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Sequencing-Related NSF Grants Awarded Sept. 22 - Oct. 20, 2007

Microbial Inventory Research Across Diverse Aquatic LTERs
Start Date: Sept. 15, 2007
Expires: Aug. 31, 2008
Awarded Amount to Date: $440,000
Principal Investigator: Linda Amaral Zettler
Sponsor: Marine Biological Laboratory, Woods Hole
This project will establish a Microbial Biodiversity Survey and Inventory across all 13 of the major aquatic (marine and freshwater) Long Term Ecological Research (LTER) sites established by the NSF US LTER Program. The long-term objective of the study is to document and describe baseline diversity and relative abundance data for both common and rare members of microbial communities located in aquatic LTER sites and to relate this diversity to the underlying physical and chemical environment. The project employs a new, high-volume DNA-sequencing technology based on the sequencing of small ribosomal RNA regions that are especially variable, which could enable researchers to discover novel microbial diversity in bacteria, archaea, and eukaryotes, according to the grant abstract.

Using Combined-Evidence Phylogenetics to Inform a Revised Classification of Spittlebugs (Insecta: Hemiptera: Cercopoidea)
Start Date: Sept. 15, 2007
Expires: Aug. 31, 2008
Awarded Amount to Date: $136,706
Principal Investigator: Jason Cryan
Sponsor: New York State Museum Institute
This project represents a large-scale investigation into the evolution of spittlebugs using both traditional comparative morphological methods and modern DNA-sequencing technology. The results of this project will include a reconstruction of evolutionary relationships among the major lineages of spittlebugs, interpretations of observed patterns of worldwide spittlebug geographical distribution and host-plant affiliations, and improved, internet-accessible tools for spittlebug identification.

Physiological Advantages of the Development of Bacterial Morphology
Start Date: Oct. 1, 2007
Expires: Sept. 30, 2010
Awarded Amount to Date: $700,002
Principal Investigator: Yves Brun
Sponsor: Indiana University
The goal of this project is to produce a high-quality draft sequence of nine genomes of prosthecate bacteria, and one closely related non-prosthecate bacterium, selected to represent an increasingly complex collection of morphologies. The genomes will be analyzed with respect to mechanisms for the biosynthesis and function of stalks, the extent of conservation of regulatory pathways for stalk biosynthesis, and the interesting and potentially useful physiological properties of these organisms. Comparative analysis of the genome sequences of the stalked bacteria will further the understanding of the mechanisms of stalk synthesis. The results will provide the information necessary to engineer stalked bacteria with new metabolic pathways, or to engineer other bacteria to synthesize stalks. The genomic sequence information obtained in this study will aid the research of many investigators who study the cell biology, developmental biology, and cell shape determination and function of bacteria. The knowledge acquired in this project could also have uses in industry, according to the grant abstract. For example, engineering these bacteria to synthesize stalks to quicken the uptake of a substrate molecule could improve drug production.

Comparative Genome Analysis of Foliar and Root-Infecting Members of the Magnaporthaceae
Start Date: Oct. 1, 2007
Expires: Sept. 30, 2009
Awarded Amount to Date: $1,009,625
Principal Investigator: Ralph Dean
Sponsor: North Carolina State University
This project builds on work supported by the NSF-USDA Microbial Genome Sequencing Program that characterized the genome of the rice blast fungus Magnaporthe oryzae. The current grant will support comparative analysis of the genome of M. oryzae with its close relatives Gaeumannomyces graminis var tritici and Magnaporthe poae. The project objectives are to generate 7X draft genome assemblies for G. graminis var. tritici and M. poae to generate ESTs from cDNA pools derived from G. graminis var. tritici and M. oryzae using 454 sequencing; to provide a public database for each genome complete with automated gene predictions and annotations; and to create a user-friendly genome browser to enable phylogenomic analyses between G. graminis var. tritici, M. poae, and M. oryzae. Comparative genome analyses will enable rigorous evaluation of the genetic and evolutionary basis of structure-functional relationships associated with their different developmental patterns and different disease pathologies caused by these three fungi.

Metagenomic Exploration of Virus-Host Interactions in Deep-Sea Hydrothermal Vent Environments
Start Date: Dec. 15, 2007
Expires: Nov. 30, 2010
Awarded Amount to Date: $1,199,999
Principal Investigator: K. Wommack
Sponsor: University of Delaware
The objective of this research program is to explore the abundant, but largely unknown, assemblages of viruses within the hostile environments of deep-sea hydrothermal vents. Because viruses can significantly alter the biological characteristics of their microbial hosts, in some cases changing benign bacteria into pathogens, it is possible that viruses at the deep-sea vents are intimately involved in assisting microbial life cope with the challenging conditions of deep-sea hydrothermal vents. DNA sequence data from this project will reveal thousands of new genes and protein groups and possibly entirely new viral clades existing at the vents. Outreach and education efforts during the project will include all levels of science education.

The Scan

Mosquitos Genetically Modified to Prevent Malaria Spread

A gene drive approach could be used to render mosquitos unable to spread malaria, researchers report in Science Advances.

Gut Microbiomes Allow Bears to Grow to Similar Sizes Despite Differing Diets

Researchers in Scientific Reports find that the makeup of brown bears' gut microbiomes allows them to reach similar sizes even when feasting on different foods.

Finding Safe Harbor in the Human Genome

In Genome Biology, researchers present a new approach to identify genomic safe harbors where transgenes can be expressed without affecting host cell function.

New Data Point to Nuanced Relationship Between Major Depression, Bipolar Disorder

Lund University researchers in JAMA Psychiatry uncover overlapping genetic liabilities for major depression and bipolar disorder.