Genome Center Core Facility Pilot Projects

The Genome Center is pleased to announce the request for proposals for the next round of pilot projects to use the technology service cores.

Program Scope:

This program will allocate up to $2,000 worth of service to UC Davis researchers to be used in one or more of the five Genome Center core facilities:

• DNA Technologies (http://genomecenter.ucdavis.edu/dna_technologies/)
• Expression Analysis (http://genomecenter.ucdavis.edu/expression_analysis/)
• Proteomics (http://proteomics.ucdavis.edu/)
• Metabolomics (http://metabolomics-core.ucdavis.edu/)
• Bioinformatics (http://bioinformatics.ucdavis.edu)

This support is designed to allow investigators to generate preliminary data for grant proposals or to explore how the expertise and equipment in the genome center core facilities can be utilized in their research. It is not intended to supplement on-going projects taking place in the cores.

Procedure:

For consideration in this round, principal investigators should submit a one page proposal by June 15, 2008 to the core manager(s) of the facility(ies) that they wish to access. PIs are strongly encouraged to consult the webpage for each core to see how the funds could be best utilized within the context of the services provided. Further discussions with the core facility manager(s) prior to submission can occur if necessary. There is a three month deadline from awards to project initiation (see below); therefore experimental materials to be analyzed should be in hand or readily obtainable. Since requests for pilot grant proposals are made approximately every six months, investigators should wait until the next call if materials are not ready or imminently available for analysis. Proposals will be reviewed and prioritized by the advisory committee for each core. Proposals will be evaluated on their feasibility, appropriateness for the facility, and the likelihood of the data generated leading to a paper or successful grant proposal. Support for on-going use of the cores or to cover training fees for operation of core equipment will not be considered. It is anticipated at least five pilot projects from each core facility will be funded. In past rounds the majority of proposals have been supported. Investigators receiving previous pilot grant awards can apply but depending on the number of application may receive lower rankings. Selected projects will be performed in order of priority set by the advisory committee and subject to availability of resources in the facility in excess of work commissioned at the normal recharge rates.

Provisions:

• Pilot Projects should be initiated within three months of the award and should be completed within six months of initiation. If the funds are not used within this period of time, the award will expire and the PI may re-apply in the next round of pilot projects.
• It is expected that grant proposals submitted using data generated from this program will request funding for continued use of one or more core facilities.
• Applicants may apply for projects costing more than $2,000. In these cases excess costs will be recovered through normal recharges to the PI. If pilot project award does not cover all costs associated with reagents, chips or analytical standards, additional funds may be required from the PI.
• At the end of the project a one page summary report should be provided by the PI noting any publications or submitted grants that include data from the pilot project.
• Publications resulting from use of the cores will acknowledge the services provided.
• Some pilot projects may be appropriately considered collaborative projects between the PI and facility personnel. Such expectations should be discussed and agreed upon at the outset of the project. Facility personnel who contribute significantly intellectually to the project should be acknowledged by inclusion as authors on publications according to standard scientific rules for authorship.
• Pilot Projects are for researchers that are new users of a particular core facility or new projects from a current user. Support for projects that are currently ongoing in a core facility will not be considered.

Free Genome Analysis

The Korf laboratory has recently developed a software pipeline called CEGMA in order to study the many whole genome shotgun genome sequences (WGS) that are available. In a recently submitted manuscript that looks at the utility and completeness of WGS genomes, they have shown that the genome annotations of these sequences frequently miss important, and highly-conserved genes. As a free service, they will run their CEGMA pipeline software against your (eukaryotic) genome sequence to:

• assess how many genes are likely to be present/absent in that assembly
• accurately predict the structures of a set of conserved genes that are present in all eukaryotes.

Email korflab@ucdavis.edu for more information or visit http://korflab.ucdavis.edu

Genome Center Scientist in the news

Janine LaSalle, Professor of Microbiology and Immunology at the UC Davis School of Medicine, and Peggy Farnham, Professor of Pharmacology at the UCDMC as well as the Associate Director of Genomics at the Genome Center, recently completed a study on MECP2, an X-linked gene which, when mutated, can lead to Rett Syndrome. What they found surprised them and will undoubtedly lead to a more accurate understanding of Rett Syndrome genetics and the role of the MECP2 protein. The study, which appeared in the December 4 issue of Proceedings of the National Academy of Sciences is discussed in an article from the UC Davis health system.

2007/2008 Genome Center Colloquium Series

Forefronts of Genomics
All seminars take place at 10am in GBSF Auditorium unless otherwise noted

May 23 Dr. Mike Snyder (sponsored by the Storer Endowment in Life Sciences; faculty host: Peggy Farnham)
Professor; Department of Molecular, Cellular, and Developmental Biology
Yale University

June 27 Dr. Kelly Frazer (faculty host: Katie Pollard)
Director of Genomic Biology
Scripps Genomic Medicine

Sept 26 Dr. Drew Endy
Assistant Professor, Biological Engineering Division
Massachusetts Institute of Technology

For more information about the series, please contact Emily Riley (530) 752-3472.

Upcoming Seminars

Weekly Bioinformatics Tech Forums - Thursdays 11:00am-12:00pm, Room 4202

The purpose of the Thursday Bioinformatics Technology Forum (BTF) meeting series at the Genome Center is to provide a campus-wide venue to show and tell how bioinformatics tools or related information technology actually work. To present your practical problems and ask bioinformatics help is also an appropriate thing to do. In the meeting, people are encouraged to do live demonstrations as well as brief introductions of their work or problems. All talks are informal (although introduction slides are often helpful) and active interactions are expected. BTF is operating by a committee, which consists of Kyoungmi Kim, Jennifer Lee, Dawei Lin, and Kristian Stevens. If you want to talk at BTF, please send an email to lhslin@ucdavis.edu to schedule your talk. BTF meetings are usually held at 11:00am-12:00pm on Thursdays in room 4202, GBSF.

ENCYCLOPEDIA OF DNA PUBLISHED

A consortium of U.S. and international researchers, including a team led by Peggy Farnham, Professor of Pharmacology and Associate Director at the Genome Center, has completed a detailed study of a piece of the human genome. The study, which was carried out by 35 groups from 80 organizations around the world, was published in the June 14 issue of Nature and in 28 companion papers published in the June issue of Genome Research.

Recent Publications from the Genome Center

CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes, 2007, Bioinformatics, 23, 9, Genis Parra, Keith Bradnam, and Ian Korf The numbers of finished and ongoing genome projects are increasing at a rapid rate, and providing the catalog of genes for these new genomes is a key challenge.. read more ...

Structure- based redesign of the dimerization interface reduces the toxicity of zinc-finger nucleases Nature Biotechnology, 25:786-793. Cover article
The Segal Lab, with collaborator Toni Cathomen at Charite´ Medical School in Berlin, Germany, describe an important advance in methods for editing the genomes of living cells. read more...

Genome-Wide Analysis of KAP1 Binding Suggests Autoregulation of KRAB-ZNFs
We performed a genome-scale chromatin immunoprecipitation (ChIP)-chip comparison of two modifications (trimethylation of lysine 9 [H3me3K9] and trimethylation of lysine 27 [H3me3K27]) of histone H3 in Ntera2 testicular carcinoma cells and in three different anatomical sources of primary human fibroblasts.read more...

Folding free-energy landscape of villin headpiece subdomain from molecular dynamics simulations. PNAS, in-press (published online)
Lei et al studied the folding process of a protein called villin headpiece (HP35) using molecular dynamics simulation and achieved high accuracy ab initio folding to as close as 0.46 Å. The achievement marks the first time that ab initio simulations can reach this level. The simulation demonstrated a comprehensive picture on the kinetics and thermodynamics of HP35 folding. read more ...

Forces Shaping the Fastest Evolving Regions in the Human Genome. PLoS Genetics, 2: e168.
Katherine Pollard and colleagues identified 202 genome sequences that are highly conserved between chimpanzee and other vertebrates, but changed significantly in the human lineage since divergence from the chimp-human ancestor. These Human Accelerated Regions (HARs) are mostly in non-coding DNA, often nearby proteins involved in transcription. There is some evidence of positive selection in the most accelerated HARs. In addition, the human-specific changes show a strong bias for AT to GC nucleotide changes, suggesting either biased gene conversion or isochore selection. read more ...

"Macronuclear Genome Sequence of the Ciliate Tetrahymena thermophila, a Model Eukaryote." PLoS Biol. 2006 Aug 29;4(9).
In the September issue of PLoS Biology, Jonathan Eisen and colleagues report on the sequencing and
analysis of the macronuclear genome of the ciliate Tetrahymena thermophila. read more ...

"An RNA gene expressed during cortical development evolved rapidly in humans." Nature. 2006 Aug 16.
Pollard and colleagues scanned the human genome for DNA sequences that have been nearly frozen throughout vertebrate evolution but changed rapidly in the human lineage since the chimp-human ancestor. read more ...

"Structure of Aart, a Designed Six-Finger Zinc Finger Peptide, bound to DNA" J. Mol. Biol. Aug 2006. doi:10.1016/j.jmb.2006.08.016
The Segal Lab, in collaboration with crystallographer Nancy Horton at U. Arizona, present the first crystal structure of an engineered, 6-zinc finger DNA-binding protein bound to DNA. read more ...

"Suz12 binds to silenced regions of the genome in a cell-type-specific manner." Genome Res. published online Jun 2, 2006.
In this manuscript, Squazzo and colleagues use the technique of genome-wide ChIP-chip to identify thousands of promoters that are silenced by Polycomb Group Repression Complexes (PRCs). read more ...