Download Bagby CV website - Valentine Lab - University of California, Santa

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