The most exciting phrase to hear in science, the one that heralds new discoveries, is not 'Eureka!' but 'That's funny...' --Isaac Asimov
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Curriculum Vitae


R. ERIC COLLINS, PH.D.

Earth and Planetary Sciences, Room 304
McGill University, Montréal, QC, CANADA



EDUCATION AND RESEARCH EXPERIENCE


Postdoctoral Fellow in Astrobiology, McMaster University (November 2009-Present)

  • Early Earth Genomics: I study the evolution of microbes by comparative genomics and mathematical modeling. One such project involves modeling the duplication, deletion, and invention of gene families in Bacteria and Archaea, with the end goal being better constraints on the rates of gene invention versus horizontal gene transfer. Another project uses an infinitely-many-genes model of neutral evolution to predict the sizes of the core and pan-genomes of bacteria. Additional field- and wet-lab-based projects include isolating toluene-degrading halophilic bacteria from saline lakes to investigate the distribution of plasmids associated with BTEX degradation and using bioinformatics to detect genes specifically associated with sulfur isotope fractionation by sulfate reducing bacteria. PIs: Dr. Paul Higgs (McMaster), Dr. Greg Slater (McMaster), Dr. Boswell Wing (McGill)


Ph.D. Biological Oceanography, University of Washington (September 2009)

  • Microbial Evolution In Sea Ice–Communities To Genes: I investigated the diversity of Bacterial and Archaeal communities in winter sea ice utilizing web-enabled software I wrote for the project. I found Archaea and Bacteria from seawater persisted through the winter season with no change in richness and limited changes in the structure of either community. During the Circumpolar Flaw Lead Systems Study I measured the abundances of viruses, bacteria, and dissolved DNA in newly formed sea ice to explore the potential for horizontal gene transfer there. Genomics analyses of the psychrophilic bacterium Colwellia psychrerythraea strain 34H revealed evidence of horizontal gene transfer of a genomic island involved in compatible solute degradation. Advisor: Dr. Jody W. Deming


Certificate in Astrobiology, University of Washington (2009)

  • In vitro microsensor measurements of AOM: I used microsensors to measure the rate of anaerobic oxidation of methane (AOM) in microbial mats from the Black Sea. Advisors: Dr. Dirk de Beer (MPI-Bremen), Dr. Antje Boetius (MPI-Bremen)


M.S. Biological Oceanography, University of Washington (2006)

  • Microbial persistence over an Arctic winter season: I investigated the abundances of bacteria, particles, and particulate extracellular polymeric substances (pEPS) in Arctic winter sea ice during the Canadian Arctic Shelf Exchange study. I observed a significant decline in microbial abundance in the coldest ice, a significant production of pEPS was also detected in all of the ice measured, implying microbial activity in winter sea ice. Advisor: Dr. Jody W. Deming


B.S. Biochemistry with Honors, Washington State University (2002)


PEER-REVIEWED PUBLICATIONS



  • Collins RE, Deming JW (2011) Abundant dissolved genetic material in Arctic sea ice, Part I: Extracellular DNA. Polar Biology

  • Collins RE, Deming JW (2011) Abundant dissolved genetic material in Arctic sea ice, Part II: Viral dynamics during autumn freeze-up. Polar Biology

  • Miller LA, Papakyriakou TN, Collins RE, Deming JW, Ehn, JK, Macdonald RW, Mucci A, Owens O, Raudsepp M, and N Sutherland (2011) Carbon dynamics in sea ice: A winter flux time series. Journal of Geophysical Research 116:C02028. doi:10.1029/2009JC006058

  • Collins RE, Rocap G, Deming JW (2010) Persistence of bacterial and archaeal communities in sea ice through an Arctic winter. Environmental Microbiology 7:1828-1841. Open Access. doi:10.1111/j.1462-2920.2010.02179.x

  • Collins RE, Carpenter S, Deming JW (2008) Spatial and temporal dynamics of particles, bacteria, and extracellular polymeric substances in Arctic winter sea ice. Journal of Marine Systems 74:902-917. doi:10.1016/j.jmarsys.2007.09.005.

  • Collins RE, Rocap G (2007) REPK: an analytical web server to select restriction endonucleases for terminal restriction fragment length polymorphism analysis. Nucleic Acids Research 35 (Database issue): W58-W62. Open Access. doi:10.1093/nar/gkm384

  • Ehlmann BL, Chowdhury J, Marzullo TC, Collins RE, Litzenberger J, Ibsen S, Krauser WR, DeKock B, Hannon M, Kinnevan J, Shepard R, Grant FD (2005) Humans to Mars: a feasibility and cost-benefit analysis. Acta Astronautica 56:851.

  • Costa MA, Collins RE, Anterola AM, Cochrane FC, Davin LB, Lewis NG (2003) An in silico assessment of gene function and organization of the phenylpropanoid pathway metabolic networks in Arabidopsis thaliana and limitations thereof. Phytochemistry 64:1097-1112.



FORTHCOMING MANUSCRIPTS



  • Collins RE, Hughes M, Higgs PA (submitted) Origin and Evolution of Gene Families in Bacteria and Archaea. For submission to BMC Bioinformatics

  • Collins RE, Higgs PA (in preparation) Comparing Models of the Bacterial Pangenome

  • Collins RE, Deming JW (in preparation) Horizontal transfer of a genomic island encoding the degradation of sarcosine in Colwellia psychrerythraea strain 34H.

  • Fuchsman CA, Brazelton WJ, Collins RE, Horner-Devine MC, Rocap G (in preparation) Vertical descent or lateral transfer? Unravelling the large number of whole-genome reciprocal BLAST hits between anaerobic, thermophilic Bacteria and Archaea.



SELECTED PRESENTATIONS



  • Collins RE and JW Deming (2010) Microbial evolution and the potential for horizontal gene transfer in sea ice. IPY Science Conference, Oslo, Norway. Speaker.

  • Collins RE (2010) Proposal for an education and public outreach curriculum linking polar climate change and astrobiology. IPY Science Conference, Oslo, Norway. Poster.

  • Collins RE (2010) Astrobiology and Bioinformatics: Past, Present, and Future. McGill University, Montreal, Canada. Speaker.

  • Collins RE (2010) Astrobiology and Bioinformatics. Computational Astrobiology Summer School, Honolulu, Hawaii. Speaker.

  • Collins RE, Merz H, and P Higgs (2010) Modeling Microbial Genome Evolution. Sharcnet Research Conference. York University, Toronto, Canada. Poster.

  • Collins RE and JW Deming (2008) Icy Evolution: Lateral gene transfer in the Arctic? Polar and Alpine Microbiology Meeting, Banff, Alberta, Canada. Speaker.

  • Anderson RA, Brazelton WJ, Collins RE, Ewert Sarmiento M, Fuchsman CA, Goldman AD, Harnmeijer JP, Lin M, Opatkiewicz AD, Som SM, and E Stueeken (2008) A course in the origin of life as a model for meeting the goals of an astrobiology curriculum. Astrobiology Science Conference, Santa Clara, California. Poster.

  • Som S, Collins RE, Schreiber BC, Montgomery DR (2008) Salts on Mars: New perspectives in planetary geomorphology and astrobiological implications. 59th International Astronautical Congress, Paper IAC-08-A1.6.12, Glasgow, Scotland. Paper.

  • Fuchsman CA, Brazelton WJ, Collins RE, Horner-Devine MC, Rocap G (2007) Vertical descent or lateral transfer? Unravelling the large number of whole-genome reciprocal BLAST hits between anaerobic, thermophilic Bacteria and Archaea. American Society for Microbiology General Meeting, Toronto, Canada. Poster.

  • Collins RE and JW Deming (2007) Lateral gene transfer in Arctic sea ice? Polar Marine Science Gordon Research Conference, Ventura, California. Poster.

  • Collins RE and JW Deming (2006) Persistence of Archaea in sea ice. Astrobiology 6: 174-221. doi:10.1089/ast.2006.6.174. Astrobiology Science Conference, Washington, DC. Poster.

  • Collins RE and JW Deming (2006) Archaea in Arctic Winter Sea Ice. American Society for Microbiology Northwest Meeting, Seattle, Washington. Speaker.

  • Collins RE and JW Deming (2004) Potential changes in sea-ice microbial community composition during an Arctic winter. International Conference on Arctic Microbiology, Rovaniemi, Finland. Poster.



TEACHING EXPERIENCE



  • Winter 2011:
    Environmental Genomics Workshop: Designed and delivered two-day workshops on Web-Enabled Environmental Genomics and Metagenomics at McGill University in Montreal, Canada. Course participants included 16 students, postdocs, and faculty from microbiology, geochemistry, and oceanography. Course wiki: http://openwetware.org/wiki/User:R._Eric_Collins/GenomicsTutorial

  • 2010-2011:
    Astrobiology Journal Club: Organizer of a bi-weekly meeting of interested undergraduates, graduate students, postdocs and faculty members on topics as diverse as the bioenergetic control of microbial genome size to the presence of methane on Mars. Guest lecturer in `Life in the Universe’ course.

  • Autumn 2008:
    Oceanography 430: Senior undergraduate core course in Biological Oceanography. Teaching Assistantship. Led weekly review sessions and gave lectures. Assisted in adaptation of curriculum towards discovery-based learning approaches.

  • Winter/Spring 2008:
    Oceanography 443/444: Senior undergraduate thesis course. Teaching Assistantship. Mentored students in the development and execution of individual research projects which were then carried out aboard the R/V Thomas G. Thompson in March 2008.

  • Spring 2007:
    Communicating Ocean Sciences outreach course. Constructed and presented pre-planned kits for science outreach to 2nd grade classroom, then designed, constructed, presented, and evaluated implementation of a new kit with a team member.

  • Autumn 2005:
    Astrobiology Exchange Workshop at Friday Harbor Labs. Assisted in planning and execution of 4-day hands-on scientific workshop involving 20 students and faculty from the Astrobiology programs at the University of Washington and the University of Arizona.

  • Spring 2004:
    Oceanography 101: Introduction to Oceanography for non-majors. Teaching Assistantship. Lectured and taught 3 lab sections of 15 students each, culminating in a research cruise in Puget Sound.



PROFESSIONAL SERVICE



  • Referee for quality journals in polar and marine microbiology: Environmental Microbiology, Marine Ecology Progress Series, Polar Biology, Aquatic Sciences

  • Organizer of the Association of Polar Early Career Scientists (APECS) Polar Microbial Ecology Research Group

  • Science Judge for the Women in Science and Engineering Conference (2010-2011)

  • Graduate student representative to the UW Oceanography Faculty Search Committee (2008)

  • Graduate student representative to the UW Astrobiology Steering Group (2006)

  • Interviewer for NASA Academy Selection Panel



FIELD EXPERIENCE



  • I’ve spent more than 20 weeks in the field for various projects–most were in the Arctic or other cold regions, including 3 months in the Northwest Territories during fall and winter, and several weeks in Barrow, Alaska and Hokkaido, Japan during winter.

  • Autumn 2007: Six-week cruise in the Beaufort Sea aboard the CCGS Amundsen as part of the Circumpolar Flaw Lead Systems Study(CFL). Conducted measurements on bacterial abundance, viral abundance, extracellular polymeric substances (EPS), dissolved DNA, suspended particulate matter (SPM), chlorophyll a, particulate organic carbon (POC), particulate nitrogen (PN), sea ice temperature and salinity, and sea ice microstructure.

  • Winter 2004: Six-week overwintering cruise in Franklin Bay, Northwest Territories aboard the CCGS Amundsen as part of the Canadian Arctic Shelf Exchange Study (CASES). Conducted measurements on bacterial abundance, EPS, bacterial and archaeal diversity (16S rRNA gene sequencing), bacterial and archaeal community structure (T-RFLP of 16S rRNA gene), fluorescence in situ hybridization (FISH), and sea ice temperature and salinity.

  • Winter 2006: Two-week sea ice field course in Hokkaido, Japan through the University of Alaska-Fairbanks. Conducted measurements of ice algal abundance and preliminary identification, and pulse amplitude modulation (PAM) fluorometry of ice algal communities in Saroma-ko lagoon.

  • Summer 2003: Two-week cruise in the Chukchi Sea on the R/V Xuelong with the Chinese National Arctic/Antarctic Research Expedition (CHINARE) program. Conducted measurements of bacterial abundance and EPS, and isolated marine bacteria using environmental-shock approach.

  • Spring 2008: Two-week cruise to Glacier Bay National Park, Alaska, aboard the R/V Thomas G. Thompson while TA’ing the UW Oceanography Senior Thesis course. Sampled glacier and lake ice for student projects involving microbial diversity in Glacier Bay. Operated standard oceanographic instruments including the CTD-rosette, Niskin bottles, GO-FLO bottles, and plankton nets.

  • Winter 2003: One-week workshop with the NASA Astrobiology Institute Europa Focus Group in Barrow, Alaska.

  • Spring 2004: One week of daily student cruises in Puget Sound aboard the R/V Barnes while TA’ing Oceanography 101. Operated standard oceanographic instruments including the CTD-rosette, Niskin bottles, secchi disc, and plankton nets.

  • Summer 2007: Multiple one-day student cruises with the Ocean Inquiry Project in Puget Sound, Washington. Operated standard oceanographic instruments including the CTD-rosette, secchi disc, and plankton nets.

  • Autumn 2002-2009: UW Astrobiology Workshops at Easton Glacier on Mt. Baker, the Mojave Desert Research Station, Mount St. Helens, San Juan Islands, Yellowstone National Park, University of Arizona Kitt Peak Observatory, and the Channeled Scablands.

  • Summer 2010: One week of sampling at the Pavilion Lake Research Station in British Columbia for the MARSLIFE project, aimed at detecting nucleic acids in small samples as analogs to searches for life on other planets.



COMPUTATIONAL PROFICIENCIES



  • Bioinformatics and Statistics: R, PRIMER-E, Matlab, blast, mcl, BioPerl, Galaxy, KEGG, IMG, CAMERA, PAUP*, ARB, PHYLIP, MrBayes, fastDNAml, MAFFT, MUSCLE

  • General: Perl, C++, Javascript, PHP, HTML, XML, LATEX, MySQL, Linux sysadmin, high-performance computing on large datasets

  • Web-accessible Software Products
    Two web-accessible programs were written to aid in fingerprinting analyses of complex microbial communities, gaining frequent use both within the Center for Environmental Genomics and by external users.

    REPK: http://rocaplab.ocean.washington.edu/tools/repk [150 runs/month]

    Dakster: http://rocaplab.ocean.washington.edu/cgi/dakster/index.html

    Two interactive web-accessible databases were engineered to facilitate data-sharing both among scientists and between scientists and the public. The Lab Sampling Database will make information about my sampling efforts easily accessible to the public and to other scientists with whom collaborations might be initiated.

    Deming Lab Sampling Database: http://reric.org/deminglab

    Seattle Crow Project: http://depts.washington.edu/uwcrows [1500 visitors/yr]




PUBLIC OUTREACH



  • I consider science outreach an important part of my scientific development and have volunteered my time to a variety of outreach activities, including dozens of hours giving demonstrations at Polar Science Weekend at the Seattle Science Center, the annual School of Oceanography Open House, inside K-6 classrooms, and at sea with the Ocean Inquiry Project. I am currently co-mentoring two `at-risk’ high school students conducting a science fair project on isolating halophilic BTEX-degrading bacteria. In partnership with the Centers for Ocean Sciences Educational Excellence-Ocean Learning Communities (COSEE-OLC), a fellow student and I designed and implemented an ocean sciences curriculum with a local grade school teacher, and I participated in workshops to improve my ability to communicate with citizen scientists, a goal shared by another project I developed to allow engaged amateurs to report and track crows banded by Dr. John Marzluff in the College of Forest Resources at the University of Washington. I have also written articles and shared photographs for publication in non-technical science forums, one of which was subsequently translated and published in Catalan.