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Environmental Factor, November 2012

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Genomics day highlights the new resources available to intramural researchers

By Sonika Patial

Kevin Gerrish, Ph.D.

Gerrish, above, and his team keep themselves abreast of new developments in the rapidly advancing fields of genomic technologies and bioinformatics. (Photo courtesy of Steve McCaw)

David Fargo, Ph.D.

Fargo said he hopes to help empower researchers to work as independently as they want. (Photo courtesy of Steve McCaw)

NIEHS celebrated Genomics Day Sept. 27, by showcasing new resources for high-throughput assessment and the advanced research these resources make possible. Scientists and trainees from NIEHS and the adjacent U.S. Environmental Protection Agency (EPA) gathered in Rodbell Auditorium for a series of talks followed by a stimulating poster session.

Kevin Gerrish, Ph.D., deputy director of the NIEHS Molecular Genomics Core, opened the event with a synopsis of the agenda for the day’s activities and emphasized that the main goal of Genomics Day is to increase awareness and promote discussion about advances in genomic methods and software technology, as well as to inform researchers at NIEHS about the sophisticated bioinformatics resources available to them. Describing the array of genomic techniques scientists can access, Gerrish said, “I think we have a really robust program here at NIEHS.”

In addition, Gerrish briefly described the restructuring that will combine the Microarray core, Molecular Genetics core, and Sequencing lab group into a consolidated core lab that will be called the Molecular Genomics Core.

NIEHS Sequencing Lab Group Manager Greg Solomon presented an overview of the new NextGen facilities available at NIEHS. Solomon proudly showcased the new MiSeq instrument, which is capable of a range of assays, from targeted resequencing, small genome sequencing, and RNA sequencing to methylated DNA sequencing.

Describing the new features of the versatile and virtually self-reliant little unit, Solomon said, “This technology is changing almost daily.”

A final resource presentation by David Fargo, Ph.D., director of the Integrative Bioinformatics Group in the NIEHS Office of the Scientific Director, featured an overview of the bioinformatics support for the research programs at NIEHS, as well as the general and individually tailored bioinformatics training and mentoring. Fargo pointed to support available from his colleagues, Biostatistics Branch staff scientists Pierre Bushel, Ph.D., and Grace Kissling, Ph.D., as well as contractor Ruchir Shah, Ph.D.

Fellows took center stage with Genomics Day presentations

When it came time to show off the results of genomics support at NIEHS, fellows outnumbered senior researchers in sharing their work this year. Out of a total of seven presentations, five were made by fellows and two by group leaders (see text box). These oral presentations highlighted the wide range of different genomics technologies currently available to researchers and underscored the scope of these techniques, as well as how they are bound to revolutionize the field of biomedical research.

Presenters were among the lead authors of the 41 posters that were displayed in the afternoon poster session. The poster session was structured so the researchers who were not selected for oral presentations would still be able to present their work. Organizers intermingled vendor posters with the NIEHS and EPA ones, to increase exposure and create dialogue with the companies that provide the reagents and platforms for performing genomic studies.

As Gerrish explained, the Genomics Day talks and poster session promote interaction between the NIEHS and EPA research communities.

(Sonika Patial, D.V.M., Ph.D., is a visiting fellow in the NIEHS Laboratory of Signal Transduction.)

Jennifer Nichols, Ph.D.

Using gene expression patterns, Nichols looked at windows of susceptibility for oxidative lung injury in infants. (Photo courtesy of Steve McCaw)

Steve Kleeberger, Ph.D., Greg Solomon, and Ken Korach, Ph.D.

The poster session offered NIEHS scientists an opportunity to huddle in impromptu conversations. Shown, left to right, are lead researcher Steve Kleeberger, Ph.D., Solomon, and lead researcher Ken Korach, Ph.D. (Photo courtesy of Steve McCaw)

Anne Lai, Ph.D.

As part of her study, Lai assessed differences in DNA methylation during activation and differentiation of B cell subsets from inflamed tonsils. (Photo courtesy of Steve McCaw)

Carmen Williams, M.D., Ph.D., and Kristin Lichti-Kaiser, Ph.D.

Kristin Lichti-Kaiser, Ph.D., a fellow in the NIEHS Cell Biology Group, right, discusses her work on thyroid hormone synthesis with lead researcher Carmen Williams, M.D., Ph.D. (Photo courtesy of Steve McCaw)

Research highlights of the genomics day presentations

  • “450K epigenome-wide scanning to identify DNA methylations in newborns related to maternal smoke during pregnancy,” by Bonnie Joubert, Ph.D., research fellow in the NIEHS Genetics, Environment, and Respiratory Disease Group. Joubert and colleagues are the first at NIEHS to use Infinium HumanMethylation450 BeadChip (450K) technology (see story).
  • “Dynamics of DNA methylation during B lymphocyte activation and differentiation using methyl-binding domain enrichment, Nimblegen promoter arrays, and NextGen sequencing,” by Anne Lai, Ph.D., postdoctoral fellow in the NIEHS Eukaryotic Transcriptional Regulation Group.
  • “Expression QTL (eQTL) analysis in lung development and hyperoxic lung injury in the neonatal inbred mouse using Illumina gene expression microarrays,” by Jennifer Nichols, Ph.D., EPA postdoctoral fellow and a former predoctoral fellow in the NIEHS Environmental Genetics Group.
  • “Artificial butter flavoring and a rat model of obliterans bronchiolitis (OB) using laser capture micro-dissection and Affymetrix gene expression,” by Dan Morgan, Ph.D., group leader in the NTP Respiratory Toxicology Group.
  • “Chromatin structure controls glucocorticoid receptor recruitment using formaldehyde assisted isolation of regulatory elements (FAIRE) and NextGen sequencing,” by Craig Burd, Ph.D., postdoctoral fellow in the NIEHS Chromatin and Gene Expression Group.
  • “The pervasive effects of Pol II pausing on stimulus-responsive gene networks using ChIP-chip with Nimblegen promoter microarrays and NextGen sequencing,” by Dan Gilchrist, Ph.D., postdoctoral fellow in the NIEHS Transcriptional Responses to the Environment Group.
  • "Meta-analysis identifies determinants of embryonic stem cell identity," by Raja Jothi, Ph.D., lead researcher in the NIEHS Systems Biology Group - Stem Cells, Epigenetics, and Gene Regulation.

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