eDNA Sampler | Updates | Senior Design Updates | Github | ednaUI | ednaServer

Current Project Team:

Lead: Riley Prince

Mechanical: Hendy, Joshua Iler

Software: Nathan Jesudason, Marc Belinga

Electrical: Jacob Field, Kai Roy

Overview

Organisms leave traces of DNA as they move through their environments. The extraction of these DNA traces is known as environmental DNA (eDNA). eDNA provides scientists and researchers with a non-invasive and sensitive way to detect and quantify species. However, traditional eDNA sampling consists of manually filtering water, which is labor and cost-intensive for remote locations. Furthermore, commercialized solutions are expensive and require a field operator. This eDNA sampler project aims to provide an affordable, open-sourced, remotely deployable, fully automated, and customizable alternative.

Description

The eDNA Sampler can run up to 24 inline filter units with support for different conditions including pressure, time, and volume limit. The pumps can deliver a maximum of 350mL/min of flow with each solenoid valve separating the filter housings to minimize cross-contamination. At the end of each sample, the desired stabilizing solution can be injected to fully submerge the filter for long-term storage. An optional river depth sensor can provide a proxy for flow to correct eDNA concentrations to allow for improved quantification of organisms. Data acquired during operation including water depth, pressure, temperature, and flow rate will be stored on a microSD card as a CSV file, which allows easier data export and analysis. A web application is specially designed for the eDNA Sampler for in-field programming, real-time sensor updates, scheduling tasks, and manual operations. The full sampler is estimated to be ~$5000 each, with an add-on river depth sensor and 10ah 12V battery.

Objectives

• Determining the cross-contamination between filters (samples)

• Drafting a HardwareX Paper

Outcomes

We are currently working on the electronic hardware and software side of the project. More tests will be performed on the system as a whole to determine the level of cross-contamination between different filters.

Main Control Board

Browser Application

Future

The main things that we are currently working on are:

• Brainstorming ways to increase cross-contamination if it falls below desired margins.
• Implementing a better way of monitoring the amount of volume sampled.

In addition to the previously mentioned tasks, we are planning to work on the following in the near future:

• Redesign of the main control board/electronics hardware.
• Making the User Interface more friendly to less technical users.
• Decreasing the amount of cross-contamination between samples (depending on the testing currently happening).
• Adding a Depth Sensor

Resource List

• A Build Guide for the current version (V4) of the eDNA Sampler (Work in Progress)
• How to update an assembly in Fusion360

Problems & Solutions

What problem we have encountered in the development of the series and the solution that we have come up with:

• Reducing motor noise

• Alcohol retention for unclogged filter

• Sending large website package

• Troubleshoot?

Feel free to contact the lab/developer if you have other ideas to solve, improve, or upgrade the eDNA sampler.

Riley Prince: princeri@oregonstate.edu

Keywords

eDNA, genomic, sampling, sampler, sample, environmental DNA

Former Team Members:

Electrical: Bao Nguyen, Sean Booth

Programming: Kawin Pechetratanapanit, Emannuel Moncada

Mechanical: Torrey Menne, Aaron S Arvidson, Nikhil Wandhekar, Ethan Pohlschneider, Tilford Li, Danil Kryuchkov, Dylan Heisey

Reference

• Types of Hydraulic Pumps

• eDNA AGU 2019 Poster | ESSOAR | 10.1002/essoar.10501740.1

• Inline Pressure Sensor (Outdated)

• Inline Flow Sensor (Outdated)