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Sequencing-Related NSF Grants Awarded March 26 – Aug. 15, 2008

Ecological Genomics of a Global Amphibian Pathogen
Start Date: Sept. 1, 2008
Expires: Aug. 31, 2009
Awarded Amount to Date: $50,000
Principal Investigator: Erica Rosenblum
Sponsor: University of Idaho
This project will use genomic-based techniques to study chytrid, a fungus that has infected hundreds of species of frogs around the world, according to its abstract. Whole-genome sequences will be obtained for chytrid strains from different parts of the world and from different environmental conditions. This work is designed to help understand why certain strains of chytrid are more deadly than others, and will help identify particular genes that are important for chytrid's ability to attack frogs, the abstract states.

New Generation of Lab on Chip Separators Based on Independent Fluid and Analyte Control
Start Date: Sept. 1, 2008
Expires: Aug. 31, 2011
Awarded Amount to Date: $417,592
Principal Investigator: Dimiter Petsev
Sponsor: University of New Mexico
The objective of this project is to develop a novel method for separating and sensing biomolecules, such as large DNA fragments and proteins, by decoupling the electro-osmotic transport of the fluid from the electrophoretic migration of the solutes, according to the abstract. This will be accomplished by means of new elements that the investigators developed recently: semiconductor diode pumps powered by an alternating current field.
The analytes will be independently manipulated electrophoretically by a direct current. In addition, the researchers propose to explore the fabrication and properties of a new class of microscopic device-like particles that can move, sense, and respond to biochemical stimuli on their own, according to the abstract.
The self-propelling particles will be microdiodes that harvest energy for their motion from a global AC field or mesostructured entities that are driven by osmotic gradients through a controlled solute release.
The successful execution of the proposed research program could open a new range of opportunities in the areas of biomedical engineering, proteomics, and DNA sequencing, medical diagnostics, microfluidic reactor design, sensing, and detection, according to the abstract. A major object for separation in the devices to be developed will be megabase DNA, which is important for genomic applications such as genotyping and purification of clone libraries. DNA in the megabase range (109 Da) is commonly separated using slab gel electrophoresis; however, standard gels only resolve fragments up to 75 kb, since resolution for larger fragments is poor. The new technique will avoid this problem and can become a key in rapid prototyping on a chip, according to the abstract.

Acquisition of a Genome Sequencer System for Research and Education
Start Date: Sept. 1, 2008
Expires: Aug. 31, 2011
Awarded Amount to Date: $511,736
Principal Investigator: Linda Strausbaugh
Sponsor: University of Connecticut
Acquisition of a genome sequencer will enable faculty, staff, and student members of more than 30 research groups across multiple campuses at the university to conduct transformative research, according to the abstract.
Research foci include: the genomic basis and evolution of pathogenesis/symbiosis; adaptation to extreme environments; novel regulation of proper development; genetic basis of complex characteristics; measurement and conservation of biodiversity; forensic identity typing; and innovative computational approaches to genome science applications, according to the abstract.

Genome Sequence of Wolbachia/Drosophila Lateral Gene Transfer
Start Date: Sept. 1, 2008
Expires: Aug. 31, 2010
Awarded Amount to Date: $313,498
Principal Investigator: Julie Hotopp
Sponsor: University of Maryland at Baltimore
The goal of this project is to examine the genomic changes in the fruit fly Drosophila due to lateral gene transfer from the bacterium Wolbachia, according to the abstract.
More than 70 percent of the genomes of Wolbachia-infected insects have evidence of lateral gene transfer from bacterium to animal. The DNA of both the fruit fly insert and the resident bacterial genome will be sequenced using second-generation sequencing technologies, according to the abstract.
Bioinformatic techniques will be used to decipher the role and impact of the transferred DNA in flies. Wolbachia are very abundant bacteria because their hosts are among the most abundant animals on earth. These hosts include parasitic worms and disease-spreading pests like mosquitoes and tsetse flies, according to the abstract
Current drugs and pesticides targeting these organisms can be toxic to humans because the worm/insect genes are similar to human genes. However, LGT genes are more closely related to bacterial genes, and as such, can be targeted with less toxic drugs or pesticides similar to antibiotics, the abstract states.

Transitions in the Surface Layer and the Role of Vertically Stratified Microbial Communities in the Carbon Cycle- An Oceanic Microbial Observatory
Start Date: Aug. 15, 2008
Expires: July 31, 2013
This grant has been awarded to two investigative teams:
  • Stephan Giovannoni; Oregon State University; $479,208
  • Craig Carlson; University of California-Santa Barbara; $803,765
The focus of this proposal is the role of bacterioplankton microbial community stratification in the ocean carbon cycle, according to the abstract. The premise of the proposal is that stratified bacterioplankton clades engage in specialized biogeochemical activities that can be identified by integrated oceanographic and microbiological approaches.
Specifically, the objective is to assess if the mesopelagic microbial community rely on diagenetically altered organic matter and subcellular fragments that are produced by microbial processes in the euphotic zone and delivered into the upper mesopelagic by sinking or mixing.
Among other goals, complete genome sequences from key organisms will be sought and used as queries to study patterns of natural variation in genes and populations that have been associated with biogeochemically important functions. This project will make cultures of novel bacterioplankton and genome sequences available to the scientific community, according to the abstract.
Findings from this research may be used directly in foodweb and ocean carbon-cycle models.

Linking Dissolved Organic Matter Composition to Prokaryotic Community Structure
Start Date: Aug. 1, 2008
Expires: July 31, 2009
Awarded Amount to Date: $47,000
Principal Investigator: Jennifer Edmonds
Sponsor: University of Alabama Tuscaloosa
In this study, the researcher will use 454 pyrosequencing to characterize bacterial community diversity and to identify the roles that diverse microbial species play in the cycling of different types of organic matter, according to the abstract.
The resulting data will be analyzed to determine if bacteria specialize on particular types of carbon and to test hypotheses on specific metabolic functions of participating species, the abstract states.

Acquisition of an Illumina/Solexa Genome Analyzer
Start Date: Aug.1, 2008
Expires: July 31, 2011
Awarded Amount to Date: $484,395
Principal Investigator: Leslie Sieburth
Sponsor: University of Utah
The University of Utah will obtain a next-generation genome analysis machine “such as the Illumina/Solexa Genome Analyzer,” according to the abstract.
The equipment will support a diverse base of users, and will contribute “significantly” to many NSF-supported research programs. In addition, the equipment will also be used for undergraduate education, according to the abstract.
The PIs and major users of this equipment will address several different basic research questions, including natural variation and genome evolution; genetic networks and basic molecular mechanisms; and behavioral genetics and molecular characterization of “subtle mutant phenotypes,” the abstract states.
The  sequencer will be placed into a new genomics facility in the biology department at the University of Utah. It will be made available to researchers in the Great Basin Region, for instance Idaho, Wyoming, Montana, Nevada, and New Mexico, according to the abstract.

Integrated Nanosystem Combining Engineered Nanopore Devices and Hierarchical Model-Based Diagnosis Algorithms for Ultra-Rapid Biomolecule Analysis
Start Date: June 15, 2008
Expires: May 31, 2009
Awarded Amount to Date: $176,482
Principal Investigator: Sankar Nair
Sponsor: GA Tech Research Corporation - GA Institute of Technology
The objective of this research is to create a nanoscale system that achieves ultra-rapid, high-resolution analysis of biomolecules such as nucleic acids and proteins, according to the abstract.
The approach is based on a combination of nanopore device fabrication, predictive physics-based diagnostic algorithms to control biomolecule transport in the device, and integration of these subsystems to demonstrate high-speed biomolecule analysis with much higher resolution than currently possible.
This work addresses the challenge of developing nucleic acid and protein sequencing platforms that achieve orders-of-magnitude savings in time and cost, according to the abstract.
The approach combines a wafer-scale process (based on electron-beam and atomic layer deposition techniques) to fabricate reproducible arrays of engineered nanopore devices, with a computational diagnosis platform that couples hierarchically detailed simulation engines and mathematical algorithms to adaptively refine the nanopore device performance for single-nucleotide resolution.

Practical Chimera Detection for High-Throughput Sequencing Methods
Start Date: June 1, 2008
Expires: May 31, 2009
Awarded Amount to Date: $5,637
Principal Investigator: Micah Hamady
Sponsor: Hamady Micah
This award supports a US graduate student to conduct an individual research project at one of seven locations in East Asia and the Pacific region, including Australia, China, Japan, Korea, New Zealand, Singapore, and Taiwan, according to the abstract.
The research project, called the East Asia Summer Institute, is designed to provide the student with a first-hand mentored research experience, an introduction to science and science policy infrastructure, and an orientation to the culture and language of the location, the abstract states.

Anthropological Genomics and Phylogeny in New World Monkeys (Platyrrhini)
Start Date: June 1, 2008
Expires: May 31, 2009
This grant was awarded to two investigative teams:
  • Soojin Yi; Georgia Tech Research Corporation; $42,553
  • Derek Wildman; Wayne State University; $42,447
In this study, phylogeny of New World monkeys will be inferred using innovative and efficient genomic and computational techniques. Random genomic libraries, generated from a representative species of each family, will provide up 100 markers of approximately 650 base pairs in length. These unlinked markers, which are estimated to encompass up to 65 kilobases of non-coding, non-genic, non-repetitive nuclear DNA, will be sequenced in at least one representative species of every platyrrhine genus, according to the abstract.
This dataset will be combined with and compared to data from traditional molecular markers such as protein coding loci from the nuclear and mitochondrial genomes. Data will be analyzed with a likelihood-based method, taking into account phylogenetic incongruence among markers caused by ancestral polymorphism and rapid divergence in the early stage of diversification of platyrrhine families, according to the abstract.
Without an accurate New World monkey phylogeny in place, evolutionary reconstructions of anthropoid genomes, phenotypes, and behaviors will be hampered, according to the abstract, which notes that the proposed study  introduces new approaches to determine the branching order and timing of divergence among all platyrrhine genera.
A “high-throughput method” will be used to generate a large amount of non-coding phylogenetic sequence data for analysis, according to the abstract.

Assembling the Liverwort Tree of Life: A Window into the Evolution and Diversification of Early Land Plants
Start Date: Jan. 30, 2008
Expires: Dec. 31, 2010 (Estimated)
Awarded Amount to Date: $335,458
Principal Investigator: Reed Beaman
Sponsor: University of Florida
This project aims to resolve the liverwort “Tree of Life,” according to the abstract. It brings together experts from around the world for a multidisciplinary, highly integrated approach that combines anatomical and developmental features with DNA sequence and genome structural characters to resolve phylogenetic relationships across the entire spectrum of liverwort diversity.
Three general types of data will be compiled: 1) conservative morphological and genome characters to resolve deep "backbone" relationships, 2) anatomical/developmental data to resolve intermediate-depth lineages, and 3) morphological and DNA sequence characters to resolve relationships among a sample of 800 taxa representing all genera of liverworts, according to the abstract.
A second major goal of the project is to integrate phylogenetic inferences and bionformatic efforts between this and other ongoing NSF-supported projects, including several funded ATOL programs. These integrative activities include contributions to studies of genome structure and evolution across land plants, expansions of novel informatic tools to make methods, results, and implications widely accessible, and continued development of DNA sequence utilities that will benefit a broad range of scientists working on diverse organisms, according to the abstract.

The Scan

Positive Framing of Genetic Studies Can Spark Mistrust Among Underrepresented Groups

Researchers in Human Genetics and Genomics Advances report that how researchers describe genomic studies may alienate potential participants.

Small Study of Gene Editing to Treat Sickle Cell Disease

In a Novartis-sponsored study in the New England Journal of Medicine, researchers found that a CRISPR-Cas9-based treatment targeting promoters of genes encoding fetal hemoglobin could reduce disease symptoms.

Gut Microbiome Changes Appear in Infants Before They Develop Eczema, Study Finds

Researchers report in mSystems that infants experienced an enrichment in Clostridium sensu stricto 1 and Finegoldia and a depletion of Bacteroides before developing eczema.

Acute Myeloid Leukemia Treatment Specificity Enhanced With Stem Cell Editing

A study in Nature suggests epitope editing in donor stem cells prior to bone marrow transplants can stave off toxicity when targeting acute myeloid leukemia with immunotherapy.