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Courtesy of Caltech Information Science and Technology Initiative – Wierman Cray 2 Supercomputer

Grants List


Courtesy of Jon Kaye

Monterey Bay Aquarium Research Institute

Microfluidic chip technologies to enhance environmental monitoring

In support of developing microfluidic chip technology to detect the presence and function of biological organisms in environmental settings. Funding will be used to dramatically increase current analytical throughput (reaction speed and total number of samples), decrease reagent and sample amounts, and to deploy this technology on the Environmental Sample Processor for extended periods in remote locations.

Title: Microfluidic chip technologies to enhance environmental monitoring
Date Awarded: Sep 2010
Amount: $3,060,000
Term: 49 months
Grant ID: GBMF2728
Funding Area: Science, Special Projects in Science



Marine microbes play a key role in cycling matter and energy throughout the global ocean. These organisms and the cycles they mediate are central to structuring marine ecosystems and maintaining the habitability of our planet. Laboratory techniques that reveal the genetic content and metabolic capacity of these organisms have revolutionized our understanding of the diversity and functions of oceanic microbial communities. Generally such studies depend on large ocean-going ships to access particular locations and collect samples for analysis. The material obtained is then returned to shore-based laboratories where scientists perform tests and analyze results.  This traditional approach has proven effective, but is also costly and subject to many constraints; the time one can spend at any one location and the number of locations that can be visited repeatedly is inherently limited. For these reasons we are developing an ocean-deployable robotic laboratory, the Environmental Sample Processor (ESP), which automatically collects samples of seawater and performs tests to assess the diversity, abundance and activities of wide range of microbes.  The ESP can also be used to preserve samples for later laboratory studies in situations where the desired tests are not yet practical to automate for in-water operations.

The ESP has undergone a number of developmental steps in recent years.  At present, the “second generation” (2G) device is deployed on moorings, drifters, benthic stations and piers ( It has served to validate the concept of utilizing analytical technologies such as DNA and protein probe arrays and quantitative PCR in remote ocean settings (Scholin et al., Preston et al.). However, its large size restricts application on small, mobile platforms, and the analytical capacity is constrained by available hardware and fluidic layout. A “third generation” (3G) ESP is being developed to overcome those limitations.  Like the 2G device, the 3G system allows for the collection and concentration of particulate matter and its preparation for analysis, but the new design is much more compact.  The goals of this project are to develop new PCR and probe array “analytical modules” for the 3G sampler, and deploy the new system on a long-range autonomous underwater vehicle (LRAUV; The current focus of this work is the design of a digital PCR module (Ray et al.) to increase the ESP’s analytical throughput by enhancing both processing speed and the total number of targets that can be detected in a single sample. This new analytical capability will allow the ESP to use fewer reagents and stay deployed for longer periods of time.  When deployed on the LRAUV, it will be possible to track dynamic ocean features and their associated microbial communities with respect to space and time.


Read more:

Preston, C. M., A. Harris, J. P. Ryan, B. Roman, R. Marin, 3rd, S. Jensen, C. Everlove, J. Birch, J. M. Dzenitis, D. Pargett, M. Adachi, K. Turk, J. P. Zehr, & C. A. Scholin. (2011). Underwater application of quantitative PCR on an ocean mooring. PLoS One, 6(8), e22522. doi: 10.1371/journal.pone.0022522

Scholin, C. A., G. Doucette, S. Jensen, B. Roman, D. Pargett, R. Marin III, C. Preston, W.  Jones, J. Feldman, C. Everlove, A. Harris, N. Alvarado, E. I. Massion, J. Birch, D. Greenfield, R. Vrijenhoek, C. Mikuliso, & K. Jones. (2009). Remote Detection of Marine Microbes, Small Invertebrates, Harmful, Algae and Biotoxins Using the Environmental Sample Processor (ESP). Oceanography, 22(2), 158-167. doi: 10.5670/oceanog.2009.46

Return to the Main Marine Microbiology Initiative Page

Other grants to Monterey Bay Aquarium Research Institute (4)

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