diff --git a/contact.qmd b/contact.qmd index 0d5f3f7..dc169da 100644 --- a/contact.qmd +++ b/contact.qmd @@ -10,6 +10,8 @@ Feel free to email any lab member - you can find that information [here](people. If you have a query related to wet lab work or data analysis - please submit a [GitHub Issue in RobertsLab/resources.](https://github.com/RobertsLab/resources/issues) + +
Physical Address: (for walking, etc) University of Washington \ diff --git a/docs/contact.html b/docs/contact.html index b2cabf8..8f13ab3 100644 --- a/docs/contact.html +++ b/docs/contact.html @@ -326,6 +326,9 @@

Contact Us

Steven Roberts - 206-866-5141; sr320@uw.edu

Feel free to email any lab member - you can find that information here.

If you have a query related to wet lab work or data analysis - please submit a GitHub Issue in RobertsLab/resources.

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Physical Address: (for walking, etc) University of Washington
1140 NE Boat Street
diff --git a/docs/listings.json b/docs/listings.json index a4e168c..cdb866b 100644 --- a/docs/listings.json +++ b/docs/listings.json @@ -62,6 +62,28 @@ "/publications/articles/rajan2021.html" ] }, + { + "listing": "/projects.html", + "items": [ + "/research/crabcod.html", + "/research/safs.html", + "/research/aquamine.html", + "/research/usda.html", + "/research/nprb.html", + "/research/cod.html", + "/research/wsg-ec.html", + "/research/nrsp8.html", + "/research/vernon.html", + "/research/ffar.html", + "/research/wsg-sc.html", + "/research/art.html", + "/research/wsg-clam.html", + "/research/ceabigr.html", + "/research/aust.html", + "/research/e5.html", + "/research/psmfc.html" + ] + }, { "listing": "/research.html", "items": [ @@ -94,27 +116,5 @@ "/posts/frontpage/sr320-intertidal/index.html", "/posts/frontpage/ariana-hatchery/index.html" ] - }, - { - "listing": "/projects.html", - "items": [ - "/research/crabcod.html", - "/research/safs.html", - "/research/aquamine.html", - "/research/usda.html", - "/research/nprb.html", - "/research/cod.html", - "/research/wsg-ec.html", - "/research/nrsp8.html", - "/research/vernon.html", - "/research/ffar.html", - "/research/wsg-sc.html", - "/research/art.html", - "/research/wsg-clam.html", - "/research/ceabigr.html", - "/research/aust.html", - "/research/e5.html", - "/research/psmfc.html" - ] } ] \ No newline at end of file diff --git a/docs/posts/frontpage/sr320-handbook/index.html b/docs/posts/frontpage/sr320-handbook/index.html deleted file mode 100644 index bcb9e40..0000000 --- a/docs/posts/frontpage/sr320-handbook/index.html +++ /dev/null @@ -1,1446 +0,0 @@ - - - - - - - - - - - -Deep dive into the handbook – robertslab.info - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

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Deep dive into the handbook

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September 14, 2024

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A unique perspective. You will never guess what they reveal!

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Welcome to The Deep Dive, where we dig into the nitty gritty of fascinating topics.

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Today, we’re taking a deep dive into the Roberts Lab at the University of Washington, and we’re doing that through the lens of their handbook.

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It’s more than just a rule book, though, isn’t it?

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Oh, absolutely.

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It’s like a window into their whole approach to science.

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Everything from, like, groundbreaking research to how they actually build their research culture.

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And they’re known for being incredibly transparent, which this handbook really embodies.

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Yeah, it’s refreshing.

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And speaking of refreshing, I have to ask you about this freezer alarm situation.

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Oh, yes.

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So they have, like, a dedicated alarm for their ultra-low temperature freezers, right?

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Yeah.

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But there’s this 15-minute delay before anyone actually gets notified if it goes off.

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Can you imagine?

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It’s like a slow-motion heart attack for a researcher.

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Right.

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All those precious samples.

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I’d be a wreck.

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It really highlights the fragility of these biological materials they’re working with.

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RNA, proteins, these things have to be stored at, like, negative 80 degrees Celsius.

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Wow.

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Even a short power outage could be disastrous.

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So is that delay, like, a safety net to give the system a chance to recover?

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Exactly.

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It’s a calculated risk.

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They’re trying to balance preventing false alarms while also, you know, protecting those invaluable research materials.

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Makes sense.

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Yeah.

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And it seems like that emphasis on meticulousness, on minimizing risk, it really comes through in the whole handbook, especially when they talk about lab safety and chemicals.

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It’s serious business.

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Right.

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Like with Arnazole RT, they’re very clear about it being corrosive, potentially harmful if you inhale it, even disposing of it.

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It’s a whole multi-step process.

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Well, they’re dealing with some pretty potent stuff.

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It underscores their dedication to, you know, not just scientific rigor, but the actual well-being of their researchers.

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Absolutely.

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It’s like they’re creating an environment where cutting-edge science can happen, but it can happen safely.

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Safety first.

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Yeah.

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And that meticulousness, that doing things by the book, it goes beyond just lab safety, you know.

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Right.

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It’s woven into their whole research philosophy, which makes you wonder, if they’re this careful with safety, how does that translate to, say, data management or collaboration?

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Good question.

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And as luck would have it, that’s exactly what we’re going to be digging into in the rest of this deep dive.

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You know, it’s funny you should mention that because the next thing that really struck me about this handbook was their code of conduct.

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Oh, interesting.

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How so?

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Well, for one, it’s incredibly detailed, even for like their diversity, equity, and inclusion meetings.

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You don’t always see that level of, I don’t know, formality in a lab handbook.

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What kinds of things are we talking about here?

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They have these great phrases like, “Elevate impact above intent,” and, “Expect and accept non-closure.”

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Like, really specific guidelines.

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Huh.

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It sounds like they’re trying to foster a very specific kind of research environment.

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Right.

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One where people feel comfortable admitting they don’t know everything, which, let’s be honest, is most of the time in research, right?

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Oh, absolutely.

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Science is all about embracing uncertainty.

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But it takes a certain culture to really allow for that.

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Totally.

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And it seems like they’re putting a lot of emphasis on making sure everyone feels heard and respected, especially in those DEI meetings.

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Well, and that makes sense, right?

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If you want to have those tough conversations about diversity and inclusion, you need to create a space where people feel safe to speak their minds.

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Yeah.

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No, you’re right.

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It all ties together.

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And then there’s this whole thing about mentorship.

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They really encourage lab members to have multiple mentors, not just one.

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That’s interesting.

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Most labs I’ve seen, it’s pretty standard to have one primary mentor.

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Right.

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Yeah.

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So I thought that was really unique.

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It kind of speaks to this idea of providing a well-rounded experience, right?

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Absolutely.

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Different mentors bring different perspectives, different areas of expertise.

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It can really enrich a researcher’s training.

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Okay, so we’ve got meticulous safety protocols, a very deliberate approach to their lab culture.

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But we also know they’re dealing with a massive amount of data.

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Like their handbook mentions Nightingale for sequencing this whole network attached storage system called Gannett.

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Don’t forget the supercomputer.

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MOCs, was it?

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Oh, right.

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MOCs.

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I mean, it’s a lot.

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It really makes you wonder how they manage it all.

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It’s a data tsunami.

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How do they keep from drowning?

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Well, for one thing, they’re incredibly organized.

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Like religiously organized.

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Give me the details.

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Think detailed metadata for every single experiment, strict folder structures on their network.

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They even have readme files.

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Readme files for every folder, seriously.

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Seriously.

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And it’s all part of this commitment to open science.

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They want their research to be accessible, transparent.

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So anyone could theoretically go in and understand their data, their methods.

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That’s the idea.

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It’s about breaking down those silos, you know, fostering collaboration, avoiding unnecessary redundancy, ultimately speeding up discoveries.

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It’s kind of inspiring, actually.

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It’s like they’re playing the long game, advancing science as a whole, not just their own work.

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Exactly.

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But okay, even with perfect organization, all that data analysis, it’s got to be intense.

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They mentioned Jupiter notebooks in the handbook.

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Right, and mocks the supercomputer.

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And they even talk about using like the command line.

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Hard course, so they’re not messing around.

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Well, they’re equipping their researchers with a seriously powerful toolkit.

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But it goes beyond just the tech.

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They even recommend this book, Getting Things Done.

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Time management.

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Time management.

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It’s all about efficiency.

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They don’t just give them the tools.

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They give them the training, the resources to actually use them well.

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It’s like they’ve thought of everything.

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Yeah.

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And it doesn’t stop there.

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They have a whole section on conferences, funding opportunities, even like travel grants.

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They want their researchers to be well-rounded, right?

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Not just stuck in the lab, but out there presenting, collaborating, getting their work funded.

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It’s impressive, I have to say.

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Looking at the Roberts Lab this way, through their handbook, you really get a sense of the thoughtfulness, the care that goes into building a successful research environment.

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It’s not just about, you know, the results, the discoveries.

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It’s the people, the culture.

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And that commitment to moving science forward in a way that’s open and collaborative, it’s really something.

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Makes you wonder what they’ll accomplish, what amazing discoveries are on the horizon for them.

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It does, doesn’t it?

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And that’s something to ponder as we wrap up this deep dive into the world of the Roberts Lab.

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Until next time, keep exploring, keep questioning, and keep diving deep.

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- - - - - - \ No newline at end of file diff --git a/docs/projects.xml b/docs/projects.xml deleted file mode 100644 index dad63de..0000000 --- a/docs/projects.xml +++ /dev/null @@ -1,794 +0,0 @@ - - - -robertslab.info -https://faculty.washington.edu/sr320/projects.html - - -quarto-1.6.40 -Sat, 08 Feb 2025 20:50:45 GMT - - Using next-generation sequencing techniques to assess adaptive capacity and illuminate mechanisms underlying the effects of high pCO2 on Alaskan crab and fish species - https://faculty.washington.edu/sr320/research/crabcod.html - -

Collaborators

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Ingrid Spies

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Summary

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Researchers at the Alaska Fisheries Science Center (AFSC) and the University of Washington are interested in the effects of ocean acidification (OA) on commercially and economically important crab and fish species. It appears that many species are negatively affected by exposure to pH levels predicted to occur throughout their ranges under climate change.  The effects of OA include physiological consequences including decreased growth, altered embryonic development, reduced exoskeleton strength, increased metabolic rate, altered immune system, altered behavior, and increased mortality.  Environmental changes may select for adapted individuals, resulting in populations that are less vulnerable to OA than the current population. Estimating the degree to which acclimation and adaptation will alter the experimental effects of OA and combined effects with other stressors is thus critical to accurately predicting how these stressors will affect future fisheries yields.  We are using next-generation sequencing techniques to identify the specific alterations in the molecular, metabolic, and physiological pathways of individuals exposed to OA. We are looking for a post-doctoral researcher to perform bioinformatics on RNA transcriptomic data of Pacific cod and crabs exposed to OA conditions in an experimental setting. In addition, the researcher will be responsible for writing up their methods and results and drafting peer-reviewed manuscripts.

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Data Availability

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Notes

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AWD-004600 Grant Revenue (RC1054) (Line 143)
-GR014801 TASK II SEQ TECHNIQUES - 62-7490 - 2021

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AWD-004600 Grant Revenue (RC1054) (Line 151)
-GR015296 TASK II SEQ TECH PD - 62-8482 - 2021

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UW CICOES Task II Seq Techniques (62-7490) / Seq Tech PD (62-8482) NOAA - NA20OAR4320271

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7/1/2022 – 6/30/2025

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$328,323

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- crab - cod - Alaska - acidification - 02-RBE - open - https://faculty.washington.edu/sr320/research/crabcod.html - Sat, 08 Feb 2025 20:50:45 GMT -
- - Field-based Education and Research at Regional Aquaculture Sites (FERRAS) - https://faculty.washington.edu/sr320/research/safs.html - -

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Summary

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Aquaculture operations serve as a vital cog in our local economy, playing an integral role in conservation efforts and holding cultural significance. Primarily, my laboratory’s research program is devoted to enhancing aquaculture practices in the Pacific Northwest, having received several research awards in collaboration with tribes, industry players, and conservation organizations.

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Despite having various projects involving shellfish transfer to the field for commercial or conservation purposes, budget constraints and directives in specific Requests for Proposals (RFPs) have hindered us from leveraging these opportunities to engage students and staff in fieldwork components. Thus, the purpose of this proposal is to request funds that would facilitate student and staff involvement in ongoing field grow-outs, thereby creating unique opportunities for SAFS community members. The funding will cover travel expenses, field sampling, and reagents and equipment for physiological analysis.

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Our partnerships span both local and regional scopes, enabling a range of experiences. For instance, local sites include shellfish farms in Puget Sound, as well as with sites associated with the MusselWatch program via UW Tacoma. These local sites provide a platform for integrating field research into courses like FISH 441/541 Integrative Environmental Physiology. Traditionally, the lab has exclusively engaged in lab-based environmental manipulation. However, this funding would enable us to shift focus to comparative studies across different field sites, offering students a more immersive experience in data collection and physiological assessment. Additionally, students would gain the invaluable experience of observing active aquaculture operations, providing them with practical insights into the application of their classroom knowledge. With some necessary constraints, students would be given the freedom to design their experiments. For instance, they could assess the stress response in oysters from two different field sites, formulating hypotheses to test based on natural conditions.

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Moreover, as part of a recent USDA award, we are dispatching oysters to commercial producers in Oregon. These field sites would provide an excellent framework for studies, which may be more apt for graduate students or scientific staff due to the need for accommodation. This experience would also illuminate the variations in environmental conditions and aquaculture practices across the region, fostering the expansion of research networks for our students.

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Data Availability

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- oyster - aquaculture - 03-ARD - https://faculty.washington.edu/sr320/research/safs.html - Sat, 08 Feb 2025 20:50:45 GMT -
- - FACT: AquaMine - A High Performance Genomic Data Mining System for Species of Importance to US Aquaculture - https://faculty.washington.edu/sr320/research/aquamine.html - -

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PI: Christine G. Elsik, University of Missouri

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AquaMine is a data mining system that integrates genome assemblies and gene annotation data for aquatic eumetazoan species of importance to US aquaculture and fisheries, with the goal of enabling researchers to create customized annotation datasets integrated with their own data. AquaMine was developed using the InterMine genomic data mining platform, which includes a web application with several search tools, including a simple key word search, predefined template queries, a QueryBuilder Tool for creating custom queries, a Regions Search Tool for coordinate-based queries, and a List Tool for uploading and searching with lists of identifiers. AquaMinev1.2 contains genomes of 37 aquatic species, including Arctic char, Atlantic salmon, California yellowtail, channel catfish, coho salmon, eastern oyster, giant tiger prawn, Nile tilapia, Pacific oyster, Pacific white shrimp, rainbow trout, striped sea bass and yellow perch. Annotation data includes RefSeq genes and additional data sources that may be available for each species, including Ensembl, KEGG, UniProt, Gene Ontology (GO), PubMed, and OrthoDB. Genes of human, fruit fly, owl limpet and zebrafish are included so model organism information can be leveraged using orthology. A precomputed orthology dataset called AquaMine-Ortho encompasses all species, including those not found in OrthoDB or Ensembl. New in AquaMinev1.2 is a comprehensive GO annotation dataset, covering all species, that can be used with a built-in gene enrichment analysis tool. AquaMinev1.2 also includes new genomic variant data from the Ensembl Variation Archive and RNA-seq-based gene expression levels for some species. We are currently developing new JBrowse genome browsers with Apollo manual genome annotation tools for the aquaculture species and will present the rainbow trout genome browser. We seek beta-testers from the research community to provide feedback on the AquaMine data mining tools and genome browsers.

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Data Availability

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- genomics - aquaculture - 03-ARD - https://faculty.washington.edu/sr320/research/aquamine.html - Sat, 08 Feb 2025 20:50:45 GMT -
- - Improved climate resilience in oysters through optimization of hatchery-based environmental conditioning practices - https://faculty.washington.edu/sr320/research/usda.html - -

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Matt George

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Summary

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As academic, industry, and tribal stakeholders, our collective goal is to ensure the sustainable expansion of oyster aquaculture within the U.S. by reducing the frequency and severity of mass mortality events by improving the climate resilience of oyster stocks. The specific research objectives are: Optimize early-life stage environmental conditioning to improve climate resilience Assess carry-over benefits of broodstock husbandry practices on offspring performance Objective 1. Optimize early-life stage environmental conditioning to improve climate resilience. Developmental plasticity occurs when the environment experienced by an organism during development alters the phenotype of the same organism during later life-stages (Figure). To assess the potential for developmental plasticity to produce positive carry-over effects that improve resilience, we will expose oysters to a variety of environmental stressors at nonlethal levels during larval rearing. The performance of larvae will be assessed during early development and compared with performance after summer deployment at grow-out sites.

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Objective 2. Assess carry-over benefits of broodstock husbandry practices on offspring performance. Transgenerational plasticity occurs when the environment experienced by parents influences the phenotype of their offspring (Fig. 4B). To assess the potential for transgenerational plasticity to produce positive carry-over effects that improve offspring resilience, we will expose oyster broodstock to a variety of environmental stressors at nonlethal levels prior to broodstock conditioning and spawning. The performance of offspring will then be assessed during the pre- and post-settlement larval stages and compared with performance after summer deployment at grow-out site

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Data Availability

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Notes

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AWD-008583 Grant Revenue (RC1054) (Line 1)
-GR014587 CLIMATE RESILIENCE - 62-7174 - 2021021

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9/1/2022 – 8/31/2024

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$299,374

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- oyster - carryover - aquaculture - 03-ARD - open - https://faculty.washington.edu/sr320/research/usda.html - Sat, 08 Feb 2025 20:50:45 GMT -
- - Effects of temperature change and Hematodinium sp. infection (Bitter Crab Disease) on Tanner crab (Chionoecetes bairdi) - https://faculty.washington.edu/sr320/research/nprb.html - -

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Pamela Jensen

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Changing climate conditions, due to increasing releases of CO2 into the atmosphere, are causing warming of the world’s oceans. Changes in seawater temperatures are predicted to cause a shift in the distribution and a change in the abundance of most plants and animals. For most species, the magnitude of the impact, the potential for adaptation to future temperatures, and the mechanisms for adaptation are unknown. Features of parasite/disease ecology are also predicted to change as oceans warm, including susceptibility of hosts to disease, host ability to combat disease once infected, and alterations in pathogen virulence. Alaskan Tanner crab stocks, supporting fisheries worth $21 million in 2014, are expected to be significantly impacted directly and indirectly by warming temperatures. The Alaska Department of Fish and Game considers bitter crab disease, caused by a parasitic dinoflagellate, Hematodinium, to be the ‘principle threat’ to Alaskan Tanner crab stocks. Infection rates in the Bering Sea and southeast Alaska range from 2-5% and 0-100%, respectively. In heavily infected hosts, the meat is soft and chalky with a bitter taste, rendering the crabs unmarketable. The disease is believed fatal, although the time from infection to death remains uncertain. Recent worldwide spread of Hematodinium infections appears to have closely followed warming trends in the Atlantic and Pacific Oceans. We postulate that increased temperature in the North Pacific will physiologically stress Tanner crabs and also lead to increased prevalence of Hematodinium infections, either of which may lead to increased mortality in Tanner crabs. We propose to hold healthy and Hematodinium-infected Tanner crabs under different temperature regimes testing for a genetic response to infection and temperature. Our research will provide insight into the underlying mechanistic linkages between potential effects of climate change and important processes such as recruitment, growth and natural mortality on Alaskan Tanner crab stocks.

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Data Availability

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- crab - disease - Alaska - 02-RBE - https://faculty.washington.edu/sr320/research/nprb.html - Sat, 08 Feb 2025 20:50:45 GMT -
- - Gene activity and genetic selection in Pacific cod reared under thermal stress - https://faculty.washington.edu/sr320/research/cod.html - -

Collaborators

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Louise Copeman (co-PI)

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Ben Laurel (co-PI)

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Krista Nichols (co-PI)

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Ingrid Spies (co-PI)

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Recent heat wave stress in the Gulf of Alaska has resulted in significant declines of Pacific cod, Gadus macrocephalus, in that region. In particular, overwintering success of juveniles is hypothesized to represent a critical bottleneck with food availability the previous summer affecting juvenile lipid reserves and thus, their ability to survive winter. The physiological and transcriptional responses of Pacific cod and whether selective mortality is present under thermal stress are unknown. The proposed project will address these questions critical to their survival under climate change by identifying regions of the genome and epigenome that respond to thermal stress and starvation. Juvenile Pacific cod will be reared in three temperatures under feeding and non-feeding conditions, then an integrated genomic approach will identify genes, gene variants, and epigenetic markers that respond to thermal stress and confer resilience. To complement the genomic approaches and further investigate temperature influences on energy resources, we will perform lipid analyses. This work will inform predictions of genetic selection and molecular response of Pacific cod in the Gulf of Alaska under climate change.

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Data Availability

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Notes

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AWD-008727 Grant Revenue (RC1054) (Line 1)
-GR031727 COD THERMAL STRESS - 66-9283 - 2021

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Pacific States Marine Fisheries Commission / 23-084G (66-9283)

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11/1/2022 – 7/31/2025

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$524,788

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- cod - Alaska - epigenetics - 01-EE - 02-RBE - open - https://faculty.washington.edu/sr320/research/cod.html - Sat, 08 Feb 2025 20:50:45 GMT -
- - A collaborative partnership to address mass mortalities in oyster aquaculture through improved field monitoring, husbandry practices, and workforce development - https://faculty.washington.edu/sr320/research/wsg-ec.html - -

Collaborators

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Emily Carrington

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As a collaborative partnership, our collective goal is to ensure the sustainable expansion of oyster aquaculture within Washington State by reducing the frequency and severity of mass mortality events that result from the interaction between OsHV-1 infection and extreme climate events such as marine and aerial heatwaves. The specific research and outreach objectives we will use to achieve this goal are:

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Objective 1. Determine susceptibility of Washington shellfish farms to heatwaves. Air and water temperatures experienced by oysters during grow-out will be monitored at farms within the Salish Sea and Willapa Bay in collaboration with industry partners. Continuous monitoring of environmental conditions in combination with oyster mortality data will be used to generate a climate risk assessment model for commercial growing areas within Washington State.

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Objective 2. Develop a commercially viable hatchery husbandry protocol that improves oyster heat tolerance. Oyster seed (“spat”) from OsHV-1 resistant families supplied by the USDA-ARS’ Pacific Shellfish Breeding Center (PSBC) will undergo sublethal exposure to simulated marine and aerial heat waves within a hatchery setting. The summer survival of stress-primed spat out-planted at farms with Puget Sound and Willapa Bay will inform the creation of a husbandry protocol that improves oyster climate resilience.

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Objective 3. Develop an enhanced workforce training curriculum for shellfish industry technicians. To address the industry’s need for skilled technicians, students from Bellingham Technical College’s (BTC) Fisheries and Aquaculture Sciences Program will be integrated into research objectives; this collaboration will be used to generate an enhanced workforce training curriculum that uses OsHV-1 and heat waves as case studies. Students will also gain exposure to training opportunities by serving as hatchery technicians, summer interns at shellfish farms, and student ambassadors during regular partner meetings.

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Data Availability

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Notes

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TBD

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TBD

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2/2024 – 1/2026

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$280,000

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- oyster - aquaculture - disease - 03-ARD - https://faculty.washington.edu/sr320/research/wsg-ec.html - Sat, 08 Feb 2025 20:50:45 GMT -
- - Identifying genomic architecture features that contribute to critical phenotypes in shellfish - https://faculty.washington.edu/sr320/research/nrsp8.html - -

Collaborators

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Mackenzie Gavery, Matt George

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Summary

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Shellfish are a key component of domestic seafood production. Shellfish aquaculture is one of the most economically important sectors of the US industry, with major species including oysters and clams. As is the case with all farmed species, there are a suite of desirable phenotypes that directly correspond to increased environmental and economic sustainability. The ability to identify genomic predictors of phenotype offer a framework to increase aquaculture production. In shellfish aquaculture key phenotypes continue to be resilience and stress tolerance. Understanding the physiological underpinnings of these phenotypes in oysters and clams has been a focus in our group. To this end we have archived hundreds of samples from families with diverse phenotypic responses to stress. For example, as part of one effort to examine the influence of ploidy on oyster stress tolerance we have Standard Metabolic Rate (SMR) and enzyme activity data on oysters that reveal diverse physiological profiles. In response to the NRSP-8 Small Funding Possibilities for US Aquaculture Groups, we are proposing to 1) identify genomic architecture variation contributing to desired phenotypes in shellfish and 2) develop a community platform to share data and analytical approaches. These objectives are in direct response to Program Objective 2: Advance genome-to-phenome prediction by implementing strategies and tools to identify and validate genes and allelic variants predictive of biologically and economically important phenotypes and traits. Additionally the proposed work will address Program Objective 1, by … providing a deep functional annotation of assemblies, and comparison across species to understand structure and function of animal genomes.

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Data Availability

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- oyster - triploidy - acidification - aquaculture - epigenetics - 01-EE - https://faculty.washington.edu/sr320/research/nrsp8.html - Sat, 08 Feb 2025 20:50:45 GMT -
- - Vernon: Development of innovative approaches to support sustainable aquaculture and understand the effects of ocean acidification on marine species - https://faculty.washington.edu/sr320/research/vernon.html - -

Collaborators

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Mackenzie Gavery

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Summary

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Environmental variability due to climate change and ocean acidification (OA) are having multifaceted impacts on marine species, ecosystems and human industries such as marine aquaculture. It is absolutely critical to understand how marine organisms, and industries that rely on them, will respond to these changing conditions. Arguably, it will be just as important to provide tools and best practices to mitigate these effects, and in the case of marine aquaculture – find solutions to increase sustainability of the sector broadly, to create resilience even in the face of environmental uncertainty. Innovative scientific solutions are required to meet these ongoing and future challenges. In this project, we will add capacity to collaborative research between partners at the University of Washington and the Northwest Fisheries Science Center, addressing objectives of key importance to the National Marine Fisheries Service mission. These include innovative problem-solving approaches to address challenges facing sustainable aquaculture development, understanding the impacts of climate variability on marine fish and shellfish, and woven throughout these research activities is the development of ’omics and bioinformatics workflows for both data generation and data analysis (bioinformatics). Through this composite project, our goal is to contribute to applications to support sustainable aquaculture, increase our understanding of the effects of OA on marine fish and shellfish and contribute bioinformatic capacity, tools and workflows for research related to aquaculture, genomics and climate change.

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Data Availability

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Notes

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AWD-004600 Grant Revenue (RC1054) (Line 128)
-GR012147 TASK II VERNON - 62-3837 - 2021

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AWD-004600 Grant Revenue (RC1054) (Line 3)
-GR011321 TASK II OMICS TECH - 62-2795 - 2021

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UW CICOES Task II Vernon (62-3837) / NOAA - NA20OAR4320271

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7/2022 – 6/2024

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$1,182,294

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- oyster - acidification - aquaculture - 03-ARD - open - https://faculty.washington.edu/sr320/research/vernon.html - Sat, 08 Feb 2025 20:50:45 GMT -
- - Development of environmental conditioning practices to decrease impacts of climate change on shellfish aquaculture - https://faculty.washington.edu/sr320/research/ffar.html - -

Collaborators

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Hollie Putnam

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Summary

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The project will be completed using commercial hatchery rearing of geoduck clams. We will test and implement shellfish performance enhancement methods through the use of environmental stressor preconditioning, or “hardening”. The objectives of this work are to A) Identify key stages in the geoduck life cycle when environmental conditioning can be applied for optimal benefits to productivity, including: – Broodstock conditioning and reproductive performance, – Larval growth and survivorship, and – Juvenile resistance to stress through repeated exposures, B) Use genomics and epigenomics to identify underlying mechanisms involved in enhanced performance. This will provide mechanistic information that enables the application of optimal preconditioning approaches in other shellfish species. This project directly addresses the research topics of genomics, quantitative genetics, and phenomics in the less studied, yet viable, geoduck clam. The proposed work is based on our group’s prior finding that some exposure to low pH conditions can improve larval and juvenile performance traits. The research proposed will integrate and further test these findings in a commercial shellfish hatchery setting and determine the genetic and epigenetic markers associated with improved performance. In addition, we will explore how the “memory” of prior exposure increases later performance such that epigenetic markers could be leveraged in broodstock management and hatchery practices. A number of phenotypes will be assessed, as well as the underlying genomic factors, including fecundity, survival, and growth.

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Data Availability

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- clam - epigenetics - aquaculture - 03-ARD - https://faculty.washington.edu/sr320/research/ffar.html - Sat, 08 Feb 2025 20:50:45 GMT -
- - Enhancing sustainability of shellfish aquaculture through streamlined maturation control - https://faculty.washington.edu/sr320/research/wsg-sc.html - -

Collaborators

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Mackenzie Gavery

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Summary

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The proposed objectives cover the essential first steps toward generating sterile bivalves via molecular disruption of germ cell formation. The first step in the process is the identification of genes involved in primordial germ cell (PGC) specification in bivalves via single-cell RNA sequencing (scRNA- Seq). This cutting-edge technique is particularly suited to identify germ cell markers in bivalves, since germ cell precursors represent a small number of cells in developing embryos. This information is integral to being able to control germ cell fate for reproductive sterilization of aquaculture species, and our proposed use of scRNA-Seq for directed application to aquaculture is both novel and potentially highly beneficial to the broader shellfish aquaculture community. Our first specific research aim is to characterize genomic processes involved in germ cell specification in Pacific oysters. A second fundamental step in the process is the optimization of techniques to deliver targeted, gene-regulating molecules to embryos to inhibit germ cell formation. Methods to optimize delivery techniques, including the use of CRISPR-Cas9 and morpholino constructs, have yet to be developed for bivalve embryos. Therefore, our second specific research aim is to optimize delivery techniques of custom gene-regulating molecules to oyster embryos. The completion of these objectives sets the stage for a more effective and sustainable approach for sterilization of shellfish.

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Data Availability

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- oyster - scRNAseq - aquaculture - 02-RBE - https://faculty.washington.edu/sr320/research/wsg-sc.html - Sat, 08 Feb 2025 20:50:45 GMT -
- - Increasing Environmental Connection, Literacy and Engagement through an Art + Science Collaborative Education Practice - https://faculty.washington.edu/sr320/research/art.html - -

Collaborators

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Research Team:
-Principal Investigator: Steven Roberts, UW Seattle, College of the Environment, Aquatic & Fishery Science
-Community Lead: Tiara Moore, CEO, Black in Marine Science
-Student: Chris Mantegna, UW Seattle, College of the Environment, Aquatic & Fishery Science
-Collaborators: Tivon Rice, UW Seattle College of Arts & Sciences, Digital Arts & Experimental Media
-Symone Barkley, Black in Marine Science
-Rosalind Echols, UW Seattle College of the Environment, Aquatic & Fishery Science
-Savannah Smith, Sea Potential
-Ebony Welborn, Sea Potential
-Ángel Quimbita, Sea Potential

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Summary

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As the country comes to a reckoning on education and the environment, we are forced to interrogate the historic events that have led to such crises and how we can support inclusive solutions. Covid-19 has offered us an unprecedented glimpse into the challenges students face in the K-12 education system. It has also profoundly impacted socio-economically disadvantaged communities through the exposure of crippled or missing infrastructure. These same communities have been deliberately disconnected from building relationships with the natural world. In the face of complex problems like climate change, which will disproportionately impact these communities, we must act urgently to support the students who have historically been excluded from environmental science education. Our project starts with reconnecting community to environment, followed by engaging learners dynamically through the co-production of place-based knowledge. Although disadvantaged communities are highly engaged in climate change mitigation, this is often limited to anecdotes about water quality during trash pick-ups or community beautification projects led by outside non-profit volunteers, rather than building knowledge and strength within the community. Rarely do students have the opportunity to access their local environment through a non- problem solving lens and participate as equal partners. We want to change who is leading the learning as well as how the learning is done. Partnering with Sea Potential and Black in Marine Science, our team of scientists and digital arts experts will co-produce an arts based learning approach to increase environmental literacy in the communities most regularly overlooked. We will empower students to engage with the intertidal ecosystem, a defining feature of all coastlines and an accessible and dynamic place to learn about ocean science, organismal resilience, and community composition. Student projects will demonstrate how they understand the intertidal ecosystem, their connection to it, and its relationship to their home neighborhoods. Each of the projects will be presented to their academic and familial communities as well as used to create a teaching toolkit for local and national educators to replicate our art- and science-integrated student centered learning model for intertidal ecology.

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Data Availability

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Drive

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Notes

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- education - 02-RBE - https://faculty.washington.edu/sr320/research/art.html - Sat, 08 Feb 2025 20:50:45 GMT -
- - Readying sustainable aquaculture for a changing ocean: uncovering the mechanisms associated with intergenerational carryover effects to enhance bivalve resilience to acidification - https://faculty.washington.edu/sr320/research/wsg-clam.html - -

Collaborators

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Mackenzie Gavery

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Summary

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The proposed effort will identify how parental environmental conditions drive shellfish offspring performance, including describing underlying mechanisms. To do this we will examine intergenerational effects of ocean acidification in the Manila clam, a globally cultured species that will serve as a model for marine bivalves and related taxa. By comprehensively investigating gamete status following parental pCO2 exposures, this project will uncover the non-genetic carriers of information across generations while simultaneously identifying factors that predict high performance of larvae in acidified conditions. By leveraging and working closely on a complementary NOAA supported project, we are able to expand our traditional research objectives with an objective centered around increasing diversity and inclusion in marine sciences. The specific objectives include 1) Characterize carryover performance in clams in response to ocean acidification, 2) Identify maternal macromolecule contribution of intergenerational plasticity and carryover performance, 3) Identify paternal epigenetic signatures associated with intergenerational plasticity and carryover performance, and 4) Develop inclusive educational experiences and products for underserved groups. The proposed work supports Washington Sea Grants commitment to cultivating partnerships and practicing a commitment to diversity, equity and inclusion. The objectives directly align with the critical program areas of Sustainable Fisheries and Aquaculture, Ocean Literacy and Workforce Development, and Healthy Coastal Ecosystems.

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Data Availability

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notes

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Notes

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AWD-007435 Grant Revenue (RC1054) (Line 14)
-GR013472 SG ROBERTS_R_SFA15 - 62-5534 - 2021

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AWD-001657 Grant Revenue (RC1054) (Line 51)
-GR014879 SG ROBERTS_VADOPALAS - 62-7661 - 2021

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Washington Sea Grant / R_SFA-15 (62-5534) and Puget Sound Partnership (co-funding) / 2022-44 (63-5817)

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02/2022 – 1/2024

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$279,374

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- clam - acidification - carryover - aquaculture - epigenetics - 03-ARD - 01-EE - open - https://faculty.washington.edu/sr320/research/wsg-clam.html - Sat, 08 Feb 2025 20:50:45 GMT -
- - Collaborative Research: Does ocean acidification induce a methylation response that affects the fitness of the next generation in oysters? - https://faculty.washington.edu/sr320/research/ceabigr.html - -

Collaborators

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Katie Lotterhos

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Summary

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Living organisms may acclimate to environmental changes through epigenetic modifications to DNA, which alter the way genetic instructions are interpreted without altering the DNA code itself. While these modifications to organismal phenotype or function can be reversible, some of them may be inherited by offspring, potentially producing multiple, heritable outcomes from a single genome and affecting ecological and evolutionary outcomes. This project uses symbiotic, metabolically complex reef building corals as a model system to test the connections between physiological, epigenetic, and metabolic states, and predict how population and community dynamics are influenced by epigenetically-modulated phenotypes. This work will advance biological knowledge by delineating fundamental links (Rules of Life) between ubiquitous organismal energetic processes, epigenetics, and eco-evolutionary outcomes. The Broader Impacts activities parallel the project’s integrative approach, linking insights from Environment x Energetics x Epigenetics x Ecology for Education into an E5 platform. The E5 platform will provide i) early career STEM training, ii) local and global community education, and iii) educational resources for open science, quantitative approaches, and research reproducibility. Further, this E5 platform will train and inform the next generation of diverse scientists and public by combining local and global initiatives focusing on groups underrepresented in STEM.

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This project examines how nutrient metabolism in the mitochondria generates cofactors and energy that will instruct the epigenetic machinery in the cell nucleus to modulate genome function to appropriately respond to environmental conditions. Environmentally-responsive metabolic function and energetic-epigenetic linkages act as drivers of complex emergent phenotypes. To elucidate relationships that are the basis for Rules of Life with respect to epigenetics, this project will use integrative experimental and modeling approaches focused on reef building corals to: 1) link nutritionally-provisioned metabolites with epigenetic and organismal state through seasonal sampling across environmental gradients; 2) expand current Dynamic Energy Budget (DEB) models for symbiotic organisms to further integrate critical facets of nutritional symbiosis and calcification; 3) experimentally modulate metabolic and therefore epigenetic states through repeated exposure to increased temperature and nutrients, to test intra- and trans-generational epigenetic inheritance; 4) use DEB theory to identify shifts in energetics associated with epigenetic modulation, and link these sub-organismal processes to higher levels of organization; and 5) integrate findings into a generalizable, predictive eco-evolutionary model that links nutritional interactions, metabolic states, and subsequent epigenetic effects to the timescales regulating organismal processes and eco-evolutionary outcomes. This effort will provide characterization of environmental epigenetic phenomena in ecosystem-engineering marine invertebrates. This characterization includes determining the mechanisms and the degree of epigenetic ‘memory’ both within and across generations. By including information on environmental legacies, propagated by epigenetics, this project will advance both organismal and population-based models and improve capacity to predict responses to acute and chronic environmental signals.

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Data Availability

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The online version contains supplementary material available at https://doi.org/10.5281/zenodo.4563060

- - -
- - ]]>
- oyster - epigenetics - acidification - aquaculture - 01-EE - https://faculty.washington.edu/sr320/research/ceabigr.html - Sat, 08 Feb 2025 20:50:45 GMT -
- - Oyster adaptation to climate change via transgenerational plasticity - https://faculty.washington.edu/sr320/research/aust.html - -

Collaborators

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Dr Laura Parker
-Chief Investigator

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Dr Wayne O’Connor
-Prof Pauline Ross
-Prof Thiyagarajan Vengatesen

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Summary

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Summary: Across the globe, oysters need to rapidly respond to climate change. Increased concentrations of atmospheric carbon dioxide (CO2) are warming and acidifying estuaries, especially along the south-eastern coast of Australia, at a rate an order of magnitude greater than that predicted for oceans (Collins et al. 2013; Scanes et al. 2020). For Indigenous Australians, oysters create an unbroken connection with the coast and sea that has persisted over time (National Oceans Office 2002) and are the focus of Aboriginal-led reef restoration projects. Assessing the capacity of oysters and other marine organisms to acclimate or adapt to global climate change stressors presents one of the most important research challenges of our time. Acclimation through the mechanism of transgenerational plasticity (TGP) is now at the leading edge of research providing hope that oysters and other marine organisms may persist into the future (Parker et al. 2012, 2015, 2017a, Gibbs et al. accepted a, b). This project takes the next critical step in research: to identify whether the TGP response of oysters differ across genotypes, the capacity of TGP responses to persist within and across generations, and the epigenetic mechanisms which underlie them. How well we understand this, will determine our ability to ensure marine food security into the future and to protect the cultural heritage of Indigenous Australians – identified as a major concern for Indigenous people (National Oceans Office 2002). Globally, oysters form large aquaculture industries worth $6.8 billion per annum (Food and Agriculture Organization 2014) and provide services vital to the ecosystem (Lemasson et al. 2017).
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-AIM: Focussing on the ecologically, economically, and culturally important Sydney rock oyster, Saccostrea glomerata – we will use an innovative combination of state-of-the-art climate change mesocosm exposure systems and internationally established epigenetic and genetic techniques, with an ultimate aim to protect and conserve oysters against climate change to the benefit of Australians. Specific aims: Using the unique resource of pair-mated family lines of the Sydney rock oyster, S. glomerata, we will:
-1. Measure the variation in transgenerational plasticity responses to ocean warming and acidification within and among genotypes
-2. Characterise the role of epigenetic inheritance (DNA methylation) in transgenerational plasticity responses
-3. Assess the capacity of transgenerational plasticity responses to persist across life stages and generations

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Data Availability

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Notes

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AWD-006084 Grant Revenue (RC1054) (Line 1)
-GR032859 UNSW-OYSTER - 68-7511 - 2021

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University of New South Wales via ARC / IN220100054 (68-7511)

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5/2/2023 – 12/31/2024

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$90,255

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- genomics - epigenetics - 03-ARD - 01-EE - open - https://faculty.washington.edu/sr320/research/aust.html - Sat, 08 Feb 2025 20:50:45 GMT -
- - Collaborative Research: URoL : Epigenetics 2: Predicting phenotypic and eco-evolutionary consequences of environmental-energetic-epigenetic linkages - https://faculty.washington.edu/sr320/research/e5.html - -

Collaborators

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Hollie Putnam
-Jose Eirin-Lopez
-Roger Nisbet
-Holly Moeller
-Ross Cunning

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Summary

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Living organisms may acclimate to environmental changes through epigenetic modifications to DNA, which alter the way genetic instructions are interpreted without altering the DNA code itself. While these modifications to organismal phenotype or function can be reversible, some of them may be inherited by offspring, potentially producing multiple, heritable outcomes from a single genome and affecting ecological and evolutionary outcomes. This project uses symbiotic, metabolically complex reef building corals as a model system to test the connections between physiological, epigenetic, and metabolic states, and predict how population and community dynamics are influenced by epigenetically-modulated phenotypes. This work will advance biological knowledge by delineating fundamental links (Rules of Life) between ubiquitous organismal energetic processes, epigenetics, and eco-evolutionary outcomes. The Broader Impacts activities parallel the project’s integrative approach, linking insights from Environment x Energetics x Epigenetics x Ecology for Education into an E5 platform. The E5 platform will provide i) early career STEM training, ii) local and global community education, and iii) educational resources for open science, quantitative approaches, and research reproducibility. Further, this E5 platform will train and inform the next generation of diverse scientists and public by combining local and global initiatives focusing on groups underrepresented in STEM.

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This project examines how nutrient metabolism in the mitochondria generates cofactors and energy that will instruct the epigenetic machinery in the cell nucleus to modulate genome function to appropriately respond to environmental conditions. Environmentally-responsive metabolic function and energetic-epigenetic linkages act as drivers of complex emergent phenotypes. To elucidate relationships that are the basis for Rules of Life with respect to epigenetics, this project will use integrative experimental and modeling approaches focused on reef building corals to: 1) link nutritionally-provisioned metabolites with epigenetic and organismal state through seasonal sampling across environmental gradients; 2) expand current Dynamic Energy Budget (DEB) models for symbiotic organisms to further integrate critical facets of nutritional symbiosis and calcification; 3) experimentally modulate metabolic and therefore epigenetic states through repeated exposure to increased temperature and nutrients, to test intra- and trans-generational epigenetic inheritance; 4) use DEB theory to identify shifts in energetics associated with epigenetic modulation, and link these sub-organismal processes to higher levels of organization; and 5) integrate findings into a generalizable, predictive eco-evolutionary model that links nutritional interactions, metabolic states, and subsequent epigenetic effects to the timescales regulating organismal processes and eco-evolutionary outcomes. This effort will provide characterization of environmental epigenetic phenomena in ecosystem-engineering marine invertebrates. This characterization includes determining the mechanisms and the degree of epigenetic ‘memory’ both within and across generations. By including information on environmental legacies, propagated by epigenetics, this project will advance both organismal and population-based models and improve capacity to predict responses to acute and chronic environmental signals.

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Data Availability

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The online version contains supplementary material available at https://doi.org/10.5281/zenodo.4563060

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Notes

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AWD-002762 Grant Revenue (RC1054) (Line 1)
-GR006094 NSF-ROL - 61-0552 - 2021

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NSF / EF-1921149

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09/2019-8/2024

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$871,336

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- - ]]>
- coral - epigenetics - 01-EE - open - https://faculty.washington.edu/sr320/research/e5.html - Sat, 08 Feb 2025 20:50:45 GMT -
- - Applying cutting-edge technology for reproductive control in emerging bivalve species - https://faculty.washington.edu/sr320/research/psmfc.html - -

Collaborators

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Mackenzie Gavery

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Summary

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Given the supreme importance of maintaining ecological security in expanding shellfish farming to meet the global demand for environmentally sustainable protein, our goal is to engage a novel mix of disciplines to create new knowledge leading to an optimal approach for conferring sterility in emerging shellfish species. We have assembled an interdisciplinary team including aquaculture specialists, molecular physiologists, and single cell genomicists to tackle the critical initial step in this approach: the identification of genes involved in germ cell fate at the earliest developmental stages in geoducks. We anticipate identifying several germ cell- specific genes that when disrupted effectively turn off germ cell differentiation, yielding sterile products that do not undergo gonadogenesis, exhibit superior performance, and cannot disrupt genetic structure of ecosystems. Identification of these genes will be the measure of success for the proposed work. These gene targets will be the focus of future stages of research that determines how to best disrupt reproductive function without impacting growth performance.

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Data Availability

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Notes

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AWD-002979 Grant Revenue (RC1054) (Line 1)
-GR019591 BIVALVE REPRO CONTROL - 63-9405 - 2021

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Pacific States Marine Fisheries Commission / 20-04G-1 (63-9405)

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7/8/2019 – 4/30/2024 (NCE)

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$93,400

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- - ]]>
- clam - scRNAseq - aquaculture - 02-RBE - 03-ARD - open - https://faculty.washington.edu/sr320/research/psmfc.html - Sat, 08 Feb 2025 20:50:45 GMT -
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diff --git a/docs/research.html b/docs/research.html index 79e4561..5427d20 100644 --- a/docs/research.html +++ b/docs/research.html @@ -556,7 +556,7 @@

Research Projects

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  • +
  • Improved climate resilience in oysters through optimization of hatchery-based environmental conditioning practices
    diff --git a/docs/search.json b/docs/search.json index 6eb777d..3e9758d 100644 --- a/docs/search.json +++ b/docs/search.json @@ -20,536 +20,557 @@ ] }, { - "objectID": "publications/notebooks/crandall2022.html", - "href": "publications/notebooks/crandall2022.html", - "title": "Proteomic response of early juvenile Pacific oysters (Crassostrea gigas) to temperature", + "objectID": "projects.html", + "href": "projects.html", + "title": "Research Projects", "section": "", - "text": "Crandall G, Elliott Thompson R, Eudeline B, Vadopalas B, Timmins-Schiffman E, Roberts S. 2022. Proteomic response of early juvenile Pacific oysters (Crassostrea gigas) to temperature. PeerJ 10:e14158 https://doi.org/10.7717/peerj.14158" + "text": "Using next-generation sequencing techniques to assess adaptive capacity and illuminate mechanisms underlying the effects of high pCO2 on Alaskan crab and fish species\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\nField-based Education and Research at Regional Aquaculture Sites (FERRAS)\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\nFACT: AquaMine - A High Performance Genomic Data Mining System for Species of Importance to US Aquaculture\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\nImproved climate resilience in oysters through optimization of hatchery-based environmental conditioning practices\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\nEffects of temperature change and Hematodinium sp. infection (Bitter Crab Disease) on Tanner crab (Chionoecetes bairdi)\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\nGene activity and genetic selection in Pacific cod reared under thermal stress\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\nA collaborative partnership to address mass mortalities in oyster aquaculture through improved field monitoring, husbandry practices, and workforce development\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\nIdentifying genomic architecture features that contribute to critical phenotypes in shellfish\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\nVernon: Development of innovative approaches to support sustainable aquaculture and understand the effects of ocean acidification on marine species\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\nDevelopment of environmental conditioning practices to decrease impacts of climate change on shellfish aquaculture\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\nEnhancing sustainability of shellfish aquaculture through streamlined maturation control\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\nIncreasing Environmental Connection, Literacy and Engagement through an Art + Science Collaborative Education Practice\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\nReadying sustainable aquaculture for a changing ocean: uncovering the mechanisms associated with intergenerational carryover effects to enhance bivalve resilience to acidification\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\nCollaborative Research: Does ocean acidification induce a methylation response that affects the fitness of the next generation in oysters?\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\nOyster adaptation to climate change via transgenerational plasticity\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\nCollaborative Research: URoL : Epigenetics 2: Predicting phenotypic and eco-evolutionary consequences of environmental-energetic-epigenetic linkages\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\nApplying cutting-edge technology for reproductive control in emerging bivalve species\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\nNo matching items" }, { - "objectID": "publications/notebooks/crandall2022.html#citation", - "href": "publications/notebooks/crandall2022.html#citation", - "title": "Proteomic response of early juvenile Pacific oysters (Crassostrea gigas) to temperature", + "objectID": "publications/articles/crandall2022.html", + "href": "publications/articles/crandall2022.html", + "title": "Characterization of the Gene Repertoire and Environmentally Driven Expression Patterns in Tanner Crab (Chionoecetes bairdi)", "section": "", - "text": "Crandall G, Elliott Thompson R, Eudeline B, Vadopalas B, Timmins-Schiffman E, Roberts S. 2022. Proteomic response of early juvenile Pacific oysters (Crassostrea gigas) to temperature. PeerJ 10:e14158 https://doi.org/10.7717/peerj.14158" + "text": "Crandall, G., Jensen, P.C., White, S.J. et al. Characterization of the Gene Repertoire and Environmentally Driven Expression Patterns in Tanner Crab (Chionoecetes bairdi). Mar Biotechnol 24, 216–225 (2022). https://doi.org/10.1007/s10126-022-10100-8" }, { - "objectID": "publications/notebooks/crandall2022.html#abstract", - "href": "publications/notebooks/crandall2022.html#abstract", - "title": "Proteomic response of early juvenile Pacific oysters (Crassostrea gigas) to temperature", + "objectID": "publications/articles/crandall2022.html#citation", + "href": "publications/articles/crandall2022.html#citation", + "title": "Characterization of the Gene Repertoire and Environmentally Driven Expression Patterns in Tanner Crab (Chionoecetes bairdi)", + "section": "", + "text": "Crandall, G., Jensen, P.C., White, S.J. et al. Characterization of the Gene Repertoire and Environmentally Driven Expression Patterns in Tanner Crab (Chionoecetes bairdi). Mar Biotechnol 24, 216–225 (2022). https://doi.org/10.1007/s10126-022-10100-8" + }, + { + "objectID": "publications/articles/crandall2022.html#abstract", + "href": "publications/articles/crandall2022.html#abstract", + "title": "Characterization of the Gene Repertoire and Environmentally Driven Expression Patterns in Tanner Crab (Chionoecetes bairdi)", "section": "Abstract", - "text": "Abstract\nPacific oysters (Crassostrea gigas) are a valuable aquaculture product that provides important ecosystem benefits. Among other threats, climate-driven changes in ocean temperature can impact oyster metabolism, survivorship, and immune function. We investigated how elevated temperature impacts larval oysters during settlement (19–33 days post-fertilization), using shotgun proteomics with data-independent acquisition to identify proteins present in the oysters after 2 weeks of exposure to 23 °C or 29 °C. Oysters maintained at elevated temperatures were larger and had a higher settlement rate, with 86% surviving to the end of the experiment; these oysters also had higher abundance trends of proteins related to metabolism and growth. Oysters held at 23 °C were smaller, had a decreased settlement rate, displayed 100% mortality, and had elevated abundance trends of proteins related to immune response. This novel use of proteomics was able to capture characteristic shifts in protein abundance that hint at important differences in the phenotypic response of Pacific oysters to temperature regimes. Additionally, this work has produced a robust proteomic product that will be the basis for future research on bivalve developmental processes." + "text": "Abstract\nTanner crab (Chionoecetes bairdi) is an economically important species that is threatened by ocean warming and bitter crab disease, which is caused by an endoparasitic dinoflagellate, Hematodinium. Little is known about disease transmission or its link to host mortality, or how ocean warming will affect pathogenicity or host susceptibility. To provide a transcriptomic resource for the Tanner crab, we generated a suite of RNA-seq libraries encompassing pooled hemolymph samples from crab displaying differing infection statuses and maintained at different temperatures (ambient (7.5˚C), elevated (10˚C), or decreased (4˚C)). After assembling a transcriptome and performing a multifactor differential gene expression analysis, we found genes influenced by temperature in relation to infection and detected some of those genes over time at the individual level using RNA-seq data from one crab. Biological processes associated with those genes include lipid storage, transcription, response to oxidative stress, cell adhesion, and morphogenesis. Alteration in lipid storage and transcription provide insight into how temperature impacts energy allocation in Hematodinium infected crabs. Alteration in expression patterns in genes associated with morphogenesis could suggest that hemocytes were changing morphology and/or type in response to temperature. This project provides insight into how Hematodinium infection could influence crab physiology as oceans warm." }, { - "objectID": "publications/notebooks/crandall2022.html#data-availability", - "href": "publications/notebooks/crandall2022.html#data-availability", - "title": "Proteomic response of early juvenile Pacific oysters (Crassostrea gigas) to temperature", + "objectID": "publications/articles/crandall2022.html#data-availability", + "href": "publications/articles/crandall2022.html#data-availability", + "title": "Characterization of the Gene Repertoire and Environmentally Driven Expression Patterns in Tanner Crab (Chionoecetes bairdi)", "section": "Data Availability", - "text": "Data Availability\nThe following information was supplied regarding data availability:\nAdditional files, scripts, and data are available at Zenodo: grace-ac, & Steven Roberts. (2021). grace-ac/paper-pacific.oyster-larvae: release for PeerJ submission (v2.1.0). Zenodo. https://doi.org/10.5281/zenodo.5708415.\nThe proteomic data is available at PRIDE: PXD015434." + "text": "Data Availability\nThe online version contains supplementary material available at https://doi.org/10.5281/zenodo.4563060" }, { - "objectID": "publications/articles/rajan2021.html", - "href": "publications/articles/rajan2021.html", - "title": "Oyster biomineralisation under ocean acidification: from genes to shell", + "objectID": "publications/articles/arredondo-espinoza2023.html", + "href": "publications/articles/arredondo-espinoza2023.html", + "title": "Transcriptome profile in heat resilient Pacific oyster Crassostrea gigas families under thermal challenge", "section": "", - "text": "Chandra Rajan, K., Yuan, M., Yu, Z., Roberts, S.B. and Thiyagarajan, V. (2021) Oyster biomineralisation under ocean acidification: from genes to shell Global Change Biology. doi:10.1111/gcb.15675" + "text": ">Arredondo-Espinoza R, Ibarra AM, Roberts SB, Sicard-González MT, Escobedo-Fregoso C. Transcriptome profile in heat resilient Pacific oyster Crassostrea gigas families under thermal challenge. Comp Biochem Physiol Part D Genomics Proteomics. 2023 Sep;47:101089. doi: 10.1016/j.cbd.2023.101089. Epub 2023 May 26. PMID: 37269757." }, { - "objectID": "publications/articles/rajan2021.html#citation", - "href": "publications/articles/rajan2021.html#citation", - "title": "Oyster biomineralisation under ocean acidification: from genes to shell", + "objectID": "publications/articles/arredondo-espinoza2023.html#citation", + "href": "publications/articles/arredondo-espinoza2023.html#citation", + "title": "Transcriptome profile in heat resilient Pacific oyster Crassostrea gigas families under thermal challenge", "section": "", - "text": "Chandra Rajan, K., Yuan, M., Yu, Z., Roberts, S.B. and Thiyagarajan, V. (2021) Oyster biomineralisation under ocean acidification: from genes to shell Global Change Biology. doi:10.1111/gcb.15675" + "text": ">Arredondo-Espinoza R, Ibarra AM, Roberts SB, Sicard-González MT, Escobedo-Fregoso C. Transcriptome profile in heat resilient Pacific oyster Crassostrea gigas families under thermal challenge. Comp Biochem Physiol Part D Genomics Proteomics. 2023 Sep;47:101089. doi: 10.1016/j.cbd.2023.101089. Epub 2023 May 26. PMID: 37269757." }, { - "objectID": "publications/articles/rajan2021.html#abstract", - "href": "publications/articles/rajan2021.html#abstract", - "title": "Oyster biomineralisation under ocean acidification: from genes to shell", + "objectID": "publications/articles/arredondo-espinoza2023.html#abstract", + "href": "publications/articles/arredondo-espinoza2023.html#abstract", + "title": "Transcriptome profile in heat resilient Pacific oyster Crassostrea gigas families under thermal challenge", "section": "Abstract", - "text": "Abstract\nBiomineralization is one of the key processes that is notably affected in marine calcifiers such as oysters under ocean acidification (OA). Understanding molecular changes in the biomineralization process under OA and its heritability, therefore, is key to developing conservation strategies for protecting ecologically and economically important oyster species. To do this, in this study, we have explicitly chosen the tissue involved in biomineralization (mantle) of an estuarine commercial oyster species, Crassostrea hongkongensis. The primary aim of this study is to understand the influence of DNA methylation over gene expression of mantle tissue under decreased ~pH 7.4, a proxy of OA, and to extrapolate if these molecular changes can be observed in the product of biomineralization—the shell. We grew early juvenile C. hongkongensis, under decreased ~pH 7.4 and control ~pH 8.0 over 4.5 months and studied OA-induced DNA methylation and gene expression patterns along with shell properties such as microstructure, crystal orientation and hardness. The population of oysters used in this study was found to be moderately resilient to OA at the end of the experiment. The expression of key biomineralization-related genes such as carbonic anhydrase and alkaline phosphatase remained unaffected; thus, the mechanical properties of the shell (shell growth rate, hardness and crystal orientation) were also maintained without any significant difference between control and OA conditions with signs of severe dissolution. In addition, this study makes three major conclusions: (1) higher expression of Ca2+ binding/signalling-related genes in the mantle plays a key role in maintaining biomineralization under OA; (2) DNA methylation changes occur in response to OA; however, these methylation changes do not directly control gene expression; and (3) OA would be more of a 'dissolution problem' rather than a 'biomineralization problem' for resilient species that maintain calcification rate with normal shell growth and mechanical properties." + "text": "Abstract\nSince the introduction of the Pacific oyster Crassostrea gigas in Baja California Sur, Mexico, its culture has faced environmental challenges, specifically increasing temperatures that result in high mortalities. The inter-tidal zone seawater temperature during a year at the Baja California Peninsula broadly ranges from 7 °C to 39 °C. Therefore, to understand how oysters respond to heat stress during daily temperature oscillations, heat-resistant (RR, father, and mother resistant) and heat-susceptible (SS, both parents susceptible) phenotypes families from a C. gigas breeding program were exposed to a thermal challenge. Based on a laboratory-simulated daily oscillatory thermal challenge (26 to 34 °C) for 30 days, RR phenotype presented differences compared to SS phenotype since the beginning (day 0) of the thermal challenge. Gene expression analyses revealed 1822 differentially expressed up-regulated transcripts in RR, related to functions of metabolic processes, biological regulation, and response to stimulus and signaling. At the end of the experiment (day 30), 2660 differentially expressed up-regulated transcripts were identified in RR. Functional analysis of the genes expressed indicates responses of regulation of biological processes and response to a stimulus. Additionally, 340 genes were differentially expressed among RR vs. SS from the beginning to the end of the thermal challenge, where 170 genes were up-regulated, and 170 were down-regulated. These transcriptomic profiles represent the first report to identify gene expression markers associated with RR phenotypes for the Pacific oyster to the future broodstock selection.\n\n\n\nga" }, { - "objectID": "publications/articles/rajan2021.html#data-availability", - "href": "publications/articles/rajan2021.html#data-availability", - "title": "Oyster biomineralisation under ocean acidification: from genes to shell", + "objectID": "publications/articles/arredondo-espinoza2023.html#data-availability", + "href": "publications/articles/arredondo-espinoza2023.html#data-availability", + "title": "Transcriptome profile in heat resilient Pacific oyster Crassostrea gigas families under thermal challenge", "section": "Data Availability", - "text": "Data Availability\nThe RNA-Seq and Methyl RAD data are available under the NCBI Bio-project ID: PRJNA643001. Supporting Information files including the R and perl scripts are provided together with this manuscript." + "text": "Data Availability" }, { - "objectID": "publications/articles/arredondo-espinoza2021.html", - "href": "publications/articles/arredondo-espinoza2021.html", - "title": "Differentially methylated gene regions between resistant and susceptible heat-phenotypes of the Pacific oyster Crassostrea gigas", + "objectID": "publications/articles/silliman2023.html", + "href": "publications/articles/silliman2023.html", + "title": "Epigenetic and genetic population structure is coupled in a marine invertebrate", "section": "", - "text": ">Arredondo-Espinoza Roberto, Ibarra Ana M., Roberts B. Steven, Sicard-Gonzalez Maria Teresa, Escobedo-Fregoso Cristina (2021) Differentially methylated gene regions between resistant and susceptible heat-phenotypes of the Pacific oyster Crassostrea gigas Aquaculture Vol 543. doi:10.1016/j.aquaculture.2021.736923." + "text": "Katherine Silliman and others, Epigenetic and Genetic Population Structure is Coupled in a Marine Invertebrate, Genome Biology and Evolution, Volume 15, Issue 2, February 2023, evad013, https://doi.org/10.1093/gbe/evad013" }, { - "objectID": "publications/articles/arredondo-espinoza2021.html#citation", - "href": "publications/articles/arredondo-espinoza2021.html#citation", - "title": "Differentially methylated gene regions between resistant and susceptible heat-phenotypes of the Pacific oyster Crassostrea gigas", + "objectID": "publications/articles/silliman2023.html#citation", + "href": "publications/articles/silliman2023.html#citation", + "title": "Epigenetic and genetic population structure is coupled in a marine invertebrate", "section": "", - "text": ">Arredondo-Espinoza Roberto, Ibarra Ana M., Roberts B. Steven, Sicard-Gonzalez Maria Teresa, Escobedo-Fregoso Cristina (2021) Differentially methylated gene regions between resistant and susceptible heat-phenotypes of the Pacific oyster Crassostrea gigas Aquaculture Vol 543. doi:10.1016/j.aquaculture.2021.736923." + "text": "Katherine Silliman and others, Epigenetic and Genetic Population Structure is Coupled in a Marine Invertebrate, Genome Biology and Evolution, Volume 15, Issue 2, February 2023, evad013, https://doi.org/10.1093/gbe/evad013" }, { - "objectID": "publications/articles/arredondo-espinoza2021.html#abstract", - "href": "publications/articles/arredondo-espinoza2021.html#abstract", - "title": "Differentially methylated gene regions between resistant and susceptible heat-phenotypes of the Pacific oyster Crassostrea gigas", + "objectID": "publications/articles/silliman2023.html#abstract", + "href": "publications/articles/silliman2023.html#abstract", + "title": "Epigenetic and genetic population structure is coupled in a marine invertebrate", "section": "Abstract", - "text": "Abstract\nHeat stress is one of the factors that affect aquaculture production of the Pacific oyster Crassostrea gigas in Mexico, and research aiming to improve heat tolerance is required. C. gigas breeding stock, produced for genetic improvement, is being implemented, and breeding lines available with 50 families were characterized for their heat-tolerance, selecting the two-most heat-resistant and the two-most heat-susceptible families. These families were analyzed for differences in their DNA methylation patterns after maintaining them for 30 days in a regime of oscillating temperatures (26 °C to 34 °C), similar to what is found in culture areas of Mexico. Whereas no differences were found in global methylation among heat-phenotypes, differentially methylated regions (DMRs) were found between phenotypes. Temperature modifies the methylation in gene bodies of C. gigas, where the heat-resistant phenotype (RR) showed more genes with DMRs in promoters (3672), exons (6340), and introns (18,685). Hyper-methylated genes among phenotypes were more abundant in RR introns (122), followed by exons (23), and promoters (2), whereas hypo-methylated regions corresponded to ten in introns, three in exons, and one in promoters. Hyper-methylated DMRs were mostly found in genes associated with processes such as regulation of gene expression, ions interactions, metabolism, and production of cellular components. This suggests that DMRs among heat-phenotypes in C. gigas families are involved in the heat-shock stress response regulated by methylation. The DMRs reported in this study could be used as methylation markers for a future broodstock selection." + "text": "Abstract\nDelineating the relative influence of genotype and the environment on DNA methylation is critical for characterizing the spectrum of organism fitness as driven by adaptation and phenotypic plasticity. In this study, we integrated genomic and DNA methylation data for two distinct Olympia oyster (Ostrea lurida) populations while controlling for within-generation environmental influences. In addition to providing the first characterization of genome-wide DNA methylation patterns in the oyster genus Ostrea, we identified 3,963 differentially methylated loci between populations. Our results show a clear coupling between genetic and epigenetic patterns of variation, with 27% of variation in interindividual methylation differences explained by genotype. Underlying this association are both direct genetic changes in CpGs (CpG-SNPs) and genetic variation with indirect influence on methylation (mQTLs). When comparing measures of genetic and epigenetic population divergence at specific genomic regions this relationship surprisingly breaks down, which has implications for the methods commonly used to study epigenetic and genetic coupling in marine invertebrates.\n\n\n\nfig7" }, { - "objectID": "publications/articles/arredondo-espinoza2021.html#data-availability", - "href": "publications/articles/arredondo-espinoza2021.html#data-availability", - "title": "Differentially methylated gene regions between resistant and susceptible heat-phenotypes of the Pacific oyster Crassostrea gigas", + "objectID": "publications/articles/silliman2023.html#significance", + "href": "publications/articles/silliman2023.html#significance", + "title": "Epigenetic and genetic population structure is coupled in a marine invertebrate", + "section": "Significance", + "text": "Significance\nWe know that genotype and epigenetic patterns are primarily responsible for phenotype, yet there is a lack of understanding to what degree the two are linked. Here, we characterized the degree by which genetic variation and DNA methylation variation are coupled in a marine invertebrate and identified potential mechanisms, with almost a third of the methylation variation attributable to genotype. This study provides a framework for future studies in environmental epigenetics to take genetic variation into account when teasing apart the drivers of phenotypic variation. By identifying methylation variation that cannot be attributed to genotype or environmental changes during development, our results also highlight the need for future research to characterize molecular mechanisms adjacent to genetic adaptation for producing long-term shifts in phenotype." + }, + { + "objectID": "publications/articles/silliman2023.html#data-availability", + "href": "publications/articles/silliman2023.html#data-availability", + "title": "Epigenetic and genetic population structure is coupled in a marine invertebrate", "section": "Data Availability", - "text": "Data Availability" + "text": "Data Availability\nCode, intermediate analysis files, and genome annotation files used in this study are available in the accompanying repository https://github.com/sr320/paper-oly-mbdbs-gen (https://doi.org/10.5281/zenodo.7083311). The genome assembly can be found at ENA under the accession PRJEB39287 and the raw data are available at NCBI Sequence Read Archive (SRA) at BioProject PRJNA316624. Raw 2b-RAD data are available on SRA at BioProject PRJNA851765. Raw MBD-BS data are available on SRA at BioProject PRJNA849214." }, { - "objectID": "publications/articles/venkataraman2024.html", - "href": "publications/articles/venkataraman2024.html", - "title": "DNA methylation correlates with transcriptional noise in response to elevated pCO2 in the eastern oyster (Crassostrea virginica)", + "objectID": "publications/articles/venkataraman2022.html", + "href": "publications/articles/venkataraman2022.html", + "title": "Differential DNA methylation in Pacific oyster reproductive tissue in response to ocean acidification", "section": "", - "text": "DNA methylation correlates with transcriptional noise in response to elevated pCO2 in the eastern oyster (Crassostrea virginica)\nYaamini R. Venkataraman, Ariana S. Huffmyer, Samuel J. White, Alan Downey-Wall, JillAshey, Danielle M. Becker, Zachary Bengtsson, Hollie M. Putnam, Emma Strand, Javier A. Rodríguez-Casariego, Shelly A. Wanamaker, Kathleen E. Lotterhos, Steven B. Roberts\nbioRxiv 2024.04.04.588108; doi: https://doi.org/10.1101/2024.04.04.588108" + "text": "Venkataraman, Y.R., White, S.J. & Roberts, S.B. Differential DNA methylation in Pacific oyster reproductive tissue in response to ocean acidification. BMC Genomics 23, 556 (2022). https://doi.org/10.1186/s12864-022-08781-5" }, { - "objectID": "publications/articles/venkataraman2024.html#citation", - "href": "publications/articles/venkataraman2024.html#citation", - "title": "DNA methylation correlates with transcriptional noise in response to elevated pCO2 in the eastern oyster (Crassostrea virginica)", + "objectID": "publications/articles/venkataraman2022.html#citation", + "href": "publications/articles/venkataraman2022.html#citation", + "title": "Differential DNA methylation in Pacific oyster reproductive tissue in response to ocean acidification", "section": "", - "text": "DNA methylation correlates with transcriptional noise in response to elevated pCO2 in the eastern oyster (Crassostrea virginica)\nYaamini R. Venkataraman, Ariana S. Huffmyer, Samuel J. White, Alan Downey-Wall, JillAshey, Danielle M. Becker, Zachary Bengtsson, Hollie M. Putnam, Emma Strand, Javier A. Rodríguez-Casariego, Shelly A. Wanamaker, Kathleen E. Lotterhos, Steven B. Roberts\nbioRxiv 2024.04.04.588108; doi: https://doi.org/10.1101/2024.04.04.588108" + "text": "Venkataraman, Y.R., White, S.J. & Roberts, S.B. Differential DNA methylation in Pacific oyster reproductive tissue in response to ocean acidification. BMC Genomics 23, 556 (2022). https://doi.org/10.1186/s12864-022-08781-5" }, { - "objectID": "publications/articles/venkataraman2024.html#abstract", - "href": "publications/articles/venkataraman2024.html#abstract", - "title": "DNA methylation correlates with transcriptional noise in response to elevated pCO2 in the eastern oyster (Crassostrea virginica)", + "objectID": "publications/articles/venkataraman2022.html#abstract", + "href": "publications/articles/venkataraman2022.html#abstract", + "title": "Differential DNA methylation in Pacific oyster reproductive tissue in response to ocean acidification", "section": "Abstract", - "text": "Abstract\nOcean acidification significantly affects marine calcifiers like oysters, warranting the study of molecular mechanisms like DNA methylation that contribute to adaptive plasticity in response to environmental change. However, a consensus has not been reached on the extent to which methylation modules gene expression, and in turn plasticity, in marine invertebrates. In this study, we investigated the impact of pCO2 on gene expression and DNA methylation in the eastern oyster, Crassostrea virginica. After a 30-day exposure to control (572 ppm) or elevated pCO2 (2,827 ppm), whole genome bisulfite sequencing (WGBS) and RNA-Seq data were generated from adult female gonad tissue and male sperm samples. Although differentially methylated loci (DML) were identified in females (89) and males (2,916), there were no differentially expressed genes, and only one differentially expressed transcript in females. However, gene body methylation impacted other forms of gene activity in sperm, such as the maximum number of transcripts expressed per gene and changes in the predominant transcript expressed. Elevated pCO2 exposure increased gene expression variability (transcriptional noise) in males but decreased noise in females, suggesting a sex-specific role of methylation in gene expression regulation. Functional annotation of genes with changes in transcript-level expression or containing DML revealed several enriched biological processes potentially involved in elevated pCO2 response, including apoptotic pathways and signal transduction, as well as reproductive functions. Taken together, these results suggest that DNA methylation may regulate gene expression variability to maintain homeostasis in elevated pCO2 conditions and could play a key role in environmental resilience in marine invertebrates." + "text": "Abstract\nBackground There is a need to investigate mechanisms of phenotypic plasticity in marine invertebrates as negative effects of climate change, like ocean acidification, are experienced by coastal ecosystems. Environmentally-induced changes to the methylome may regulate gene expression, but methylome responses can be species- and tissue-specific. Tissue-specificity has implications for gonad tissue, as gonad-specific methylation patterns may be inherited by offspring. We used the Pacific oyster (Crassostrea gigas) — a model for understanding pH impacts on bivalve molecular physiology due to its genomic resources and importance in global aquaculture— to assess how low pH could impact the gonad methylome. Oysters were exposed to either low pH (7.31 ± 0.02) or ambient pH (7.82 ± 0.02) conditions for 7 weeks. Whole genome bisulfite sequencing was used to identify methylated regions in female oyster gonad samples. C- > T single nucleotide polymorphisms were identified and removed to ensure accurate methylation characterization. Results Analysis of gonad methylomes revealed a total of 1284 differentially methylated loci (DML) found primarily in genes, with several genes containing multiple DML. Gene ontologies for genes containing DML were involved in development and stress response, suggesting methylation may promote gonad growth homeostasis in low pH conditions. Additionally, several of these genes were associated with cytoskeletal structure regulation, metabolism, and protein ubiquitination — commonly-observed responses to ocean acidification. Comparison of these DML with other Crassostrea spp. exposed to ocean acidification demonstrates that similar pathways, but not identical genes, are impacted by methylation. Conclusions Our work suggests DNA methylation may have a regulatory role in gonad and larval development, which would shape adult and offspring responses to low pH stress. Combined with existing molluscan methylome research, our work further supports the need for tissue- and species-specific studies to understand the potential regulatory role of DNA methylation." }, { - "objectID": "publications/articles/venkataraman2024.html#data-availability", - "href": "publications/articles/venkataraman2024.html#data-availability", - "title": "DNA methylation correlates with transcriptional noise in response to elevated pCO2 in the eastern oyster (Crassostrea virginica)", + "objectID": "publications/articles/venkataraman2022.html#data-availability", + "href": "publications/articles/venkataraman2022.html#data-availability", + "title": "Differential DNA methylation in Pacific oyster reproductive tissue in response to ocean acidification", "section": "Data Availability", - "text": "Data Availability\n\nhttps://github.com/sr320/ceabigr\nhttps://osf.io/xuy2f/" + "text": "Data Availability\nAll data, genome feature tracks, scripts, and a supplementary materials list are available in the Oyster Gonad Methylation repository, doi.org/10.17605/OSF.IO/YGCTB. All raw data can be accessed at the NCBI Sequence Read Archive under BioProject accession number PRJNA806944 (https://www.ncbi.nlm.nih.gov/bioproject/806944)." }, { - "objectID": "publications/articles/dimond2021.html", - "href": "publications/articles/dimond2021.html", - "title": "DNA methylation profiling of a cnidarian-algal symbiosis using nanopore sequencing", + "objectID": "publications/articles/dang2022.html", + "href": "publications/articles/dang2022.html", + "title": "Epigenetic-associated phenotypic plasticity of the ocean acidification-acclimated edible oyster in the mariculture environment", "section": "", - "text": "James L Dimond and others, DNA methylation profiling of a cnidarian-algal symbiosis using nanopore sequencing, G3 Genes|Genomes|Genetics, Volume 11, Issue 7, July 2021, jkab148, https://doi.org/10.1093/g3journal/jkab148" + "text": "Dang, X., Lim, Y.-K., Li, Y., Roberts, S. B., Li, L., & Thiyagarajan, V. (2023). Epigenetic-associated phenotypic plasticity of the ocean acidification-acclimated edible oyster in the mariculture environment. Molecular Ecology, 32, 412– 427. https://doi.org/10.1111/mec.16751" }, { - "objectID": "publications/articles/dimond2021.html#citation", - "href": "publications/articles/dimond2021.html#citation", - "title": "DNA methylation profiling of a cnidarian-algal symbiosis using nanopore sequencing", + "objectID": "publications/articles/dang2022.html#citation", + "href": "publications/articles/dang2022.html#citation", + "title": "Epigenetic-associated phenotypic plasticity of the ocean acidification-acclimated edible oyster in the mariculture environment", "section": "", - "text": "James L Dimond and others, DNA methylation profiling of a cnidarian-algal symbiosis using nanopore sequencing, G3 Genes|Genomes|Genetics, Volume 11, Issue 7, July 2021, jkab148, https://doi.org/10.1093/g3journal/jkab148" + "text": "Dang, X., Lim, Y.-K., Li, Y., Roberts, S. B., Li, L., & Thiyagarajan, V. (2023). Epigenetic-associated phenotypic plasticity of the ocean acidification-acclimated edible oyster in the mariculture environment. Molecular Ecology, 32, 412– 427. https://doi.org/10.1111/mec.16751" }, { - "objectID": "publications/articles/dimond2021.html#abstract", - "href": "publications/articles/dimond2021.html#abstract", - "title": "DNA methylation profiling of a cnidarian-algal symbiosis using nanopore sequencing", + "objectID": "publications/articles/dang2022.html#abstract", + "href": "publications/articles/dang2022.html#abstract", + "title": "Epigenetic-associated phenotypic plasticity of the ocean acidification-acclimated edible oyster in the mariculture environment", "section": "Abstract", - "text": "Abstract\nSymbiosis with protists is common among cnidarians such as corals and sea anemones and is associated with homeostatic and phenotypic changes in the host that could have epigenetic underpinnings, such as methylation of CpG dinucleotides. We leveraged the sensitivity to base modifications of nanopore sequencing to probe the effect of symbiosis with the chlorophyte Elliptochloris marina on methylation in the sea anemone Anthopleura elegantissima. We first validated the approach by comparison of nanopore-derived methylation levels with CpG depletion analysis of a published transcriptome, finding that high methylation levels are associated with CpG depletion as expected. Next, using reads generated exclusively from aposymbiotic anemones, a largely complete draft genome comprising 243 Mb was assembled. Reads from aposymbiotic and symbiotic sea anemones were then mapped to this genome and assessed for methylation using the program Nanopolish, which detects signal disruptions from base modifications as they pass through the nanopore. Based on assessment of 452,841 CpGs for which there was adequate read coverage (approximately 8% of the CpGs in the genome), symbiosis with E. marina was, surprisingly, associated with only subtle changes in the host methylome. However, we did identify one extended genomic region with consistently higher methylation among symbiotic individuals. The region was associated with a DNA polymerase zeta that is noted for its role in translesion synthesis, which opens interesting questions about the biology of this symbiosis. Our study highlights the power and relative simplicity of nanopore sequencing for studies of nucleic acid base modifications in non-model species." + "text": "Abstract\nFor marine invertebrates with a pelagic–benthic life cycle, larval exposure to ocean acidification (OA) can affect adult performance in response to another environmental stressor. This carry-over effect has the potential to alter phenotypic traits. However, the molecular mechanisms that mediate “OA”-triggered carry-over effects have not been explored despite such information being key to improving species fitness and management strategies for aquafarming. This study integrated the genome-wide DNA methylome and transcriptome to examine epigenetic modification-mediated carry-over OA impacts on phenotypic traits of the ecologically and commercially important oyster species Crassostrea hongkongensis under field conditions. Larvae of C. hongkongensis were exposed to control pH 8.0 and low pH 7.4 conditions, mimicking near future OA scenario in their habitat, before being outplanted as post-metamorphic juveniles at two mariculture field sites with contrasting environmental stressors for 9 months. The larval carry-over OA effect was found to have persistent impacts on the growth and survival trade-off traits on the outplanted juveniles, although the beneficial or adverse effect depended on the environmental conditions at the outplanted sites. Site-specific plasticity was demonstrated with a diverse DNA methylation-associated gene expression profile, with signal transduction and the endocrine system being the most common and highly enriched functions. Highly methylated exons prevailed in the key genes related to general metabolic and endocytic responses and these genes are evolutionarily conserved in various marine invertebrates in response to OA. These results suggest that oysters with prior larval exposure history to OA had the ability to trigger rapid local adaptive responses via epigenetic modification to cope with multiple stressors in the field." }, { - "objectID": "publications/articles/dimond2021.html#data-availability", - "href": "publications/articles/dimond2021.html#data-availability", - "title": "DNA methylation profiling of a cnidarian-algal symbiosis using nanopore sequencing", + "objectID": "publications/articles/dang2022.html#data-availability", + "href": "publications/articles/dang2022.html#data-availability", + "title": "Epigenetic-associated phenotypic plasticity of the ocean acidification-acclimated edible oyster in the mariculture environment", "section": "Data Availability", - "text": "Data Availability\nA repository containing datasets, notebooks, scripts, and output files, including the draft genome, is publicly available at https://doi.org/10.5281/zenodo.4677448. Raw sequencing reads are available at NCBI under BioProject PRJNA700526 (https://www.ncbi.nlm.nih.gov/sra/PRJNA700526). Supplemental Material available at figshare: https://doi.org/10.25387/g3.14485401." + "text": "Data Availability\nThe methylRAD and RNA-seq data are available under NCBI Bio-project ID PRJNA741860 and PRJNA741374, respectively. Supporting Information including R and Perl scripts are provided." }, { - "objectID": "publications/articles/silliman-bogan2023.html", - "href": "publications/articles/silliman-bogan2023.html", - "title": "A dynamic web resource for robust and reproducible genomics in non-model species: marineomics.io", + "objectID": "publications/articles/huffmyer2024.html", + "href": "publications/articles/huffmyer2024.html", + "title": "Coral larvae increase nitrogen assimilation to stabilize algal symbiosis and combat bleaching under increased temperature", "section": "", - "text": "Bogan, S. N., Johns, J., Griffiths, J. S., Davenport, D., Smith, S. J., Schaal, S. M., Downey-Wall, A., Lou, R. N., Lotterhos, K., Guidry, M. E., Rivera, H. E., McGirr, J. A., Puritz, J. B., Roberts, S. B., & Silliman, K. (2023). A dynamic web resource for robust and reproducible genomics in nonmodel species: marineomics.io. Methods in Ecology and Evolution, 00, 1–8. https://doi.org/10.1111/2041-210X.14219" + "text": ">Huffmyer AS, J Ashey, E Strand, E Chiles, X Su, HM Putnam. (2024) Coral larvae increase nitrogen assimilation to stabilize algal symbiosis and combat bleaching under increased temperature. PLoS Biology 22(11): e3002875. doi: https://doi.org/10.1371/journal.pbio.3002875" }, { - "objectID": "publications/articles/silliman-bogan2023.html#citation", - "href": "publications/articles/silliman-bogan2023.html#citation", - "title": "A dynamic web resource for robust and reproducible genomics in non-model species: marineomics.io", + "objectID": "publications/articles/huffmyer2024.html#citation", + "href": "publications/articles/huffmyer2024.html#citation", + "title": "Coral larvae increase nitrogen assimilation to stabilize algal symbiosis and combat bleaching under increased temperature", "section": "", - "text": "Bogan, S. N., Johns, J., Griffiths, J. S., Davenport, D., Smith, S. J., Schaal, S. M., Downey-Wall, A., Lou, R. N., Lotterhos, K., Guidry, M. E., Rivera, H. E., McGirr, J. A., Puritz, J. B., Roberts, S. B., & Silliman, K. (2023). A dynamic web resource for robust and reproducible genomics in nonmodel species: marineomics.io. Methods in Ecology and Evolution, 00, 1–8. https://doi.org/10.1111/2041-210X.14219" + "text": ">Huffmyer AS, J Ashey, E Strand, E Chiles, X Su, HM Putnam. (2024) Coral larvae increase nitrogen assimilation to stabilize algal symbiosis and combat bleaching under increased temperature. PLoS Biology 22(11): e3002875. doi: https://doi.org/10.1371/journal.pbio.3002875" }, { - "objectID": "publications/articles/silliman-bogan2023.html#abstract", - "href": "publications/articles/silliman-bogan2023.html#abstract", - "title": "A dynamic web resource for robust and reproducible genomics in non-model species: marineomics.io", + "objectID": "publications/articles/huffmyer2024.html#abstract", + "href": "publications/articles/huffmyer2024.html#abstract", + "title": "Coral larvae increase nitrogen assimilation to stabilize algal symbiosis and combat bleaching under increased temperature", "section": "Abstract", - "text": "Abstract\n\nGenomic methods are becoming increasingly valuable and established in eco- logical research, particularly in nonmodel species. Supporting their progress and adoption requires investment in resources that promote (i) reproducibility of genomic analyses, (ii) accessibility of learning tools and (iii) keeping pace with rapidly developing methods and principles.\nWe introduce marineomics.io, an open-source, living document to disseminate tutorials, reproducibility tools and best principles for ecological genomic research in marine and nonmodel systems.\nThe website’s existing content spans population and functional genomics, includ- ing current recommendations for whole-genome sequencing, RAD-seq, Pool-seq and RNA-seq. With the goal to facilitate the development of new, similar re- sources, we describe our process for aggregating and synthesizing methodologi- cal principles from the ecological genomics community to inform website content. We also detail steps for authorship and submission of new website content, as well as protocols for providing feedback and topic requests from the community.\nThese web resources were constructed with guidance for doing rigorous, repro- ducible science. Collaboration and contributions to the website are encouraged from scientists of all skill sets and levels of expertise." + "text": "Abstract\nRising sea surface temperatures are increasingly causing breakdown in the nutritional relationship between corals and algal endosymbionts (Symbiodiniaceae), threatening the basis of coral reef ecosystems and highlighting the critical role of coral reproduction in reef maintenance. The effects of thermal stress on metabolic exchange (i.e., transfer of fixed carbon photosynthates from symbiont to host) during sensitive early life stages, however, remains understudied. We exposed symbiotic Montipora capitata coral larvae in Hawaiʻi to high temperature (+2.5°C for 3 days), assessed rates of photosynthesis and respiration, and used stable isotope tracing (4 mM 13C sodium bicarbonate; 4.5 h) to quantify metabolite exchange. While larvae did not show any signs of bleaching and did not experience declines in survival and settlement, metabolic depression was significant under high temperature, indicated by a 19% reduction in respiration rates, but with no change in photosynthesis. Larvae exposed to high temperature showed evidence for maintained translocation of a major photosynthate, glucose, from the symbiont, but there was reduced metabolism of glucose through central carbon metabolism (i.e., glycolysis). The larval host invested in nitrogen cycling by increasing ammonium assimilation, urea metabolism, and sequestration of nitrogen into dipeptides, a mechanism that may support the maintenance of glucose translocation under thermal stress. Host nitrogen assimilation via dipeptide synthesis appears to be used for nitrogen limitation to the Symbiodiniaceae, and we hypothesize that nitrogen limitation contributes to retention of fixed carbon by favoring photosynthate translocation to the host. Collectively, our findings indicate that although these larvae are susceptible to metabolic stress under high temperature, diverting energy to nitrogen assimilation to maintain symbiont population density, photosynthesis, and carbon translocation may allow larvae to avoid bleaching and highlights potential life stage specific metabolic responses to stress." }, { - "objectID": "publications/articles/silliman-bogan2023.html#data-availability", - "href": "publications/articles/silliman-bogan2023.html#data-availability", - "title": "A dynamic web resource for robust and reproducible genomics in non-model species: marineomics.io", + "objectID": "publications/articles/huffmyer2024.html#data-availability", + "href": "publications/articles/huffmyer2024.html#data-availability", + "title": "Coral larvae increase nitrogen assimilation to stabilize algal symbiosis and combat bleaching under increased temperature", "section": "Data Availability", - "text": "Data Availability\nThe website can be found at http://marineomics.github.io/ and the source repository for contributors is located at https://github.com/ MarineOmics/marineomics.github.io. A snapshot of the site’s source code at the time of submission is available via Zenodo: https://doi. org/10.5281/zenodo.8289843 (Roberts et al., 2023)." + "text": "Data Availability\nhttps://github.com/AHuffmyer/SymbioticIntegration" }, { - "objectID": "publications/articles/putnam2022.html", - "href": "publications/articles/putnam2022.html", - "title": "Dynamic DNA methylation contributes to carryover effects and beneficial acclimatization in geoduck clams", + "objectID": "publications/articles/spencer2023.html", + "href": "publications/articles/spencer2023.html", + "title": "Population-specific effects of ocean acidification in the Olympia oyster", "section": "", - "text": "Dynamic DNA methylation contributes to carryover effects and beneficial acclimatization in geoduck clams Hollie M. Putnam, Shelly A. Wanamaker , Samuel J. White, Laura H. Spencer, Brent Vadopalas, Aparna Natarajan, Jonathan Hetzel, Erich Jaeger, Jonathan Soohoo, Cristian Gallardo-Escárate, Frederick W. Goetz, Steven B. Roberts bioRxiv 2022.06.24.497506; doi: https://doi.org/10.1101/2022.06.24.497506" + "text": "Population-specific effects of ocean acidification in the Olympia oyster Laura H Spencer, Steven B Roberts, Katherine Silliman bioRxiv 2023.09.08.556443; doi: https://doi.org/10.1101/2023.09.08.556443" }, { - "objectID": "publications/articles/putnam2022.html#citation", - "href": "publications/articles/putnam2022.html#citation", - "title": "Dynamic DNA methylation contributes to carryover effects and beneficial acclimatization in geoduck clams", + "objectID": "publications/articles/spencer2023.html#citation", + "href": "publications/articles/spencer2023.html#citation", + "title": "Population-specific effects of ocean acidification in the Olympia oyster", "section": "", - "text": "Dynamic DNA methylation contributes to carryover effects and beneficial acclimatization in geoduck clams Hollie M. Putnam, Shelly A. Wanamaker , Samuel J. White, Laura H. Spencer, Brent Vadopalas, Aparna Natarajan, Jonathan Hetzel, Erich Jaeger, Jonathan Soohoo, Cristian Gallardo-Escárate, Frederick W. Goetz, Steven B. Roberts bioRxiv 2022.06.24.497506; doi: https://doi.org/10.1101/2022.06.24.497506" + "text": "Population-specific effects of ocean acidification in the Olympia oyster Laura H Spencer, Steven B Roberts, Katherine Silliman bioRxiv 2023.09.08.556443; doi: https://doi.org/10.1101/2023.09.08.556443" }, { - "objectID": "publications/articles/putnam2022.html#abstract", - "href": "publications/articles/putnam2022.html#abstract", - "title": "Dynamic DNA methylation contributes to carryover effects and beneficial acclimatization in geoduck clams", + "objectID": "publications/articles/spencer2023.html#abstract", + "href": "publications/articles/spencer2023.html#abstract", + "title": "Population-specific effects of ocean acidification in the Olympia oyster", "section": "Abstract", - "text": "Abstract\nGiven the rapidly changing global climate, there is a growing need to understand the acclimatory basis of animal response to environmental change. To investigate the role of DNA methylation in environmental acclimatization, we generated a reference genome and surveyed the physiology and DNA methylomes of juvenile geoduck clams, Panopea generosa, under differing seawater pH regimes. Juveniles were initially exposed to one of three seawater pH conditions, followed by ambient common-garden conditions, then a second reciprocal exposure to ambient pH or pH 7.4. Within 10 days of the initial low pH exposure, juvenile clams showed decreased shell size relative to ambient pH with corresponding differential DNA methylation. Following four months of ambient common-garden conditions, juveniles initially exposed to low pH compensatorily grew larger, with DNA methylation indicative of these phenotypic differences, demonstrating epigenetic carryover effects persisted months after initial exposure. Functional enrichment analysis of differentially methylated genes revealed regulation of signal transduction through widespread changes in the Wnt signaling pathways that influence cell growth, proliferation, tissue and skeletal formation, and cytoskeletal change. After 10 days of secondary exposure to pH 7.4, naive juvenile clams were more sensitive to low pH compared to those initially exposed, showing reduced growth and having nearly a 2-fold greater change in DNA methylation. Collectively, this new genomic resource and coordinated phenotypic and methylomic response support that epigenetic mechanisms underlie acclimatization to provide beneficial phenotypes." + "text": "Abstract\nPopulations of marine species that respond differently to ocean acidification offer natural reservoirs of biodiversity that can be leveraged for conservation efforts and to sustain marine food systems. The molecular and physiological traits associated with tolerance to acidification must first be identified. This study leveraged oysters from three phenotypically-distinct populations of the Olympia oyster, Ostrea lurida, but that were bred and reared in common conditions for four years. We assessed their growth, reproductive development, and transcriptional response to acidification within and across generations. Responses reveal energetic trade-offs that reflect unique physiotypes previously observed among populations. The population with the slowest growth but high survival rates, oysters from Dabob Bay, mounted the largest transcriptional response to acidification without effects to growth and reproduction. A moderate response was observed in the population with fastest growth rate but lowest fecundity (Fidalgo Bay). Oyster Bay, the population with highest fecundity but lowest survival rates, did not respond at the transcript level. Oyster Bay was also the only population for which acidification negatively affected growth and reproductive development. While exposure to acidification did not affect gene expression in the next generation’s larval stage, it did result in larger larvae in the Oyster Bay population, which could partially alleviate negative effects of acidification in the wild for that population. Given the distinct transcriptional response of the Dabob Bay population to acidification and its high survival rates in previous studies, we then identified genes that were uniquely expressed in Dabob Bay oysters compared to the other populations. Genes involved in antibacterial and antiviral processes, metabolism, growth, and reproduction were uniquely expressed in Dabob Bay, and many similar functions were identified in both adults and larvae, which provides insight into the mechanisms behind a stress-tolerant oyster population. The population-specific physiotypes and responses to acidification illustrate the diversity of physiological strategies in O. lurida that balance the energetic demands of growth, reproduction, cellular maintenance, and offspring viability. Taken together this study reveals that there are distinct physiotypes among marine invertebrate populations on small geographic scales with implications for species resilience to acidification and other environmental stressors." }, { - "objectID": "publications/articles/putnam2022.html#data-availability", - "href": "publications/articles/putnam2022.html#data-availability", - "title": "Dynamic DNA methylation contributes to carryover effects and beneficial acclimatization in geoduck clams", + "objectID": "publications/articles/spencer2023.html#data-availability", + "href": "publications/articles/spencer2023.html#data-availability", + "title": "Population-specific effects of ocean acidification in the Olympia oyster", "section": "Data Availability", - "text": "Data Availability\nThe genomic DNA, transcriptomic, and DNA bisulfite sequence data generated in this study have been submitted to the NCBI BioProject database (https://www.ncbi.nlm.nih.gov/bioproject/) under accession numbers PRJNA316601; PRJNA529226 and PRJNA646071; and PRJNA566166, respectively. All intermediate data files and raw experimental data and statistical code are also available at OSF https://osf.io/yem8n/ (Roberts et al. 2020)." + "text": "Data Availability" }, { - "objectID": "publications/articles/gurr2022.html", - "href": "publications/articles/gurr2022.html", - "title": "Acclimatory gene expression of primed clams enhances robustness to elevated pCO2", + "objectID": "publications/articles/spencer2021.html", + "href": "publications/articles/spencer2021.html", + "title": "Latent effects of winter warming on Olympia oyster reproduction and larval viability", "section": "", - "text": "Gurr, S. J., Wanamaker , S. A., Vadopalas, B., Roberts, S. B., & Putnam, H. M. (2022). Acclimatory gene expression of primed clams enhances robustness to elevated pCO2. Molecular Ecology, 31, 5005– 5023. https://doi.org/10.1111/mec.16644" + "text": "Laura H. Spencer, Erin Horkan, Ryan Crim, Steven B. Roberts (2021) Latent effects of winter warming on Olympia oyster reproduction and larval viability Journal of Experimental Marine Biology and Ecology. doi:10.1016/j.jembe.2021.151604" }, { - "objectID": "publications/articles/gurr2022.html#citation", - "href": "publications/articles/gurr2022.html#citation", - "title": "Acclimatory gene expression of primed clams enhances robustness to elevated pCO2", + "objectID": "publications/articles/spencer2021.html#citation", + "href": "publications/articles/spencer2021.html#citation", + "title": "Latent effects of winter warming on Olympia oyster reproduction and larval viability", "section": "", - "text": "Gurr, S. J., Wanamaker , S. A., Vadopalas, B., Roberts, S. B., & Putnam, H. M. (2022). Acclimatory gene expression of primed clams enhances robustness to elevated pCO2. Molecular Ecology, 31, 5005– 5023. https://doi.org/10.1111/mec.16644" + "text": "Laura H. Spencer, Erin Horkan, Ryan Crim, Steven B. Roberts (2021) Latent effects of winter warming on Olympia oyster reproduction and larval viability Journal of Experimental Marine Biology and Ecology. doi:10.1016/j.jembe.2021.151604" }, { - "objectID": "publications/articles/gurr2022.html#abstract", - "href": "publications/articles/gurr2022.html#abstract", - "title": "Acclimatory gene expression of primed clams enhances robustness to elevated pCO2", + "objectID": "publications/articles/spencer2021.html#highlights", + "href": "publications/articles/spencer2021.html#highlights", + "title": "Latent effects of winter warming on Olympia oyster reproduction and larval viability", + "section": "Highlights", + "text": "Highlights\n• Gametes were more developed following elevated winter temperature.\n• Oocytes and larvae were larger following elevated winter temperature.\n• Larval production and survival were unaffected by winter temperature.\n• O. lurida reproduction is relatively resilient to increasing winter temperatures.\n• In the wild increased larval size due to winter warming could increase recruitment." + }, + { + "objectID": "publications/articles/spencer2021.html#abstract", + "href": "publications/articles/spencer2021.html#abstract", + "title": "Latent effects of winter warming on Olympia oyster reproduction and larval viability", "section": "Abstract", - "text": "Abstract\nBackground Sublethal exposure to environmental challenges may enhance ability to cope with chronic or repeated change, a process known as priming. In a previous study, pre-exposure to seawater enriched with pCO2 improved growth and reduced antioxidant capacity of juvenile Pacific geoduck Panopea generosa clams, suggesting that transcriptional shifts may drive phenotypic modifications post-priming. To this end, juvenile clams were sampled and TagSeq gene expression data were analysed after (i) a 110-day acclimation under ambient (921 μatm, naïve) and moderately elevated pCO2 (2870 μatm, pre-exposed); then following (ii) a second 7-day exposure to three pCO2 treatments (ambient: 754 μatm; moderately elevated: 2750 μatm; severely elevated: 4940 μatm), a 7-day return to ambient pCO2 and a third 7-day exposure to two pCO2 treatments (ambient: 967 μatm; moderately elevated: 3030 μatm). Pre-exposed geoducks frontloaded genes for stress and apoptosis/innate immune response, homeostatic processes, protein degradation and transcriptional modifiers. Pre-exposed geoducks were also responsive to subsequent encounters, with gene sets enriched for mitochondrial recycling and immune defence under elevated pCO2 and energy metabolism and biosynthesis under ambient recovery. In contrast, gene sets with higher expression in naïve clams were enriched for fatty-acid degradation and glutathione components, suggesting naïve clams could be depleting endogenous fuels, with unsustainable energetic requirements if changes in carbonate chemistry persist. Collectively, our transcriptomic data indicate that pCO2 priming during post-larval periods could, via gene expression regulation, enhance robustness in bivalves to environmental change. Such priming approaches may be beneficial for aquaculture, as seafood demand intensifies concurrent with increasing climate change in marine systems." + "text": "Abstract\nFor ectothermic marine invertebrates living in temperate regions, impacts of ocean warming will vary considerably by season. In many species, reproductive and metabolic processes are tightly linked to the seasonal change from winter to spring, yet we know little about how these processes will shift as winters become milder. This study examined latent effects of winter warming on spring reproduction in the Olympia oyster, Ostrea lurida. Adults were collected in autumn from central Puget Sound, WA, USA, and exposed to two winter temperatures (7 °C, 10 °C) in the presence of food limited (5 k algal cells/mL) and food abundant (50 k algal cells/mL) environments. Following treatments, adults exposed to elevated winter temperature contained larger oocytes regardless of feeding regime, and those also fed abundant food contained more developed sperm. Adults then spawned in common conditions, and larvae were reared through settlement to assess carryover effects of winter treatments on larval viability. Adults previously exposed to elevated winter temperature (10 °C) produced larger larvae, particularly if they were also fed high food levels. More developed gametes and larger larvae suggest that gametogenesis occurred at low levels throughout the winter, possibly resulting in increased maternal provisioning to influence larval size. Interestingly, winter temperature did not impact larval survival, or the timing or magnitude of larval production. In the wild, more developed gametes and larger larvae following milder winters could greatly impact recruitment patterns, possibly benefitting O. lurida populations. In the hatchery setting, larval production and survival is not contingent upon winter conditions, and larval survival does not correlate with oocyte and larval size. Our results suggest that O. lurida reproduction is resilient to winter warming. Furthermore, as global temperature continues to rise, winter conditions should not be overlooked when examining reproduction in O. lurida and other temperate marine invertebrates with similar reproductive cycles." }, { - "objectID": "publications/articles/gurr2022.html#data-availability", - "href": "publications/articles/gurr2022.html#data-availability", - "title": "Acclimatory gene expression of primed clams enhances robustness to elevated pCO2", + "objectID": "publications/articles/spencer2021.html#data-availability", + "href": "publications/articles/spencer2021.html#data-availability", + "title": "Latent effects of winter warming on Olympia oyster reproduction and larval viability", "section": "Data Availability", - "text": "Data Availability\n\n\n\n\n\n\nOpen Data\n\n\n\nThis article has earned an Open Data Badge for making publicly available the digitally-shareable data necessary to reproduce the reported results\n\n\nThe data is available at https://doi.org/10.5281/zenodo.6908630.\nRaw sequence reads are deposited in the SRA (Accession: PRJNA740307; BioProject: Transcriptome profiles of Panopea generosa under hypercapnic seawater). All data have been submitted as a public Zenodo repository https://doi.org/10.5281/zenodo.6908630." + "text": "Data Availability\nAll data and code associated with this project are publicly available https://doi.org/10.6084/m9.figshare.14066498.v3\nL.H. Spencer, E. Horkan, R. Crim, S.B. Roberts Paper-olurida-latent-effects. figshare. Dataset (2021), 10.6084/m9.figshare.14066498.v3" }, { - "objectID": "publications/articles/george2023.html", - "href": "publications/articles/george2023.html", - "title": "Triploid Pacific oysters exhibit stress response dysregulation and elevated mortality following heatwaves", + "objectID": "publications/articles/gurr2021.html", + "href": "publications/articles/gurr2021.html", + "title": "Repeat exposure to hypercapnic seawater modifies growth and oxidative status in a tolerant burrowing clam", "section": "", - "text": "George, M. N.,  Cattau, O.,  Middleton, M. A.,  Lawson, D.,  Vadopalas, B.,  Gavery, M., &  Roberts, S. B. (2023). Triploid Pacific oysters exhibit stress response dysregulation and elevated mortality following heatwaves. Global Change Biology,  00,  1–19. https://doi.org/10.1111/gcb.16880" + "text": "Samuel J. Gurr, Shelly A. Wanamaker, Brent Vadopalas, Steven B. Roberts, Hollie M. Putnam; Repeat exposure to hypercapnic seawater modifies growth and oxidative status in a tolerant burrowing clam. J Exp Biol 1 July 2021; 224 (13): jeb233932. doi: https://doi.org/10.1242/jeb.233932" }, { - "objectID": "publications/articles/george2023.html#citation", - "href": "publications/articles/george2023.html#citation", - "title": "Triploid Pacific oysters exhibit stress response dysregulation and elevated mortality following heatwaves", + "objectID": "publications/articles/gurr2021.html#citation", + "href": "publications/articles/gurr2021.html#citation", + "title": "Repeat exposure to hypercapnic seawater modifies growth and oxidative status in a tolerant burrowing clam", "section": "", - "text": "George, M. N.,  Cattau, O.,  Middleton, M. A.,  Lawson, D.,  Vadopalas, B.,  Gavery, M., &  Roberts, S. B. (2023). Triploid Pacific oysters exhibit stress response dysregulation and elevated mortality following heatwaves. Global Change Biology,  00,  1–19. https://doi.org/10.1111/gcb.16880" + "text": "Samuel J. Gurr, Shelly A. Wanamaker, Brent Vadopalas, Steven B. Roberts, Hollie M. Putnam; Repeat exposure to hypercapnic seawater modifies growth and oxidative status in a tolerant burrowing clam. J Exp Biol 1 July 2021; 224 (13): jeb233932. doi: https://doi.org/10.1242/jeb.233932" }, { - "objectID": "publications/articles/george2023.html#abstract", - "href": "publications/articles/george2023.html#abstract", - "title": "Triploid Pacific oysters exhibit stress response dysregulation and elevated mortality following heatwaves", + "objectID": "publications/articles/gurr2021.html#abstract", + "href": "publications/articles/gurr2021.html#abstract", + "title": "Repeat exposure to hypercapnic seawater modifies growth and oxidative status in a tolerant burrowing clam", "section": "Abstract", - "text": "Abstract\nPolyploidy has been shown to negatively impact environmental stress tolerance, resulting in increased susceptibility to extreme climate events such as marine heatwaves (MHWs). In this study, we used the response of the Pacific oyster Crassostrea gigas to MHWs as a model system to identify key ploidy-specific differences in the physiological and transcriptomic response of oysters to environmental stress. In this study, adult diploid (2n) and triploid (3n) oysters were exposed to elevated seawater temperature (single stressor; 30°C), elevated temperature followed by acute desiccation stress (multiple stressor; 30°C + emersion at an aerial temperature of 44°C for 4h), or a control (17°C) within a hatchery setting. Oyster mortality rate was elevated within stress treatments with respect to the control and was significantly higher in triploids than diploids following multiple stress exposure (36.4% vs. 14.8%). Triploids within the multiple stressor treatment exhibited signs of energetic limitation, including metabolic depression, a significant reduction in ctenidium Na+/K+ ATPase activity, and the dysregulated expression of key genes associated with heat tolerance, the inhibition of apoptosis, and mitochondrial function. Functional enrichment analysis of ploidy-specific gene sets identified that biological processes associated with metabolism, stress tolerance, and immune function were overrepresented within triploids across stress treatments. Our results demonstrate that triploidy impacts the transcriptional regulation of key metabolic processes that underly the environmental stress response of Pacific oysters, resulting in downstream shifts in physiological tolerance limits that may be detrimental to survival. The impact of chromosome set manipulation on the climate resilience of marine populations has important implications for the adaptability of marine populations and domestic food security within future climate scenarios, especially as triploidy induction becomes an increasingly popular tool to elicit reproductive control across a wide range of marine organisms used within marine aquaculture." + "text": "Abstract\nAlthough low levels of thermal stress, irradiance and dietary restriction can have beneficial effects for many taxa, stress acclimation remains little studied in marine invertebrates, even though they are threatened by climate change stressors such as ocean acidification. To test the role of life-stage and stress-intensity dependence in eliciting enhanced tolerance under subsequent stress encounters, we initially conditioned pediveliger Pacific geoduck (Panopea generosa) larvae to ambient and moderately elevated PCO2 (920 µatm and 2800 µatm, respectively) for 110 days. Then, clams were exposed to ambient, moderate or severely elevated PCO2 (750, 2800 or 4900 µatm, respectively) for 7 days and, following 7 days in ambient conditions, a 7-day third exposure to ambient (970 µatm) or moderate PCO2 (3000 µatm). Initial conditioning to moderate PCO2 stress followed by second and third exposure to severe and moderate PCO2 stress increased respiration rate, organic biomass and shell size, suggesting a stress-intensity-dependent effect on energetics. Additionally, stress-acclimated clams had lower antioxidant capacity compared with clams under ambient conditions, supporting the hypothesis that stress over postlarval-to-juvenile development affects oxidative status later in life. Time series and stress intensity-specific approaches can reveal life-stages and magnitudes of exposure, respectively, that may elicit beneficial phenotypic variation." }, { - "objectID": "publications/articles/george2023.html#data-availability", - "href": "publications/articles/george2023.html#data-availability", - "title": "Triploid Pacific oysters exhibit stress response dysregulation and elevated mortality following heatwaves", + "objectID": "publications/articles/gurr2021.html#data-availability", + "href": "publications/articles/gurr2021.html#data-availability", + "title": "Repeat exposure to hypercapnic seawater modifies growth and oxidative status in a tolerant burrowing clam", "section": "Data Availability", - "text": "Data Availability\nThe data that support the findings of this study are openly available at https://doi.org/10.5281/zenodo.7693092 (George et al., 2023). Tag-seq data are available under the NCBI BioProject ID 913164. Supporting tables and figures are provided together with this manuscript." + "text": "Data Availability\nAll raw data and statistical code are openly available in the Zenodo repository at: http://doi.org/10.5281/zenodo.3903019." }, { - "objectID": "publications/articles/gallardo2021.html", - "href": "publications/articles/gallardo2021.html", - "title": "Chromosome-scale genome assembly of the sea louse Caligus rogercresseyi by SMRT sequencing and Hi-C analysis", + "objectID": "publications/articles/trigg2021.html", + "href": "publications/articles/trigg2021.html", + "title": "Invertebrate methylomes provide insight into mechanisms of environmental tolerance and reveal methodological biases", "section": "", - "text": "Gallardo-Escárate, C., Valenzuela-Muñoz, V., Nuñez-Acuña, G. et al. Chromosome-scale genome assembly of the sea louse Caligus rogercresseyi by SMRT sequencing and Hi-C analysis. Sci Data 8, 60 (2021). https://doi.org/10.1038/s41597-021-00842-w" + "text": "Wanamaker , S. A., Venkataraman, Y. R., Gavery, M. R., Roberts, S. B., Bhattacharya, D., Downey-Wall, A., Eirin-Lopez, J. M., Johnson, K. M., Lotterhos, K. E., Puritz, J. B., & Putnam, H. M. (2022). Invertebrate methylomes provide insight into mechanisms of environmental tolerance and reveal methodological biases. Molecular Ecology Resources, 22, 1247– 1261. https://doi.org/10.1111/1755-0998.13542" }, { - "objectID": "publications/articles/gallardo2021.html#citation", - "href": "publications/articles/gallardo2021.html#citation", - "title": "Chromosome-scale genome assembly of the sea louse Caligus rogercresseyi by SMRT sequencing and Hi-C analysis", + "objectID": "publications/articles/trigg2021.html#citation", + "href": "publications/articles/trigg2021.html#citation", + "title": "Invertebrate methylomes provide insight into mechanisms of environmental tolerance and reveal methodological biases", "section": "", - "text": "Gallardo-Escárate, C., Valenzuela-Muñoz, V., Nuñez-Acuña, G. et al. Chromosome-scale genome assembly of the sea louse Caligus rogercresseyi by SMRT sequencing and Hi-C analysis. Sci Data 8, 60 (2021). https://doi.org/10.1038/s41597-021-00842-w" + "text": "Wanamaker , S. A., Venkataraman, Y. R., Gavery, M. R., Roberts, S. B., Bhattacharya, D., Downey-Wall, A., Eirin-Lopez, J. M., Johnson, K. M., Lotterhos, K. E., Puritz, J. B., & Putnam, H. M. (2022). Invertebrate methylomes provide insight into mechanisms of environmental tolerance and reveal methodological biases. Molecular Ecology Resources, 22, 1247– 1261. https://doi.org/10.1111/1755-0998.13542" }, { - "objectID": "publications/articles/gallardo2021.html#abstract", - "href": "publications/articles/gallardo2021.html#abstract", - "title": "Chromosome-scale genome assembly of the sea louse Caligus rogercresseyi by SMRT sequencing and Hi-C analysis", + "objectID": "publications/articles/trigg2021.html#abstract", + "href": "publications/articles/trigg2021.html#abstract", + "title": "Invertebrate methylomes provide insight into mechanisms of environmental tolerance and reveal methodological biases", "section": "Abstract", - "text": "Abstract\nCaligus rogercresseyi, commonly known as sea louse, is an ectoparasite copepod that impacts the salmon aquaculture in Chile, causing losses of hundreds of million dollars per year. In this study, we report a chromosome-scale assembly of the sea louse (C. rogercresseyi) genome based on single-molecule real-time sequencing (SMRT) and proximity ligation (Hi-C) analysis. Coding RNAs and non-coding RNAs, and specifically long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) were identified through whole transcriptome sequencing from different life stages. A total of 23,686 protein-coding genes and 12,558 non-coding RNAs were annotated. In addition, 6,308 lncRNAs and 5,774 miRNAs were found to be transcriptionally active from larvae to adult stages. Taken together, this genomic resource for C. rogercresseyi represents a valuable tool to develop sustainable control strategies in the salmon aquaculture industry." + "text": "Abstract\nThere is a growing focus on the role of DNA methylation in the ability of marine invertebrates to rapidly respond to changing environmental factors and anthropogenic impacts. However, genome-wide DNA methylation studies in nonmodel organisms are currently hampered by a limited understanding of methodological biases. Here, we compare three methods for quantifying DNA methylation at single base-pair resolution—whole genome bisulfite sequencing (WGBS), reduced representation bisulfite sequencing (RRBS), and methyl-CpG binding domain bisulfite sequencing (MBDBS)—using multiple individuals from two reef-building coral species with contrasting environmental sensitivity. All methods reveal substantially greater methylation in Montipora capitata (11.4%) than the more sensitive Pocillopora acuta (2.9%). The majority of CpG methylation in both species occurs in gene bodies and flanking regions. In both species, MBDBS has the greatest capacity for detecting CpGs in coding regions at our sequencing depth, but MBDBS may be influenced by intrasample methylation heterogeneity. RRBS yields robust information for specific loci albeit without enrichment of any particular genome feature and with significantly reduced genome coverage. Relative genome size strongly influences the number and location of CpGs detected by each method when sequencing depth is limited, illuminating nuances in cross-species comparisons. As genome-wide methylation differences, supported by data across bisulfite sequencing methods, may contribute to environmental sensitivity phenotypes in critical marine invertebrate taxa, these data provide a genomic resource for investigating the functional role of DNA methylation in environmental tolerance." }, { - "objectID": "publications/articles/gallardo2021.html#data-availability", - "href": "publications/articles/gallardo2021.html#data-availability", - "title": "Chromosome-scale genome assembly of the sea louse Caligus rogercresseyi by SMRT sequencing and Hi-C analysis", + "objectID": "publications/articles/trigg2021.html#data-availability", + "href": "publications/articles/trigg2021.html#data-availability", + "title": "Invertebrate methylomes provide insight into mechanisms of environmental tolerance and reveal methodological biases", "section": "Data Availability", - "text": "Data Availability\nDNA and RNA sequencing runs were deposited to NCBI Sequence Read Archive (SRA)1(https://www.nature.com/articles/s41597-021-00842-w#ref-CR50 “NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP229458\n (2019).\"),[51](https://www.nature.com/articles/s41597-021-00842-w#ref-CR51 \"NCBI Sequence Read Archive \n https://identifiers.org/ncbi/insdc.sra:SRP212140\n \n (2019).\"),[52](https://www.nature.com/articles/s41597-021-00842-w#ref-CR52 \"NCBI Sequence Read Archive \n https://identifiers.org/ncbi/insdc.sra:SRP067375\n \n (2015).\")^. The assembled genome has been deposited at NCBI assembly with the accession number ASM1338718v1^[53](https://www.nature.com/articles/s41597-021-00842-w#ref-CR53 \"NCBI Assembly \n https://identifiers.org/insdc.gca:GCA_013387185.1\n \n (2020).\")^. Additional files containing repeated sequences, gene structure, and functional prediction were deposited in the *Figshare*database^[54](https://www.nature.com/articles/s41597-021-00842-w#ref-CR54 \"Gallardo-Escárate, C. Additional annotation files_GenSAS. figshare \n https://doi.org/10.6084/m9.figshare.12847493\n \n (2020).\")^." - }, - { - "objectID": "publications/articles/gallardo2021.html#footnotes", - "href": "publications/articles/gallardo2021.html#footnotes", - "title": "Chromosome-scale genome assembly of the sea louse Caligus rogercresseyi by SMRT sequencing and Hi-C analysis", - "section": "Footnotes", - "text": "Footnotes\n\n\n50↩︎" + "text": "Data Availability\n\n\n\n\n\n\nOpen Data\n\n\n\nThis article has earned an Open Data Badge for making publicly available the digitally-shareable data necessary to reproduce the reported results\n\n\nThe data sets supporting the conclusions of this article are available in the Coral Methylation Methods Comparison repository, http://doi.org/10.17605/OSF.IO/X5WAZ, and included within the article and its additional files. All raw data can be accessed under NCBI Bioproject PRJNA691891." }, { - "objectID": "publications/articles/buckley2023.html", - "href": "publications/articles/buckley2023.html", - "title": "Characterizing biological responses to climate variability and extremes to improve biodiversity projections", + "objectID": "publications/articles/crandall2022b.html", + "href": "publications/articles/crandall2022b.html", + "title": "Proteomic response of early juvenile Pacific oysters (Crassostrea gigas) to temperature", "section": "", - "text": "Buckley LB, Carrington E, Dillon ME, García-Robledo C, Roberts SB, Wegrzyn JL, et al. (2023) Characterizing biological responses to climate variability and extremes to improve biodiversity projections. PLOS Clim 2(6): e0000226. https://doi.org/10.1371/journal.pclm.0000226" + "text": "Crandall G, Elliott Thompson R, Eudeline B, Vadopalas B, Timmins-Schiffman E, Roberts S. 2022. Proteomic response of early juvenile Pacific oysters (Crassostrea gigas) to temperature. PeerJ 10:e14158 https://doi.org/10.7717/peerj.14158" }, { - "objectID": "publications/articles/buckley2023.html#citation", - "href": "publications/articles/buckley2023.html#citation", - "title": "Characterizing biological responses to climate variability and extremes to improve biodiversity projections", + "objectID": "publications/articles/crandall2022b.html#citation", + "href": "publications/articles/crandall2022b.html#citation", + "title": "Proteomic response of early juvenile Pacific oysters (Crassostrea gigas) to temperature", "section": "", - "text": "Buckley LB, Carrington E, Dillon ME, García-Robledo C, Roberts SB, Wegrzyn JL, et al. (2023) Characterizing biological responses to climate variability and extremes to improve biodiversity projections. PLOS Clim 2(6): e0000226. https://doi.org/10.1371/journal.pclm.0000226" + "text": "Crandall G, Elliott Thompson R, Eudeline B, Vadopalas B, Timmins-Schiffman E, Roberts S. 2022. Proteomic response of early juvenile Pacific oysters (Crassostrea gigas) to temperature. PeerJ 10:e14158 https://doi.org/10.7717/peerj.14158" }, { - "objectID": "publications/articles/buckley2023.html#abstract", - "href": "publications/articles/buckley2023.html#abstract", - "title": "Characterizing biological responses to climate variability and extremes to improve biodiversity projections", + "objectID": "publications/articles/crandall2022b.html#abstract", + "href": "publications/articles/crandall2022b.html#abstract", + "title": "Proteomic response of early juvenile Pacific oysters (Crassostrea gigas) to temperature", "section": "Abstract", - "text": "Abstract\nProjecting ecological and evolutionary responses to variable and changing environments is central to anticipating and managing impacts to biodiversity and ecosystems. Current modeling approaches are largely phenomenological and often fail to accurately project responses due to numerous biological processes at multiple levels of biological organization responding to environmental variation at varied spatial and temporal scales. Limited mechanistic understanding of organismal responses to environmental variability and extremes also restricts predictive capacity. We outline a strategy for identifying and modeling the key organismal mechanisms across levels of biological organization that mediate ecological and evolutionary responses to environmental variation. A central component of this strategy is quantifying timescales and magnitudes of climatic variability and how organisms experience them. We highlight recent empirical research that builds this information and suggest how to design future experiments that can produce more generalizable principles. We discuss how to create biologically informed projections in a feasible way by combining statistical and mechanistic approaches. Predictions will inform both fundamental and practical questions at the interface of ecology, evolution, and Earth science such as how organisms experience, adapt to, and respond to environmental variation at multiple hierarchical spatial and temporal scales." + "text": "Abstract\nPacific oysters (Crassostrea gigas) are a valuable aquaculture product that provides important ecosystem benefits. Among other threats, climate-driven changes in ocean temperature can impact oyster metabolism, survivorship, and immune function. We investigated how elevated temperature impacts larval oysters during settlement (19–33 days post-fertilization), using shotgun proteomics with data-independent acquisition to identify proteins present in the oysters after 2 weeks of exposure to 23 °C or 29 °C. Oysters maintained at elevated temperatures were larger and had a higher settlement rate, with 86% surviving to the end of the experiment; these oysters also had higher abundance trends of proteins related to metabolism and growth. Oysters held at 23 °C were smaller, had a decreased settlement rate, displayed 100% mortality, and had elevated abundance trends of proteins related to immune response. This novel use of proteomics was able to capture characteristic shifts in protein abundance that hint at important differences in the phenotypic response of Pacific oysters to temperature regimes. Additionally, this work has produced a robust proteomic product that will be the basis for future research on bivalve developmental processes." }, { - "objectID": "publications/articles/buckley2023.html#data-availability", - "href": "publications/articles/buckley2023.html#data-availability", - "title": "Characterizing biological responses to climate variability and extremes to improve biodiversity projections", + "objectID": "publications/articles/crandall2022b.html#data-availability", + "href": "publications/articles/crandall2022b.html#data-availability", + "title": "Proteomic response of early juvenile Pacific oysters (Crassostrea gigas) to temperature", "section": "Data Availability", - "text": "Data Availability\nS1 Text.Supplementary methods for fitting data on the temperature dependence of mussel assimilation rate.\nhttps://doi.org/10.1371/journal.pclm.0000226.s001\n(DOCX)" + "text": "Data Availability\nThe following information was supplied regarding data availability:\nAdditional files, scripts, and data are available at Zenodo: grace-ac, & Steven Roberts. (2021). grace-ac/paper-pacific.oyster-larvae: release for PeerJ submission (v2.1.0). Zenodo. https://doi.org/10.5281/zenodo.5708415.\nThe proteomic data is available at PRIDE: PXD015434." }, { - "objectID": "publications/articles/gallardo2023.html", - "href": "publications/articles/gallardo2023.html", - "title": "Chromosome-Level Genome Assembly of the Blue Mussel Mytilus chilensis Reveals Molecular Signatures Facing the Marine Environment", + "objectID": "publications/articles/timmins-schiffman2021.html", + "href": "publications/articles/timmins-schiffman2021.html", + "title": "Coupled microbiome analyses highlights relative functional roles of bacteria in a bivalve hatchery", "section": "", - "text": "Gallardo-Escárate, C.; Valenzuela-Muñoz, V.; Nuñez-Acuña, G.; Valenzuela-Miranda, D.; Tapia, F.J.; Yévenes, M.; Gajardo, G.; Toro, J.E.; Oyarzún, P.A.; Arriagada, G.; et al. Chromosome-Level Genome Assembly of the Blue Mussel Mytilus chilensis Reveals Molecular Signatures Facing the Marine Environment. Genes 2023, 14, 876. https://doi.org/10.3390/genes14040876" + "text": "Timmins-Schiffman, E., White, S.J., Thompson, R.E. et al. Coupled microbiome analyses highlights relative functional roles of bacteria in a bivalve hatchery. Environmental Microbiome 16, 7 (2021). https://doi.org/10.1186/s40793-021-00376-z" }, { - "objectID": "publications/articles/gallardo2023.html#citation", - "href": "publications/articles/gallardo2023.html#citation", - "title": "Chromosome-Level Genome Assembly of the Blue Mussel Mytilus chilensis Reveals Molecular Signatures Facing the Marine Environment", + "objectID": "publications/articles/timmins-schiffman2021.html#citation", + "href": "publications/articles/timmins-schiffman2021.html#citation", + "title": "Coupled microbiome analyses highlights relative functional roles of bacteria in a bivalve hatchery", "section": "", - "text": "Gallardo-Escárate, C.; Valenzuela-Muñoz, V.; Nuñez-Acuña, G.; Valenzuela-Miranda, D.; Tapia, F.J.; Yévenes, M.; Gajardo, G.; Toro, J.E.; Oyarzún, P.A.; Arriagada, G.; et al. Chromosome-Level Genome Assembly of the Blue Mussel Mytilus chilensis Reveals Molecular Signatures Facing the Marine Environment. Genes 2023, 14, 876. https://doi.org/10.3390/genes14040876" + "text": "Timmins-Schiffman, E., White, S.J., Thompson, R.E. et al. Coupled microbiome analyses highlights relative functional roles of bacteria in a bivalve hatchery. Environmental Microbiome 16, 7 (2021). https://doi.org/10.1186/s40793-021-00376-z" }, { - "objectID": "publications/articles/gallardo2023.html#abstract", - "href": "publications/articles/gallardo2023.html#abstract", - "title": "Chromosome-Level Genome Assembly of the Blue Mussel Mytilus chilensis Reveals Molecular Signatures Facing the Marine Environment", + "objectID": "publications/articles/timmins-schiffman2021.html#abstract", + "href": "publications/articles/timmins-schiffman2021.html#abstract", + "title": "Coupled microbiome analyses highlights relative functional roles of bacteria in a bivalve hatchery", "section": "Abstract", - "text": "Abstract\nThe blue mussel Mytilus chilensis is an endemic and key socioeconomic species inhabiting the southern coast of Chile. This bivalve species supports a booming aquaculture industry, which entirely relies on artificially collected seeds from natural beds that are translocated to diverse physical–chemical ocean farming conditions. Furthermore, mussel production is threatened by a broad range of microorganisms, pollution, and environmental stressors that eventually impact its survival and growth. Herein, understanding the genomic basis of the local adaption is pivotal to developing sustainable shellfish aquaculture. We present a high-quality reference genome of M. chilensis, which is the first chromosome-level genome for a Mytilidae member in South America. The assembled genome size was 1.93 Gb, with a contig N50 of 134 Mb. Through Hi-C proximity ligation, 11,868 contigs were clustered, ordered, and assembled into 14 chromosomes in congruence with the karyological evidence. The M. chilensis genome comprises 34,530 genes and 4795 non-coding RNAs. A total of 57% of the genome contains repetitive sequences with predominancy of LTR-retrotransposons and unknown elements. Comparative genome analysis of M. chilensis and M. coruscus was conducted, revealing genic rearrangements distributed into the whole genome. Notably, transposable Steamer-like elements associated with horizontal transmissible cancer were explored in reference genomes, suggesting putative relationships at the chromosome level in Bivalvia. Genome expression analysis was also conducted, showing putative genomic differences between two ecologically different mussel populations. The evidence suggests that local genome adaptation and physiological plasticity can be analyzed to develop sustainable mussel production. The genome of M. chilensis provides pivotal molecular knowledge for the Mytilus complex." + "text": "Abstract\nBackground Microbial communities are ubiquitous throughout ecosystems and are commensal with hosts across taxonomic boundaries. Environmental and species-specific microbiomes are instrumental in maintaining ecosystem and host health, respectively. The introduction of pathogenic microbes that shift microbiome community structure can lead to illness and death. Understanding the dynamics of microbiomes across a diversity of environments and hosts will help us to better understand which taxa forecast survival and which forecast mortality events. Results We characterized the bacterial community microbiome in the water of a commercial shellfish hatchery in Washington state, USA, where the hatchery has been plagued by recurring and unexplained larval mortality events. By applying the complementary methods of metagenomics and metaproteomics we were able to more fully characterize the bacterial taxa in the hatchery at high (pH 8.2) and low (pH 7.1) pH that were metabolically active versus present but not contributing metabolically. There were shifts in the taxonomy and functional profile of the microbiome between pH and over time. Based on detected metagenomic reads and metaproteomic peptide spectral matches, some taxa were more metabolically active than expected based on presence alone (Deltaproteobacteria, Alphaproteobacteria) and some were less metabolically active than expected (e.g., Betaproteobacteria, Cytophagia). There was little correlation between potential and realized metabolic function based on Gene Ontology analysis of detected genes and peptides. Conclusion The complementary methods of metagenomics and metaproteomics contribute to a more full characterization of bacterial taxa that are potentially active versus truly metabolically active and thus impact water quality and inter-trophic relationships." }, { - "objectID": "publications/articles/gallardo2023.html#data-availability", - "href": "publications/articles/gallardo2023.html#data-availability", - "title": "Chromosome-Level Genome Assembly of the Blue Mussel Mytilus chilensis Reveals Molecular Signatures Facing the Marine Environment", + "objectID": "publications/articles/timmins-schiffman2021.html#data-availability", + "href": "publications/articles/timmins-schiffman2021.html#data-availability", + "title": "Coupled microbiome analyses highlights relative functional roles of bacteria in a bivalve hatchery", "section": "Data Availability", - "text": "Data Availability\nThe Mytilus chilensis whole-genome sequencing data supporting this study’s findings are available from NCBI under BioProject PRJNA861856. The sequencing data supporting this study’s findings are available in SRA at SRR20966976, SRR20593343, and SRP261955. The benefits from this study accrue from sharing our data and results on public databases as described above. The assembled genome and the genome annotation results were deposited in the Figshare database [93]." + "text": "Data Availability\nThe sequenced metagenomics data can be found in NCBI’s Short Read Archive under BioProject PRJNA649049. The metaproteomics dataset can be found in the ProteomeXchange PRIDE repository under accession PXD020692." }, { - "objectID": "publications/articles/valenzuela2024.html", - "href": "publications/articles/valenzuela2024.html", - "title": "Environmental influence on the Atlantic salmon transcriptome and methylome during sea lice infestations", + "objectID": "notebooks.html", + "href": "notebooks.html", + "title": "Lab Notebooks", "section": "", - "text": "Valenzuela-Muñoz, V., Wanamaker, S., Núñez-Acuña, G., Roberts, S., Garcia, A., Valdés, J. A., Valenzuela-Miranda, D., & Gallardo-Escarate, C. (2024). Environmental influence on the Atlantic salmon transcriptome and methylome during sea lice infestations. Full Length Article, FSIM-D-24-00599R2." + "text": "Person\nNotebook\nCommitment\n\n\n\n\nSteven Roberts\nsr320.github.io\n\n\n\nSam White\nrobertslab.github.io\n\n\n\nMatt George\nmattgeorgephd.github.io\n\n\n\nAspen Coyle\naspencoyle.github.io\n\n\n\nAriana Huffmyer\nahuffmyer.github.io\n\n\n\nChris Mantegna\nchrismantegna.github.io\n\n\n\nZach Bengtsson\nzbengt.github.io\n\n\n\nCeleste Valdivia\nvaleste.github.io\n\n\n\nGrace Crandall\ngrace-ac.github.io\n\n\n\nKathleen Durkin\nshedurkin.github.io\n\n\n\nMegan Ewing\nmewing-notebook" }, { - "objectID": "publications/articles/valenzuela2024.html#citation", - "href": "publications/articles/valenzuela2024.html#citation", - "title": "Environmental influence on the Atlantic salmon transcriptome and methylome during sea lice infestations", + "objectID": "posts/sr320-marineomics/index.html", + "href": "posts/sr320-marineomics/index.html", + "title": "MarineOmics.io", "section": "", - "text": "Valenzuela-Muñoz, V., Wanamaker, S., Núñez-Acuña, G., Roberts, S., Garcia, A., Valdés, J. A., Valenzuela-Miranda, D., & Gallardo-Escarate, C. (2024). Environmental influence on the Atlantic salmon transcriptome and methylome during sea lice infestations. Full Length Article, FSIM-D-24-00599R2." + "text": "In an era where ecological genomics is garnering increased recognition, particularly within nonmodel species, the necessity for robust, reproducible, and accessible resources has never been more apparent. A recent publication led by a consortium of researchers introduces MarineOmics.io, a dynamic web resource tailored to meet the burgeoning needs of this scientific domain. This open-source platform aims to foster a collaborative environment for researchers at various stages of their career, promoting reproducibility, accessibility, and adaptability in genomic analyses.\nMarineOmics.io emerges as a living document, meticulously curated to disseminate vital tutorials, reproducibility tools, and best principles pivotal for genomic research in marine and other nonmodel ecosystems. This endeavor is a testament to the collaborative spirit of the ecological genomics community, as the platform encapsulates current methodologies and recommendations across a myriad of genomic studies including whole-genome sequencing, RAD-seq, Pool-seq, and RNA-seq.\n\n\n\nF I G U R E 1 Screenshot of one web page concerning a RAD-seq pipeline serving as an example of tutorial structure.\n\n\nWhat sets MarineOmics.io apart is its dynamic nature. Not only does it provide a repository of existing knowledge, but it also outlines a structured process for the aggregation and synthesis of methodological principles derived from the community. The platform invites submissions of new content, feedback, and topic requests from the community, thereby ensuring its content remains updated, relevant, and in tune with the rapidly evolving field of genomics.\nThe meticulous planning invested in MarineOmics.io is reflective in its guidelines for authorship, submission of new content, and protocols for community feedback. These guidelines are drafted with a vision to uphold the rigor and reproducibility in scientific inquiries, encouraging contributions from scientists spanning various skill sets and expertise levels. This collaborative ethos is further underscored by the availability of the site’s source code for contributors on GitHub, and a snapshot of the source code as of the time of submission, hosted on Zenodo.\nThe data and resources available through MarineOmics.io are not merely a contribution but a cornerstone for advancing ecological genomic research in nonmodel marine systems. By providing a structured, collaborative platform, MarineOmics.io is poised to catalyze a new wave of discoveries, fostering a community of researchers equipped to navigate the challenges and opportunities that lay ahead in the genomic era.\nCitation: Bogan, S. N., Johns, J., Griffiths, J. S., Davenport, D., Smith, S. J., Schaal, S. M., Downey-Wall, A., Lou, R. N., Lotterhos, K., Guidry, M. E., Rivera, H. E., McGirr, J. A., Puritz, J. B., Roberts, S. B., & Silliman, K. (2023). A dynamic web resource for robust and reproducible genomics in nonmodel species: marineomics.io. Methods in Ecology and Evolution, 00, 1–8. https://doi.org/10.1111/2041-210X.14219" }, { - "objectID": "publications/articles/valenzuela2024.html#abstract", - "href": "publications/articles/valenzuela2024.html#abstract", - "title": "Environmental influence on the Atlantic salmon transcriptome and methylome during sea lice infestations", - "section": "Abstract", - "text": "Abstract\nThe fish’s immune response is affected by different factors, including a wide range of environmental conditions that can also disrupt or promote changes in the host- pathogen interactions. How environmental conditions modulate the salmon genome during parasitism is poorly understood here. This study aimed to explore the environmental influence on the Salmo salar transcriptome and methylome infected with the sea louse Caligus rogercresseyi. Atlantic salmon were experimentally infected with lice at two temperatures (8 and 16oC) and salinity conditions (32 and 26PSU). Fish tissues were collected from the infected Atlantic salmon for reduced representation bisulfite sequencing (RRBS) and whole transcriptome sequencing (RNAseq) analysis. The parasitic load was highly divergent in the evaluated environmental conditions, where the lowest lice abundance was observed in fish infected at 8oC/26PSU. Notably, transcriptome profile differences were statistically associated with the number of alternative splicing events in fish exposed to low temperature/salinity conditions. Furthermore, the temperature significantly affected the methylation level, where high values of differential methylation regions were observed at 16oC. Also, the association between expression levels of spliced transcripts and their methylation levels was determined, revealing significant correlations with Ferroptosis and TLR KEEG pathways. This study supports the relevance of the environmental conditions during host-parasite interactions in marine ecosystems. The discovery of alternative splicing transcripts associated with DMRs is also discussed as a novel player in fish biology." + "objectID": "posts/grace_L_WSN/index.html", + "href": "posts/grace_L_WSN/index.html", + "title": "Western Society of Naturalists", + "section": "", + "text": "I presented some data from a summer pilot project that didn’t end up being significant, but sparked some good conversations! Flow rate is known to influence the amount of threads that mussels produce to stick onto rocky surfaces, so I was wondering if it influenced the actual composition of the threads as well! I kept mussels under three different flow rates and measured their attachment strength. Didn’t find anything significant, but saw some trends.\n\n\n\nimg\n\n\nI haven’t ever presented data in person at a conference before (relic of being a college covid baby), so this was really exciting for me to get feedback from other ecomechanics people and brainstorm future directions for my work, especially as I’m trying to propose my thesis this spring." }, { - "objectID": "publications/articles/valenzuela2024.html#data-availability", - "href": "publications/articles/valenzuela2024.html#data-availability", - "title": "Environmental influence on the Atlantic salmon transcriptome and methylome during sea lice infestations", - "section": "Data Availability", - "text": "Data Availability" + "objectID": "posts/grace_L_WSN/index.html#poster-presentation", + "href": "posts/grace_L_WSN/index.html#poster-presentation", + "title": "Western Society of Naturalists", + "section": "", + "text": "I presented some data from a summer pilot project that didn’t end up being significant, but sparked some good conversations! Flow rate is known to influence the amount of threads that mussels produce to stick onto rocky surfaces, so I was wondering if it influenced the actual composition of the threads as well! I kept mussels under three different flow rates and measured their attachment strength. Didn’t find anything significant, but saw some trends.\n\n\n\nimg\n\n\nI haven’t ever presented data in person at a conference before (relic of being a college covid baby), so this was really exciting for me to get feedback from other ecomechanics people and brainstorm future directions for my work, especially as I’m trying to propose my thesis this spring." }, { - "objectID": "posts/sr320-george-paper/index.html", - "href": "posts/sr320-george-paper/index.html", - "title": "The Double-Edged Sword of Triploidy in Pacific Oysters", + "objectID": "posts/sr320-prep/index.html", + "href": "posts/sr320-prep/index.html", + "title": "Are you really prepared?", "section": "", - "text": "The issue of climate change and its cascading effects on marine ecosystems is a growing concern for researchers, conservationists, and policymakers alike. One of the intriguing avenues of research in marine science involves the impact of polyploidy, a genetic variation where organisms have extra sets of chromosomes, on stress tolerance in marine species. A recent study led by Matthew N. George from the School of Aquatic & Fishery Sciences at the University of Washington, along with affiliations from the Environmental and Fisheries Sciences Division at the Northwest Fisheries Science Center, sheds new light on the vulnerability of triploid Pacific oysters to climate stressors.\n\n\n\nThe study, titled “Triploid Pacific oysters exhibit stress response dysregulation and elevated mortality following heatwaves,” focuses on the comparison of diploid (2n) and triploid (3n) Pacific oysters (Crassostrea gigas) in response to environmental conditions akin to a heatwave. By exposing these oysters to different stressors such as elevated seawater temperature and aerial emersion, the researchers found that triploid oysters had a significantly higher mortality rate than their diploid counterparts when subjected to multiple stressors.\n\n\n\nHigher Mortality Rates in Triploids: The mortality rate in triploid oysters exposed to multiple stressors was 36.4% compared to 14.8% in diploid oysters.\nMetabolic and Physiological Limitations: Triploid oysters showed signs of metabolic depression, a reduction in ctenidium Na+/K+ ATPase activity, and dysregulated expression of stress response genes.\nFunctional Genomics Insights: Gene sets enriched in biological processes like metabolism, stress tolerance, and immune function were disproportionately represented in triploids across stress treatments.\n\n\n\n\nThe increased vulnerability of triploid Pacific oysters to climate stressors has far-reaching implications. Triploidy is often induced to achieve reproductive control in species used for marine aquaculture. While this serves to boost production and control unwanted reproduction, the study highlights that it may also render these organisms more susceptible to environmental extremes. This, in turn, could impact food security in regions dependent on marine aquaculture.\n\n\n\n\nThe findings of this study present a clear need for further research to fully understand the complexities of triploidy and its relationship with environmental stress tolerance. As climate change continues to bring about more frequent and severe heatwaves, understanding the impact on marine organisms is crucial. Future research should explore the possibility of developing stress-resilient triploid species and consider alternative strategies for reproductive control in aquaculture.\n\n\n\nWhile triploidy offers some benefits for controlling reproduction in marine aquaculture, this genetic modification may inadvertently make these organisms more susceptible to the threats posed by climate change. As we continue to grapple with the realities of a changing climate, research like this serves as an invaluable resource for better understanding the complex interactions between genetic variation and environmental stressors, thereby informing both conservation strategies and aquaculture practices.\n\n\n\nGeorge, M. N.,  Cattau, O.,  Middleton, M. A.,  Lawson, D.,  Vadopalas, B.,  Gavery, M., &  Roberts, S. B. (2023). Triploid Pacific oysters exhibit stress response dysregulation and elevated mortality following heatwaves. Global Change Biology,  00,  1–19. https://doi.org/10.1111/gcb.16880\n\nFeel free to dive into the full paper for a more detailed understanding of our findings." + "text": "Ariana lead a great tutorial on being prepared and planning for science. The narrative underscored the importance of thorough preparation and planning, including considering alternative uses for collected data, planning for potential pitfalls, and ensuring that experimental designs are robust against unforeseen challenges. This includes the practical aspects of laboratory work, field studies, and data analysis, emphasizing the value of learning from past experiences and being flexible in research approaches.\n\nDesigning scientific experiments requires extensive planning to ensure projects run smoothly and yield meaningful results. Here are some important aspects to consider when preparing for research:\nClearly Define Your Hypothesis and Objectives: Having a clear hypothesis drives your experimental design and analysis approach. Define what you aim to test upfront.\nPrepare Detailed Protocols: Write step-by-step protocols for all procedures well before starting. Practice techniques on mock datasets to work out kinks.\nPlan Your Data Collection: Design data sheets, name conventions, and metadata standards early. Consider sample sizes and ensure you collect the right data to answer your questions.\nSchedule Carefully: Block out experiment timelines, factoring permitting needs and collaborator availability. Leave buffer time for unexpected issues.\nCreate Organizational Systems: Use checklists, spreadsheets, and visual aids to track tasks and ensure all preparation steps are completed thoroughly.\nAnticipate Challenges: Brainstorm potential pitfalls and have contingency plans. Run test analyses to flag problems before using real data.\nProper preparation is key to running successful, high-quality experiments that yield meaningful scientific insights. Taking the time to carefully plan experimental design and logistics pays off in efficient, productive research." }, { - "objectID": "posts/sr320-george-paper/index.html#introduction", - "href": "posts/sr320-george-paper/index.html#introduction", - "title": "The Double-Edged Sword of Triploidy in Pacific Oysters", + "objectID": "posts/frontpage/ariana-paper/index.html", + "href": "posts/frontpage/ariana-paper/index.html", + "title": "Coral Larvae and Thermal Stress", "section": "", - "text": "The issue of climate change and its cascading effects on marine ecosystems is a growing concern for researchers, conservationists, and policymakers alike. One of the intriguing avenues of research in marine science involves the impact of polyploidy, a genetic variation where organisms have extra sets of chromosomes, on stress tolerance in marine species. A recent study led by Matthew N. George from the School of Aquatic & Fishery Sciences at the University of Washington, along with affiliations from the Environmental and Fisheries Sciences Division at the Northwest Fisheries Science Center, sheds new light on the vulnerability of triploid Pacific oysters to climate stressors." + "text": "As climate change continues to drive rising ocean temperatures, coral reef ecosystems face an unprecedented crisis. Coral bleaching events, characterized by the breakdown of the mutualistic relationship between corals and their algal endosymbionts (Symbiodiniaceae), have become increasingly common, threatening the persistence of coral reefs worldwide. While much research has focused on adult corals, new studies are shedding light on how early life stages respond to thermal stress. A recent study by Huffmyer et al. (2024), published in PLOS Biology, provides novel insights into how coral larvae cope with increased temperatures by modifying nitrogen assimilation to stabilize symbiotic relationships and mitigate bleaching risk.\n\nThe Crucial Role of Coral Larvae in Reef Resilience\nReef-building corals rely on their symbionts to produce energy-rich photosynthates that fuel metabolic processes. However, when subjected to thermal stress, this delicate exchange can be disrupted, leading to the expulsion of symbionts and loss of critical energy sources. Understanding how coral larvae respond to environmental stress is particularly important, as their ability to establish symbiosis and successfully settle onto reefs determines the future of coral populations.\nThe study focused on Montipora capitata, a dominant reef-building coral in Hawai‘i that vertically transmits Symbiodiniaceae to its offspring. The researchers subjected symbiotic larvae to a 2.5°C increase in temperature for three days and assessed metabolic responses, photosynthetic performance, and stable isotope-labeled metabolite exchange.\n\n\nKey Findings: Nitrogen Assimilation as a Protective Mechanism\nContrary to expectations, the study found that while larvae exhibited significant metabolic depression under high temperatures—indicated by a 19% reduction in respiration rates—they did not experience bleaching or a decline in survival and settlement rates. Photosynthetic activity remained stable, and the symbiont population density was maintained despite thermal stress.\nA crucial discovery was that coral larvae increased ammonium assimilation and urea metabolism while sequestering nitrogen into dipeptides. This shift suggests that larvae actively modulate nitrogen cycling to maintain symbiotic balance. By limiting nitrogen availability to the symbionts, the coral hosts may be promoting sustained photosynthate translocation, ensuring that energy supply remains uninterrupted under heat stress.\n\n\nMetabolic Trade-offs and Implications for Coral Survival\nWhile glucose translocation from symbiont to host was maintained, the study revealed reduced metabolism of glucose through central carbon pathways such as glycolysis. This metabolic shift implies a trade-off: larvae prioritize nitrogen assimilation over carbohydrate breakdown, potentially conserving energy for essential physiological functions.\nThe authors propose that nitrogen limitation imposed on Symbiodiniaceae encourages continued carbon transfer to the host, preventing the symbionts from hoarding fixed carbon, which could otherwise disrupt the mutualistic relationship. This mechanism highlights a potential resilience strategy in coral early life stages that may influence reef recovery following bleaching events.\n\n\nFuture Directions and Conservation Implications\nUnderstanding the physiological mechanisms that allow coral larvae to withstand heat stress has significant implications for reef conservation and restoration efforts. If coral larvae can naturally modulate nitrogen metabolism to maintain symbiosis, selective breeding or assisted evolution approaches may enhance these traits in vulnerable species.\nAdditionally, further research should investigate whether similar nitrogen assimilation strategies are present in adult corals or if this is a life-stage-specific adaptation. Given the increasing frequency of marine heatwaves, identifying and promoting heat-resilient traits in corals could be a crucial component of future conservation strategies.\n\n\nConclusion\nHuffmyer et al. (2024) provide compelling evidence that coral larvae can mitigate thermal stress through nitrogen assimilation, maintaining stable symbiosis even under elevated temperatures. By uncovering this metabolic adaptation, the study advances our understanding of coral resilience mechanisms and underscores the importance of protecting early life stages in reef conservation efforts. As climate change accelerates, these insights may inform new strategies to support coral reef survival in a warming world." }, { - "objectID": "posts/sr320-george-paper/index.html#summary-of-the-paper", - "href": "posts/sr320-george-paper/index.html#summary-of-the-paper", - "title": "The Double-Edged Sword of Triploidy in Pacific Oysters", + "objectID": "posts/frontpage/sr320-usda-report/index.html", + "href": "posts/frontpage/sr320-usda-report/index.html", + "title": "Hatchery-based Environmental Conditioning Activities", "section": "", - "text": "The study, titled “Triploid Pacific oysters exhibit stress response dysregulation and elevated mortality following heatwaves,” focuses on the comparison of diploid (2n) and triploid (3n) Pacific oysters (Crassostrea gigas) in response to environmental conditions akin to a heatwave. By exposing these oysters to different stressors such as elevated seawater temperature and aerial emersion, the researchers found that triploid oysters had a significantly higher mortality rate than their diploid counterparts when subjected to multiple stressors.\n\n\n\nHigher Mortality Rates in Triploids: The mortality rate in triploid oysters exposed to multiple stressors was 36.4% compared to 14.8% in diploid oysters.\nMetabolic and Physiological Limitations: Triploid oysters showed signs of metabolic depression, a reduction in ctenidium Na+/K+ ATPase activity, and dysregulated expression of stress response genes.\nFunctional Genomics Insights: Gene sets enriched in biological processes like metabolism, stress tolerance, and immune function were disproportionately represented in triploids across stress treatments.\n\n\n\n\nThe increased vulnerability of triploid Pacific oysters to climate stressors has far-reaching implications. Triploidy is often induced to achieve reproductive control in species used for marine aquaculture. While this serves to boost production and control unwanted reproduction, the study highlights that it may also render these organisms more susceptible to environmental extremes. This, in turn, could impact food security in regions dependent on marine aquaculture." + "text": "During this past year a series of hatchery-based environmental conditioning activities (referred to as hardening) were completed with oysters out-planted onto three farms to evaluate performance. Additionally, climate resiliency was assessed in hardened oysters under controlled conditions.\n\n\n\nExperimental Overview\n\n\n\nFarm Outplanting\nEarly in the season, a cohort of oysters were subject to (a) daily thermal hardening for approximately two weeks prior to out planting in hanging bags on a farm in Sequim Bay, alongside a control group. These oyster will be assessed in early Autumn 2024. Later in the season oysters were subjected to a more diverse series of hardening conditions with oyster split between two commercial farms, one located in Willapa Bay and a second in the San Juan Islands. The combination of age classes and hardening conditions were as follows: b) small seed / daily thermal hardening, c) adult / daily thermal hardening, d) small seed / weekly thermal hardening, e1) large seed / weekly thermal hardening, e2) large seed / weekly zero salinity hardening. These hardening activities spanned from several weeks to months. For all hardening efforts controls were also outplanted. Oysters out planted in Willapa Bay will be assessed for survival and growth in early September 2024. Oysters out planted in the San Juan Islands have be subject to more routine monitoring. At this site we are currently observing a trend where oysters subjected to the daily hardening regime are surviving better than controls.\n\n\n\nWescott Bay Outplanting\n\n\n\n\nPhysiological Assessment 1\nTo assess the effectiveness of hardening within a hatchery setting, four ages classes of oysters were examined: adults (40-100mm), juveniles (20-55mm), seed (6-15mm), and spat ()1-6mm). In order to assess hardening potential and environmental memory, oysters were subject to an initial chronic temperature stress, then subjected to a secondary stress to see if the response to secondary stress was impacted by initial exposure. During the chronic temperature stress period, oysters from each age class were exposed to a daily 25ºC temperature spike. This repeated for 14 days starting on October 1. Control oysters from each cohort were maintained at an ambient temperature of approximately 17ºC during the same time period.\n\n\n\nHardening and acute stress temperature timeline\n\n\nAdult oysters in stress conditions were also subject to mechanical stress at day 1, 7, and 48, which was induced by 15 minutes. At day 147 (7 weeks after initial chronic stress), both stressed and non-stressed adult, juvenile, spat, and seed were subjected to a secondary stress of 30 minutes in 32ºC. Gill tissue was sampled immediately after and placed into RNAlater. Spat and seed that were too small to dissect gill tissue were sampled whole with all tissue used in gene expression assays. To date we have analyzed gene expression data from seed and spat. There was no mortality during this trial. Hardening increased growth (compared to controls) in spat. Further there was a reduced transcriptional response in spat. These data suggest temperature hardening of spat could result in a resiliency to later temperature stress whereby energy resources could favor growth.\n\n\n\nGrowth Performance\n\n\n\n\n\nGene expression profiles (spat)\n\n\n\n\n\nSchematic physiology explanation when hardened spat are exposed to acute temperature stress.\n\n\n\n\nPhysiological Assessment 2\nIn a second experimental regime, juvenile oysters were subjected to four hardening conditions 1) high temperature (35°C), 2) high temperature and freshwater, 3) freshwater, and 4) poly I:C immersion. These were exposures that occurred every other day for about 3 weeks. Approximately 1 month after hardening, oysters were brought to the lab and subjected to metabolic assessment using resazurin at 18°C and 42°C. Resazurin is a dye that is commonly used in cell viability, and it works by changing color as an organism consumes oxygen. Survival was assessed during the resazurin assay and 24 hours later. To date, our analysis suggests metabolic activity of the 42°C oysters was higher in the control oysters than previously hardened oysters. In the near future we will assess the relationship of metabolic activity and survival however it appears higher metabolic rate directly correlates with mortality. Taken together these sets of controlled experiments suggest hardening does have an impact on resiliency, though dependent on age, hardening duration, and subsequent environmental conditions." }, { - "objectID": "posts/sr320-george-paper/index.html#discussion-and-future-directions", - "href": "posts/sr320-george-paper/index.html#discussion-and-future-directions", - "title": "The Double-Edged Sword of Triploidy in Pacific Oysters", + "objectID": "posts/frontpage/sr320-intertidal/index.html", + "href": "posts/frontpage/sr320-intertidal/index.html", + "title": "Intertidal Innovators", "section": "", - "text": "The findings of this study present a clear need for further research to fully understand the complexities of triploidy and its relationship with environmental stress tolerance. As climate change continues to bring about more frequent and severe heatwaves, understanding the impact on marine organisms is crucial. Future research should explore the possibility of developing stress-resilient triploid species and consider alternative strategies for reproductive control in aquaculture." + "text": "On August 16, participants in the Intertidal Innovators program presented their work to the community. The program, which was a collaboration sponsored by the UW Earthlab program, provided students with the opportunity to learn about marine science and conservation through art.\n\n\n\n\n\n\n\nQuote\n\n\n\nThis program has lasted for 10 days, but during those days we have learned and worked very hard to give you this project. And we are proud to say that there are a bunch of hard working members in our program that have learned new skills and have gained knowledge in this program So in this journey, you will learn a lot about our work and marine life.\n\n\nAt the community showcase, students guide small groups around the intertidal, sharing their art with tablets and speakers. It was a great experience that showcased videos, poems, live demonostrations, and stories. Anyone can checkout their guided tour at Golden Garden Park via the echoes app - https://explore.echoes.xyz/collections/jJtrYdYIdtZ8eCpC\nBelow is a video that takes you behind the scenes on the 10-day experience students participated in." }, { - "objectID": "posts/sr320-george-paper/index.html#conclusion", - "href": "posts/sr320-george-paper/index.html#conclusion", - "title": "The Double-Edged Sword of Triploidy in Pacific Oysters", + "objectID": "posts/mytilus-genome/index.html", + "href": "posts/mytilus-genome/index.html", + "title": "Unveiling the Blueprints of the Sea", "section": "", - "text": "While triploidy offers some benefits for controlling reproduction in marine aquaculture, this genetic modification may inadvertently make these organisms more susceptible to the threats posed by climate change. As we continue to grapple with the realities of a changing climate, research like this serves as an invaluable resource for better understanding the complex interactions between genetic variation and environmental stressors, thereby informing both conservation strategies and aquaculture practices.\n\n\n\nGeorge, M. N.,  Cattau, O.,  Middleton, M. A.,  Lawson, D.,  Vadopalas, B.,  Gavery, M., &  Roberts, S. B. (2023). Triploid Pacific oysters exhibit stress response dysregulation and elevated mortality following heatwaves. Global Change Biology,  00,  1–19. https://doi.org/10.1111/gcb.16880\n\nFeel free to dive into the full paper for a more detailed understanding of our findings." + "text": "The blue mussel, Mytilus chilensis, is not only a delicacy on dinner plates but also a cornerstone of the booming aquaculture industry along the southern coast of Chile. Its iridescent shells and robust nature make it a favorite, but beneath the waves, this bivalve is locked in a constant battle against environmental stressors, diseases, and the effects of pollution. The secret to its resilience lies in its genetic code, a treasure trove of information until now largely uncharted.\n\n\nIn a groundbreaking study, researchers have presented the first chromosome-level genome assembly for a Mytilidae family member in South America. This scientific feat, detailed in a recent publication, offers a high-quality reference genome for M. chilensis. It’s a leap forward in our understanding of this species, providing a detailed map of the genetic factors that contribute to its survival and adaptation in a changing marine environment.\n\n\n\nImagine having a detailed instruction manual for building and maintaining an organism, one that could tell you how it can survive freezing waters, resist certain pathogens, or how it might react to the shifting chemistry of its habitat. That’s what a genome assembly provides. For aquaculture, this information is invaluable. It can lead to the development of hardier mussel strains, inform conservation efforts, and enhance the industry’s sustainability.\n\n\n\nThe aquaculture industry relies heavily on mussel farming, but it’s an enterprise not without its risks. With seeds collected from natural beds and translocated to varied farming conditions, the industry has been seeking ways to reduce losses and improve yields. The newly unveiled genome paves the way for breeding programs that can select for desirable traits, such as disease resistance or faster growth rates, potentially revolutionizing mussel farming.\n\n\n\nBut the implications of this research extend beyond the realm of economics. Mussels serve as a filter for the ocean, playing a critical role in maintaining the health of marine ecosystems. Understanding their genetic makeup helps us appreciate not only how they contribute to their environment but also how they might be affected by our actions—be it through climate change or pollution.\n\n\n\nThe journey of understanding Mytilus chilensis at the genomic level is just beginning. This initial assembly is a scaffold for future discoveries, a reference for comparative genomics, and a baseline for monitoring the genetic health of populations. As scientists continue to unravel the mysteries locked in its DNA, we move closer to a future where the blue mussel can continue to thrive, both as a species and an industry.\nThe study in discussion is not just a scientific achievement; it’s a testament to the intricate dance of life adapted to the ebb and flow of the sea. As we delve into the genome of Mytilus chilensis, we’re reminded of the resilience of life and the ingenuity of those who seek to understand and preserve it. The blueprints of the sea are laid bare, and with them, a new chapter in sustainable aquaculture beckons.\nCITATION: Gallardo-Escárate, C.; Valenzuela-Muñoz, V.; Nuñez-Acuña, G.; Valenzuela-Miranda, D.; Tapia, F.J.; Yévenes, M.; Gajardo, G.; Toro, J.E.; Oyarzún, P.A.; Arriagada, G.; et al. Chromosome-Level Genome Assembly of the Blue Mussel Mytilus chilensis Reveals Molecular Signatures Facing the Marine Environment. Genes 2023, 14, 876. https://doi.org/10.3390/genes14040876" }, { - "objectID": "posts/sr320-enrich/index.html", - "href": "posts/sr320-enrich/index.html", - "title": "Unraveling the Intricacies of Enrichment Analysis", + "objectID": "posts/mytilus-genome/index.html#a-genomic-milestone", + "href": "posts/mytilus-genome/index.html#a-genomic-milestone", + "title": "Unveiling the Blueprints of the Sea", "section": "", - "text": "In our most recent lab meeting, we delved into the fascinating world of enrichment analysis. This statistical method is a cornerstone of our research, helping us identify significantly over-represented subsets of proteins or genes within our data." + "text": "In a groundbreaking study, researchers have presented the first chromosome-level genome assembly for a Mytilidae family member in South America. This scientific feat, detailed in a recent publication, offers a high-quality reference genome for M. chilensis. It’s a leap forward in our understanding of this species, providing a detailed map of the genetic factors that contribute to its survival and adaptation in a changing marine environment." }, { - "objectID": "posts/sr320-enrich/index.html#the-power-of-enrichment-analysis", - "href": "posts/sr320-enrich/index.html#the-power-of-enrichment-analysis", - "title": "Unraveling the Intricacies of Enrichment Analysis", - "section": "The Power of Enrichment Analysis", - "text": "The Power of Enrichment Analysis\nEnrichment analysis allows us to compare a small subset of genes or proteins to a larger set, identifying overrepresentation. This can provide valuable insights into the biological processes that are most relevant to our research." + "objectID": "posts/mytilus-genome/index.html#why-genome-matters", + "href": "posts/mytilus-genome/index.html#why-genome-matters", + "title": "Unveiling the Blueprints of the Sea", + "section": "", + "text": "Imagine having a detailed instruction manual for building and maintaining an organism, one that could tell you how it can survive freezing waters, resist certain pathogens, or how it might react to the shifting chemistry of its habitat. That’s what a genome assembly provides. For aquaculture, this information is invaluable. It can lead to the development of hardier mussel strains, inform conservation efforts, and enhance the industry’s sustainability." }, { - "objectID": "posts/sr320-enrich/index.html#a-deep-dive-into-david", - "href": "posts/sr320-enrich/index.html#a-deep-dive-into-david", - "title": "Unraveling the Intricacies of Enrichment Analysis", - "section": "A Deep Dive into David", - "text": "A Deep Dive into David\nOne of the tools we use for enrichment analysis is David. During the meeting, we explored how to upload gene lists and backgrounds into David, and how to interpret the results it provides. This tool is invaluable in helping us understand the complex relationships and patterns within our data." + "objectID": "posts/mytilus-genome/index.html#the-economic-and-ecological-impact", + "href": "posts/mytilus-genome/index.html#the-economic-and-ecological-impact", + "title": "Unveiling the Blueprints of the Sea", + "section": "", + "text": "The aquaculture industry relies heavily on mussel farming, but it’s an enterprise not without its risks. With seeds collected from natural beds and translocated to varied farming conditions, the industry has been seeking ways to reduce losses and improve yields. The newly unveiled genome paves the way for breeding programs that can select for desirable traits, such as disease resistance or faster growth rates, potentially revolutionizing mussel farming." }, { - "objectID": "posts/sr320-enrich/index.html#the-reference-list-debate", - "href": "posts/sr320-enrich/index.html#the-reference-list-debate", - "title": "Unraveling the Intricacies of Enrichment Analysis", - "section": "The Reference List Debate", - "text": "The Reference List Debate\nAn interesting discussion arose around what to use as a reference list in enrichment analysis. Should it be all the genes detected in the data set, or all genes in a reference genome? This question sparked a lively debate, highlighting the complexities and nuances of enrichment analysis." + "objectID": "posts/mytilus-genome/index.html#beyond-the-economic-horizon", + "href": "posts/mytilus-genome/index.html#beyond-the-economic-horizon", + "title": "Unveiling the Blueprints of the Sea", + "section": "", + "text": "But the implications of this research extend beyond the realm of economics. Mussels serve as a filter for the ocean, playing a critical role in maintaining the health of marine ecosystems. Understanding their genetic makeup helps us appreciate not only how they contribute to their environment but also how they might be affected by our actions—be it through climate change or pollution." }, { - "objectID": "posts/sr320-enrich/index.html#visualizing-gene-ontology-with-revigo", - "href": "posts/sr320-enrich/index.html#visualizing-gene-ontology-with-revigo", - "title": "Unraveling the Intricacies of Enrichment Analysis", - "section": "Visualizing Gene Ontology with Revigo", - "text": "Visualizing Gene Ontology with Revigo\nTo help us visualize gene ontology, we use a tool called Revigo. This tool provides a visual representation of the relationships between genes, making it easier to understand the complex data we work with." + "objectID": "posts/mytilus-genome/index.html#looking-forward", + "href": "posts/mytilus-genome/index.html#looking-forward", + "title": "Unveiling the Blueprints of the Sea", + "section": "", + "text": "The journey of understanding Mytilus chilensis at the genomic level is just beginning. This initial assembly is a scaffold for future discoveries, a reference for comparative genomics, and a baseline for monitoring the genetic health of populations. As scientists continue to unravel the mysteries locked in its DNA, we move closer to a future where the blue mussel can continue to thrive, both as a species and an industry.\nThe study in discussion is not just a scientific achievement; it’s a testament to the intricate dance of life adapted to the ebb and flow of the sea. As we delve into the genome of Mytilus chilensis, we’re reminded of the resilience of life and the ingenuity of those who seek to understand and preserve it. The blueprints of the sea are laid bare, and with them, a new chapter in sustainable aquaculture beckons.\nCITATION: Gallardo-Escárate, C.; Valenzuela-Muñoz, V.; Nuñez-Acuña, G.; Valenzuela-Miranda, D.; Tapia, F.J.; Yévenes, M.; Gajardo, G.; Toro, J.E.; Oyarzún, P.A.; Arriagada, G.; et al. Chromosome-Level Genome Assembly of the Blue Mussel Mytilus chilensis Reveals Molecular Signatures Facing the Marine Environment. Genes 2023, 14, 876. https://doi.org/10.3390/genes14040876" }, { - "objectID": "posts/sr320-enrich/index.html#a-lighter-moment", - "href": "posts/sr320-enrich/index.html#a-lighter-moment", - "title": "Unraveling the Intricacies of Enrichment Analysis", - "section": "A Lighter Moment", - "text": "A Lighter Moment\nAmidst the serious scientific discussions, we also had a lighter moment when a team member shared a story about narrowly avoiding a parking ticket. It’s moments like these that remind us of the importance of camaraderie and humor in the lab.\n\nOur lab meetings are a crucial part of our research process, providing a space for us to discuss, debate, and learn together. Stay tuned for more insights from our lab meetings in future posts!" + "objectID": "posts/grace-ac-WSN/index.html", + "href": "posts/grace-ac-WSN/index.html", + "title": "Western Society of Naturalists", + "section": "", + "text": "Had an amazing week last week! See post for details!" }, { - "objectID": "posts/sr320-asi/index.html", - "href": "posts/sr320-asi/index.html", - "title": "Sharing the Good Word of Marine Epigenetics", - "section": "", - "text": "The University of Concepción recently offered an eye-opening course that dove deep into the realms of climate change, epigenetics, and marine biology. Titled “Epigenetic Phenomena Connecting Climate Change and Coastal Marine Species,” this graduate-level course provided an intensive one-week journey into the fascinating interplay between our changing climate and the genetic mechanisms of marine invertebrates.\n\nUnraveling the Mysteries of Marine Invertebrates\nThe course, designed for students with a foundational understanding of genetics and climate science, began by establishing a strong base in epigenetics, climate change, and marine invertebrate physiology. The highlight was on the often-overlooked role of marine invertebrates in coastal ecosystems, emphasizing their ecological importance and responses to climate change at an epigenetic level.\n\n\nReal-World Applications and Functional Genomics\nA significant focus of the course was the application of functional genomics. Students explored how climate change leads to alterations in epigenetic mechanisms of various coastal marine invertebrates through real-world examples. This approach helped in understanding the broader implications of these changes for marine ecosystems.\n\n\nComprehensive Course Objectives\nThe course had three primary objectives:\n\nUnderstanding Climate Change and Epigenetics: Gaining a comprehensive understanding of how climate change impacts marine invertebrates’ physiological processes through an epigenetic lens.\nProficiency in Functional Genomics: Learning about genomic techniques and their applications in studying epigenetic changes in marine invertebrates due to climate stressors.\nAnalyzing Scientific Research: Developing skills to critically analyze and evaluate scientific literature in marine invertebrate epigenetics and climate change.\n\n\n\nCourse Content: A Rich Blend of Science and Research\nThe course content was diverse and in-depth:\n\nBasics of Epigenetics and Climate Change: Introduced the intersection of these fields and the concept of environmental epigenetics.\nPhysiology of Marine Invertebrates: Covered essential aspects like feeding, digestion, reproduction, and stress response.\nImpact of Climate Change on Physiology: Explored the specific impacts of climate factors on marine invertebrates.\nFunctional Genomics and Epigenetics: Delved into genomic methodologies and applications.\nCase Studies and Current Research: Involved critical examination of recent research studies, emphasizing practical understanding.\n\n\n\nMethodology: Interactive and Engaging\nThe course used a mix of lectures, discussions, and interactive data analysis. It emphasized hands-on learning, particularly in the afternoons, where students engaged in data analysis using R and bash, providing a practical edge to the theoretical knowledge gained.\n\n\nScholarly Contributions: A Rich Bibliography\nThe course drew from a rich bibliography, featuring works by renowned researchers like Grace Crandall, Steven B. Roberts, and Cristian Gallardo-Escárate. These publications covered various aspects, from the proteomic responses of Pacific Oysters to the genomic assembly of the Blue Mussel, offering students a comprehensive view of current research in the field.\n\n\nConclusion: A Step Forward in Marine Biology Education\nThis course at the University of Concepción marked a significant step in educating the next generation of marine biologists, geneticists, and climate scientists. By bridging the gap between climate change and epigenetic phenomena in marine species, it not only enhanced understanding but also prepared students to contribute meaningfully to marine conservation efforts in the face of global climate challenges." + "objectID": "posts/grace-ac-WSN/index.html#eelgrass-workshop", + "href": "posts/grace-ac-WSN/index.html#eelgrass-workshop", + "title": "Western Society of Naturalists", + "section": "Eelgrass Workshop", + "text": "Eelgrass Workshop\nFor the past year+ I’ve been fortunate to be part of an awesome team of folks working on an NSF Grant studying Eelgrass Wasting Disease, mostly centered in the Puget Sound/San Juan Islands, but also spanning along the West Coast. We had a great workshop pre-WSN where we chatted about the various aspects of the grant that folks have been working on and made plans and outlines for writing up the various projects. It was a great time and I’m looking forward to all the cool stuff coming up - keep an eye out!\nHere’s the team!\n\n\n\nimg\n\n\nDr. Lindsay Alma, Dr. Colleen Burge, Dr. Drew Harvell, Dr. Eileen Hoffman, Dr. Maya Groner, Me, Dr. Becca Maher, and Dr. Olivia Graham!" }, { - "objectID": "posts/frontpage/ariana-hatchery/index.html", - "href": "posts/frontpage/ariana-hatchery/index.html", - "title": "Hatchery Field Day at Point Whitney", - "section": "", - "text": "On May 6, 2024, Dr. Ariana Huffmyer, an NSF Ocean Sciences Postdoctoral Fellow from the University of Rhode Island and University of Washington, shared insights from a field day at Point Whitney. This comprehensive post revealed the detailed process of managing and monitoring oyster growth and stress testing, providing a clear framework for hatchery management.\n\n\n\n\n\n\nLink to Full Notebook Post\n\n\n\nhttps://ahuffmyer.github.io/ASH_Putnam_Lab_Notebook/Hatchery-field-day-at-Point-Whitney-May-6-2024/\n\n\nOverview of Field Day Activities The objective was to monitor the health and stress responses of oyster cohorts at the hatchery. Key activities included calibrating monitoring equipment, feeding the oysters, and assessing the impacts of temperature and freshwater stress.\n\nMonitoring Equipment Calibration: Dr. Huffmyer set up and calibrated an Orion Star A325 probe to measure pH, temperature, and conductivity. By using buffers of varying pH and a conductivity solution, she ensured accurate measurements. The pH was measured on the NBS scale, considered sufficient since ocean acidification experiments weren’t being conducted.\nFeeding Protocol: The oysters were pulse-fed, where approximately 1/3 of a 5-gallon bucket was distributed among the tanks. This ensured that the animals received sufficient nutrition.\nFluorometry and Physiochemical Measurements: Fluorometry measurements were conducted before and after feeding, providing data on oyster metabolic activity. Additionally, pH, temperature, and conductivity were measured across different tanks, offering valuable weekly insights into water quality.\nStress Testing Regimen: Dr. Huffmyer conducted a 30-minute stress test for specific oyster cohorts using freshwater and elevated temperature exposures. Animals were subjected to 25°C temperature and freshwater immersion, replicating environmental stressors they might face. Trays were labeled and organized by stressor type.\nGrowth Characterization: Size measurements were taken using a waterproof digital caliper. Cohorts were categorized based on their respective stressors, creating a comprehensive understanding of their growth patterns.\nPloidy Testing Preparations: A selection of oysters from different cohorts was collected for ploidy testing to distinguish between diploid and triploid oysters. They were stored in mesh bags, and the testing results would provide critical information for future breeding programs.\n\n\n\n\nheath-tray\n\n\nTakeaways for Hatchery Science Dr. Huffmyer’s systematic approach highlights the significance of precise monitoring and stress testing in hatchery science. Understanding oyster resilience to environmental stressors is crucial for aquaculture sustainability. Her work at Point Whitney offers a detailed protocol that could be replicated or adapted by other researchers to monitor and improve hatchery operations.\nThe future of hatchery management will depend heavily on such frameworks, where real-time data collection and analysis enable researchers to respond promptly to environmental changes." + "objectID": "posts/grace-ac-WSN/index.html#wsn-monterey-ca", + "href": "posts/grace-ac-WSN/index.html#wsn-monterey-ca", + "title": "Western Society of Naturalists", + "section": "WSN, Monterey, CA", + "text": "WSN, Monterey, CA\nI haven’t been to a conference since the Alaska Marine Science Symposium in Anchorage, AK, January 2020… so it was a little nerve-wracking to head to my first one in so long! It was amazing, though! So much cool science, so many interesting and engaging talks and posters, and I had so much fun. Made some new connections that I’m excited to foster.\nDr. Olivia Graham did an amazing job putting together THREE Marine Disease Ecology sessions!! There were two sessions on Saturday - an eelgrass session during which a lot of the team pictured in the above section presented amazing work, and a miscellaneous section that had some great talks as well.\nI was part of the Sunday morning session that was all about Pycnopodia helianthoides! Below is a photo of everyone who presented. My talk went well - I ended up getting Honorable Mention for it!\n\n\n\nimg\n\n\nDr. Lauren Schiebelhut, Dr. Jason Hodin, Dr. Alyssa Gehman, Me, Dr. Melanie Prentice, Tiffany Rudek, Dr. Drew Harvell, and Dr. Olivia Graham.\nFor fun, here’s a pretty photo of one of our adult Pycnopodia helianthoides from our Summer 2021 work that made many appearances in my talk:" }, { - "objectID": "posts/frontpage/sr320-usda-report/index.html", - "href": "posts/frontpage/sr320-usda-report/index.html", - "title": "Hatchery-based Environmental Conditioning Activities", + "objectID": "posts/cool-paper/index.html", + "href": "posts/cool-paper/index.html", + "title": "Genetics: Does it really matter?", "section": "", - "text": "During this past year a series of hatchery-based environmental conditioning activities (referred to as hardening) were completed with oysters out-planted onto three farms to evaluate performance. Additionally, climate resiliency was assessed in hardened oysters under controlled conditions.\n\n\n\nExperimental Overview\n\n\n\nFarm Outplanting\nEarly in the season, a cohort of oysters were subject to (a) daily thermal hardening for approximately two weeks prior to out planting in hanging bags on a farm in Sequim Bay, alongside a control group. These oyster will be assessed in early Autumn 2024. Later in the season oysters were subjected to a more diverse series of hardening conditions with oyster split between two commercial farms, one located in Willapa Bay and a second in the San Juan Islands. The combination of age classes and hardening conditions were as follows: b) small seed / daily thermal hardening, c) adult / daily thermal hardening, d) small seed / weekly thermal hardening, e1) large seed / weekly thermal hardening, e2) large seed / weekly zero salinity hardening. These hardening activities spanned from several weeks to months. For all hardening efforts controls were also outplanted. Oysters out planted in Willapa Bay will be assessed for survival and growth in early September 2024. Oysters out planted in the San Juan Islands have be subject to more routine monitoring. At this site we are currently observing a trend where oysters subjected to the daily hardening regime are surviving better than controls.\n\n\n\nWescott Bay Outplanting\n\n\n\n\nPhysiological Assessment 1\nTo assess the effectiveness of hardening within a hatchery setting, four ages classes of oysters were examined: adults (40-100mm), juveniles (20-55mm), seed (6-15mm), and spat ()1-6mm). In order to assess hardening potential and environmental memory, oysters were subject to an initial chronic temperature stress, then subjected to a secondary stress to see if the response to secondary stress was impacted by initial exposure. During the chronic temperature stress period, oysters from each age class were exposed to a daily 25ºC temperature spike. This repeated for 14 days starting on October 1. Control oysters from each cohort were maintained at an ambient temperature of approximately 17ºC during the same time period.\n\n\n\nHardening and acute stress temperature timeline\n\n\nAdult oysters in stress conditions were also subject to mechanical stress at day 1, 7, and 48, which was induced by 15 minutes. At day 147 (7 weeks after initial chronic stress), both stressed and non-stressed adult, juvenile, spat, and seed were subjected to a secondary stress of 30 minutes in 32ºC. Gill tissue was sampled immediately after and placed into RNAlater. Spat and seed that were too small to dissect gill tissue were sampled whole with all tissue used in gene expression assays. To date we have analyzed gene expression data from seed and spat. There was no mortality during this trial. Hardening increased growth (compared to controls) in spat. Further there was a reduced transcriptional response in spat. These data suggest temperature hardening of spat could result in a resiliency to later temperature stress whereby energy resources could favor growth.\n\n\n\nGrowth Performance\n\n\n\n\n\nGene expression profiles (spat)\n\n\n\n\n\nSchematic physiology explanation when hardened spat are exposed to acute temperature stress.\n\n\n\n\nPhysiological Assessment 2\nIn a second experimental regime, juvenile oysters were subjected to four hardening conditions 1) high temperature (35°C), 2) high temperature and freshwater, 3) freshwater, and 4) poly I:C immersion. These were exposures that occurred every other day for about 3 weeks. Approximately 1 month after hardening, oysters were brought to the lab and subjected to metabolic assessment using resazurin at 18°C and 42°C. Resazurin is a dye that is commonly used in cell viability, and it works by changing color as an organism consumes oxygen. Survival was assessed during the resazurin assay and 24 hours later. To date, our analysis suggests metabolic activity of the 42°C oysters was higher in the control oysters than previously hardened oysters. In the near future we will assess the relationship of metabolic activity and survival however it appears higher metabolic rate directly correlates with mortality. Taken together these sets of controlled experiments suggest hardening does have an impact on resiliency, though dependent on age, hardening duration, and subsequent environmental conditions." + "text": "Here I will describe a recent, cool paper and try to also highlight 1) some of the material covered in our class on Proposal Writing and Professional Development, and 2) some of the features of using Quarto.\nThe paper characterizes the relationship of genetics and epigenetics in the Olympia oysters. The two primary authors are Katherine Silliman and Laura Spencer. Silliman et al. (2023)" + }, + { + "objectID": "posts/cool-paper/index.html#so-why-does-it-matter", + "href": "posts/cool-paper/index.html#so-why-does-it-matter", + "title": "Genetics: Does it really matter?", + "section": "So why does it matter?", + "text": "So why does it matter?\n\nStudies of plasticity and epigenetic variation among groups from different environments must also account for genetic variation, rather than attributing all differences to the environment.\nGenetic variation is clearly heritable, our results suggest that some proportion of DNA methylation (and likely associated phenotypes) are also heritable.\nDespite our two populations being raised in the same environment, 73% of the epigenetic variation in our system was not attributable to genetics." }, { - "objectID": "posts/frontpage/sr320-boundless/index.html", - "href": "posts/frontpage/sr320-boundless/index.html", - "title": "Exploring Pacific Cod Resilience in a Warming Ocean", - "section": "", - "text": "In our latest update on the Pacific cod juvenile temperature study, we've gained deeper insights into how these remarkable fish respond to different temperatures. This research is part of a larger effort to understand the resilience of marine species in changing environments.\nGenetic Insights Reveal Population Origins\nWe began with genetic analyses, using data from thousands of genetic markers to determine the origin of our experimental fish. All our test fish were linked to the spawning grounds in the western Gulf of Alaska (wGOA) and the Eastern Bering Sea (EBS). This finding allows us to focus on the thermal resilience of cod from this particular region, which is vital as they face shifts in temperature in their natural habitats.\n\nTemperature's Role in Energy and Lipid Storage\nOur collaborator Louise Copement analyzed liver lipids in these juvenile cod, focusing on triglycerides and other key lipid types that are crucial for overwinter survival. The results showed a clear trend: energy storage, primarily in the form of triglycerides, peaked at 9°C, then dropped sharply at higher temperatures, especially at 16°C. This suggests that extreme warmth could deplete essential energy reserves, reducing the fish's survival prospects in the cold winter months.\n\nOptimal Growth Temperatures and Physiological Responses\nWe also observed that juvenile cod exhibit optimal growth at approximately 12.3°C, slightly higher than previous findings. With higher temperatures, growth rates plateau or decline, mirroring the energy storage patterns. Interestingly, the gene expression data from liver tissues revealed significant temperature-driven shifts, especially in energy production, lipid metabolism, and immune response genes. This molecular data adds a new layer to our understanding of temperature tolerance.\n\nIntegrated Data: A Pathway to Genomic Resilience Markers\nCombining growth, lipid, and gene expression data, we've started identifying genes that correlate with enhanced resilience at specific temperatures. This approach could spotlight genetic markers for thermal resilience, offering clues about cod populations best suited to future ocean conditions.\nIn summary, this research underscores the delicate balance juvenile Pacific cod must maintain in their energy reserves and growth under variable temperatures. These findings will help guide conservation and management efforts as we work to protect Pacific cod populations in a warming world." + "objectID": "posts/cool-paper/index.html#how-are-you-including-images", + "href": "posts/cool-paper/index.html#how-are-you-including-images", + "title": "Genetics: Does it really matter?", + "section": "How are you including images?", + "text": "How are you including images?\n\nknitr::include_graphics(\"img/skitch.gif\")\n\n\n\n\n\n\n\n\nBut what is the code in the Quarto file to render what we are seeing above?\n\nknitr::include_graphics(\"img/skitch.gif\")\n\n\n\n\n\n\n\n\nEssentially you just need to include an image (here it is within the post directory) and use R code to display, highly leveraging code chunk options.\nExplore the entirety of the code behind this page at https://github.com/sr320/tumbling-oysters/blob/main/posts/cool-paper/index.qmd" }, { - "objectID": "posts/sr320-altsplice/index.html", - "href": "posts/sr320-altsplice/index.html", - "title": "Cmplexities of Gene Expression", + "objectID": "posts/sr320-DM/index.html", + "href": "posts/sr320-DM/index.html", + "title": "Insights from Pacific Oysters in a Heating Ocean", "section": "", - "text": "In a recent meeting focused on gene expression analysis, we delved into the intricacies of examining expression at the exon level, a crucial but complex aspect of understanding gene function and regulation. The discussion provided deep insights into both the challenges and potential breakthroughs in the field of genomics. Here’s a detailed recap of the key points and future directions highlighted during the conversation.\n\n\nEmphasis on Gene Expression Analysis\nGene expression analysis remains a cornerstone of genomic studies, serving as a gateway to understanding the roles of genes in various biological processes and disease states. The meeting opened with a reaffirmation of the importance of mastering the techniques and tools that allow for such analysis, emphasizing that comprehensive understanding is necessary to advance research.\n\n\nWorkflow and Tools\nA significant portion of the discussion revolved around the workflow used in the analysis. The researchers outlined their use of HiSat for alignment—a choice reflecting HiSat’s efficiency in handling high-throughput RNA-seq data. StringTie was then introduced as the tool for identifying transcript units, highlighting its capability to assemble transcripts effectively. The differential expression analysis was conducted using DC2, a tool favored for its robust statistical methods in handling variance among biological replicates.\n\n\nChallenges in Interpretation\nOne of the central themes of the meeting was the challenge of interpreting results where genes do not show differential expression overall but do exhibit variations at the exon level. This scenario often leads to questions about alternative splicing or differential exon usage, which can have significant implications for gene function.\nThe group discussed several hypothetical situations:\n- Alternative Splicing: If only certain exons within a gene are differentially expressed, this might suggest alternative splicing, a process where the same gene can lead to different protein variants.\n- Alternative Start Sites: Differentially expressed exons at the gene’s boundaries might indicate alternative transcription start sites, affecting how transcription is initiated.\n\n\nBiological Implications and Interpretation\nThe biological implications of these findings are profound, potentially impacting everything from gene regulation to the development of therapeutic strategies. For example, alternative splicing can result in proteins with differing, sometimes antagonistic functions. Understanding these nuances is essential for the development of targeted therapies.\n\n\nThe Role of Visual Aids\nA noteworthy suggestion from the meeting was the use of visual aids to better explain complex data and analysis. Presentations with graphical representations of data can facilitate a clearer understanding, aiding in the interpretation of intricate patterns of gene expression that might otherwise be overlooked in raw numerical data.\n\n\nFuture Directions\nLooking to the future, the participants agreed on the need for more refined tools and methodologies to enhance the accuracy and granularity of exon-level expression analysis. They highlighted the potential for developing new computational tools that can integrate more complex layers of data, such as epigenetic modifications and non-coding RNA interactions, which could provide a more comprehensive view of gene regulation.\nThe meeting concluded with a sense of optimism about the path forward, acknowledging that while challenges remain, the ongoing advancements in technology and methodology will continue to illuminate the complexities of the genome.\nThis deep dive into exon-level analysis not only underscores the complexity inherent in genetic studies but also highlights the meticulous detail and sophisticated understanding required to truly grasp the implications of gene expression data. As researchers continue to unravel these complexities, each discussion and discovery adds a valuable piece to the puzzle of life sciences." + "text": "In a recent commentary by Donal T. Manahan, the magnified effects of marine heatwaves on the mortality of triploid Pacific oysters have been thrust into the spotlight, underscoring the urgent need for deeper understanding of marine life’s tolerance to heat stress. Manahan’s piece, a commentary our recent work led by Matt George, delves into the realm where climate change meets marine biology and aquaculture." }, { - "objectID": "posts/sr320-cod/index.html", - "href": "posts/sr320-cod/index.html", - "title": "Exploring the Impact of Marine Heatwaves on Pacific Cod", - "section": "", - "text": "In recent years, the Northeastern Pacific has been hit by a series of unprecedented marine heatwaves, notably “The Blob” from 2014-2016 and another in 2019, causing significant ecological disruptions. A compelling article titled “Beyond the Blob: Pinpointing the Mechanisms of Pacific Cod Population Decline” by the CICOES staff, delves into the alarming decline of Pacific cod populations in the Gulf of Alaska, a critical concern given the species’ ecological and economic significance.\nThe Pacific cod, a vital component of Alaska’s groundfish fishery, generating over $100 million annually, faced a dramatic 71% reduction in population between 2015 and 2017 surveys. This decline coincides with the marine heatwaves, raising urgent questions about the survival of early life stages of Pacific cod in a rapidly changing climate.\nResearchers from CICOES, the University of Washington’s School of Aquatic and Fishery Sciences, Oregon State University, and NOAA are collaborating to unravel how increased temperatures impact Pacific cod. Their focus is on the vulnerable early life stages – developing eggs, larvae, and juveniles. Intriguingly, higher temperatures, while accelerating growth, also diminish liver size and alter key metabolic enzymes in young Pacific cod, hinting at deeper metabolic disruptions.\nOne innovative approach used by these researchers is RNA-Seq, a next-generation sequencing technology. It allows for a comprehensive analysis of gene activity, shedding light on how warming affects Pacific cod at a molecular level. Initial findings suggest that high temperatures during larval rearing disrupt lipid metabolism processes, potentially reducing energy availability, a crucial resource during this stage.\nThe ultimate goal of these studies is to identify the mechanisms driving the mortality of Pacific cod post marine heatwaves. If these mechanisms are more clearly understood, it could lead to the identification of populations or individuals with a better genetic and physiological predisposition to withstand warmer conditions.\nFor anyone interested in marine biology, climate change impacts, or fisheries management, this article is a must-read. It not only provides a deep dive into the challenges faced by Pacific cod but also highlights the cutting-edge research being conducted to safeguard these vital marine populations. To explore this topic further and understand the intricacies of this crucial research, I highly recommend reading the full article in the CICOES Magazine 2023 issue. Read the full article below to gain a deeper understanding of the interplay between marine heatwaves and marine life.\nUnable to display PDF file. Download instead." + "objectID": "posts/sr320-DM/index.html#the-rising-heat-and-its-victims", + "href": "posts/sr320-DM/index.html#the-rising-heat-and-its-victims", + "title": "Insights from Pacific Oysters in a Heating Ocean", + "section": "The Rising Heat and Its Victims", + "text": "The Rising Heat and Its Victims\nThe context is alarming: with ocean temperatures breaking records and coastal heatwaves causing mass marine mortality, researchers like Manahan stress the importance of grasping how different organisms will survive in this changing environment. The Pacific Northwest, as noted by White et al. (2023), has witnessed temperatures soaring to nearly 50°C, resulting in the death of over a million bivalve mussels in a mere 100-meter stretch." }, { - "objectID": "posts/megan-rna/index.html", - "href": "posts/megan-rna/index.html", - "title": "Clam Gonad RNAseq Analysis", - "section": "", - "text": "Write up for this github issue\nGithub repo available here but each step’s chunk is also linked in workflow write up.\n\nThe Data\nThe RNA-seq data that was analyzed for this issue was from manila clam (Ruditapes philippinarum) samples of a control and treatment group. There were 15 control samples and 15 treatment samples, each with 2 reads. Each fasta file had the naming scheme M-?-###_R#_001 where ? = C (control) or T(treatment), ### = sample number, and R# = R1 (read 1) or R2 (read 2). Raw files can be found here.\n\n\nThe Workflow\n\nRetrieving Files From Gannet\nTo start the analysis, I retrieved the raw reads from gannet using wget.\nCode on Github\n\n\nChecking File Integrity via MD5sums\nTypically, the next step would be to check the file integrity by comparing the md5sums of the downloaded files with those on the remote server (gannet). However, the directory containing our reads did not have a text file of the md5sums for me to run md5sum on. So we skipped this step.\nCode on Github\n\n\nFastQC and MultiQC\nThe next step was to evaluate the quality of our sequences using FastQC and MultiQC. I generated a FastQC file for each of the reads, and then combined all of those using MultiQC to look at the quality of all of our reads together. The MultiQC report can be found here (note to view the “pretty version” you will need to download the html file and open the local file since github just shows the raw). Here’s some of the results from that:\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\nSoftware Used:\n\nFastQC (v0.12.1)\n\nCode on Github\n\n\nPsuedo Alignment with Kallisto\nNext I pseudo aligned the reads and quantified expression using Kallisto. I did not trim prior to this as it is not wholly necessary for pseudo alignment. An index for alignment and quantification was created using a reference transcriptome for Ruditapes philippinarum (note: ensure to select for RNA file). Paired end reads for each sample were then aligned and quantified against this index.\nFollowing pseudo alignment and quantification, a trinity matrix was created with the Kallisto output to build an abundance matrix.\nSoftware Used:\n\nKallisto (Linux)(v0.50.1)\nTrinityRNAseq (v2.12.0)\n\nCode on Github\n\n\nDifferential Expression and Visualization with DESeq2\nUsing the quantification in the trinity matrix created, I ran DESeq2 to show deferentially expressed genes, and filtering for those who’s expression showed a difference with a p value <= 0.05. Differential expression was also visualized via a volcano plot and heatmap of the top 25 deferentially expressed genes)\n\n\n\n\n\n\n\n\n\n\nAlong with the visualzations, I created a dataframe with the differentially expressed genes and associated statistics (base mean, log 2fold change, lfcSE, stat, pvalue, padj) and saved as a tab file for the next steps.\nSoftware used:\n\nBiocManager (v1.30.22)\nDESeq2 (v1.38.3)\npheatmap (v1.0.12)\n\nCode on GitHub\n\n\nIdentifying DEG Functions with Blastx\nOnce we had a tab file with differentially expressed genes, we could run blast on our reference genome (note: be sure to select for RNA file). Doing this creates a list of all of the genes (and gene short names) in our reference genome for us to get the names of our DEGs in the next step.\nSoftware used:\n\nNCBI Blast (v2.11.0)\n\nCode on Github\n\n\nJoining DEG with Blast Results and UniProt Gene Ontology Annotations\nUsing the file created from the reference genome Blast, I combined the Blast results with the DEG file by the common gene names. This dataframe contained the gene ID, gene short name, base mean, log 2fold change, pvalue, and padj. I isolated the UniProt IDs from the gene short names in order to retrieve the gene ontology (GO) annotations of interest.\nI looked up the annotations on UniProt’s web interface and saved the output as a tab file. Finally, I merged the Blast/DEG data frame with the GO data frame by the common UniProt ID’s/Entries to get a file of our GO annotations for the significantly deferentially expressed genes. The annotation file is available here.\nCode on Github\n\n\nGeneral (non-step specific) software and hardware info:\nComputer: 2016 MacBook Pro 8GB 13” with macOS Big Sur (v11.2)\nIDE: R Studio (v4.2.3)(via raven)" + "objectID": "posts/sr320-DM/index.html#the-pacific-oyster-at-the-heart-of-study", + "href": "posts/sr320-DM/index.html#the-pacific-oyster-at-the-heart-of-study", + "title": "Insights from Pacific Oysters in a Heating Ocean", + "section": "The Pacific Oyster at the Heart of Study", + "text": "The Pacific Oyster at the Heart of Study\nMatt’s study, referenced by Manahan, brings under scrutiny the Pacific oyster, Crassostrea gigas, an organism of commercial significance and genetic interest. Their work dissects the responses of diploid and triploid oysters to heatwaves, revealing that the mortality rate among triploid oysters was 2.5 times higher than their diploid counterparts." }, { - "objectID": "posts/sr320-lsamp/index.html", - "href": "posts/sr320-lsamp/index.html", - "title": "Assessing Oyster Viability Under Environmental Stress", - "section": "", - "text": "As part of our ongoing commitment to fostering innovative research, this summer was particularly thrilling due to the strides made in the LSAMP Scientist Program. One of our standout projects, led by an ambitious student researcher, Colby Elvrum, brought new insights into the resilience of oysters against environmental stressors. Get a first hand account of all of Colby’s science from his notebook!\n\nThe Genesis of the Study\nOysters, a crucial component of aquatic ecosystems, serve as indicators of environmental health and sustainability. Recognizing their role and the urgent need to understand how environmental changes affect these organisms, we embarked on a project to utilize a novel application of the resazurin assay, traditionally a cell viability test in microbiology. This assay, which exploits the color-changing properties of the resazurin dye in response to oxygen consumption, was adapted to measure the metabolic activity of oysters under stress.\n\n\nWhat We Aimed to Discover\nOur research was driven by two pivotal questions: Can resazurin effectively measure metabolism in oysters, and does prior exposure to stress (stress hardening) alter their metabolic response to subsequent stressors? Through meticulously designed experiments, Colby led the charge in optimizing the assay conditions, ensuring the reliability and accuracy of our measurements.\n\n\n\nColby presenting his research at the Summer Research Symposium\n\n\n\n\nKey Findings and Methodological Innovations\nOur findings were enlightening. We observed that resazurin is not only a viable marker for oyster metabolism but also that it clearly illustrates the metabolic shifts caused by environmental stressors such as temperature fluctuations. Notably, oysters exposed to elevated temperatures displayed a rapid increase in metabolic rate, which was a precursor to subsequent mortality. This initial surge and later plateau in metabolism provided critical clues about the stress thresholds of these organisms.\nMoreover, the study also highlighted how oysters previously conditioned to withstand stress exhibited altered survival rates under extreme temperatures, suggesting a potential sensitization rather than hardening effect. These insights are crucial for understanding how oysters might respond to the escalating challenges of climate change.\n\n\nLooking Ahead\nThe implications of this research extend beyond the academic sphere. They beckon a reevaluation of how we manage and conserve our aquatic resources in the face of rapid environmental changes. The potential to scale up this assay and automate aspects of the procedure could revolutionize aquaculture, and provide a more dynamic understanding of environmental impacts on marine life.\n\n\nGratitude and Acknowledgments\nThis research was made possible through the support of the National Science Foundation. We are immensely proud of Colby and all associated researchers for their dedication and hard work.\nPoster (download hi-res pdf)" + "objectID": "posts/sr320-DM/index.html#a-triploid-dilemma", + "href": "posts/sr320-DM/index.html#a-triploid-dilemma", + "title": "Insights from Pacific Oysters in a Heating Ocean", + "section": "A Triploid Dilemma", + "text": "A Triploid Dilemma\nTriploid oysters, engineered for their superior growth and yield, seem to face greater peril under thermal stress. Manahan points out that these oysters show signs of metabolic depression, reduced ATP production, and a slump in essential biological processes like glucose metabolism and immunity responses. This finding poses serious implications for aquaculture, as triploids are widely cultivated for food production." }, { - "objectID": "posts/sr320-LGBTQ/index.html", - "href": "posts/sr320-LGBTQ/index.html", - "title": "Celebrating LGBTQ+ in STEM", - "section": "", - "text": "Full Article\n\n\n\nThe following is an excerpt from a post on the SAFS Website: https://fish.uw.edu/2023/11/celebrating-lgbtq-in-stem\nCelebrating and highlighting the work of LGBTQ+ people in science, technology, engineering, and math (STEM) has a special day on the calendar: November 18. Why this date? It is based on the 60th anniversary of American Astronomer and gay activist Frank Kameny’s fight against workplace discrimination, which he took to the U.S. Supreme Court.\nScience is a place of innovation, research, and progress, but many communities are still marginalized in these spaces. Pride in STEM notes that 28% of LGBT+ people have considered leaving their jobs because of discrimination or workplace hostility.\nOn LGBTQ+ in STEM Day, we celebrate the contribution of LGBTQ+ scientists, while also recognizing that barriers are still faced and that efforts have to continue to break these down. We spoke with SAFS graduate student, Aspen Coyle, who shared her thoughts on her journey so far in academia, what inclusion means for her, and some of the barriers and highlights she’s experienced. She also shares some advice for those concerned about a lack of representation in marine science." + "objectID": "posts/sr320-DM/index.html#the-challenge-of-predicting-phenotypes", + "href": "posts/sr320-DM/index.html#the-challenge-of-predicting-phenotypes", + "title": "Insights from Pacific Oysters in a Heating Ocean", + "section": "The Challenge of Predicting Phenotypes", + "text": "The Challenge of Predicting Phenotypes\nManahan underscores a crucial challenge in marine biology: the prediction of phenotypes from gene expression. The commentary reflects on how data from different biological levels may not always align, and he calls for a cautious interpretation of such analyses. Integrative approaches are necessary for a comprehensive understanding of how organisms function and respond to environmental stress." }, { - "objectID": "posts/sr320-LGBTQ/index.html#what-led-you-to-pursue-studies-in-science", - "href": "posts/sr320-LGBTQ/index.html#what-led-you-to-pursue-studies-in-science", - "title": "Celebrating LGBTQ+ in STEM", - "section": "What led you to pursue studies in science?", - "text": "What led you to pursue studies in science?\n\nI’m one of those people that’s wanted to be a marine biologist ever since I was a little kid. I grew up in a fishing town in coastal Alaska, and my favorite thing in the world was scrambling along the intertidal, peering into tidepools and turning over rocks, trying to find the neatest critters. That base delight in hunting for cool creatures was augmented in undergrad with a deeper understanding of the ecological importance, and then after getting a job in another Alaskan fishing town, the economic importance." + "objectID": "posts/sr320-DM/index.html#energy-allocation-and-the-cost-of-reproduction", + "href": "posts/sr320-DM/index.html#energy-allocation-and-the-cost-of-reproduction", + "title": "Insights from Pacific Oysters in a Heating Ocean", + "section": "Energy Allocation and the Cost of Reproduction", + "text": "Energy Allocation and the Cost of Reproduction\nThe commentary also touches upon the energetic cost of being a triploid organism. With triploids being functionally sterile, Manahan questions whether there’s an unaccounted metabolic cost involved in maintaining redundant biosynthetic pathways." }, { - "objectID": "posts/sr320-LGBTQ/index.html#what-are-some-of-the-positive-experiences-as-lgbtq-in-stem-that-youve-had", - "href": "posts/sr320-LGBTQ/index.html#what-are-some-of-the-positive-experiences-as-lgbtq-in-stem-that-youve-had", - "title": "Celebrating LGBTQ+ in STEM", - "section": "What are some of the positive experiences as LGBTQ+ in STEM that you’ve had?", - "text": "What are some of the positive experiences as LGBTQ+ in STEM that you’ve had?\nFrom an outside perspective, I’ve existed in several different modes as a queer person in STEM – up until recently as a queer guy, and for the last six months or so as a transfemme. Before grad school, I was working for the Alaska Department of Fish and Game in a variety of fieldwork positions. Being queer in rural Alaska, especially around the fishing industry, is often met with confusion (and occasionally, mild hostility), but I never felt much of that from my coworkers.\nHere at SAFS, my lab is mostly other queer people, which has been wonderful. When I was living as a queer guy, it was really great to have a bunch of people around with this shared experience and perspective. And since queer cis people are usually around more trans people than straight cis people, it really wasn’t that big of a deal when I started transitioning." + "objectID": "posts/sr320-DM/index.html#a-path-forward", + "href": "posts/sr320-DM/index.html#a-path-forward", + "title": "Insights from Pacific Oysters in a Heating Ocean", + "section": "A Path Forward", + "text": "A Path Forward\nManahan highlights the value of multi-year, trans-generational breeding programs and commends the collaborative efforts exemplified by the team behind our study. Such partnerships across universities, governments, and industry are vital for sustained research and for breeding marine species that can withstand the pressures of climate change.\nIn summary, Manahan’s commentary not only sheds light on the specific challenges faced by triploid Pacific oysters under heat stress but also casts a wider net on the complexities of studying marine life’s response to a warming world. The findings are a crucial piece of the puzzle in our pursuit of sustainable “Blue Food” production and the broader understanding of marine ecosystem resilience.\nCitation: Manahan, D. T. (2023). Marine heatwaves impact mortality of triploid Pacific oysters. Global Change Biology. https://doi.org/10.1111/gcb.16980" }, { - "objectID": "posts/sr320-LGBTQ/index.html#what-does-inclusion-look-like-for-you", - "href": "posts/sr320-LGBTQ/index.html#what-does-inclusion-look-like-for-you", - "title": "Celebrating LGBTQ+ in STEM", - "section": "What does inclusion look like for you?", - "text": "What does inclusion look like for you?\n\n\n\n\n\n\nFull Article\n\n\n\nTo see the answer to this and other questions read the full article at https://fish.uw.edu/2023/11/celebrating-lgbtq-in-stem" + "objectID": "posts/sr320-handbook/index.html", + "href": "posts/sr320-handbook/index.html", + "title": "Deep dive into the handbook", + "section": "", + "text": "A unique perspective. You will never guess what they reveal!\n\nAudio\n\n\n\nTranscript\nWelcome to The Deep Dive, where we dig into the nitty gritty of fascinating topics.\nToday, we’re taking a deep dive into the Roberts Lab at the University of Washington, and we’re doing that through the lens of their handbook.\nIt’s more than just a rule book, though, isn’t it?\nOh, absolutely.\nIt’s like a window into their whole approach to science.\nEverything from, like, groundbreaking research to how they actually build their research culture.\nAnd they’re known for being incredibly transparent, which this handbook really embodies.\nYeah, it’s refreshing.\nAnd speaking of refreshing, I have to ask you about this freezer alarm situation.\nOh, yes.\nSo they have, like, a dedicated alarm for their ultra-low temperature freezers, right?\nYeah.\nBut there’s this 15-minute delay before anyone actually gets notified if it goes off.\nCan you imagine?\nIt’s like a slow-motion heart attack for a researcher.\nRight.\nAll those precious samples.\nI’d be a wreck.\nIt really highlights the fragility of these biological materials they’re working with.\nRNA, proteins, these things have to be stored at, like, negative 80 degrees Celsius.\nWow.\nEven a short power outage could be disastrous.\nSo is that delay, like, a safety net to give the system a chance to recover?\nExactly.\nIt’s a calculated risk.\nThey’re trying to balance preventing false alarms while also, you know, protecting those invaluable research materials.\nMakes sense.\nYeah.\nAnd it seems like that emphasis on meticulousness, on minimizing risk, it really comes through in the whole handbook, especially when they talk about lab safety and chemicals.\nIt’s serious business.\nRight.\nLike with Arnazole RT, they’re very clear about it being corrosive, potentially harmful if you inhale it, even disposing of it.\nIt’s a whole multi-step process.\nWell, they’re dealing with some pretty potent stuff.\nIt underscores their dedication to, you know, not just scientific rigor, but the actual well-being of their researchers.\nAbsolutely.\nIt’s like they’re creating an environment where cutting-edge science can happen, but it can happen safely.\nSafety first.\nYeah.\nAnd that meticulousness, that doing things by the book, it goes beyond just lab safety, you know.\nRight.\nIt’s woven into their whole research philosophy, which makes you wonder, if they’re this careful with safety, how does that translate to, say, data management or collaboration?\nGood question.\nAnd as luck would have it, that’s exactly what we’re going to be digging into in the rest of this deep dive.\nYou know, it’s funny you should mention that because the next thing that really struck me about this handbook was their code of conduct.\nOh, interesting.\nHow so?\nWell, for one, it’s incredibly detailed, even for like their diversity, equity, and inclusion meetings.\nYou don’t always see that level of, I don’t know, formality in a lab handbook.\nWhat kinds of things are we talking about here?\nThey have these great phrases like, “Elevate impact above intent,” and, “Expect and accept non-closure.”\nLike, really specific guidelines.\nHuh.\nIt sounds like they’re trying to foster a very specific kind of research environment.\nRight.\nOne where people feel comfortable admitting they don’t know everything, which, let’s be honest, is most of the time in research, right?\nOh, absolutely.\nScience is all about embracing uncertainty.\nBut it takes a certain culture to really allow for that.\nTotally.\nAnd it seems like they’re putting a lot of emphasis on making sure everyone feels heard and respected, especially in those DEI meetings.\nWell, and that makes sense, right?\nIf you want to have those tough conversations about diversity and inclusion, you need to create a space where people feel safe to speak their minds.\nYeah.\nNo, you’re right.\nIt all ties together.\nAnd then there’s this whole thing about mentorship.\nThey really encourage lab members to have multiple mentors, not just one.\nThat’s interesting.\nMost labs I’ve seen, it’s pretty standard to have one primary mentor.\nRight.\nYeah.\nSo I thought that was really unique.\nIt kind of speaks to this idea of providing a well-rounded experience, right?\nAbsolutely.\nDifferent mentors bring different perspectives, different areas of expertise.\nIt can really enrich a researcher’s training.\nOkay, so we’ve got meticulous safety protocols, a very deliberate approach to their lab culture.\nBut we also know they’re dealing with a massive amount of data.\nLike their handbook mentions Nightingale for sequencing this whole network attached storage system called Gannett.\nDon’t forget the supercomputer.\nMOCs, was it?\nOh, right.\nMOCs.\nI mean, it’s a lot.\nIt really makes you wonder how they manage it all.\nIt’s a data tsunami.\nHow do they keep from drowning?\nWell, for one thing, they’re incredibly organized.\nLike religiously organized.\nGive me the details.\nThink detailed metadata for every single experiment, strict folder structures on their network.\nThey even have readme files.\nReadme files for every folder, seriously.\nSeriously.\nAnd it’s all part of this commitment to open science.\nThey want their research to be accessible, transparent.\nSo anyone could theoretically go in and understand their data, their methods.\nThat’s the idea.\nIt’s about breaking down those silos, you know, fostering collaboration, avoiding unnecessary redundancy, ultimately speeding up discoveries.\nIt’s kind of inspiring, actually.\nIt’s like they’re playing the long game, advancing science as a whole, not just their own work.\nExactly.\nBut okay, even with perfect organization, all that data analysis, it’s got to be intense.\nThey mentioned Jupiter notebooks in the handbook.\nRight, and mocks the supercomputer.\nAnd they even talk about using like the command line.\nHard course, so they’re not messing around.\nWell, they’re equipping their researchers with a seriously powerful toolkit.\nBut it goes beyond just the tech.\nThey even recommend this book, Getting Things Done.\nTime management.\nTime management.\nIt’s all about efficiency.\nThey don’t just give them the tools.\nThey give them the training, the resources to actually use them well.\nIt’s like they’ve thought of everything.\nYeah.\nAnd it doesn’t stop there.\nThey have a whole section on conferences, funding opportunities, even like travel grants.\nThey want their researchers to be well-rounded, right?\nNot just stuck in the lab, but out there presenting, collaborating, getting their work funded.\nIt’s impressive, I have to say.\nLooking at the Roberts Lab this way, through their handbook, you really get a sense of the thoughtfulness, the care that goes into building a successful research environment.\nIt’s not just about, you know, the results, the discoveries.\nIt’s the people, the culture.\nAnd that commitment to moving science forward in a way that’s open and collaborative, it’s really something.\nMakes you wonder what they’ll accomplish, what amazing discoveries are on the horizon for them.\nIt does, doesn’t it?\nAnd that’s something to ponder as we wrap up this deep dive into the world of the Roberts Lab.\nUntil next time, keep exploring, keep questioning, and keep diving deep." }, { "objectID": "posts/sr320-fhl/index.html", @@ -577,7 +598,7 @@ "href": "contact.html", "title": "Contact Us", "section": "", - "text": "Steven Roberts - 206-866-5141; sr320@uw.edu\nFeel free to email any lab member - you can find that information here.\nIf you have a query related to wet lab work or data analysis - please submit a GitHub Issue in RobertsLab/resources.\n\nPhysical Address: (for walking, etc) University of Washington \n1140 NE Boat Street\nFisheries Research and Teaching Building\nRoom # 232\nSeattle, WA 98105\nGoogle Map Link\n\n\nShipping Address:\nUniversity of Washington\nSchool of Aquatic and Fishery Sciences\n1122 Boat Street\nSeattle, WA 98105-5020\nCampus Mail Address:\nUniversity of Washington\nSchool of Aquatic and Fishery Sciences\nBox 355020\nSeattle, WA 98195" + "text": "Steven Roberts - 206-866-5141; sr320@uw.edu\nFeel free to email any lab member - you can find that information here.\nIf you have a query related to wet lab work or data analysis - please submit a GitHub Issue in RobertsLab/resources.\n\nLoading…\n\n\nPhysical Address: (for walking, etc) University of Washington \n1140 NE Boat Street\nFisheries Research and Teaching Building\nRoom # 232\nSeattle, WA 98105\nGoogle Map Link\n\n\nShipping Address:\nUniversity of Washington\nSchool of Aquatic and Fishery Sciences\n1122 Boat Street\nSeattle, WA 98105-5020\nCampus Mail Address:\nUniversity of Washington\nSchool of Aquatic and Fishery Sciences\nBox 355020\nSeattle, WA 98195" }, { "objectID": "research.html", @@ -1266,543 +1287,536 @@ "text": "In the meticulously orchestrated world of marine science, a groundbreaking experiment has unfolded in the hands of Eric Essington, casting the spotlight on an unlikely protagonist: the oyster. This narrative begins with the arrival of 235 adult oysters from Pacific Hybreed, their sizes ranging impressively from 40 to 100mm, and further complemented by a diverse younger contingent—120 juveniles, 120 seed, and approximately 120 spat, all courtesy of the USDA’s 2023 spawn.\nThe experimental setup divided these oysters into two groups: one destined for a control tank, mirroring their natural aquatic environment at a serene 17ºC, and the other for a treatment tank, where conditions were significantly altered. The latter group was subjected to a deliberate increase in temperature, a gradual ascent of 2ºC per hour until the water reached a stress-inducing 26ºC, maintained for six hours daily over a seven-week span (began 10 2 2023, ended 11 21 2023). This thermal regimen aimed to simulate the increasingly erratic and harsh conditions wrought by climate change.\n\nAdding a layer of complexity, adults and juveniles were subjected to mechanical stress, an innovative use of a salad spinner for 15 minutes on selected dates (10/2/2023, 10/4/2023, 10/11/2023). This unusual methodology aimed to mimic the physical disturbances oysters might face in their natural habitats, from tumbling in currents to encounters with predators and debris.\nThe culmination of this phase was marked by a meticulous sampling process on November 21, 2023. Selected groups of oysters were divided for detailed analysis, with some undergoing immediate tissue sampling for RNA and DNA analysis, while others faced an additional stress test—a 30-minute immersion in 32ºC water followed by a tumbling session in the salad spinner. This process was designed to simulate an acute stress event, allowing researchers to gauge the oysters’ physiological responses to compounded stressors.\nSeveral months later, on February 28, 2024, the experiment was revisited with a focused approach. This time, the younger generation of oysters was spotlighted, undergoing tissue sampling without the prior mechanical stress, to isolate the effects of thermal stress.\n\nTake-away to date - Stress hardening in spat in October and November resulted in increased growth compared to controls in February.\nThis experiment is not merely an investigation into the resilience of oysters to thermal and mechanical stress; it’s a narrative about adaptation, survival, and the intricate dance of life beneath the waves.\nSee Eric’s Post for more details." }, { - "objectID": "posts/sr320-DM/index.html", - "href": "posts/sr320-DM/index.html", - "title": "Insights from Pacific Oysters in a Heating Ocean", + "objectID": "posts/sr320-LGBTQ/index.html", + "href": "posts/sr320-LGBTQ/index.html", + "title": "Celebrating LGBTQ+ in STEM", "section": "", - "text": "In a recent commentary by Donal T. Manahan, the magnified effects of marine heatwaves on the mortality of triploid Pacific oysters have been thrust into the spotlight, underscoring the urgent need for deeper understanding of marine life’s tolerance to heat stress. Manahan’s piece, a commentary our recent work led by Matt George, delves into the realm where climate change meets marine biology and aquaculture." + "text": "Full Article\n\n\n\nThe following is an excerpt from a post on the SAFS Website: https://fish.uw.edu/2023/11/celebrating-lgbtq-in-stem\nCelebrating and highlighting the work of LGBTQ+ people in science, technology, engineering, and math (STEM) has a special day on the calendar: November 18. Why this date? It is based on the 60th anniversary of American Astronomer and gay activist Frank Kameny’s fight against workplace discrimination, which he took to the U.S. Supreme Court.\nScience is a place of innovation, research, and progress, but many communities are still marginalized in these spaces. Pride in STEM notes that 28% of LGBT+ people have considered leaving their jobs because of discrimination or workplace hostility.\nOn LGBTQ+ in STEM Day, we celebrate the contribution of LGBTQ+ scientists, while also recognizing that barriers are still faced and that efforts have to continue to break these down. We spoke with SAFS graduate student, Aspen Coyle, who shared her thoughts on her journey so far in academia, what inclusion means for her, and some of the barriers and highlights she’s experienced. She also shares some advice for those concerned about a lack of representation in marine science." }, { - "objectID": "posts/sr320-DM/index.html#the-rising-heat-and-its-victims", - "href": "posts/sr320-DM/index.html#the-rising-heat-and-its-victims", - "title": "Insights from Pacific Oysters in a Heating Ocean", - "section": "The Rising Heat and Its Victims", - "text": "The Rising Heat and Its Victims\nThe context is alarming: with ocean temperatures breaking records and coastal heatwaves causing mass marine mortality, researchers like Manahan stress the importance of grasping how different organisms will survive in this changing environment. The Pacific Northwest, as noted by White et al. (2023), has witnessed temperatures soaring to nearly 50°C, resulting in the death of over a million bivalve mussels in a mere 100-meter stretch." + "objectID": "posts/sr320-LGBTQ/index.html#what-led-you-to-pursue-studies-in-science", + "href": "posts/sr320-LGBTQ/index.html#what-led-you-to-pursue-studies-in-science", + "title": "Celebrating LGBTQ+ in STEM", + "section": "What led you to pursue studies in science?", + "text": "What led you to pursue studies in science?\n\nI’m one of those people that’s wanted to be a marine biologist ever since I was a little kid. I grew up in a fishing town in coastal Alaska, and my favorite thing in the world was scrambling along the intertidal, peering into tidepools and turning over rocks, trying to find the neatest critters. That base delight in hunting for cool creatures was augmented in undergrad with a deeper understanding of the ecological importance, and then after getting a job in another Alaskan fishing town, the economic importance." }, { - "objectID": "posts/sr320-DM/index.html#the-pacific-oyster-at-the-heart-of-study", - "href": "posts/sr320-DM/index.html#the-pacific-oyster-at-the-heart-of-study", - "title": "Insights from Pacific Oysters in a Heating Ocean", - "section": "The Pacific Oyster at the Heart of Study", - "text": "The Pacific Oyster at the Heart of Study\nMatt’s study, referenced by Manahan, brings under scrutiny the Pacific oyster, Crassostrea gigas, an organism of commercial significance and genetic interest. Their work dissects the responses of diploid and triploid oysters to heatwaves, revealing that the mortality rate among triploid oysters was 2.5 times higher than their diploid counterparts." + "objectID": "posts/sr320-LGBTQ/index.html#what-are-some-of-the-positive-experiences-as-lgbtq-in-stem-that-youve-had", + "href": "posts/sr320-LGBTQ/index.html#what-are-some-of-the-positive-experiences-as-lgbtq-in-stem-that-youve-had", + "title": "Celebrating LGBTQ+ in STEM", + "section": "What are some of the positive experiences as LGBTQ+ in STEM that you’ve had?", + "text": "What are some of the positive experiences as LGBTQ+ in STEM that you’ve had?\nFrom an outside perspective, I’ve existed in several different modes as a queer person in STEM – up until recently as a queer guy, and for the last six months or so as a transfemme. Before grad school, I was working for the Alaska Department of Fish and Game in a variety of fieldwork positions. Being queer in rural Alaska, especially around the fishing industry, is often met with confusion (and occasionally, mild hostility), but I never felt much of that from my coworkers.\nHere at SAFS, my lab is mostly other queer people, which has been wonderful. When I was living as a queer guy, it was really great to have a bunch of people around with this shared experience and perspective. And since queer cis people are usually around more trans people than straight cis people, it really wasn’t that big of a deal when I started transitioning." }, { - "objectID": "posts/sr320-DM/index.html#a-triploid-dilemma", - "href": "posts/sr320-DM/index.html#a-triploid-dilemma", - "title": "Insights from Pacific Oysters in a Heating Ocean", - "section": "A Triploid Dilemma", - "text": "A Triploid Dilemma\nTriploid oysters, engineered for their superior growth and yield, seem to face greater peril under thermal stress. Manahan points out that these oysters show signs of metabolic depression, reduced ATP production, and a slump in essential biological processes like glucose metabolism and immunity responses. This finding poses serious implications for aquaculture, as triploids are widely cultivated for food production." + "objectID": "posts/sr320-LGBTQ/index.html#what-does-inclusion-look-like-for-you", + "href": "posts/sr320-LGBTQ/index.html#what-does-inclusion-look-like-for-you", + "title": "Celebrating LGBTQ+ in STEM", + "section": "What does inclusion look like for you?", + "text": "What does inclusion look like for you?\n\n\n\n\n\n\nFull Article\n\n\n\nTo see the answer to this and other questions read the full article at https://fish.uw.edu/2023/11/celebrating-lgbtq-in-stem" }, { - "objectID": "posts/sr320-DM/index.html#the-challenge-of-predicting-phenotypes", - "href": "posts/sr320-DM/index.html#the-challenge-of-predicting-phenotypes", - "title": "Insights from Pacific Oysters in a Heating Ocean", - "section": "The Challenge of Predicting Phenotypes", - "text": "The Challenge of Predicting Phenotypes\nManahan underscores a crucial challenge in marine biology: the prediction of phenotypes from gene expression. The commentary reflects on how data from different biological levels may not always align, and he calls for a cautious interpretation of such analyses. Integrative approaches are necessary for a comprehensive understanding of how organisms function and respond to environmental stress." + "objectID": "posts/sr320-lsamp/index.html", + "href": "posts/sr320-lsamp/index.html", + "title": "Assessing Oyster Viability Under Environmental Stress", + "section": "", + "text": "As part of our ongoing commitment to fostering innovative research, this summer was particularly thrilling due to the strides made in the LSAMP Scientist Program. One of our standout projects, led by an ambitious student researcher, Colby Elvrum, brought new insights into the resilience of oysters against environmental stressors. Get a first hand account of all of Colby’s science from his notebook!\n\nThe Genesis of the Study\nOysters, a crucial component of aquatic ecosystems, serve as indicators of environmental health and sustainability. Recognizing their role and the urgent need to understand how environmental changes affect these organisms, we embarked on a project to utilize a novel application of the resazurin assay, traditionally a cell viability test in microbiology. This assay, which exploits the color-changing properties of the resazurin dye in response to oxygen consumption, was adapted to measure the metabolic activity of oysters under stress.\n\n\nWhat We Aimed to Discover\nOur research was driven by two pivotal questions: Can resazurin effectively measure metabolism in oysters, and does prior exposure to stress (stress hardening) alter their metabolic response to subsequent stressors? Through meticulously designed experiments, Colby led the charge in optimizing the assay conditions, ensuring the reliability and accuracy of our measurements.\n\n\n\nColby presenting his research at the Summer Research Symposium\n\n\n\n\nKey Findings and Methodological Innovations\nOur findings were enlightening. We observed that resazurin is not only a viable marker for oyster metabolism but also that it clearly illustrates the metabolic shifts caused by environmental stressors such as temperature fluctuations. Notably, oysters exposed to elevated temperatures displayed a rapid increase in metabolic rate, which was a precursor to subsequent mortality. This initial surge and later plateau in metabolism provided critical clues about the stress thresholds of these organisms.\nMoreover, the study also highlighted how oysters previously conditioned to withstand stress exhibited altered survival rates under extreme temperatures, suggesting a potential sensitization rather than hardening effect. These insights are crucial for understanding how oysters might respond to the escalating challenges of climate change.\n\n\nLooking Ahead\nThe implications of this research extend beyond the academic sphere. They beckon a reevaluation of how we manage and conserve our aquatic resources in the face of rapid environmental changes. The potential to scale up this assay and automate aspects of the procedure could revolutionize aquaculture, and provide a more dynamic understanding of environmental impacts on marine life.\n\n\nGratitude and Acknowledgments\nThis research was made possible through the support of the National Science Foundation. We are immensely proud of Colby and all associated researchers for their dedication and hard work.\nPoster (download hi-res pdf)" }, { - "objectID": "posts/sr320-DM/index.html#energy-allocation-and-the-cost-of-reproduction", - "href": "posts/sr320-DM/index.html#energy-allocation-and-the-cost-of-reproduction", - "title": "Insights from Pacific Oysters in a Heating Ocean", - "section": "Energy Allocation and the Cost of Reproduction", - "text": "Energy Allocation and the Cost of Reproduction\nThe commentary also touches upon the energetic cost of being a triploid organism. With triploids being functionally sterile, Manahan questions whether there’s an unaccounted metabolic cost involved in maintaining redundant biosynthetic pathways." + "objectID": "posts/megan-rna/index.html", + "href": "posts/megan-rna/index.html", + "title": "Clam Gonad RNAseq Analysis", + "section": "", + "text": "Write up for this github issue\nGithub repo available here but each step’s chunk is also linked in workflow write up.\n\nThe Data\nThe RNA-seq data that was analyzed for this issue was from manila clam (Ruditapes philippinarum) samples of a control and treatment group. There were 15 control samples and 15 treatment samples, each with 2 reads. Each fasta file had the naming scheme M-?-###_R#_001 where ? = C (control) or T(treatment), ### = sample number, and R# = R1 (read 1) or R2 (read 2). Raw files can be found here.\n\n\nThe Workflow\n\nRetrieving Files From Gannet\nTo start the analysis, I retrieved the raw reads from gannet using wget.\nCode on Github\n\n\nChecking File Integrity via MD5sums\nTypically, the next step would be to check the file integrity by comparing the md5sums of the downloaded files with those on the remote server (gannet). However, the directory containing our reads did not have a text file of the md5sums for me to run md5sum on. So we skipped this step.\nCode on Github\n\n\nFastQC and MultiQC\nThe next step was to evaluate the quality of our sequences using FastQC and MultiQC. I generated a FastQC file for each of the reads, and then combined all of those using MultiQC to look at the quality of all of our reads together. The MultiQC report can be found here (note to view the “pretty version” you will need to download the html file and open the local file since github just shows the raw). Here’s some of the results from that:\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\nSoftware Used:\n\nFastQC (v0.12.1)\n\nCode on Github\n\n\nPsuedo Alignment with Kallisto\nNext I pseudo aligned the reads and quantified expression using Kallisto. I did not trim prior to this as it is not wholly necessary for pseudo alignment. An index for alignment and quantification was created using a reference transcriptome for Ruditapes philippinarum (note: ensure to select for RNA file). Paired end reads for each sample were then aligned and quantified against this index.\nFollowing pseudo alignment and quantification, a trinity matrix was created with the Kallisto output to build an abundance matrix.\nSoftware Used:\n\nKallisto (Linux)(v0.50.1)\nTrinityRNAseq (v2.12.0)\n\nCode on Github\n\n\nDifferential Expression and Visualization with DESeq2\nUsing the quantification in the trinity matrix created, I ran DESeq2 to show deferentially expressed genes, and filtering for those who’s expression showed a difference with a p value <= 0.05. Differential expression was also visualized via a volcano plot and heatmap of the top 25 deferentially expressed genes)\n\n\n\n\n\n\n\n\n\n\nAlong with the visualzations, I created a dataframe with the differentially expressed genes and associated statistics (base mean, log 2fold change, lfcSE, stat, pvalue, padj) and saved as a tab file for the next steps.\nSoftware used:\n\nBiocManager (v1.30.22)\nDESeq2 (v1.38.3)\npheatmap (v1.0.12)\n\nCode on GitHub\n\n\nIdentifying DEG Functions with Blastx\nOnce we had a tab file with differentially expressed genes, we could run blast on our reference genome (note: be sure to select for RNA file). Doing this creates a list of all of the genes (and gene short names) in our reference genome for us to get the names of our DEGs in the next step.\nSoftware used:\n\nNCBI Blast (v2.11.0)\n\nCode on Github\n\n\nJoining DEG with Blast Results and UniProt Gene Ontology Annotations\nUsing the file created from the reference genome Blast, I combined the Blast results with the DEG file by the common gene names. This dataframe contained the gene ID, gene short name, base mean, log 2fold change, pvalue, and padj. I isolated the UniProt IDs from the gene short names in order to retrieve the gene ontology (GO) annotations of interest.\nI looked up the annotations on UniProt’s web interface and saved the output as a tab file. Finally, I merged the Blast/DEG data frame with the GO data frame by the common UniProt ID’s/Entries to get a file of our GO annotations for the significantly deferentially expressed genes. The annotation file is available here.\nCode on Github\n\n\nGeneral (non-step specific) software and hardware info:\nComputer: 2016 MacBook Pro 8GB 13” with macOS Big Sur (v11.2)\nIDE: R Studio (v4.2.3)(via raven)" }, { - "objectID": "posts/sr320-DM/index.html#a-path-forward", - "href": "posts/sr320-DM/index.html#a-path-forward", - "title": "Insights from Pacific Oysters in a Heating Ocean", - "section": "A Path Forward", - "text": "A Path Forward\nManahan highlights the value of multi-year, trans-generational breeding programs and commends the collaborative efforts exemplified by the team behind our study. Such partnerships across universities, governments, and industry are vital for sustained research and for breeding marine species that can withstand the pressures of climate change.\nIn summary, Manahan’s commentary not only sheds light on the specific challenges faced by triploid Pacific oysters under heat stress but also casts a wider net on the complexities of studying marine life’s response to a warming world. The findings are a crucial piece of the puzzle in our pursuit of sustainable “Blue Food” production and the broader understanding of marine ecosystem resilience.\nCitation: Manahan, D. T. (2023). Marine heatwaves impact mortality of triploid Pacific oysters. Global Change Biology. https://doi.org/10.1111/gcb.16980" + "objectID": "posts/sr320-cod/index.html", + "href": "posts/sr320-cod/index.html", + "title": "Exploring the Impact of Marine Heatwaves on Pacific Cod", + "section": "", + "text": "In recent years, the Northeastern Pacific has been hit by a series of unprecedented marine heatwaves, notably “The Blob” from 2014-2016 and another in 2019, causing significant ecological disruptions. A compelling article titled “Beyond the Blob: Pinpointing the Mechanisms of Pacific Cod Population Decline” by the CICOES staff, delves into the alarming decline of Pacific cod populations in the Gulf of Alaska, a critical concern given the species’ ecological and economic significance.\nThe Pacific cod, a vital component of Alaska’s groundfish fishery, generating over $100 million annually, faced a dramatic 71% reduction in population between 2015 and 2017 surveys. This decline coincides with the marine heatwaves, raising urgent questions about the survival of early life stages of Pacific cod in a rapidly changing climate.\nResearchers from CICOES, the University of Washington’s School of Aquatic and Fishery Sciences, Oregon State University, and NOAA are collaborating to unravel how increased temperatures impact Pacific cod. Their focus is on the vulnerable early life stages – developing eggs, larvae, and juveniles. Intriguingly, higher temperatures, while accelerating growth, also diminish liver size and alter key metabolic enzymes in young Pacific cod, hinting at deeper metabolic disruptions.\nOne innovative approach used by these researchers is RNA-Seq, a next-generation sequencing technology. It allows for a comprehensive analysis of gene activity, shedding light on how warming affects Pacific cod at a molecular level. Initial findings suggest that high temperatures during larval rearing disrupt lipid metabolism processes, potentially reducing energy availability, a crucial resource during this stage.\nThe ultimate goal of these studies is to identify the mechanisms driving the mortality of Pacific cod post marine heatwaves. If these mechanisms are more clearly understood, it could lead to the identification of populations or individuals with a better genetic and physiological predisposition to withstand warmer conditions.\nFor anyone interested in marine biology, climate change impacts, or fisheries management, this article is a must-read. It not only provides a deep dive into the challenges faced by Pacific cod but also highlights the cutting-edge research being conducted to safeguard these vital marine populations. To explore this topic further and understand the intricacies of this crucial research, I highly recommend reading the full article in the CICOES Magazine 2023 issue. Read the full article below to gain a deeper understanding of the interplay between marine heatwaves and marine life.\nUnable to display PDF file. Download instead." }, { - "objectID": "posts/cool-paper/index.html", - "href": "posts/cool-paper/index.html", - "title": "Genetics: Does it really matter?", + "objectID": "posts/sr320-altsplice/index.html", + "href": "posts/sr320-altsplice/index.html", + "title": "Cmplexities of Gene Expression", "section": "", - "text": "Here I will describe a recent, cool paper and try to also highlight 1) some of the material covered in our class on Proposal Writing and Professional Development, and 2) some of the features of using Quarto.\nThe paper characterizes the relationship of genetics and epigenetics in the Olympia oysters. The two primary authors are Katherine Silliman and Laura Spencer. Silliman et al. (2023)" + "text": "In a recent meeting focused on gene expression analysis, we delved into the intricacies of examining expression at the exon level, a crucial but complex aspect of understanding gene function and regulation. The discussion provided deep insights into both the challenges and potential breakthroughs in the field of genomics. Here’s a detailed recap of the key points and future directions highlighted during the conversation.\n\n\nEmphasis on Gene Expression Analysis\nGene expression analysis remains a cornerstone of genomic studies, serving as a gateway to understanding the roles of genes in various biological processes and disease states. The meeting opened with a reaffirmation of the importance of mastering the techniques and tools that allow for such analysis, emphasizing that comprehensive understanding is necessary to advance research.\n\n\nWorkflow and Tools\nA significant portion of the discussion revolved around the workflow used in the analysis. The researchers outlined their use of HiSat for alignment—a choice reflecting HiSat’s efficiency in handling high-throughput RNA-seq data. StringTie was then introduced as the tool for identifying transcript units, highlighting its capability to assemble transcripts effectively. The differential expression analysis was conducted using DC2, a tool favored for its robust statistical methods in handling variance among biological replicates.\n\n\nChallenges in Interpretation\nOne of the central themes of the meeting was the challenge of interpreting results where genes do not show differential expression overall but do exhibit variations at the exon level. This scenario often leads to questions about alternative splicing or differential exon usage, which can have significant implications for gene function.\nThe group discussed several hypothetical situations:\n- Alternative Splicing: If only certain exons within a gene are differentially expressed, this might suggest alternative splicing, a process where the same gene can lead to different protein variants.\n- Alternative Start Sites: Differentially expressed exons at the gene’s boundaries might indicate alternative transcription start sites, affecting how transcription is initiated.\n\n\nBiological Implications and Interpretation\nThe biological implications of these findings are profound, potentially impacting everything from gene regulation to the development of therapeutic strategies. For example, alternative splicing can result in proteins with differing, sometimes antagonistic functions. Understanding these nuances is essential for the development of targeted therapies.\n\n\nThe Role of Visual Aids\nA noteworthy suggestion from the meeting was the use of visual aids to better explain complex data and analysis. Presentations with graphical representations of data can facilitate a clearer understanding, aiding in the interpretation of intricate patterns of gene expression that might otherwise be overlooked in raw numerical data.\n\n\nFuture Directions\nLooking to the future, the participants agreed on the need for more refined tools and methodologies to enhance the accuracy and granularity of exon-level expression analysis. They highlighted the potential for developing new computational tools that can integrate more complex layers of data, such as epigenetic modifications and non-coding RNA interactions, which could provide a more comprehensive view of gene regulation.\nThe meeting concluded with a sense of optimism about the path forward, acknowledging that while challenges remain, the ongoing advancements in technology and methodology will continue to illuminate the complexities of the genome.\nThis deep dive into exon-level analysis not only underscores the complexity inherent in genetic studies but also highlights the meticulous detail and sophisticated understanding required to truly grasp the implications of gene expression data. As researchers continue to unravel these complexities, each discussion and discovery adds a valuable piece to the puzzle of life sciences." }, { - "objectID": "posts/cool-paper/index.html#so-why-does-it-matter", - "href": "posts/cool-paper/index.html#so-why-does-it-matter", - "title": "Genetics: Does it really matter?", - "section": "So why does it matter?", - "text": "So why does it matter?\n\nStudies of plasticity and epigenetic variation among groups from different environments must also account for genetic variation, rather than attributing all differences to the environment.\nGenetic variation is clearly heritable, our results suggest that some proportion of DNA methylation (and likely associated phenotypes) are also heritable.\nDespite our two populations being raised in the same environment, 73% of the epigenetic variation in our system was not attributable to genetics." + "objectID": "posts/frontpage/sr320-boundless/index.html", + "href": "posts/frontpage/sr320-boundless/index.html", + "title": "Exploring Pacific Cod Resilience in a Warming Ocean", + "section": "", + "text": "In our latest update on the Pacific cod juvenile temperature study, we've gained deeper insights into how these remarkable fish respond to different temperatures. This research is part of a larger effort to understand the resilience of marine species in changing environments.\nGenetic Insights Reveal Population Origins\nWe began with genetic analyses, using data from thousands of genetic markers to determine the origin of our experimental fish. All our test fish were linked to the spawning grounds in the western Gulf of Alaska (wGOA) and the Eastern Bering Sea (EBS). This finding allows us to focus on the thermal resilience of cod from this particular region, which is vital as they face shifts in temperature in their natural habitats.\n\nTemperature's Role in Energy and Lipid Storage\nOur collaborator Louise Copement analyzed liver lipids in these juvenile cod, focusing on triglycerides and other key lipid types that are crucial for overwinter survival. The results showed a clear trend: energy storage, primarily in the form of triglycerides, peaked at 9°C, then dropped sharply at higher temperatures, especially at 16°C. This suggests that extreme warmth could deplete essential energy reserves, reducing the fish's survival prospects in the cold winter months.\n\nOptimal Growth Temperatures and Physiological Responses\nWe also observed that juvenile cod exhibit optimal growth at approximately 12.3°C, slightly higher than previous findings. With higher temperatures, growth rates plateau or decline, mirroring the energy storage patterns. Interestingly, the gene expression data from liver tissues revealed significant temperature-driven shifts, especially in energy production, lipid metabolism, and immune response genes. This molecular data adds a new layer to our understanding of temperature tolerance.\n\nIntegrated Data: A Pathway to Genomic Resilience Markers\nCombining growth, lipid, and gene expression data, we've started identifying genes that correlate with enhanced resilience at specific temperatures. This approach could spotlight genetic markers for thermal resilience, offering clues about cod populations best suited to future ocean conditions.\nIn summary, this research underscores the delicate balance juvenile Pacific cod must maintain in their energy reserves and growth under variable temperatures. These findings will help guide conservation and management efforts as we work to protect Pacific cod populations in a warming world." }, { - "objectID": "posts/cool-paper/index.html#how-are-you-including-images", - "href": "posts/cool-paper/index.html#how-are-you-including-images", - "title": "Genetics: Does it really matter?", - "section": "How are you including images?", - "text": "How are you including images?\n\nknitr::include_graphics(\"img/skitch.gif\")\n\n\n\n\n\n\n\n\nBut what is the code in the Quarto file to render what we are seeing above?\n\nknitr::include_graphics(\"img/skitch.gif\")\n\n\n\n\n\n\n\n\nEssentially you just need to include an image (here it is within the post directory) and use R code to display, highly leveraging code chunk options.\nExplore the entirety of the code behind this page at https://github.com/sr320/tumbling-oysters/blob/main/posts/cool-paper/index.qmd" + "objectID": "posts/frontpage/lspencer-cod/index.html", + "href": "posts/frontpage/lspencer-cod/index.html", + "title": "Turning the tide", + "section": "", + "text": "Chris is featured on UW’s “Be Boundless” site. Read full article here. Below is a short snippet of the feature along with an amazing video!\nOn a windy June afternoon, Chris Mantegna, ’21, encourages a half-dozen undergraduates to flip over barnacle-studded rocks and sift through seaweed. Equipped with clipboards to record their findings, they’re creating a snapshot of the organisms in the island’s intertidal zone — from orange sea cucumbers to the camouflaged armored mollusks called chitons.\nMantegna, a third-year graduate student in aquatic and fishery sciences, has spent the past three summers in Washington’s San Juan Islands, mentoring undergrads here on Yellow Island — a pristine 11-acre nature preserve owned by the Nature Conservancy. She created this eight-week program for students to get their hands dirty in the field and learn cutting-edge lab techniques at the UW Friday Harbor Laboratories — where she had a transformational research experience herself as a Husky undergrad.\nThis mentorship program reflects Mantegna’s passion both for advancing the science and for making it more inclusive and accessible to others. Her face lights up when she spots a small chiton (her favorite) clinging to the bottom of a rock, and she invites others to feel the mollusk’s tough plated back. Even Mantegna’s doctoral work — examining the genetic response of shellfish to contaminants in Puget Sound waterways — has a focus on community outreach and environmental literacy.\n\nMantegna says we have a better chance at fighting climate change when everyone — scientists and community members — feels connected to their environment and each other. “I can tell you that the ocean is dying or that we have too much acidification,” says Mantegna, a U.S. Navy veteran who is the first in her family to graduate from college. “But it doesn’t matter if you’ve never had the chance to feel the joy that comes from this place.”\nFinish feature here." }, { - "objectID": "posts/grace-ac-WSN/index.html", - "href": "posts/grace-ac-WSN/index.html", - "title": "Western Society of Naturalists", + "objectID": "posts/frontpage/ariana-hatchery/index.html", + "href": "posts/frontpage/ariana-hatchery/index.html", + "title": "Hatchery Field Day at Point Whitney", "section": "", - "text": "Had an amazing week last week! See post for details!" + "text": "On May 6, 2024, Dr. Ariana Huffmyer, an NSF Ocean Sciences Postdoctoral Fellow from the University of Rhode Island and University of Washington, shared insights from a field day at Point Whitney. This comprehensive post revealed the detailed process of managing and monitoring oyster growth and stress testing, providing a clear framework for hatchery management.\n\n\n\n\n\n\nLink to Full Notebook Post\n\n\n\nhttps://ahuffmyer.github.io/ASH_Putnam_Lab_Notebook/Hatchery-field-day-at-Point-Whitney-May-6-2024/\n\n\nOverview of Field Day Activities The objective was to monitor the health and stress responses of oyster cohorts at the hatchery. Key activities included calibrating monitoring equipment, feeding the oysters, and assessing the impacts of temperature and freshwater stress.\n\nMonitoring Equipment Calibration: Dr. Huffmyer set up and calibrated an Orion Star A325 probe to measure pH, temperature, and conductivity. By using buffers of varying pH and a conductivity solution, she ensured accurate measurements. The pH was measured on the NBS scale, considered sufficient since ocean acidification experiments weren’t being conducted.\nFeeding Protocol: The oysters were pulse-fed, where approximately 1/3 of a 5-gallon bucket was distributed among the tanks. This ensured that the animals received sufficient nutrition.\nFluorometry and Physiochemical Measurements: Fluorometry measurements were conducted before and after feeding, providing data on oyster metabolic activity. Additionally, pH, temperature, and conductivity were measured across different tanks, offering valuable weekly insights into water quality.\nStress Testing Regimen: Dr. Huffmyer conducted a 30-minute stress test for specific oyster cohorts using freshwater and elevated temperature exposures. Animals were subjected to 25°C temperature and freshwater immersion, replicating environmental stressors they might face. Trays were labeled and organized by stressor type.\nGrowth Characterization: Size measurements were taken using a waterproof digital caliper. Cohorts were categorized based on their respective stressors, creating a comprehensive understanding of their growth patterns.\nPloidy Testing Preparations: A selection of oysters from different cohorts was collected for ploidy testing to distinguish between diploid and triploid oysters. They were stored in mesh bags, and the testing results would provide critical information for future breeding programs.\n\n\n\n\nheath-tray\n\n\nTakeaways for Hatchery Science Dr. Huffmyer’s systematic approach highlights the significance of precise monitoring and stress testing in hatchery science. Understanding oyster resilience to environmental stressors is crucial for aquaculture sustainability. Her work at Point Whitney offers a detailed protocol that could be replicated or adapted by other researchers to monitor and improve hatchery operations.\nThe future of hatchery management will depend heavily on such frameworks, where real-time data collection and analysis enable researchers to respond promptly to environmental changes." }, { - "objectID": "posts/grace-ac-WSN/index.html#eelgrass-workshop", - "href": "posts/grace-ac-WSN/index.html#eelgrass-workshop", - "title": "Western Society of Naturalists", - "section": "Eelgrass Workshop", - "text": "Eelgrass Workshop\nFor the past year+ I’ve been fortunate to be part of an awesome team of folks working on an NSF Grant studying Eelgrass Wasting Disease, mostly centered in the Puget Sound/San Juan Islands, but also spanning along the West Coast. We had a great workshop pre-WSN where we chatted about the various aspects of the grant that folks have been working on and made plans and outlines for writing up the various projects. It was a great time and I’m looking forward to all the cool stuff coming up - keep an eye out!\nHere’s the team!\n\n\n\nimg\n\n\nDr. Lindsay Alma, Dr. Colleen Burge, Dr. Drew Harvell, Dr. Eileen Hoffman, Dr. Maya Groner, Me, Dr. Becca Maher, and Dr. Olivia Graham!" + "objectID": "posts/sr320-asi/index.html", + "href": "posts/sr320-asi/index.html", + "title": "Sharing the Good Word of Marine Epigenetics", + "section": "", + "text": "The University of Concepción recently offered an eye-opening course that dove deep into the realms of climate change, epigenetics, and marine biology. Titled “Epigenetic Phenomena Connecting Climate Change and Coastal Marine Species,” this graduate-level course provided an intensive one-week journey into the fascinating interplay between our changing climate and the genetic mechanisms of marine invertebrates.\n\nUnraveling the Mysteries of Marine Invertebrates\nThe course, designed for students with a foundational understanding of genetics and climate science, began by establishing a strong base in epigenetics, climate change, and marine invertebrate physiology. The highlight was on the often-overlooked role of marine invertebrates in coastal ecosystems, emphasizing their ecological importance and responses to climate change at an epigenetic level.\n\n\nReal-World Applications and Functional Genomics\nA significant focus of the course was the application of functional genomics. Students explored how climate change leads to alterations in epigenetic mechanisms of various coastal marine invertebrates through real-world examples. This approach helped in understanding the broader implications of these changes for marine ecosystems.\n\n\nComprehensive Course Objectives\nThe course had three primary objectives:\n\nUnderstanding Climate Change and Epigenetics: Gaining a comprehensive understanding of how climate change impacts marine invertebrates’ physiological processes through an epigenetic lens.\nProficiency in Functional Genomics: Learning about genomic techniques and their applications in studying epigenetic changes in marine invertebrates due to climate stressors.\nAnalyzing Scientific Research: Developing skills to critically analyze and evaluate scientific literature in marine invertebrate epigenetics and climate change.\n\n\n\nCourse Content: A Rich Blend of Science and Research\nThe course content was diverse and in-depth:\n\nBasics of Epigenetics and Climate Change: Introduced the intersection of these fields and the concept of environmental epigenetics.\nPhysiology of Marine Invertebrates: Covered essential aspects like feeding, digestion, reproduction, and stress response.\nImpact of Climate Change on Physiology: Explored the specific impacts of climate factors on marine invertebrates.\nFunctional Genomics and Epigenetics: Delved into genomic methodologies and applications.\nCase Studies and Current Research: Involved critical examination of recent research studies, emphasizing practical understanding.\n\n\n\nMethodology: Interactive and Engaging\nThe course used a mix of lectures, discussions, and interactive data analysis. It emphasized hands-on learning, particularly in the afternoons, where students engaged in data analysis using R and bash, providing a practical edge to the theoretical knowledge gained.\n\n\nScholarly Contributions: A Rich Bibliography\nThe course drew from a rich bibliography, featuring works by renowned researchers like Grace Crandall, Steven B. Roberts, and Cristian Gallardo-Escárate. These publications covered various aspects, from the proteomic responses of Pacific Oysters to the genomic assembly of the Blue Mussel, offering students a comprehensive view of current research in the field.\n\n\nConclusion: A Step Forward in Marine Biology Education\nThis course at the University of Concepción marked a significant step in educating the next generation of marine biologists, geneticists, and climate scientists. By bridging the gap between climate change and epigenetic phenomena in marine species, it not only enhanced understanding but also prepared students to contribute meaningfully to marine conservation efforts in the face of global climate challenges." }, { - "objectID": "posts/grace-ac-WSN/index.html#wsn-monterey-ca", - "href": "posts/grace-ac-WSN/index.html#wsn-monterey-ca", - "title": "Western Society of Naturalists", - "section": "WSN, Monterey, CA", - "text": "WSN, Monterey, CA\nI haven’t been to a conference since the Alaska Marine Science Symposium in Anchorage, AK, January 2020… so it was a little nerve-wracking to head to my first one in so long! It was amazing, though! So much cool science, so many interesting and engaging talks and posters, and I had so much fun. Made some new connections that I’m excited to foster.\nDr. Olivia Graham did an amazing job putting together THREE Marine Disease Ecology sessions!! There were two sessions on Saturday - an eelgrass session during which a lot of the team pictured in the above section presented amazing work, and a miscellaneous section that had some great talks as well.\nI was part of the Sunday morning session that was all about Pycnopodia helianthoides! Below is a photo of everyone who presented. My talk went well - I ended up getting Honorable Mention for it!\n\n\n\nimg\n\n\nDr. Lauren Schiebelhut, Dr. Jason Hodin, Dr. Alyssa Gehman, Me, Dr. Melanie Prentice, Tiffany Rudek, Dr. Drew Harvell, and Dr. Olivia Graham.\nFor fun, here’s a pretty photo of one of our adult Pycnopodia helianthoides from our Summer 2021 work that made many appearances in my talk:" + "objectID": "posts/sr320-enrich/index.html", + "href": "posts/sr320-enrich/index.html", + "title": "Unraveling the Intricacies of Enrichment Analysis", + "section": "", + "text": "In our most recent lab meeting, we delved into the fascinating world of enrichment analysis. This statistical method is a cornerstone of our research, helping us identify significantly over-represented subsets of proteins or genes within our data." }, { - "objectID": "posts/mytilus-genome/index.html", - "href": "posts/mytilus-genome/index.html", - "title": "Unveiling the Blueprints of the Sea", - "section": "", - "text": "The blue mussel, Mytilus chilensis, is not only a delicacy on dinner plates but also a cornerstone of the booming aquaculture industry along the southern coast of Chile. Its iridescent shells and robust nature make it a favorite, but beneath the waves, this bivalve is locked in a constant battle against environmental stressors, diseases, and the effects of pollution. The secret to its resilience lies in its genetic code, a treasure trove of information until now largely uncharted.\n\n\nIn a groundbreaking study, researchers have presented the first chromosome-level genome assembly for a Mytilidae family member in South America. This scientific feat, detailed in a recent publication, offers a high-quality reference genome for M. chilensis. It’s a leap forward in our understanding of this species, providing a detailed map of the genetic factors that contribute to its survival and adaptation in a changing marine environment.\n\n\n\nImagine having a detailed instruction manual for building and maintaining an organism, one that could tell you how it can survive freezing waters, resist certain pathogens, or how it might react to the shifting chemistry of its habitat. That’s what a genome assembly provides. For aquaculture, this information is invaluable. It can lead to the development of hardier mussel strains, inform conservation efforts, and enhance the industry’s sustainability.\n\n\n\nThe aquaculture industry relies heavily on mussel farming, but it’s an enterprise not without its risks. With seeds collected from natural beds and translocated to varied farming conditions, the industry has been seeking ways to reduce losses and improve yields. The newly unveiled genome paves the way for breeding programs that can select for desirable traits, such as disease resistance or faster growth rates, potentially revolutionizing mussel farming.\n\n\n\nBut the implications of this research extend beyond the realm of economics. Mussels serve as a filter for the ocean, playing a critical role in maintaining the health of marine ecosystems. Understanding their genetic makeup helps us appreciate not only how they contribute to their environment but also how they might be affected by our actions—be it through climate change or pollution.\n\n\n\nThe journey of understanding Mytilus chilensis at the genomic level is just beginning. This initial assembly is a scaffold for future discoveries, a reference for comparative genomics, and a baseline for monitoring the genetic health of populations. As scientists continue to unravel the mysteries locked in its DNA, we move closer to a future where the blue mussel can continue to thrive, both as a species and an industry.\nThe study in discussion is not just a scientific achievement; it’s a testament to the intricate dance of life adapted to the ebb and flow of the sea. As we delve into the genome of Mytilus chilensis, we’re reminded of the resilience of life and the ingenuity of those who seek to understand and preserve it. The blueprints of the sea are laid bare, and with them, a new chapter in sustainable aquaculture beckons.\nCITATION: Gallardo-Escárate, C.; Valenzuela-Muñoz, V.; Nuñez-Acuña, G.; Valenzuela-Miranda, D.; Tapia, F.J.; Yévenes, M.; Gajardo, G.; Toro, J.E.; Oyarzún, P.A.; Arriagada, G.; et al. Chromosome-Level Genome Assembly of the Blue Mussel Mytilus chilensis Reveals Molecular Signatures Facing the Marine Environment. Genes 2023, 14, 876. https://doi.org/10.3390/genes14040876" + "objectID": "posts/sr320-enrich/index.html#the-power-of-enrichment-analysis", + "href": "posts/sr320-enrich/index.html#the-power-of-enrichment-analysis", + "title": "Unraveling the Intricacies of Enrichment Analysis", + "section": "The Power of Enrichment Analysis", + "text": "The Power of Enrichment Analysis\nEnrichment analysis allows us to compare a small subset of genes or proteins to a larger set, identifying overrepresentation. This can provide valuable insights into the biological processes that are most relevant to our research." }, { - "objectID": "posts/mytilus-genome/index.html#a-genomic-milestone", - "href": "posts/mytilus-genome/index.html#a-genomic-milestone", - "title": "Unveiling the Blueprints of the Sea", - "section": "", - "text": "In a groundbreaking study, researchers have presented the first chromosome-level genome assembly for a Mytilidae family member in South America. This scientific feat, detailed in a recent publication, offers a high-quality reference genome for M. chilensis. It’s a leap forward in our understanding of this species, providing a detailed map of the genetic factors that contribute to its survival and adaptation in a changing marine environment." + "objectID": "posts/sr320-enrich/index.html#a-deep-dive-into-david", + "href": "posts/sr320-enrich/index.html#a-deep-dive-into-david", + "title": "Unraveling the Intricacies of Enrichment Analysis", + "section": "A Deep Dive into David", + "text": "A Deep Dive into David\nOne of the tools we use for enrichment analysis is David. During the meeting, we explored how to upload gene lists and backgrounds into David, and how to interpret the results it provides. This tool is invaluable in helping us understand the complex relationships and patterns within our data." }, { - "objectID": "posts/mytilus-genome/index.html#why-genome-matters", - "href": "posts/mytilus-genome/index.html#why-genome-matters", - "title": "Unveiling the Blueprints of the Sea", - "section": "", - "text": "Imagine having a detailed instruction manual for building and maintaining an organism, one that could tell you how it can survive freezing waters, resist certain pathogens, or how it might react to the shifting chemistry of its habitat. That’s what a genome assembly provides. For aquaculture, this information is invaluable. It can lead to the development of hardier mussel strains, inform conservation efforts, and enhance the industry’s sustainability." + "objectID": "posts/sr320-enrich/index.html#the-reference-list-debate", + "href": "posts/sr320-enrich/index.html#the-reference-list-debate", + "title": "Unraveling the Intricacies of Enrichment Analysis", + "section": "The Reference List Debate", + "text": "The Reference List Debate\nAn interesting discussion arose around what to use as a reference list in enrichment analysis. Should it be all the genes detected in the data set, or all genes in a reference genome? This question sparked a lively debate, highlighting the complexities and nuances of enrichment analysis." }, { - "objectID": "posts/mytilus-genome/index.html#the-economic-and-ecological-impact", - "href": "posts/mytilus-genome/index.html#the-economic-and-ecological-impact", - "title": "Unveiling the Blueprints of the Sea", - "section": "", - "text": "The aquaculture industry relies heavily on mussel farming, but it’s an enterprise not without its risks. With seeds collected from natural beds and translocated to varied farming conditions, the industry has been seeking ways to reduce losses and improve yields. The newly unveiled genome paves the way for breeding programs that can select for desirable traits, such as disease resistance or faster growth rates, potentially revolutionizing mussel farming." + "objectID": "posts/sr320-enrich/index.html#visualizing-gene-ontology-with-revigo", + "href": "posts/sr320-enrich/index.html#visualizing-gene-ontology-with-revigo", + "title": "Unraveling the Intricacies of Enrichment Analysis", + "section": "Visualizing Gene Ontology with Revigo", + "text": "Visualizing Gene Ontology with Revigo\nTo help us visualize gene ontology, we use a tool called Revigo. This tool provides a visual representation of the relationships between genes, making it easier to understand the complex data we work with." }, { - "objectID": "posts/mytilus-genome/index.html#beyond-the-economic-horizon", - "href": "posts/mytilus-genome/index.html#beyond-the-economic-horizon", - "title": "Unveiling the Blueprints of the Sea", - "section": "", - "text": "But the implications of this research extend beyond the realm of economics. Mussels serve as a filter for the ocean, playing a critical role in maintaining the health of marine ecosystems. Understanding their genetic makeup helps us appreciate not only how they contribute to their environment but also how they might be affected by our actions—be it through climate change or pollution." + "objectID": "posts/sr320-enrich/index.html#a-lighter-moment", + "href": "posts/sr320-enrich/index.html#a-lighter-moment", + "title": "Unraveling the Intricacies of Enrichment Analysis", + "section": "A Lighter Moment", + "text": "A Lighter Moment\nAmidst the serious scientific discussions, we also had a lighter moment when a team member shared a story about narrowly avoiding a parking ticket. It’s moments like these that remind us of the importance of camaraderie and humor in the lab.\n\nOur lab meetings are a crucial part of our research process, providing a space for us to discuss, debate, and learn together. Stay tuned for more insights from our lab meetings in future posts!" }, { - "objectID": "posts/mytilus-genome/index.html#looking-forward", - "href": "posts/mytilus-genome/index.html#looking-forward", - "title": "Unveiling the Blueprints of the Sea", + "objectID": "posts/sr320-george-paper/index.html", + "href": "posts/sr320-george-paper/index.html", + "title": "The Double-Edged Sword of Triploidy in Pacific Oysters", "section": "", - "text": "The journey of understanding Mytilus chilensis at the genomic level is just beginning. This initial assembly is a scaffold for future discoveries, a reference for comparative genomics, and a baseline for monitoring the genetic health of populations. As scientists continue to unravel the mysteries locked in its DNA, we move closer to a future where the blue mussel can continue to thrive, both as a species and an industry.\nThe study in discussion is not just a scientific achievement; it’s a testament to the intricate dance of life adapted to the ebb and flow of the sea. As we delve into the genome of Mytilus chilensis, we’re reminded of the resilience of life and the ingenuity of those who seek to understand and preserve it. The blueprints of the sea are laid bare, and with them, a new chapter in sustainable aquaculture beckons.\nCITATION: Gallardo-Escárate, C.; Valenzuela-Muñoz, V.; Nuñez-Acuña, G.; Valenzuela-Miranda, D.; Tapia, F.J.; Yévenes, M.; Gajardo, G.; Toro, J.E.; Oyarzún, P.A.; Arriagada, G.; et al. Chromosome-Level Genome Assembly of the Blue Mussel Mytilus chilensis Reveals Molecular Signatures Facing the Marine Environment. Genes 2023, 14, 876. https://doi.org/10.3390/genes14040876" + "text": "The issue of climate change and its cascading effects on marine ecosystems is a growing concern for researchers, conservationists, and policymakers alike. One of the intriguing avenues of research in marine science involves the impact of polyploidy, a genetic variation where organisms have extra sets of chromosomes, on stress tolerance in marine species. A recent study led by Matthew N. George from the School of Aquatic & Fishery Sciences at the University of Washington, along with affiliations from the Environmental and Fisheries Sciences Division at the Northwest Fisheries Science Center, sheds new light on the vulnerability of triploid Pacific oysters to climate stressors.\n\n\n\nThe study, titled “Triploid Pacific oysters exhibit stress response dysregulation and elevated mortality following heatwaves,” focuses on the comparison of diploid (2n) and triploid (3n) Pacific oysters (Crassostrea gigas) in response to environmental conditions akin to a heatwave. By exposing these oysters to different stressors such as elevated seawater temperature and aerial emersion, the researchers found that triploid oysters had a significantly higher mortality rate than their diploid counterparts when subjected to multiple stressors.\n\n\n\nHigher Mortality Rates in Triploids: The mortality rate in triploid oysters exposed to multiple stressors was 36.4% compared to 14.8% in diploid oysters.\nMetabolic and Physiological Limitations: Triploid oysters showed signs of metabolic depression, a reduction in ctenidium Na+/K+ ATPase activity, and dysregulated expression of stress response genes.\nFunctional Genomics Insights: Gene sets enriched in biological processes like metabolism, stress tolerance, and immune function were disproportionately represented in triploids across stress treatments.\n\n\n\n\nThe increased vulnerability of triploid Pacific oysters to climate stressors has far-reaching implications. Triploidy is often induced to achieve reproductive control in species used for marine aquaculture. While this serves to boost production and control unwanted reproduction, the study highlights that it may also render these organisms more susceptible to environmental extremes. This, in turn, could impact food security in regions dependent on marine aquaculture.\n\n\n\n\nThe findings of this study present a clear need for further research to fully understand the complexities of triploidy and its relationship with environmental stress tolerance. As climate change continues to bring about more frequent and severe heatwaves, understanding the impact on marine organisms is crucial. Future research should explore the possibility of developing stress-resilient triploid species and consider alternative strategies for reproductive control in aquaculture.\n\n\n\nWhile triploidy offers some benefits for controlling reproduction in marine aquaculture, this genetic modification may inadvertently make these organisms more susceptible to the threats posed by climate change. As we continue to grapple with the realities of a changing climate, research like this serves as an invaluable resource for better understanding the complex interactions between genetic variation and environmental stressors, thereby informing both conservation strategies and aquaculture practices.\n\n\n\nGeorge, M. N.,  Cattau, O.,  Middleton, M. A.,  Lawson, D.,  Vadopalas, B.,  Gavery, M., &  Roberts, S. B. (2023). Triploid Pacific oysters exhibit stress response dysregulation and elevated mortality following heatwaves. Global Change Biology,  00,  1–19. https://doi.org/10.1111/gcb.16880\n\nFeel free to dive into the full paper for a more detailed understanding of our findings." }, { - "objectID": "posts/frontpage/sr320-intertidal/index.html", - "href": "posts/frontpage/sr320-intertidal/index.html", - "title": "Intertidal Innovators", + "objectID": "posts/sr320-george-paper/index.html#introduction", + "href": "posts/sr320-george-paper/index.html#introduction", + "title": "The Double-Edged Sword of Triploidy in Pacific Oysters", "section": "", - "text": "On August 16, participants in the Intertidal Innovators program presented their work to the community. The program, which was a collaboration sponsored by the UW Earthlab program, provided students with the opportunity to learn about marine science and conservation through art.\n\n\n\n\n\n\n\nQuote\n\n\n\nThis program has lasted for 10 days, but during those days we have learned and worked very hard to give you this project. And we are proud to say that there are a bunch of hard working members in our program that have learned new skills and have gained knowledge in this program So in this journey, you will learn a lot about our work and marine life.\n\n\nAt the community showcase, students guide small groups around the intertidal, sharing their art with tablets and speakers. It was a great experience that showcased videos, poems, live demonostrations, and stories. Anyone can checkout their guided tour at Golden Garden Park via the echoes app - https://explore.echoes.xyz/collections/jJtrYdYIdtZ8eCpC\nBelow is a video that takes you behind the scenes on the 10-day experience students participated in." + "text": "The issue of climate change and its cascading effects on marine ecosystems is a growing concern for researchers, conservationists, and policymakers alike. One of the intriguing avenues of research in marine science involves the impact of polyploidy, a genetic variation where organisms have extra sets of chromosomes, on stress tolerance in marine species. A recent study led by Matthew N. George from the School of Aquatic & Fishery Sciences at the University of Washington, along with affiliations from the Environmental and Fisheries Sciences Division at the Northwest Fisheries Science Center, sheds new light on the vulnerability of triploid Pacific oysters to climate stressors." }, { - "objectID": "posts/frontpage/sr320-handbook/index.html", - "href": "posts/frontpage/sr320-handbook/index.html", - "title": "Deep dive into the handbook", + "objectID": "posts/sr320-george-paper/index.html#summary-of-the-paper", + "href": "posts/sr320-george-paper/index.html#summary-of-the-paper", + "title": "The Double-Edged Sword of Triploidy in Pacific Oysters", "section": "", - "text": "A unique perspective. You will never guess what they reveal!\n\nAudio\n\n\n\nTranscript\nWelcome to The Deep Dive, where we dig into the nitty gritty of fascinating topics.\nToday, we’re taking a deep dive into the Roberts Lab at the University of Washington, and we’re doing that through the lens of their handbook.\nIt’s more than just a rule book, though, isn’t it?\nOh, absolutely.\nIt’s like a window into their whole approach to science.\nEverything from, like, groundbreaking research to how they actually build their research culture.\nAnd they’re known for being incredibly transparent, which this handbook really embodies.\nYeah, it’s refreshing.\nAnd speaking of refreshing, I have to ask you about this freezer alarm situation.\nOh, yes.\nSo they have, like, a dedicated alarm for their ultra-low temperature freezers, right?\nYeah.\nBut there’s this 15-minute delay before anyone actually gets notified if it goes off.\nCan you imagine?\nIt’s like a slow-motion heart attack for a researcher.\nRight.\nAll those precious samples.\nI’d be a wreck.\nIt really highlights the fragility of these biological materials they’re working with.\nRNA, proteins, these things have to be stored at, like, negative 80 degrees Celsius.\nWow.\nEven a short power outage could be disastrous.\nSo is that delay, like, a safety net to give the system a chance to recover?\nExactly.\nIt’s a calculated risk.\nThey’re trying to balance preventing false alarms while also, you know, protecting those invaluable research materials.\nMakes sense.\nYeah.\nAnd it seems like that emphasis on meticulousness, on minimizing risk, it really comes through in the whole handbook, especially when they talk about lab safety and chemicals.\nIt’s serious business.\nRight.\nLike with Arnazole RT, they’re very clear about it being corrosive, potentially harmful if you inhale it, even disposing of it.\nIt’s a whole multi-step process.\nWell, they’re dealing with some pretty potent stuff.\nIt underscores their dedication to, you know, not just scientific rigor, but the actual well-being of their researchers.\nAbsolutely.\nIt’s like they’re creating an environment where cutting-edge science can happen, but it can happen safely.\nSafety first.\nYeah.\nAnd that meticulousness, that doing things by the book, it goes beyond just lab safety, you know.\nRight.\nIt’s woven into their whole research philosophy, which makes you wonder, if they’re this careful with safety, how does that translate to, say, data management or collaboration?\nGood question.\nAnd as luck would have it, that’s exactly what we’re going to be digging into in the rest of this deep dive.\nYou know, it’s funny you should mention that because the next thing that really struck me about this handbook was their code of conduct.\nOh, interesting.\nHow so?\nWell, for one, it’s incredibly detailed, even for like their diversity, equity, and inclusion meetings.\nYou don’t always see that level of, I don’t know, formality in a lab handbook.\nWhat kinds of things are we talking about here?\nThey have these great phrases like, “Elevate impact above intent,” and, “Expect and accept non-closure.”\nLike, really specific guidelines.\nHuh.\nIt sounds like they’re trying to foster a very specific kind of research environment.\nRight.\nOne where people feel comfortable admitting they don’t know everything, which, let’s be honest, is most of the time in research, right?\nOh, absolutely.\nScience is all about embracing uncertainty.\nBut it takes a certain culture to really allow for that.\nTotally.\nAnd it seems like they’re putting a lot of emphasis on making sure everyone feels heard and respected, especially in those DEI meetings.\nWell, and that makes sense, right?\nIf you want to have those tough conversations about diversity and inclusion, you need to create a space where people feel safe to speak their minds.\nYeah.\nNo, you’re right.\nIt all ties together.\nAnd then there’s this whole thing about mentorship.\nThey really encourage lab members to have multiple mentors, not just one.\nThat’s interesting.\nMost labs I’ve seen, it’s pretty standard to have one primary mentor.\nRight.\nYeah.\nSo I thought that was really unique.\nIt kind of speaks to this idea of providing a well-rounded experience, right?\nAbsolutely.\nDifferent mentors bring different perspectives, different areas of expertise.\nIt can really enrich a researcher’s training.\nOkay, so we’ve got meticulous safety protocols, a very deliberate approach to their lab culture.\nBut we also know they’re dealing with a massive amount of data.\nLike their handbook mentions Nightingale for sequencing this whole network attached storage system called Gannett.\nDon’t forget the supercomputer.\nMOCs, was it?\nOh, right.\nMOCs.\nI mean, it’s a lot.\nIt really makes you wonder how they manage it all.\nIt’s a data tsunami.\nHow do they keep from drowning?\nWell, for one thing, they’re incredibly organized.\nLike religiously organized.\nGive me the details.\nThink detailed metadata for every single experiment, strict folder structures on their network.\nThey even have readme files.\nReadme files for every folder, seriously.\nSeriously.\nAnd it’s all part of this commitment to open science.\nThey want their research to be accessible, transparent.\nSo anyone could theoretically go in and understand their data, their methods.\nThat’s the idea.\nIt’s about breaking down those silos, you know, fostering collaboration, avoiding unnecessary redundancy, ultimately speeding up discoveries.\nIt’s kind of inspiring, actually.\nIt’s like they’re playing the long game, advancing science as a whole, not just their own work.\nExactly.\nBut okay, even with perfect organization, all that data analysis, it’s got to be intense.\nThey mentioned Jupiter notebooks in the handbook.\nRight, and mocks the supercomputer.\nAnd they even talk about using like the command line.\nHard course, so they’re not messing around.\nWell, they’re equipping their researchers with a seriously powerful toolkit.\nBut it goes beyond just the tech.\nThey even recommend this book, Getting Things Done.\nTime management.\nTime management.\nIt’s all about efficiency.\nThey don’t just give them the tools.\nThey give them the training, the resources to actually use them well.\nIt’s like they’ve thought of everything.\nYeah.\nAnd it doesn’t stop there.\nThey have a whole section on conferences, funding opportunities, even like travel grants.\nThey want their researchers to be well-rounded, right?\nNot just stuck in the lab, but out there presenting, collaborating, getting their work funded.\nIt’s impressive, I have to say.\nLooking at the Roberts Lab this way, through their handbook, you really get a sense of the thoughtfulness, the care that goes into building a successful research environment.\nIt’s not just about, you know, the results, the discoveries.\nIt’s the people, the culture.\nAnd that commitment to moving science forward in a way that’s open and collaborative, it’s really something.\nMakes you wonder what they’ll accomplish, what amazing discoveries are on the horizon for them.\nIt does, doesn’t it?\nAnd that’s something to ponder as we wrap up this deep dive into the world of the Roberts Lab.\nUntil next time, keep exploring, keep questioning, and keep diving deep." + "text": "The study, titled “Triploid Pacific oysters exhibit stress response dysregulation and elevated mortality following heatwaves,” focuses on the comparison of diploid (2n) and triploid (3n) Pacific oysters (Crassostrea gigas) in response to environmental conditions akin to a heatwave. By exposing these oysters to different stressors such as elevated seawater temperature and aerial emersion, the researchers found that triploid oysters had a significantly higher mortality rate than their diploid counterparts when subjected to multiple stressors.\n\n\n\nHigher Mortality Rates in Triploids: The mortality rate in triploid oysters exposed to multiple stressors was 36.4% compared to 14.8% in diploid oysters.\nMetabolic and Physiological Limitations: Triploid oysters showed signs of metabolic depression, a reduction in ctenidium Na+/K+ ATPase activity, and dysregulated expression of stress response genes.\nFunctional Genomics Insights: Gene sets enriched in biological processes like metabolism, stress tolerance, and immune function were disproportionately represented in triploids across stress treatments.\n\n\n\n\nThe increased vulnerability of triploid Pacific oysters to climate stressors has far-reaching implications. Triploidy is often induced to achieve reproductive control in species used for marine aquaculture. While this serves to boost production and control unwanted reproduction, the study highlights that it may also render these organisms more susceptible to environmental extremes. This, in turn, could impact food security in regions dependent on marine aquaculture." }, { - "objectID": "posts/frontpage/lspencer-cod/index.html", - "href": "posts/frontpage/lspencer-cod/index.html", - "title": "Turning the tide", + "objectID": "posts/sr320-george-paper/index.html#discussion-and-future-directions", + "href": "posts/sr320-george-paper/index.html#discussion-and-future-directions", + "title": "The Double-Edged Sword of Triploidy in Pacific Oysters", "section": "", - "text": "Chris is featured on UW’s “Be Boundless” site. Read full article here. Below is a short snippet of the feature along with an amazing video!\nOn a windy June afternoon, Chris Mantegna, ’21, encourages a half-dozen undergraduates to flip over barnacle-studded rocks and sift through seaweed. Equipped with clipboards to record their findings, they’re creating a snapshot of the organisms in the island’s intertidal zone — from orange sea cucumbers to the camouflaged armored mollusks called chitons.\nMantegna, a third-year graduate student in aquatic and fishery sciences, has spent the past three summers in Washington’s San Juan Islands, mentoring undergrads here on Yellow Island — a pristine 11-acre nature preserve owned by the Nature Conservancy. She created this eight-week program for students to get their hands dirty in the field and learn cutting-edge lab techniques at the UW Friday Harbor Laboratories — where she had a transformational research experience herself as a Husky undergrad.\nThis mentorship program reflects Mantegna’s passion both for advancing the science and for making it more inclusive and accessible to others. Her face lights up when she spots a small chiton (her favorite) clinging to the bottom of a rock, and she invites others to feel the mollusk’s tough plated back. Even Mantegna’s doctoral work — examining the genetic response of shellfish to contaminants in Puget Sound waterways — has a focus on community outreach and environmental literacy.\n\nMantegna says we have a better chance at fighting climate change when everyone — scientists and community members — feels connected to their environment and each other. “I can tell you that the ocean is dying or that we have too much acidification,” says Mantegna, a U.S. Navy veteran who is the first in her family to graduate from college. “But it doesn’t matter if you’ve never had the chance to feel the joy that comes from this place.”\nFinish feature here." + "text": "The findings of this study present a clear need for further research to fully understand the complexities of triploidy and its relationship with environmental stress tolerance. As climate change continues to bring about more frequent and severe heatwaves, understanding the impact on marine organisms is crucial. Future research should explore the possibility of developing stress-resilient triploid species and consider alternative strategies for reproductive control in aquaculture." }, { - "objectID": "posts/sr320-prep/index.html", - "href": "posts/sr320-prep/index.html", - "title": "Are you really prepared?", + "objectID": "posts/sr320-george-paper/index.html#conclusion", + "href": "posts/sr320-george-paper/index.html#conclusion", + "title": "The Double-Edged Sword of Triploidy in Pacific Oysters", "section": "", - "text": "Ariana lead a great tutorial on being prepared and planning for science. The narrative underscored the importance of thorough preparation and planning, including considering alternative uses for collected data, planning for potential pitfalls, and ensuring that experimental designs are robust against unforeseen challenges. This includes the practical aspects of laboratory work, field studies, and data analysis, emphasizing the value of learning from past experiences and being flexible in research approaches.\n\nDesigning scientific experiments requires extensive planning to ensure projects run smoothly and yield meaningful results. Here are some important aspects to consider when preparing for research:\nClearly Define Your Hypothesis and Objectives: Having a clear hypothesis drives your experimental design and analysis approach. Define what you aim to test upfront.\nPrepare Detailed Protocols: Write step-by-step protocols for all procedures well before starting. Practice techniques on mock datasets to work out kinks.\nPlan Your Data Collection: Design data sheets, name conventions, and metadata standards early. Consider sample sizes and ensure you collect the right data to answer your questions.\nSchedule Carefully: Block out experiment timelines, factoring permitting needs and collaborator availability. Leave buffer time for unexpected issues.\nCreate Organizational Systems: Use checklists, spreadsheets, and visual aids to track tasks and ensure all preparation steps are completed thoroughly.\nAnticipate Challenges: Brainstorm potential pitfalls and have contingency plans. Run test analyses to flag problems before using real data.\nProper preparation is key to running successful, high-quality experiments that yield meaningful scientific insights. Taking the time to carefully plan experimental design and logistics pays off in efficient, productive research." + "text": "While triploidy offers some benefits for controlling reproduction in marine aquaculture, this genetic modification may inadvertently make these organisms more susceptible to the threats posed by climate change. As we continue to grapple with the realities of a changing climate, research like this serves as an invaluable resource for better understanding the complex interactions between genetic variation and environmental stressors, thereby informing both conservation strategies and aquaculture practices.\n\n\n\nGeorge, M. N.,  Cattau, O.,  Middleton, M. A.,  Lawson, D.,  Vadopalas, B.,  Gavery, M., &  Roberts, S. B. (2023). Triploid Pacific oysters exhibit stress response dysregulation and elevated mortality following heatwaves. Global Change Biology,  00,  1–19. https://doi.org/10.1111/gcb.16880\n\nFeel free to dive into the full paper for a more detailed understanding of our findings." }, { - "objectID": "posts/grace_L_WSN/index.html", - "href": "posts/grace_L_WSN/index.html", - "title": "Western Society of Naturalists", + "objectID": "publications/articles/valenzuela2024.html", + "href": "publications/articles/valenzuela2024.html", + "title": "Environmental influence on the Atlantic salmon transcriptome and methylome during sea lice infestations", "section": "", - "text": "I presented some data from a summer pilot project that didn’t end up being significant, but sparked some good conversations! Flow rate is known to influence the amount of threads that mussels produce to stick onto rocky surfaces, so I was wondering if it influenced the actual composition of the threads as well! I kept mussels under three different flow rates and measured their attachment strength. Didn’t find anything significant, but saw some trends.\n\n\n\nimg\n\n\nI haven’t ever presented data in person at a conference before (relic of being a college covid baby), so this was really exciting for me to get feedback from other ecomechanics people and brainstorm future directions for my work, especially as I’m trying to propose my thesis this spring." + "text": "Valenzuela-Muñoz, V., Wanamaker, S., Núñez-Acuña, G., Roberts, S., Garcia, A., Valdés, J. A., Valenzuela-Miranda, D., & Gallardo-Escarate, C. (2024). Environmental influence on the Atlantic salmon transcriptome and methylome during sea lice infestations. Full Length Article, FSIM-D-24-00599R2." }, { - "objectID": "posts/grace_L_WSN/index.html#poster-presentation", - "href": "posts/grace_L_WSN/index.html#poster-presentation", - "title": "Western Society of Naturalists", + "objectID": "publications/articles/valenzuela2024.html#citation", + "href": "publications/articles/valenzuela2024.html#citation", + "title": "Environmental influence on the Atlantic salmon transcriptome and methylome during sea lice infestations", "section": "", - "text": "I presented some data from a summer pilot project that didn’t end up being significant, but sparked some good conversations! Flow rate is known to influence the amount of threads that mussels produce to stick onto rocky surfaces, so I was wondering if it influenced the actual composition of the threads as well! I kept mussels under three different flow rates and measured their attachment strength. Didn’t find anything significant, but saw some trends.\n\n\n\nimg\n\n\nI haven’t ever presented data in person at a conference before (relic of being a college covid baby), so this was really exciting for me to get feedback from other ecomechanics people and brainstorm future directions for my work, especially as I’m trying to propose my thesis this spring." + "text": "Valenzuela-Muñoz, V., Wanamaker, S., Núñez-Acuña, G., Roberts, S., Garcia, A., Valdés, J. A., Valenzuela-Miranda, D., & Gallardo-Escarate, C. (2024). Environmental influence on the Atlantic salmon transcriptome and methylome during sea lice infestations. Full Length Article, FSIM-D-24-00599R2." }, { - "objectID": "posts/sr320-marineomics/index.html", - "href": "posts/sr320-marineomics/index.html", - "title": "MarineOmics.io", - "section": "", - "text": "In an era where ecological genomics is garnering increased recognition, particularly within nonmodel species, the necessity for robust, reproducible, and accessible resources has never been more apparent. A recent publication led by a consortium of researchers introduces MarineOmics.io, a dynamic web resource tailored to meet the burgeoning needs of this scientific domain. This open-source platform aims to foster a collaborative environment for researchers at various stages of their career, promoting reproducibility, accessibility, and adaptability in genomic analyses.\nMarineOmics.io emerges as a living document, meticulously curated to disseminate vital tutorials, reproducibility tools, and best principles pivotal for genomic research in marine and other nonmodel ecosystems. This endeavor is a testament to the collaborative spirit of the ecological genomics community, as the platform encapsulates current methodologies and recommendations across a myriad of genomic studies including whole-genome sequencing, RAD-seq, Pool-seq, and RNA-seq.\n\n\n\nF I G U R E 1 Screenshot of one web page concerning a RAD-seq pipeline serving as an example of tutorial structure.\n\n\nWhat sets MarineOmics.io apart is its dynamic nature. Not only does it provide a repository of existing knowledge, but it also outlines a structured process for the aggregation and synthesis of methodological principles derived from the community. The platform invites submissions of new content, feedback, and topic requests from the community, thereby ensuring its content remains updated, relevant, and in tune with the rapidly evolving field of genomics.\nThe meticulous planning invested in MarineOmics.io is reflective in its guidelines for authorship, submission of new content, and protocols for community feedback. These guidelines are drafted with a vision to uphold the rigor and reproducibility in scientific inquiries, encouraging contributions from scientists spanning various skill sets and expertise levels. This collaborative ethos is further underscored by the availability of the site’s source code for contributors on GitHub, and a snapshot of the source code as of the time of submission, hosted on Zenodo.\nThe data and resources available through MarineOmics.io are not merely a contribution but a cornerstone for advancing ecological genomic research in nonmodel marine systems. By providing a structured, collaborative platform, MarineOmics.io is poised to catalyze a new wave of discoveries, fostering a community of researchers equipped to navigate the challenges and opportunities that lay ahead in the genomic era.\nCitation: Bogan, S. N., Johns, J., Griffiths, J. S., Davenport, D., Smith, S. J., Schaal, S. M., Downey-Wall, A., Lou, R. N., Lotterhos, K., Guidry, M. E., Rivera, H. E., McGirr, J. A., Puritz, J. B., Roberts, S. B., & Silliman, K. (2023). A dynamic web resource for robust and reproducible genomics in nonmodel species: marineomics.io. Methods in Ecology and Evolution, 00, 1–8. https://doi.org/10.1111/2041-210X.14219" + "objectID": "publications/articles/valenzuela2024.html#abstract", + "href": "publications/articles/valenzuela2024.html#abstract", + "title": "Environmental influence on the Atlantic salmon transcriptome and methylome during sea lice infestations", + "section": "Abstract", + "text": "Abstract\nThe fish’s immune response is affected by different factors, including a wide range of environmental conditions that can also disrupt or promote changes in the host- pathogen interactions. How environmental conditions modulate the salmon genome during parasitism is poorly understood here. This study aimed to explore the environmental influence on the Salmo salar transcriptome and methylome infected with the sea louse Caligus rogercresseyi. Atlantic salmon were experimentally infected with lice at two temperatures (8 and 16oC) and salinity conditions (32 and 26PSU). Fish tissues were collected from the infected Atlantic salmon for reduced representation bisulfite sequencing (RRBS) and whole transcriptome sequencing (RNAseq) analysis. The parasitic load was highly divergent in the evaluated environmental conditions, where the lowest lice abundance was observed in fish infected at 8oC/26PSU. Notably, transcriptome profile differences were statistically associated with the number of alternative splicing events in fish exposed to low temperature/salinity conditions. Furthermore, the temperature significantly affected the methylation level, where high values of differential methylation regions were observed at 16oC. Also, the association between expression levels of spliced transcripts and their methylation levels was determined, revealing significant correlations with Ferroptosis and TLR KEEG pathways. This study supports the relevance of the environmental conditions during host-parasite interactions in marine ecosystems. The discovery of alternative splicing transcripts associated with DMRs is also discussed as a novel player in fish biology." }, { - "objectID": "notebooks.html", - "href": "notebooks.html", - "title": "Lab Notebooks", - "section": "", - "text": "Person\nNotebook\nCommitment\n\n\n\n\nSteven Roberts\nsr320.github.io\n\n\n\nSam White\nrobertslab.github.io\n\n\n\nMatt George\nmattgeorgephd.github.io\n\n\n\nAspen Coyle\naspencoyle.github.io\n\n\n\nAriana Huffmyer\nahuffmyer.github.io\n\n\n\nChris Mantegna\nchrismantegna.github.io\n\n\n\nZach Bengtsson\nzbengt.github.io\n\n\n\nCeleste Valdivia\nvaleste.github.io\n\n\n\nGrace Crandall\ngrace-ac.github.io\n\n\n\nKathleen Durkin\nshedurkin.github.io\n\n\n\nMegan Ewing\nmewing-notebook" + "objectID": "publications/articles/valenzuela2024.html#data-availability", + "href": "publications/articles/valenzuela2024.html#data-availability", + "title": "Environmental influence on the Atlantic salmon transcriptome and methylome during sea lice infestations", + "section": "Data Availability", + "text": "Data Availability" }, { - "objectID": "publications/articles/timmins-schiffman2021.html", - "href": "publications/articles/timmins-schiffman2021.html", - "title": "Coupled microbiome analyses highlights relative functional roles of bacteria in a bivalve hatchery", + "objectID": "publications/articles/gallardo2023.html", + "href": "publications/articles/gallardo2023.html", + "title": "Chromosome-Level Genome Assembly of the Blue Mussel Mytilus chilensis Reveals Molecular Signatures Facing the Marine Environment", "section": "", - "text": "Timmins-Schiffman, E., White, S.J., Thompson, R.E. et al. Coupled microbiome analyses highlights relative functional roles of bacteria in a bivalve hatchery. Environmental Microbiome 16, 7 (2021). https://doi.org/10.1186/s40793-021-00376-z" + "text": "Gallardo-Escárate, C.; Valenzuela-Muñoz, V.; Nuñez-Acuña, G.; Valenzuela-Miranda, D.; Tapia, F.J.; Yévenes, M.; Gajardo, G.; Toro, J.E.; Oyarzún, P.A.; Arriagada, G.; et al. Chromosome-Level Genome Assembly of the Blue Mussel Mytilus chilensis Reveals Molecular Signatures Facing the Marine Environment. Genes 2023, 14, 876. https://doi.org/10.3390/genes14040876" }, { - "objectID": "publications/articles/timmins-schiffman2021.html#citation", - "href": "publications/articles/timmins-schiffman2021.html#citation", - "title": "Coupled microbiome analyses highlights relative functional roles of bacteria in a bivalve hatchery", + "objectID": "publications/articles/gallardo2023.html#citation", + "href": "publications/articles/gallardo2023.html#citation", + "title": "Chromosome-Level Genome Assembly of the Blue Mussel Mytilus chilensis Reveals Molecular Signatures Facing the Marine Environment", "section": "", - "text": "Timmins-Schiffman, E., White, S.J., Thompson, R.E. et al. Coupled microbiome analyses highlights relative functional roles of bacteria in a bivalve hatchery. Environmental Microbiome 16, 7 (2021). https://doi.org/10.1186/s40793-021-00376-z" + "text": "Gallardo-Escárate, C.; Valenzuela-Muñoz, V.; Nuñez-Acuña, G.; Valenzuela-Miranda, D.; Tapia, F.J.; Yévenes, M.; Gajardo, G.; Toro, J.E.; Oyarzún, P.A.; Arriagada, G.; et al. Chromosome-Level Genome Assembly of the Blue Mussel Mytilus chilensis Reveals Molecular Signatures Facing the Marine Environment. Genes 2023, 14, 876. https://doi.org/10.3390/genes14040876" }, { - "objectID": "publications/articles/timmins-schiffman2021.html#abstract", - "href": "publications/articles/timmins-schiffman2021.html#abstract", - "title": "Coupled microbiome analyses highlights relative functional roles of bacteria in a bivalve hatchery", + "objectID": "publications/articles/gallardo2023.html#abstract", + "href": "publications/articles/gallardo2023.html#abstract", + "title": "Chromosome-Level Genome Assembly of the Blue Mussel Mytilus chilensis Reveals Molecular Signatures Facing the Marine Environment", "section": "Abstract", - "text": "Abstract\nBackground Microbial communities are ubiquitous throughout ecosystems and are commensal with hosts across taxonomic boundaries. Environmental and species-specific microbiomes are instrumental in maintaining ecosystem and host health, respectively. The introduction of pathogenic microbes that shift microbiome community structure can lead to illness and death. Understanding the dynamics of microbiomes across a diversity of environments and hosts will help us to better understand which taxa forecast survival and which forecast mortality events. Results We characterized the bacterial community microbiome in the water of a commercial shellfish hatchery in Washington state, USA, where the hatchery has been plagued by recurring and unexplained larval mortality events. By applying the complementary methods of metagenomics and metaproteomics we were able to more fully characterize the bacterial taxa in the hatchery at high (pH 8.2) and low (pH 7.1) pH that were metabolically active versus present but not contributing metabolically. There were shifts in the taxonomy and functional profile of the microbiome between pH and over time. Based on detected metagenomic reads and metaproteomic peptide spectral matches, some taxa were more metabolically active than expected based on presence alone (Deltaproteobacteria, Alphaproteobacteria) and some were less metabolically active than expected (e.g., Betaproteobacteria, Cytophagia). There was little correlation between potential and realized metabolic function based on Gene Ontology analysis of detected genes and peptides. Conclusion The complementary methods of metagenomics and metaproteomics contribute to a more full characterization of bacterial taxa that are potentially active versus truly metabolically active and thus impact water quality and inter-trophic relationships." + "text": "Abstract\nThe blue mussel Mytilus chilensis is an endemic and key socioeconomic species inhabiting the southern coast of Chile. This bivalve species supports a booming aquaculture industry, which entirely relies on artificially collected seeds from natural beds that are translocated to diverse physical–chemical ocean farming conditions. Furthermore, mussel production is threatened by a broad range of microorganisms, pollution, and environmental stressors that eventually impact its survival and growth. Herein, understanding the genomic basis of the local adaption is pivotal to developing sustainable shellfish aquaculture. We present a high-quality reference genome of M. chilensis, which is the first chromosome-level genome for a Mytilidae member in South America. The assembled genome size was 1.93 Gb, with a contig N50 of 134 Mb. Through Hi-C proximity ligation, 11,868 contigs were clustered, ordered, and assembled into 14 chromosomes in congruence with the karyological evidence. The M. chilensis genome comprises 34,530 genes and 4795 non-coding RNAs. A total of 57% of the genome contains repetitive sequences with predominancy of LTR-retrotransposons and unknown elements. Comparative genome analysis of M. chilensis and M. coruscus was conducted, revealing genic rearrangements distributed into the whole genome. Notably, transposable Steamer-like elements associated with horizontal transmissible cancer were explored in reference genomes, suggesting putative relationships at the chromosome level in Bivalvia. Genome expression analysis was also conducted, showing putative genomic differences between two ecologically different mussel populations. The evidence suggests that local genome adaptation and physiological plasticity can be analyzed to develop sustainable mussel production. The genome of M. chilensis provides pivotal molecular knowledge for the Mytilus complex." }, { - "objectID": "publications/articles/timmins-schiffman2021.html#data-availability", - "href": "publications/articles/timmins-schiffman2021.html#data-availability", - "title": "Coupled microbiome analyses highlights relative functional roles of bacteria in a bivalve hatchery", + "objectID": "publications/articles/gallardo2023.html#data-availability", + "href": "publications/articles/gallardo2023.html#data-availability", + "title": "Chromosome-Level Genome Assembly of the Blue Mussel Mytilus chilensis Reveals Molecular Signatures Facing the Marine Environment", "section": "Data Availability", - "text": "Data Availability\nThe sequenced metagenomics data can be found in NCBI’s Short Read Archive under BioProject PRJNA649049. The metaproteomics dataset can be found in the ProteomeXchange PRIDE repository under accession PXD020692." + "text": "Data Availability\nThe Mytilus chilensis whole-genome sequencing data supporting this study’s findings are available from NCBI under BioProject PRJNA861856. The sequencing data supporting this study’s findings are available in SRA at SRR20966976, SRR20593343, and SRP261955. The benefits from this study accrue from sharing our data and results on public databases as described above. The assembled genome and the genome annotation results were deposited in the Figshare database [93]." }, { - "objectID": "publications/articles/crandall2022b.html", - "href": "publications/articles/crandall2022b.html", - "title": "Proteomic response of early juvenile Pacific oysters (Crassostrea gigas) to temperature", + "objectID": "publications/articles/buckley2023.html", + "href": "publications/articles/buckley2023.html", + "title": "Characterizing biological responses to climate variability and extremes to improve biodiversity projections", "section": "", - "text": "Crandall G, Elliott Thompson R, Eudeline B, Vadopalas B, Timmins-Schiffman E, Roberts S. 2022. Proteomic response of early juvenile Pacific oysters (Crassostrea gigas) to temperature. PeerJ 10:e14158 https://doi.org/10.7717/peerj.14158" + "text": "Buckley LB, Carrington E, Dillon ME, García-Robledo C, Roberts SB, Wegrzyn JL, et al. (2023) Characterizing biological responses to climate variability and extremes to improve biodiversity projections. PLOS Clim 2(6): e0000226. https://doi.org/10.1371/journal.pclm.0000226" }, { - "objectID": "publications/articles/crandall2022b.html#citation", - "href": "publications/articles/crandall2022b.html#citation", - "title": "Proteomic response of early juvenile Pacific oysters (Crassostrea gigas) to temperature", + "objectID": "publications/articles/buckley2023.html#citation", + "href": "publications/articles/buckley2023.html#citation", + "title": "Characterizing biological responses to climate variability and extremes to improve biodiversity projections", "section": "", - "text": "Crandall G, Elliott Thompson R, Eudeline B, Vadopalas B, Timmins-Schiffman E, Roberts S. 2022. Proteomic response of early juvenile Pacific oysters (Crassostrea gigas) to temperature. PeerJ 10:e14158 https://doi.org/10.7717/peerj.14158" + "text": "Buckley LB, Carrington E, Dillon ME, García-Robledo C, Roberts SB, Wegrzyn JL, et al. (2023) Characterizing biological responses to climate variability and extremes to improve biodiversity projections. PLOS Clim 2(6): e0000226. https://doi.org/10.1371/journal.pclm.0000226" }, { - "objectID": "publications/articles/crandall2022b.html#abstract", - "href": "publications/articles/crandall2022b.html#abstract", - "title": "Proteomic response of early juvenile Pacific oysters (Crassostrea gigas) to temperature", + "objectID": "publications/articles/buckley2023.html#abstract", + "href": "publications/articles/buckley2023.html#abstract", + "title": "Characterizing biological responses to climate variability and extremes to improve biodiversity projections", "section": "Abstract", - "text": "Abstract\nPacific oysters (Crassostrea gigas) are a valuable aquaculture product that provides important ecosystem benefits. Among other threats, climate-driven changes in ocean temperature can impact oyster metabolism, survivorship, and immune function. We investigated how elevated temperature impacts larval oysters during settlement (19–33 days post-fertilization), using shotgun proteomics with data-independent acquisition to identify proteins present in the oysters after 2 weeks of exposure to 23 °C or 29 °C. Oysters maintained at elevated temperatures were larger and had a higher settlement rate, with 86% surviving to the end of the experiment; these oysters also had higher abundance trends of proteins related to metabolism and growth. Oysters held at 23 °C were smaller, had a decreased settlement rate, displayed 100% mortality, and had elevated abundance trends of proteins related to immune response. This novel use of proteomics was able to capture characteristic shifts in protein abundance that hint at important differences in the phenotypic response of Pacific oysters to temperature regimes. Additionally, this work has produced a robust proteomic product that will be the basis for future research on bivalve developmental processes." + "text": "Abstract\nProjecting ecological and evolutionary responses to variable and changing environments is central to anticipating and managing impacts to biodiversity and ecosystems. Current modeling approaches are largely phenomenological and often fail to accurately project responses due to numerous biological processes at multiple levels of biological organization responding to environmental variation at varied spatial and temporal scales. Limited mechanistic understanding of organismal responses to environmental variability and extremes also restricts predictive capacity. We outline a strategy for identifying and modeling the key organismal mechanisms across levels of biological organization that mediate ecological and evolutionary responses to environmental variation. A central component of this strategy is quantifying timescales and magnitudes of climatic variability and how organisms experience them. We highlight recent empirical research that builds this information and suggest how to design future experiments that can produce more generalizable principles. We discuss how to create biologically informed projections in a feasible way by combining statistical and mechanistic approaches. Predictions will inform both fundamental and practical questions at the interface of ecology, evolution, and Earth science such as how organisms experience, adapt to, and respond to environmental variation at multiple hierarchical spatial and temporal scales." }, { - "objectID": "publications/articles/crandall2022b.html#data-availability", - "href": "publications/articles/crandall2022b.html#data-availability", - "title": "Proteomic response of early juvenile Pacific oysters (Crassostrea gigas) to temperature", + "objectID": "publications/articles/buckley2023.html#data-availability", + "href": "publications/articles/buckley2023.html#data-availability", + "title": "Characterizing biological responses to climate variability and extremes to improve biodiversity projections", "section": "Data Availability", - "text": "Data Availability\nThe following information was supplied regarding data availability:\nAdditional files, scripts, and data are available at Zenodo: grace-ac, & Steven Roberts. (2021). grace-ac/paper-pacific.oyster-larvae: release for PeerJ submission (v2.1.0). Zenodo. https://doi.org/10.5281/zenodo.5708415.\nThe proteomic data is available at PRIDE: PXD015434." + "text": "Data Availability\nS1 Text.Supplementary methods for fitting data on the temperature dependence of mussel assimilation rate.\nhttps://doi.org/10.1371/journal.pclm.0000226.s001\n(DOCX)" }, { - "objectID": "publications/articles/trigg2021.html", - "href": "publications/articles/trigg2021.html", - "title": "Invertebrate methylomes provide insight into mechanisms of environmental tolerance and reveal methodological biases", + "objectID": "publications/articles/gallardo2021.html", + "href": "publications/articles/gallardo2021.html", + "title": "Chromosome-scale genome assembly of the sea louse Caligus rogercresseyi by SMRT sequencing and Hi-C analysis", "section": "", - "text": "Wanamaker , S. A., Venkataraman, Y. R., Gavery, M. R., Roberts, S. B., Bhattacharya, D., Downey-Wall, A., Eirin-Lopez, J. M., Johnson, K. M., Lotterhos, K. E., Puritz, J. B., & Putnam, H. M. (2022). Invertebrate methylomes provide insight into mechanisms of environmental tolerance and reveal methodological biases. Molecular Ecology Resources, 22, 1247– 1261. https://doi.org/10.1111/1755-0998.13542" + "text": "Gallardo-Escárate, C., Valenzuela-Muñoz, V., Nuñez-Acuña, G. et al. Chromosome-scale genome assembly of the sea louse Caligus rogercresseyi by SMRT sequencing and Hi-C analysis. Sci Data 8, 60 (2021). https://doi.org/10.1038/s41597-021-00842-w" }, { - "objectID": "publications/articles/trigg2021.html#citation", - "href": "publications/articles/trigg2021.html#citation", - "title": "Invertebrate methylomes provide insight into mechanisms of environmental tolerance and reveal methodological biases", + "objectID": "publications/articles/gallardo2021.html#citation", + "href": "publications/articles/gallardo2021.html#citation", + "title": "Chromosome-scale genome assembly of the sea louse Caligus rogercresseyi by SMRT sequencing and Hi-C analysis", "section": "", - "text": "Wanamaker , S. A., Venkataraman, Y. R., Gavery, M. R., Roberts, S. B., Bhattacharya, D., Downey-Wall, A., Eirin-Lopez, J. M., Johnson, K. M., Lotterhos, K. E., Puritz, J. B., & Putnam, H. M. (2022). Invertebrate methylomes provide insight into mechanisms of environmental tolerance and reveal methodological biases. Molecular Ecology Resources, 22, 1247– 1261. https://doi.org/10.1111/1755-0998.13542" + "text": "Gallardo-Escárate, C., Valenzuela-Muñoz, V., Nuñez-Acuña, G. et al. Chromosome-scale genome assembly of the sea louse Caligus rogercresseyi by SMRT sequencing and Hi-C analysis. Sci Data 8, 60 (2021). https://doi.org/10.1038/s41597-021-00842-w" }, { - "objectID": "publications/articles/trigg2021.html#abstract", - "href": "publications/articles/trigg2021.html#abstract", - "title": "Invertebrate methylomes provide insight into mechanisms of environmental tolerance and reveal methodological biases", + "objectID": "publications/articles/gallardo2021.html#abstract", + "href": "publications/articles/gallardo2021.html#abstract", + "title": "Chromosome-scale genome assembly of the sea louse Caligus rogercresseyi by SMRT sequencing and Hi-C analysis", "section": "Abstract", - "text": "Abstract\nThere is a growing focus on the role of DNA methylation in the ability of marine invertebrates to rapidly respond to changing environmental factors and anthropogenic impacts. However, genome-wide DNA methylation studies in nonmodel organisms are currently hampered by a limited understanding of methodological biases. Here, we compare three methods for quantifying DNA methylation at single base-pair resolution—whole genome bisulfite sequencing (WGBS), reduced representation bisulfite sequencing (RRBS), and methyl-CpG binding domain bisulfite sequencing (MBDBS)—using multiple individuals from two reef-building coral species with contrasting environmental sensitivity. All methods reveal substantially greater methylation in Montipora capitata (11.4%) than the more sensitive Pocillopora acuta (2.9%). The majority of CpG methylation in both species occurs in gene bodies and flanking regions. In both species, MBDBS has the greatest capacity for detecting CpGs in coding regions at our sequencing depth, but MBDBS may be influenced by intrasample methylation heterogeneity. RRBS yields robust information for specific loci albeit without enrichment of any particular genome feature and with significantly reduced genome coverage. Relative genome size strongly influences the number and location of CpGs detected by each method when sequencing depth is limited, illuminating nuances in cross-species comparisons. As genome-wide methylation differences, supported by data across bisulfite sequencing methods, may contribute to environmental sensitivity phenotypes in critical marine invertebrate taxa, these data provide a genomic resource for investigating the functional role of DNA methylation in environmental tolerance." + "text": "Abstract\nCaligus rogercresseyi, commonly known as sea louse, is an ectoparasite copepod that impacts the salmon aquaculture in Chile, causing losses of hundreds of million dollars per year. In this study, we report a chromosome-scale assembly of the sea louse (C. rogercresseyi) genome based on single-molecule real-time sequencing (SMRT) and proximity ligation (Hi-C) analysis. Coding RNAs and non-coding RNAs, and specifically long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) were identified through whole transcriptome sequencing from different life stages. A total of 23,686 protein-coding genes and 12,558 non-coding RNAs were annotated. In addition, 6,308 lncRNAs and 5,774 miRNAs were found to be transcriptionally active from larvae to adult stages. Taken together, this genomic resource for C. rogercresseyi represents a valuable tool to develop sustainable control strategies in the salmon aquaculture industry." }, { - "objectID": "publications/articles/trigg2021.html#data-availability", - "href": "publications/articles/trigg2021.html#data-availability", - "title": "Invertebrate methylomes provide insight into mechanisms of environmental tolerance and reveal methodological biases", + "objectID": "publications/articles/gallardo2021.html#data-availability", + "href": "publications/articles/gallardo2021.html#data-availability", + "title": "Chromosome-scale genome assembly of the sea louse Caligus rogercresseyi by SMRT sequencing and Hi-C analysis", "section": "Data Availability", - "text": "Data Availability\n\n\n\n\n\n\nOpen Data\n\n\n\nThis article has earned an Open Data Badge for making publicly available the digitally-shareable data necessary to reproduce the reported results\n\n\nThe data sets supporting the conclusions of this article are available in the Coral Methylation Methods Comparison repository, http://doi.org/10.17605/OSF.IO/X5WAZ, and included within the article and its additional files. All raw data can be accessed under NCBI Bioproject PRJNA691891." + "text": "Data Availability\nDNA and RNA sequencing runs were deposited to NCBI Sequence Read Archive (SRA)1(https://www.nature.com/articles/s41597-021-00842-w#ref-CR50 “NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP229458\n (2019).\"),[51](https://www.nature.com/articles/s41597-021-00842-w#ref-CR51 \"NCBI Sequence Read Archive \n https://identifiers.org/ncbi/insdc.sra:SRP212140\n \n (2019).\"),[52](https://www.nature.com/articles/s41597-021-00842-w#ref-CR52 \"NCBI Sequence Read Archive \n https://identifiers.org/ncbi/insdc.sra:SRP067375\n \n (2015).\")^. The assembled genome has been deposited at NCBI assembly with the accession number ASM1338718v1^[53](https://www.nature.com/articles/s41597-021-00842-w#ref-CR53 \"NCBI Assembly \n https://identifiers.org/insdc.gca:GCA_013387185.1\n \n (2020).\")^. Additional files containing repeated sequences, gene structure, and functional prediction were deposited in the *Figshare*database^[54](https://www.nature.com/articles/s41597-021-00842-w#ref-CR54 \"Gallardo-Escárate, C. Additional annotation files_GenSAS. figshare \n https://doi.org/10.6084/m9.figshare.12847493\n \n (2020).\")^." }, { - "objectID": "publications/articles/gurr2021.html", - "href": "publications/articles/gurr2021.html", - "title": "Repeat exposure to hypercapnic seawater modifies growth and oxidative status in a tolerant burrowing clam", + "objectID": "publications/articles/gallardo2021.html#footnotes", + "href": "publications/articles/gallardo2021.html#footnotes", + "title": "Chromosome-scale genome assembly of the sea louse Caligus rogercresseyi by SMRT sequencing and Hi-C analysis", + "section": "Footnotes", + "text": "Footnotes\n\n\n50↩︎" + }, + { + "objectID": "publications/articles/george2023.html", + "href": "publications/articles/george2023.html", + "title": "Triploid Pacific oysters exhibit stress response dysregulation and elevated mortality following heatwaves", "section": "", - "text": "Samuel J. Gurr, Shelly A. Wanamaker, Brent Vadopalas, Steven B. Roberts, Hollie M. Putnam; Repeat exposure to hypercapnic seawater modifies growth and oxidative status in a tolerant burrowing clam. J Exp Biol 1 July 2021; 224 (13): jeb233932. doi: https://doi.org/10.1242/jeb.233932" + "text": "George, M. N.,  Cattau, O.,  Middleton, M. A.,  Lawson, D.,  Vadopalas, B.,  Gavery, M., &  Roberts, S. B. (2023). Triploid Pacific oysters exhibit stress response dysregulation and elevated mortality following heatwaves. Global Change Biology,  00,  1–19. https://doi.org/10.1111/gcb.16880" }, { - "objectID": "publications/articles/gurr2021.html#citation", - "href": "publications/articles/gurr2021.html#citation", - "title": "Repeat exposure to hypercapnic seawater modifies growth and oxidative status in a tolerant burrowing clam", + "objectID": "publications/articles/george2023.html#citation", + "href": "publications/articles/george2023.html#citation", + "title": "Triploid Pacific oysters exhibit stress response dysregulation and elevated mortality following heatwaves", "section": "", - "text": "Samuel J. Gurr, Shelly A. Wanamaker, Brent Vadopalas, Steven B. Roberts, Hollie M. Putnam; Repeat exposure to hypercapnic seawater modifies growth and oxidative status in a tolerant burrowing clam. J Exp Biol 1 July 2021; 224 (13): jeb233932. doi: https://doi.org/10.1242/jeb.233932" + "text": "George, M. N.,  Cattau, O.,  Middleton, M. A.,  Lawson, D.,  Vadopalas, B.,  Gavery, M., &  Roberts, S. B. (2023). Triploid Pacific oysters exhibit stress response dysregulation and elevated mortality following heatwaves. Global Change Biology,  00,  1–19. https://doi.org/10.1111/gcb.16880" }, { - "objectID": "publications/articles/gurr2021.html#abstract", - "href": "publications/articles/gurr2021.html#abstract", - "title": "Repeat exposure to hypercapnic seawater modifies growth and oxidative status in a tolerant burrowing clam", + "objectID": "publications/articles/george2023.html#abstract", + "href": "publications/articles/george2023.html#abstract", + "title": "Triploid Pacific oysters exhibit stress response dysregulation and elevated mortality following heatwaves", "section": "Abstract", - "text": "Abstract\nAlthough low levels of thermal stress, irradiance and dietary restriction can have beneficial effects for many taxa, stress acclimation remains little studied in marine invertebrates, even though they are threatened by climate change stressors such as ocean acidification. To test the role of life-stage and stress-intensity dependence in eliciting enhanced tolerance under subsequent stress encounters, we initially conditioned pediveliger Pacific geoduck (Panopea generosa) larvae to ambient and moderately elevated PCO2 (920 µatm and 2800 µatm, respectively) for 110 days. Then, clams were exposed to ambient, moderate or severely elevated PCO2 (750, 2800 or 4900 µatm, respectively) for 7 days and, following 7 days in ambient conditions, a 7-day third exposure to ambient (970 µatm) or moderate PCO2 (3000 µatm). Initial conditioning to moderate PCO2 stress followed by second and third exposure to severe and moderate PCO2 stress increased respiration rate, organic biomass and shell size, suggesting a stress-intensity-dependent effect on energetics. Additionally, stress-acclimated clams had lower antioxidant capacity compared with clams under ambient conditions, supporting the hypothesis that stress over postlarval-to-juvenile development affects oxidative status later in life. Time series and stress intensity-specific approaches can reveal life-stages and magnitudes of exposure, respectively, that may elicit beneficial phenotypic variation." + "text": "Abstract\nPolyploidy has been shown to negatively impact environmental stress tolerance, resulting in increased susceptibility to extreme climate events such as marine heatwaves (MHWs). In this study, we used the response of the Pacific oyster Crassostrea gigas to MHWs as a model system to identify key ploidy-specific differences in the physiological and transcriptomic response of oysters to environmental stress. In this study, adult diploid (2n) and triploid (3n) oysters were exposed to elevated seawater temperature (single stressor; 30°C), elevated temperature followed by acute desiccation stress (multiple stressor; 30°C + emersion at an aerial temperature of 44°C for 4h), or a control (17°C) within a hatchery setting. Oyster mortality rate was elevated within stress treatments with respect to the control and was significantly higher in triploids than diploids following multiple stress exposure (36.4% vs. 14.8%). Triploids within the multiple stressor treatment exhibited signs of energetic limitation, including metabolic depression, a significant reduction in ctenidium Na+/K+ ATPase activity, and the dysregulated expression of key genes associated with heat tolerance, the inhibition of apoptosis, and mitochondrial function. Functional enrichment analysis of ploidy-specific gene sets identified that biological processes associated with metabolism, stress tolerance, and immune function were overrepresented within triploids across stress treatments. Our results demonstrate that triploidy impacts the transcriptional regulation of key metabolic processes that underly the environmental stress response of Pacific oysters, resulting in downstream shifts in physiological tolerance limits that may be detrimental to survival. The impact of chromosome set manipulation on the climate resilience of marine populations has important implications for the adaptability of marine populations and domestic food security within future climate scenarios, especially as triploidy induction becomes an increasingly popular tool to elicit reproductive control across a wide range of marine organisms used within marine aquaculture." }, { - "objectID": "publications/articles/gurr2021.html#data-availability", - "href": "publications/articles/gurr2021.html#data-availability", - "title": "Repeat exposure to hypercapnic seawater modifies growth and oxidative status in a tolerant burrowing clam", + "objectID": "publications/articles/george2023.html#data-availability", + "href": "publications/articles/george2023.html#data-availability", + "title": "Triploid Pacific oysters exhibit stress response dysregulation and elevated mortality following heatwaves", "section": "Data Availability", - "text": "Data Availability\nAll raw data and statistical code are openly available in the Zenodo repository at: http://doi.org/10.5281/zenodo.3903019." + "text": "Data Availability\nThe data that support the findings of this study are openly available at https://doi.org/10.5281/zenodo.7693092 (George et al., 2023). Tag-seq data are available under the NCBI BioProject ID 913164. Supporting tables and figures are provided together with this manuscript." }, { - "objectID": "publications/articles/spencer2021.html", - "href": "publications/articles/spencer2021.html", - "title": "Latent effects of winter warming on Olympia oyster reproduction and larval viability", + "objectID": "publications/articles/gurr2022.html", + "href": "publications/articles/gurr2022.html", + "title": "Acclimatory gene expression of primed clams enhances robustness to elevated pCO2", "section": "", - "text": "Laura H. Spencer, Erin Horkan, Ryan Crim, Steven B. Roberts (2021) Latent effects of winter warming on Olympia oyster reproduction and larval viability Journal of Experimental Marine Biology and Ecology. doi:10.1016/j.jembe.2021.151604" + "text": "Gurr, S. J., Wanamaker , S. A., Vadopalas, B., Roberts, S. B., & Putnam, H. M. (2022). Acclimatory gene expression of primed clams enhances robustness to elevated pCO2. Molecular Ecology, 31, 5005– 5023. https://doi.org/10.1111/mec.16644" }, { - "objectID": "publications/articles/spencer2021.html#citation", - "href": "publications/articles/spencer2021.html#citation", - "title": "Latent effects of winter warming on Olympia oyster reproduction and larval viability", + "objectID": "publications/articles/gurr2022.html#citation", + "href": "publications/articles/gurr2022.html#citation", + "title": "Acclimatory gene expression of primed clams enhances robustness to elevated pCO2", "section": "", - "text": "Laura H. Spencer, Erin Horkan, Ryan Crim, Steven B. Roberts (2021) Latent effects of winter warming on Olympia oyster reproduction and larval viability Journal of Experimental Marine Biology and Ecology. doi:10.1016/j.jembe.2021.151604" - }, - { - "objectID": "publications/articles/spencer2021.html#highlights", - "href": "publications/articles/spencer2021.html#highlights", - "title": "Latent effects of winter warming on Olympia oyster reproduction and larval viability", - "section": "Highlights", - "text": "Highlights\n• Gametes were more developed following elevated winter temperature.\n• Oocytes and larvae were larger following elevated winter temperature.\n• Larval production and survival were unaffected by winter temperature.\n• O. lurida reproduction is relatively resilient to increasing winter temperatures.\n• In the wild increased larval size due to winter warming could increase recruitment." + "text": "Gurr, S. J., Wanamaker , S. A., Vadopalas, B., Roberts, S. B., & Putnam, H. M. (2022). Acclimatory gene expression of primed clams enhances robustness to elevated pCO2. Molecular Ecology, 31, 5005– 5023. https://doi.org/10.1111/mec.16644" }, { - "objectID": "publications/articles/spencer2021.html#abstract", - "href": "publications/articles/spencer2021.html#abstract", - "title": "Latent effects of winter warming on Olympia oyster reproduction and larval viability", + "objectID": "publications/articles/gurr2022.html#abstract", + "href": "publications/articles/gurr2022.html#abstract", + "title": "Acclimatory gene expression of primed clams enhances robustness to elevated pCO2", "section": "Abstract", - "text": "Abstract\nFor ectothermic marine invertebrates living in temperate regions, impacts of ocean warming will vary considerably by season. In many species, reproductive and metabolic processes are tightly linked to the seasonal change from winter to spring, yet we know little about how these processes will shift as winters become milder. This study examined latent effects of winter warming on spring reproduction in the Olympia oyster, Ostrea lurida. Adults were collected in autumn from central Puget Sound, WA, USA, and exposed to two winter temperatures (7 °C, 10 °C) in the presence of food limited (5 k algal cells/mL) and food abundant (50 k algal cells/mL) environments. Following treatments, adults exposed to elevated winter temperature contained larger oocytes regardless of feeding regime, and those also fed abundant food contained more developed sperm. Adults then spawned in common conditions, and larvae were reared through settlement to assess carryover effects of winter treatments on larval viability. Adults previously exposed to elevated winter temperature (10 °C) produced larger larvae, particularly if they were also fed high food levels. More developed gametes and larger larvae suggest that gametogenesis occurred at low levels throughout the winter, possibly resulting in increased maternal provisioning to influence larval size. Interestingly, winter temperature did not impact larval survival, or the timing or magnitude of larval production. In the wild, more developed gametes and larger larvae following milder winters could greatly impact recruitment patterns, possibly benefitting O. lurida populations. In the hatchery setting, larval production and survival is not contingent upon winter conditions, and larval survival does not correlate with oocyte and larval size. Our results suggest that O. lurida reproduction is resilient to winter warming. Furthermore, as global temperature continues to rise, winter conditions should not be overlooked when examining reproduction in O. lurida and other temperate marine invertebrates with similar reproductive cycles." + "text": "Abstract\nBackground Sublethal exposure to environmental challenges may enhance ability to cope with chronic or repeated change, a process known as priming. In a previous study, pre-exposure to seawater enriched with pCO2 improved growth and reduced antioxidant capacity of juvenile Pacific geoduck Panopea generosa clams, suggesting that transcriptional shifts may drive phenotypic modifications post-priming. To this end, juvenile clams were sampled and TagSeq gene expression data were analysed after (i) a 110-day acclimation under ambient (921 μatm, naïve) and moderately elevated pCO2 (2870 μatm, pre-exposed); then following (ii) a second 7-day exposure to three pCO2 treatments (ambient: 754 μatm; moderately elevated: 2750 μatm; severely elevated: 4940 μatm), a 7-day return to ambient pCO2 and a third 7-day exposure to two pCO2 treatments (ambient: 967 μatm; moderately elevated: 3030 μatm). Pre-exposed geoducks frontloaded genes for stress and apoptosis/innate immune response, homeostatic processes, protein degradation and transcriptional modifiers. Pre-exposed geoducks were also responsive to subsequent encounters, with gene sets enriched for mitochondrial recycling and immune defence under elevated pCO2 and energy metabolism and biosynthesis under ambient recovery. In contrast, gene sets with higher expression in naïve clams were enriched for fatty-acid degradation and glutathione components, suggesting naïve clams could be depleting endogenous fuels, with unsustainable energetic requirements if changes in carbonate chemistry persist. Collectively, our transcriptomic data indicate that pCO2 priming during post-larval periods could, via gene expression regulation, enhance robustness in bivalves to environmental change. Such priming approaches may be beneficial for aquaculture, as seafood demand intensifies concurrent with increasing climate change in marine systems." }, { - "objectID": "publications/articles/spencer2021.html#data-availability", - "href": "publications/articles/spencer2021.html#data-availability", - "title": "Latent effects of winter warming on Olympia oyster reproduction and larval viability", + "objectID": "publications/articles/gurr2022.html#data-availability", + "href": "publications/articles/gurr2022.html#data-availability", + "title": "Acclimatory gene expression of primed clams enhances robustness to elevated pCO2", "section": "Data Availability", - "text": "Data Availability\nAll data and code associated with this project are publicly available https://doi.org/10.6084/m9.figshare.14066498.v3\nL.H. Spencer, E. Horkan, R. Crim, S.B. Roberts Paper-olurida-latent-effects. figshare. Dataset (2021), 10.6084/m9.figshare.14066498.v3" + "text": "Data Availability\n\n\n\n\n\n\nOpen Data\n\n\n\nThis article has earned an Open Data Badge for making publicly available the digitally-shareable data necessary to reproduce the reported results\n\n\nThe data is available at https://doi.org/10.5281/zenodo.6908630.\nRaw sequence reads are deposited in the SRA (Accession: PRJNA740307; BioProject: Transcriptome profiles of Panopea generosa under hypercapnic seawater). All data have been submitted as a public Zenodo repository https://doi.org/10.5281/zenodo.6908630." }, { - "objectID": "publications/articles/spencer2023.html", - "href": "publications/articles/spencer2023.html", - "title": "Population-specific effects of ocean acidification in the Olympia oyster", + "objectID": "publications/articles/putnam2022.html", + "href": "publications/articles/putnam2022.html", + "title": "Dynamic DNA methylation contributes to carryover effects and beneficial acclimatization in geoduck clams", "section": "", - "text": "Population-specific effects of ocean acidification in the Olympia oyster Laura H Spencer, Steven B Roberts, Katherine Silliman bioRxiv 2023.09.08.556443; doi: https://doi.org/10.1101/2023.09.08.556443" + "text": "Dynamic DNA methylation contributes to carryover effects and beneficial acclimatization in geoduck clams Hollie M. Putnam, Shelly A. Wanamaker , Samuel J. White, Laura H. Spencer, Brent Vadopalas, Aparna Natarajan, Jonathan Hetzel, Erich Jaeger, Jonathan Soohoo, Cristian Gallardo-Escárate, Frederick W. Goetz, Steven B. Roberts bioRxiv 2022.06.24.497506; doi: https://doi.org/10.1101/2022.06.24.497506" }, { - "objectID": "publications/articles/spencer2023.html#citation", - "href": "publications/articles/spencer2023.html#citation", - "title": "Population-specific effects of ocean acidification in the Olympia oyster", + "objectID": "publications/articles/putnam2022.html#citation", + "href": "publications/articles/putnam2022.html#citation", + "title": "Dynamic DNA methylation contributes to carryover effects and beneficial acclimatization in geoduck clams", "section": "", - "text": "Population-specific effects of ocean acidification in the Olympia oyster Laura H Spencer, Steven B Roberts, Katherine Silliman bioRxiv 2023.09.08.556443; doi: https://doi.org/10.1101/2023.09.08.556443" + "text": "Dynamic DNA methylation contributes to carryover effects and beneficial acclimatization in geoduck clams Hollie M. Putnam, Shelly A. Wanamaker , Samuel J. White, Laura H. Spencer, Brent Vadopalas, Aparna Natarajan, Jonathan Hetzel, Erich Jaeger, Jonathan Soohoo, Cristian Gallardo-Escárate, Frederick W. Goetz, Steven B. Roberts bioRxiv 2022.06.24.497506; doi: https://doi.org/10.1101/2022.06.24.497506" }, { - "objectID": "publications/articles/spencer2023.html#abstract", - "href": "publications/articles/spencer2023.html#abstract", - "title": "Population-specific effects of ocean acidification in the Olympia oyster", + "objectID": "publications/articles/putnam2022.html#abstract", + "href": "publications/articles/putnam2022.html#abstract", + "title": "Dynamic DNA methylation contributes to carryover effects and beneficial acclimatization in geoduck clams", "section": "Abstract", - "text": "Abstract\nPopulations of marine species that respond differently to ocean acidification offer natural reservoirs of biodiversity that can be leveraged for conservation efforts and to sustain marine food systems. The molecular and physiological traits associated with tolerance to acidification must first be identified. This study leveraged oysters from three phenotypically-distinct populations of the Olympia oyster, Ostrea lurida, but that were bred and reared in common conditions for four years. We assessed their growth, reproductive development, and transcriptional response to acidification within and across generations. Responses reveal energetic trade-offs that reflect unique physiotypes previously observed among populations. The population with the slowest growth but high survival rates, oysters from Dabob Bay, mounted the largest transcriptional response to acidification without effects to growth and reproduction. A moderate response was observed in the population with fastest growth rate but lowest fecundity (Fidalgo Bay). Oyster Bay, the population with highest fecundity but lowest survival rates, did not respond at the transcript level. Oyster Bay was also the only population for which acidification negatively affected growth and reproductive development. While exposure to acidification did not affect gene expression in the next generation’s larval stage, it did result in larger larvae in the Oyster Bay population, which could partially alleviate negative effects of acidification in the wild for that population. Given the distinct transcriptional response of the Dabob Bay population to acidification and its high survival rates in previous studies, we then identified genes that were uniquely expressed in Dabob Bay oysters compared to the other populations. Genes involved in antibacterial and antiviral processes, metabolism, growth, and reproduction were uniquely expressed in Dabob Bay, and many similar functions were identified in both adults and larvae, which provides insight into the mechanisms behind a stress-tolerant oyster population. The population-specific physiotypes and responses to acidification illustrate the diversity of physiological strategies in O. lurida that balance the energetic demands of growth, reproduction, cellular maintenance, and offspring viability. Taken together this study reveals that there are distinct physiotypes among marine invertebrate populations on small geographic scales with implications for species resilience to acidification and other environmental stressors." + "text": "Abstract\nGiven the rapidly changing global climate, there is a growing need to understand the acclimatory basis of animal response to environmental change. To investigate the role of DNA methylation in environmental acclimatization, we generated a reference genome and surveyed the physiology and DNA methylomes of juvenile geoduck clams, Panopea generosa, under differing seawater pH regimes. Juveniles were initially exposed to one of three seawater pH conditions, followed by ambient common-garden conditions, then a second reciprocal exposure to ambient pH or pH 7.4. Within 10 days of the initial low pH exposure, juvenile clams showed decreased shell size relative to ambient pH with corresponding differential DNA methylation. Following four months of ambient common-garden conditions, juveniles initially exposed to low pH compensatorily grew larger, with DNA methylation indicative of these phenotypic differences, demonstrating epigenetic carryover effects persisted months after initial exposure. Functional enrichment analysis of differentially methylated genes revealed regulation of signal transduction through widespread changes in the Wnt signaling pathways that influence cell growth, proliferation, tissue and skeletal formation, and cytoskeletal change. After 10 days of secondary exposure to pH 7.4, naive juvenile clams were more sensitive to low pH compared to those initially exposed, showing reduced growth and having nearly a 2-fold greater change in DNA methylation. Collectively, this new genomic resource and coordinated phenotypic and methylomic response support that epigenetic mechanisms underlie acclimatization to provide beneficial phenotypes." }, { - "objectID": "publications/articles/spencer2023.html#data-availability", - "href": "publications/articles/spencer2023.html#data-availability", - "title": "Population-specific effects of ocean acidification in the Olympia oyster", + "objectID": "publications/articles/putnam2022.html#data-availability", + "href": "publications/articles/putnam2022.html#data-availability", + "title": "Dynamic DNA methylation contributes to carryover effects and beneficial acclimatization in geoduck clams", "section": "Data Availability", - "text": "Data Availability" + "text": "Data Availability\nThe genomic DNA, transcriptomic, and DNA bisulfite sequence data generated in this study have been submitted to the NCBI BioProject database (https://www.ncbi.nlm.nih.gov/bioproject/) under accession numbers PRJNA316601; PRJNA529226 and PRJNA646071; and PRJNA566166, respectively. All intermediate data files and raw experimental data and statistical code are also available at OSF https://osf.io/yem8n/ (Roberts et al. 2020)." }, { - "objectID": "publications/articles/huffmyer2024.html", - "href": "publications/articles/huffmyer2024.html", - "title": "Coral larvae increase nitrogen assimilation to stabilize algal symbiosis and combat bleaching under increased temperature", + "objectID": "publications/articles/silliman-bogan2023.html", + "href": "publications/articles/silliman-bogan2023.html", + "title": "A dynamic web resource for robust and reproducible genomics in non-model species: marineomics.io", "section": "", - "text": ">Huffmyer AS, J Ashey, E Strand, E Chiles, X Su, HM Putnam. (2024) Coral larvae increase nitrogen assimilation to stabilize algal symbiosis and combat bleaching under increased temperature. PLoS Biology 22(11): e3002875. doi: https://doi.org/10.1371/journal.pbio.3002875" + "text": "Bogan, S. N., Johns, J., Griffiths, J. S., Davenport, D., Smith, S. J., Schaal, S. M., Downey-Wall, A., Lou, R. N., Lotterhos, K., Guidry, M. E., Rivera, H. E., McGirr, J. A., Puritz, J. B., Roberts, S. B., & Silliman, K. (2023). A dynamic web resource for robust and reproducible genomics in nonmodel species: marineomics.io. Methods in Ecology and Evolution, 00, 1–8. https://doi.org/10.1111/2041-210X.14219" }, { - "objectID": "publications/articles/huffmyer2024.html#citation", - "href": "publications/articles/huffmyer2024.html#citation", - "title": "Coral larvae increase nitrogen assimilation to stabilize algal symbiosis and combat bleaching under increased temperature", + "objectID": "publications/articles/silliman-bogan2023.html#citation", + "href": "publications/articles/silliman-bogan2023.html#citation", + "title": "A dynamic web resource for robust and reproducible genomics in non-model species: marineomics.io", "section": "", - "text": ">Huffmyer AS, J Ashey, E Strand, E Chiles, X Su, HM Putnam. (2024) Coral larvae increase nitrogen assimilation to stabilize algal symbiosis and combat bleaching under increased temperature. PLoS Biology 22(11): e3002875. doi: https://doi.org/10.1371/journal.pbio.3002875" + "text": "Bogan, S. N., Johns, J., Griffiths, J. S., Davenport, D., Smith, S. J., Schaal, S. M., Downey-Wall, A., Lou, R. N., Lotterhos, K., Guidry, M. E., Rivera, H. E., McGirr, J. A., Puritz, J. B., Roberts, S. B., & Silliman, K. (2023). A dynamic web resource for robust and reproducible genomics in nonmodel species: marineomics.io. Methods in Ecology and Evolution, 00, 1–8. https://doi.org/10.1111/2041-210X.14219" }, { - "objectID": "publications/articles/huffmyer2024.html#abstract", - "href": "publications/articles/huffmyer2024.html#abstract", - "title": "Coral larvae increase nitrogen assimilation to stabilize algal symbiosis and combat bleaching under increased temperature", + "objectID": "publications/articles/silliman-bogan2023.html#abstract", + "href": "publications/articles/silliman-bogan2023.html#abstract", + "title": "A dynamic web resource for robust and reproducible genomics in non-model species: marineomics.io", "section": "Abstract", - "text": "Abstract\nRising sea surface temperatures are increasingly causing breakdown in the nutritional relationship between corals and algal endosymbionts (Symbiodiniaceae), threatening the basis of coral reef ecosystems and highlighting the critical role of coral reproduction in reef maintenance. The effects of thermal stress on metabolic exchange (i.e., transfer of fixed carbon photosynthates from symbiont to host) during sensitive early life stages, however, remains understudied. We exposed symbiotic Montipora capitata coral larvae in Hawaiʻi to high temperature (+2.5°C for 3 days), assessed rates of photosynthesis and respiration, and used stable isotope tracing (4 mM 13C sodium bicarbonate; 4.5 h) to quantify metabolite exchange. While larvae did not show any signs of bleaching and did not experience declines in survival and settlement, metabolic depression was significant under high temperature, indicated by a 19% reduction in respiration rates, but with no change in photosynthesis. Larvae exposed to high temperature showed evidence for maintained translocation of a major photosynthate, glucose, from the symbiont, but there was reduced metabolism of glucose through central carbon metabolism (i.e., glycolysis). The larval host invested in nitrogen cycling by increasing ammonium assimilation, urea metabolism, and sequestration of nitrogen into dipeptides, a mechanism that may support the maintenance of glucose translocation under thermal stress. Host nitrogen assimilation via dipeptide synthesis appears to be used for nitrogen limitation to the Symbiodiniaceae, and we hypothesize that nitrogen limitation contributes to retention of fixed carbon by favoring photosynthate translocation to the host. Collectively, our findings indicate that although these larvae are susceptible to metabolic stress under high temperature, diverting energy to nitrogen assimilation to maintain symbiont population density, photosynthesis, and carbon translocation may allow larvae to avoid bleaching and highlights potential life stage specific metabolic responses to stress." + "text": "Abstract\n\nGenomic methods are becoming increasingly valuable and established in eco- logical research, particularly in nonmodel species. Supporting their progress and adoption requires investment in resources that promote (i) reproducibility of genomic analyses, (ii) accessibility of learning tools and (iii) keeping pace with rapidly developing methods and principles.\nWe introduce marineomics.io, an open-source, living document to disseminate tutorials, reproducibility tools and best principles for ecological genomic research in marine and nonmodel systems.\nThe website’s existing content spans population and functional genomics, includ- ing current recommendations for whole-genome sequencing, RAD-seq, Pool-seq and RNA-seq. With the goal to facilitate the development of new, similar re- sources, we describe our process for aggregating and synthesizing methodologi- cal principles from the ecological genomics community to inform website content. We also detail steps for authorship and submission of new website content, as well as protocols for providing feedback and topic requests from the community.\nThese web resources were constructed with guidance for doing rigorous, repro- ducible science. Collaboration and contributions to the website are encouraged from scientists of all skill sets and levels of expertise." }, { - "objectID": "publications/articles/huffmyer2024.html#data-availability", - "href": "publications/articles/huffmyer2024.html#data-availability", - "title": "Coral larvae increase nitrogen assimilation to stabilize algal symbiosis and combat bleaching under increased temperature", + "objectID": "publications/articles/silliman-bogan2023.html#data-availability", + "href": "publications/articles/silliman-bogan2023.html#data-availability", + "title": "A dynamic web resource for robust and reproducible genomics in non-model species: marineomics.io", "section": "Data Availability", - "text": "Data Availability\nhttps://github.com/AHuffmyer/SymbioticIntegration" + "text": "Data Availability\nThe website can be found at http://marineomics.github.io/ and the source repository for contributors is located at https://github.com/ MarineOmics/marineomics.github.io. A snapshot of the site’s source code at the time of submission is available via Zenodo: https://doi. org/10.5281/zenodo.8289843 (Roberts et al., 2023)." }, { - "objectID": "publications/articles/dang2022.html", - "href": "publications/articles/dang2022.html", - "title": "Epigenetic-associated phenotypic plasticity of the ocean acidification-acclimated edible oyster in the mariculture environment", + "objectID": "publications/articles/dimond2021.html", + "href": "publications/articles/dimond2021.html", + "title": "DNA methylation profiling of a cnidarian-algal symbiosis using nanopore sequencing", "section": "", - "text": "Dang, X., Lim, Y.-K., Li, Y., Roberts, S. B., Li, L., & Thiyagarajan, V. (2023). Epigenetic-associated phenotypic plasticity of the ocean acidification-acclimated edible oyster in the mariculture environment. Molecular Ecology, 32, 412– 427. https://doi.org/10.1111/mec.16751" + "text": "James L Dimond and others, DNA methylation profiling of a cnidarian-algal symbiosis using nanopore sequencing, G3 Genes|Genomes|Genetics, Volume 11, Issue 7, July 2021, jkab148, https://doi.org/10.1093/g3journal/jkab148" }, { - "objectID": "publications/articles/dang2022.html#citation", - "href": "publications/articles/dang2022.html#citation", - "title": "Epigenetic-associated phenotypic plasticity of the ocean acidification-acclimated edible oyster in the mariculture environment", + "objectID": "publications/articles/dimond2021.html#citation", + "href": "publications/articles/dimond2021.html#citation", + "title": "DNA methylation profiling of a cnidarian-algal symbiosis using nanopore sequencing", "section": "", - "text": "Dang, X., Lim, Y.-K., Li, Y., Roberts, S. B., Li, L., & Thiyagarajan, V. (2023). Epigenetic-associated phenotypic plasticity of the ocean acidification-acclimated edible oyster in the mariculture environment. Molecular Ecology, 32, 412– 427. https://doi.org/10.1111/mec.16751" + "text": "James L Dimond and others, DNA methylation profiling of a cnidarian-algal symbiosis using nanopore sequencing, G3 Genes|Genomes|Genetics, Volume 11, Issue 7, July 2021, jkab148, https://doi.org/10.1093/g3journal/jkab148" }, { - "objectID": "publications/articles/dang2022.html#abstract", - "href": "publications/articles/dang2022.html#abstract", - "title": "Epigenetic-associated phenotypic plasticity of the ocean acidification-acclimated edible oyster in the mariculture environment", + "objectID": "publications/articles/dimond2021.html#abstract", + "href": "publications/articles/dimond2021.html#abstract", + "title": "DNA methylation profiling of a cnidarian-algal symbiosis using nanopore sequencing", "section": "Abstract", - "text": "Abstract\nFor marine invertebrates with a pelagic–benthic life cycle, larval exposure to ocean acidification (OA) can affect adult performance in response to another environmental stressor. This carry-over effect has the potential to alter phenotypic traits. However, the molecular mechanisms that mediate “OA”-triggered carry-over effects have not been explored despite such information being key to improving species fitness and management strategies for aquafarming. This study integrated the genome-wide DNA methylome and transcriptome to examine epigenetic modification-mediated carry-over OA impacts on phenotypic traits of the ecologically and commercially important oyster species Crassostrea hongkongensis under field conditions. Larvae of C. hongkongensis were exposed to control pH 8.0 and low pH 7.4 conditions, mimicking near future OA scenario in their habitat, before being outplanted as post-metamorphic juveniles at two mariculture field sites with contrasting environmental stressors for 9 months. The larval carry-over OA effect was found to have persistent impacts on the growth and survival trade-off traits on the outplanted juveniles, although the beneficial or adverse effect depended on the environmental conditions at the outplanted sites. Site-specific plasticity was demonstrated with a diverse DNA methylation-associated gene expression profile, with signal transduction and the endocrine system being the most common and highly enriched functions. Highly methylated exons prevailed in the key genes related to general metabolic and endocytic responses and these genes are evolutionarily conserved in various marine invertebrates in response to OA. These results suggest that oysters with prior larval exposure history to OA had the ability to trigger rapid local adaptive responses via epigenetic modification to cope with multiple stressors in the field." + "text": "Abstract\nSymbiosis with protists is common among cnidarians such as corals and sea anemones and is associated with homeostatic and phenotypic changes in the host that could have epigenetic underpinnings, such as methylation of CpG dinucleotides. We leveraged the sensitivity to base modifications of nanopore sequencing to probe the effect of symbiosis with the chlorophyte Elliptochloris marina on methylation in the sea anemone Anthopleura elegantissima. We first validated the approach by comparison of nanopore-derived methylation levels with CpG depletion analysis of a published transcriptome, finding that high methylation levels are associated with CpG depletion as expected. Next, using reads generated exclusively from aposymbiotic anemones, a largely complete draft genome comprising 243 Mb was assembled. Reads from aposymbiotic and symbiotic sea anemones were then mapped to this genome and assessed for methylation using the program Nanopolish, which detects signal disruptions from base modifications as they pass through the nanopore. Based on assessment of 452,841 CpGs for which there was adequate read coverage (approximately 8% of the CpGs in the genome), symbiosis with E. marina was, surprisingly, associated with only subtle changes in the host methylome. However, we did identify one extended genomic region with consistently higher methylation among symbiotic individuals. The region was associated with a DNA polymerase zeta that is noted for its role in translesion synthesis, which opens interesting questions about the biology of this symbiosis. Our study highlights the power and relative simplicity of nanopore sequencing for studies of nucleic acid base modifications in non-model species." }, { - "objectID": "publications/articles/dang2022.html#data-availability", - "href": "publications/articles/dang2022.html#data-availability", - "title": "Epigenetic-associated phenotypic plasticity of the ocean acidification-acclimated edible oyster in the mariculture environment", + "objectID": "publications/articles/dimond2021.html#data-availability", + "href": "publications/articles/dimond2021.html#data-availability", + "title": "DNA methylation profiling of a cnidarian-algal symbiosis using nanopore sequencing", "section": "Data Availability", - "text": "Data Availability\nThe methylRAD and RNA-seq data are available under NCBI Bio-project ID PRJNA741860 and PRJNA741374, respectively. Supporting Information including R and Perl scripts are provided." + "text": "Data Availability\nA repository containing datasets, notebooks, scripts, and output files, including the draft genome, is publicly available at https://doi.org/10.5281/zenodo.4677448. Raw sequencing reads are available at NCBI under BioProject PRJNA700526 (https://www.ncbi.nlm.nih.gov/sra/PRJNA700526). Supplemental Material available at figshare: https://doi.org/10.25387/g3.14485401." }, { - "objectID": "publications/articles/venkataraman2022.html", - "href": "publications/articles/venkataraman2022.html", - "title": "Differential DNA methylation in Pacific oyster reproductive tissue in response to ocean acidification", + "objectID": "publications/articles/venkataraman2024.html", + "href": "publications/articles/venkataraman2024.html", + "title": "DNA methylation correlates with transcriptional noise in response to elevated pCO2 in the eastern oyster (Crassostrea virginica)", "section": "", - "text": "Venkataraman, Y.R., White, S.J. & Roberts, S.B. Differential DNA methylation in Pacific oyster reproductive tissue in response to ocean acidification. BMC Genomics 23, 556 (2022). https://doi.org/10.1186/s12864-022-08781-5" + "text": "DNA methylation correlates with transcriptional noise in response to elevated pCO2 in the eastern oyster (Crassostrea virginica)\nYaamini R. Venkataraman, Ariana S. Huffmyer, Samuel J. White, Alan Downey-Wall, JillAshey, Danielle M. Becker, Zachary Bengtsson, Hollie M. Putnam, Emma Strand, Javier A. Rodríguez-Casariego, Shelly A. Wanamaker, Kathleen E. Lotterhos, Steven B. Roberts\nbioRxiv 2024.04.04.588108; doi: https://doi.org/10.1101/2024.04.04.588108" }, { - "objectID": "publications/articles/venkataraman2022.html#citation", - "href": "publications/articles/venkataraman2022.html#citation", - "title": "Differential DNA methylation in Pacific oyster reproductive tissue in response to ocean acidification", + "objectID": "publications/articles/venkataraman2024.html#citation", + "href": "publications/articles/venkataraman2024.html#citation", + "title": "DNA methylation correlates with transcriptional noise in response to elevated pCO2 in the eastern oyster (Crassostrea virginica)", "section": "", - "text": "Venkataraman, Y.R., White, S.J. & Roberts, S.B. Differential DNA methylation in Pacific oyster reproductive tissue in response to ocean acidification. BMC Genomics 23, 556 (2022). https://doi.org/10.1186/s12864-022-08781-5" + "text": "DNA methylation correlates with transcriptional noise in response to elevated pCO2 in the eastern oyster (Crassostrea virginica)\nYaamini R. Venkataraman, Ariana S. Huffmyer, Samuel J. White, Alan Downey-Wall, JillAshey, Danielle M. Becker, Zachary Bengtsson, Hollie M. Putnam, Emma Strand, Javier A. Rodríguez-Casariego, Shelly A. Wanamaker, Kathleen E. Lotterhos, Steven B. Roberts\nbioRxiv 2024.04.04.588108; doi: https://doi.org/10.1101/2024.04.04.588108" }, { - "objectID": "publications/articles/venkataraman2022.html#abstract", - "href": "publications/articles/venkataraman2022.html#abstract", - "title": "Differential DNA methylation in Pacific oyster reproductive tissue in response to ocean acidification", + "objectID": "publications/articles/venkataraman2024.html#abstract", + "href": "publications/articles/venkataraman2024.html#abstract", + "title": "DNA methylation correlates with transcriptional noise in response to elevated pCO2 in the eastern oyster (Crassostrea virginica)", "section": "Abstract", - "text": "Abstract\nBackground There is a need to investigate mechanisms of phenotypic plasticity in marine invertebrates as negative effects of climate change, like ocean acidification, are experienced by coastal ecosystems. Environmentally-induced changes to the methylome may regulate gene expression, but methylome responses can be species- and tissue-specific. Tissue-specificity has implications for gonad tissue, as gonad-specific methylation patterns may be inherited by offspring. We used the Pacific oyster (Crassostrea gigas) — a model for understanding pH impacts on bivalve molecular physiology due to its genomic resources and importance in global aquaculture— to assess how low pH could impact the gonad methylome. Oysters were exposed to either low pH (7.31 ± 0.02) or ambient pH (7.82 ± 0.02) conditions for 7 weeks. Whole genome bisulfite sequencing was used to identify methylated regions in female oyster gonad samples. C- > T single nucleotide polymorphisms were identified and removed to ensure accurate methylation characterization. Results Analysis of gonad methylomes revealed a total of 1284 differentially methylated loci (DML) found primarily in genes, with several genes containing multiple DML. Gene ontologies for genes containing DML were involved in development and stress response, suggesting methylation may promote gonad growth homeostasis in low pH conditions. Additionally, several of these genes were associated with cytoskeletal structure regulation, metabolism, and protein ubiquitination — commonly-observed responses to ocean acidification. Comparison of these DML with other Crassostrea spp. exposed to ocean acidification demonstrates that similar pathways, but not identical genes, are impacted by methylation. Conclusions Our work suggests DNA methylation may have a regulatory role in gonad and larval development, which would shape adult and offspring responses to low pH stress. Combined with existing molluscan methylome research, our work further supports the need for tissue- and species-specific studies to understand the potential regulatory role of DNA methylation." + "text": "Abstract\nOcean acidification significantly affects marine calcifiers like oysters, warranting the study of molecular mechanisms like DNA methylation that contribute to adaptive plasticity in response to environmental change. However, a consensus has not been reached on the extent to which methylation modules gene expression, and in turn plasticity, in marine invertebrates. In this study, we investigated the impact of pCO2 on gene expression and DNA methylation in the eastern oyster, Crassostrea virginica. After a 30-day exposure to control (572 ppm) or elevated pCO2 (2,827 ppm), whole genome bisulfite sequencing (WGBS) and RNA-Seq data were generated from adult female gonad tissue and male sperm samples. Although differentially methylated loci (DML) were identified in females (89) and males (2,916), there were no differentially expressed genes, and only one differentially expressed transcript in females. However, gene body methylation impacted other forms of gene activity in sperm, such as the maximum number of transcripts expressed per gene and changes in the predominant transcript expressed. Elevated pCO2 exposure increased gene expression variability (transcriptional noise) in males but decreased noise in females, suggesting a sex-specific role of methylation in gene expression regulation. Functional annotation of genes with changes in transcript-level expression or containing DML revealed several enriched biological processes potentially involved in elevated pCO2 response, including apoptotic pathways and signal transduction, as well as reproductive functions. Taken together, these results suggest that DNA methylation may regulate gene expression variability to maintain homeostasis in elevated pCO2 conditions and could play a key role in environmental resilience in marine invertebrates." }, { - "objectID": "publications/articles/venkataraman2022.html#data-availability", - "href": "publications/articles/venkataraman2022.html#data-availability", - "title": "Differential DNA methylation in Pacific oyster reproductive tissue in response to ocean acidification", + "objectID": "publications/articles/venkataraman2024.html#data-availability", + "href": "publications/articles/venkataraman2024.html#data-availability", + "title": "DNA methylation correlates with transcriptional noise in response to elevated pCO2 in the eastern oyster (Crassostrea virginica)", "section": "Data Availability", - "text": "Data Availability\nAll data, genome feature tracks, scripts, and a supplementary materials list are available in the Oyster Gonad Methylation repository, doi.org/10.17605/OSF.IO/YGCTB. All raw data can be accessed at the NCBI Sequence Read Archive under BioProject accession number PRJNA806944 (https://www.ncbi.nlm.nih.gov/bioproject/806944)." + "text": "Data Availability\n\nhttps://github.com/sr320/ceabigr\nhttps://osf.io/xuy2f/" }, { - "objectID": "publications/articles/silliman2023.html", - "href": "publications/articles/silliman2023.html", - "title": "Epigenetic and genetic population structure is coupled in a marine invertebrate", + "objectID": "publications/articles/arredondo-espinoza2021.html", + "href": "publications/articles/arredondo-espinoza2021.html", + "title": "Differentially methylated gene regions between resistant and susceptible heat-phenotypes of the Pacific oyster Crassostrea gigas", "section": "", - "text": "Katherine Silliman and others, Epigenetic and Genetic Population Structure is Coupled in a Marine Invertebrate, Genome Biology and Evolution, Volume 15, Issue 2, February 2023, evad013, https://doi.org/10.1093/gbe/evad013" + "text": ">Arredondo-Espinoza Roberto, Ibarra Ana M., Roberts B. Steven, Sicard-Gonzalez Maria Teresa, Escobedo-Fregoso Cristina (2021) Differentially methylated gene regions between resistant and susceptible heat-phenotypes of the Pacific oyster Crassostrea gigas Aquaculture Vol 543. doi:10.1016/j.aquaculture.2021.736923." }, { - "objectID": "publications/articles/silliman2023.html#citation", - "href": "publications/articles/silliman2023.html#citation", - "title": "Epigenetic and genetic population structure is coupled in a marine invertebrate", + "objectID": "publications/articles/arredondo-espinoza2021.html#citation", + "href": "publications/articles/arredondo-espinoza2021.html#citation", + "title": "Differentially methylated gene regions between resistant and susceptible heat-phenotypes of the Pacific oyster Crassostrea gigas", "section": "", - "text": "Katherine Silliman and others, Epigenetic and Genetic Population Structure is Coupled in a Marine Invertebrate, Genome Biology and Evolution, Volume 15, Issue 2, February 2023, evad013, https://doi.org/10.1093/gbe/evad013" + "text": ">Arredondo-Espinoza Roberto, Ibarra Ana M., Roberts B. Steven, Sicard-Gonzalez Maria Teresa, Escobedo-Fregoso Cristina (2021) Differentially methylated gene regions between resistant and susceptible heat-phenotypes of the Pacific oyster Crassostrea gigas Aquaculture Vol 543. doi:10.1016/j.aquaculture.2021.736923." }, { - "objectID": "publications/articles/silliman2023.html#abstract", - "href": "publications/articles/silliman2023.html#abstract", - "title": "Epigenetic and genetic population structure is coupled in a marine invertebrate", + "objectID": "publications/articles/arredondo-espinoza2021.html#abstract", + "href": "publications/articles/arredondo-espinoza2021.html#abstract", + "title": "Differentially methylated gene regions between resistant and susceptible heat-phenotypes of the Pacific oyster Crassostrea gigas", "section": "Abstract", - "text": "Abstract\nDelineating the relative influence of genotype and the environment on DNA methylation is critical for characterizing the spectrum of organism fitness as driven by adaptation and phenotypic plasticity. In this study, we integrated genomic and DNA methylation data for two distinct Olympia oyster (Ostrea lurida) populations while controlling for within-generation environmental influences. In addition to providing the first characterization of genome-wide DNA methylation patterns in the oyster genus Ostrea, we identified 3,963 differentially methylated loci between populations. Our results show a clear coupling between genetic and epigenetic patterns of variation, with 27% of variation in interindividual methylation differences explained by genotype. Underlying this association are both direct genetic changes in CpGs (CpG-SNPs) and genetic variation with indirect influence on methylation (mQTLs). When comparing measures of genetic and epigenetic population divergence at specific genomic regions this relationship surprisingly breaks down, which has implications for the methods commonly used to study epigenetic and genetic coupling in marine invertebrates.\n\n\n\nfig7" - }, - { - "objectID": "publications/articles/silliman2023.html#significance", - "href": "publications/articles/silliman2023.html#significance", - "title": "Epigenetic and genetic population structure is coupled in a marine invertebrate", - "section": "Significance", - "text": "Significance\nWe know that genotype and epigenetic patterns are primarily responsible for phenotype, yet there is a lack of understanding to what degree the two are linked. Here, we characterized the degree by which genetic variation and DNA methylation variation are coupled in a marine invertebrate and identified potential mechanisms, with almost a third of the methylation variation attributable to genotype. This study provides a framework for future studies in environmental epigenetics to take genetic variation into account when teasing apart the drivers of phenotypic variation. By identifying methylation variation that cannot be attributed to genotype or environmental changes during development, our results also highlight the need for future research to characterize molecular mechanisms adjacent to genetic adaptation for producing long-term shifts in phenotype." + "text": "Abstract\nHeat stress is one of the factors that affect aquaculture production of the Pacific oyster Crassostrea gigas in Mexico, and research aiming to improve heat tolerance is required. C. gigas breeding stock, produced for genetic improvement, is being implemented, and breeding lines available with 50 families were characterized for their heat-tolerance, selecting the two-most heat-resistant and the two-most heat-susceptible families. These families were analyzed for differences in their DNA methylation patterns after maintaining them for 30 days in a regime of oscillating temperatures (26 °C to 34 °C), similar to what is found in culture areas of Mexico. Whereas no differences were found in global methylation among heat-phenotypes, differentially methylated regions (DMRs) were found between phenotypes. Temperature modifies the methylation in gene bodies of C. gigas, where the heat-resistant phenotype (RR) showed more genes with DMRs in promoters (3672), exons (6340), and introns (18,685). Hyper-methylated genes among phenotypes were more abundant in RR introns (122), followed by exons (23), and promoters (2), whereas hypo-methylated regions corresponded to ten in introns, three in exons, and one in promoters. Hyper-methylated DMRs were mostly found in genes associated with processes such as regulation of gene expression, ions interactions, metabolism, and production of cellular components. This suggests that DMRs among heat-phenotypes in C. gigas families are involved in the heat-shock stress response regulated by methylation. The DMRs reported in this study could be used as methylation markers for a future broodstock selection." }, { - "objectID": "publications/articles/silliman2023.html#data-availability", - "href": "publications/articles/silliman2023.html#data-availability", - "title": "Epigenetic and genetic population structure is coupled in a marine invertebrate", + "objectID": "publications/articles/arredondo-espinoza2021.html#data-availability", + "href": "publications/articles/arredondo-espinoza2021.html#data-availability", + "title": "Differentially methylated gene regions between resistant and susceptible heat-phenotypes of the Pacific oyster Crassostrea gigas", "section": "Data Availability", - "text": "Data Availability\nCode, intermediate analysis files, and genome annotation files used in this study are available in the accompanying repository https://github.com/sr320/paper-oly-mbdbs-gen (https://doi.org/10.5281/zenodo.7083311). The genome assembly can be found at ENA under the accession PRJEB39287 and the raw data are available at NCBI Sequence Read Archive (SRA) at BioProject PRJNA316624. Raw 2b-RAD data are available on SRA at BioProject PRJNA851765. Raw MBD-BS data are available on SRA at BioProject PRJNA849214." + "text": "Data Availability" }, { - "objectID": "publications/articles/arredondo-espinoza2023.html", - "href": "publications/articles/arredondo-espinoza2023.html", - "title": "Transcriptome profile in heat resilient Pacific oyster Crassostrea gigas families under thermal challenge", + "objectID": "publications/articles/rajan2021.html", + "href": "publications/articles/rajan2021.html", + "title": "Oyster biomineralisation under ocean acidification: from genes to shell", "section": "", - "text": ">Arredondo-Espinoza R, Ibarra AM, Roberts SB, Sicard-González MT, Escobedo-Fregoso C. Transcriptome profile in heat resilient Pacific oyster Crassostrea gigas families under thermal challenge. Comp Biochem Physiol Part D Genomics Proteomics. 2023 Sep;47:101089. doi: 10.1016/j.cbd.2023.101089. Epub 2023 May 26. PMID: 37269757." + "text": "Chandra Rajan, K., Yuan, M., Yu, Z., Roberts, S.B. and Thiyagarajan, V. (2021) Oyster biomineralisation under ocean acidification: from genes to shell Global Change Biology. doi:10.1111/gcb.15675" }, { - "objectID": "publications/articles/arredondo-espinoza2023.html#citation", - "href": "publications/articles/arredondo-espinoza2023.html#citation", - "title": "Transcriptome profile in heat resilient Pacific oyster Crassostrea gigas families under thermal challenge", + "objectID": "publications/articles/rajan2021.html#citation", + "href": "publications/articles/rajan2021.html#citation", + "title": "Oyster biomineralisation under ocean acidification: from genes to shell", "section": "", - "text": ">Arredondo-Espinoza R, Ibarra AM, Roberts SB, Sicard-González MT, Escobedo-Fregoso C. Transcriptome profile in heat resilient Pacific oyster Crassostrea gigas families under thermal challenge. Comp Biochem Physiol Part D Genomics Proteomics. 2023 Sep;47:101089. doi: 10.1016/j.cbd.2023.101089. Epub 2023 May 26. PMID: 37269757." + "text": "Chandra Rajan, K., Yuan, M., Yu, Z., Roberts, S.B. and Thiyagarajan, V. (2021) Oyster biomineralisation under ocean acidification: from genes to shell Global Change Biology. doi:10.1111/gcb.15675" }, { - "objectID": "publications/articles/arredondo-espinoza2023.html#abstract", - "href": "publications/articles/arredondo-espinoza2023.html#abstract", - "title": "Transcriptome profile in heat resilient Pacific oyster Crassostrea gigas families under thermal challenge", + "objectID": "publications/articles/rajan2021.html#abstract", + "href": "publications/articles/rajan2021.html#abstract", + "title": "Oyster biomineralisation under ocean acidification: from genes to shell", "section": "Abstract", - "text": "Abstract\nSince the introduction of the Pacific oyster Crassostrea gigas in Baja California Sur, Mexico, its culture has faced environmental challenges, specifically increasing temperatures that result in high mortalities. The inter-tidal zone seawater temperature during a year at the Baja California Peninsula broadly ranges from 7 °C to 39 °C. Therefore, to understand how oysters respond to heat stress during daily temperature oscillations, heat-resistant (RR, father, and mother resistant) and heat-susceptible (SS, both parents susceptible) phenotypes families from a C. gigas breeding program were exposed to a thermal challenge. Based on a laboratory-simulated daily oscillatory thermal challenge (26 to 34 °C) for 30 days, RR phenotype presented differences compared to SS phenotype since the beginning (day 0) of the thermal challenge. Gene expression analyses revealed 1822 differentially expressed up-regulated transcripts in RR, related to functions of metabolic processes, biological regulation, and response to stimulus and signaling. At the end of the experiment (day 30), 2660 differentially expressed up-regulated transcripts were identified in RR. Functional analysis of the genes expressed indicates responses of regulation of biological processes and response to a stimulus. Additionally, 340 genes were differentially expressed among RR vs. SS from the beginning to the end of the thermal challenge, where 170 genes were up-regulated, and 170 were down-regulated. These transcriptomic profiles represent the first report to identify gene expression markers associated with RR phenotypes for the Pacific oyster to the future broodstock selection.\n\n\n\nga" + "text": "Abstract\nBiomineralization is one of the key processes that is notably affected in marine calcifiers such as oysters under ocean acidification (OA). Understanding molecular changes in the biomineralization process under OA and its heritability, therefore, is key to developing conservation strategies for protecting ecologically and economically important oyster species. To do this, in this study, we have explicitly chosen the tissue involved in biomineralization (mantle) of an estuarine commercial oyster species, Crassostrea hongkongensis. The primary aim of this study is to understand the influence of DNA methylation over gene expression of mantle tissue under decreased ~pH 7.4, a proxy of OA, and to extrapolate if these molecular changes can be observed in the product of biomineralization—the shell. We grew early juvenile C. hongkongensis, under decreased ~pH 7.4 and control ~pH 8.0 over 4.5 months and studied OA-induced DNA methylation and gene expression patterns along with shell properties such as microstructure, crystal orientation and hardness. The population of oysters used in this study was found to be moderately resilient to OA at the end of the experiment. The expression of key biomineralization-related genes such as carbonic anhydrase and alkaline phosphatase remained unaffected; thus, the mechanical properties of the shell (shell growth rate, hardness and crystal orientation) were also maintained without any significant difference between control and OA conditions with signs of severe dissolution. In addition, this study makes three major conclusions: (1) higher expression of Ca2+ binding/signalling-related genes in the mantle plays a key role in maintaining biomineralization under OA; (2) DNA methylation changes occur in response to OA; however, these methylation changes do not directly control gene expression; and (3) OA would be more of a 'dissolution problem' rather than a 'biomineralization problem' for resilient species that maintain calcification rate with normal shell growth and mechanical properties." }, { - "objectID": "publications/articles/arredondo-espinoza2023.html#data-availability", - "href": "publications/articles/arredondo-espinoza2023.html#data-availability", - "title": "Transcriptome profile in heat resilient Pacific oyster Crassostrea gigas families under thermal challenge", + "objectID": "publications/articles/rajan2021.html#data-availability", + "href": "publications/articles/rajan2021.html#data-availability", + "title": "Oyster biomineralisation under ocean acidification: from genes to shell", "section": "Data Availability", - "text": "Data Availability" + "text": "Data Availability\nThe RNA-Seq and Methyl RAD data are available under the NCBI Bio-project ID: PRJNA643001. Supporting Information files including the R and perl scripts are provided together with this manuscript." }, { - "objectID": "publications/articles/crandall2022.html", - "href": "publications/articles/crandall2022.html", - "title": "Characterization of the Gene Repertoire and Environmentally Driven Expression Patterns in Tanner Crab (Chionoecetes bairdi)", + "objectID": "publications/notebooks/crandall2022.html", + "href": "publications/notebooks/crandall2022.html", + "title": "Proteomic response of early juvenile Pacific oysters (Crassostrea gigas) to temperature", "section": "", - "text": "Crandall, G., Jensen, P.C., White, S.J. et al. Characterization of the Gene Repertoire and Environmentally Driven Expression Patterns in Tanner Crab (Chionoecetes bairdi). Mar Biotechnol 24, 216–225 (2022). https://doi.org/10.1007/s10126-022-10100-8" + "text": "Crandall G, Elliott Thompson R, Eudeline B, Vadopalas B, Timmins-Schiffman E, Roberts S. 2022. Proteomic response of early juvenile Pacific oysters (Crassostrea gigas) to temperature. PeerJ 10:e14158 https://doi.org/10.7717/peerj.14158" }, { - "objectID": "publications/articles/crandall2022.html#citation", - "href": "publications/articles/crandall2022.html#citation", - "title": "Characterization of the Gene Repertoire and Environmentally Driven Expression Patterns in Tanner Crab (Chionoecetes bairdi)", + "objectID": "publications/notebooks/crandall2022.html#citation", + "href": "publications/notebooks/crandall2022.html#citation", + "title": "Proteomic response of early juvenile Pacific oysters (Crassostrea gigas) to temperature", "section": "", - "text": "Crandall, G., Jensen, P.C., White, S.J. et al. Characterization of the Gene Repertoire and Environmentally Driven Expression Patterns in Tanner Crab (Chionoecetes bairdi). Mar Biotechnol 24, 216–225 (2022). https://doi.org/10.1007/s10126-022-10100-8" + "text": "Crandall G, Elliott Thompson R, Eudeline B, Vadopalas B, Timmins-Schiffman E, Roberts S. 2022. Proteomic response of early juvenile Pacific oysters (Crassostrea gigas) to temperature. PeerJ 10:e14158 https://doi.org/10.7717/peerj.14158" }, { - "objectID": "publications/articles/crandall2022.html#abstract", - "href": "publications/articles/crandall2022.html#abstract", - "title": "Characterization of the Gene Repertoire and Environmentally Driven Expression Patterns in Tanner Crab (Chionoecetes bairdi)", + "objectID": "publications/notebooks/crandall2022.html#abstract", + "href": "publications/notebooks/crandall2022.html#abstract", + "title": "Proteomic response of early juvenile Pacific oysters (Crassostrea gigas) to temperature", "section": "Abstract", - "text": "Abstract\nTanner crab (Chionoecetes bairdi) is an economically important species that is threatened by ocean warming and bitter crab disease, which is caused by an endoparasitic dinoflagellate, Hematodinium. Little is known about disease transmission or its link to host mortality, or how ocean warming will affect pathogenicity or host susceptibility. To provide a transcriptomic resource for the Tanner crab, we generated a suite of RNA-seq libraries encompassing pooled hemolymph samples from crab displaying differing infection statuses and maintained at different temperatures (ambient (7.5˚C), elevated (10˚C), or decreased (4˚C)). After assembling a transcriptome and performing a multifactor differential gene expression analysis, we found genes influenced by temperature in relation to infection and detected some of those genes over time at the individual level using RNA-seq data from one crab. Biological processes associated with those genes include lipid storage, transcription, response to oxidative stress, cell adhesion, and morphogenesis. Alteration in lipid storage and transcription provide insight into how temperature impacts energy allocation in Hematodinium infected crabs. Alteration in expression patterns in genes associated with morphogenesis could suggest that hemocytes were changing morphology and/or type in response to temperature. This project provides insight into how Hematodinium infection could influence crab physiology as oceans warm." + "text": "Abstract\nPacific oysters (Crassostrea gigas) are a valuable aquaculture product that provides important ecosystem benefits. Among other threats, climate-driven changes in ocean temperature can impact oyster metabolism, survivorship, and immune function. We investigated how elevated temperature impacts larval oysters during settlement (19–33 days post-fertilization), using shotgun proteomics with data-independent acquisition to identify proteins present in the oysters after 2 weeks of exposure to 23 °C or 29 °C. Oysters maintained at elevated temperatures were larger and had a higher settlement rate, with 86% surviving to the end of the experiment; these oysters also had higher abundance trends of proteins related to metabolism and growth. Oysters held at 23 °C were smaller, had a decreased settlement rate, displayed 100% mortality, and had elevated abundance trends of proteins related to immune response. This novel use of proteomics was able to capture characteristic shifts in protein abundance that hint at important differences in the phenotypic response of Pacific oysters to temperature regimes. Additionally, this work has produced a robust proteomic product that will be the basis for future research on bivalve developmental processes." }, { - "objectID": "publications/articles/crandall2022.html#data-availability", - "href": "publications/articles/crandall2022.html#data-availability", - "title": "Characterization of the Gene Repertoire and Environmentally Driven Expression Patterns in Tanner Crab (Chionoecetes bairdi)", + "objectID": "publications/notebooks/crandall2022.html#data-availability", + "href": "publications/notebooks/crandall2022.html#data-availability", + "title": "Proteomic response of early juvenile Pacific oysters (Crassostrea gigas) to temperature", "section": "Data Availability", - "text": "Data Availability\nThe online version contains supplementary material available at https://doi.org/10.5281/zenodo.4563060" + "text": "Data Availability\nThe following information was supplied regarding data availability:\nAdditional files, scripts, and data are available at Zenodo: grace-ac, & Steven Roberts. (2021). grace-ac/paper-pacific.oyster-larvae: release for PeerJ submission (v2.1.0). Zenodo. https://doi.org/10.5281/zenodo.5708415.\nThe proteomic data is available at PRIDE: PXD015434." }, { "objectID": "index.html", @@ -1960,26 +1974,5 @@ "crumbs": [ "Diversity, Equity, and Inclusion" ] - }, - { - "objectID": "posts/frontpage/ariana-paper/index.html", - "href": "posts/frontpage/ariana-paper/index.html", - "title": "Coral Larvae and Thermal Stress", - "section": "", - "text": "As climate change continues to drive rising ocean temperatures, coral reef ecosystems face an unprecedented crisis. Coral bleaching events, characterized by the breakdown of the mutualistic relationship between corals and their algal endosymbionts (Symbiodiniaceae), have become increasingly common, threatening the persistence of coral reefs worldwide. While much research has focused on adult corals, new studies are shedding light on how early life stages respond to thermal stress. A recent study by Huffmyer et al. (2024), published in PLOS Biology, provides novel insights into how coral larvae cope with increased temperatures by modifying nitrogen assimilation to stabilize symbiotic relationships and mitigate bleaching risk.\n\nThe Crucial Role of Coral Larvae in Reef Resilience\nReef-building corals rely on their symbionts to produce energy-rich photosynthates that fuel metabolic processes. However, when subjected to thermal stress, this delicate exchange can be disrupted, leading to the expulsion of symbionts and loss of critical energy sources. Understanding how coral larvae respond to environmental stress is particularly important, as their ability to establish symbiosis and successfully settle onto reefs determines the future of coral populations.\nThe study focused on Montipora capitata, a dominant reef-building coral in Hawai‘i that vertically transmits Symbiodiniaceae to its offspring. The researchers subjected symbiotic larvae to a 2.5°C increase in temperature for three days and assessed metabolic responses, photosynthetic performance, and stable isotope-labeled metabolite exchange.\n\n\nKey Findings: Nitrogen Assimilation as a Protective Mechanism\nContrary to expectations, the study found that while larvae exhibited significant metabolic depression under high temperatures—indicated by a 19% reduction in respiration rates—they did not experience bleaching or a decline in survival and settlement rates. Photosynthetic activity remained stable, and the symbiont population density was maintained despite thermal stress.\nA crucial discovery was that coral larvae increased ammonium assimilation and urea metabolism while sequestering nitrogen into dipeptides. This shift suggests that larvae actively modulate nitrogen cycling to maintain symbiotic balance. By limiting nitrogen availability to the symbionts, the coral hosts may be promoting sustained photosynthate translocation, ensuring that energy supply remains uninterrupted under heat stress.\n\n\nMetabolic Trade-offs and Implications for Coral Survival\nWhile glucose translocation from symbiont to host was maintained, the study revealed reduced metabolism of glucose through central carbon pathways such as glycolysis. This metabolic shift implies a trade-off: larvae prioritize nitrogen assimilation over carbohydrate breakdown, potentially conserving energy for essential physiological functions.\nThe authors propose that nitrogen limitation imposed on Symbiodiniaceae encourages continued carbon transfer to the host, preventing the symbionts from hoarding fixed carbon, which could otherwise disrupt the mutualistic relationship. This mechanism highlights a potential resilience strategy in coral early life stages that may influence reef recovery following bleaching events.\n\n\nFuture Directions and Conservation Implications\nUnderstanding the physiological mechanisms that allow coral larvae to withstand heat stress has significant implications for reef conservation and restoration efforts. If coral larvae can naturally modulate nitrogen metabolism to maintain symbiosis, selective breeding or assisted evolution approaches may enhance these traits in vulnerable species.\nAdditionally, further research should investigate whether similar nitrogen assimilation strategies are present in adult corals or if this is a life-stage-specific adaptation. Given the increasing frequency of marine heatwaves, identifying and promoting heat-resilient traits in corals could be a crucial component of future conservation strategies.\n\n\nConclusion\nHuffmyer et al. (2024) provide compelling evidence that coral larvae can mitigate thermal stress through nitrogen assimilation, maintaining stable symbiosis even under elevated temperatures. By uncovering this metabolic adaptation, the study advances our understanding of coral resilience mechanisms and underscores the importance of protecting early life stages in reef conservation efforts. As climate change accelerates, these insights may inform new strategies to support coral reef survival in a warming world." - }, - { - "objectID": "posts/sr320-handbook/index.html", - "href": "posts/sr320-handbook/index.html", - "title": "Deep dive into the handbook", - "section": "", - "text": "A unique perspective. You will never guess what they reveal!\n\nAudio\n\n\n\nTranscript\nWelcome to The Deep Dive, where we dig into the nitty gritty of fascinating topics.\nToday, we’re taking a deep dive into the Roberts Lab at the University of Washington, and we’re doing that through the lens of their handbook.\nIt’s more than just a rule book, though, isn’t it?\nOh, absolutely.\nIt’s like a window into their whole approach to science.\nEverything from, like, groundbreaking research to how they actually build their research culture.\nAnd they’re known for being incredibly transparent, which this handbook really embodies.\nYeah, it’s refreshing.\nAnd speaking of refreshing, I have to ask you about this freezer alarm situation.\nOh, yes.\nSo they have, like, a dedicated alarm for their ultra-low temperature freezers, right?\nYeah.\nBut there’s this 15-minute delay before anyone actually gets notified if it goes off.\nCan you imagine?\nIt’s like a slow-motion heart attack for a researcher.\nRight.\nAll those precious samples.\nI’d be a wreck.\nIt really highlights the fragility of these biological materials they’re working with.\nRNA, proteins, these things have to be stored at, like, negative 80 degrees Celsius.\nWow.\nEven a short power outage could be disastrous.\nSo is that delay, like, a safety net to give the system a chance to recover?\nExactly.\nIt’s a calculated risk.\nThey’re trying to balance preventing false alarms while also, you know, protecting those invaluable research materials.\nMakes sense.\nYeah.\nAnd it seems like that emphasis on meticulousness, on minimizing risk, it really comes through in the whole handbook, especially when they talk about lab safety and chemicals.\nIt’s serious business.\nRight.\nLike with Arnazole RT, they’re very clear about it being corrosive, potentially harmful if you inhale it, even disposing of it.\nIt’s a whole multi-step process.\nWell, they’re dealing with some pretty potent stuff.\nIt underscores their dedication to, you know, not just scientific rigor, but the actual well-being of their researchers.\nAbsolutely.\nIt’s like they’re creating an environment where cutting-edge science can happen, but it can happen safely.\nSafety first.\nYeah.\nAnd that meticulousness, that doing things by the book, it goes beyond just lab safety, you know.\nRight.\nIt’s woven into their whole research philosophy, which makes you wonder, if they’re this careful with safety, how does that translate to, say, data management or collaboration?\nGood question.\nAnd as luck would have it, that’s exactly what we’re going to be digging into in the rest of this deep dive.\nYou know, it’s funny you should mention that because the next thing that really struck me about this handbook was their code of conduct.\nOh, interesting.\nHow so?\nWell, for one, it’s incredibly detailed, even for like their diversity, equity, and inclusion meetings.\nYou don’t always see that level of, I don’t know, formality in a lab handbook.\nWhat kinds of things are we talking about here?\nThey have these great phrases like, “Elevate impact above intent,” and, “Expect and accept non-closure.”\nLike, really specific guidelines.\nHuh.\nIt sounds like they’re trying to foster a very specific kind of research environment.\nRight.\nOne where people feel comfortable admitting they don’t know everything, which, let’s be honest, is most of the time in research, right?\nOh, absolutely.\nScience is all about embracing uncertainty.\nBut it takes a certain culture to really allow for that.\nTotally.\nAnd it seems like they’re putting a lot of emphasis on making sure everyone feels heard and respected, especially in those DEI meetings.\nWell, and that makes sense, right?\nIf you want to have those tough conversations about diversity and inclusion, you need to create a space where people feel safe to speak their minds.\nYeah.\nNo, you’re right.\nIt all ties together.\nAnd then there’s this whole thing about mentorship.\nThey really encourage lab members to have multiple mentors, not just one.\nThat’s interesting.\nMost labs I’ve seen, it’s pretty standard to have one primary mentor.\nRight.\nYeah.\nSo I thought that was really unique.\nIt kind of speaks to this idea of providing a well-rounded experience, right?\nAbsolutely.\nDifferent mentors bring different perspectives, different areas of expertise.\nIt can really enrich a researcher’s training.\nOkay, so we’ve got meticulous safety protocols, a very deliberate approach to their lab culture.\nBut we also know they’re dealing with a massive amount of data.\nLike their handbook mentions Nightingale for sequencing this whole network attached storage system called Gannett.\nDon’t forget the supercomputer.\nMOCs, was it?\nOh, right.\nMOCs.\nI mean, it’s a lot.\nIt really makes you wonder how they manage it all.\nIt’s a data tsunami.\nHow do they keep from drowning?\nWell, for one thing, they’re incredibly organized.\nLike religiously organized.\nGive me the details.\nThink detailed metadata for every single experiment, strict folder structures on their network.\nThey even have readme files.\nReadme files for every folder, seriously.\nSeriously.\nAnd it’s all part of this commitment to open science.\nThey want their research to be accessible, transparent.\nSo anyone could theoretically go in and understand their data, their methods.\nThat’s the idea.\nIt’s about breaking down those silos, you know, fostering collaboration, avoiding unnecessary redundancy, ultimately speeding up discoveries.\nIt’s kind of inspiring, actually.\nIt’s like they’re playing the long game, advancing science as a whole, not just their own work.\nExactly.\nBut okay, even with perfect organization, all that data analysis, it’s got to be intense.\nThey mentioned Jupiter notebooks in the handbook.\nRight, and mocks the supercomputer.\nAnd they even talk about using like the command line.\nHard course, so they’re not messing around.\nWell, they’re equipping their researchers with a seriously powerful toolkit.\nBut it goes beyond just the tech.\nThey even recommend this book, Getting Things Done.\nTime management.\nTime management.\nIt’s all about efficiency.\nThey don’t just give them the tools.\nThey give them the training, the resources to actually use them well.\nIt’s like they’ve thought of everything.\nYeah.\nAnd it doesn’t stop there.\nThey have a whole section on conferences, funding opportunities, even like travel grants.\nThey want their researchers to be well-rounded, right?\nNot just stuck in the lab, but out there presenting, collaborating, getting their work funded.\nIt’s impressive, I have to say.\nLooking at the Roberts Lab this way, through their handbook, you really get a sense of the thoughtfulness, the care that goes into building a successful research environment.\nIt’s not just about, you know, the results, the discoveries.\nIt’s the people, the culture.\nAnd that commitment to moving science forward in a way that’s open and collaborative, it’s really something.\nMakes you wonder what they’ll accomplish, what amazing discoveries are on the horizon for them.\nIt does, doesn’t it?\nAnd that’s something to ponder as we wrap up this deep dive into the world of the Roberts Lab.\nUntil next time, keep exploring, keep questioning, and keep diving deep." - }, - { - "objectID": "projects.html", - "href": "projects.html", - "title": "Research Projects", - "section": "", - "text": "Using next-generation sequencing techniques to assess adaptive capacity and illuminate mechanisms underlying the effects of high pCO2 on Alaskan crab and fish species\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\nField-based Education and Research at Regional Aquaculture Sites (FERRAS)\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\nFACT: AquaMine - A High Performance Genomic Data Mining System for Species of Importance to US Aquaculture\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\nImproved climate resilience in oysters through optimization of hatchery-based environmental conditioning practices\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\nEffects of temperature change and Hematodinium sp. infection (Bitter Crab Disease) on Tanner crab (Chionoecetes bairdi)\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\nGene activity and genetic selection in Pacific cod reared under thermal stress\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\nA collaborative partnership to address mass mortalities in oyster aquaculture through improved field monitoring, husbandry practices, and workforce development\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\nIdentifying genomic architecture features that contribute to critical phenotypes in shellfish\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\nVernon: Development of innovative approaches to support sustainable aquaculture and understand the effects of ocean acidification on marine species\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\nDevelopment of environmental conditioning practices to decrease impacts of climate change on shellfish aquaculture\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\nEnhancing sustainability of shellfish aquaculture through streamlined maturation control\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\nIncreasing Environmental Connection, Literacy and Engagement through an Art + Science Collaborative Education Practice\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\nReadying sustainable aquaculture for a changing ocean: uncovering the mechanisms associated with intergenerational carryover effects to enhance bivalve resilience to acidification\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\nCollaborative Research: Does ocean acidification induce a methylation response that affects the fitness of the next generation in oysters?\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\nOyster adaptation to climate change via transgenerational plasticity\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\nCollaborative Research: URoL : Epigenetics 2: Predicting phenotypic and eco-evolutionary consequences of environmental-energetic-epigenetic linkages\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\nApplying cutting-edge technology for reproductive control in emerging bivalve species\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\nNo matching items" } ] \ No newline at end of file diff --git a/docs/sitemap.xml b/docs/sitemap.xml index 8884834..cb94b0b 100644 --- a/docs/sitemap.xml +++ b/docs/sitemap.xml @@ -13,100 +13,104 @@ 2025-02-08T20:25:09.721Z - https://faculty.washington.edu/sr320/publications/notebooks/crandall2022.html - 2023-06-23T22:34:15.026Z + https://faculty.washington.edu/sr320/projects.html + 2025-02-08T21:03:17.032Z - https://faculty.washington.edu/sr320/publications/articles/rajan2021.html - 2023-09-08T02:07:45.825Z + https://faculty.washington.edu/sr320/publications/articles/crandall2022.html + 2023-10-16T14:46:00.505Z - https://faculty.washington.edu/sr320/publications/articles/arredondo-espinoza2021.html - 2023-09-08T02:11:25.474Z + https://faculty.washington.edu/sr320/publications/articles/arredondo-espinoza2023.html + 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