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Sequencing-Related NSF Grants Awarded Aug. 16 – Oct. 24, 2008

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Collaborative Proposal: Are Abundant Bacteria More Active Than Rare Bacteria in the Sargasso Sea?
Start Date: Oct. 1, 2008
Expires: Sept. 30, 2011 
This grant was awarded to two investigative teams:
— John Heidelberg, University of Southern California, $337,367
— Barbara Campbell, University of Delaware, $445,461
 
The project will investigate what bacteria are most active in open oceanic environments like the Sargasso Sea, and what metabolic processes are represented by the most commonly expressed genes. It will use a combination of pyrosequencing and qPCR approaches to examine rRNA to rDNA ratios, BrdU incorporating cells, and transcript types and amounts in the metatranscriptome of Sargasso Sea surface water. According to the abstract, pyrosequencing using 454’s platform avoids amplification and cloning artifacts and is cost-effective. Preliminary analyses indicate that the sequence length of 454 reads and the proposed number of sequences are ideal for addressing the questions raised in this project. The investigators will also use Micro-FISH to examine incorporation of thymidine, leucine, and PO4. Samples will be collected twice yearly during the spring phytoplankton bloom when heterotrophic bacterial production is lowest and during the peak of bacterial production in summer.
 

 
Collaborative Research: Genetic Bases for the Evolution of Human Diet
Start Date: Oct. 1, 2008
Expires: Sept. 30, 2009
This grant was awarded to two investigative teams:
— Sarah Tishkoff, University of Pennsylvania, $175,000
— Gregory Wray, Duke University, $324,945
 
This project will focus on the evolution of human diet. An interdisciplinary team of anthropologists and human geneticists will integrate genetic, organismal, and ecological information to better understand the genetic basis for the evolution of dietary traits in humans. The goals of this project are to screen the human genome for relevant genes using two approaches: Measuring gene expression across the entire genome from humans and chimpanzees in several tissues of dietary significance using ultra high-throughput sequencing and testing for adaptation in DNA sequences across the entire genome based on patterns of mutation. The project plans to conduct integrative case studies of diet-related genes implicated in trait changes during human origins through extensive DNA sequence comparisons among great ape species, detailed characterization of gene expression, experimental tests of functional differences, and associations between gene expression and specific dietary traits, and to conduct integrative case studies of diet-related genes among modern African human populations that are diverse with respect to diet and local climate, through detailed analyses of genetic variation, tests for natural selection, and genetic associations with specific dietary traits.
 

 
Genetic, Genomic, and Biochemical Approaches to Elucidate Control of Sulfur Deprivation Responses
Start Date: Oct. 1, 2008
Expires: Sept. 30, 2009
Awarded Amount to Date: $149,141
Principal Investigator: Arthur Grossman
Sponsor: Carnegie Institution of Washington
 
The work proposed in this grant continues an exploration of the regulatory aspects of sulfur deprivation responses in the alga Chlamydomonas. Wild-type and various mutant strains will be queried with genome-wide methods for examining the transcriptome under nutrient-replete and sulfur-starvation conditions, using both microarray and Solexa sequencing technologies. A diversity of protein-protein interaction assays, including the yeast two-hybrid system, the split ubiquitin and split GFP systems and classical co-immunoprecipitation assays will facilitate these studies. Finally, analyses will be performed to help understand the two tiers of the sulfur-deprivation response that have recently been discovered; one is protein synthesis-independent while the other is protein synthesis-dependent.
 

 
POPcorn — A Project Portal for Corn
Start Date: Sept. 15, 2008
Expires: Aug. 31, 2010
Awarded Amount to Date: $451,356
Principal Investigator: Carolyn Lawrence
Sponsor: Iowa State University
 
This project, in collaboration with the community of maize researchers, will launch POPcorn (PrOject Portal for corn), a resource and data pipeline. POPcorn will make available a centralized web-accessible resource to search and browse ongoing maize genomics projects; a single, stand-alone tool that makes use of web services and minimal data warehousing to enable researchers to carry out sequence searches at one location that return matches for all participating projects’ related resources; a set of tools that enable collaborators to migrate their data to MaizeGDB, the long-term model organism database for maize genetic and genomic information, at their projects’ conclusion; and generalized, freely available code that other research communities could use to meet similar needs.
 

 
The Development of a Collaborative Research Plan for NIST and the Semiconductor Industry for Nanoelectronics Research in the Bio-Sciences
Start Date: Sept. 15, 2008
Expires: Aug. 31, 2009
Awarded Amount to Date: $49,900
Principal Investigator: Ralph Cavin
Sponsor: Semiconductor Research Corporation
 
A research plan will be developed to directly couple the semiconductor industry and NIST in the support of bio-sciences research through the application of the industries' technological capabilities to pressing bio-science needs. The applicants believe that new electronic technologies can be developed for rapid DNA sequencing, to identify and quantify proteins, to detect toxins, and for molecular mass spectroscopy. As a specific example, nanopores may have application for rapid DNA sequencing, for protein denaturation detection, for anthrax detection, for understanding how cells respond to proteins, and possibly for total cell analysis for system biology and for future medical applications. The proposed planning process will define potential technology application areas, and identify specific technology needs and their associated time horizons.
 

 
After the Sequencing: Curating the Medicago Truncatula Genome
Start Date: Sept. 15, 2008
Expires: Aug. 31, 2009
Awarded Amount to Date: $1,171,114
Principal Investigator: Christopher Town 
Sponsor: J. Craig Venter Institute
 
Medicago truncatula has been the target of an international sequencing initiative for the past five years. When the international sequencing efforts wind down in the fall of 2008, there will be approximately 280 megabases of high quality DNA sequence distributed across the plant’s eight chromosomes, each with blocks of sequence ranging in size from a few hundred thousand bases to between five and 10 million bases in length and with 10 to 30 gaps in each of the euchromatic arms. Based upon the projected capture rate of expressed sequence tags, the euchromatic, gene-rich portion of genome will be around 80 percent complete. There will also be approximately 200 megabases of unsequenced DNA in the centromeres that is gene-poor and was not targeted for sequencing. This project will integrate, manage, and enhance the understanding of both the structure and annotation of the Medicago genome, and comprises three goals: Creation of the best possible sequence-based representation of the M. truncatula genome, which will involve construction of an optical map; capturing and localizing as much as possible of the remaining gene-containing regions of M. truncatula genome in the most cost-efficient fashion; and supporting and maintaining the International Medicago Genome Annotation Group annotation pipeline that represents a consensus annotation process for the entire Medicago and legume community, and enriching the annotation of the M. truncatula genome by overlaying other data types including expression data, both from microarrays and next-generation sequencing, proteomic data, locations of transposon, fast-neutron induced mutations, links to genetic resources, et cetera.
 

 
Efficient Identification of Induced Mutations in Crop Species by Ultra-High Throughput DNA Sequencing
Start Date: Sept. 15, 2008
Expires: Aug. 31, 2010
Awarded Amount to Date: $1,966,061
Principal Investigator: Luca Comai
Sponsor: University of California-Davis
 
This project will apply ultra-high throughput sequencing to Targeting Induced Local Lesions IN Genomes, or TILLING, a general method for the discovery of induced mutations in genes of interest. Working with rice and wheat TILLING lines, it will employ PCR-mediated amplification from pooled genomic templates to target dozens to hundreds of genes. The research will test and implement several technical and computational methods to resolve real mutations from errors in highly complex templates. To target hundreds to thousands of genes, the project will use sequence barcoding to create DNA pools of short adapter-ligated random fragments from hundreds or thousands of existing TILLING lines of Arabidopsis, and later rice and wheat. Aliquots from an amplified pool will be subjected to a capture procedure using custom programmable arrays or long oligos attached to either microarrays or beads, and the eluted fragments subjected to Solexa sequencing.
 

 
Acquisition of Automated Genetic Analyzer for Interdisciplinary Research, Teaching and Training in Molecular Phylogenetics, Biology, and Bioinformatics in an Undergraduate College
Start Date: Sept. 1, 2008
Expires: Aug. 31, 2009
Awarded Amount to Date: $117,080
Principal Investigator: Aaron Best
Sponsor: Hope College
 
Hope College has received the grant to purchase an automated genetic analyzer for research and training in evolutionary biology, microbiology, molecular biology, and bioinformatics. The instrument, which will be used by both faculty and students, will significantly impact multiple areas of research and teaching. First, it will be used to collect DNA sequence data for evolutionary studies of the pineapple family, whose species have been under increasing risk of extinction due to extensive habitat loss. Second, it will be used to examine genome evolution in the primitive eukaryote Giardia lamblia, the parasite that causes giardiasis. Third, the instrument will be used to learn more about how genes are regulated by fatty acids through a study in yeast. Lastly, it will be used in a comparative analysis of virus genomes as part of the HHMI-funded Phage Genomics Research Initiative
 

 
MRI: Aquisition of Genome Sequencer FLX System
Start Date: Sept. 1, 2008
Expires: Aug. 31, 2011 
Awarded Amount to Date: $630,000
Principal Investigator: Joshua Udall
Sponsor: Brigham Young University
 
Brigham Young University has received the grant for the acquisition of a next-generation DNA genome sequencer. The sequencer will have three primary uses at Brigham Young University. It will promote and enhance the scope of research capability to a large group of researchers on and off campus; provide state-of-the-art equipment training and familiarity to a large group of undergraduate and graduate students involved in NSF, NIH, USDA, and university-sponsored mentored research experiences; and increase and enhance the involvement of student researchers in data analyses and bioinformatics that will be useful to them after graduation. The impacted research includes plant and animal systematics, nematode co-evolution, crop improvement, conservation biology, molecular ecology, and novel algorithms for genome and transciptome sequence assembly. The instrument will be housed in the College of Life Sciences DNA Sequencing Center.
 

 
Single Cell Genome Sequencing of Uncultured Prokaryotes From the South Atlantic Mesopelagic
 
Start Date: Sept. 1, 2008
Expires: Aug. 31, 2011
Awarded Amount to Date: $976,747
Principal Investigator: Ramunas Stepanauskas
Sponsor: Bigelow Laboratory for Ocean Sciences
 
As a new approach to the study deep dwelling ocean communities, scientists at the Bigelow Laboratory for Ocean Sciences will employ single amplified genomics, or SAG, a novel technology which enables the reconstruction of the entire genome of an uncultured microorganism collected from the environment. The scientists will couple SAG with flow cytometry, which is used for sorting cells, to apply this procedure in the ocean. This technology is transformative, according to the grantees, because it allows scientists to study a microbe, through its genome, without the need for first bringing the organism into culture. These investigators will use samples from the mesopelagic zone in the South Atlantic Gyre and through a careful screening procedure, produce hundreds of SAGs from these samples, which can then be sequenced. These researchers will be particularly interested in characterizing the identities and genomic composition of the microorganisms that are involved in the degradation of complex biomolecules and in the transformations of nitrogen compounds that control the productivity of the ocean. These SAG sequences will also be interrogated with metagenomic sequence datasets, such as the Global Ocean Survey dataset, to postulate the metabolism, physiology and evolutionary history of these organisms.
 

 
Whole Genome Sequencing and Annotation of Representative Strains of Spiroplasma Mirum
Start Date: Sept. 1, 2008
Expires: Aug. 31, 2010
Awarded Amount to Date: $185,000
Principal Investigator: Frank Bastian
Sponsor: Louisiana State University Agricultural Center
 
Frank Bastian and Ronald Thune of Louisiana State University Agricultural Center will be obtaining a finished, complete sequence of three spiroplasma genomes: Spiroplasma mirum, a rabbit tick isolate; a Spiroplasma sp. isolated recently from scrapie-infected sheep brain and closely related to S. mirum; and a non-pathogenic spiroplasma, Spiroplasma montanense. To this point, only partial Spiroplasma kunkelii and Spiroplasma citri genomes have been sequenced. However, these spiroplasma are plant pathogens and widely divergent from S. mirum. S. mirum is the only Spiroplasma sp. to experimentally cause persistent infection in animals, including mice, rats and ruminants. These investigators postulate that direct comparison of the genomes of S. mirum, an S. mirum-like spiroplasma from TSE-affected ruminant brain, and a non-pathogenic spiroplasma will provide evidence for the pathogenesis of TSE in some animals and in humans.
 

 
MRI: Acquisition of a Massively Parallel Sequencing Instrument System
Start Date: Sept. 1, 2008
Expires: Aug. 31, 2011
Awarded Amount to Date: $600,000
Principal Investigator: George Grills
Sponsor: Cornell University
 
Cornell University has received a grant for a Roche 454 Genome Sequencer FLX. This new DNA sequencing instrument will enable creative research with potential for breakthrough discoveries. The 454 system enables massively parallel DNA sequence detection and analysis. The instrument will be operated by the Cornell University Life Sciences Core Laboratories Center as a university-wide shared research resource, which will enable cost-effective access to this new technology. The instrument will be used for whole genome assembly, sequencing of targeted regions, mutation detection, genotyping, and genome-wide measurements of gene expression and gene regulation. The instrument will be an essential tool in research that includes studies on genetic markers for improved crop breeding, bacterial and fungal pathogens capable of causing disease in plants and animals, insecticide and fungicide resistance, the regulation of metabolism and of the immune response, the regulation of fertility, flowering and fruit ripening in plants, and genome level regulation of crop biomass.
 

 
MRI: Acquisition of High Capacity DNA Sequencing System
Start Date: Sept. 1, 2008
Expires: Aug. 31, 2011
Awarded Amount to Date: $714,750
Principal Investigator: Michael Fromm
Sponsor: University of Nebraska-Lincoln
 
The University of Nebraska has received a grant to purchase a next-generation high-throughput DNA sequencing system. This type of system has the capacity to obtain over 1 billion base pairs of DNA sequence per analysis, which is expected to accelerate research in genomics projects in all the life sciences research programs at Nebraska. In particular, a new NSF-funded program on understanding how changes in chromatin modifications affect gene expression will be able to obtain larger amounts of data more quickly using this machine. Additional uses will be to determine mRNA structures and expression in green algae, as a potential source of biofuels; to extend research on chromatin modifications into corn for the purpose of improving drought tolerance; and, on improving the understanding of how dietary molecules can improve human health through specific signaling pathways and changes in chromatin modifications.
 

 
Unlocking the Mysteries of Plastid Origin Through Comparative Genomic Analysis of Two Paulinella Species
Start Date: Sept. 1, 2008
Expires: Aug. 31, 2010
Awarded Amount to Date: $993,911
Principal Investigator: Hwan Su Yoon
Sponsor: Bigelow Laboratory for Ocean Sciences
 
Paulinella chromatophora is a green amoeba that is remarkable because it very recently acquired a plastid via an independent primary endosymbiosis involving a Prochlorococcus or Synechococcus-like cyanobacterium. The closely related Paulinella ovalis lacks a plastid but feeds actively on cyanobacteria. Using these model organisms, this project will sequence genomic DNA and generate a transcriptome database from the photosynthetic amoeba Paulinella chromatophora and sequence genomic DNA from the plastid-lacking Paulinella ovalis using the most modern high-throughput pyrosequencing methods; compare the gene inventories between P. chromatophora and P. ovalis; and make freely available to the public the Paulinella genome sequences.
 

 
III-CXT-Small: Graphs to Diversity: Extracting Genomic Variation from Sequence Graphs
Start Date: Sept. 1, 2008
Expires: Aug. 31, 2010
Awarded Amount to Date: $293,074
Principal Investigator: Mihai Pop
Sponsor: University of Maryland College Park
 
This proposal aims to develop the theoretical and computational infrastructure for the study of genomic variation within mixtures of organisms. The proposed research relies on both theoretical and empirical analyses of the structure of genome assembly graphs in order to characterize graph signatures that are correlated with intra- and inter- species polymorphisms. A particular focus is placed on understanding and using the information provided by next-generation sequencing technologies as well as other high-throughput experimental techniques.
 

 
MRI: Acquisition of Genomic Sequencing Instrumentation
Start Date: Sept. 1, 2008
Expires: Aug. 31, 2011
Awarded Amount to Date: $1,257,184
Principal Investigator: Peter Houde
Sponsor: New Mexico State University
 
New Mexico State University has received funding to acquire major research instrumentation in the form of emulsion PCR pyrosequencing. The technology reduces the time and cost of DNA sequencing to about 1 percent of existing technologies, according to the grantees, and allows exploratory genetic characterization of environmental samples. The multi-user genome sequencing core facility will allow NMSU researchers to pioneer the understanding of how mutations in a few genes can affect the expression of hundreds of others, how certain viruses ameliorate the pathogenicity of some diseases, how genes that allow beneficial bacteria to live in hosts can change to allow pathogenicity, the changes in microbial communities of severely polluted and remediated soils, mutations that drive ongoing speciation in natural populations of plants and insects, and genome-level genetic characterization of non-model organisms.
 

 
Phylogeny of Apidae (Hymenoptera) with an Emphasis on the Evolution and Antiquity of Eusociality
Start Date: Sept. 1, 2008
Expires: Aug. 31, 2011
Awarded Amount to Date: $393,736
Principal Investigator: Bryan Danforth
Sponsor: Cornell University
 
Understanding the evolutionary history of social behavior in apid bees requires a phylogeny at the tribal and generic levels. This project will combine data from morphology, the fossil record, and large molecular data sets generated with novel 454 Life Sciences sequencing technology to resolve the conflicting results obtained by previous studies. The research will allow a re-assessment of the morphological data, and a re-examination of apid fossils from Dominican, Baltic, and North American amber deposits. The combination of fossil data and DNA sequence data will allow application of relaxed-clock dating methods to estimate the antiquity of the apid bees and the antiquity of eusociality. The project will lead to a revised classification for the family and improved understanding of the evolutionary history of bees.
 

 
Phylogenetic Systematics of Orthoptera (Insecta): Evolution of Male Genitalia and Study of Nuclear Mitochondrial Pseudogenes
Start Date: Sept. 1, 2008
Expires: Aug. 31, 2011
Awarded Amount to Date: $400,000
Principal Investigator: Hojun Song 
Sponsor: Brigham Young University
 
A team of entomologists at Brigham Young University will investigate the evolutionary relationships within Orthoptera, an insect group that contains grasshoppers, crickets, and katydids. They will generate DNA sequences from 168 species to address three fundamental questions: How are the major groups of Orthoptera related to each other? How has the male reproductive system, one of the most important characters in orthopteran classification, evolved? How do non-functional copies of mitochondrial genes evolve in Orthoptera? Investigators will conduct international field studies to collect specimens and then analyze the data using advanced analytic software and high-resolution digital imaging technology.
 

 
Physical Mapping of the Wheat D Genome
Start Date: Sept. 1, 2008
Expires: Aug. 31, 2009
Awarded Amount to Date: $2,907,481
Principal Investigator: Jan Dvorak
Sponsor: University of California-Davis
 
The goal of this project is to develop genomic resources for physical mapping of wheat chromosomes and to deploy them in physical mapping of chromosomes of the wheat D genome. A physical map of a chromosome is a physical representation of the linear order of genes and other landmarks along the chromosome. To construct a physical map, genomic DNA is fragmented, DNA fragments are cloned and each clone is “fingerprinted.” Overlaps between fingerprints are used to identify DNA fragments from neighboring regions of a chromosome. The location of genes and other markers in these fragments is determined and the sequence of overlapping DNA fragments is aligned to the linear order of markers along a chromosome. Wheat polyploidy and large genomes require the use of novel strategies in the physical mapping of its chromosomes. Instead of attempting to construct wheat physical maps globally, the physical maps of the chromosomes of Aegilops tauschii, the diploid ancestor of the wheat D genome, will be constructed first. These maps will then be used as templates for the construction of the physical maps of three individual chromosomes of the wheat D genome in the cultivar Chinese Spring. This step will be facilitated by international collaboration with the Institute of Experimental Botany, Czech Republic, which developed a technique for the isolation of individual wheat chromosomes by chromosome flow-sorting. This project complements ongoing national and international work toward wheat genome sequencing.
 

 
Deep Trench Single-cell Genomics
Start Date: Sept. 1, 2008
Expires: August 31, 2011
Awarded Amount to Date: $658,000
Principal Investigator: Douglas Bartlett
Sponsor: University of California-San Diego Scripps Institute of Oceanography
 
Scientists from the University of California San Diego and University of Puerto Rico-Mayaguez will explore the biodiversity of microorganisms of particularly extreme deep-sea environments — deep-sea trenches — by focusing on one site, the Puerto Rico Trench, the deepest part of the Atlantic Ocean. Deep trench prokaryotes are expected to possess novel enzymes and cell properties which allow them to survive and grow under these extreme conditions. One major goal of this project is to study the genomes of these microorganisms to understand what capabilities they have evolved to live in this harsh environment. Another goal is to evaluate the extent and diversity of novel protein families in the genomes of these deep trench microbes. Water samples collected from the trench and maintained under very high pressure will be examined using single-cell genomic technology. A careful sorting procedure will be developed to avoid contamination, chimeras, and other artifacts of sample handling. These researchers will collect two hundred individual cells from the water sample by micromanipulation and amplify their genomic DNA in nanoliter volume microfluidic chambers. They will perform 16S rDNA sequencing on each sample as an independent genetic identifier. They will then select genomic DNA candidates with novel phylogenetic characteristics for further full genome sequencing. The closed and assembled genome sequences will be annotated to assign gene function. These researchers will compare these genome sequences with sequences from various marine metagenomic datasets and will also compare the extent and diversity of novel protein families in these genomes to the large number of protein families identified in the Global Ocean Survey dataset.
 

 
High-Throughput Small RNA Sequencing in Archaea
Start Date: Sept. 1, 2008
Expires: Aug. 31, 2011
Awarded Amount to Date: $809,428
Principal Investigator: Todd Lowe
 
This project seeks to apply the latest new gene sequencing technology to discover thousands of unknown RNA genes across a broad sampling of 24 key species of Archaea. The new data will also enable creation of new probabilistic models for new RNA gene families, and vastly improve automated RNA gene annotation for newly decoded species. This project will catalyze many areas of archaeal RNA gene research, including discovery of novel structural and regulatory RNAs, the mechanism and evolution of Clustered Regularly Interspaced Short Palindrome Repeat cell immunity, RNA gene processing motifs, and locating genes regulated by RNA "antisense" transcripts.
 

 
SGER: Development of a Novel Strategy for De Novo Sequencing of Wheat BACs Using the SOLiD Sequencing Platform
Start Date: Sept. 1, 2008
Expires: Aug. 31, 2009
Awarded Amount to Date: $195,958
Principal Investigator: Jan Dvorak
Sponsor: University of California-Davis
 
Complete BAC-by-BAC sequencing of large plant genomes, such as those of wheat, barley, and other economically important plants, is currently prohibitively expensive. Next generation sequencing technologies offer sequencing with much higher throughputs and at greatly reduced costs, but the short read-lengths complicate the use of these techniques in de novo sequencing of eukaryotic genomes. That is particularly true for large plant genomes that contain vast amounts of repeated DNA sequences. The goal of this project is to assess a novel strategy for de novo sequencing with the SOLiD platform in collaboration with Applied Biosystems. This strategy will employ sequencing of two-dimensional pools of bacterial artificial chromosome clones of genomic DNA. The strategy will be evaluated using two-dimensional pools of BAC clones of Aegilops tauschii, one of the diploid ancestors of polyploid wheat. A program will be written to deconvolute the pools and assemble sequences of individual clones.
 

 
MO Collaborative Research: A Genomics and Cultivation-Based Study on Novel Candidate Divisions OD1, SR1, OP11, and TM7 in a Sulfur-Rich Spring (Zodletone Spring, OK)
Start Date: Aug. 15, 2008
Expires: July 31, 2013
This grant was awarded to two investigative teams:
— Mostafa Elshahed, Oklahoma State University, $800,001 
— Lee Krumholz, University of Oklahoma, $500,000
 
The goal of this project is to investigate the physiological characteristics, metabolic abilities, and potential ecological roles of four of these important bacterial groups, termed candidate divisions, OD1, SR1, OP11, and TM7. These four groups have been shown to be relatively abundant in Zodletone spring, a low temperature sulfide and sulfur-rich spring in southwestern Oklahoma and they are thought to be important members of the community in terms of facilitating the biological processes that are occurring in this spring. These processes include degradation of hydrocarbons, formation of minerals and photosynthesis. Zodletone spring will be used as a microbial observatory to study these groups. A set of genomic techniques will be used, which involve sequencing DNA from the genome of one individual microbial cell, literally fished from the spring using a flow cytometer. The results will allow identification of the genes and assembly of the metabolic pathways that may be used for the above processes. Ultimately the data will be used to understand the chemical reactions and the ecological roles performed by members of each these groups. Along with genomic studies, these groups of bacteria will be cultivated and studied in the laboratory. These bacteria come from an environment in which oxygen is rarely present and as a result, oxygen is likely toxic to these cells. Sophisticated isolation strategies will be used for isolating and growing bacteria that would not normally grow in the laboratory and these will be adapted to work with microorganisms that are oxygen sensitive. These cultivation studies will allow us to verify that the bacteria are able to catalyze the reactions that have been proposed for them and will allow us to study individual reactions to understand how each process occurs.
 

 
IWGSC-IBSC Workshop on Genome Sequencing Strategies
Start Date: Aug. 15, 2008
Expires: July 31, 2009
Awarded Amount to Date: $28,260
Principal Investigator: Gary Muehlbauer
Sponsor: University of Minnesota-Twin Cities
 
The recent advances in the development of next generation DNA sequencing technologies are opening the prospect for tackling large, complex genomes such as wheat and barley in a reasonable time frame and for tractable cost. It is timely to discuss the use of these technologies to sequence the wheat and barley genomes. To this end, the International Wheat Genome Sequencing Consortium and the International Barley Sequencing Consortium will convene an international workshop on wheat and barley genome sequencing. This workshop will bring together international experts in the human and agriculturally-important genome sequencing projects, developers of genome sequencing technologies, scientists with extensive knowledge of the structure and organization of the wheat and barley genomes, representatives of international genome sequencing centers interested in de novo sequencing of plant species, as well as representatives of governmental funding agencies. The workshop will last two days and will result in a summary document that will be distributed to all participants as well as others interested in advances in wheat and barley genomics.

The Scan

Guidelines for Ancient DNA Work

More than two dozen researchers have developed new ethical guidelines for conducting ancient DNA research, which they present in Nature.

And Cleared

A UK regulator has cleared former UK Prime Minister David Cameron in concerns he should have registered as a consultant-lobbyist for his work with Illumina, according to the Financial Times.

Suit Over Allegations

The Boston Globe reports that David Sabatini, who was placed on leave from MIT after allegations of sexual harassment, is suing his accuser, the Whitehead Institute, and the institute's director.

Nature Papers on Esophageal Cancer, Origin of Modern Horses, Exome Sequencing of UK Biobank Participants

In Nature this week: genetic and environmental influences of esophageal cancer, domestic horse origin traced to Western Eurasian steppes, and more.