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An initial exploration of in-situ underwater genetic sequencing

$3,700
Raised of $3,600 Goal
102%
Funded on 7/12/21
Successfully Funded
  • $3,700
    pledged
  • 102%
    funded
  • Funded
    on 7/12/21

About This Project

Our goal is to adapt portable genome sequencing technology for high-pressure, underwater environments. Currently, deep-sea organisms are sequenced at near 1 atmosphere of pressure, a pressure many of them would never live in naturally. If successful, this technology will enable researchers to sequence deep-sea organisms in their natural environment and thereby gain valuable information about how organisms express their genes in response to their unique environments.

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What is the context of this research?

Scientists have been able to culture less than 1% of the bacteria species on Earth [1]. Many of the most interesting bacteria live at the bottom of the ocean in high-pressure environments with no oxygen and no light. We currently know nothing about these bacteria or how their genomes are expressed in the context of their environment, questions which can only be answered in situ using underwater biosensors. The first step is to understand the effects of pressure on nanopore sequencing technology: how does pressure create errors in mobile genome sequencing? We believe that developing underwater nanopore biosensors will open entirely new areas of research.

[1] Schloss and Handelsman. “Status of the microbial census.” Microbiol Mol Biol Rev (2004) vol. 68 (4): 686–91.

What is the significance of this project?

The aim of this project is to adapt portable genome sequencing technology for high-pressure deep-sea environments. If successful, it will dramatically expand our knowledge of deep-sea species, the functioning of deep-sea ecosystems, and ultimately the planet. Biosensors adapted for deep-sea use would allow researchers to study how deep-sea organisms express their genomes in their natural environment while reducing or eliminating the need for physical samples to be brought up from the deep. This modular, portable sensor technology can be integrated with existing exploration survey platforms (ROVs, UMS, terrestrial and marine NASA landers, etc.) and could be used to develop time-series data that would lead to the discovery of important new attributes of ocean environments.

What are the goals of the project?

The goals of this project are to perform proof-of-concept experiments showing how the nanopore flow cell can perform at varying pressure. First we will complete the construction of a pressure vesselwith a nanopore sensor. Our preliminary design has been approved by our collaborators at Scripps Institution of Oceanography, Oxford Nanopore Technologies, and Global Ocean Design. We will then sequence three types of DNA at varying pressure, including a metagenomic sample mixture, simulating the diversity of environmental DNA found in the ocean [2]. We have allowed time for iterative technology development in our workflow.

[2] Matthew A. Barnes, et al. “Environmental Conditions Influence eDNA Persistence in Aquatic Systems.” Environ. Sci. Technol. 2014 48 (3): 1819–1827.

Budget

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Supplies and Materials:

(1) We will purchase all DNA from New England BioLabs. The total cost of DNA is around: $69.00+$66.00=$135.00.

(2) We plan to conduct eight proof-of-concept experiments. Three starter kits using the Oxford Nanopore Sensor (the MinION) will cost $3,276.00 ($1092.00 each).

(3) Additionally, modifying the pressure vessel at Scripps Institute of Oceanography so that it contains a USB-3 power connection�data link will cost approximately $275. This cost is a rough, extremely conservative estimate. We will need to bring the USB-3 cable through the existing bulkhead connector on the pressure vessel. Global Ocean Dynamics, has years of experience adapting high pressure systems and foresees that this task is possible by fitting an existing connector from the group at no cost.

Endorsed by

This project is a clever and creative way to get deeper into bacterial genomics. Science doesn't know nearly as much about bacteria as it should - bacteria are arguably the dominant form of life on Earth, and their genomes contain amazing secrets. (CRISPR was discovered in a bacterial genome!)

Flag iconProject Timeline

Phase 1: Using existing lab facilities, confirm nanopore sensor can operate at high pressure.

Phase 2: Confirm nanopore sensor can operate in the sea. This is imagined as a series of shallow water tests, 200-300m, of moderate duration to see what fluid pumps may need to be created, including, perhaps, a reverse flow, back flush/cleaning stream, or possibly shutters that close for the nanopore sensor head.

Phase 3: Field deployment of the advanced prototype.

May 15, 2021

Project Launched

Apr 01, 2022

Confirm nanopore sensor can operate at high pressure.

Apr 01, 2023

Confirm nanopore sensor can operate in the sea.

Apr 01, 2024

Field deployment of the advanced prototype.

Meet the Team

Keolu Fox, PhD
Keolu Fox, PhD
Assistant Professor

Affiliates

University of California, San Diego
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Keolu Fox, PhD

Keolu Fox Ph.D., Kānaka Maoli (Native Hawaiian) is an assistant professor at University of California, San Diego, affiliated with the Department of Anthropology, the Global Health Program, the Halıcıoğlu Data Science Institute, the Climate Action Lab, and the Indigenous Futures Institute. He holds a Ph.D. in Genome Sciences from the University of Washington, Seattle (2016). Dr. Fox’s multi-disciplinary research interests include genome sequencing, genome engineering, computational biology, evolutionary genetics, paleogenetics, and Indigenizing biomedical research. His primary research focuses on questions of functionalizing genomics, testing theories of natural selection by editing genes and determining the functions of mutations.

Dr. Fox has published numerous articles on human genetics, biomedicine, ancient genomics, and Indigenous data sovereignty, most recently in the New England Journal of Medicine, Nature, and the Proceedings of the Royal Society B.

Dr. Fox is a recipient of grants from numerous organizations including the National Institutes of Health, the National Science Foundation, National Geographic, the American Association for Physical Anthropology, Emerson Collective, the Social Science Research Council the Massachusetts Institute of Technology, SOLVE Initiative.

Lab Notes

Nothing posted yet.

Additional Information

We believe this exploratory series of experiments will be the first to quantify the effects of pressure on mobile nanopore-based genomic sensors. The experiments will serve as a proof of concept, generate preliminary data on the effects of pressure on nanopore-based genome sequencing�sensors, and move towards the long term goal of engineering a deployable in situ nanopore genome sequencing sensor. It will complement the development of solid-state nanopores for deep-sea genetic sequencers.


Project Backers

  • 17Backers
  • 102%Funded
  • $3,700Total Donations
  • $217.65Average Donation
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