June 2011

On May 31st sixteen undergraduates arrived at Duke to begin the IGSP & Center for Systems Biology Summer Fellowship Program. These select students will conduct faculty-mentored research on major questions in genome sciences and policy currently under investigation within the IGSP & Center for Systems Biology, attend weekly IGSP faculty-led seminars and workshops, and participate in a research presentation at the end of the 10-week program. In addition to spending the summer in an IGSP lab, fellows receive a stipend and on-campus housing for the length of the program. This year's group is comprised of nine Duke students, five students from North Carolina Central University (NCCU), one student from North Carolina State University (NCSU), and one student from Rice University. Fellows have been placed in Duke labs based on their interest in specific fields of genome sciences research and the participating faculty member's interest in mentoring undergraduates.

Please join us in welcoming the 2011 Summer Research Fellows to the IGSP! Keep an eye on the plasma screens for profiles of this year's fellows and updates on their summer research experience. And don't forget to mark your calendars for the August 5th undergraduate research presentation in the lobby outside CIEMAS 2240 from 10 am – 12 noon.

As 454 Preps Launch of Sanger-Length Reads, Early Customers Highlight Utility for De Novo Assembly
A GenomeWeb article highlighting 454 Life Sciences’ upcoming launch of the XL+ kit, which supports shotgun sequencing, transcriptome sequencing, and paired-end sequencing, features commentary from Erich Jarvis.

IP Rules for Synthetic Bio Generate More Questions Than Answers
“If and when standardization is realized, then we could see the same sorts of IP issues that we see in information technology regarding standards,” Arti Rai tells Genetic Engineering & Biotechnology News in an article reporting on the bioethical issues facing the field of synthetic biology. “Right now—i.e., absent standardization—I am not sure I see a set of issues distinct from those that face biological research more generally.”

Should Human Genes be Patented?
In an article in The Mark, Bob Cook-Deegan offers commentary on the details, legal issues, and potential consequences surrounding a landmark case working its way through U.S. courts involving the American Civil Liberties Union and Public Patent Foundation’s challenge of Myriad Genetics’ practice of gene patenting.

Polysome Profiling of the Malaria Parasite Plasmodium falciparum
In Molecular and Biochemical Parasitology, Ashley Chi and colleagues suggest a powerful approach for polysome profiling in P. falciparum that opens translational regulation in malaria to genome-wide analysis.

Public Perspectives on Returning Genetics and Genomics Research Results
In Public Health Genomics, Susanne Haga and Julianne O’Daniel suggest that providing the option to learn research results may help strengthen relationships between investigators and participants in genetics and genomics research.

Evolutionary Genetics of Plant Adaptation
Tom Mitchell-Olds and collaborators provide a review of the evolutionary genetics of plant adaptation and emphasize the importance of field studies for understanding the evolutionary dynamics of model and non-model systems in Trends in Genetics.

Identification of Tat-SF1 Cellular Targets by Exon Array Analysis Reveals Dual Roles in Transcription and Splicing
Alex Hartemink and colleagues present finding is in RNA that suggest Tat-SF1 functions independently in transcription and splicing of cellular genes.

Circular Polymerase Extension Cloning for High-throughput Cloning of Complex and Combinatorial DNA Libraries
Jingdong Tian and colleague provide a protocol for a sequence-independent approach for cloning complex individual or combinatorial DNA libraries and routine or high-throughput cloning of single or multiple DNA fragments in Nature Protocols.

Pathway-based Classification of Lung Cancer: A Strategy to Guide Therapeutic Selection
In Proceedings of the American Thoracic Society, Joe Nevins discusses how genomic signatures of oncogenic signaling pathways provide an opportunity to dissect the complexity of lung cancer and serve as tools to direct the use of targeted therapeutic agents.

Genomic Profiles Specific to Patient Ethnicity in Lung Adenocarcinoma
In Clinical Cancer Research, Patrick Tan and collaborators from Duke-NUS explore novel molecular differences between non-small-cell lung cancers (NSCLC) from East Asian and Western European patients, identify ethnic-specific chromosomal aberrations in lung adenocarcinoma, and suggest patient ethnicity should be considered when evaluating future NSCLC therapies targeting genes located on these areas.

Using Noisy Gene Expression Mediated by Engineered Adenovirus to Probe Signaling Dynamics in Mammalian Cells
Lingchong You, Joseph Nevins, and collaborators describe how variability in adenoviral-mediated gene expression provides an effective means to map dose responses of signaling pathways in Methods in Enzymology.

Origin of Bistability Underlying Mammalian Cell Cycle Entry
Lingchong You, Joseph Nevins, and colleagues suggest basic design principles for the robust control of the bistable cell cycle entry at the R-point in Molecular Systems Biology.

Ecological Genetics and Genomics of Plant Defenses: Evidence and Approaches
Tom Mitchell-Olds is a collaborator on a paper in Functional Ecology that reviews ecogenomics techniques and emphasizes how this framework can address long-standing and emerging questions relating to anti-herbivore defenses in plants.

Algorithms in Structural Molecular Biology. Bruce Donald’s upcoming book, called an “essential guide for young scientists on their way to research success” in the field of computational structural biology, will be released by The MIT Press in August 2011.

Susanne Haga and Beth Sullivan were two of three genetics scientists honored with Trustee Alumni awards during the May 1 Senior Investiture and Honors Convocation at McDaniel College.

Waters Corporation added Duke University Proteomics Core Facility, directed by Arthur Moseley, into its Centers of Innovation Program. “Our relationship with Arthur epitomizes a successful corporate/academic collaboration,” said Tim Riley, Vice President and Director, Centers of Innovation Program at Waters.

The NHGRI seeks to provide access to full-service high-throughput genotyping, sequencing or other genetic tools to aid the discovery of genetic elements important in health and disease.

NHGRI is soliciting grant applications to develop new and improved technologies for the efficient, comprehensive and high-throughput identification, validation and characterization of all types of sequence-based functional elements in eukaryotic genomes