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Funding Update: May 28, 2009 (rev. 1)

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Sequencing-Related NSF Grants Awarded April 29 — June 2, 2009

Dissertation Research: Evolution of moss organellar genomes and gene transfer from mosses to Amborella

Start Date: July 1, 2009
Expires: June 30, 2010
Awarded Amount to Date: $14,815
Principal Investigator: Jeffrey Palmer
Sponsor: Indiana University

This project will sequence the entire mitochondrial genome from each of ten diverse species of moss, and will assess genome size, gene order, and DNA mutation rate. All these properties vary among mitochondrial genomes of larger plants, but are largely unknown in the mosses. The project will also permit interpretation of a biological phenomenon in which the mitochondria of a small tree known as Amborella have acquired the entire mitochondrial DNA from two separate species of moss. The researchers plan to compare the sequences of the moss DNA in Amborella with the sequences being generated in this project.


Dissertation Research: Edaphic endemism in Eriogonum (Polygonaceae): A molecular phylogenetic approach

Start Date: June 1, 2009
Expires: May 31, 2011
Awarded Amount to Date: $10,429
Principal Investigator: Kenneth Sytsma
Sponsor: University of Wisconsin-Madison

The wild buckwheats (Eriogonum) are a group of plants that include many soil specialists. This project uses modern DNA sequencing and classic greenhouse experiments to determine if there is an evolutionary pattern relating to these soil specialists. It will also address whether these species are specifically adapted to their soils, or if they can survive on a variety of soils.


Dissertation Research: A Genomic Approach to Resolving the Origin of and Evolution of Turtles

Start Date: July 1, 2009
Expires: June 30, 2011
Awarded Amount to Date: $13,576
Principal Investigator: Jimmy McGuire
Sponsor: University of California-Berkeley

This project will develop a method to sequence 25 nuclear genes for fish, amphibians, reptiles, and mammals. These DNA data, along with the use of fossils, will help determine the position of turtles in the tree of life, resolve relationships within turtles, and provide insight into the tempo and mode of turtle evolution. According to the grantees, the DNA technique developed in this project will provide a simple, efficient method for small laboratories to begin collecting genomic-level data previously restricted to large, high-budget laboratories.


Integrated Biological Sequence Data Management

Start Date: Sept. 1, 2008
Expires: Sept. 30, 2009
Awarded Amount to Date: $406,613
Principal Investigator: Jignesh Patel
Sponsor: University of Wisconsin-Madison

The project aims to develop a comprehensive system called SEQ that can support complex declarative and efficient querying on biological sequences. The approach extends a relational database engine with methods for querying on sequences. SEQ will be implemented by extending the existing Postgres database engine. The collaboration between the investigators — computer scientists and biomedical researchers — will also facilitate deployment of the SEQ system in a project that will analyze various genomes for transcriptional regulatory elements related to genes essential for eye development and visual function. The SEQ project will lead to new computer science methods for sequence query processing, according to the grantees. It will also directly assist in the analysis of downstream targets for a transcription factor critical for rod photoreceptor development and function. The project will result in a free open-source OSI-certified release of the SEQ system using the ECL license.

The Scan

Not Yet a Permanent One

NPR says the lack of a permanent Food and Drug Administration commissioner has "flummoxed" public health officials.

Unfair Targeting

Technology Review writes that a new report says the US has been unfairly targeting Chinese and Chinese-American individuals in economic espionage cases.

Limited Rapid Testing

The New York Times wonders why rapid tests for COVID-19 are not widely available in the US.

Genome Research Papers on IPAFinder, Structural Variant Expression Effects, Single-Cell RNA-Seq Markers

In Genome Research this week: IPAFinder method to detect intronic polyadenylation, influence of structural variants on gene expression, and more.