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454, Roche, NHGRI, New England Biolabs, Integrated Genomics, JGI

454 Revenues Increase 43 Percent in Q1 as Unit Awaits Sale to Roche
454 Life Sciences’ first-quarter revenues increased 43 percent compared to the prior-year period, according to information CuraGen disclosed in a filing with the US Securities and Exchange Commission last week.
Curagen included 454’s first-quarter financial results under “discontinued operations” in a 10-Q filing last week. In late March, Curagen agreed to sell 454 to Roche for up to $154.9 million in cash. The sale is expected to close this quarter.
According to the SEC filing, 454 had $12.9 million in revenues in the first quarter, up from $8.8 million during the same period last year.
Of those revenues, $8.4 million derived from products, up from $4.5 million during the year-ago quarter. Sequencing service revenue remained almost flat, at $2.6 million, compared to $2.4 million last year. 454 also recorded $375,000 in collaboration revenue, the same amount as a year ago, and $1.5 million in milestone revenues, up from $950,000 during last year’s first quarter.
Research and development costs increased to $4.4 million during the quarter, up from $3.3 million during the year-ago period.
454’s loss for the quarter increased to $1.1 million, from $55,000 during the year-ago quarter. This increase was due to rising R&D expenses as well as higher general and administrative expenses, primarily from consulting and legal fees in connection with the sale to Roche.
The increase was partially offset by a higher profit margin 454 earned on product, grant, and milestone revenue, according to the filing.
As of March 31, 454 had $5.9 million in cash and cash equivalents, $1.1 million in short-term investments, and $28,000 in marketable securities.
CuraGen said it expects to shoulder most of 454’s net loss during the second quarter, prior to the completion of the sale of the business to Roche, but does not anticipate the amount to be material.

NHGRI Awards $57M in modENCODE Grants for Drosophila, C. elegans Studies
The National Human Genome Research Institute this week awarded $57 million in grants to 10 projects under its modENCODE Project, which aims to study the functional elements in the genomes of the model organisms Drosophila melanogaster and Caenorhabditis elegans. The funding will be spread over four years.
The effort will build upon the ENCyclopedia Of DNA Elements (ENCODE) project, which NHGRI launched in 2003 with the goal of building a catalog of all elements in the human genome crucial to biological function.
“This parallel effort in the fruit fly and worm genomes will provide us with information about the functional landscape of two key model organisms, which should aid our efforts to tackle such questions in humans,” NHGRI director Francis Collins said in a statement.
The following is a list of modENCODE grant recipients the NIH named this week:
Susan Celniker, Lawrence Berkeley National Laboratory
First year, $3.6 million; total funds, $14.5 million
“Comprehensive Characterization of the Drosophila Transcriptome”
Steven Henikoff, Fred Hutchinson Cancer Research Center
First-year funds, $429,000; total funds, $7.4 million
“Genome-Wide Profiling of Histone Variants in Drosophila and Caenorhabditis
Gary Karpen, Lawrence Berkeley National Laboratory
First -year funds, $1.8 million; total funds, $7.2 million
 “Genome-Wide Mapping of Chromosomal Proteins in Drosophila
Eric Lai, Memorial Sloan-Kettering Cancer Center
First-year funds, $470,000; total funds, $1.9 million
 “Annotation of the Small RNA/microRNA Component in the Drosophila Genome“
Jason Lieb, The University of North Carolina at Chapel Hill
First-year funds, $1.8 million; total funds, $9.1 million
“Identification of DNA Elements Governing Chromatin Function in C. elegans
David MacAlpine, Duke University
First-year funds, $469,000; total funds, $1.9 million
“The Systematic Identification and Analysis of Replication Origins in Drosophila
Fabio Piano, New York University.
First-year funds, $397,000; total funds, $1.6 million
“Encyclopedia of C. elegans 3’UTRs and Their Regulatory Elements”
Michael Snyder, Yale University
First-year funds, $1.7 million; total funds, $6.6 million
 “Global Identification of Transcription Factor Binding Sites in C. elegans
Robert Waterston, University of Washington
 First-year funds, $1.4 million; total funds, $5.4 million
“Global Identification of Transcribed Elements in the C. elegans Genome”
Kevin White, University of Chicago
First-year funds, $2.3 million; total funds, $9.1 million
“A Cis Regulatory Map of the Drosophila Genome”

New England Biolabs To Use Integrated Genomics’ ERGO
New England Biolabs has licensed Integrated Genomics’ ERGO bioinformatics software platform, Integrated Genomics said this week.
NEB will use the software for gene annotation, metabolic reconstruction, enzyme data-mining, and comparative genomics.
ERGO integrates data from genomics, biochemistry, gene expression studies, genetics, and the literature. It includes more than 1,180 genomes at “various stages of completion,” the company said.

JGI Hits 100-Genome Milestone
The Department of Energy’s Joint Genome Institute said last week that it has finished sequencing its 100th genome sequence – that of Shewanella baltica OS185, a microbe that lives in the Baltic Sea and shows promise for cleaning up radioactive contamination.
Chris Detter, leader of the JGI Sequencing Technology Team, said that S. baltica might be useful for cleaning up uranium-contaminated areas, such as the laboratory's legacy waste sites.
S. baltica is able to convert uranium dissolved in groundwater into uranium dioxide, which is insoluble and therefore does not migrate into groundwater.

The Scan

New Study Highlights Role of Genetics in ADHD

Researchers report in Nature Genetics on differences in genetic architecture between ADHD affecting children versus ADHD that persists into adulthood or is diagnosed in adults.

Study Highlights Pitfall of Large Gene Panels in Clinical Genomic Analysis

An analysis in Genetics in Medicine finds that as gene panels get larger, there is an increased chance of uncovering benign candidate variants.

Single-Cell Atlas of Drosophila Embryogenesis

A new paper in Science presents a single-cell atlas of fruit fly embryonic development over time.

Phage Cocktail Holds Promise for IBD

Researchers uncovered a combination phage therapy that targets Klebsiella pneumonia strains among individuals experiencing inflammatory bowel disease flare ups, as they report in Cell.