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James M. Birch 2011 7700 Sandholdt Rd, Moss Landing, CA 95039 831-775-2062 [email protected]

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James M. Birch 2011 7700 Sandholdt Rd, Moss Landing, CA 95039 831-775-2062 Jbirch@Mbari.Org James M. Birch 2011 7700 Sandholdt Rd, Moss Landing, CA 95039 831-775-2062 [email protected] EMPLOYMENT / POSITIONS MONTEREY BAY AQUARIUM RESEARCH INSTITUTE Director, SURF Center, Sensors: Underwater Research of the Future (2009-PRESENT) MONTEREY BAY AQUARIUM RESEARCH INSTITUTE Instrument Engineering and Development Group Leader (2007-2009) LAWRENCE LIVERMORE NATIONAL LABORATORY Associate Program Leader (acting)—Assays, and (AUGUST, 2005-MARCH, 2007) Project Manager for Influenza assay and instrument development LAWRENCE LIVERMORE NATIONAL LABORATORY Staff Scientist, Medical Physics and Biophysics Division (2003-2005) UNIVERSITY OF CALIFORNIA Research Associate III Berkeley (1999-2003) NORTHERN ARIZONA UNIVERSITY Post-Doctoral Researcher Flagstaff (1995 – 1999) RESEARCH EXPERIENCE BIOENGINEERING / BIOPHYSICS 2007-present I am the Project Manager of the Environmental Sample Processor project (ESP) and have been responsible for the first networked deployment (3 machines deployed simultaneously), the development of 4000m depth capability, and the addition of DNA analysis via PCR on the ESP. 2005-2007 As Project Manager, I oversaw the development of a respiratory assay and FluIDx, an autonomous, self-contained respiratory virus diagnostic instrument. Oversaw team of 5 with 3 direct reports. I will directed the instrument deployment to UC-Davis Medical Center for field testing December, 2006. Instrument utilizes ‘zone fluidics’ and custom software to autonomously move fluid and perform PCR and detection of target nucleic acid sequences. 2003-2005 I helped design and test a new inlet for a bioagent detector, the BioAerosol Mass Spectrometer (BAMS). This was a dual-polarity TOF mass spectrometer. Our goal was to create a nozzle that more accurately focused 1-10 µm particles into the laser desorption chamber for ionization. BIOLOGICAL FLUID MECHANICS 1999-2003 Helped discover the mechanisms of lift generation in insects, and the aerodynamic parameter space in which flies (Drosophila) operate by using ‘Robofly’, a dynamically scaled 3 DOF robot flapping in mineral oil for comparable Reynolds number scaling. Designed and developed a fluid visualization system to elucidate wake structure and function during insect hovering. Performed particle-image velocimetry and designed custom software for data analysis. Proficient with class IV laser usage. Designed and constructed second-generation Robofly to study translation. BIOMECHANICS 1995-1999 Created biomechanical models to understand feeding systems utilizing high-speed video filming and analysis. SELECTED PUBLICATIONS Preston, C., A. Harris, J. Ryan, B. Roman, R. Marin III, S. Jensen, C. Everlove, J. Birch, J. Dzenitis, D. Pargett, M. Adachi, K. Turk, J. Zehr, C. Scholin. 2011. Underwater application of quantitative PCR on an ocean mooring. PLoS ONE 6(8): e22522. http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0022522. Ryan, J., D. Greenfield, R. Marin III, C. Preston, B. Roman, S. Jensen, D. Pargett, J. Birch, C. Mikulski, G. Doucette, C. Scholin. 2011. Harmful phytoplankton ecology studies using an autonomous molecular analytical and ocean observing network. Limnol. Oceanogr. 56(4): 1255-1272. Regan, J., S. Létant, K. Adams, N. Nguyen, R. Derlet, S. Cohen, E. Vitalis, L. Tammero, J. Ortiz, M. McBride, J. Birch. 2010. A sample-in-answer-out instrument for the detection of multiple respiratory pathogens in unprepared nasopharyngeal swab samples. Analyst, 135: 2316-2322. Scholin, C, G. Doucette, S. Jensen, B. Roman, D. Pargett, R. Marin III, C. Preston, W. Jones, J. Feldman, C. Everlove, A. Harris, N. Avarado, E. Massion, J. Birch, D. Greenfield, R. Vrijenhoek, C. Mikulski, K. Jones. 2009. Remote detection of marine microbes, small invertebrates, harmful algae and biotoxins using the Environmental Sample Processor (ESP). Oceanography 22: 158-167. Preston, C., R. Marin III, S. Jensen, J. Feldman, J. Birch, E. Massion, E. DeLong, M. Suzuki, K. Wheeler, and C. Scholin. Near real- time, autonomous detection of marine bacterioplankton on a coastal mooring in Monterey Bay, California, using rRNA-targeted DNA probes. Environmental Microbiology 11:1168-1180. Regan, J., S. Létant, L. Bentley Tammero, J. Ortiz, R. Derlet, S. Cohen, N. Nguyen, K. Adams, E. Vitalis, B. Colston, M. McBride, J. Birch. 2009. Development and evaluation of an automated multiplex RT-PCR liquid array instrument for the detection of respiratory pathogens. Submitted to Biosensors and Bioelectronics. Le´tant, S.E., J.I. Ortiz, L.F. Bentley Tammero, J.M. Birch, R.W. Derlet, S. Cohen, D. Manning, and M.T. McBride. 2007. Multiplexed reverse transcriptase PCR assay for identification of viral respiratory pathogens at the point of care. J. Clinical Microbiology 45 (11): 3498-3505. Birch, J.M., W.B Dickson, and M.H. Dickinson. 2004. Force production and flow structure of the leading edge vortex on flapping wings at high and low Reynolds numbers. J. Experimental Biology 207: 1063-1072. Wang, Z.J., J.M. Birch, and M.H. Dickinson. 2004. Unsteady forces and flows in low Reynolds numbers hovering flight: two dimensional computations vs. robotic wing experiments. J. Experimental Biology 207: 449-460. Birch, J.M. and M.H. Dickinson. 2003. The influence of wing-wake interactions on the production of aerodynamic forces in flapping flight. J. Experimental Biology, 206:2257-2272. Myers, J.J., A. Herrel, and J.M. Birch. 2002. Scaling of morphology, bite force, and feeding kinematics in an iguanian and a scleroglossan lizard. In: Topics in Functional and Ecological Vertebrate Morphology. P. Aerts, K. D’Août, A. Herrel, and R. Van Damme, (eds.), pp. 47-62. Maastricht: Shaker Publishing. Yan, J., S.A Avadhanula, M.H. Dickinson, J.M. Birch, M. Sitti, T. Su, and R.S. Fearing. 2002. Wing transmission for a micromechanical flying insect. J. of Micromechatronics, 1 (3): 221-37. J. Yan, S.Avadhanula, J. Birch, M.H. Dickinson, M. Menon, E. Park, T.D. Sands, S.Sane, M. Sitti, T. Su, R.J. Wood, and R.S. Fearing. The Micromechanical Flying Insect. Video Proc. of IEEE Intl. Conf. on Robotics and Automation, Washington, D.C., May 11-15, 2002. (Co-winner Best Video Award) Birch, J.M. and M.H. Dickinson. 2001. Spanwise flow and the attachment of the leading-edge vortex on insect wings. Nature, 412:729-733. Mallett, E.S., G.T. Yamaguchi, J.M. Birch, and K.C. Nishikawa. 2001. Feeding motor patterns in anurans: Insights from biomechanical modeling. American Zoologist 41:1364-1374. SELECTED PRESENTATIONS Birch, J., C. Preston, D. Pargett, S. Jensen, B. Roman, C. Everlove, R. Marin III, V. Orphan, P. Girguis, C. Scholin. Searching for microbes in deep-sea and hydrothermal vents using the Environmental Sample Processor. Astrobiology Science Conference, League City, TX, May 26-29, 2010. Birch, J. Innovative ocean monitoring; the ESP as a persistent presence in the ocean. Arizona State University, School of Engineering, Tempe, AZ March 10, 2010. Scholin, C. and J. Birch. Development of ecogenomic sensors for use with coastal and global ocean observatories. Ocean Sciences, Portland, OR. February 22-26, 2010. Birch, J., C. Preston, A. Harris, R. Marin III, S. Jensen, B. Roman, C. Everlove, C. Scholin. Detecting and identifying microbial communities with a remote, in situ sensor, the Environmental Sample Processor. Advancing the Science of Limnology and Oceanography, ASLO, Nice France, January 26-30, 2009. Sherman, A.D., P. McGill, B. Hobson, R. Henthorn, A. Chase, and K. Smith. Rover: a mobile platform for long-term deep ocean ecological research. Ocean Sciences, March 2-7, 2008, Orlando, FL. Presented for A. Sherman. ABSTRACTS / OTHERS Scholin, C., C. Preston, A. Harris, J. Birch, R. Marin III, S. Jensen, B. Roman, C. Everlove, A. Makarewicz, J. Dzenitis, V. Riot, D. Headley. Development of Ecogenomic sensors for remote detection of marine microbes, their genes and gene products. American Geophysical Union, San Francisco, CA, December 15-19, 2008. Preston, C., C. Scholin, S. Jensen, B. Roman, R. Marin III, D. Pargett, J. Birch, A. Harris J. Dzenitis, C. Frendl, M. Parker, C. Everlove. Near real-time detection of marine bacterioplankton with an autonomous robotic device, the Environmental Sample Processor. American Society for Microbiology, Boston, MA, June 1-5, 2008. Birch, J., R. Mahnke, S. Letant, R. Derlet, S. Cohen, D. Manning, M. McBride. A multiplexed diagnostic platform for Point-of- Care Pathogen detection. Improving health care accessibility through Point-of-Care technologies, NIH/NSF, Arlington, VA, April 11-12, 2006 (poster). Slezak, T., J. Birch, R. Derlet, M. McBride. Rapid Prototype detection technologies for emerging and engineered pathogens. DOD BioMarker Conference, Fairborn, Ohio, March 28-29, 2006. Birch, J., M. McBride, J. Ortiz, L. Tammero, R. Derlet, S. Cohen. A Multiplexed diagnostic platform for point-of-care pathogen detection. Biosecurity Science and Technology Directorate Review Committee, LLNL, November 14, 2005 (poster). Frank M., J. Birch, A. Srivastava, P. Steele, K. Coffee, D. Fergenson, H. Tobias, M. Pitesky, V. Riot, S. Martin, E. Gard, C. Lebrilla, G. Czerwieniec, S. Russell,and E. McJimpsey. Real-time characterization of individual bioaerosol particles with bioaerosol mass spectrometry. Annual Conference of the German Mass Spectrometry Society (DGMS), Rostock, Germany, March 7-9, 2005 Frank M.A., E. E. Gard, D. P. Fergenson, M. Pitesky, H. J. Tobias, P. T. Steele, A. Srivastava, K. Coffee, J. M. Birch, J. M. Horn, C. B. Lebrilla, G. Czerwieniec, S. Russell. SPIE, Optics and Photonics in Global Homeland Security.
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