Home

Annual Report 2006

PROGRESS REPORT – Year 2


COMPUTATIONAL AND GENOME BIOLOGY INITIATIVE
NOVEMBER 3, 2006

1.  What was accomplished in 2005-2006?  Several goals were articulated in the previous report.
A.  Goal - Hiring and Start-Up of New Faculty.  Hiring and starting-up five new faculty, in close collaboration with two colleges and four departments, was the top priority over the past year. The search and recruitment phases occurred in year one (2005) and offers were made.  All new faculty relocated to Corvallis and initiated appointments.  Major start-up purchases and fiscal coordination are being coordinated by Rosa Hill (CGRB), who is managing most start-up phase salary, equipment and supply funds, and facilitating group purchases at substantial discounts.  Three faculty initiated minor or major laboratory renovations. 
  • Dee Denver  (Assistant Professor, Zoology) arrived in March, 2006.  Major renovations for his laboratory space Cordley 2001 (885 sq. ft.), Cordley 2004 (183 sq. ft.) and Cordley 2011B (80 sq. ft.) were coordinated by the Department of Zoology, and funded mainly by CoS but with approximately ¼ funding from CGBI.  One postdoctoral scientist and one Molecular and Cellular Biology Program Ph.D student were successfully recruited to the Denver lab.
  • Todd Mockler (Assistant Professor, Botany and Plant Pathology) arrived in June, 2006  and is occupying temporary office and lab space in Cordley Hall.  Major renovation of his primary laboratory, Cordley 3060 (624 sq. ft), and office/computational space, Cordley 3054 (553 sq. ft.) were initiated and coordinated by the Department of Botany and Plant Pathology.  The CGBI is estimated to contribute approximately ¼ of renovation costs.  Additionally, a new plant growth room will be funded and built using an existing conference room space provided by Botany and Plant Pathology.
  • Jeff Chang (Assistant Professor, Botany & Plant Pathology) arrived in March, 2006 after a search done by the Department of Botany and Plant Pathology.  The Department of Botany and Plant Pathology funded a modest laboratory renovation in Cordley 3097 (630 sq. ft.), Cordley 3097A (321 sq. ft.), Cordley 3097B (97sq. ft.), Cordley 3097C (63 sq. ft), and  several additional shared rooms for computers, radioactive work, plant growth, and other purposes.   The CGBI will partially fund renovations to a growth chamber room 4015K (85 sq. ft) shared with Todd Mockler.
  • Michael Freitag (Assistant Professor, Biochemistry & Biophysics) arrived June, 2006.  He has office and lab space (ALS 2045 and ALS 2034) that require no significant renovation.  He is scheduled to move into larger laboratory facilities upon subsequent retirements in Biochemistry and Biophysics (ALS 2071).
  • Erica Bakker (Assistant Professor, Horticulture) arrived June, 2006.  She occupied high-quality laboratory and office space in ALS 4031 and ALS 4031C, which required no renovation.  She will be using recently renovated greenhouse space, along with Jeff Chang and Todd Mockler, provided by Botany and Plant Pathology.
Success in grant awards is being realized quickly.  The grants portfolio for the new CGBI faculty is provided below:
  • Dee Denver
    NIH R01 GM072639.  Evolutionary Causes and Consequences of Mutational Variation
    05/01/06 - 04/31/11
    PI:  C. Baer (Univ. of Florida)
    Co-PI:  D. Denver (OSU)

    Statement: Approximately 30,000 PCR products generated from two sets each of Caenorhabditis elegans (N2, PB306) and Caenorhabditis briggsae (HK104, PB800) mutation-accumulation lines will be amplified, purified, and then directly sequenced at the OSU Center for Genome Research and Biocomputing for molecular mutation detection.  In addition to the MA lines, the same set of genomic regions will be surveyed in natural isolates for each Caenorhabditis species to compare mutation patterns in the MA lines to natural molecular variation patterns. 
  • Todd Mockler
    NSF DBI 0605240.  Comparative Genomic Analysis of Diurnal and Circadian Gene Expression Regulation
    09/01/06 – 08/31/09
    PI:  Todd Mockler (OSU)
    Co-PI:  Joanne Chory (Salk Institute)
    Co-PI:  Steve Kay (Scripps Research Institute)

    Statement: The ability to appropriately phase gene expression to match the environment is critical to plant growth, confers improved fitness and ultimately allows a plant to survive. We are interested in understanding is how specific regulatory DNA elements and the proteins that bind to them confer phase-specific gene expression depending upon the external light/temperature conditions. In this project we will couple computational approaches with in vivo confirmations of promoter element predictions and the identification of the transcription factors that bind to these elements. We will compare genomic sequences between Arabidopsis, rice and poplar to infer the role of phased gene expression in adaptation to different light/temperature environments.

    DOE-JGI Community Sequencing Program #CSP_LOI_19183.  Deep EST Sequencing of the Brachypodium distachyon Transcriptome
    PIs:  Todd Mockler (OSU), Todd Michael, Samuel Hazen, and Jeff Chang (OSU)

    Statement: Todd Mockler and Jeff Chang are working closely with an international team of collaborators to develop the grass Brachypodium distachyon as a model monocot plant. The Mockler Lab is leading the transcriptome sequencing efforts for the DOE-JGI Brachypodium sequencing project, including the preparation of normalized cDNA libraries from which JGI will be sequencing ~180,000 ESTs. These libraries include a variety of tissues, developmental stages, and stress treatments. Co-PI Jeff Chang's lab is providing samples representing various biotic stress treatments. We anticipate that the sequencing will commence in early 2007.

  • Jeff Chang
    DOE-JGI Community Sequencing Program #CSP_LOI_19183.  Deep EST Sequencing of the Brachypodium distachyon Transcriptome
    PIs:  Todd Mockler (OSU), Todd Michael, Samuel Hazen, and Jeff Chang (OSU)

    Statement: Todd Mockler and Jeff Chang are working closely with an international team of collaborators to develop the grass Brachypodium distachyon as a model monocot plant. The Mockler Lab is leading the transcriptome sequencing efforts for the DOE-JGI Brachypodium sequencing project, including the preparation of normalized cDNA libraries from which JGI will be sequencing ~180,000 ESTs. These libraries include a variety of tissues, developmental stages, and stress treatments. Co-PI Jeff Chang's lab is providing samples representing various biotic stress treatments. We anticipate that the sequencing will commence in early 2007.
  • Michael Freitag
    Medical Research Foundation of Oregon.  Centromeres of filamentous fungi: DNA structure and epigenetic modifications.
    12/01/06 - 11/30/07
    PI:  Michael Freitag (OSU)

    Statement: Centromeres form the foundation for the cellular machinery that transports chromosomes into daughter nuclei during nuclear division, an essential process in all eukaryotes. We are carrying out experiments that directly test the contribution of repeated DNA vs. epigenetic modifications to the placement of functional centromeres in two filamentous fungi, Neurospora crassa and Gibberella zeae. We are testing if Gibberella centromeres - which are devoid of repeated DNA - are entirely defined epigenetically and thus more dynamic than those of other organisms by isolating and sequencing centromeric DNA and determining the distribution of epigenetic modifications found in associated chromatin by “ChIP on chip” microarray technology. Aside from our mechanistic studies we hope to gain new insights into centromere evolution, which will potentially identify novel ways to inhibit invasive growth of fungi by targeting diverged centromere proteins.

B.  Goal - Development of New Computational Facility:  Due to the lack of expansion capacity, cooling, reliable electricity and security in the former space in Cordley used for the CGRB computational infrastructure (distributed server system, disc arrays, parallel compute cluster and network gear), a major renovation was made to ALS 30XX to accommodate the infrastructure within CGRB facilities.  A new cooling system, major electrical upgrade, generator-backup capacity and plumbing were installed.  The facility came online in Spring, 2006, with installation of the entire CGRB computational infrastructure.  The facility was funded partially by CGBI funds and RERF funds from the Research Office.  Expansion of this facility is now on-going to increase computing speed, and to expand back-up and disk array capacity.  This is being done with contributions of CGBI funds, grant funds and CGRB funds.

C. Goal – Attract MCB Graduate Students in Computational and Genome Biology:  Computational and genome biology was stressed as a focal point in new recruitment materials for the MCB Ph.D program.  Among eight new students in the 2006 incoming class, three had interests in computation or genome biology, and two were funded by CGBI first-year fellowships.

D.  Goal – Initiate Renovation of MCB Graduate Program Curriculum:  A systematic review of the MCB Program curriculum was initiated.  Content of two core courses (MCB554 – Genome Organization, Structure and Maintenance;  MCB555 – Eukaryotic Molecular Genetics) was reviewed, content revised, and new contributing instructors identified.  An MCB faculty workshop to continue planning and implementing necessary changes, and to plan integration of CGBI faculty into the curriculum, is scheduled for December 12-13, 2007.

E. Goal – Develop CGBI Website:  The CGBI website (http://cgbi.cgrb.oregonstate.edu/) was developed to provide up-to-date information about the initiative, links to faculty pages, and information about and access to software developed through the initiative.  The CGBI website is integrated in format and content with the CGRB and MCB Graduate Program websites.


2.  Goals for 2006-07

A.   New Graduate Students in MCB Program.  We will continue attracting and elevating the profile of graduate students in computational and genome biology in the MCB Graduate Program.

B.   Continue Renovation of MCB Curriculum.  Plans for the new faculty to teach in the MCB Graduate Program will be finalized by December, 2006.  We are specifically interested in upgrading four existing courses and initiating new courses in computational and genome biology.  

C:  MCB Faculty Workshop.  This is scheduled for December 12-13, 2007.  A primary objective of the workshop is to finalize plans for increased practical and theoretical instruction in computational and genome biology.  

D.  Computational Infrastructure Expansion.   We intend to upgrade several components within the CGRB computational infrastructure, including addition of new cluster nodes that are dedicated for use by new faculty programs.  

E.  New Grant Funding.  Besides grants to individual CGBI faculty, we seek to obtain a group grant to develop a high-throughput sequencing facility with next-generation sequencing technology.


3.  Where you want to be when your initiative is fully developed/matured?
  • Major strength in Computational and Genome Biology at OSU.  Strong impact on existing departments and programs through infusion of new faculty, new graduate students and new or revised core facilities.  We envision OSU being recognized as a major force in these areas of science, which will serve to attract students, faculty, postdoctorals and stature to OSU.
  • Recognition as an excellent destination for graduate students in computational and genome-based biology.  They will be accommodated through formulation of a new track – Computational and Genome Biology – within the MCB Graduate Program. 
  • Major new community resources and core facilities, primarily through the CGRB, enabling high-throughput and computation-intensive bioscience.  This will serve to attract new grant money broadly across OSU.
  • Recognition as a center of high-impact discovery, attracting donors and gift-givers to OSU.

4.  A few simplified metrics that will be easy for others to understand
  • Leveraged approximately $3.1 million from CGRB, Research Office and Colleges to combine with Provost’s Initiative funds.
  • Funds originally proposed for THREE new faculty were leveraged to provide support for FIVE new faculty in four departments.
  • Within five years, each faculty is projected to generate $450,000/yr in external grant funding.
  • Both salary and start-up packages offered are recognized as peer-competitive by our external advisors (Brian Staskawicz of UC Berkeley, and Steve Kay of The Scripps Research Institute).
  • Five new or revised courses to be offered by MCB Graduate Program within two years.

5.  Other helpful information (examples include student credit hours that will be/could be generated; new dollars that will be generated from the dollars invested; a summary of what OSU gets for this investment)
  • In addition to research funding to new faculty, the Initiative and new CGRB investment will continue to fuel high-value, grant-generating activities from existing programs.  Examples of early payoffs from these investments include funding for projects like the Ocean Microbial Genome project ($3.3 million, Moore Foundation; PI:  Giovannoni, CGBI co-coordinator), Arabidopsis Small RNA project (Total $2.9 million over 6 years, NSF; PI: Carrington, CGBI co-coordinator), and new grants for CGBI faculty (see above)

Progress Report prepared by:  

James C. Carrington
Director, Center for Genome Research and Biocomputing, and
Co-coordinator, Computational and Genome Biology Initiative