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Sequencing-Related NSF Grants Awarded Aug. 14 – Sept. 21, 2007

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Identification and Functional Characterization of Novel Expressed Transcripts in the Rosaceae
 
Start Date: Sept. 1, 2007
Expires: Aug. 31, 2010
Awarded Amount to Date: $1,005,853
Principal Investigator: Kevin Folta
Sponsor: University of Florida
 
The species within the family Rosaceae represent economically valuable fruit, nut and ornamental crops, according to the grantees. Over the last five years there has been a rapid expansion in the DNA sequence information in this family. By focusing on a plant family known and valued for its diversity of plant and plant-product forms (strawberry, raspberry, peach, almond, cherry, apple, pear, rose, and others), this project complements and significantly extends model system studies aimed at illuminating the functions of all plant genes. The research leverages available knowledge of expressed DNA sequences, innovative methods of new sequence capture, the agility of the recombination-based cloning systems, and the efficient genetic transformation capacities of strawberry and the model species Arabidopsis. Specifically, strawberry (Fragaria) and other Rosaceae expressed sequences cloned in Gateway vectors will be subjected to homology searches against GenBank databases to identify sequences that either have no apparent homologous counterparts outside of the Rosaceae family, or that have model system homologues that remain functionally uncharacterized.
 

 
Reconstruction and Annotation of Transcribed Sequences in Plants
 
Start Date: Sept. 1, 2007
Expires: Aug. 31, 2008
Awarded Amount to Date: $641,500
Principal Investigator: John Quackenbush
Sponsor: Dana-Farber Cancer Institute
 
The Gene Index (TGI) databases were developed to provide a high-quality, publicly available analysis of EST sequences and currently represent more than 34 different plant species. This project will more than double the number of plant and plant parasite species represented in the TGI databases.
 

 
Phylogeny and Chloroplast Genome Evolution in Geraniaceae
 
Start Date: Sept. 1, 2007
Expires: Aug. 31, 2008
Awarded Amount to Date: $117,000
Principal Investigator: Robert Jansen
Sponsor: University of Texas at Austin
 
This study will generate an evolutionary tree for the flowering plant family Geraniaceae using multiple genes, which will enable the development of the first classification for the family based on evolutionary history. The first goal of this project is to construct a family-wide evolutionary tree using sequences of four chloroplast and two nuclear genes and chloroplast genome rearrangements for 110 species of Geraniaceae from all major groups within each of the five genera and from four related families. The second goal involves sequencing entire chloroplast genomes for four species of Geraniaceae to add to the nine genomes sequenced or in progress.
 

 
Understanding the Rice Epigenome: From Genes to Genomes
 
Start Date: Sept. 1, 2007
Expires: Aug. 31, 2008
Awarded Amount to Date: $1,320,690
Principal Investigator: Blake Meyers
Sponsor: University of Delaware
 
The goal of this project is to apply novel methods to understand the rice epigenome, with the fundamental objective of transferring the extensive knowledge about plant epigenetics to rice. The data generated by this project will include genome-wide measurements of DNA methylation, histone methylation, small RNA, and mRNA profiles for a comparative set of rice tissues and genotypes. The research will utilize novel laboratory and bioinformatics methods for whole-genome chromatin analysis and for the deep sequencing of small RNAs.
 

 
A Genomic and Physiology Approach to Understanding the Impact of Fungal Colonization on Root Metabolism and Nutrient Acquisition
 
Start Date: Sept. 1, 2007
Expires: Aug. 31, 2010
Awarded Amount to Date: $934,996
Principal Investigator: Daniel Schachtman
Sponsor: Donald Danforth Plant Science Center
 
This project will focus on using genomic tools to understand how the interaction between mycorrhizal fungi and roots alters the way in which roots function in soils where there are localized patches of nutrients, as is typical in most soils, by using tomatoes in soil with and without enrichment with several important nutrients: nitrate, ammonium, zinc, and phosphorus. The PIs will compare the gene expression profiles in mycorrhizal and in non-mycorrhizal tomato roots to the addition of nutrient patches to the soil. The PIs will also use an ultra-high throughput sequencing method, which provides comprehensive data sets for both the discovery of new genes and for comparative gene expression between treatments and tomato genotypes.
 

 
Bacterial Communication in Microbial Mats: A Metagenomic Approach to Understanding Quorum Sensing Gene Diversity and Expression
 
Start Date: Sept. 1, 2007
Expires: Aug. 31, 2010
Awarded Amount to Date: $773,860
Principal Investigator: Robert Norman
Sponsor: University of South Carolina Research Foundation
 
This project will sequence all of the bacteria in the microbial mat (the so-called “microbial metagenome”) and look for possible quorum sensing genes. Then QS gene expression will be followed over time and space to determine what factors control their activities. Finally, QS gene expression will be correlated with major groups of bacteria in the mat in order to determine which groups are the key regulators in the mat.
 

 
Biochemical Genomics: Quizzing the Chemical Factories of Oilseeds
 
Start Date: Sept. 1, 2007
Expires: Aug. 31, 2008
Awarded Amount to Date: $1,196,279
Principal Investigator: John Browse
Sponsor: Washington State University
 
The goal of this project is to use genomics to access the network of genes and proteins that operate chemical factories to synthesize and accumulate novel fatty acids in seeds. Providing a detailed description of genes and proteins required for optimal pathway function will require the integrated deployment of four strategies: a) Investigate and optimize the activities of enzymes for unusual fatty acid synthesis using bioinformatics and protein engineering. b) Carry out extensive sequencing of seeds sampled through the period of oil synthesis, and use functional genomic screens to identify co-evolved enzymes and other protein functions required for incorporation of the novel fatty acid into the oil. c) Perform biochemical analysis of the identified proteins and quantify their contributions to the accumulation of unusual fatty acids through expression in transgenic plants. d) Analyze protein-protein interactions in membranes to gain insight into how these pathways are physically organized.
 

 
The Parasitic Plant Genome Project
 
Start Date: Sept. 15, 2007
Expires: Aug. 31, 2010
Awarded Amount to Date: $1,528,815
Principal Investigator: James Westwood
Sponsor: Virginia Polytechnic Institute and State University
 
The project will produce a comparative genomic analysis of three related genera that span the spectrum of parasitism: a facultative parasite (Triphysaria versicolor), a photosynthetically competent obligate parasite (Striga hermonthica), and an obligate holoparasite (Orobanche ramosa). The availability of a sequenced genome for the closely related non-parasite Mimulus provides a fully autotrophic outgroup to further enhance this approach. The project will sequence cDNAs representing transcripts from key life stages of each parasitic species and conduct cursory comparative analysis of expression patterns based on sequence diversity and abundance.
 

 
Computing Regulatory DNA by Comparing Plant Genomes
 
Start Date: Sept. 15, 2007
Expires: Aug. 31, 2008 (Estimated)
Awarded Amount to Date: $504,060
Principal Investigator: Michael Freeling
Sponsor: University of California-Berkeley
 
This project will provide databases of regulatory DNA sequences, mapping tools, and software needed by the plant breeding and research community. The primary biological research activity is to align each gene in sorghum with its orthologous gene in rice, evaluate exon annotations, and then define and store those noncoding sequences that have been conserved over evolutionary time, called "CNSs". These sequences are expected to comprise DNA sites that bind proteins and small RNAs that regulate gene availability or expression.
 

 
Comparative Genomic and Proteomic Survey of Major Antarctic Marine Phytoplankton: A Foundation for Polar Phytoplankton Genomics
 
Start Date: Sept. 15, 2007
Expires: Aug. 31, 2010
This grant was awarded to two investigative teams:
  • Sponsor: Institute for Genomic Research (now J. Craig Venter Institute).
    Awarded Amount to Date: $546,810.
    Principal Investigator: Andrew Allen
  • Sponsor: Woods Hole Oceanographic Institution.
    Awarded Amount to Date: $425,416.
    Principal Investigator: Mak Saito
The research project will create a foundation for polar marine phytoplankton genomics and proteomics, by surveying three major taxa common to Antarctic waters using primarily expressed sequence tag libraries. These EST libraries will be developed under environmentally relevant conditions, in particular under iron limitation, to improve gene models of key genes involved in important polar biogeochemical processes. In addition, the investigators will use this sequencing project to begin to address research questions related to the interactions of phytoplankton with the biogeochemical cycling of carbon and iron.
 

 
Phytophthora sojae: A High Quality Reference Sequence for the Oomycetes
 
Start Date: Sept. 15, 2007
Expires: Aug. 31, 2009
Awarded Amount to Date: $750,000
Principal Investigator: Brett Tyler
Sponsor: Virginia Polytechnic Institute and State University
 
This project, which will also be funded by the USDA/CSREES, will create a comprehensive genetic resource for oomycete pathogens by creating a high-quality DNA sequence of the soybean pathogen Phytophthora sojae. The Ph. sojae sequence will be integrated with draft sequences for five other oomycete pathogens: Ph. Ramorum; Ph.infestans; the pepper and cucurbit pathogen Ph. Capsici; the downy mildew Hyaloperonospora parasitica; and the broad host range opportunistic pathogen Pythium ultimum.
 

 
Evolutionary Analysis of Speciation in a Marine Species Flock
 
Start Date: Sept. 15, 2007
Expires: Aug. 31, 2009
Awarded Amount to Date: $149,568
Principal Investigator: Andres Aguilar
Sponsor: University of California, Merced
 
The proposed project will identify genes related to reproductive isolation and phenotypic differentiation in a highly diverse group of marine fishes, the rockfish (genus Sebastes). Genes that play a role in pigmentation will be targeted. These include genes for gamete recognition and sperm competition. In other species similar genes display signals of natural selection and evolve in a rapid manner. Genes expressed in the gonads and skin of selected rockfish species will be sequenced to generate large sequence databases. This DNA sequence information will be analyzed in a comparative genomic framework to identify genes that are rapidly evolving and subject to selection. Further analysis of genes across a larger set of rockfish species will elucidate the mode and timing of selective events.
 

 
Genomic Resources for the Study of Cotton-Reniform Nematode Interactions
 
Start Date: Sept. 15, 2007
Expires: Aug. 31, 2008
Awarded Amount to Date: $315,588
Principal Investigator: Ramesh Kantety
Sponsor: Alabama A&M University
 
Various cotton species will be characterized for their responses to the reniform nematode infection while building functional genomic resources. The project will develop and sequence cDNA and small RNA libraries from cotton roots infected with reniform or root-knot nematodes as well as from cotton roots treated with various elicitors of plant defense responses. Four cotton species that react differently to the reniform nematode infection will be included in these studies. Sequences generated will be used in the development of microarrays that can then be used in the functional genomic studies of cotton-reniform nematode interactions. EST sequences will be deposited at the National Center for Biotechnology Information.
 

 
Metatranscriptomic Analysis of Puget Sound Phytoplankton Populations: SGER Complement to the Pacific NW Center for Human Health and Ocean Studies
 
Start Date: Sept. 15, 2007
Expires: Aug. 31, 2009
Awarded Amount to Date: $125,000
Principal Investigator: Andrew Allen
Sponsor: J. Craig Venter Institute
 
With support from this Small Grant for Exploratory Research, researchers at the J. Craig Venter Institute and the University of Washington will use metagenome and transcriptome sequencing of the coastal microbial and phytoplankton communities to investigate how environmental stressors (some related to human activities) might tip the ecological balance toward an increase in harmful algal blooms.
 

 
Genomic Analysis of Unculturable Microbial Eukaryotic Plankton of the San Pedro Ocean Time Series Station
 
Start Date: Sept. 15, 2007
Expires: Aug. 31, 2009
Awarded Amount to Date: $499,999
Principal Investigator: Karla Heidelberg
Sponsor: University of Southern California
 
The program described here is designed to obtain large quantities of detailed DNA sequence data linked to known organisms. Data will be obtained for four previously understudied marine taxa from the Kingdoms Euglenozoa, Alveolata, Stramenopila, and Cercozoa. These more detailed data will significantly increase genomic information on environmental microbial eukaryotes in the public domain and begin to allow detailed studies of relationships between and among prokaryote and eukaryote taxa.
 

 
Genome Sequencing of Mutualistic Bacteria Associated With Fungus-growing Ants
 
Start Date: Sept. 15, 2007
Expires: Aug. 31, 2009
Awarded Amount to Date: $656,963
Principal Investigator: Cameron Currie
Sponsor: University of Wisconsin-Madison
 
Fungus-growing ants and their microbial partners form a complex symbiosis. The ant-fungus mutualism is parasitized by microfungi in the genus Escovopsis, and to defend against infection, the ants have a mutualistic association with antibiotic-producing filamentous bacteria in the genus Pseudonocardia. The genomes for three strains of Pseudonocardia that span the diversity of the mutualism will be sequenced, as well as the genome of P. saturnea, a closely related non-symbiotic species. In addition, optical maps for the genomes of 20 Pseudonocardia strains will be generated.
 

 
A Taxonomic Revision and Phylogenetic Investigation of Five Groups of Species in the Genus Vorticella (Protista, Ciliophora, Oligohymenophorea)
 
Start Date: Sept. 15, 2007
Expires: Aug. 31, 2008
Awarded Amount to Date: $140,000
Principal Investigator: John Clamp
Sponsor: North Carolina Central University
 
Ciliated protists in the genus Vorticella are widespread, well-known, aquatic microorganisms, but identification of individual kinds is difficult and little is known about their evolution, according to the grantees. American and Chinese collaborators will use a wide variety of new information (especially gene sequences) to sort out classification and evolutionary relationships of five groups of Vorticella species to begin solving this problem. Activities will include sequencing a variety of genes.
 

 
Functional Genomic Investigations of Dissolved Organic Carbon Cyling at the Sapelo Island Microbial Observatory
 
Start Date: Sept. 15, 2007
Expires: Aug. 31, 2010
Awarded Amount to Date: $656,336
Principal Investigator: Mary Ann Moran
Sponsor: University of Georgia Research Foundation
 
This project will use gene expression patterns in bacterial communities at the Sapelo Island, Ga., Long Term Ecological Research site to identify the components of terrestrial- and marine-derived organic matter that are assimilated and metabolized in the coastal ocean. By sequencing expressed genes directly from seawater at times when ecosystem inputs are the most distinct, the patterns of dissolved organic carbon supply and flux will be discerned.
 

 
Reconstruction of Human Genetic History Along the North Slope
 
Start Date: Sept. 15, 2007
Expires: Aug. 31, 2010
This grant was awarded to two investigative teams:
  • Sponsor: Northwestern University at Chicago.
    Awarded Amount to Date: $504,819
    Principal Investigator: Geoffrey Hayes.
  • Sponsor: University of Utah.
    Awarded Amount to Date: $552,543.
    Principal Investigator: Dennis O'Rourke
This collaborative project will document geographic patterns of genetic variation in both prehistoric and modern human populations along the North Slope of Alaska and assess how the ancient residents of arctic Alaska are related to contemporary Inupiaq populations throughout the circumarctic region. This will be achieved by the characterization of maternally inherited mitochondrial DNA sequences, paternally inherited Y-chromosome markers, as well as biparentally inherited autosomal genetic markers in both the archaeologically derived prehistoric samples and the contemporary populations of the North coast of Alaska.
 

 
Coordinated Shotgun Metagenomic Sequencing and Proteomics: A Double-Barreled Approach to Cyanobacterial Community Analysis
 
Start Date: Oct. 1, 2007
Expires: Sept. 30, 2009
Awarded Amount to Date: $508,391
Principal Investigator: Brian Palenik
Sponsor: University of California,San Diego; Scripps Institute of Oceanography
 
Marine cyanobacteria contribute perhaps 25 percent of global primary productivity and are thus of major importance in the global carbon and other element cycles, according to the grantees. Multiple whole genomes are now available for model isolated strains of these organisms. This research seeks to perform metagenomic sequencing using 454 sequencing technology. Coastal marine cyanobacteria are sorted out of the sample before sequencing, increasing the information available to understand the genetic diversity of these microbes. In this way the pan-genome of two major marine cyanobacteria (Synechococcus) species will be investigated and likely lead to the discovery of novel genes in these microorganisms.
 

 
A Comprehensive Comparative Genomic Approach for Identifying the Saxitoxin Synthesis Genes
 
Start Date: Oct. 1, 2007
Expires: Sept. 30, 2009
Awarded Amount to Date: $1,064,352
Principal Investigator: F. Gerald Plumley
Sponsor: Bermuda Biological Station for Research
 
The project will use high-throughput DNA sequencing to study the genes responsible for the production of saxitoxin, a compound produced by microalgae that is responsible for paralytic shellfish poisoning. Saxitoxin is produced by several freshwater cyanobacteria, or blue green algae, and by several eukaryotic phytoplankton called dinoflagellates. It is hypothesized that the same genes in these very different groups of algae are involved in the synthesis of the toxin. The researchers will sequence the entire genomes of the cyanobacteria, as well as the set of genes involved in protein production in the dinoflagellates.
 

 
Complete Genomic Characterization of Mycoplasma gallisepticum Isolates from a 12-Year Epizootic in House Finches: Evolution of a Pathogen
 
Start Date: Oct. 1, 2007
Expires: Sept. 30, 2009
Awarded Amount to Date: $605,699
Principal Investigator: Steven Geary
Sponsor: University of Connecticut
 
Mycoplasma gallisepticum is a bacterial pathogen that causes respiratory diseases in domestic poultry. Recently, especially over the last 12 years, this bacterial infection has jumped species and emerged as a disease and spread to a wild songbird host, the house finch. The objective of this project is to sequence and analyze the genomes of five key Mycoplasma strains from 1994 to the present and of isolates from different disease outbreak locations across the US.
 

 
The PhyloFacts Phylogenomic Encyclopedia of Microbial Protein Families
 
Start Date: Nov. 1, 2007
Expires: Oct. 31, 2010
Awarded Amount to Date: $1,899,499
Principal Investigator: Kimmen Sjolander
Sponsor: University of California, Berkeley
 
The resource to be developed under this grant, the PhyloFacts Microbial Encyclopedia, will provide pre-computed phylogenomic analyses of millions of microbial genes. It will use new bioinformatics methods to reconstruct the evolutionary histories of these ancient gene families, predict protein structure, molecular function, and cellular localization, and link genes to metabolic networks and signaling pathways. New sequences generated by genome sequencing projects will be classified to families and subfamilies using a database of hidden Markov models, statistical models representing the preferred amino acids at each position in the consensus structure of these macromolecules.
 

 
Genomics of Terrestrial Microbial Communities Associated with the Production and Consumption of Greenhouse Gases
 
Start Date: Nov. 1, 2007
Expires: Oct. 31, 2010
Awarded Amount to Date: $1,695,687
Principal Investigator: Thomas Schmidt
Sponsor: Michigan State University
 
This research project will catalog a large fraction of the genetic diversity in soil through metagenomic approaches and address specific questions about the relationships between the genetic structure of microbial communities in soil and the production and consumption of two greenhouse gases — nitrous oxide and methane.
 

 
EST Sequencing and Comparative Genomics of the Globally Significant Marine Phytoplankton Phaeocystis Globosa
 
Start Date: Jan. 1, 2008
Expires: Dec. 31, 2009
Awarded Amount to Date: $629,588
Principal Investigator: Andrew Allen
Sponsor: Institute for Genomic Research (now J. Craig Venter Institute)
 
The researchers plan to evaluate gene expression responses to ecological stresses and stimuli of Phaeocystis globosa, a globally important species of marine phytoplankton that forms massive blooms that export significant amounts of carbon to the deep sea. Further, the genomic and gene-expression databases from this project will be a community resource and will support many projects on the ecology and evolution of this organism.
 

The Scan

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For Flu and More

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To Boost Women

China's Ministry of Science and Technology aims to boost the number of female researchers through a new policy, reports the South China Morning Post.

Science Papers Describe Approach to Predict Chemotherapeutic Response, Role of Transcriptional Noise

In Science this week: neural network to predict chemotherapeutic response in cancer patients, and more.