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Research Spending & Results

Award Detail

Awardee:UNIVERSITY OF WASHINGTON
Doing Business As Name:University of Washington
PD/PI:
  • E. Virginia Armbrust
  • (206) 616-1783
  • armbrust@ocean.washington.edu
Co-PD(s)/co-PI(s):
  • Robert Morris Dr.~000525534
Award Date:05/21/2012
Estimated Total Award Amount: $ 873,930
Funds Obligated to Date: $ 873,930
  • FY 2012=$873,930
Start Date:06/01/2012
End Date:05/31/2016
Transaction Type:Grant
Agency:NSF
Awarding Agency Code:4900
Funding Agency Code:4900
CFDA Number:47.050
Primary Program Source:040100 NSF RESEARCH & RELATED ACTIVIT
Award Title or Description:Implementation of continuous flow cytometry for high resolution mapping of microbial distributions in surface waters
Federal Award ID Number:1154074
DUNS ID:605799469
Parent DUNS ID:042803536
Program:OCEAN TECH & INTERDISC COORDIN
Program Officer:
  • Kandace S. Binkley
  • (703) 292-8581
  • kbinkley@nsf.gov

Awardee Location

Street:4333 Brooklyn Ave NE
City:Seattle
State:WA
ZIP:98195-0001
County:Seattle
Country:US
Awardee Cong. District:07

Primary Place of Performance

Organization Name:University of Washington
Street:4333 Brooklyn Ave NE
City:Seattle
State:WA
ZIP:98195-1202
County:Seattle
Country:US
Cong. District:07

Abstract at Time of Award

The PI's request funding to complete the development of instrumentation that allows continuous high-resolution mapping of microbial (both autotrophic and heterotrophic) communities in surface waters. With this proposal they propose to transition SeaFlow into the final development stage where it will be permanently installed and operated on the R/V Thompson, requiring minimal support of shipboard marine technicians. This instrument will build upon SeaFlow optics and fluidics and will be the first instrument to continuously measure the distribution of heterotrophic microbes in surface waters. They will also develop a collaborative data processing, management and analysis platform to allow scalable, interactive analysis of our rapidly expanding data sets both on-vessel and on-shore, during and after the cruise. Broader Impacts: A successful outcome from this proposal could pioneer the routine use of flow cytometry on ships of opportunity and on research cruises where a specialist in this technique was not present. The increased frequency and coverage of sampling, and the proposed ease of access to the data, is likely to stimulate interest in marine microbial ecology in the wider oceanographic community. The proposed research will provide great training opportunities for undergraduates and post doctoral researchers directly and will presumably include graduate students in some of the real time testing and feedback. This project is definitely interdisciplinary and pulls in undergraduates from different disciplines.

Publications Produced as a Result of this Research

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Howe, B., F. Ribalet, S. Chitnis, E. V. Armbrust "SQLShare: Scientific Workflow Management via Relational View Sharing" Computing in Science and Engineering, IEEE computer Society Digital Library. IEEE Computer Society,, v.42, 2013, p.10.1109. doi:http://doi.ieeecomputersociety.org/10.1109/MCSE.2013.42 

Bill Howe, Daniel Halperin, Francois Ribalet, Sagar Chitnis, E. Virginia Armbrust, "Collaborative Science Workflows in SQL" Computing in Science and Engineering, v.15, 2013, p.22.

Ribalet, F., Swalwell, J., C. Ellis, V. Jimenez, L. Yajuan, Z. Johnson, A. Z. Worden and E. V. Armbrust "Light-driven synchrony of Prochlorococcus growth and mortality in the subtropical Pacific gyre" PNAS, v.112, 2015, p.8008.

Ribalet, F., Swalwell, J., Clayton, S., Jimenez, V., Sudek, S., Lin, Y., Johnson, Z.I., Worden, A.Z. and Armbrust, E.V. "Light-driven synchrony of Prochlorococcus cell growth and mortality in the subtropical Pacific gyre" Proceedings of the National Academy of Sciences USA, v.112, 2015, p.8008.

Hyrkas, J., Clayton, S., Ribalet, F., Halperin, D., Armbrust, E.V. and Howe, B. "Scalable clustering algorithms for continuous environmental flow cytometry." Bioinformatics, v., 2016, p.btv594v1.


Project Outcomes Report

Disclaimer

This Project Outcomes Report for the General Public is displayed verbatim as submitted by the Principal Investigator (PI) for this award. Any opinions, findings, and conclusions or recommendations expressed in this Report are those of the PI and do not necessarily reflect the views of the National Science Foundation; NSF has not approved or endorsed its content.

Phytoplankton are tiny single celled organisms that live in the surface of the ocean relying on sunlight, carbon dioxide, and nutrients for their growth. They are responsible for creating roughly half of the earth's oxygen produced each year and most of the food for life in the sea. Understanding the distribution of these organisms over space and time informs how marine ecosystems function both today and under future ocean conditions.  In response to this need, we developed a novel flow cytometer called SeaFlow that creates “fingerprints” of individual phytoplankton cells based on their ability to scatter or re-emit specific wavelengths of light.  This light can be detected and used to estimate cell size and the combination of photosynthetic pigments of individual cells. Together, these properties can then be used to identify different types of phytoplankton. SeaFlow thus allows a continuous counting of these different groups of phytoplankton.  SeaFlow performs measurements of surface waters on board a ship continuously in real time, which allows the unprecedented collection of an enormous amount of data on a very fine scale. The resulting data can be automatically linked by time and the ship's location and compared to other data such as nutrient measurements. SeaFlow can detect even very small phytoplankton with comparable sensitivity to the best commercial flow cytometers. In addition, it can be operated and adjusted remotely through an internet connection. Over the course of this research grant, we optimized instrument capabilities to further ease operations and we developed advanced software tools to manage and analyze the large SeaFlow data sets.  We also developed software that allow the data generated at sea to be transmitted to shore in near-real time for display over a public web site.  Data from over twenty research cruises have been collected, spanning about 100km of the North Pacific Ocean. This project resulted in the training of numerous undergraduates with backgrounds in engineering, computer science, biology and oceanography. These students gained experience in conducting collaborative cross-disciplinary research.

 


Last Modified: 01/06/2017
Modified by: E. Virginia Armbrust

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