Lab Members

Picture of Natasha Talago (Bonilla)
  • Natasha Talago (Bonilla)
  • natasha.science@gmail.com
  • Area of Study: Mucosal Immunology, Phage, Microbiology
  • Interests: My area of expertise used to be in environmental microbiology, but now I'm currently obsessed in trying to identify novel phage-mediated immune responses. As hobbies I like to do art & craft, painting, cooking Puerto Rican dishes, exercise, biking and hiking with my kids : )
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    EDUCATION
    San Diego State Univesity, San Diego, California
    Master of Science in Microbiology
    Expected May 2015

    University of Puerto Rico, Rio Piedras, Puerto Rico
    Bachelor of Science in Biology
    June 2011

    Colegio La Piedad High School, Isla Verde, Carolina,  Puerto Rico
    High School Diploma
    May 2006

    PROFESSIONAL EXPERIENCE
    University of Puerto Rico, Rio Piedras Campus – San Juan, PR
    June 2008 – June 2011

    -Environmental Sample collection and water analysis specialist
    -Environmental Microbiology Laboratory instructor and supervisor of undergraduate students
    -Microbe World Podcasts (‘’El mundo de los microbios’’) Spanish speaker for the American Society for Microbiology (ASM) webpage

    San Diego State University, Main Campus – San Diego, CA, June 2012 – Present
    Bacteriophage and mucosal immune system

    Procedures and Techniques:
    Aseptic techniques, sterilization  and bacteriology procedures
    Characterization and detection of microbial indicators of fecal contamination
    Detection of antibiotic resistant genes and virulence factors in bacteriophages
    Preparation of lab reagents and ordering lab chemicals/supplies
    DNA extraction, purification and quantification
    PCR and gel electrophoresis
    Biochemical and physiological identification methods for methicillin-resistant Staphylococcus aureus (MRSA)
    Epifluorescent microscopy of bacteria and viruses
    Tissue culture
    Protein extraction, precipitation and purification

    RESEARCH EXPERIENCE
    San Diego State University – San Diego, CA, June 2012 – Present
    Graduate student in the Rohwer Lab and Teaching Assistant (TA) in Microbiology

    University of Puerto Rico, Rio Piedras Campus – San Juan, PR
    BS student and assistant in the Environmental Microbiology Laboratory
    May 2008 - June 2011

    University of Washington – Seattle, WA
    Environmental Health Research Experience Program (EH REP)
    Summer 2010


    PUBLICATIONS IN PEER-REVIEWED JOURNALS
    N. Bonilla, T. Santiago, P. Marcos, M. Urdaneta, J. Santo Domingo and Gary Toranzos.  2010. Enterophages, a group of phages infecting Enterococcus faecalis and their potential as alternate indicators of human fecal contamination. 2010. Water Science and Technology.  61:293-300.

    Tasha M. Santiago-Rodríguez, Catalina Dávila, Joel González, Natasha Bonilla, Patricia Marcos,, Miguel Urdaneta, Manuela Cadete, Sílvia Monteiro, Ricardo Santos, Jorge Santo Domingo and Gary A. Toranzos.  2010.  Characterization of Enterococcus faecalis-infecting phages (enterophages) as markers of human fecal pollution in recreational waters.  Water Research. 44:4716-4725.

    Emily Levin-Edens, Natasha Bonilla, J. Scott Mescke and  Marilyn C. Roberts. 2011. Survival of environmental and clinical strains of methicillin-resistant Staphylococcus aureus (MRSA) in marine and fresh waters. Water Research. 45:5681-5686.

    PRESENTATIONS IN LOCAL, NATIONAL, AND INTERNATIONAL CONFERENCES

    Poster presentations:
    Natasha Bonilla, Tasha Santiago, Patricia Marcos, Ricardo Santos, Silvia Monteiro, Miguel Urdaneta and Gary A. Toranzos. Developing methods for the detection of Enterococcus faecalis-infecting phages (Enterophages) as Microbial Indicators of Water Contamination at the 29th Puerto Rico Interdisciplinary Scientific Meeting / 44th Junior Technical Meeting (December, 2008)

    Natasha Bonilla, Tasha Santiago, Patricia Marcos, Ricardo Santos, Silvia Monteiro, Miguel Urdaneta and Gary A. Toranzos. Ecology and prevalence of a novel group of viruses infecting Enterococcus faecalis at PRMS Semiannual Convention (December 2009) and ABRCMS (November 2009).

    Catalina Dávila, Tasha Santiago, Natasha Bonilla, Miguel Urdaneta, Joel Gonzalez, Carlos Toledo, Patricia Marcos, Manuela Cadete, Ricardo Santos, Silvia Monteiroand Gary Toranzos. Prevalence, survival and characterization of enterophages at the Water Research Conference, Portugal (April 2010).

    T. M. Santiago-Rodríguez, C. Dávila, J. González, N. Bonilla, P. Marcos, M. Urdaneta, M. Cadete, S. Monteiro, R. Santo, J. Santo Domingo and G.A. Toranzos. Enterococcus faecalis-infecting phages: their characterization as markers of human fecal pollution in recreational waters at Viruses of Microbes Conference, Institute Pasteur, France (June 2010).

    Natasha Bonilla, Emily Levin-Edens and Marilyn C. Roberts. Survival of clinical and environmental strains of methicillin-resistant Staphylococcus aureus (MRSA) in marine waters at University of Washington Summer Undergraduate Research Poster Session, Seattle (August 2010) and ABRCMS (November 2010).

    Natasha Bonilla, Jessica Rivera, Jean M. Carraquillo, Marilyn C. Roberts and Gary A. Toranzos. Prevalence of Methicillin-resistant Staphylococcus aureus (MRSA) in Tropical Marine, Fresh and Sewage Waters at EPA’s National Beach Conference, Miami, Florida (March 2011).

    Emily Levin-Edens, Natasha Bonilla, J. Scott Meschke and Marilyn C. Roberts. Survival of methicillin-resistant Staphylococcus aureus [MRSA] in Pacific Northwest marine and fresh water at ASM General Meeting, New Orleans, LA (May 2011).

    Jessica Rivera, Natasha Bonilla, Jean M. Carrasquillo, Mariel Coradin, Tasha Santiago, Marilyn C. Roberts and Gary A. Toranzos. Prevalence of Methicillin-resistance genes and Methicillin-resistant Staphylococcus aureus (MRSA) in tropical recreational waters and sewage in the 16th International Health-Related Water Microbiology at Rotorua, New Zealand (September, 2011).

    Talago (Bonilla), N., Rohwer, F. and Barr, J. The interaction of bacteriophage with the human mucosal immune system at the SDSU 2013 Cell Molecular Biology Graduate Student Symposium (April 2013).

    Oral presentations:
    Bonilla, N., C. Dávila,  J. Cuevas, P. Marcos, J. Rosado, D. Vargas, A. Silva and G.A., Toranzos. Prevalence of enterophages as indicators of fecal water contamination in tropical waters at 29th Puerto Rico Interdisciplinary Scientific Meeting / 44th Junior Technical Meeting

    Bonilla, N.  Fecal contamination on El Balneario de Carolina in Alliance for the Teaching in Science and Math at University of Puerto Rico, Rio Piedras Campus (Summer 2008).

    Bonilla, N., T. Santiago, C. Dávila,  J. Cuevas, P. Marcos, J. Rosado, M. Urdaneta and G.A., Toranzos.  Enterophages, a group of phages infecting Enterococcus faecalis and their potential as alternate indicators of human fecal contamination in the 15th International Health-Related Water Microbiology at Naxos, Greece (June, 2009).  Winner of Best Oral Presentation.

    Talago (Bonilla), N., Rohwer, F. and Barr, J. The interaction of bacteriophage with the human mucosal immune system at the SDSU 2013 Student Research Symposium (March 2013).

    AWARDS
    MARC NIH PROGRAM (Minority Access to Research Careers), June 2009 – May 2011

    Best Oral Presentation at the 15th International Health-related Water Microbiology, International Water Association (IWA) in Naxos, Greece, June 2010

    Award from the Notre Dame College at Maryland, Baltimore as the most outstanding undergraduate researcher in biology at the University of Puerto Rico, Rio Piedras, November 2010

    Puerto Rico Math and Science Partnership (ALACiMA) Undergraduate Fellow, Summer 2005

    COMPUTER/STATISTICAL SKILLS
    Introduction of Statistics with computers course
    Minitab                          
    The R Project for Statistical Computing
    Endnote
    Microsoft Office
    Power Point for oral and poster presentations
    Creating Excel Worksheets for data analysis

    LANGUAGES
    Spanish
    English

Picture of Rita Auro
  • Rita Auro
  • rita.auro89@gmail.com
  • Area of Study: Biology, phage, mucus, tissue culture
  • Interests: traveling/exploring, baking, music, documentaries, kittens
Picture of Jeremy Barr
  • Jeremy Barr
  • jeremybarr85@gmail.com
  • Area of Study:

    Phage, Mucus, and Microfluidic Model systems
    Website (http://www.jeremyjbarr.com

  • Interests: Sports, Beer and Vegemite (oh and science)
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    Address
    Dept. of Biology San Diego State University, 302 North Life Sciences 5500 Campanile Dr., San Diego, CA 92182

    Academic History

    • 2013 – Present - Adjunct Assistant Professor, San Diego, CA San Diego State University, The Rohwer Lab.
    • 2011 – 2013  - Post-doctoral Research Fellow San Diego, CA San Diego State University, The Rohwer Lab.
    • 2007 – 2011 - Doctorate of Philosophy Brisbane, QLD The University of Queensland, Advanced Water Management Centre. Thesis; The Microbial Ecology of Granular Sludge in Enhanced Biological Phosphorus Removal.
    • 2009 – 2010 - Graduate Certificate in Research Commercialisation Brisbane, QLD The University of Queensland, School of Business.
    • 2005 – 2006 - Honours Class I - Microbiology Brisbane, QLD The University of Queensland, School of Chemistry and Molecular Biosciences. Thesis: Stability of the Violacein Antitumour Antibiotic Gene Cluster in a RecA Mutant of Rhodobacter sphaeroides.
    • 2002 – 2005 - Bachelor of Biotechnology - Microbiology Brisbane, QLD The University of Queensland, School of Chemistry and Molecular Biosciences.


    Publications

    1. J. J. Barr, R. Auro, M. Furlan, K. L. Whiteson, M. L. Erb, J. Pogliano, A. Stotland, R. Wolkowicz, A. S. Cutting, K. S. Doran, P. Salamon, M. Youle & F. Rohwer (2013). Bacteriophage adhering to mucus provide a non-host-derived immunity. Proceedings of the National Academy of Sciences.
    2. J. J. Barr, M. Youle & F. Rohwer (2013). Innate and acquired bacteriophage-mediated immunity. Bacteriophage, 3(3).
    3. J. J. Barr, F. Slater, T. Fukushima & P. L. Bond (2010). Bacteriophage-host interactions cause community and performance changes in a mixed-culture activated sludge system. FEMS Microbiology Ecology, 74, 631 – 642.
    4. J. J. Barr, L. L. Blackall & P. L. Bond (2010). Further limitations of phylogenetic group-specific probes used for the detection of bacteria in environmental samples. The ISME Journal, 4(8), 959 – 961.
    5. J. J. Barr, A. E. Cook & P. L. Bond (2010). Granule formation mechanisms within an aerobic wastewater system operating for phosphorus removal. Applied and Environmental Microbiology, 76(22), 7588 – 7597. *Figure published as Journal Cover.
    6. J. J. Barr, A. E. Cook, T. Fukushima & P. L. Bond (2010). Chapter 11.4: Clone Library Generation. In: The Microbiology Ecology of Activated Sludge. Eds. R. J. Seviour & P. H. Nielsen.
    7. C. M. Wright, J. E. Larsen, M. L. Colosimo, J. J. Barr, L. Chen, R. E. McLachlan, I. A. Yang, R. V. Bowman & K. M. Fong (2010). Genetic association study of CYP1A1 polymorphisms identifies risk haplotypes in nonsmall cell lung cancer. European Respiratory Journal, 35(1), 152-159.
    8. F. R. Slater, A. C. Singer, S. Turner, J. J. Barr & P. L. Bond (2010). Pandemic pharmaceutical dosing effects on wastewater treatment: no adaptation of activated sludge bacteria to degrade the antiviral drug Oseltamivir (Tamiflu) and loss of nutrient removal performance. FEMS Microbiology Letters, 315(1), 17-22.
    9. J. Mohanakrishnan, M. V. W. Kofoed, J. J. Barr, Z. Yuan, A. Schramm & R. L. Meyer (2011). Dynamic microbial response of sulfidogenic wastewater biofilm to nitrate. Applied Microbial Biotechnology, 91(6), 1647-57.


    Awards and Acheivements

    • 2010 – AusBiotech-GSK Student Excellence Award, National finalist for post-graduate biotechnology students, Melbourne, Australia.
    • 2010 – Teaching Excellence Award, Student evaluation of teaching excellence, Avg: 4.9 (scale 1-5, 5 highest), The University of Queensland, Brisbane, Australia.
    • 2010 – Commercial Training Scheme Scholarship, Competitive government grant for the undertaking of a Business School Graduate Certificate, Brisbane, Australia.
    • 2009 - ASM Becton-Dickinson PhD Award, National award for post-graduate microbiology students, Perth, Australia.
    • 2009 – Best Student Platform Presentation Award, Best Student presentation at ASPD5 conference, Aalborg, Denmark
    • 2009 - ISME Student Award, Best Presentation of a proffered microbial ecology paper at The 50th  ASM conference, Perth, Australia

    Work History
     
    • 2006 – 2010 Practical Demonstrator and Presenter, Brisbane, QLD The University of Queensland, School of Chemistry and Molecular Biosciences. Subjects: Environmental Engineering, Microbiology, Genetics, Medicine, Dentistry and Biotechnology.
    • 2004 – 2007 Laboratory Technician, Brisbane, QLD The Prince Charles Hospital, Thoracic Medicine Cancer Research Department.
Picture of Lance Boling
  • Lance Boling
  • liquidgrey@gmail.com
  • Area of Study: Cell and Molecular Biology
  • Interests: Nutrition, Gene therapy, music
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    Education
    B.S. Food and Nutrition from San Diego State University
    SDSU Biotechnology Certification

Picture of Sandi Calhoun
  • Sandi Calhoun
  • sandi.calhoun@gmail.com
  • Area of Study: Phage, coral immunology, mucus, viromes, bioinformatics
  • Interests: Pretty much anything outdoors, dancing, hooping, caving, traveling
Picture of Mike Furlan
  • Mike Furlan
  • mikefurlan@gmail.com
  • Area of Study: Viruses related to Cystic Fibrosis
  • Interests: Pulmonary medicine & CF related topics MOTORCYCLES & INSANE SPEEDS!!!!! Working on motorcycles that are broken from insane speeds. Human Anatomy & related topics, OLD books about Human Anatomy. COMPUTERS (MACS RULE).
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    Education
    Graduate student in Dr. Rohwer's Labratory (Fall 2005)
    B.S. S.D.S.U. 2005

    Professional Experience

    Human Anatomy Instructor (2005- Currently)
    Laboratory tech. (2004-2005)
    Lead Anatomy Tutor (1999-2004)
    Human Anatomy Tutor (1996-1999)

    Publications
    Dinsdale EA, RA Edwards, D Hall, F Angly, M Breitbart, JM Brulc, M Furlan, C Desnues, M Haynes, L Li, L McDaniel, MA Moran , KE Nelson, C Nilsson, R Olson, J Paul, B Rodriguez-Brito, Y Ruan, BK Swan, R Stevens, DL Valentine, RV Thurber, L Wegley, BA White, F Rohwer (2008) Functional metagenomic profiling of nine biomes. Nature. 452. 629-632. > Correction to manuscript published in September 2008. 

Picture of Emma George
  • Emma George
  • 3mma6eorg3@gmail.com
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    EDUCATION

     B.S. Biology with Honors, minor Journalism, College of Idaho (2008-2012)

     

    EXPERIENCE AND PREVIOUS EMPLOYMENT

    • Research Assistant/Lab Technician – San Diego State University, Research Foundation, Dr. Forest Rohwer (April 2013-Present).
    • Teaching Assistant – College of Idaho, Department of Biology, Australia Expedition (2013)
    • Research Assistant – College of Idaho, Dr. Don Mansfield. Phylogenetic studies of Lomatium and Cymopterus, two genera in the carrot family, Apiaceae (2011-2012)
    • Survey Assistant – Dr. Chris Walser, Stream invertebrate survey to determine effects of low water levels in Boise River on salmon food supply (2012)
    • Survey Assistant – Ecosystem Sciences, Environmental Consultant Agency (2012)    


    PUBLICATIONS

    George E.E., D.H. Mansfield, J.F. Smith, R.L. Hartman, S.R. Downie, C.E. Hinchliff (In Press) Phylogenetic Analysis Reveals Multiple Cases of Morphological Parallelism and Taxonomic Polyphyly in Lomatium (Apiaceae). Systematic Botany.

     

    FIELD EXPEDITIONS

    • NOAA RAMP Cruise, Main Hawaiian Islands (2013)
    • C of I Biology Australia Expedition, Heron Island Research Station (2013 and 2010)
    • Middle Fork of the Malheur River, Fish Survey, (2012)
    • Botany Collection Expeditions, Owyhee Mountains, (2011 and 2012)

     

    HONORS/AWARDS

    • Biology Departmental Honors, 2012
    • Biology Department Outstanding Student Award, 2012
    • Patricia Packard Award for Excellence in Botany, 2011
    • First Place for Best Poster Presentation, Idaho Academy of Science Symposium, 2011
    • Best Female Junior Writer, Coyote (Student Newspaper), 2011

     

    PRESENTATIONS

    Oral Presentation

    • 2012 College of Idaho Student Research Conference

    Poster

    • 2012 Murdock College Science Research Conference
    • 2012 Idaho Academy of Science Symposium
    • 2011 Murdock College Science Research Conference
    • 2011 College of Idaho Day at the Idaho State Capitol
    • 2011 College of Idaho Student Research Conference
    • 2010 College of Idaho Student Research Conference
Picture of Andi Haas
  • Andi Haas
  • andreas.florian.haas@gmail.com
  • Area of Study: Coral reef ecology, coral algae interactions, DOC, oxygen dynamics
  • Interests: Skiing in MY Alps
Picture of Arron Hartmann
  • Arron Hartmann
  • Area of Study: Marine ecology, invertebrate physiology and reproductive ecology, energetic tradeoffs, symbioses
  • Interests: Coral reefs, traveling, playing guitar, changing light bulbs
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    Curriculum vitae


    Scripps Institution of Oceanography, University of California San Diego – La Jolla, California (2007–present)

    • M.S. in Oceanography, 2010
    • Ph.D. in Marine Biology, expected 03/2014

    University of Vermont – Burlington, Vermont (2002–2007)

    • Bachelor of Science, Cum Laude
    • Major: Biology, Minor: Environmental Science

    Södertörns högskola (University of Southern Stockholm) – Huddinge, Sweden (2006–2007)

    • Study abroad student

    The Center for Coastal Studies Puerto San Carlos, Mexico (Jun–Jul 2005)

    • Classroom and fieldwork in sea turtle biology and ecology


    RECENT RESEARCH EXPERIENCE

    Ph.D. Student Researcher – CARMABI Research Station, Willemstad, Curaçao (2008–present)

    • Investigating how local and global change influences reproductive investment, lipid energetics and skeletal formation in Caribbean corals.

    Graduate Student Intern – Division of Aquatic Resources, Maui, Hawai’i (Jun–Aug 2009)

    • Examined the impact of wastewater pollution on the integrity of coral communities.


    TEACHING AND MENTORING

    • National Science Foundation GK-12 Fellow – High Tech High North County, San Marcos, California (2012– 2013). Taught weekly lessons on marine biology and coral husbandry to sixty students while overseeing a fifteen-tank coral health experiment in the classroom.
    • Coach for National Ocean Sciences Bowl La Jolla, California (2007–present). Coach and provide lessons for a team of high school students as they prepare for San Diego County’s annual ocean science scholars’ bowl competition.
    • Invited Speaker for Escondido Charter High School Leadership Conference Escondido, California (2013). Lectured to ~350 high school students on what I have learned about effective leadership from living with Marfan syndrome and being a marine biologist.
    • Graduate Student Mentor – Scripps Institution of Oceanography (2009–2012). Worked one-on-one in the laboratory with four summer and term-long undergraduate interns.


    VOLUNTEERING AND SERVICE

    • Volunteer at Birch Aquarium at Scripps Institution of Oceanography La Jolla, California (2009–2012). Assisted Aquarium Curator, Fernando Nosratpour, by maintaining and caring for organisms throughout the aquarium, in particular the stony corals and other coral reef organisms.
    • Reviewer for Coral Reefs and Marine Biology (2011–present). Reviewer of eight manuscripts to date.
    • Professional Memberships: International Society of Reef Studies, Ecological Society of America, Society for Conservation Biology


    ACADEMIC AWARDS AND FELLOWSHIPS

    • National Science Foundation GK-12 Fellow (2012-2013)
    • National Science Foundation Graduate Research Fellow (2009-2012)
    • National Science Foundation IGERT Fellow (2007-2009)


    RESEARCH PUBLICATIONS

    1. Trentacoste EM, RP Shrestha, SR Smith, C Gle, AC Hartmann, M Hildebrand, WH Gerwick (2013) Metabolic engineering of lipid catabolism increases microalgal lipid accumulation without compromising growth. Proceedings of the National Academy of the Sciences 110(49): 19748-19753

    2. Hartmann AC, KL Marhaver, VF Chamberland, SA Sandin, MJA Vermeij (2013) Large birth size does not reduce the negative latent effects of harsh environmental conditions across early life stages in two coral species. Ecology 94(9): 1966-1976.

    3. Carilli J, Donner SD, Hartmann AC (2012) Historical temperature variability affects coral response to heat stress. PLoS ONE 7(3): e34418. doi:10.1371/journal.pone.0034418

    4. Hartmann AC, Carilli JE, Norris RD, Charles C, Deheyn DD (2010) Stable isotopic records of bleaching and endolithic algae blooms in the skeleton of the boulder forming coral Montastraea faveolata. Coral Reefs 29:1079-1089

    5. Han S, Narasingarao P, Obraztsova A, Gieskes J, Hartmann AC, Tebo BM, Allen EE, Deheyn DD (2010) Mercury Speciation in Marine Sediments under Sulfate-Limited Conditions. Environmental Science and Technology 44: 3752-3757.

    6. Druschel GK, Hartmann A, Lomonaco R, Oldrid K (2005) Determination of sediment phosphorus concentrations in St. Albans Bay, Lake Champlain: Assessment of internal loading and seasonal variations of phosphorus sediment-water column cycling. Report to the Vermont Agency of Natural Resources, 71 p.


    COMMENTARY PUBLICATIONS

    • Hartmann, AC (2013) Education: Science literacy benefits all. Nature 498: 171.

    • Hartmann, AC, Levin LA (2012) Conservation Concerns in the Deep. Science 336: 668-669.


    SCIENCE WRITING FOR BROAD AUDIENCES

    • Hartmann, AC (2012) Science Minded on UT-San Diego. Authored a blog to introduce students, parents and teachers to many aspects of science through experiences as a marine biologist. All posts: http://bit.ly/13TMZd0.

    • Hartmann, AC (2012) The Lightning of Catatumbo in Sage Magazine. Creative non-fiction piece about the complex relationship between human needs and coral reef conservation on Curaçao (available at: http://bit.ly/YIq3wr). Selected for the 2013 Sage Magazine print edition.


    PRESS COVERAGE

    • Socrates Fellow Brings Coral Research to Local High School (2013) This Week @ UC San Diego. Available at: http://bit.ly/1aw8v8m

    • Population convinced of importance of nature conservation (2013) Amigoe newspaper. Available at: http://bit.ly/16ho6bg

    • Protest mail from America (2013) Amigoe newspaper. Available at: http://bit.ly/16ho7Mo

    • Oostpunt Plans: Fatal Impact On Reefs Along The Entire South-Eastern Coast (2013) Curacao Chronicle. Available at: http://bit.ly/17YR6c2

    • Reefs will die with development of Oostpunt (2012) Amigoe newspaper. Available at: http://bit.ly/19SLoJb



    LABORATORY AND FIELD SKILLS

    • Lipid extraction and class analysis (TLC-FID), fatty acid analysis (GC-MS), stable isotope analyses of organic and inorganic materials (IRMS), stable isotope labeling studies, rearing of marine invertebrate larvae, advanced aquarium husbandry skills, marine field experimental design and implementation, public speaking, scientific writing, writing about science for broad audiences, curriculum development.


    CONFERENCE PRESENTATIONS

    • 12th International Coral Reef Symposium – July 2012 in Cairns, Australia – 15-minute oral presentation: Linking parental energetics and larval recruitment success in Agaricia humilis (with K. Marhaver, M. Vermeij).
    • 26th International Congress for Conservation Biology – July 2013 in Baltimore, USA – 15-minute oral presentation: High energy content and fecundity of healthy coral reefs in Curaçao (with K. Marhaver, M. Vermeij). Selected as 4th place winner in the Student Award Symposium out of over 100 applicants.
Picture of Mark Hatay
  • Mark Hatay
  • mhatay@sciences.sdsu.edu
  • Area of Study: Making toys!
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    Publications
    Dinsdale, EA, O Pantos, S Smriga, RA Edwards, F Angly, L Wegley, M Hatay, D Hall, E Brown, M Haynes, L Krause, E Sala, SA Sandin, RV Thurber, BL Willis, F Azam, N Knowlton, F Rohwer (2008) Microbial ecology of four coral atolls in the Northern Line Islands. PLoS One. 3(2) e1584. 1-17.

    Smith JE, M Shaw, RA Edwards, M Hatay, D Obura, O Pantos, E Sala, SA Sandin, S Smriga, F Rohwer (2006) Effects of algae on coral: Algal-mediated, microbe-induced coral mortality. Ecology Letters. 9 (7). 835-845.

    Hatay, M, N Kuntz, F Rohwer (2005) SPIDERS: A syringe pump system for long-term dosing underwater. Limnology and Oceanography Methods. 3. 38-45

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Picture of Nao Hisakawa
  • Nao Hisakawa
  • nghisakawa@gmail.com
  • Area of Study: Geographic Information Science (GIS), data visualization, bioinformatics
  • Interests: Traveling, dogs, drawing, maps, tennis, piano
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    Education
    M.S. Geography with emphasis on Geographic Information Science, San Diego State University, 2011
    B.S. Animal Science, UC Davis, 2006 


    Research Experience
    Research Specialist at Rohwer Lab, San Diego State University, Dec 2012 to present
    Research Assistant at Rohwer Lab, San Diego State University, Dec 2009 to Dec 2011
    Researcher at Department of Geoinformation, Carinthia University of Applied Sciences, Austria, June to September 2011
    Research Assistant at Department of Geography, San Diego State University, June to August 2010

    Publication
    Hisakawa N, Jankowski P, Paulus G. 2013. Mapping the porosity of international border to pedestrian traffic: a comparative data classification approach to a study of the border region in Austria, Italy, and Slovenia. Cartography and Geographic Information Science. 40(1): 18-27.

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  • Victoria Hosford
  • Hosford.Victoria@gmail.com
  • Area of Study: Marine Microbiology
  • Interests: Surfing, Video Games, camping and cooking
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    Education
    B.S. in Marine Microbiology at San Diego State University (in progress)

Picture of Shr-Hau Hung
  • Shr-Hau Hung
  • sky.hon@gmail.com
  • Area of Study: Phage, Marine Microbiology
  • Interests: Sports, cooking, playing clarinet
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    EDUCATION
    SDSU-UCSD Joint Doctoral Program in Cellular and Molecular Biology
    , Biology Department, San Diego State University, California, USA (2013- present)

    Cell and Molecular Biology Master's Program, Biology Department, San Diego State University, California, USA (2012-2013)

    M.S. in Marine Environmental Chemistry and Ecology (MECE), National Taiwan Ocean University (NTOU), Keelung, Taiwan (2007-2009)

    B.S. in Microbiology, Soochow University, Taipei, Taiwan (2002-2007)

     

    RELEVEANT EXPERIENCE
    Teaching assistant: general chemistry lab, Department of Chemistry and Biochemistry, SDSU (2012)
    Teaching assistant: microbiology lab, Department of Biology, SDSU (2013-present)
    Research Assistant, supervisor: Prof. Jeng Chang (Inst. of Marine Biology) and Prof. Gwo-Ching Gong (Inst. of MECE), NTOU (2010-2012)

     

    HONORS & AWARDS
    Scholarship to study abroad, Ministry of Education, Taiwan (2012)
    Excellence in performance award from Army Command headquarters, Taiwan (2010)
    Travel Scholarship for oversea meetings, NTOU (2009)
    First Prize in the student poster competition, NTOU (2008)
    Second Prize in the student poster competition of Ocean Science Meeting of National Science Council, Taiwan (2008)

     

    RESEARCH PUBLICATION
    S.-H. Hung, C.-C. Chung, G.-C. Gong, and J. Chang. The phosphate transporter gene expression, alkaline phosphatase activity, and maximum quantum efficiency of photosynthesis of Skeletonema costatum under phosphate limitation and starvation. In preparation.

    S.-H. Hung, C.-C. Chung, C.-W. Liao, G.-C. Gong, and J. Chang. 2013. Sequence diversity and expression levels of Synechococcus phosphate transporter gene in the East China Sea. J. Exp. Mar. Biol. 440: 90-99
     

    PRESENTATION
    2012 SDSU Graduate Research Symposium
    2011 Ocean Science Meeting of National Science Council, Taiwan.
    2009 ASLO, Aquatic Science meeting, Nice, France
    2008 The Center of Excellence for Marine Bioenvironment and Biotechnology, NTOU
    2008 Ocean Science Meeting of National Science Council, Taiwan.
    2007 Student research exhibition, Inst. of Marine Biology, NTOU

     
    PROFESSIONAL SKILLS
    Molecular biology
    PCR, cloning, southern blotting, reverse transcription, real-time PCR

    Oceanographic sampling
    phytoplankton cell collecting, Size fraction, DNA & RNA sample preservation, on-deck incubation

    Phytoplankton physiological assays
    Flow cytometry, alkaline phosphatase activity, maximum quantum yield for PSII (Fv/Fm)

     

    LEADERSHIP & ACTIVITIES
    Public Performance, Chinese New Year’s Eve Party (Pachelbel Canon; clarinet, violin and piano trio), Chinese Student and Scholar Associate, SDSU, San Diego, CA (9 Feb., 2013)

    1st clarinetist, Cool-phone Wind band, Keelung, Taiwan (2010-2012)       

    Leader of Vacation Transportation affairs of R.O.C. Army in Lieyu (Lesser Kinmen) Regional Commander Center (2009-2010)                                                          

    Public Performance, NTOU Orchestra (Concerto piece No.2 for Two Solo Clarinets / F. Mendelssohn), Keelung Culture Center, Taiwan (Jun. 2009)                                                                          

     

    LANGUAGES
    English, Mandarin, Taiwanese

Picture of Jan Janouskovec
  • Jan Janouskovec
  • janjan.cz@gmail.com
  • Area of Study:

    Apicomplexan parasites (malaria), Applications of phylogenetics Microbial diversity, Origins of parasitism, Principles of molecular evolution

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    EDUCATION & RESEARCH                                                                       

    • 2014 Jan - present, Postdoctoral Fellow. San Diego State University, USA (F.L. Rohwer)            
    • 2013 Aug - 2013 Dec ,Postdoctoral Fellow. University of British Columbia, Canada (P.J. Keeling)            
    • 2008 May - 2013 Jul, PhD (Botany). University of British Columbia, Canada (P.J. Keeling) Topic: Free-living alveolates and the evolution of apicomplexan parasites
    • 2008 Feb - 2008 Apr, Research Assistant. Biology Centre, Academy of Sciences, Czech Rep. (J. Lukeš)      
    • 2007 Sep - 2007 Dec, Research Assistant (volunteer). University of Glasgow, Scotland (S. Muller)
    • 2005 Sep - 2008 Jan, MSc (Molecular biology). University of South Bohemia, Czech Rep. (M. Oborník)         Topic: The plastid of Chromera velia, the photosynthetic relative of apicomplexan parasites
    • 2001 Sep 2005 May, BSc (Biology). University of South Bohemia, Czech Republic (J. Zrzavý) Topic: Evolutionary position of moss animals (Bryozoa) and phylogeny of ringed worms (Annelida)

    MAJOR AWARDS

    • Governor General Gold Medal , Univ. of BC, May 2014
    • CIFAR Global Scholar Fellowship (2 year), CIFAR, Nov 2012
    • AWARDS
    • Four Year Fellowship (FYF) for PhD students, Univ. of BC, Sep 2009
    • Faculty of Science Graduate Award, Univ. of BC, Mar 2014
    • Kit Malkin Scholarship, Univ. of BC, Feb 2013
    • Edith Ashton Memorial Scholarship, Univ. of BC,   Mar 2011
    • Jahn-Bovee Award for Best Student Oral Presentation, ISOP*, Aug 2011
    • CMDE Best Poster Presentation, CMDE**, May 2010
    • Faculty of Science Graduate Award, Univ. of BC, May 2009
    • Conference Travel Awards PSA/ISOP 2011, Seattle, WA, USA ISEP XVIII 2010, Kanazawa, Japan SMBE 2007, Halifax, NS, Canada *Awarded by International Society of Protistologists for the talk "Photosynthetic alveolates and the evolution of apicomlexan parasites" at  PSA/ISOP conference 2011, Seattle, WA, US **Awarded by Centre for Microbial Diversity and Evolution for the poster presentation "Unexpected diversity of novel eukaryotes with plastids associated with coral reefs” in 2010 at annual meeting at Halfmoon Bay, BC, Canada


    PUBLICATIONS

    1. Tikhonenkov, D.V., Janouškovec, J., Mylnikov, A.P., Mikhailov, K.V., Simdyanov, T.G., Aleoshin, V.V., Keeling, P.J. (2014) Description of Colponema vietnamica sp.n. and Acavomonas peruviana n. gen. n. sp., two new alveolate phyla (Colponemidia nom. nov. and Acavomonidia nom. nov.) and their contributions to reconstructing the ancestral state of alveolates and eukaryotes. PLoS One 9(4): e95467.
    2. Janouškovec, J.*, Tikhonenkov, D.V.*, Mikhailov, K.V., Mylnikov, A.P., Simdyanov, T.G., Aleoshin, V.V., Keeling, P.J. (2013) Colponemids represent multiple ancient alveolate lineages. Current Biology 23:1–7. *Authors contributed equally.
    3. Pombert J.-F., Smirnov, A., James, E.R., Janouškovec, J., Gray, M.W., Keeling, P.J. (2013). The complete mitochondrial genome from an unidentified Phalansterium species. Protist Genomics 1:25–32
    4. Janouškovec, J.*, Sobotka, R.*, Lai, D.-H.*, Flegontov, P., Koník, P, Komenda, J, Ali, S., Prášil, O., Pain, A., Oborník, M., Lukeš, J., Keeling, P.J. (2013). Split photosystem protein, linear-mapping topology and growth of structural complexity in the plastid genome of Chromera velia. Molecular Biology and Evolution 30(11):2447–2462. *Authors contributed equally.
    5. Janouškovec, J., Liu, S.-L., Martone, P.T., Carré, W., Leblanc, C., Collén, J., Keeling, P.J. (2013) Evolution of red algal plastid genomes: ancient architectures, introns, horizontal gene transfer and taxonomic utility of plastid markers. PLoS One 8(3):e59001.
    6. Pombert, J.-F., James, E.R., Janouškovec, J., Keeling, P.J.. 2012. Evidence for transitional stages in the evolution of euglenid group II introns and twintrons in the Monomorphina aenigmatica plastid genome. PLoS ONE 7:e53433.
    7. Janouškovec, J., Horák, A., Barott, K.L., Rohwer, F.L., Keeling, P.J. (2012) Environmental distribution of coral-associated relatives of apicomplexan parasites. The ISME Journal 7:444-7.
    8. Worden, A.Z., Janouškovec, J., Engman, A., McRose, D., Welsh, R.M., Malfatti, S., Tringe, S.G., Keeling, P.J. (2012) Global distribution of a marine alga revealed by targeted metagenomics. Current Biology 22(17):R675-7.
    9. Janouškovec, J., Horák, A., Barott, K.L., Rohwer, F.L., Keeling, P.J. (2012) Global analysis of plastid diversity reveals apicomplexan-related lineages in coral reefs. Current Biology 22(13):R518–9.
    10. Barott, K.L., Rodriguez-Brito, B., Janouškovec, J., Marhaver, K., Smith, J.E., Keeling, P., Rohwer, F.L. (2011) Microbial diversity associated with four functional groups of benthic reef algae and the reef-building coral Montastraea annularis. Environmental Microbiology 13:1192–1204.
    11. Botté, C.Y., Yamaryo-Botté, Y., Janouškovec, J., Rupasinghe, T., Keeling, P.J., Crellin, P., Coppel, R.L., Maréchal, E., McConville, M.J., McFadden, G.I. (2011) Identification of plant-like galactolipids in Chromera velia, a photosynthetic relative of malaria parasites. Journal of Biological Chemistry 286:29893–903.
    12. Koblížek, M., Janouškovec, J., Oborník, M., Johnson, J.H., Ferriera, S., Falkowski, P.G. (2011) Genome sequence of the marine photoheterotrophic bacterium Erythrobacter sp. strain NAP1. Journal of Bacteriology 193:5881–2.
    13. Oborník, M., Vancová, M., Lai, D.-H., Janouškovec J., Keeling, P.J., Lukeš, J. (2011) Morphology and ultrastructure of multiple life cycle stages of the photosynthetic relative of apicomplexa, Chromera velia. Protist 162:115–30.
    14. Kořený, L., Sobotka, R., Janouškovec, J., Keeling, P.J., Oborník, M. (2011) Tetrapyrrole synthesis of photosynthetic chromerids is likely homologous to the unusual pathway of apicomplexan parasites. Plant Cell 23:3454–62.
    15. Janouškovec, J., Horák, A., Oborník, M., Lukeš, J., Keeling, P.J. (2010) A common red algal origin of the apicomplexan, dinoflagellate, and heterokont plastids. Proceedings of the National Academy of Science of the United States of America 107:10949–54.
    16. Zrzavý, J., Říha, P., Piálek, L., Janouškovec, J. (2009) Phylogeny of Annelida (Lophotrochozoa): total-evidence analysis of morphology and six genes. BMC Evolutionary Biology 9:189.
    17. Oborník, M., Janouškovec, J., Chrudimský, T., Lukeš, J. (2009) Evolution of the apicoplast and its hosts: from heterotrophy to autotrophy and back again. International Journal for Parasitology 39:1–12.
    18. Moore, R.B., Oborník, M., Janouškovec, J., Chrudimský, T., Vancová, M., Green, D.H., Wright, S.W., Davies, N.W., Bolch, C.J.S., Heimann, K., Šlapeta, J., Hoegh-Guldberg, O., Logsdon, J.M., Carter, D.A. (2008) A photosynthetic alveolate closely related to apicomplexan parasites. Nature 451:959–63.


    PROFESSIONAL EXPERIENCE
    (international meetings only)

    ●  11 Talks (2 invited *) Chromera II 2014*, Ceske Budejovice, Czech Republic  CIFAR-IMB 2014, Liblice, Czech Republic ICOP 2013, Vancouver, BC, Canada (2x) NWAS 2012, Vancouver, BC, Canada PSA/ISOP 2011, Seattle, WA, USA ISEP 2010, Kanazawa, Japan CIFAR-IMB 2009, Asilomar, CA, USA Protist 2008, Halifax, NS, Canada ISP 2008*, Tsukuba, Japan SMBE 2007, Halifax, NS, Canada.

    ●  2 Posters CSM 2012 Vancouver, BC, Canada ISEP 2006 Wroclaw, Poland.

    ●  4 Workshops Genomics Transcriptomics Big data Tree of life.

    ●  9 Invited manuscript reviews Molecular Biology and Evolution (4x) PLOS One (2x) Protist (1x) Molecular Genetic Elements (1x) Journal of Phycology (1x)

    ●  Community Volunteer at ICOP 2013 Meeting, Vancouver, BC, Canada Member of International Society of Protistologists (ISOP): 2008, 2010-2014    Member of International Society for Evolutionary. Protistology (ISEP): 2010-2014   Member of Society for Molecular Biology and Evolution (SMBE): 2007



    TEACHING TRAINING

    ●  Teaching assistant. BIOL 332 (Protistology). Univ. of BC, Canada (2010).

    ●  Instructional Skills Workshop and Instructional Skills Program for International Teaching Assistants. Univ. of BC, Canada (2008).

    ●  Certificate: Biology Teaching for High Schools. 4 semesters of 12 classes + 30 hours of teaching practice at a high school. Univ. of South Bohemia, Czech Republic (2005-2008).

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  • Ben Knowles
  • enhalus@gmail.com
  • Area of Study: Marine Biology and Ecology
  • Interests: Camping, traveling, and the ocean
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    Education

    SDSU-UCSD Joint Doctoral Program in Cellular and Molecular Biology (2011-2017)
    Biology Department, San Diego State University, California, USA
    Field of Interest: Microbial dynamics of tropical marine systems

    Bachelor of Science Honours Degree in the Field of Botany (2004-2005)
    University of Queensland, Australia
    NB: an Honors degree is the equivalent of a one-year Research MSc

    Bachelor of Science in the Fields of Ecology and Marine Biology (2001-2003)
    School of Life Sciences, University of Queensland, Australia

Picture of Yan Wei Lim
  • Yan Wei Lim
  • ywlim.s@gmail.com
  • Area of Study: Microbial Metatrascriptomics. Viral Metagenomic in animals, human and vectors
  • Interests: Diving, Swimming, Camping, Running
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    EXPERIENCE AND PREVIOUS EMPLOYMENT

    09/2012 – current Graduate Research (Joint Doctoral Program in Cell and Molecular Biology) Department of Biology, San Diego State University, United States.

    01/2013 – 05/2013 Teaching Assistant for Ecological Metagenomics Department of Biology, San Diego State University, United States

    09/2009 – 08/2012 Graduate Research (Cell and Molecular Biology Master’s Program Department of Biology, San Diego State University, United States
    Project title: Understanding the dynamics of viral and microbial communities in Cystic Fibrosis lungs using metagenomic and metatranscriptomic approaches

    08/2011 – 12/2011 Teaching Assistant for Biochemistry and Molecular Biology Laboratory
    Department of Biology, San Diego State University, United States

    03/2009 – 07/2011 Research Assistant
    Global Viral Forecasting Initiative, San Diego State University, United States

    1. Viral Discovery and Viral Community Characterization Projects - Characterizing viral community in human nasopharhyngeal swab samples from patients with flu-like symptoms and tested negative with known viruses
    2. Setting up and facilitating Roche 454-GSFLX sequencing machine in SDSU

    11/2006 – 02/2009 Research Assistant
    Genome Technology and Biology Group, Genome Institute of Singapore, Singapore 

    1. Metagenomic studies of mosquito-associated viruses using high-throughput sequencing
    2. Studies of bacterial flora in health and disease through gastric and oral samples from patients with and without gastric pathology and characterizing microbial flora in pre-term birth using 16S rRNA sequence analysis
    3. Bacterial genome sequencing using Paired-End diTagging (gPET) of highly virulent Burkholderia pseudomallei isolate, Streptococcus pneumonia, and Neisseria spp. 
    4. Laboratory Risk Management

    As a member of the Risk Assessment committee, responsible in risk assessment of the various projects performed within the group

    09/2005 – 06/2006 Bachelor Research
    School of Health, Nature and Social Sciences, University of Sunderland, United Kingdom

    Developing a real-time quantitative gene expression assay by using the RT-PCR standard curve method to investigate NDST-2 gene expression in HMEC-1 cell line


    HONORS AND AWARDS

    The CSUPERB student travel award, 2012
    The International Symposium on Microbial Ecology (ISME) travel grant award, 2012
    Mabel Myers Memorial Scholarship, San Diego State University, 2011-2012
    The President’s Prize, Institute of Biomedical Science, United Kingdom, 2006
    North East Region Symposium Prize, University of Sunderland, United Kingdom, 2006


    PUBLICATIONS

    1. Lim Y. W., Cuevas D., Silva G., Hass A., Sanchez, S., Aguinaldo K., Wegley L., …. Rohwer, F., Edwards R. (In revision) Sequencing At Sea: Challenges and Experiences in Ion Torrent Sequencing during the 2013 Southern Line Islands Research Expedition.
    2. Lim Y.W., Haynes M., Furlan M., Robertson C.E., Harris J.K., Rohwer F. (2014) Purifying the impure: Sequencing metagenomes and metatranscriptomes from complex animal-associated samples. Journal of Visualized Experiment
    3. Haas A.F., Knowles B., Lim Y.W., McDole Somera T., Kelly L.W., Hatay M., Rohwer F. (2014) Unraveling the unseen players in the ocean – a field guide to water chemistry and marine microbiology. Journal of Visualized Experiment
    4. Garg N., Kapono C., Lim Y.W., Koyama N., Vermeij M., Conrad D., Rohwer F., Dorrestein P. (2014) Mass spectral similarity for untargeted metabolomics data analysis of complex mixtures. International Journal of Mass Spectrometry
    5. Kelly L.W., Williams G., Barott K., Calson C., …. Lim Y.W., …. Rohwer F. (2014) Local genomic adaptation of coral reef-associated microbiomes to gradients of natural variability and anthropogenic stressor. Proceedings of the National Academy of Sciences
    6. Whiteson K., Bailey B., Bergkessel M., Conrad D., Delhaes L., Felts B., Harris J.K., Hunter R., Lim Y.W., Maughan H., Quinn R., Salamon P., Sullivan J., Wagner B.D., and Rainey P.D. (2014) The upper respiratory tract as a microbial source for pulmonary infections in Cystic Fibrosis: Parallels from Island Biogeography. American Journal of Respiratory and Critical Care Medicine
    7. Quinn R., Lim Y.W., Maughan H., Rohwer F., Whiteson K.L. (2014) Biogeochemical Forces Shape the Composition and Physiology of Polymicrobial Communities in the Cystic Fibrosis Lung. mBio Journal
    8. Whiteson K.L., Meinardi S., Lim Y.W., Schmieder R., Maughan H., Quinn R., Blake D., Conrad D., Rohwer F. (2014) Breath gas metabolites and bacterial metagenomes from cystic fibrosis airways indicate active pH neutral 2,3-butanedione fermentation. ISME Journal
    9. Lim Y.W., Evangelista J.S III, Schmieder R., Bailey B., Haynes M.R., Furlan M., Maughan H., Edwards R., Rohwer F., Conrad D. (2014) Clinical insights from metagenomic analysis of sputum samples from patients with cystic fibrosis. Journal of Clinical Microbiology
    10. Lim Y.W. (2013) Sequencing at sea. http://coralreefsystems.org/http%3A/%252Fcoralreefsystems.org/expedition-year/2013/sequencing-at-sea
    11. Lim Y.W., Schmieder R., Haynes M.R., Furlan M., Matthews T. D., Whiteson K., Poole S. J., Hayes C. S., Low D. A., Maughan H., Edwards R., Conrad D., Rohwer F. (2013) Mechanistic model of Rothia mucilaginosa adaptation toward persistence in the CF lung, based on a genome reconstructed from metagenomic data. PLoS ONE
    12. Mokili J.L., Dutilh B.E., Lim Y.W., Schneider B.S., Taylor T, et al. (2013) Identification of a novel human papillomavirus by metagenomic analysis of samples from patients with febrile respiratory illness. PLoS ONE 8(3): e58404.
    13. Lim Y.W., Schmieder R., Haynes M.R., Willner D., Furlan M., Youle M., Abbott K., Edwards R., Evangelista J., Conrad D., Rohwer F. (2012) Metagenomics and metatranscriptomics: Windows on CF-associated viral and microbial communities. Journal of Cystic Fibrosis
    14. Schmieder R., Lim Y.W., Edwards R. (2011) Identification and removal of ribosomal RNA sequences from metatranscriptomes Bioinformatics
    15. Willner D., Haynes M.R., Furlan M., Hanson N., Kirby B., Lim Y.W., Rainey P.B., Schmieder R., Youle M., Conrad D., Rohwer F.  (2011) Case studies of the spatial heterogeneity of DNA viruses in the cystic fibrosis lung. American Journal of Respiratory Cell and Molecular Biology.
    16. Willner D., Haynes M.R., Furlan M., Schmieder R., Lim Y.W., Rainey P.B., Rohwer F., Conrad D. (2011) Spatial distribution of microbial communities in the cystic fibrosis lung. ISMEJ. 2011.104
    17. Ng T.F.F., Willner D., Lim Y.W., Schmieder R., Chau B., Nilsson C., Anthony S., Ruan Y., Rohwer F., Breitbart. (2011) Broad surveys of DNA viral diversity obtained through viral metagenomics of mosquitoes. PLoS ONE 6(6): e20579.
    18. Schmieder R., Lim Y.W., Rohwer F. and Edwards R. (2010) TagCleaner: Identification and removal of tag sequences from genomic and metagenomic datasets. BMC Bioinformatics, 11(1), 341.
    19. Rosario K., Nilsson C., Lim Y.W., Ruan Y., Breitbart M. (2009) Metagenomic analysis of viruses in reclaimed water. Environmental Microbiology, 1462-2920

    TECHNICAL AND IT SKILLS

    • Scanning and Transmission Electron Microscopy
    • Operating Roche-454 pyrosequencer, Ion Torrent PGM, and Illumina MiSeq Sequencer


    LANGUAGES (WRITTEN AND SPOKEN)
    English, Mandarin, Malay, Hokkien (Spoken), Cantonese (Spoken)


    PRESENTATION

    Oral presentation:

    2014 American Society of Microbiology Conference (Boston)
    2013 Cystic Fibrosis: Ecology, Evolution, and Eradication Workshop, Telluride Science Research Center
    2012 North American Cystic Fibrosis Conference
    2012 Liverpool Alder Hey Children’s Hospital
    2012 International Society for Microbial Ecology (ISME-Copenhagen)
    2012 Copenhagen CF workshop
    2011 Cystic Fibrosis: Ecology, Evolution, and Eradication Workshop, Telluride Science Research Center
    2010 SDSU Student Research Symposium

    Poster:
    2013 SDSU Graduate Research Symposium
    2012 SDSU Graduate Research Symposium
    2011 SDSU Graduate Research Symposium
    2011 SDSU Student Research Symposium
    2008 International Metagenomic Conference
    2008 Genome Institute of Singapore SAB meeting

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  • Mark Little
  • marklittle1989@gmail.com
  • Area of Study:

    Marine Microbial Ecology

  • Interests: Music, soccer, diving, guitars
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    Education
    B.S Biology with Marine Emphasis (in progress)

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  • John Mokili
  • jmokili2@msn.com
  • Area of Study: Virus discovery: Liver failure of unknown origin; risk-assessment of pig-to-baboon xenotransplantation; flu-like illnesses of unknown origin; diffuse large B-cell lymphoma of unknown origin; HIV diversity and transmission
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    Education
    Post-doc, HIV/SIV Vaccine at Los Alamos National Lab,  2001 - 2004
    Post-doc, HIV phylogeny at Henry M. Jackson Foundation. 1999 - 2001
    Phd, Virology, University of Edinburgh, 1998
    Master of Science, Medical Microbiology, University of London, 1992
    B.A. Biology/Chemistry, Université Pédagogique Nationale, 1988

    Professional Experience
    Senior Scientific Fellow at Global Viral Forecasting Initiative, 2009 - present
    Assistant Research Professor at San Diego State University, 2007 - present
    Research Scientist at La Jolla Institute for Allergy and Immunology, Division of Vaccine Discovery, 
        2005 - 2007
    Consultant Scientific Officer at Univ. of Natal, South Africa, 1998
    Acting Director/Research Fellow at Project Nkebolo, DR Congo/University of Edinburgh, UK,
        1993 - 1998

    Publications
    Macke J, Calef C, Yusim K, Funkhouser R, Leitner T, Szinger J, Gaschen B, Abfalterer W, Mokili J, Foley B, Korber B, Kuiken C (2007). Search Tools in the HIV Databases pp. 37-57 in HIV Sequence. Compendium 2006/2007. Edited by: Thomas Leitner T, Foley B, Hahn B, Marx P, McCutchan F, Mellors J,Wolinsky S, Korber B. Published by: Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM. LA-UR 07-4826.

    Rong R, S. Gnanakaran, Julie M. Decker, Frederic Bibollet-Ruche, Jesse Taylor, Jeffrey N. Sfakianos, John L. Mokili, Mark Muldoon, Joseph Mulenga, Susan Allen, Beatrice H. Hahn, George M. Shaw, Jerry L. Blackwell, Bette T. Korber, Eric Hunter, and Cynthia A. Derdeyn. Unique Mutational Patterns in the Envelope alpha-2 Amphipathic Helix and Acquisition of Length in gp120 Hyper-variable Domains are Associated with Resistance to Autologous Neutralization of Subtype C Human Immunodeficiency Virus type 1. J Virol. 2007 Jun;81(11):5658-68.

    Olins J.C., Kokolamami J, Lepira B.F., Kashamuka M., Mupenda B., Lubaki M., Maman S., Bollinger R.C., Nachega J.B., Mokili J. Community Preparedness for HIV Vaccine Trials in the Democratic Republic of Congo: Formative Research for Phase I and II Trials.Culture, health and Sexuality, November-December 2006; 8 (6): 529-544.

    Mokili JL, Korber B; The Spread of HIV in Africa. Journal of NeuroVirology, 11(suppl.1): 66-75, 2005 (Review).

    Yang C, Li M, Mokili JL, Winter J, Ndongala ML, Kashamuka MM, Kasali MJ, Atibu LJ, Quinn TC, Bollinger RC, and Lal RB. Genetic diversification and recombination of HIV-1 group M in Kinshasa, Democratic Republic of Congo. AIDS Research and Human Retroviruses, 2005 21(7):661-6.

    Compendium: Nonhuman Primates HIV/SIV Vaccine Trials Database 2003. Editors: John Mokili, Brian Foley, Norman Letvin, Kalpana Gupta, Marta L. Marthas, and Bette T. M. Korber. Los Alamos National Laboratory, December 2004.

    Cynthia A. Derdeyn, Julie M. Decker, Frederic Bibollet-Ruche, John L. Mokili, Mark Muldoon, Scott A. Denham, Marintha L. Heil, Jeannette Y. Lee, Francis Kasolo, Rosemary Musonda, Beatrice H. Hahn, George M. Shaw, Bette T. Korber, Susan Allen, and Eric Hunter. Heterosexual Transmission of Envelope-Constrained, Neutralization-Sensitive HIV-1. Science 2004; 303: 2019-2022.

    Mokili JLK, Rogers M, Carr JK, Simmonds P, Bopopi JM, Foley BT, Korber BT, Birx DL, McCutchan FE. Identification of a novel clade of human immunodeficiency virus type 1 in Democratic Republic of Congo. AIDS Res Hum Retroviruses. 2002 Jul 20; 18(11): 817-23.

    Papathanasopoulos MA, Cilliers T, Morris L, Mokili JLK, Dowling W, Birx DL, McCutchan FE. Full-length genome analysis of HIV-1 subtype C utilizing CXCR4 and intersubtype recombinants isolated in South Africa. AIDS Res Hum Retroviruses. 2002 Aug 10; 18(12): 879-86.

    Randi Vita, Kerrie Vaughan, Laura Zarebski, Nima Salimi, Ward Fleri, Howard Grey, Muthu Sathiamurthy, John Mokili, Huynh-Hoa Bui, Philip E Bourne, Julia Ponomarenko, Romulo DE Castro Jr, Russell K Chan, John Sidney, Stephen S Wilson, Scott Stewart, Scott Way, Bjoern Peters, Alessandro Sette. Curation of complex, context-dependent immunological data. BMC Bioinformatics 2006, 7:341.

    Sathiamurthy M, Peters B, Bui HH, Sidney J, Mokili J, Wilson SS, Fleri W, McGuinness DL, Bourne PE, Sette A. An ontology for immune epitopes: application to the design of a broad scope database of immune reactivities. Immunome Res. 2005 Sep 20;1(1):2.

    Pillay T, Adhikari M, Mokili JLK, Moodley D, Connoly C, Doorasamy T, Coovadia HM. Severe, rapidly progressive human immunodeficiency virus type 1 disease in newborns with co-infection. Pediatric Infectious Disease Journal. 2001.

    Anderson TJ, Haubold B, Williams JT, Estrada-Franco JG, Richardson L, Mollinedo R, Bockarie M, Mokili JLK, Mharakurwa S, French N, Whitworth J, Velez ID, Brockman AH, Nosten F, Ferreira MU, Day KP. Microsatellite markers reveal a spectrum of population structures in the malaria parasite Plasmodium falciparum. Mol Biol Evol. (2000)17(10):1467-82.

    Mokili JLK, Wade CM, Burns SM, Cutting WAM, Bopopi JM, Green SDR, Peutherer JF, Simmonds P. Genetic heterogeneity of HIV type 1 subtypes in Kimpese, rural Democratic Republic of Congo. AIDS Research and Human Retroviruses. (1999), 15: 655-664.

    Prescott LE, MacDonald DM, Davidson F, Mokili JLK, Pritchard DI, Arnot DE, Riley EM, Greewood BM, Hamid S, Saeed AA, McClure MO, Smith DB, Simmonds P. Sequence diversity of TT virus in geographically disperse human population. Journal of General Virology (1999), 80:1751-1758.

    Davidson F, MacDonald D, Mokili JLK, Prescott LE, Graham S, Simmonds P. Early acquisition of TT virus (TTV) in area endemic for TTV infection. Journal of Infectious Diseases. (1999), 179: 1070-1076.

    Prescott L E, Simmonds P, Pritchard D I, Riley EM, Greenwood B M, Hamid S, Saeed A A, McClure M O, Lewis J C M and Mokili JLK. Global distribution of transfusion transmitted (TT) virus (1998). New England Journal Med, 339, 776-777.

    Smith DB, Cucaenu N, Davidson F, Jarvis L, Mokili JLK, Hamid S, Ludlam C, Simmonds P. Discrimination of Hepatitis G virus / GBV-C geographical variants by analysis of the 5í non-coding region. Journal of General Virology (1997), 78: 1533-1542.

    Mokili JLK, Connell JA, Parry JV, Green SDR, Davies AG, Cutting WAM. How valuable are IgA and IgM anti-HIV testing for the diagnosis of mother to child transmission of HIV in an African setting? Clinical and Diagnostic Virology (1996), 5: 3-12.

    Boivin MJ, Green SDR, Davies AG, Giordani B, Mokili JLK and WAM Cutting. A preliminary evaluation of the cognitive and motor effects of pediatric HIV infection in Zairian children. Health Psychology. (1995), 14 (1), 13-21

    Green SDR, Cutting WAM, Mokili JLK, Nganzi M, Hargreaves FD, Davies AG, Bopopi JM, Elton RA, Hardy IRB, Jackson DJ, Klee EB. Stable seroprevalence of HIV-1 in antenatal women in rural Bas-ZaÔre, 1988-1993. AIDS (1994) 8(3): 397-398.

    Jackson DJ, Klee EB, Green SDR, Mokili JLK, Elton RA and Cutting WAM. Severe anaemia in pregnancy - A problem of primigravidae in an area endemic for falciparum malaria in ZaÔre. Trans R Soc Trop Med Hyg. (1991), 85: 829-832.

    Jackson DJ, Klee EB, Green SDR, Mokili JLK, Cutting WAM. Immunoglobulins and Beta-2 microglobulin in HIV-1 infected children in rural ZaÔre., AIDS. (1991); 5 (8): 1032-34.

Picture of Sophie Nguyen
  • Sophie Nguyen
  • sofanguyen@gmail.com
  • Area of Study: bacteriophage, immunology, microbiology
  • Interests: biology, swimming, hiking, music, reading, coffee
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  • Lauren Paul
  • lololauren26862@gmail.com
  • Area of Study: Microbiology
  • Interests: Photography, traveling/exploring, music, diving, anything in the water
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  • Robert Quinn
  • quinnr1234@gmail.com
  • Area of Study: Microbial ecology of human and animal disease
  • Interests: Understanding microbes, understanding baseball, just understanding things in general
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    CURRENT POSITION
    Postdoctoral Scholar. San Diego State University. Specialization: Microbial Ecology of Cystic Fibrosis. Fellowship funding awarded by the Cystic Fibrosis Research Inc. May 2012-present.

    RESEARCH INTERESTS
    My research interests are the microbiology and microbial ecology of animal and human disease, and the physiology and dynamics of microbial communities.

    EDUCATION

    • Ph. D. in Biology, University of Louisiana at Lafayette, Lafayette, Louisiana, 2008 – 2012. Specialization: Microbiology of Aquatic Animal Disease. Advisor: Dr. Andrei Y. Chistoserdov. Dissertation: Shell Disease in the American Lobster (Homarus americanus): Microbiology and Microbial Ecology of a Complex Polymicrobial Disease
    • M. Sc. in Microbiology, University of Guelph, Guelph, Ontario, 2005-2007. Specialization: Molecular and Microbiological Diagnostics of Finfish Disease. Advisor: Dr. Roselynn M.W. Stevenson Thesis: Non-lethal Detection of Bacterial Fish Pathogens with DGGE and the Molecular Epizootiology of Aeromonas salmonicida
    • B. Sc. Microbiology with Honors, University of Guelph, Guelph, Ontario, 2001 - 2005. Department of Molecular and Cellular Biology. Specialization in Microbiology and Molecular Biology of Bacteria, Fungi and Viruses.


    ACADEMIC AWARDS AND HONORS

    • Elizabeth Nash Memorial Postdoctoral Fellowship. December, 2011. Awarded a postdoctoral fellowship grant from the Cystic Fibrosis Research Inc. to work in Dr. Forest Rohwer’s lab at San Diego State University based on my research proposal “Metagenomic signals characteristic of cystic fibrosis exacerbation onset”.
    • J. V. Huner Award. 2010. University of Louisiana at Lafayette, travel fund award.
    • Best Ph.D. Presentation. Southeast/Texas Branch of the American Society of Microbiology Annual Meeting, November 8-11, 2008, University of Texas at Austin.
    • Best Student Presentation. Eastern Fish Health Workshop, April 28-May 1st, 2009. Lake Placid New York.
    • University of Guelph Travel Award. 2007.


    PUBLICATIONS

    1. Smolowitz, R, R. A. Quinn, R.J. Cawthorn, R.L. Summerfield and A. Y. Chistoserdov. 2014. Pathology of two forms of shell disease in the American lobster Homarus americanus Milne Edwards in Atlandtic Canada. J. Fish Dis. 37:577-581. Doi:10.1111/jfd.12136
    2. Quinn, R.A., Lim, Y.W., Maughan, H., Conrad, D., Rohwer, F and K. L. Whiteson. 2014. Biogeochemical forces shape the composition and physiology of polymicrobial communities in the cystic fibrosis lung. mBio 5(2):e00956-13. doi:10.1128/mBio.00956-13 Article Highlighted in: Molloy, S. 2014. A metabolic milieu. Nat. Rev. Microbiol. 12:315. doi:10.1038/nrmicro3268
    3. Whiteson, K., Bailey, B., Bergkessel, M., Conrad, D.,
    4. Delhaes, L., Felts, B., Harris, J.K., Hunter, R., Lim, Y.W., Maughan, H., Quinn, R., Salamon, P., Sullivan, J., Wagner, B., and P.B. Rainey. 2014. The upper respiratory tract as a microbial source for pulmonary infections in cystic fibrosis patients: parallels from island biogeography. Am. J. Resp. Clin. Care Med. 189(11):1309-1315.
    5. Whiteson, K., Meinardi, S., Lim, Y.W., Schmieder, R., Maughan, H., Quinn, R.A., Black, D., Conrad, D., and F. Rohwer. 2014. Breath gas metabolites and bacterial metagenomes from cystic fibrosis airways indicated active pH neutral 2,3-butanedione fermentation. ISME. 8:1247-1258.
    6. Cheng-Chi Hsu, Mariam S. El Naggar, Yao Peng, Jinshu Fang, Laura M. Sanchez, Samantha J. Mascuch, Amalie Møller, Emad K. Alazzeh, Jiri Pikula, Robert A. Quinn, Yi Zeng, Benjamin E. Wolfe, Rachel J. Dutton, Lena Gerwick, Lixin Zhang, Xueting Liu, Maria Månsson, and Pieter C. Dorrestein. 2013. Real-Time Metabolomics on Living Microorganisms Using Ambient Electrospray Ionization Flow-Probe. Analytical Chemistry. July 11th, doi:10.1021/ac401613x
    7. Quinn, R.A., R.J. Cawthorn, R.L. Summerfield, R. Smolowitz and A.Y Chistoserdov. 2013. Bacterial communities associated with lesions of two forms of shell disease in the American lobster (Homarus americanus, Milne Edwards) from Atlantic Canada. Canadian Journal of Microbiology. 59(6):380-390.
    8. Quinn, R. A., R. M. Smolowitz, S. L. Gubbala and A. Y. Chistoserdov. 2013. Culture-independent analysis of bacterial communities in the hemolymph of American lobsters with epizootic shell disease using PCR-DGGE. Diseases of Aquatic Organisms. 103:141-148.
    9. Quinn, R. A, A. Metzler, R. M. Smolowitz, M. Tlusty and A. Y. Chistoserdov. 2012. Exposures of Homarus americanus shell to three bacteria isolated from naturally occurring epizootic shell disease lesions. Journal of Shellfish Research. 31(2):485-493.
    10. Chistoserdov, A., R. A. Quinn, S.L. Gubbala and R. Smolowitz. 2012. Bacterial communities associated with lesions of shell disease in the American lobster (Homarus americanus, Milne-Edwards). Journal of Shellfish Research. 31(2):449-462.
    11. Quinn, R. A., A. Metzler, M. Tlusty, R. M. Smolowitz, P. Leberg and A. Y. Chistoserdov. 2012. Lesion bacterial communities of American lobsters with diet induced shell disease. Diseases of Aquatic Organisms. 98:221-233.
    12. Quinn, R.A. and R. Stevenson. 2012. Denaturing gradient gel electrophoresis for nonlethal detection of Aeromonas salmonicida in salmonid mucus and its potential for other bacterial fish pathogens. Canadian Journal of Microbiology. 58(5):563-571. Quinn, R.A., R.M. Smolowitz and A.Y. Chistoserdov. 2009. Analysis of eukaryotic communities of American lobsters with epizootic shell disease using PCR-DGGE. Journal of Shellfish Research. 28:913-922.


    PUBLICATIONS IN REVIEW/PREPARATION

    • Quinn, R.A., Lim, Y.W., Maughan, H., Conrad, D., Rohwer, F., Whiteson, K. 2013. Targeted and Untargeted metabolomics of cystic fibrosis sputum guided by molecular networking. ISME. In Prep.
    • Quinn, R.A., Whiteson, K., Lim, Y.W., Salamon, P., Mienardi, S., Blake, D., Conrad, D., and F. Rohwer. 2014. A Winogradsky-based culture model of the cystic fibrosis microbial community reveals an association of microbial fermentation with pulmonary exacerbation. ISME. In prep.


    INVITED TALKS

    1. Quinn, R.A., Dorrestein, P., and Rohwer, F. ISME 2014 August 24th-29th, 2014. ‘Omics methods reveal how chemistry governs the biology of cystic fibrosis lung infections.
    2. Quinn, R.A. Southern Line Islands Cruise Meeting. May 29th-30th. Scripps Institute of Oceanography, La Jolla, CA. Metabolomics of Coral Reef Benthic Interactions.
    3. Quinn, R.A. and Dorrestein, P. Bioinformatics Workshop. San Diego State University, Nov 18, 2013. Bioinformatic challenges in metabolomics.
    4. Quinn, R.A., Phelan, V., Whiteson, K., Lim, Y.W., Conrad, D., Dorrestein, P., and Rohwer, F. Microbial Ecology of the Cystic Fibrosis Lung. August 2-4th, 2013. Telluride Sciences: Cystic Fibrosis Ecology and Eradication Conference. Telluride, CO. Novel Culture Models, Metagenomics and Metabolomics of Cystic Fibrosis.
    5. Quinn, R.A. Cystic Fibrosis Research Inc. National CF Family Education Conference. San Francisco, CA, Aug 3rd, 2013. Microbial Community Dynamics Through Cystic Fibrosis Pulmonary Exacerbations.
    6. Quinn, R.A. World Equine Airways Symposium. Calgary, Alberta, Canada. July 15, 2013. Microbial Ecology of the Cystic Fibrosis Lung.
    7. Quinn, R.A. Cystic Fibrosis Research Inc. National CF Family Education Conference. San Francisco, CA, July 28, 2012. The Microbial Ecology of Cystic Fibrosis: Novel Approaches to a Complex Microbial Infection.
    8. Quinn, R.A. Invited Talk for the laboratory of Dr. Forest Rohwer. San Diego State University, April 12, 2011. The makings of an Ugly Lobster: Epizootic Shell Disease in the American lobster.
    9. Quinn, R. A., D. Felder, A. Chistoserdov*, A. Metzler, M. Tlusty and R. Smolowitz. Rhode Island Sea Grant, Lobster Initiative Meeting. August 3-5, 2009. Microbes and Shell Disease.
    10. Quinn, R.A. and A. Y. Chistoserdov. New England Aquarium Research Seminar, July 8, 2009. Microbiology of Epizootic Shell Disease. Presented to scientists at the New England Aquarium
    11. Quinn, R.A. March, 2007. Graduate Student Seminar Series, University of Guelph. Guelph, Ontario. Molecular epizootiology and evolution of Viral Haemorrhagic Septicaemia virus.


    CONFERENCE PRESENTATIONS AND POSTERS

    1. Quinn, R.A.1 Phelan, V., Whiteson, K., Meehan, M., Conrad, D., Rohwer, F, and Dorrestein, P. Mass Spectrometry Applications to the Clinical Lab. March 1st-4th, 2014. Target and untargeted metabolomics of cystic fibrosis sputum guided by molecular networking. Poster.
    2. Quinn, R.A., Phelan, V., Whiteson, K., Lim, Y.W., Conrad, D., Dorrestein, P., and Rohwer, F. Microbial Ecology of the Cystic Fibrosis Lung. August 2-4th, 2013. Cystic Fibrosis Research Inc. National CF Family Education Conference. San Francisco, CA. Microbial Ecology of the Cystic Fibrosis Lung. Presentation.
    3. Rath, C., Phelan, V., Yurong, G., Watrous, J., Wang, M., Quinn, R.A., Lim, Y.W., Dorrestein, K., Bandeira, N., Alexandrov, T., and Pieter C. Dorrestein. June 8-9. 2013. American Society of Mass Spectrometry Annual Meeting, Minneapolis, MN. Understanding the biology of higher organisms through GoogleMAPS-type visualization of specialized metabolites found to be associated with microbial communities. Presentation.
    4. Quinn, R.A., Lim, YW, Whiteson, K., and F. Rohwer. July 28, 2012. Cystic Fibrosis Research Inc. National CF Family Education Conference. San Francisco, CA. The Microbial Ecology of Cystic Fibrosis: Novel Approaches to A Complex Microbial Infection. Presentation.
    5. Quinn, R. A., A. Metzler, M. Tlusty, R. Smolowitz and A. Chistoserdov. Sept 25st-30th, 2011. Joint Genome Institute Microbial Metagenomics Workshop. Walnut Creek, CA. Microbial communities of epizootic shell disease lesions of the American lobster (Homarus americanus). Poster.
    6. Quinn, R. A., A. Metzler, M. Tlusty, R. Smolowitz and A. Chistoserdov. May 21st-24th, 2011. 111th Annual General Meeting of the American Society of Microbiology, New Orleans, Louisiana. Characterization of the microbial community of epizootic shell disease lesions of the American lobster (Homarus americanus). Poster.
    7. Quinn, R. A., A. Metzler, M. Tlusty, R. Smolowitz and A. Chistoserdov. May 21st-24th, 2011. 111th Annual General Meeting of the American Society of Microbiology, New Orleans, Louisiana. A role for an Aquimarina sp. in shell disease of the American lobster (Homarus americanus). Poster.
    8. Quinn. R. A., A. Chistoserdov, A. Meltzer, M. Tlusty and R. Smolowitz. May 23-28th, 2010. 35th Annual Eastern Fish Health Workshop, Shephardstown, West Virginia. Localization of the Shell Disease Pathogen in the Environment: A Quantitative Approach. Presentation.
    9. Quinn, R.A., A. Metzler, M. Tlusty, R.M. Smolowitz and A. Chistoserdov. November 6-9, 2009. Southcentral Branch of the American Society of Microbiology Annual Meeting. Lobster Shell Disease: Interactions at the Host, Pathogen and Environmental Interface. Presentation.
    10. Quinn R. A., A. Chistoserdov, A. Meltzer, M. Tlusty and R. Smolowitz. April 28th-May1st, 2009. 34th Eastern Fish Health Workshop, Lake Placid, New York. Bacteroidetes and Epizootic Shell Disease: Microbial Community Analysis Can Reveal Potential Etiological Agents. Presentation.
    11. Quinn, R. A., A. Y. Chistoserdov*, A.Y., S. L. Gubbala, and R. M. Smolowitz. March 22-26, 2009. The 101th Annual Meeting of National Shellfisheries Association.Various forms and stages of shell disease in the American lobster share a common bacterial pathogen in their lesions. Presentation. Abstract published in: J. Shellfish Res. 28:689.
    12. Quinn, R. A., A. Y. Chistoserdov*, A.Y., S. L. Gubbala, and R. M. Smolowitz. March 22-26, 2009. The 101th Annual Meeting of National Shellfisheries Association. Protozoan and metazoan communities associated with shell lesions and healthy shell surfaces of the American lobster (Homarus americanus) afflicted by epizootic shell disease. Presentation. Abstract published in: J. Shellfish Res. 28: 722-722.
    13. Smolowitz, R.M.*, J. DeFaveri, R. A. Quinn and A. Y. Chistoserdov. 101st annual meeting of the national shellfisheries association, March 22nd-26th, 2009, Savannah Georgia. Comparative Histopathology of Shell Disease in American Lobsters (Homarus americanus) and Four Species of Crab from Coastal Waters of the Northeastern U.S. Presentation. Abstract published in: J. Shellfish Res. 28:730-730.
    14. Quinn, R.A. and A. Chistoserdov. November 8-11, 2008. Southcentral/Texas Branch of the American Society of Microbiology Annual Meeting. University of Texas at Austin, Austin, Texas. Molecular analysis of microbial communities of American lobsters with epizootic shell disease and implications for disease etiology. Presentation.
    15. Quinn, R.A. and A. Chistoserdov. October 24, 2008. University of Louisiana at Lafayette, Graduate Student Symposium. Lafayette, Louisiana. Denaturing gradient gel electrophoresis analysis of the prokaryotic and eukaryotic communities of lobster shell disease lesions. Presentation. Quinn, R.A., A.Y. Chistoserdov* and R. Smolowitz. March 20-22, 2008. Annual meeting of the National Shellfisheries Association. Providence, Rhode Island. Denaturing gradient gel electrophoresis analysis of the prokaryotic and eukaryotic communities of American lobsters with epizootic shell disease. Presentation.
    16. Quinn, R.A. and R. Stevenson. June 18-21, 2007. 32nd Eastern Fish Health Workshop. Gettysburg, PA. Comparison of lethal and non-lethal sampling techniques for the detection of Aeromonas salmonicida and other fish pathogens in populations of Ontario salmonids. Presentation.
    17. Quinn, R.A. and R. Stevenson*. February 23, 2006. Great Lakes Fish Health Committee Continuing Education Workshop, 2006, Madison, Wisconsin. Non-lethal sampling approaches for detecting pathogens in fish health monitoring. Poster.
    18. Stevenson, R*, R.A. Quinn, Indervesh, V. Harper and S. Lord. Sept 3-6, 2006. 5th International Symposium on Aquatic Animal Health. San Francisco, CA. Non-lethal approaches to pathogen detection in salmonid fish: A review and applications for Ontario freshwater fish. Poster.


    *Denotes presenting author if not R. A. Quinn.


    PROFESSIONAL AND TEACHING EXPERIENCE


    Guest Instructor, Louisiana State University at Eunice.

    • 2011. Microbiology Laboratory. Acted as an interim instructor for the microbiology laboratory at LSUE, when the current instructor left the position.


    Teaching Assistant, University of Louisiana at Lafayette, Lafayette, Louisiana,

    • 2010. Instructor. Taught lecture and lab for a sophomore microbiology laboratory worth 3 credit hours.
    • 2008, 2009 and 2011. Microbial physiology and genetics class T.A. and interim instructor.


    Teaching Assistant, University of Guelph, Guelph, Ontario.

    • 2005. Introductory Microbiology Laboratory T.A. and Coordinator.
    • 2006. Systematic Bacteriology Laboratory T.A. and Coordinator.
    • 2007. Introductory Biology Laboratory and Grading T.A.


    Research Assistant, AquaHealth Vaccine Laboratory, Victoria, Prince Edward Island, 2005.

    • Assisted in the development of recombinant viral and bacterial vaccines for the salmonid aquaculture industry. Trained in protein expression, purification and analysis, salmonid challenge experiments, RT-PCR, and other molecular techniques.


    CERTIFICATIONS AND SPECIAL TRAINING

    • Advanced Mass Spectrometry. Trained on Bruker LC-MS/MS and MALDI-TOF mass spectrometry intstruments, by members of Dr. Pieter Dorrestein’s lab. January 2013.
    • Registered and Certified Integrated Microbial Genomes User (IMG). September, 2011. Completed course on advanced assembly and analysis of microbial genomes and metagenomes using the Joint Genome Institute IMG system.


    REFERENCES

    • Dr. Forest Rohwer San Diego State University Biology Department North Life Sciences Rm301 5500 Campanile Dr. San Diego, CA 92182
    • Dr. Andrei Chistoserdov (Ph.D. Dissertation Advisor) University of Louisiana at Lafayette, Department of Biology Wharton Hall Room 505 411 East St. Mary Blvd Lafayette, LA, 70506 ayc6160@louisiana.edu 337-482-1330
    • Dr. Pieter Dorrestein University of California San Diego Skaggs School of Pharmacy and Pharmaceutical Sciences Department of Pharmacology, Chemistry and Biochemistry PSB, Room 3268 9500 Gilman Drive, MC 0751 La Jolla, CA 92093-0751 858-822-5437 pdorrestein@ucsd.edu
    • Dr. Don Ennis (Ph.D. Dissertation Committee Member) University of Louisiana at Lafayette, Department of Biology Wharton Hall, Room 520 411 East St. Mary Blvd Lafayette, LA, 70506 dge5893@louisiana.edu 337-482-5008
Picture of Steven Quistad
  • Steven Quistad
  • steven.quistad@gmail.com
  • Area of Study: Coral immunology and viruses
  • Interests: Backpacking, traveling, SCUBA diving, RV road trips
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    Education
    San Diego State University, University of California San Diego (2010-present) Joint Doctoral Program
    Cell and Molecular Biology

    University of California Santa Barbara (2006-2010) B.A. Biology, minor Global Peace and Security
    GPA: 3.85/4.0, High Honors


    Research Experience
    Doctoral student – San Diego State University, Department of Biology, Dr. Forest Rohwer (PI) (2010-Present)
    Dr. Rob Edwards (Rotation): Bioinformatic comparisons of coral and human immunity proteins
    Dr. Roland Wolkowicz (Rotation): Development of a targeted random peptide library against the furine peptide of HIV localized in the Endoplasmic Reticulum.

    Research Assistant – University of California Santa Barbara, Marine Science Institute: anaerobic propane oxidation, Stable Isotope Probing of methanotrophic viral DNA, viral metagenomics. (2009-2010)
    Advisers: Dr. David Valentine (PI) and Blair Paul (PhD Student).


    Research Assistant – University of California Santa Barbara, Marine Science Institute: Impact of ocean acidification on S. purpuratus molecular physiology. (2008) Advisers: Dr. Michael J. O'Donnell (post doc) and Dr. Gretchen Hofmann (PI)


    Research Assistant – University of California Santa Barbara, Neuroscience Research Institute: Involvement of Tau protein with Neurodegeneration and Alzheimer’s. (2007)
    Adviser: Dr. Stuart Feinstein (PI)


    Biological Science Aid – United States Geological Survey: methanogenesis and mercury cycling in wetland environments. (2006-2007)
    Adviser: Dr. Mark Marvin-DiPasquale (PI)


    Field Expeditions
    Franz Josef Land, Arctic (2013, 4 weeks)
    Southern Line Islands, central pacific (2013, 4 weeks)
    Richard B. Gump South Pacific Research Station, French Polynesia (2011, 4 weeks) NOAA RAMPS Cruise, Northern Marina Islands (2011, 4 weeks), Hi'ialakai
    Study of Ecology and Evolution of Petroleum Seeps, Southern California (2009, 2
    weeks), R/V Atlantis, Dive 4547 of the DSV Alvin


    Publications
    Quistad SD and Rohwer F. (In prep) A highly complex immune system was present at the Precambrian explosion

    Quistad S.D., Paul B.P, Bagby S., Valentine D.L. (In prep) Viral stable isotope probing of an aerobic methanotrophic community.

    Quistad SD, Stotland A, Barott KL, Hilton B, Grasis J, Wolkowicz R, and Rohwer F. (Submitted) The evolution of TNF-induced apoptosis reveals 550 million years of functional conservation.

    Quistad S. D., Valentine D. L. (2011) Anaerobic oxidation of propane in marine sediments. 75 2159-2169.


    Honors and Awards
    Most Collaborative Poster, Graduate Student Symposium, (2012)
    Presidents Award, Student Research Symposium (2012)
    National Science Foundation Graduate Research Fellowship (2010-2013)
    University of California Santa Barbara Award of Distinction (2010)
    College of Creative Studies Executive Committee Award of Excellence (2010)
    Summer Undergraduate Research Fellowship (2009)
    Innovator of the Future Scholarship, Rambus Inc. (2006-2010)


    Presentations
    Immunology 2013, Hawaii (2013)
    Symbiosis Workshop, Yosemite (2013)
    SDSU Student Research Symposium, poster (2013)
    International Coral Reef Symposium, Australia (2012)
    Lower Reef Invertebrate Symbiosis with Microorganisms, Israel, poster (2012)
    California State University Research Competition, Long Beach, oral (2012)
    SDSU Student Research Symposium, San Diego, oral (2012)
    Graduate Student Symposium, San Diego, oral (2011, 2012, 2013)

Picture of Ty Roach
  • Ty Roach
  • smokinroachjr@gmail.com
  • Area of Study: Biogeochemistry, Microbiology, Evolutionary Biology
  • Interests: Surfing, Wrestling, Freestyle Rapping
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    Education
    Ph.D. candidate, Evolutionary Biology JDP, 
    San Diego State University
    BS Biology, BS Botany, minor:genetics, microbiology 
    North Carolina State University 2004-2009

    Research Experience
    Undergraduate Research Assistant. Xie Lab
    North Carolina State University. Raleigh NC. 2008-2009 

Picture of Nate Robinett
  • Nate Robinett
  • nate.robinett@cox.net
  • Area of Study: Evolution of settlement and aggregation behaviors in invertebrates.
Picture of Savannah Sanchez
  • Savannah Sanchez
  • sanchez.s.elizabeth@gmail.com
  • Area of Study: Microbiology
  • Interests: Sports, cooking, music, dance, reading, traveling,family and collecting animals!
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    EDUCATION

    Masters of Science Candidate, Microbiology                                                                    
    San Diego State University 

    July 2013 Hopkins Microbiology Course                                                                                
    Stanford University

    June 2009 Bachelor of Science, Microbiology                                                                          
    University of California, San Diego

    May 2007 Associate in Arts, University Transfer Studies                                                           
    Grossmont-Cuyamaca College

     

    PROFESSIONAL EXPERIENCE

    Lab Manager (Forest Rohwer Lab) (Aug. 2012 – Current Date)

    SDSU Research Foundation
    San Diego, CA

    • Operational duties: Ordering, maintenance of lab equipment and budget, organization of meetings and trainings
    • Training duties: Biannual lab safety training, fundamental lab procedures and handling of common equipment
    • Mentoring duties: Of incoming PhD, MS and UG  students in techniques pertaining to microbiology, solutions and media preparations, and general metabolic theory

    April 2011 – Aug. 2012 Research Assistant                                                                          
    SDSU Research Foundation, San Diego, CA

    • Experimental work focusing on the fabrication of personalized Biolog plates.
    • Experimental work investigating isolation methods for microbes associated with the Cystic Fibrosis lung environment. 

    Aug. 2009 – Aug. 2010 Toxicology Lab Technician                                                                  
    Phamatech, Inc., San Diego, CA

    • Chemical extraction of toxins from biological samples for gas chromatography and mass spectrometry analysis.
    • Preliminary screening of biological samples for presence of toxins via ELISA methods.

    Sept. 2005 – Feb. 2006 Media Technician                                                                              
    Kay Laboratory
    La Jolla, CA

    • Preparation of molecular grade reagents and bacterial growth media.
    • Culturing of bacteria for glycerol stocks and competent cells.
    • Calibration and maintenance of common lab equipment.

     

    TEACHING EXPERIENCE

    Aug. 2012 – Dec. 2012 Advanced Molecular Biology Techniques                                                  
    San Diego State University
    San Diego, Ca

     

    PRESENTATIONS AND PUBLICATIONS

    Phage Phenomics: Characterization of Novel Viral Auxiliary Metabolic Genes

    • Poster presented at San Diego State University CMB Symposium, San Diego Ca 2014

    Mining the Great Unknown: Screening and Characterization of Novel Bacteriophage Proteins
    Savannah E. Sanchez*, Jason Rostron, Daniel Cuevas, Tiffany Y. Liang, Anca Segall, Rob Edwards, Forest Rohwer

    • Oral presentation at San Diego State University Student Research Symposium, San Diego CA 2014

    Shedding Light on the Metabolic Effects of Unknown Viral Genes
    Jason Rostron*, Savannah Sanchez*, Daniel Cuevas*, Tiff Yujing Liang, Victor Seguritan, Robert Edwards, Forest Rohwer, Anca Segall

    • Poster presented at the Analytical Genetics Meeting by Jason Rostron, Alta UT 2014

    Biomass Based Phenomic Approach for Identification of Novel Viral Proteins
    Savannah E. Sanchez*, Jason Rostron, Daniel Cuevas, Daniel Garza, Jeremy Frank, Tiffany Y. Liang, Anca Segall, Rob Edwards, Forest Rohwer

    • Poster presented at San Diego State University Student Research Symposium, San Diego CA 2013


    Dutilh, Bas E., Cassman, N., McNair, K. Sanchez, SE, et al., 2014. A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomics. Nature.com 

    Cuevas DA, Garza D, Sanchez S, et al., Manuscript in prep. Biomass growth curves for large-scale phenotype profiling and applications.

    Sanchez, SA, Rostron, J., Cuevas, DA, et al., Manuscript in prep. Phage phenomics: Physiological approaches to characterize novel viral proteins

Picture of Linda Wegley
  • Linda Wegley
  • lwegley@gmail.com
  • Area of Study: Marine microbiology
  • Interests: Investigating microbial organisms living in the sea. My hobbies include scuba diving, hiking, gardening, photography, and painting
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    Education
    Ph.D. candidate, Cell & Molecular Biology JDP, San Diego State University 
    B.S., Biology, San Diego State University, 2004 

    Professional Experience
    Lab manager and research technician, 2002-present
    San Diego State University, Forest Rohwer lab

    Research Skills:
    Molecular: DNA extraction, PCR, cloning, in situ hybridization.
    Microbiology: Light, Nomarski, epi-fluorescent, confocal, and scanning electron microscopy. I am also 
        very proficient in imaging software.
    Genomic analysis: I have experience using the SEED, Pfam, NCBI, and Clustal databases and some
        bioinformatics skills (Completed Bio 568).
    Field research: SCUBA certified. I have led fieldwork expeditions at the Hawaii Institute of Marine 
        Biology on coconut island, HI, at the Smithsonian Tropical Research Institute in Bocas del Toro, 
        Panama, and on a cruise to Kingman Reef in the northern Line Islands. 

    Publications
    Dinsdale EA, RA Edwards, D Hall, F Angly, M Breitbart, JM Brulc, M Furlan, C Desnues, M Haynes, L Li, L McDaniel, MA Moran , KE Nelson, C Nilsson, R Olson, J Paul, B Rodriguez-Brito, Y Ruan, BK Swan, R Stevens, DL Valentine, RV Thurber, L Wegley, BA White, F Rohwer (2008) Functional metagenomic profiling of nine biomes. Nature. 452. 629-632. >Correction to manuscript published in September 2008.

    Dinsdale, EA, O Pantos, S Smriga, RA Edwards, F Angly, L Wegley, M Hatay, D Hall, E Brown, M Haynes, L Krause, E Sala, SA Sandin, RV Thurber, BL Willis, F Azam, N Knowlton, F Rohwer (2008) Microbial ecology of four coral atolls in the Northern Line Islands. PLoS One. 3(2) e1584. 1-17.

    Thurber, RLV, Barott, KL, Willner-Hall, D, Liu, H, Rodriguez-Mueller, B, Desnuesa, C, Edwardsa, RA, Haynes, M, Angly, FE, Wegley, L, Rohwer, FL (2008) Metagenomic analysis indicates that stressors induce production of herpes-like viruses in the coral Porites compressa. Proceedings of the National Academy of Sciences, USA. 105 (47). 18413–18418.

    Beman, MJ, KJ Roberts, L Wegley, F Rohwer, CA Francis (2007) Distribution and diversity of archaeal ammonia monooxygenase (amoA) genes associated with corals. Applied and Environmental Microbiology. 73 (17). 5642-5647.

    Wegley, L, R Edwards, B Rodriguez-Brito, Hong Liu, F Rohwer (2007) Metagenomic analysis of the microbial community associated with the coral Porites astreoides. Environmental Microbiology. 9 (11). 2707-2719.

    Edwards RA, B Rodriguez-Brito, L Wegley, M Haynes, M Breitbart, DM Peterson, MO Saar, S Alexander, EC Alexander, Jr, F Rohwer (2006) Using pyrosequencing to shed light on deep mine microbial ecology under extreme hydrogeological conditions. BMC Genomics. 7 (57).

    Wegley L, P Mosier-Boss, S Lieberman, F Rohwer (2006) Rapid enumeration of microbes using bulk fluorescence. Environmental Microbiology. 8 (10). 1775-1782.

    Sano, E, S Carlson, L Wegley, F Rohwer (2004) Movement of viruses between biomes. Applied and Environmental Microbiology. 70 (10). 5842-5846.

    Wegley, L, Y Yu, M Breitbart, V Casas, D Kline, F Rohwer (2004) Coral-associated Archaea. Marine Ecology Progress Series. 273. 89-96.

    Casas, V, D Kline, L Wegley, Y Yu, M Breitbart, F Rohwer (2004) Bacterial communities associated with healthy and white band type I diseased Acroporid corals. Environmental Microbiology. 6(11). 1137-1148.

    Breitbart, M, Wegley, L, Leeds, S, Schoenfeld, T, and F Rohwer (2004) Phage community dynamics in hot springs. Applied and Environmental Microbiology. 70 (30). 1633-1640.

    Mosier-Boss, PA, Lieberman, SH, Andrews, JM, Rohwer, F, Wegley, LE, and M Breitbart (2003) The use of fluorescently-labeled phage in the detection/identification of bacterial species. Applied Spectroscopy. 57 (9). 1138-1144.

Picture of Katrine Whiteson
  • Katrine Whiteson
  • katrinewhiteson@gmail.com
  • Area of Study: Phage and bacterial communities that inhabit the human body. I am using metabolomics, metagenomics and ecological statistics to characterize the active, microbial or viral driven processes in polymicrobial communities.
  • Interests: Microbes, dark matter (from phage, or the universe), camping and hiking
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    Education
    Ph.D., University of Chicago, Chicago, Illinois
    Biochemistry and Molecular Biology, 2007

    B.A., University of California, Berkeley
    Molecular Cell Biology, Biochemistry, 2000

    Research Experience
    University of Geneva Hospitals, Geneva, Switzerland, 2008-2011
    Supervisors: Jacques Schrenzel and Patrice Francois
    Conducted studies of healthy and diseased human oral samples. Used both Illumina and 454 high throughput sequencing of relevant 16s rRNA variable regions to enable taxonomic classification and community structure analysis. Carried out study design, sample preparation and data analysis.

    University of Chicago, Chicago, Illinois, 2001-2007
    Advisor: Phoebe Rice
    Dissertation: “Active site chemistry and specificity of Flp recombinase”
    Exploit the trans nature of the architecture of the Flp recombinase active site to study the role of catalytically active residues, and understand how the enzyme has specificity for its DNA substrate in both binding and catalytic steps.

    Publications
    Reyes, A., Semenkovich, N.P., Whiteson, K., Rohwer, F., Gordon, J.I., 2012. Going viral: next-generation sequencing applied to phage populations in the human gut. Nat. Rev. Microbiol. 10, 607–617.

    Bolivar, I.*, Whiteson, K.*, Stadelmann, B., Baratti-Mayer, D., Gizard, Y., Mombelli, A., Pittet, D., Schrenzel, J., 2012. Bacterial diversity in oral samples of children in niger with acute noma, acute necrotizing gingivitis, and healthy controls. PLoS Negl Trop Dis 6, e1556. * contributed equally

    Fischer, A., Whiteson, K., Lazarevic, V., Hibbs, J., Francois, P., Schrenzel, J., 2012. Infant gut microbial colonization and health: recent findings from metagenomics studies. Journal of Integrated OMICS 2.

    Lazarevic, V., Whiteson, K., Gaïa, N., Gizard, Y., Hernandez, D., Farinelli, L., Osterås, M., François, P., Schrenzel, J., 2012. Analysis of the salivary microbiome using culture-independent techniques. J Clin Bioinforma 2, 4.

    Stenz, L., Francois, P., Whiteson, K., Wolz, C., Linder, P., Schrenzel, J., 2011. The CodY pleiotropic repressor controls virulence in gram-positive pathogens. FEMS Immunol. Med. Microbiol. 62, 123–139.

    Lazarevic, V., Whiteson, K., François, P., Schrenzel, J., 2010. The salivary microbiome, assessed by a high-throughput and culture-independent approach. Journal of Integrated OMICS 1, 28–35.

    Lazarevic, V., Whiteson, K., Hernandez, D., François, P., Schrenzel, J., 2010. Study of inter- and intra-individual variations in the salivary microbiota. BMC Genomics 11, 523.

    Lazarevic, V.*, Whiteson, K.*, Huse, S., Hernandez, D., Farinelli, L., Osterås, M., Schrenzel, J., François, P., 2009. Metagenomic study of the oral microbiota by Illumina high-throughput sequencing. J. Microbiol. Methods 79, 266–271. * contributed equally ** Top 25 hottest articles, #1, October – December 2009

    Whiteson, K.L., Rice, P.A., 2008. Binding and catalytic contributions to site recognition by flp recombinase. J. Biol. Chem. 283, 11414–11423.

    Whiteson, K.L., Chen, Y., Chopra, N., Raymond, A.C., Rice, P.A., 2007. Identification of a potential general acid/base in the reversible phosphoryl transfer reactions catalyzed by tyrosine recombinases: Flp H305. Chem. Biol. 14, 121–129.

    Grindley, N.D.F., Whiteson, K.L., Rice, P.A., 2006. Mechanisms of site-specific recombination. Annu. Rev. Biochem. 75, 567–605.