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NSF Microarray Grants Awarded Jan. 1 — April 8, 2008

SBIR Phase I: Silver Nanopillar patterned substrate for surface enhanced fluorescent detection of carbohydrate microarrays. Start date: Jan. 1, 2008. Expires: June 30, 2008. Awarded amount to date: $99,984. Principal investigator: Xichun Zhou. Sponsor: ADA Technologies.
Funds the development of a carbohydrate microarray platform that “takes advantage of the generation of surface plasmon by silver nanopillars to excite fluorophores above the surface of the microarray to perform detection of binding by proteins.” According to the grant abstract, a “platform for querying the binding to carbohydrate moieties would open the door to a better understanding of the important role that carbohydrates play in the regulation of cell signaling and inter cellular communication.”

Functional genomics of phosphate acquisition during virus infection of Emiliania huxleyi. Start date: Jan. 1, 2008. Expires: Dec. 31, 2010. Awarded amount to date: $808,750. Principal investigator: William Wilson. Sponsor: Bigelow Laboratory for Ocean Sciences.
Supports a study of the functional genomics of phosphate acquisition during virus infection of Emiliania huxleyi. “Microarray technology and analysis of genomes of single infected cells will be used to investigate regulation of all genes in the virus at the same time,” according to the grant abstract. Ultimately, the project aims to “help decipher how giant algal virus genes work together to achieve a successful infection under nutrient stress.”

The Vegetative Transcriptome of Arabidopsis Thaliana. Start date: Jan. 15, 2008. Expires: Dec. 31, 2008. Awarded amount to date: $423,584. Principal investigator: Scott Poethig. Sponsor: University of Pennsylvania.
Funds a study of changes in leaf morphology and physiology when a plant is induced to flower. A “genome-wide analysis of gene expression in leaves at different positions on the shoot of flowering and non-flowering plants of Arabidopsis thaliana “will be performed, according to the grant abstract. “Genes whose expression changes in accordance with the transition between juvenile and adult stages of shoot development are of particular interest” and “mRNA abundance will be determined using the Affymetrix ATH1 microarray” while “small RNA abundance will be determined by high-throughput sequencing-by-synthesis technology.”

Arabidopsis 2010: Development of an Arabidopsis Proteome Chip. Start date: Feb. 1, 2008. Expires: Dec. 31, 2009. Awarded amount to date: $1,850,000. Principal investigator: Michael Snyder. Sponsor: Yale University.
Supports the generation of an Arabidopsis thaliana expression collection containing 10,000 Arabidopsis open reading frames fused to tandem affinity purification tags. According to the grant abstract, an optimized plant-based expression system will be used to produce and purify these proteins. The proteins will be printed on various surfaces to produce Arabidopsis protein chips, which will then be screened for various biochemical assays, including protein-protein interactions, protein-phospholipids interactions, protein-nucleic acid interactions, protein-small molecule interactions, and the identification of substrates for kinases and other enzymes. The reagents and protocols generated will be made available to the scientific community through the project website, the Arabidopsis Biological Resource Center, and the Arabidopsis Information Resource.

Positional Signaling in Arabidopsis Root Epidermis Development. Start Date: April 15, 2008. Expires: March 31, 2009. Awarded Amount to Date: $120,000. Principal Investigator: John Schiefelbein. Sponsor: University of Michigan, Ann Arbor.
Funds a project to address how distinct cell types arise in appropriate patterns by using root epidermis development in Arabidopsis as a simple model. In prior work, a receptor named SCM was determined to play a role in enabling developing epidermal cells to interpret their position relative to the underlying root cells. A working model was proposed where the SCM receptor influences a network of transcriptional regulators in a position-dependent manner to generate the observed cell-type pattern in the root epidermis. According to the grant abstract, this model will be tested by “analyzing the accumulation and the specific function of the SCM receptor using molecular and genetic methods.” Additionally, “new genes that are likely to act in a SCM-related manner will be identified in a genetic screen and in a differential expression-based microarray screen.” The research results are expected to provide insights into the molecular regulation of cell specification and pattern formation during the development of multicellular organisms.

Integrated Approaches to Mapping Genome to Phenome. Start Date: April 15, 2008 Expires: March 31, 2009. Awarded Amount to Date: $123,499. Principal Investigator: Xianghong Zhou. Sponsor: University of Southern California.
Supports the development of integrated approaches for genome-to-phenome mapping. The project will use genomics data, particularly public microarray data, together with the associated phenotypic and environmental context information “to reconstruct the biological basis of phenotypes,” according to the grant abstract. The investigators note in the abstract that “traditional association studies have been relatively successful at relating genetic polymorphisms to phenotypes. However, they have met difficulties in elucidating the gene-gene interactions that contribute to complex phenotypes.” The goal of the project, therefore, is to develop methods for deriving genome-wide molecular networks of genotype-phenotype associations, termed “phenomic associations.”

The Scan

Study Reveals New Details About Genetics of Major Cause of Female Infertility

Researchers in Nature Medicine conducted a whole-exome sequencing study of mote than a thousand patients with premature ovarian insufficiency.

Circulating Tumor DNA Shows Potential as Biomarker in Rare Childhood Cancer

A study in the Journal of Clinical Oncology has found that circulating tumor DNA levels in rhabdomyosarcoma may serve as a biomarker for prognosis.

Study Recommends Cancer Screening for Dogs Beginning Age Seven, Depending on Breed

PetDx researchers report in PLOS One that annual cancer screening for dogs should begin by age seven.

White-Tailed Deer Harbor SARS-CoV-2 Variants No Longer Infecting Humans, Study Finds

A new study in PNAS has found that white-tailed deer could act as a reservoir of SARS-CoV-2 variants no longer found among humans.