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Funding Update: Oct 27, 2009

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Sequencing-Related NSF Grants Awarded Sept. 1 — Oct. 26, 2009

SBIR Phase I: Bioinformatic FPGA Appliance

Start Date: Jan. 1, 2010
Expires: June 30, 2010
Awarded Amount to Date: $150,000
Principal Investigator: Vincent Natoli
Sponsor: Stone Ridge Technology

This project will investigate the technical and commercial feasibility of a bioinformatic computing appliance based on field-programmable gate array technology. DNA sequencing machines produce large volumes of raw data with steady year-by-year increases. The initial data processing stages of alignment and mapping are computationally intense and currently present a significant and growing bottleneck. According to the grant abstract, the grantees believe that an opportunity exists for a new solution that addresses this problem. The company proposes to create an appliance using an open-source algorithm for the purpose of a feasibility study. The objective is to create a powerful and optimized engine for this algorithm that is easily operated by a user through a web interface. The work will be implemented on a PCI-e based FPGA computing board with two user FPGAs. The application will be optimized to make use of specialized features of the chip. The anticipated result is a bioinformatic appliance running 50 to 100 times faster than the standard CPU implementation, at lower power and with a smaller physical footprint.


RIG: Diversity and Biogeography of Microbial Communities in Submerged Caves

Start Date: Sept. 15, 2009
Expires: Aug. 31, 2011
Awarded Amount to Date: $199,252
Principal Investigator: Rima Franklin
Sponsor: Virginia Commonwealth University

The objective of this research is to examine the diversity and distribution of microorganisms in submerged caves using molecular genetic approaches and DNA sequence analysis. Through collaboration with the Cambrian Foundation, the principal investigator will gain access to microbial samples from several previously unstudied submerged caves in Florida, Bermuda, and Mexico. Simultaneous assessment of each site's hydrology and groundwater geochemistry will provide the environmental context for interpreting these data. In addition to discovery of novel microbial species, the research will consider the biological and geological consequences of microbial activity in these ecosystems.


Epigenetic Landscapes and Transcriptomes in Two Maize Inbred Lines and Their Heterotic Hybrids

Start Date: Sept. 15, 2009
Expires: Aug. 31, 2011
Awarded Amount to Date: $500,000
Principal Investigator: Xing-Wang Deng
Sponsor: Yale University

This project will address whether small RNAs and epigenetic modifications, such as histone modifications and DNA methylation, are involved in regulation of heterosis in maize. It will employ next-generation sequencing to provide genome-wide profiling of messenger RNA and small RNA transcriptomes and selected epigenetic modifications in two inbred lines and their reciprocal hybrid offspring. A systematic analysis of these data will provide genome-wide maps of DNA methylation, histone modification patterns, sequence polymorphisms, small RNA abundance, and gene expression levels in the maize inbred lines and their reciprocal hybrids. This in-depth analysis of a selected model pair of maize lines will aid in achieving the long-term goal of understanding the molecular mechanisms of heterosis in maize, the grant abstract states.


Pattern and Process in Human DNA Sequence Variation

Start Date: Sept. 1, 2009
Expires: Aug. 31, 2012
Awarded Amount to Date: $265,322
Principal Investigator: Jeffrey Long
Sponsor: University of New Mexico

This research will contrast and test two competing views about human genetic diversity and evolution. One view sees human genetic diversity as the outcome of founder effects that occurred as the human species expanded from Africa and filled the rest of the globe. The other view sees human genetic diversity as the outcome of genetic drift in a vast network of stable populations connected by local gene flow. To resolve these opposing views, the project will collect new DNA sequence data, and it will conduct analyses in a novel quantitative framework that is built from stochastic population genetic models. The project will produce a new body of DNA sequence data, which it will make publicly available in GenBank.

The Scan

Push Toward Approval

The Wall Street Journal reports the US Food and Drug Administration is under pressure to grant full approval to SARS-CoV-2 vaccines.

Deer Exposure

About 40 percent of deer in a handful of US states carry antibodies to SARS-CoV-2, according to Nature News.

Millions But Not Enough

NPR reports the US is set to send 110 million SARS-CoV-2 vaccine doses abroad, but that billions are needed.

PNAS Papers on CRISPR-Edited Cancer Models, Multiple Sclerosis Neuroinflammation, Parasitic Wasps

In PNAS this week: gene-editing approach for developing cancer models, role of extracellular proteins in multiple sclerosis, and more.