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Funding Update: Sep 1, 2009

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Sequencing-Related NSF Grants Awarded Aug. 1 — Aug. 31, 2009

Microbial Genome Sequencing: High-Resolution Phylogenomics of Halophilic Archaea

Start Date: Oct. 1, 2009
Expires: Sept. 30, 2011
Awarded Amount to Date: $724,678
Principal Investigator: Marc Facciotti
Sponsor: University of California-Davis

Several members of the archaeal family Halobacteriaceae are being fully sequenced by the principal investigator and his collaborators to advance the understanding of genome organization and evolution of microbial genomes and to provide a foundation for systems biology efforts to experimentally query novel aspects of microbial biochemistry, physiology, metabolism, development, and cellular biology. These genome sequences will provide sufficient coverage of this phylogenetic family — both in breadth and depth — so that comparative studies on the organization of genomes and the exchange and reshuffling of genetic information will become possible, according to the grant abstract. Because the organisms proposed for sequencing have adapted for life in hypersaline environments, the development of these as model systems will also directly shape the understanding of salt tolerance. The researchers also intend to address whether the biological species concept can be applied to archaea. The project will also investigate archaeal DNA replication, which shares aspects with both eukaryotic and prokaryotic genome replication, and genome organization.


Collaborative Research: Decoding Virus Leviathans

Two awards with this title were made:

Start Date: Oct. 1, 2009
Expires: Sept. 30, 2012
Awarded Amount to Date: $338,950
Principal Investigator: William Wilson
Sponsor: Bigelow Laboratory for Ocean Sciences

Start Date: Oct. 1, 2009
Expires: Sept. 30, 2012
Awarded Amount to Date: $275,004
Principal Investigator: Steven Wilhelm
Sponsor: University of Tennessee Knoxville

Giant viruses are loosely defined as having a genome greater than 280 kilobase pairs, and currently there are less than 20 full virus genome sequences in this size range. Four algal viruses from current collections and 16 additional giant viruses isolated from seawater are being sequenced in this project. The viruses are being isolated and sequenced by adapting single-cell sorting techniques. Once sorted, giant viruses are being amplified by multiple displacement amplification to generate giant virus single amplified genomes for downstream sequencing. To accomplish this work, the PIs are using state-of-the-art facilities for flow cytometry, at Bigelow, and sequence analysis, at the University of Tennessee/Oak Ridge National Laboratory, coupled with bioinformatics expertise from collaborator Jean-Michel Claverie.


Automated and Portable Sequence Analysis Using Virtual Machines and Cloud Computing

Start Date: Oct. 1, 2009
Expires: Sept. 30, 2011
Awarded Amount to Date: $462,774
Principal Investigator: Wolfgang Fricke
Owen White (Co-Principal Investigator)
Sponsor: University of Maryland at Baltimore

This project aims to increase the accessibility of state-of-the-art sequence analysis software to researchers without extensive bioinformatics resources. It is developing a portable and standalone software package, using virtual machines, that is incorporating readily available, open source tools for genome analysis. The VM design will provide two main advantages, according to the grant abstract, allowing users to circumvent complex software installations and avoid performance bottlenecks of local computing networks. The VM package will include fully operational bioinformatics pipelines within a single executable file that is compatible with all computer operating systems and makes further software installations unnecessary. The processing of large sequence data can be outsourced to large distributed computing networks called compute clouds. The analysis protocols provided on the VM package will replicate and extend established bioinformatics protocols and include tools for whole-genome and metagenome annotation and comparative analysis, including sequence assembly, gene prediction, functional annotation, metabolic pathway reconstruction, and phylogenetic classification. The VM package will be made available as a work in progress with at least two trial and four production releases. It will be available for download as an open source software tool through the project webpage.


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EAGER: Developing Bioinformatics Tools for the Application of Next-Generation Sequencing Technologies to Phylogeography.

Start Date: Sept. 15, 2009
Expires: Aug. 31, 2011
Awarded Amount to Date: $225,394
Principal Investigator: Bryan Carstens
Sponsor: Louisiana State University & Agricultural and Mechanical College

This proposal will develop software that facilitates investigations into the genetic diversity within and between species. Software will be tested on next-generation sequence data collected to augment existing projects in the labs of the principal investigators; these projects seek to understand the process of speciation in organisms from North and South America. The research will serve as a catalyst for the adoption of next-generation sequence data in phylogeography and will also benefit evolutionary biology, ecology, and conservation biology. This award is funded under the American Recovery and Reinvestment Act of 2009.


MRI: Acquisition of a Genome Sequencer FLX for High-Throughput Sequencing and Genotyping in Genomics Research and Student Training

Start Date: Sept. 15, 2009
Expires: Aug. 31, 2012
Awarded Amount to Date: $526,567
Principal Investigator: Pawel Michalak
Sponsor: University of Texas at Arlington

This major research instrumentation, or MRI, award funds the acquisition of a Genome Sequencer FLX system from 454 Life Sciences and Roche Applied Science to help meet the needs of an expanding group of genomics researchers at the University of Texas Arlington and the surrounding vicinity. The 454 sequencer, part of the Genome Biology Group Core Facility, can produce 400,000 DNA sequences of 200 to 400 bases in a single 6 to 8 hour run to support interdisciplinary and inter-institutional collaborative efforts spanning UTA's Department of Biology, Department of Computer Science and Engineering, and School of Nursing. Specific areas of research interest include environmental transcriptomics, transcriptional profiling of developing systems, coral biology, entomology, and plant stress physiology. This award is funded under the American Recovery and Reinvestment Act of 2009.


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MRI: Acquisition of Massively Deep-Read Sequencing Technology at NCSU

Start Date: Sept. 15, 2009
Expires: Aug. 31, 2010
Awarded Amount to Date: $452,502
Principal Investigator: William McMillan
Sponsor: North Carolina State University

The grant will be used to purchase a next-generation "deep-read" sequencer from an undisclosed vendor that generates over 20 billion bases of nucleotide sequence per run in the form of more than 400 million 50- to 72-base sequence fragments. It will be used in ongoing research requiring full genome and targeted resequencing, polymorphism detection, small RNA discovery, and transcriptional profiling. The new equipment will be operated by NCSU's Genomic Science Laboratory and will serve a diverse user community interested in understanding the connections between an organism's genotype and its phenotype, and for identifying the variation that underlies individual differences in survival and reproduction. The equipment will transform ongoing research into how microbial communities are structured, the genetic basis of complex traits, and the origins and maintenance of biodiversity. The acquisition of the new equipment is coupled with the establishment of core bioinformatics support to accelerate the transition to the new technology throughout the larger research community at NCSU. This award is funded under the American Recovery and Reinvestment Act of 2009.


EAGER: A Plant Genome Assembly Simulation Platform

Start Date: Sept. 1, 2009
Expires: Aug. 31, 2010
Awarded Amount to Date: $288,606
Principal Investigator: Steven Rounsley
Sponsor: University of Arizona

This proposal seeks to leverage the existing plant genomes in order to develop a web-based plant genome assembly simulation platform. For a given genome, a range of sequencing strategies will be simulated and the resulting data will be assembled with a number of assembly algorithms. These data will be evaluated with newly developed evaluation metrics that seek to capture the heterogeneity of uses for genome sequences, and place the results in a context that maximizes the value to the user, the grant abstract states. In addition, the platform's relevance to a larger number of plant species will be improved by introducing the concept of a virtual genome. Prototype tools will be developed that enable the construction of such a virtual genome using key genome characteristics such as size, GC content, and nature of repeats that impact genome assembly. The simulation platform generated will provide the user community with pre-computed results from common sequencing strategies on a range of plant genomes, customizable cost models to compare the costs of different strategies, standardized datasets to compare existing assemblers and to benchmark new ones, the ability to create artificial genomes through a "recipe" of defined changes to a template genome and then test sequencing strategies on it, and the ability to use the system to develop and test the feasibility of new sequencing and physical mapping strategies prior to testing in the lab.


MRI: Acquisition of a Roche 454 FLX Pyrosequencing Instrument: Development of a Nexus for Cross-Platform Next-Generation Sequencing and Bioinformatics

Start Date: Sept. 1, 2009
Expires: Aug. 31, 2012
Awarded Amount to Date: $612,019
Principal Investigator: Martin Dickman

The Roche 454 FLX will be used by more than 60 faculty members and their research staff, including post-doctoral fellows, graduate, and undergraduate students at Texas A&M University. Applications and research programs include the dissection of sorghum drought tolerance, functional and metagenomic analysis of biological communities for cattle and rumen bacteria, and disease resistance and an analysis of microflora in ocean drilling programs.


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MRI: Acquisition of Solexa Genome Analyzer to Enable Collaborative Molecular, Environmental, and Computational Research

Start Date: Sept. 1, 2009
Expires: Aug. 31, 2012
Awarded Amount to Date: $562,953
Principal Investigator: Sergey Nuzhdin
Sponsor: University of Southern California

The acquisition of a next-generation sequencing machine will allow a broad group of scientists at the University of Southern California to address a variety of questions that span the disciplines of molecular and computational biology, marine environmental biology, and neurobiology. The administration at University of Southern California has fostered an environment of innovation and collaboration, which is critical for success in the use of this next-generation platform, since the generation and analyses of this data requires expertise in disparate academic disciplines. This award is funded under the American Recovery and Reinvestment Act of 2009.


MRI: Acquisition of Next Generation Sequencers

Start Date: Sept. 1, 2009
Expires: Aug. 31, 2012
Awarded Amount to Date: $999,253
Principal Investigator: W. Richard McCombie

Funding from the MRI program has created a next-generation sequencing center, dedicated to plant genomics. The facility will be used for a wide range of projects ranging from de novo sequencing of the various plant genomes and transcriptomes to studies of epigenetics. The center will consist of an Illumina GAIIx DNA sequencer and computer equipment for data analysis and storage. This award is funded under the American Recovery and Reinvestment Act of 2009.


Assembling the Viral Tree of Life

Start Date: Sept. 1, 2009
Expires: Aug. 31, 2013
Awarded Amount to Date: $1,377,273
Principal Investigator: Mark Young
Sponsor: Montana State University

It is estimated that less than 0.01 to 0.1 percent of viruses have been discovered. The goal of this grant is to begin to overcome this deficiency by the development and implementation of tools to discover and characterize previously unknown viruses. This project will develop high-throughput DNA sequencing technology of environmental samples. This award is funded under the American Recovery and Reinvestment Act of 2009.


MRI: Acquisition of Instrumentation for a Molecular Ecology and Biosystematics Laboratory

Start Date: Sept. 1, 2009
Expires: Aug. 31, 2012
Awarded Amount to Date: $291,690
Principal Investigator: Eric Boehm
Sponsor: Kean University

Kean University plans to acquire equipment that will establish a core, multi-user DNA sequencing facility called the Molecular Ecology and Biosystematics Laboratory. The instrumentation includes an Applied Biosystems, four-capillary AB3130 Genetic Analyzer with Sequencher 4.2 software workstation; BioRad DNA Engine Peltier Thermal Cycler and Chromo-4 Real-Time PCR Detection system; Eppendorf refrigerated microcentrifuge; Eppendorf Mastercyler Thermal Gradient Cycler; Fisher Scientific Isotemp Ultralow-Temperature Freezer; Perkin Elmer Lambda 950 Spectrophotometer with UV/VIS/NIR capabilities; and Percival Scientific P-99 walk-in plant growth chamber with advanced Intellius controller and H-12 relative humidity control option. The equipment will be used by faculty and undergraduate students in research centered on the use of DNA sequence information. The research will address a broad range of questions related to the molecular ecology and biosystematics of plant-associated microfungi, marine macroalgae, melanthiaceous angiosperms, and hymenopteran insects in urban ecosystems. This award is funded under the American Recovery and Reinvestment Act of 2009.

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Fungal Genome and Transcriptomes in Phytopathogenesis

Start Date: Sept. 1, 2009
Expires: Aug. 31, 2012
Awarded Amount to Date: $693,655
Principal Investigator: Michael Perlin
Sponsor: University of Louisville Research Foundation

This project will provide a genomics infrastructure necessary for the rational design of hypothesis-driven inquiries into Microbotryum violaceum development and pathogenesis. A comprehensive and comparative view will be generated of the suites of genes that play significant roles in fungal development and successful infection. The specific objectives are to sequence and assemble the complete genome of M. violaceum, which is estimated to be 25 megabases; annotate gene structure using computational methods; analyze gene transcription profiles late in infection; promptly release publicly all reads, assemblies, and annotation; and develop education, training and outreach programs. A website will be developed at the Broad Institute to disseminate the information on the genome of M. violaceum as well as allow comparison to other genomes.


III: Small: Collaborative Research: Reconstruction of Haplotype Spectra from High-Throughput Sequencing Data

Two awards with this title were made:

Start Date: Sept. 1, 2009
Expires: Aug. 31, 2010
Awarded Amount to Date: $81,525
Principal Investigator: Aleksandr Zelikovskiy
Sponsor: Georgia State University Research Foundation

Start Date: Sept. 1, 2009
Expires: Aug. 31, 2010
Awarded Amount to Date: $94,340
Principal Investigator: Ion Mandoiu
Sponsor: University of Connecticut

This research project is aimed at developing efficient computational methods for reconstructing the full spectrum of haplotype sequences from high-throughput sequencing data. Working in collaboration with molecular biologists from the University of Connecticut Health Center and the Centers for Disease Control, the investigators will develop methods enabling three novel applications of HTS, namely reconstruction of diploid genome sequences, including complete haplotype sequences of each CNV copy; reconstruction of alternative splicing isoform sequences and their frequencies; and reconstruction of viral quasispecies sequences and their frequencies. The project will include the development of a comprehensive analytical toolkit for these problems, and open source software implementations that will be made available free of charge to the research community.


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Collaborative Research: Resolving the Phylogeny of North American Milkweeds through the Application of Massively Parallel Sequencing Technology

Two awards with this title were made:

Start Date: Aug. 15, 2009
Expires: July 31, 2013
Awarded Amount to Date: $164,955
Principal Investigator: Mark Fishbein
Sponsor: Oklahoma State University

Start Date: Aug. 15, 2009
Expires: July 31, 2013
Awarded Amount to Date: $425,171
Principal Investigator: Aaron Liston
Sponsor: Oregon State University

This project will use genomic sequencing technology to investigate how the 135 milkweed species known in North America are related to each other. DNA sequences will be obtained from complete chloroplast genomes and 10 nuclear genes from two or more samples of each species. The goal is to achieve a species-level phylogeny of a large, rapidly radiating genus.


MRI: Acquisition of an Automated DNA Sequencer to Enhance Faculty-Student Research in Molecular Biology at the University of Central Oklahoma

Start Date: Aug. 15, 2009
Expires: July 31, 2012
Awarded Amount to Date: $130,006
Principal Investigator: Michelle Haynie
Sponsor: University of Central Oklahoma

The grant will be used for the acquisition of an automated DNA sequencer. This instrument will provide the university with a fully functional molecular biology laboratory, allowing faculty and students to perform a wide array of research projects at their home institution. A large proportion of the biology department faculty perform molecular biology research that will leverage the sequencer capabilities for studies in the fields of viral/parasite-host species co-evolution, population genetics, phylogeography, molecular systematics, molecular ecology, and genome evolution. This research is conducted on a diversity of organisms, including mammals, birds, reptiles, insects, plants, and fungi.


MRI: Acquisition of Next Generation DNA Sequencing Equipment

Start Date: Aug. 15, 2009
Expires: July 31, 2012
Awarded Amount to Date: $690,110
Principal Investigator: Craig Tomlinson
Sponsor: Dartmouth College

This award funds the acquisition of a Genome Analyzer IIx sequencer to enable deep sequencing at Dartmouth College. The instrument will enable researchers to pinpoint genetic mutations and variations associated with enzymatic reactions, microbial biofilms, plant physiology, and many other biological phenomena; determine the genomic locations bound by specific DNA binding proteins involved in gene regulation; and identify and quantify differences in mRNA expression as a function of environmental, toxicological, and physiological responses.


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Exon Splice Pattern Characterization of the Whole mRNA Transcriptome

Start Date: Aug. 1, 2009
Expires: July 31, 2012
Awarded Amount to Date: $1,027,384
Principal Investigator: Jinze Liu
Sponsor: University of Kentucky Research Foundation

The grant will be used to build cyberinfrastructure to help researchers understand the messenger RNA generated using new high-throughput sequencing methods. The research team will record, analyze, and compare mRNA transcriptomes directly from high- throughput RNA sequencing data. This team will build a data-driven processing pipeline applicable to any mRNA transcriptome, requiring only a reference genome, and without dependence on a priori gene structure annotations. Identification and analysis of both known and uncharacterized splicing patterns through the unbiased assessment of splice junction tags will be a major advance. This project will bridge the gap between biological science and the analytical/computational challenges faced with the massive datasets generated using RNA-seq protocols. The suite of bioinformatics tools that will be provided has the potential to turn individual laboratories into small genome centers and to allow individual scientists to assess the mRNA transcriptome in a matter of days using samples from any organisms with a reference genome. This award is funded under the American Recovery and Reinvestment Act of 2009.


MRI: Acquisition of a Roche Genome Sequencer Titanium System for Studies of Microbial Communities

Start Date: Aug. 15, 2009
Expires: July 31, 2012
Awarded Amount to Date: $602,343
Principal Investigator: Jonathan Eisen
Sponsor: University of California-Davis

This award funds the acquisition of a Roche Genome Sequencer FLX Titanium system that allows massively high-throughput DNA sequencing at the University of California Davis. The system will form the core of a microbial diversity sequencing facility that will serve as an active center for both research and education in microbial diversity across the UC Davis campus and with outside collaborators. Microbial diversity is fundamental to many key fields of research at UC Davis, including agriculture, viticulture, microbiology, evolution, ecology, bioenergy, bioremediation, nutrition, and pathogenesis in plants, animals, and humans. The 454 instrument will build on these strengths by "revolutionizing" the research in dozens of labs across campus, facilitating productive interaction between researchers investigating different aspects of microbial communities, and recruiting new researchers to this field, according to the grant abstract. In addition, the system will be made available to others on campus and in the area through a core facility in the UC Davis Genome Center.

The Scan

WHO Seeks Booster Pause

According to CNN, the World Health Organization is calling for a moratorium on administering SARS-CoV-2 vaccine boosters until more of the world has received initial doses.

For Those Long Legs

With its genome sequence and subsequent RNAi analyses, researchers have examined the genes that give long legs to daddy longlegs, New Scientist says.

September Plans

The New York Times reports that the US Food and Drug Administration is aiming for early September for full approval of the Pfizer-BioNTech SARS-CoV-2 vaccine.

Nucleic Acids Research Papers on Targeting DNA Damage Response, TSMiner, VarSAn

In Nucleic Acids Research this week: genetic changes affecting DNA damage response inhibitor response, "time-series miner" approach, and more.