GTL/VIMSS Annual Retreat

Hotel Nikko, San Francisco

August 1-3, 2003

# Introduction

The GTL/VIMSS Annual Retreat was held at the Hotel Nikko in San
Francisco on August 1-3, 2003. The meeting was comprised of
presentations by the three core Directors, two sessions of poster
presentations, presentations from other project PIs and a roundtable
discussion of the project strategies & project planning.

# Agenda

**[Friday, August 1]{.underline}**

**8:30am - 9:00am Breakfast (served in Peninsula Room)**

**9:00am - 9:45am Welcome, Retreat Goals and Introductions 9:45am -
9:45am - 10:30am Applied Environmental Microbiology Core (Hazen)**

**10:30am - 10:45am Break (coffee/tea/water served)**

**10:45am - 11:30am Functional Genomics Core Overview (Jay Keasling)**

**11:30am - 12:15pm Computational Core Overview (Adam Arkin)**

**12:15pm - 1:15pm Lunch (served in Bay View Room)**

**1:15pm - 1:30pm Poster Setup - Group I**

**1:30pm - 3:15pm Poster Presentations - Group I**

**3:15pm - 3:30pm Poster Setup - Group II/Break**

**3:30pm - 6:00pm Poster Presentations - Group II 6:00pm - 8:00pm
Working Dinner: Hotel Nikko**

**[Saturday, August 2]{.underline}**

**8:00am - 8:30am Breakfast (served in Peninsula Room)**

**8:30am - 9:15am Bio Panning & Proteomics (M. Keller & J. Wei)**

**9:15am - 10:00am Functional Genomics (Vince Martin)**

**10:00am - 10:15am Break (coffee/tea/water served)**

**10:15am - 11:00am Functional Genomics (Anup Singh)**

**11:00am - 11:45pm Functional Genomics (Jizhong Zhou)**

**11:45am - 1:00pm Lunch (served in Big Sur Foyer)**

**1:00pm - 1:45pm Applied Environmental Microbiology (David Stahl)**

**1:45pm - 2:30pm Applied Environmental Microbiology (Judy Wall)**

**2:30pm - 3:15pm Applied Environmental Microbiology (H.Y. Holman)**

**3:15pm- 3:30pm Break (coffee/tea/water served)**

**3:30pm - 4:15pm Computational (Frank Olken)**

**4:15pm - 5:00pm Computational (Eric Alm)**

**5:00pm Dinner on your own in San Francisco**

**[Sunday, August 3]{.underline}**

**8:30am - 9:00am Breakfast (served in Peninsula Room)**

**9:00am - 10:30am Strategic Planning/Discussion of writing
assignments**

**10:30am - 10:45am Break (coffee/tea/water served)**

**10:45am -- 12:00pm Strategic Planning/Discussion of writing
assignments**

**12:00pm - 1:00pm Working Lunch served in Big Sur Foyer**

# List of Attendees

  ------------------------ ---------------------------------- -------------------------------- ------------------------
  **[Name]{.underline}**   **[Email]{.underline}**            **[Organization]{.underline}**   **[Role]{.underline}**

  Adam Arkin               <aparkin@lbl.gov>                  **LBL**                          GTL Director

  Aindrila Mukhopadhyay    aindrila@uclink.berkeley.edu       **LBL**                          Keasling Lab

  Alyssa Redding           <Aredding@uclink.berkeley.edu>     **LBL**                          Keasling Lab

  Amoolya Singh            <asingh@lbl.gov>                   **LBL**                          Arkin Grad Student

  Denise Wolf              <DMWolf@lbl.gov>                   **LBL**                          Arkin Computational
                                                                                               Programmer

  Dominique Joyner         <dcjoyner@lbl.gov>                 **LBL**                          Hazen Lab

  Eric Alm                 <EJAlm@lbl.gov>                    **LBL**                          Arkin Computational Team
                                                                                               Leader

  Frank Olken              <folken@lbl.gov>                   **LBL**                          PI, LBL

  Hoi-Ying Holman          <hyholman@lbl.gov>                 **LBL**                          Hazen\'s Co-PI

  Jay Keasling             <keasling@socrates.berkeley.edu>   **LBL**                          UCB/LBL PI

  Kat Huang                <KHHuang@lbl.gov>                  **LBL**                          Arkin Computational
                                                                                               Programmer

  Keith Keller             <Kkeller@lbl.gov>                  **LBL**                          Arkin Systems Admin

  Kevin Keck               <KDKeck@lbl.gov>                   **LBL**                          Olken Computational
                                                                                               Programmer

  Kristin Balder-Froid     <khbalder-froid@lbl.gov>           **LBL**                          Deputy Director at LBL

  Lianhong Sun             <Lsun@lbl.gov>                     **LBL**                          Keasling Lab

  Melissa Ramos            <wjramos@lbl.gov>                  **LBL**                          Assistant to Slater

  Nancy Slater             <naslater@lbl.gov>                 **LBL**                          Project Manager

  Pier Oddone              <pjoddone@lbl.gov>                 **LBL**                          Executive Committee

  Sarah Wang               <Yswang@lbl.gov>                   **LBL**                          Arkin Grad Student

  Simon Minovitsky         <Sminovitsky@lbl.gov>              **LBL**                          Arkin Computational
                                                                                               Programmer

  Terry Hazen              <tchazen@lbl.gov>                  **LBL**                          GTL Co-Director

  Vince Martin             <Vmartin@lbl.gov>                  **LBL**                          Keasling Lab Manager

  Tung Chau                <tungchau@yahoo.com>               **LBL**                          Research Associate

  Gwenyth Terry            <gaterry@lbl.gov>                  **LBL**                          Assistant to Arkin

  Kevin Costa              <kacosta@lbl.gov>                  **LBL**                          Assistant to
                                                                                               Balder-Froid

  Sharon Borglin           <seborglin@lbl.gov>                **LBL**                          Hazen lab

  Michael Banda            <mjbanda@lbl.gov>                  **LBL**                          JGI

  Todd DeSantis            <tdesantis@lbl.gov>                **LBL**                          Hazen lab

  Jing Wei                 <jwei@diversa.com>                 **Diversa**                      Diversa

  Carl Abulencia           <cabulencia@diversa.com>           **Diversa**                      Diversa

  Martin Keller            <mkeller@diversa.com>              **Diversa**                      PI, Diversa

  Dorothea Thompson        <thompsondk@ornl.gov>              **ORNL**                         ORNL

  Jizhong Zhou             <zhouj@ornl.gov>                   **ORNL**                         ORNL

  **[Name]{.underline}**   **[Email]{.underline}**            **[Organization]{.underline}**   **[Role]{.underline}**

  Matthew Fields           <fieldsm1@ornl.gov>                **ORNL**                         ORNL

  Weimin Gao               <gaown@ornl.gov>                   **ORNL**                         Post Doc

  Zhili He                 <hez@ornl.gov>                     **ORNL**                         ORNL

  Sara Gauch               <spgauch@sandia.gov>               **Sandia**                       Sandia

  Masood Hadi              <mzhadi@sandia.gov>                **Sandia**                       Sandia

  Swapnil Chhabra          <schhabr@sandia.gov>               **Sandia**                       Sandia

  Anup Singh               <aksingh@sandia.gov>               **Sandia**                       PI Sandia

  Judy Wall                <wallj@missouri.edu>               **U of Missouri**                PI, U of Missouri

  Grant M. Zane            <zaneg@missouri.edu>               **U of Missouri**                U of Missouri

  Huei-che Bill Yen        <yenh@missouri.edu>                **U of Missouri**                U of Missouri

  David Stahl              <dastahl@u.washington.edu>         **U of Washington**              PI, U of Washington

  Amoolya Singh            <asingh@lbl.gov>                   **LBL**                          Arkin Grad Student
  ------------------------ ---------------------------------- -------------------------------- ------------------------

# List of Poster Presentations

  ----------------------------- ---------------------------------- --------------------------------
  **[Presenter]{.underline}**   **[Poster Title]{.underline}**     **[Organization]{.underline}**

  Alyssa Redding                Deciphering the roles of           UC Berkeley
                                two-component systems in           
                                Desulfovibrio vulgaris             

  Anup Singh                    Reversed-Phase Chromatography of   Sandia
                                Peptides in Microchips             

  Denise Wolf                   Motifs, Modules, and Games in      LBL
                                Stressed Out Bacteria              

  Dominique Joyner              Desulfovibrio vulgaris: General    LBL
                                physiology                         

  Dorothea Thompson             Microarray Transcription Profiling ORNL
                                of Low- and High-pH Stress         
                                Tolerance in Shewanella oneidensis 
                                MR-1                               

  Eric Alm                      VIMSS Comparative Genomics Web     LBL
                                Tools                              

  Huei-Che Bill Yen             Growth characteristics of          Univ of Missouri
                                Desulfovibrio vulgaris             

  Kat Huang                     The Evolution and Maintenance of   LBL
                                Operons                            

  Matthew Fields                Novel, Iron-reducing bacterial     ORNL
                                enrichments from the NABIR-FRC     
                                Dominated by Gram-Positive         
                                Microorganisms                     

  Sara Wang                     Comparative Analysis of Gene       LBL
                                Expression in Multiple Bacterial   
                                Species                            

  Sharon Borglin                Phospholipid fatty acid signatures LBL
                                of *Desulfovibrio Vulgaris* under  
                                O~2~ stress                        

  Swapnil Chhabra               Heat Shock Response in             Sandia
                                Desulfovibrio vulgaris: A          
                                Proteomics Study                   

  Weimin Gao                    Functional annotation of a         ORNL
                                conserved hypothetical protein in  
                                Shewanella oneidensis MR-1:        
                                possible roles involved in iron    
                                homeostasis and oxidative damage   
                                protection                         

  Carl Abulencia                From Soil to Microbes to Genes     Diversa

  Linhong Sun                   Development of a Metabolomics      UC Berkeley
                                Approach for a Desulfovibrio       
                                vulgaris Research                  

  Kevin Keck                    The Biopathways Graph Data Manager LBL

  **[Presenter]{.underline}**   **[Poster Title]{.underline}**     **[Organization]{.underline}**

  Amoolya Singh                 Pathway Evolution and Modularity   LBL
                                of Bacterial Stress Responses      

  Denise Wolf                   Anatomy of a Stress Response       LBL

  Dorothea Thompson             Gene Expression Profile of         ORNL
                                Shewanella oneidensis in Response  
                                to Heat Stress                     

  Dorothea Thompson             Whole-Genome Microarray-Based      ORNL
                                Transcription Profiling of         
                                H2O2-Induced Stress Response of    
                                Shewanella oneidensis              

  Grant M. Zane                 Construction of Strep-Tagged       Univ of Missouri
                                Proteins for proteomic Analysis    

  Jing Wei                      Global Proteome Profiling of       Diversa
                                Desulfovibrio vulgaris Using       
                                Three-Dimensional LC-MS/MS         
                                Proteomic Platform                 

  Keith Keller                  Web-based File Sharing with        UC Berkeley
                                Biofiles                           

  Matthew Fields                The Diversity of Nitrite Reductase ORNL
                                Genes (nirSand nirK) from          
                                Bacterial Communities and Isolates 
                                in nitrate - and                   
                                Uranium-Contaminated Groundwater   
                                and Analysis with Artificial       
                                Neural Networks                    

  Sergey Stolyar                Syntrophic associations of         Univ of Washington
                                Desulfovibrio spp. and a           
                                hydrogenotrophic methanogen:       
                                Simple consortia for studying      
                                microbial stress responses under   
                                environmentally defensible growth  
                                conditions                         

  Swapnil Chhabra               Comparison of radiation stress     Sandia
                                response in Escherichia coli and   
                                Desulfovibrio vulgaris             

  Todd DeSantis                 Bacterial Community Composition in LBL
                                Bioareosols from Eight California  
                                Field Sites Using an Affymetric    
                                Microarray                         

  Weimin Gao                    Genomic expression profiling of    ORNL
                                Shewanella oneidensis (MR-1        
                                exposed to salt stress             

  Zhili He                      Specificity and Sensitivity        ORNL
                                Analysis of Oligonucleotide Probes 
                                for Whole-Genome Microarrays of    
                                *Desulfovibrio* *vulgaris* and     
                                *Geobacter* *metallireducens*      
  ----------------------------- ---------------------------------- --------------------------------

# Notes from the Roundtable Discussion

### Update on GTL Science

-   [Oligos]{.underline}. The *Desulfovibrio vulgaris* oligos are
    complete and ORNL will make the chips within the next few weeks.
    Mathew Fields is working with Eric Alm to determine which of the
    *Geobacter* oligos can be used; they predict that 70-80% of the
    oligos are okay.

-   [Culture Media]{.underline}. Terry Hazen's group will send the
    *Desulfovibrio vulgaris* cell cultures to the teams within one
    month. Terry will use LS media, and he will distribute the protocol
    for comment prior to making the media. Comments on the protocol
    should be returned to Terry as soon as possible. Terry has a chain
    of custody system for tracking samples, and he will bar code label
    the samples. Terry will provide the new growth curves that he gets
    from the new media. Terry and his team will perform quality control
    checks on the samples (to check for contamination), including PLFA
    and cell plating. Terry will compare his samples to Gary Anderson's
    samples. Vince and Jay will set up a conference call for the
    Functional Genomics Core to discuss cell culture needs.

-   [Physical Heterogeneity]{.underline}. There is a concern about the
    physical heterogeneity of the cell cultures. David Stahl will use
    his biofilm reactors to measure biofilm growth verses planktonic
    growth. David will send his samples in parallel with Terry's sample
    shipments.

-   [Shewanella cells]{.underline}. ORNL will send Shewanella cells to
    Diversa for Proteomics experiments.

-   [Knockouts.]{.underline} The team needs to examine the methods for
    creating knockouts. Jizhong Zhou will send Adam a target list of
    genes from his microarrays. Vince has a table of gene bar code tags.
    Anup Singh would like affinity tags for wild-type genes, not
    mutants.

### Planned Publications

1.  Salt Stress paper by Jizhong Zhou (late September completion)

2.  pH Stress paper by Jizhong Zhou (late September completion)

3.  Temperature Stress paper by Jizhong Zhou (late September completion)

4.  Oxidative Stress paper by Jizhong Zhou (December completion)

5.  Biofilms verses planktonic cell growth paper by David Stahl

6.  Nature Insight paper by Adam Arkin (November completion)

7.  Characterization of microbial communities under the stressful
    conditions of nitrate, heavy metals, and acidic pH by Mathew Fields
    (late November completion)

8.  Review of metabolomics paper by Vince Martin (October completion)

9.  Oxygen stress in Desulfovibrio vulgaris by Hoi-Ying Holman (October
    completion)

### Progress Reports

Progress Reports are due by the end of the first full week of the month.
Each report should include progress from the previous month, any
problems/challenges encountered, and the plan for progress during the
upcoming month. The PIs should enlist their GTL team members to help
with the timely writing of these reports. Information from these reports
will be used to generate a quarterly report to DOE Program Managers.

### Assessment of Finances

Each PI should assess their financial situation for the remainder of
FY03. This assessment includes determining carryover funds for FY04.
Also, an assessment of equipment needs for FY04 should be performed and
reported to Nancy.

### ASM Conference (May 2004)

We would like to apply for a session devoted to GTL work. Members of our
GTL team are encouraged to submit (abstracts or posters?) to this
session. Terry Hazen will propose this session to the ASM conference
organizers.

### Lab Notebooks

Each PI should send their lab notebook numbers to Nancy for tracking
purposes. At the end of each fiscal year, copies of the lab notebooks
must be submitted to LBNL for records maintenance. The information
contained in the GTL lab notebooks is confidential and will not be
shared or distributed.

### Email Message Groups

Email message groups will be created by Keith Keller and sent to all of
the GTL team members. There will be separate mailing lists for PIs, each
Core group and one list for all of the GTL team members. This email
group setup will record all of the messages sent, and the team members
may review the message history at any time. The Discussion Board will
still be used for posting information as well as large files that are
too large to send via email.

### GTL Data Standards Workshop

LBNL will host a GTL Data Standards Workshop on September 10-11 in San
Francisco. The invitation will be forwarded to all of the GTL PIs.
Members from each of the GTL projects will be present at the workshop. A
web link to the workshop is available through the VIMSS site.

### Technical Advisory Committee

Our GTL project is creating a Technical Advisory Committee comprised of
outside scientists who will act as advisors for our project. We've
compiled a list of candidates including Tim Tiedje, Jim Fredrickson,
Dereck Lovely, Eugene Koonin and Fitz Widdel(?) and Gerrit Voordouw(?).
Other suggestions for candidates should be forwarded to Nancy.

### Potential Collaborators with VIMSS

Terry Hazen informed the group of a project that will study deep
subsurface samples. More details are forthcoming.

End of Report