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Sarah Catherine Bagby Department of Earth Sciences / Marine Science Institute University of California–Santa Barbara Santa Barbara, CA 93106 [email protected] http://methane.geol.ucsb.edu/Sarah_Bagby.html I use field, lab, and computational methods to study the co-evolution of microbes and the Earth system: how the physical and chemical environment shapes microbial metabolic innovations, and how those innovations spread across communities and feed back into global processes. Education 2002–2009 PhD, Biology Massachusetts Institute of Technology Funded by grants from • Howard Hughes Medical Institute Pre-doctoral Fellowship Program (to SC Bagby) • NIH Pre-doctoral Training Grant Program (to the MIT Department of Biology) Additional funding from the NSF Graduate Research Fellowship Program was awarded (to SC Bagby) but could not be accepted in conjunction with the HHMI fellowship. 2000–2002 BA(Hons), Physiological Sciences Corpus Christi College, Oxford University Funded by the Marshall Scholarship (to SC Bagby) 1996–2000 BS, Biological Chemistry (special honors); BA, Chemistry; BA, Philosophy University of Chicago Funded in part by the Goldwater Scholarship (to SC Bagby) Research experience 2009–present Postdoctoral research in the laboratory of Dr. David L. Valentine, UCSB Studies of microbial hydrocarbon degradation in marine environments. • Modeled oil deposition and biodegradation following the Deepwater Horizon disaster • Designed novel ROV-deployable equipment for in situ stable-isotope probing of microbial and viral communities at seafloor methane seeps • Contributed to discovery of the first archaeal instances of diversitygenerating retroelements • Analyzed lipid and phylogenetic profiles of methanotrophic microbial mats Funded by grants from NSF Dimensions of Biodiversity (to DL Valentine; SC Bagby, named collaborator); Gordon and Betty Moore Foundation Marine Microbiology Initiative (to VJ Orphan); UCSB (to SC Bagby); Simons Foundation (to DL Valentine). Bagby CV - 2 2006–2009 Graduate research in the laboratory of Dr. Sallie W. Chisholm, MIT Studies of the globally important cyanobacterium Prochlorococcus. • Measured physiological responses to varying CO2 and O2 levels • Analyzed expression dynamics of a novel component of the carbonconcentrating mechanism • Tracked expression of phage genes related to light harvesting and photoprotection during infection Funded by grants from Gordon and Betty Moore Foundation Marine Microbiology Initiative (to SW Chisholm); MIT Energy Initiative (to SW Chisholm); Howard Hughes Medical Institute Pre-doctoral Fellowship Program (to SC Bagby). 2003–2006 Graduate research in the laboratory of Dr. David P. Bartel, MIT Studies of an in vitro–evolved ribozyme, the class I ligase. • Mapped functional groups essential for RNA catalysis • Designed and performed random permutation resampling analysis of kinetic data to detect sequence variants affecting enzyme efficiency Funded by grants from NIH (to DP Bartel); Howard Hughes Medical Institute (to DP Bartel); Howard Hughes Medical Institute Pre-doctoral Fellowship Program (to SC Bagby). 2001–2002 BA thesis research in the laboratory of Dr. James M. McDonnell, Oxford University Statistical study of receptor binding interactions in allergy and asthma. • Analyzed thermodynamic and kinetic data for a suite of mutants to identify structural features contributing to pathologically tight binding. Funded by grants from UK Medical Research Council (to B Sutton, H Gould, and JM McDonnell); UK Marshall Aid Commemoration Commission (Marshall Scholarship, to SC Bagby). 1998–2000 BA thesis research in the laboratory of Dr. Phoebe A. Rice, University of Chicago Experimental study of a cyanobacterial protein–DNA complex. • Developed crystallization conditions • Collected and analyzed x-ray data Funded by a grant from the NIH (to PA Rice). Teaching experience 2005, 2003 Teaching assistant, Graduate Biochemistry (7.51), MIT 1999 Teaching assistant, Biochemistry (Biology 201), University of Chicago 1998 Teaching assistant, Cell Biology (Biology 193), University of Chicago Field experience Bagby CV - 3 2013 Lead scientist for ROV Jason lowerings J2-735 and J2-736 during the SEEPS ’13 cruise (R/V Atlantis Leg 26-06) • Directed pilots’ use of novel equipment to inject tracer into microbial incubators in situ • Led a team of 12 postdoctoral scientists, graduate students, and undergraduates to sample a large push-core library for geochemical and biological analyses 2012 Participant, UNOLS Chief Scientist Training Cruise (R/V New Horizon Leg NH1212) • Collected multi-core samples to test storage and DNA extraction methods for Santa Monica Basin sediments 2011 Lead scientist for ROV Jason lowerings J2-599 and J2-600 during SEEPS ’11 cruise (R/V Atlantis Leg 18-11) • Directed pilots’ deployment of novel incubators at two study sites • Led the collection and processing of a library of push-cores for geochemical and biological analyses 2009 Junior scientist for DSV Alvin dive 4542 (depth 3470 m) during SEEPS '09 cruise (R/V Atlantis Leg 15-53) • Explored a potential hydrocarbon seep site • Coordinated analysis of imaging data collected by AUV Sentry to inform choice of dive targets for DSV Alvin 2006 Participant, Hawaii Ocean Time-Series (HOT) cruise (R/V Kilo Moana HOT-186) • Assisted in collection and handling of water-column samples for bacterial and viral metagenomics Publications SC Bagby and SW Chisholm (2015). Response of Prochlorococcus to varying CO2:O2 ratios. ISME J (epub ahead of print). DOI: 10.1038/ismej.2015.36 BG Paul, SC Bagby, E Czornyj, D Arambula, S Handa, A Sczyrba, P Ghosh, JF Miller, and DL Valentine (2015). Targeted diversity generation by intraterrestrial archaea and archaeal viruses. Nature Comm 6:6585. DOI: 10.1038/ncomms7585 SE Hampton, SS Anderson, SC Bagby, C Gries, X Han, EM Hart, MB Jones, WC Lenhardt, A MacDonald, WK Michener, J Mudge, A Pourmokhtarian, M Schildhauer, KH Woo, and N Zimmerman (2014). The tao of open science for ecology. Ecosphere 6:art120. DOI: 10.1890/ ES14-00402.1 DL Valentine, GB Fisher, SC Bagby, RK Nelson, CM Reddy, SP Sylva, and MA Woo (2014). A fallout plume of submerged oil from Deepwater Horizon. PNAS 111:15906. Bagby CV - 4 MD Holdom, AM Davies, JE Nettleship, SC Bagby, B Dhaliwal, E Girardi, J Hunt, HJ Gould, AJ Beavil, JM McDonnell, RJ Owens, and BJ Sutton (2011). Conformational changes in IgE contribute to its uniquely slow dissociation rate from receptor FcεRI. Nature Struct Mol Biol 18:571. DL Valentine, CM Reddy, C Farwell, TM Hill, O Pizarro, DR Yoerger, R Camilli, RK Nelson, E Peacock, SC Bagby, BA Clark, CN Roman, and M Soloway (2010). Asphalt volcanoes as a potential source of methane to late Pleistocene coastal waters. Nature Geosci 3:345. SC Bagby,* NH Bergman,* DM Shechner, C Yen, and DP Bartel (2009). A class I ligase ribozyme with reduced Mg2+ dependence: selection, sequence analysis, and tertiarystructure mapping. RNA 15:2129. (*joint first authors) DM Shechner, SC Bagby, R Grant, Y Koldobskaya, J Piccirilli, and DP Bartel (2009). Crystal structure of the catalytic core of an RNA-polymerase ribozyme. Science 326:1271. M Klein, P Zwart, SC Bagby, F Cai, SW Chisholm, S Heinhorst, G Cannon, and CA Kerfeld (2009). Identification and structural analysis of a novel carboxysome shell protein with implications for metabolite transport. J Mol Biol 392(2):319. Dammeyer, TD, SC Bagby, MB Sullivan, SW Chisholm, and N Frankenberg-Dinkel (2008). Efficient phage-mediated pigment biosynthesis in oceanic cyanobacteria. Curr Biol 18(6): 442. Manuscripts in preparation DL Valentine,* SC Bagby,* CM Reddy, C Aeppli, and GB Fisher. Persistence and biodegradation of oil at the ocean floor following Deepwater Horizon. (*joint first authors) SC Bagby and DL Valentine. An improved method of robust regression on order statistics for interval-censored data. BG Paul, H Ding, SC Bagby, M Kellermann, MC Redmond, GL Andersen, and DL Valentine. Methane-oxidizing bacteria shunt carbon to microbial mats at a marine hydrocarbon seep. Heintz, MB, JW Pohlman, SC Bagby, MJ Wooller, M Elvert, C Ruppel, and DL Valentine. Enhanced methane consumption in ice-covered arctic lakes. Meeting participation (selected) American Geophysical Union Fall Meeting, San Francisco, CA, 15–19 December 2014. Poster presentation: SC Bagby, GB Fisher, CM Reddy, and DL Valentine. Deposition and biodegradation of submerged oil from the Deepwater Horizon. Bagby CV - 5 Open Science Codefest, Santa Barbara, CA, 2–4 September 2014. ‘Unconference’ contributions: • Discussion of use cases and R package design for provenance-tracking in data analysis and for standardizing distribution of datasets as R packages • Discussion, writing, and collaborative editing of an opinion piece on adoption of ‘open science’ practices, subsequently published in Ecosphere (Hampton et al., 2014) UNOLS Council Meeting, Early Career Program, Washington, DC, 12 March 2014. Gordon and Betty Moore Foundation Marine Microbiology Initiative Research Associate and Postdoctoral Scholar Summit. San Juan, Puerto Rico, 2–6 February 2014. Poster presentation: SC Bagby, KL Lemkau, D Alden, and DL Valentine. Novel seafloor sediment samplers permit in situ and near–in situ experimental manipulations of gas phase composition and pressure. American Geophysical Union Fall Meeting, San Francisco, CA, 9–13 December 2013. Oral presentation: BG Paul, SC Bagby, and DL Valentine. Reverse transcriptase directs viral evolution in a deep ocean methane seep. Applied and Environmental Microbiology Gordon Research Conference, South Hadley, MA, 10–15 July 2011. Poster presentation: SC Bagby, BG Paul, SD Quistad, and DL Valentine. Isotope probing of hosts permits guild-targeted viral metagenomics in methanotrophic sediment communities. Molecular Basis of Microbial One-Carbon Metabolism Gordon Research Conference, Lewiston, ME, 1–6 August 2010. Poster presentation: SC Bagby and SW Chisholm. Effects of CO2:O2 balance on growth and global transcription patterns in Prochlorococcus. Service 2009–present Peer reviewer for Nature Communications, Environmental Science & Technology, Journal of Phycology, Aquatic Microbial Ecology, Limnology & Oceanography, and the National Science Foundation 2009–present Marshall Scholarship selection committee, UK Marshall Aid Commemoration Commission, Southern California region Chair, 2013–present; member, 2009–2012 Analyzed and reported on the record of gender equity in selection of Marshall Scholars, prompting an ongoing re-evaluation of the selection process to address issues of gender, racial, and socioeconomic diversity. 2008 Co-organizer, Path of Professorship workshop for MIT graduate and postdoctoral women in science 2004–2006 Graduate student member, MIT Foreign Scholarships Committee