2008 Genome Center Research Symposium

Friday, May 16, 2008

Genome Center Auditorium & Atrium

All Welcome! Short talks and posters will be presented to provide an update on the research being performed in the Genome Center.

8:00-8:30		Continental Breakfast - Sponsored By Affymetrix
8:30-8:40		Welcome By Richard Michelmore, Director
8:40-9:00		Benham Lab: Eva Strawbridge, Inverted Repeat Distributions with Attention to Potential Cruciform Formation
9:00-9:20		Comai Lab: Daniela Pignatta, Dosage and Parental Effects on Genome Regulation in Arabidopsis
9:20-9:40		Duan Lab: Ting Wang, Diffusional Encounter State Of Carazolol Within The Human Beta2-Adrenegic G-Protein Coupled Receptor
9:40-10:00		Eisen Lab: Amber Hartman, Microbial Re-Colonization Of The Transplanted Human Small Intestine
10:00-10:30		Catered Coffee Break - Sponsored By Illumina
10:40-11:00		Facciotti Lab: Marc Facciotti, Systems-level models of physiological and regulatory networks
11:00-11:20		Farnham Lab: Kim Blahnik, C2H2 zinc finger regulation by the KAP1 repressor complex
11:20-11:40		Fiehn Lab: Gert Wohlgemuth, Binbase - An Open Source Mass Spectrometry Database
11:40-12:00		Koehl Lab: David Gae, Understanding RecA family: Structure, Energetics, Chemistry
12:00-1:00		Lunch - On Your Own
1:00-1:20		Korf Lab: Shahram Emami, Intron Mediated Transcription Enhancement In Plants
1:20-1:40		Ludaescher Lab: Daniel Zinn, Modeling and Optimizing Scientific Workflows
1:40-2:00		Michelmore Lab: Leah Mchale, The Global Architecture Of Disease Resistance In Lettuce
2:00-2:20		Pollard Lab: Alisha Holloway, Accelerated Evolution In The Drosophila Genome
2:20-2:50		Catered Coffee Break - Sponsored By Sigma
3:00-3:20		Rannala Lab: Ying Wang, Bayesian Inference Of Fine-Scale Recombination Rates Using Population Genomic Data
3:20-3:40		Segal Lab: Mital Bhakta, Biochemical And Structural Characterization Of Zinc Finger-DNA Recognition
3:40-4:00		Wright Lab: Izumi Hinkson, Androgen-Mediated Phosphoprotein Profiling In Prostate Cancer

Posters: 4:00-5:00

Social Hour with live music by Minor Groove begins at 5:00

Vendors will be on hand to discuss their products and answer questions. Vendor sponsors include: Active Motif (Luis Acevedo), AffyMetrix (Griffen Lauer), Illumina (Regina Nagle), Roche/NimbleGen (Take Ogawa) & Sigma Life Science (Sharon Squazzo). We thank these vendors for sponsoring the breaks and social hour.

For more information, please contact Emily Riley, eriley@ucdavis.edu

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

Mar 21 Dr. Evan Eichler (faculty host: Luca Comai)
Associate Professor of Genome Sciences
Department of Genome Sciences,
University of Washington

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 ...