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Funding Update: Jul 19, 2011


NSF Microarray Grants Awarded March 15, 2011 — July 19, 2011

Functional structural diversity among maize haplotypes
Start date: March 15, 2011
Expires: Feb. 29, 2012
Awarded amount to date: $1,480,581
Principal investigators: Patrick Schnable
Sponsors: Iowa State University

The goal of this project is to test the hypothesis that differences in gene copy number contribute to the phenotypic diversity and plasticity of maize. The researchers argue that maize is a good model for these studies because it exhibits a rapid decay of linkage disequilibrium and because a draft genome sequence of the B73 inbred and mapping populations is available. In this project, the "Zeanome," a near-complete set of genes present in B73, other maize lines, and the wild ancestor of maize, will be defined using existing genomic sequence data and newly generated transcriptomic data. SV among maize and teosinte lines will be identified relative to the Zeanome. By mapping these copy number variants and PAVs to phenotyped RILs it will be possible to test whether structural variation contributes to phenotypic variation. The hypothesis that structural variation contributed to the domestication of maize and the success of long-term selection will be tested.

PI Patrick Schnable told BioArray News in March that his team will use Illumina sequencing and Roche NimbleGen comparative genomic-hybridization arrays in the project (BAN 4/26/2011).

Genome-wide association mapping of plant resistance to a virulent bacterial pathogen, Pseudomonas syringae
Start date: May 1, 2011
Expires: April 30, 2012
Awarded amount to date: $250,059
Principal investigators: Milton Traw and Neal Stewart
Sponsors: University of Pittsburgh and University of Tennessee

The research team has discovered that some wild collected plants of Arabidopsis thaliana are dramatically more resistant to infection by the virulent bacterial pathogen, Pseudomonas syringae pv. tomato DC3000. The focus of the current project is to understand how elevated resistance in these plants is accomplished. For this purpose, the researchers will use genome-wide association mapping, combined with mining of microarray data on gene expression, to identify focal candidate genes. RNAi knockdown lines will be created for these focal genes and characterized for defects in plant resistance. In addition, plants lacking functional copies of these genes will be complemented with resistance allele candidates and tested to determine whether resistance is restored to those lines. Finally, metabolite screening will be conducted using a subset of the experimental lines.

Barcoding-free multiplexing: leveraging combinatorial pooling for high-throughput sequencing
Start date: May 1, 2011
Expires: April 30, 2014
Awarded amount to date: $420,635
Principal investigator: Stefano Lonardi
Sponsor: University of California at Riverside

The researchers aim to develop a sequencing protocol for hierarchical genome sequencing of large eukaryotic genomes. The computational challenges require the study of combinatorial optimization problems, the development of innovative time- and space-efficient algorithms, and ultimately the implementation and deployment of user-friendly web-based software tools. The resultant combinatorial sequencing protocol is going to be tested to the cowpea genome. Cowpea Vigna unguiculata is one of the most important food legume crops in the semi-arid tropics covering Asia, Africa, and Central and South America, according to the researchers. They expect the final assembly to support applications including map-based cloning of trait determinants, development of markers for marker-assisted breeding, microarray development for gene expression studies, and analysis of synteny with related species.

Development of a sensor array for in situ real-time measurement of deep ocean and hydrothermal vent chemistry
Start date: July 15, 2011
Expires: June 30, 2012
Awarded amount to date: $200,225
Principal investigators: Samuel Kounaves and George Luther
Sponsors: Tufts University and University of Delaware

The researchers aim to develop a prototype ion-selective electrode sensor array capable of providing in situ real-time measurements of a variety of ionic chemical species at extreme depths and near vent temperatures in the ocean. The proposed sensor array will be based on the ISE sensor array that was designed, built, tested, and successfully used on the surface of Mars as part of the 2007 Phoenix Mars Mission to analyze for ionic species in an aqueous solution containing a soil sample. The longer term objective of this initial effort is to enable follow-on research that will provide the ocean sciences community with a new tool for mapping of a broad range of chemical species in seawater.

The Scan

Genetic Risk Factors for Hypertension Can Help Identify Those at Risk for Cardiovascular Disease

Genetically predicted high blood pressure risk is also associated with increased cardiovascular disease risk, a new JAMA Cardiology study says.

Circulating Tumor DNA Linked to Post-Treatment Relapse in Breast Cancer

Post-treatment detection of circulating tumor DNA may identify breast cancer patients who are more likely to relapse, a new JCO Precision Oncology study finds.

Genetics Influence Level of Depression Tied to Trauma Exposure, Study Finds

Researchers examine the interplay of trauma, genetics, and major depressive disorder in JAMA Psychiatry.

UCLA Team Reports Cost-Effective Liquid Biopsy Approach for Cancer Detection

The researchers report in Nature Communications that their liquid biopsy approach has high specificity in detecting all- and early-stage cancers.