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Sequencing-Related NSF Grants Awarded March 1 — April 9, 2007

An Integrative Approach to Understanding Speciation in Salamanders of the Ensatina Eschscholtzii Complex
Start date: 2/1/07
Expires: 1/31/10
Principal investigator: Craig Moritz
Organization: University of California, Berkeley
Amount awarded to date: $280,002
Proposal to trace the history and mechanisms of divergence in salamanders of the Ensatina eschscholtzii complex to gain “further understanding of how new species are formed.” The investigators will test hypotheses about the evolutionary processes that underlie patterns of geographic variation using “DNA sequence data at a broad scale, in concert with highly variable DNA microsatellites to scrutinize interactions between individuals at contact zones between differentiated populations,” according to the grant abstract.

Population Ecology of Amphibian Species in Relation to their Bacterial Symbionts
Start date: 2/15/07
Expires: 1/31/10
Principal investigator: Reid Harris
Organization: James Madison University
Amount awarded to date: $360,000
Funds a project to study the role of beneficial bacteria on the skin in protecting amphibians from the fungal pathogen Batrachochytrium dendrobatidis. Methods will include field sampling, experiments in large indoor amphibian habitats, culturing of bacteria and fungi, and identification of microorganisms with DNA sequencing techniques.

The Diversification of Chemical and Developmental Defenses Against Herbivores within the Genus Inga
Start date: 3/15/07
Expires: 2/28/09
Principal investigator: Phyllis Coley
Organization: University of Utah
Amount awarded to date: $370,000
Supports a project to examine how plant defenses shape plant evolution and interactions with insects by studying the genus Inga, a tropical tree in the pea family. Researchers will quantify defenses in many species of Inga from Panama, Ecuador, and Peru, and will sequence DNA to create a phylogenetic tree, according to the grant abstract.

Collaborative Research: Systematics and Evolution of Fossil and Living Delphinidans (Dolphins, Porpoises, and Kin)
Start date: 3/15/07
Expires: 2/29/08
This grant was awarded to two investigative teams:
  • University of California, Riverside. Principal investigator: John Gatesy. Amount awarded to date: $54,999
  • Georgia Southern University Research and Service Foundation. Principal investigator: Jonathan Geisler. Amount awarded to date: $44,999 
Funds a project that will integrate DNA sequences and anatomical data from living and fossil species to study the evolution of Delphinida, the group that includes oceanic dolphins, most river dolphins, porpoises, belugas, and narwhals. Research objectives include resolving evolutionary relationships among living and extinct species, estimating when the diversification of dolphins occurred, determining if behavior influenced the evolution of large brains in dolphins, and unraveling the evolution of olfactory receptor genes in aquatic animals that lack the sense of smell. “DNA will be sequenced in a state-of-the-art lab, anatomical data will be collected from museums worldwide, and computers will be used to analyze the large body of data collected,” according to the grant abstract.

Tardigrades of the LTER Sites: A Framework for the Distribution and Phylogeny of North American Tardigrada
Start date: 4/1/07
Expires 3/31/08
Principal investigator: Carl Johansson
Organization: Fresno City College
Amount awarded to date: $43,532
Proposal to study the ecology, biodiversity, and phylogeny of the phylum tardigrada through new undergraduate research programs at Baker University, Fresno City College, and Brigham Young University. Student researchers will be trained to collect, identify, sequence, and report on tardigrades at Long Term Ecological Research sites.

Molecular Basis of Mimicry in Heliconius Butterflies
Start date: 4/1/07
Expires: 3/31/10
This grant was awarded to two investigative teams:
  • North Carolina State University. Principal investigator: Owen McMillan. Amount awarded to date: $230,550
  • University of California, Irvine. Principal investigator: Robert Reed. Amount awarded to date: $59,480
Supports a study to explore how convergent morphological change is achieved in Heliconius butterflies. The project will generate genomic sequence across regions that contain genes responsible for wing pattern variation. “The targeted genomic sequence will provide the backdrop for identifying the genes that underlie wing pattern change and for exploring the history of mimetic convergence at the loci that have been the actual targets of selection,” according to the grant abstract.

DNA Amplification in a Novel Integrated Microchip Platform with Temporal Thermal Control
Start date: 4/1/07
Expires: 3/31/10
This grant was awarded to two investigative teams:
  • Brown University. Principal investigator: Anubhav Tripathi. Amount awarded to date: $286,330
  • University of Florida. Principal investigator: Anuj Chauhan. Amount awarded to date: $65,978

Funds a project to develop a microchip that can perform rapid PCR in a microchannel using a method that is based on temporal temperature cycling. The investigators intend to combine modeling and experiments “to develop a clear understanding of fundamental issues relevant to the proposed device,” which include contribution of thermal expansion-contraction, reactions on dispersion and amplification efficiency, and the effect of various design and operating parameters on the fluid-flow and mass transfer in the device.

The Scan

Single-Cell Sequencing Points to Embryo Mosaicism

Mosaicism may affect preimplantation genetic tests for aneuploidy, a single-cell sequencing-based analysis of almost three dozen embryos in PLOS Genetics finds.

Rett Syndrome Mouse Model Study Points to RNA Editing Possibilities

Investigators targeted MECP2 in mutant mouse models of Rett syndrome, showing in PNAS that they could restore its expression and dial down symptoms.

Investigators Find Shared, Distinct Genetic Contributors to Childhood Hodgkin Lymphoma

An association study in JAMA Network Open uncovers risk variants within and beyond the human leukocyte antigen locus.

Transcriptomic, Epigenetic Study Appears to Explain Anti-Viral Effects of TB Vaccine

Researchers report in Science Advances on an interferon signature and long-term shifts in monocyte cell DNA methylation in Bacille Calmette-Guérin-vaccinated infant samples.