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Funding Update: Jun 30, 2009

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Sequencing-Related NSF Grants Awarded June 3 — June 30, 2009

Collaborative Research: Evolutionary genomics of rapid adaptation in threespine stickleback

Two awards with this title were made:

Start Date: July 1, 2009
Expires: June 30, 2012
Awarded Amount to Date: $364,756
Principal Investigator: William Cresko
Sponsor: University of Oregon Eugene

Start Date: July 1, 2009
Expires: June 30, 2012
Awarded Amount to Date: $306,901
Principal Investigator: Frank von Hippel
Sponsor: University of Alaska Anchorage Campus

The goal of this research is to analyze patterns of divergence across entire genomes of multiple populations of Alaskan oceanic stickleback that colonized freshwater ponds formed during a massive earthquake in 1964. Using new sequencing technology and newly developed techniques for evaluating genome-wide patterns of genetic variation, this project will evaluate the similarity of genomic responses of each population to their new freshwater habitats. This research will provide a case study of the genomic changes that occur during the responses of organisms to both natural and human-caused environmental changes. In addition, according to the grant abstract, the results of this work will provide a better understanding of the genomic basis of how organisms respond to climate change, another environmental perturbation that could stimulate rapid evolution. The awards are funded under the American Recovery and Reinvestment Act of 2009.


Collaborative Research: New Medium for DNA Separation of Microbial Communities

Two awards with this title were made:

Start Date: July 1, 2009
Expires: June 30, 2011
Awarded Amount to Date: $255,534
Principal Investigator: Linda McGown
Sponsor: Rensselaer Polytechnic Institute, New York

Start Date: July 1, 2009
Expires: June 30, 2011
Awarded Amount to Date: $94,321
Principal Investigator: DeEtta Mills
Sponsor: Florida International University

This project investigates a new gel medium that is formed by self-association of guanosine compounds to resolve same length DNA with different sequences. Combining the new gel with conventional sieving gels in capillary gel electrophoresis will lead to "unprecedented" resolution in length and sequence of community DNA that will reveal previously masked community diversity without having to sequence the entire metagenome of the microbial community, thereby greatly reducing the time and expense compared to current methods, according to the grant abstract. The awards are funded under the American Recovery and Reinvestment Act of 2009.


EAGER: A Subtractive EST Approach to the Phylogenetics of Endosymbiotic Foraminifera

Start Date: June 1, 2009
Expires: May 31, 2010
Awarded Amount to Date: $39,772
Principal Investigator: Megan Cevasco
Sponsor: American Museum Natural History, New York

Coral reefs are home to many species of single-celled organisms known as Foraminifera, each of which contains within it multiple tiny single-celled algae. The presence of the algae has made it difficult to determine which genes are present in the foraminiferans because the algal genomes are hard to separate from those of their hosts. This research applies recent advances in genomic sequencing technology to overcome this problem by producing thousands of DNA sequences for the mixture of the foraminiferan (host) and the microalga (symbiont) together. The microalga will then be grown separately and DNA sequences generated for it. Using a computer, the set of microalgal sequences can then be subtracted from the set of foraminiferan sequences, and the subtracted sequence data can be used to determine the evolution of the two organisms in the symbiosis.

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RCN for Genomic and Metagenomic Standards

Start Date: June 1, 2009
Expires: May 31, 2010
Awarded Amount to Date: $100,000
Principal Investigator: John Wooley
Sponsor: University of California-San Diego

This grant is awarded to create a research coordination network to promote and integrate standards for genomic and metagenomic data and metadata within an international community. The network is based on the existing Genomic Standards Consortium and will be extended under this award to include ecological data standards such as Ecological Metadata Language, biodiversity standards such as Darwin Core, and environmental research programs such as the Global Lake Ecological Observatory Network and Long Term Ecological Research. The creation of this network will "ensure a worldwide, community-driven process for establishing standardized mechanisms for the electronic capture of genomic data and for obtaining willingness to participate," according to the grant abstract. Collaborations around the maturation of GCDML, Genome Rosetta Stone, and the Genome Catalogue will be an early focus. Productivity will be sustained year round by routine A.V. and web-enabled interactions, including small working group sessions and collaborations via the RCN's extant web hub. The activities will expand ongoing coordination required for implementation, including the Genome Catalog, GCDML, Genome Rosetta Stone software, Habitat-Lite and Environmental Ontology, and the eJournal Standards in Genomic Sciences. The RCN will also sustain and build upon the active, ongoing, two-way exchange between LTER and GSC, interactions arising from common goals.


Tomato Chromosome 1 and 10 Sequencing, Coordination and Bioinformatics for the International Solanaceae Genome Initiative

Start Date: June 1, 2009
Expires: May 31, 2014
Awarded Amount to Date: $2,442,430
Principal Investigator: James Giovannoni
Sponsor: Boyce Thompson Institute Plant Research

An international consortium of 10 countries has initiated sequencing of tomato as a reference genome for the Solanaceae family of crops. This project represents the US contribution to the tomato genome sequencing effort and specifically encompasses creation of a low-resolution DNA sequence of the entire tomato genome based on state-of-the-art sequencing technologies, high-quality DNA sequence of two of the twelve tomato chromosomes (chromosomes 1 and 10) to complement the remaining 10 chromosome sequences being created by international participants, and creation and enhancement of electronic web-based resources to allow characterization, analysis, and delivery of the tomato genome sequence to researchers who will exploit it for biological discovery in tomato and additional crop species important as sources of food, fiber, and energy.


CAREER: Computational Infrastructure for Full-Sequence Association Studies with Pooled Individuals

Start Date: June 1, 2009
Expires: May 31, 2014
Awarded Amount to Date: $399,999
Investigator: Itsik Pe'er
Sponsor: Columbia University

Thousands of individuals can now be sequenced for targeted regions of the genome in pools of individuals. The complete spectrum of common and rare alleles thus revealed is a key resource for understanding human origins, genomics, and heritable traits, the abstract states. Naïve tests of association of a heritable trait to a common variant are inappropriate for analysis of rare gene variants, since the contribution of each such rare variant to the trait is often statistically undetectable. The hope for finding an associated gene therefore lies in accumulating association signal across multiple functional variants. The problem of multiple-variant association is complicated by background correlations between nearby variants. This proposal involves the design of overlapping pools for recovering mutation carrier identity. Each individual will be sequenced in a unique combination of pools. Mutations observed in such a set of pools will be inferred to be carried by the corresponding individual. This proposal tackles the main task, of using individual-level mutation data for scoring of association to multiple variants in a locus, by Bayesian scoring for genomic intervals containing functional variants. Comparative genomics is used to guide a prior distribution for whether a sequenced variant is likely to be functional. The association score is further decomposed to contributions of each sample and each site, with Markovian dependency between such contributions along the genome. A dynamic-program is proposed for optimizing the causal locus boundaries.

The Scan

Interfering With Invasive Mussels

The Chicago Tribune reports that researchers are studying whether RNA interference- or CRISPR-based approaches can combat invasive freshwater mussels.

Participation Analysis

A new study finds that women tend to participate less at scientific meetings but that some changes can lead to increased involvement, the Guardian reports.

Right Whales' Decline

A research study plans to use genetic analysis to gain insight into population decline among North American right whales, according to CBC.

Science Papers Tie Rare Mutations to Short Stature, Immunodeficiency; Present Single-Cell Transcriptomics Map

In Science this week: pair of mutations in one gene uncovered in brothers with short stature and immunodeficiency, and more.