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Funding Update: Aug 4, 2009


Sequencing-Related NSF Grants Awarded July 1 — July 31, 2009

Epigenetic Modifications of the Centromeric Chromatin in Rice

Start Date: Oct. 1, 2009
Expires: Sept. 30, 2013
Awarded Amount to Date: $821,957
Principal Investigator: Jiang Jiming
Sponsor: University of Wisconsin-Madison

Using rice as a model and approaches that include chromatin immunoprecipitation and DNA sequencing, this project will reveal the location of epigenetic marks, such as cytosine DNA methylation and histone modifications, associated with centromeric chromatin. The information generated from this project will also provide information about the potential levels of transcription associated with centromeric DNA compared with DNA located outside the centromere region.

EAGER: Allopolyploidy and Photosynthesis: a Whole-transcriptome Approach

Start Date: Aug. 1, 2009
Expires: July 31, 2011
Awarded Amount to Date: $220,078
Principal Investigator: Jeffrey Doyle
Sponsor: Cornell University

The researchers will be using Illumina's high-throughput sequencer to obtain a deep and detailed profile of gene expression in three Glycine allopolyploid species and their diploid progenitors under normal light and high light stress conditions to assess which genes are involved in photoprotection, how they are regulated in diploids and polyploids, what the contribution of the two diploid progenitor genomes is at each of thousands of expressed genes in each polyploid, and whether there are shared patterns of gene expression in independently formed allopolyploids that could constitute predictable 'rules' governing photoprotection in polyploid species of Glycine and other flowering plants.

Collaborative Research at the Lau ISS: Integrating Microbial Diversity with Geochemistry Using Heat and Mass Transport Models

Two awards with this title were made:

Start Date: Aug. 1, 2009
Expires: July 31, 2011
Awarded Amount to Date: $158,346
Principal Investigator: Margaret Tivey
Sponsor: Woods Hole Oceanographic Institution

Start Date: Aug. 1, 2009
Expires: July 31, 2011
Awarded Amount to Date: $117,116
Principal Investigator: Anna-Louise Reysenbach
Sponsor: Portland State University

This research combines microbial diversity data obtained in the field from hydrothermal vent deposits at the Ridge 2000, Lau Basin Integrated Study Site with computer calculations that represent the physical and geochemical environments from which the samples were taken. Both molecular fingerprinting data and a small subset of 454 pyrosequencing data (V6 region of the 16S reran gene) from hydrothermal chimney and flange deposits are combined with computer models of vent heat and mass transport to produce estimates of temperature gradients, pore fluid compositions, and local advection rates present in the chimneys and flanges. Measured exterior and interior vent chimney temperatures, mineral compositions and textures (including porosity) are used as constraints. This award is funded under the American Recovery and Reinvestment Act of 2009.

Facile Production and Efficient Indexing of Transposon-tagged Lines Using Next-generation Sequencing Technology for Maize

Start Date: Sept. 1, 2009
Expires: Aug. 31, 2012
Awarded Amount to Date: $1,242,967
Principal Investigator: Hugo Dooner
Sponsor: Rutgers University New Brunswick

This project will develop a rapid, accurate, and cost-effective method for generating, sequencing, and indexing Ac/Ds transposable element insertions in maize based on next-generation sequencing technology. Specifically, the project will sequence-index a collection of existing lines that contain a unique transposed Ac element; complete a set of 120 roughly equidistant transgenic Ds elements that serve as launching platforms and carry easily scored markers that will allow simple visual selection of element transposition from any region of the genome and, thus, enable researchers to generate regional gene knock-out collections; sequence-index 10,000 Ds element insertion sites from model platforms using a novel method that should be applicable to any collection of insertions produced in a common genetic background; and develop a web-searchable database of insertion site sequences cross-referenced to lines that will be freely available from the Maize Genetics Stock Center. All relevant information from this project will be accessible from MaizeGDB.

EAGER: Phylogenomics

Start Date: Aug. 15, 2009
Expires: July 31, 2010
Awarded Amount to Date: $217,159
Principal Investigato: David Hillis
Sponsor: University of Texas at Austin

This project will investigate a novel method for producing large amounts of high-quality DNA sequence data for phylogenomic applications. The project will extend a strategy called "microarray-based genome selection," MGS, which is capable of enriching a DNA sample for thousands of genes, to simultaneous enrichment across distantly related species. As a result, this study has the potential to address the remaining practical obstacles to microarray hybridization across species (cross-species hybridization) and result in hugely increased scaling of MGS technology. Such a scaling up will expedite the assembly of the Tree of Life and accelerate the adoption of next-generation DNA sequencing technologies in many biological fields. Frogs, a diverse group broadly used in biology, will be the model group for this research. This award is funded under the American Recovery and Reinvestment Act of 2009.

MRI: Acquisition of an Automated Genetic Analyzer by the Department of Biology at Middle Tennessee State University

Start Date: Aug. 1, 2009
Expires: July 31, 2012
Awarded Amount to Date: $269,392
Principal Investigator: Aubrey Cahoon
Sponsor: Middle Tennessee State University

The Biology Department at Middle Tennessee State University has been awarded a grant to purchase an ABI 3130xl automated genetic analyzer with DNA sequencing and genotyping capabilities. The instrument will support instruction for students in DNA sequencing and DNA fragment analysis. "Many of the faculty in the Biology department at MTSU are engaged in research that span the breadth of sequencing and genotyping applications and the use of this equipment will allow them and their faculty mentors to answer questions related to basic molecular genetics, diagnostics, and determination of inter- and intra-species relationships," the grant abstract states. This award is funded under the American Recovery and Reinvestment Act of 2009.

CAREER: Probing the Sequence and Dynamics of Single DNA Molecules Using Solid-State Nanopores, Optical Tweezers, and Binding Proteins

Start Date: Aug. 1, 2009
Expires: July 31, 2014
Awarded Amount to Date: $400,000
Principal Investigator: Derek Stein
Sponsor: Brown University

This project plans to extract genetic information from a single molecule through a combination of three powerful techniques: First, biological binding proteins will be attached to a specific sequence along DNA molecules, and mark its locations by creating a physical bulge there. Second, the DNA molecule will be electrically threaded through a solid-state nanopore that will also serve as an electrical detector. Third, the DNA molecule will be guided through the nanopore at a controlled, steady speed using an optical tweezers instrument. As the bulky binding proteins pass through the nanopore, they will impede the flow of salt ions through the nanopore, and be detected as a measureable dip in electrical current. This ability to identify specific locations along DNA, combined with the nanometer-scale position control and pico-Newton force sensitivity of optical tweezers, will enable new fundamental studies on single molecules, according to the grant abstract. Nanoscale physics will be probed, including the role of thermal fluctuations, and whether the motion of DNA through a nanopore is continuous or proceeds in a stick-slip manner. Biological questions concerning the specificity and strength of DNA-protein interactions will also be addressed. This project will help lay the groundwork for a potentially transformative nanopore technology, capable of extracting important genetic information from single DNA molecules at high speed, the abstract claims. This award is funded under the American Recovery and Reinvestment Act of 2009.

Collaborative Research: Understanding the Role of Environmental Change on the Long-term Population Dynamics of One Surviving and Two Extinct Arctic Mammals

Three awards with this title were made:

Start Date: Aug. 1, 2009
Expires: July 31, 2012
Awarded Amount to Date: $41,135
Principal Investigator: Matthew Wooller
Sponsor: University of Alaska Fairbanks Campus

Start Date: Aug. 1, 2009
Expires: July 31, 2012
Awarded Amount to Date: $267,758
Principal Investigator: Beth Shapiro
Sponsor: Pennsylvania State University

Start Date: Aug. 1, 2009
Expires: July 31, 2012
Awarded Amount to Date: $185,310
Principal Investigator: Robert Wayne
Sponsor: University of California-Los Angeles

This project aims to produce long-term reconstructions of the population dynamics of one surviving and two extinct and arctic mammals: steppe bison, horses, and caribou. To achieve this, the "largest, most densely sampled ancient DNA data sets to date" will be produced, focusing on two environmentally distinct arctic localities with exceptional chronological control and detailed paleoenvironmental records going back at least 250,000 years, according to the grant abstract. These data will provide the first opportunity to directly evaluate the role of environmental change on the long-term dynamics and extinction risk of arctic fauna, the abstract states. A near-continuous time series detailing changes in the size and structure of bison, horse and caribou populations will be generated, spanning one complete glacial/interglacial cycle and several periods of major environmental change. Novel analytical techniques will be developed to significantly extend the temporal range of paleogenetic reconstructions; incorporate geographic and ecological data explicitly into demographic analyses; and detect and quantify the role of intrinsic and extrinsic processes in the fate of natural populations of large herbivores. In addition, a detailed analysis of evolutionary information in mitochondrial DNA sequences will be performed, using high-throughput sequencing technology and experimental methodology to develop "the first comparative temporal data set of complete mitochondrial genomes for sympatric species." This award is funded under the American Recovery and Reinvestment Act of 2009.

Rapid Electrophoretic Sorting of DNA Using Nanoemulsion Tags

Start Date: Aug. 1, 2009
Expires: July 31, 2012
Awarded Amount to Date: $329,999
Principal Investigator: James Schneider
Sponsor: Carnegie-Mellon University

The investigators propose a method of rapid DNA electrophoresis that uses dilute suspensions of nanoemulsion droplets that transiently bind to DNA in the sample. To encourage interaction of the DNA with the nanoemulsion droplets, DNA is end-modified with various nonpolar groups. This alkylated DNA can then be used as a primer for a standard Sanger DNA sequencing process, according to the grant abstract. Separations are carried out using capillary electrophoresis, a standard vehicle for many types of biomolecular characterization and DNA sequencing. Because the electrophoretic separation does not require the use of polymers or gels as a sieving matrix, the investigators "expect to provide run times that are 10 to 100 times faster than can be achieved by the current state-of-the-art, capillary gel electrophoresis." In addition, much longer DNA can be analyzed, greatly reducing the enzymatic work that must be performed in the Sanger process, the abstract states. Finally, it adds, difficulties encountered when introducing viscous polymer solutions into capillaries or microchannels are avoided using these dilute surfactant solutions. The process proposed is an extension of end-labeled free solution electrophoresis, an existing DNA separation technique that covalently attaches uncharged polymer or protein drag tags to DNA populations so that their free solution mobility is a function of DNA length. While this would remove the requirement of a sieving matrix, ELFSE methods have not been competitive with CGE as the tags need to be prohibitively monodisperse to be effective. In this system, interactions between aDNA and droplets or micelles are frequent and short lived, so that each aDNA swaps tags millions of times during the run. This confers a highly uniform average drag upon the aDNA, even though the droplets may be polydisperse. Tags can also be swapped during the run as required for separation of a given length of DNA. The research plan involves developing nanoemulsion preparation methods that are compatible with electrophoresis, quantifying and maximizing the peak resolution in high electric fields, and establishing means of switching tag sizes during the run for greater sequencing throughput. This award is funded under the American Recovery and Reinvestment Act of 2009.

The Complete Genome Sequence of the Glaucophyte Alga Cyanophora paradoxa

Start Date: July 1, 2009
Expires: Sept. 30, 2010
Awarded Amount to Date: $262,958
Principal Investigator: Debashish Bhattacharya
Sponsor: Rutgers University New Brunswick

This grant, to the University of Iowa and SymBio, aims to determine to high coverage the 140 million base pair nuclear genome sequence of the unicellular alga Cyanophora paradoxa. Cyanophora is a member of the remaining group of photosynthetic eukaryotes, Glaucophyta, that still lacks a complete genome sequence. The single cyanobacterial primary endosymbiosis that gave rise to all plastids, for example chloroplasts, occurred in the common ancestor of Cyanophora, other algae, and plants. A critical step in plastid establishment was the transfer of endosymbiont genes to the "host" nucleus. It is unclear, however, whether this massive transfer was limited to genes strictly involved in plastid metabolism or whether the host profited from the captured genome to explore other novel functions via recruitment of genes from the cyanobacterium. The Cyanophora genome sequence will enable scientists to rigorously test this idea in a relatively "simple" algal model. Beyond its contribution to understanding endosymbiosis, the Cyanophora genome sequence will allow countless other insights which include identifying a set of core genes shared by algae and plants that can be studied in detail to understand the origin of plant-specific characters. In addition, the Cyanophora genome will be invaluable for guiding the annotation of the genomes of plants and other protists.

II-NEW: A Dedicated Computing Platform for Large Spatiotemporal-scale Atomistic Simulations of DNA Translocation and Self-Assembly

Start Date: Sept. 1, 2009
Expires: Aug. 31, 2010
Awarded Amount to Date: $450,000
Principal Investigator: Priya Vashishta
Sponsor: University of Southern California

This project establishes a dedicated computing platform for microsecond simulations to study DNA self-assembly and translocation through solid-state nanopores. The project uses a predictive hierarchical petascale simulation framework to study translocation kinetics and dynamics of DNAs through solid state nanopores; electronic properties of translocating DNAs for sequencing nucleotides; ionic screening of surface charges in nanopores; pressure-driven DNA transport in confined silica channels; and shear-induced DNA self-assembly. The computing platform will also support computer science research in techniques for the parallelization of such simulations, and for the integration of multi-scale, multi-phenomena simulation codes for molecular biology and biological materials science. Petascale simulations of DNA translocation through solid-state nanopores and nanofluidic channels underlie "lab-on-a-chip" technology and solid-state nanopore "microscopy" for molecular structure and high-speed sequencing. This award is funded under the American Recovery and Reinvestment Act of 2009.

The Scan

And For Adolescents

The US Food and Drug Administration has authorized the Pfizer-BioNTech SARS-CoV-2 vaccine for children between the ages of 12 and 15 years old.

Also of Concern to WHO

The Wall Street Journal reports that the World Health Organization has classified the SARS-CoV-2 variant B.1.617 as a "variant of concern."

Test for Them All

The New York Times reports on the development of combined tests for SARS-CoV-2 and other viruses like influenza.

PNAS Papers on Oral Microbiome Evolution, Snake Toxins, Transcription Factor Binding

In PNAS this week: evolution of oral microbiomes among hominids, comparative genomic analysis of snake toxins, and more.