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Berry & Associates, Applied Biosystems, University of Iowa, Iowa State University, 454 Life Sciences, Illumina, University of Florida, Geospiza, Invitrogen, National Institute for Agricultural Research, NIMH, HortResearch, Genesis Research and Development

Berry & Associates to Supply ABI with Oligo Probe Component for SOLiD
Berry & Associates said this week that it will supply Applied Biosystems with a reagent required to make oligonucleotide probes for the SOLiD system.
Under the five-year agreement, the company, which is based in Dexter, Mich., will provide ABI with a custom nucleoside phosphoramidite that meets purity standards required for the synthesis of the oligonucleotide probes.
Jack Hodges, vice president of chemistry at Berry & Associates, said in a statement that the relationship started with an exploratory synthesis project for Agencourt Personal Genomics, which was acquired by ABI two years ago.
Berry & Associates provides a variety of nucleosides, nucleotides, and DNA/RNA synthesis monomers, as well as fluorescent markers, biotins, carbohydrates, and heterocycles for biomedical research. Recently, it added fluorous affinity products for oligonucleotide purification and BlackBerry quenchers for use in fluorogenic oligonucleotide probes.

Iowa Universities to Pool 454, Illumina Sequencing Resources
The University of Iowa has purchased a Roche 454 sequencer, Iowa State University has bought an Illumina sequencer, and the two universities have agreed to pool the new resources for joint use by researchers at the schools.
The 454 sequencer, which cost around $500,000, will be part of UI’s DNA facility, directed by Kevin Knudtson. UI said that 60 percent of that money came through the Office of the Vice President for Research and the UI Carver College of Medicine, and the remaining 40 percent was raised from CCOM departments and faculty members planning to use the technology.
Iowa State will house the Illumina Genome Analyzer II, which cost around $535,000, in the DNA Facility of the Office of Biotechnology, which is managed by Gary Polking.
Funding to buy ISU's instrument came from a group of science departments at the university, including Iowa State Plant Sciences Institute, the DNA Facility, the Office of the Vice President for Research and Economic Development, the Center for Integrated Animal Genomics, the Department of Animal Science, the Department of Agronomy, the Agricultural Experiment Station, the College of Agriculture and Life Sciences, the College of Liberal Arts and Sciences, and the College of Engineering.
"It doesn't matter that each institution only has one machine on site because this will function as one single facility," Michael Apicella, senior associate dean for scientific affairs at UI’s CCOM, said in a statement. "Researchers from either institution now have access to two machines, which have different capabilities and will be useful for different projects. We really are sharing resources at every level."
The two schools have fiber optic cables running between them that can “transfer the huge amounts of data” the sequencing projects generate, Apicella continued.
The two machines will be available to researchers at both universities, to private companies, and to other institutions on a fee-for-service basis.
The two new sequencers will make both universities “competitive for major federal funding related to new genome sequencing initiatives, including the [National Institute of Health's] microbiome project,” Apicella explained.

Florida Genomics Lab Buys Geospiza's FinchLab
The University of Florida has purchased Geospiza’s lab-management software for its genomics sequencing lab, the company said last week.
Under the agreement, the Interdisciplinary Center for Biotechnology Research's Next Generation DNA Sequencing Laboratory will use Geospiza’s FinchLab platform to manage multiple genetic analysis technologies, including capillary electrophoresis and next-generation sequencing tools from Applied Biosystems and Roche.
Bill Farmerie, associate director at ICBR, said that the center started using Geospiza’s products for managing data from its capillary sequencers eight years ago, which “allowed our bioinformatics group to focus foremost on high-level data analysis for our user community rather than divert time and energy to solving routine data management tasks."
As a result, “Geospiza’s FinchLab was the clear choice against alternative solutions when we expanded our operations to include next-gen,” he said.

Invitrogen's Acquisition of Applied Biosystems Clears Antitrust Waiting Period
Invitrogen said this week that its proposed acquisition of Applied Biosystems has cleared the waiting period under the Hart-Scott-Rodino Antitrust Improvements Act of 1976.
Invitrogen said it will “soon” begin a similar process with European regulatory authorities.
The acquisition is expected to close in late October or early November, subject to approval of both companies' shareholders.
Invitrogen said that integration team members from both companies met last week “to discuss proposed milestones and activities for the integration and further review proposed synergies.”
Mark Smedley, Invitrogen's global head of operations and leader of the integration team, said in a statement that the companies have “a clear integration model in place, and we are well on track to start delivering on the potential of our new company as soon as the transaction closes."

Illumina Plans Two-for-One Stock Split
Illumina said last week that its board of directors has approved a two-for-one stock split that will be effected in the form of a stock dividend.
The stock split is subject to shareholders approving an increase in the number of authorized shares of Illumina’s common stock from 120 million to 500 million. A special meeting is scheduled to take place on Sept. 9, at which time shareholders of record as of July 28 will be entitled to vote on the proposed amendment.
“We believe that the stock split, if effected, may place the market price of our common stock in a range that is more attractive to investors, particularly individuals, which may result in a broader market for our stock,” the firm said in a statement.
Illumina’s shares closed at $84.10 in Tuesday trade on the Nasdaq.

International Team Sequences Genome of Parasitic Nematode
An international team of 27 laboratories has published the draft genome sequence of the root-knot nematode, Meloidogyne incognita, a parasite responsible for billions of dollars in crop damage each year.
The worm infests the roots of more than 3,000 crop types, including coffee, cotton, tomatoes, melons, and cucumbers, and is currently controlled with chemical pesticides that are harmful to humans and the environment. The research team said it expects the genome sequence of the root-knot nematode will help identify new targets that will lead to less toxic pesticides.
The researchers, led by France's National Institute for Agricultural Research, published the draft sequence of the 86-megabase genome online this week in Nature Biotechnology.
The researchers used ABI 3730xl sequencers to analyze the M. incognita genome and used the Arachne algorithm to assemble the reads into 2,817 supercontigs totaling 86 Mb, which was almost twice the estimated genome size, according to the authors.
The team identified 19,212 protein-coding genes. Upon further analysis, they found that M. incognita has 61 carbohydrate-active enzymes, or CAZymes, that degrade plant cell walls — an “unprecedented” set of such enzymes, according to the authors.
“The striking similarity of these enzymes to bacterial homologs suggests that these genes were acquired by multiple [horizontal gene transfer] events,” the authors wrote in the paper, adding that the candidate horizontal transfer events in the genome “involve genes with potential roles in interactions with hosts.”
The authors noted in the paper that they are currently conducting transcriptional profiling, proteomic analysis, and high-throughput RNA interference experiments in order to further understand the processes by which these nematodes cause plant disease.
They added that M. incognita can infect the model plant Arabidopsis thaliana, and that studying functional genomics for the two organisms “should provide new insights into the intimate molecular dialog governing plant-nematode interactions and allow the further development of target-specific strategies to limit crop damage.”

NIMH to Fund Genomic Studies of Mental Illness
The National Institute of Mental Health wants to fund large-scale genomic studies that se innovative analytical designs to study genetic risk factors for mental disorders.
Investigators may propose new technologies for cost-effective whole-genome analysis and in-depth sequencing and analysis of candidate genes and genomic regions in pedigrees or in a sample of unrelated cases with mental disorders. NIMH also encourages applications for large-scale haplotype analysis and those proposing to develop new analytical methods.
NIMH said in two related funding opportunity announcements, called “Deep Sequencing and Haplotype Profiling of Mental Disorders,” that because of the nature of the proposed research, the amount of funding and the number of the awards will vary, and will be dependent upon several factors, including quality, duration, and the costs of the proposed research. Investigators should not request funding for projects lasting more than five years.
The developmental programs the investigators seek “may be evolutionary or may be fundamentally new and may lead to paradigm shifts in the field,” NIMH stated in the request.
The research will use samples from the Center for Collaborative Genetics Studies (CCGC), which was started by NIMH as a mental health disorder genetics sample and data repository. The CCGC contains DNA, cell lines, phenotypic data, clinical information, and genotyping data.
Investigators also may propose studies that use existing sample collections either alone or in a combination with CCGC samples, but this program will not fund any new data collection efforts, NIMH said.
The applications should focus on one of seven mental disorders, including anorexia nervosa, attention deficit hyperactivity disorder, autism and related autism spectrum disorders, bipolar disorder, depression, obsessive compulsive disorder, and schizophrenia.
Applications may be submitted after Sept. 5.
More information about the NIMH requests is available here and here.

Released Kiwifruit Genome Data Promises New Fruit Varieties
Two New Zealand firms said this week that they have released genomic data for the kiwifruit that can be used by fruit breeders to produce “new varieties with increased health properties” and “exciting” colors and flavors.
The New Zealand companies HortResearch and Genesis Research and Development said that they plan to release more than 130,000 expressed sequence tags from four plant species that produce the kiwifruit berry.
This genetic information also can be used by HortResearch and by other breeders to help manipulate genes that govern various characteristics, including vitamin and nutrition content, shape, ripening, and storage life.
Much of the information that the companies discovered about the kiwifruit from the expressed sequence tags was published this week by BMC Genomics.
The average sequence length of the 132,000 ESTs the companies analyzed over the course of eight years is 503 base pairs.
HortResearch said in the paper that it plans to use genomics techniques in conjunction with marker-assisted selection (MAS) and genetic transformation tools to develop the kiwifruit.
"If breeding a new fruit with a specific trait is like finding a needle in a haystack, then MAS is like having a metal detector," HortResearch scientist William Laing said in a statement. “With MAS, we can quickly ‘scan’ the seedlings and find out right away which ones are likely to have the type of fruit we want."
Laing said that the kiwifruit genus Actinidia, which covers those involved in this research, “is incredibly diverse” and has many various colors, shapes, and flavors beyond the two most commonly known kiwifruit. Laing noted that his company has a collection of 23 species of kiwifruit, and “many more” are to be found in China, where kiwifruit originated.

GE Streamlines Structure; Healthcare No Longer Standalone Unit
General Electric announced last week that it is streamlining its unit structure from six units down to four. In the process, GE Healthcare will no longer operate as a standalone unit, but it will be folded into the new GE Technology Infrastructure unit.
The reorganization is intended to align the businesses “for growth and efficiency,” the firm said in a statement. GE’s stock price has sagged over the past few months after company officials said that the firm would miss its 2008 earnings per share target of $2.42.
The Healthcare business will join Aviation, Transportation, and Enterprise Solutions as components of the Technology Infrastructure unit, which will have revenues of nearly $90 billion. Vice Chairman John Rice will lead the unit.
In advance of the reorganization, former GE Healthcare CEO Joseph Hogan left the firm two weeks ago to take over as CEO of power and automation company ABB.
The other three units are GE Energy Infrastructure, GE Capital, and NBC Universal.

Affymetrix Acquires True Materials; Posts Small Dip in Q2 Revenues
Affymetrix has acquired True Materials, a microparticle technology firm based in the University of California, San Francisco, Mission Bay Campus, for approximately $25 million in cash.
An Affymetrix spokesperson told In Sequence’s sister publication GenomeWeb Daily News via e-mail this week that True Materials founder Randy True has joined Affy as a vice president of research and development.
True Materials is developing a digitally encoded microparticle technology that will enable the array manufacturer to enter low- to mid-multiplex markets and compete with bead-based platforms. Affy said that the technology is also applicable to research, applied, and diagnostic markets.
Affy disclosed the acquisition during its second-quarter conference call last week. Steve Fodor, chairman and CEO of the firm, said the technology "is more scalable and cost-effective than bead-based approaches." It uses digital microparticles to carry out assays in solution, he said, and is "capable of multiplexing tests ranging up to several thousand markers."
Last week, Affymetrix lowered its full-year revenue forecast for the second time this year as it reported a 1.5 percent dip in second-quarter revenues to $86.9 million from $88.3 million in the comparable period of 2007.
Second-quarter product revenue rose 9.6 percent to $75 million from $68.4 million in the year-ago period. For the current quarter, array and reagent sales generated revenue of $68.9 million and instrument sales contributed $6.1 million. Affy said it shipped 22 GeneChip systems in the quarter.
Service revenue fell 25 percent to $9 million from $12 million in the second quarter of 2007, while royalties and other revenue dropped 63 percent to $2.9 million from $7.9 million.
Affy reported a net loss of $3.6 million, or $0.05 per diluted share, in the second quarter of 2008, which includes a pretax restructuring charge of $900,000, or $0.01 per diluted share. In the year-ago period, the company posted net income of $1.2 million or $0.02 per diluted share, which included a pretax restructuring charge of $1.8 million, or $0.03 per diluted share.
R&D spending was nearly flat at $19.6 million compared to $19.4 million in the second quarter of 2007, while SG&A costs decreased by 12 percent to $29.6 million from $33.6 million in the prior-year period.
The company also lowered its full-year forecast due to “predicted ongoing weakness” in pharmaceutical revenue. As a result, Affy now expects 2008 revenue to be in the range of $455 million to $460 million, including a $90 million payment from Illumina related to litigation between the firms.
The company had already lowered its revenue forecast for fiscal 2008 revenues to between $490 million and $510 million from an initial forecast of between $505 million and $525 million.
As of June 30, Affy had $326 million in cash and cash equivalents.

Genomic Vision Nets $6.3M in Series B Backing
Genomic testing company Genomic Vision said last week that it has raised €4 million ($6.3 million) in a round of Series B financing from one new and one previous investor.
The new backer, Vesalius BioCapital, joined Society Generale Asset Management Alternative Investments in providing the funding.
Genomic Vision, based in Paris, uses a technology called molecular combing for direct visualization of single molecules to detect qualitative and quantitative changes in the genomic landscape. The company exclusively licensed the technology from the Pasteur Institute.
The company said it plans to use the funds to expand its in-house R&D programs and automation, and to strengthen its ongoing collaborative programs with partners.
“This support from our investors will help us to develop our products and services more quickly and enable us to take advantage of growing market opportunities," Genomic Vision President, CEO, and Founder Aaron Bensimon said in a statement.
"We believe very strongly that [Genomic Vision’s] genomic tests will be useful for cancers, genetic diseases, viral diseases, and many other applications with wide potential markets,” SGAM AI Bioconvergence Team Managing Partner Jean-Yves Nothias said in a statement.
The company said it is focused on three areas: biomarker-based diagnostics for identifying and managing disease; testing drug compounds by studying DNA replication in cancer cells; and developing drug response biomarkers.

The Scan

Germline-Targeting HIV Vaccine Shows Promise in Phase I Trial

A National Institutes of Health-led team reports in Science that a broadly neutralizing antibody HIV vaccine induced bnAb precursors in 97 percent of those given the vaccine.

Study Uncovers Genetic Mutation in Childhood Glaucoma

A study in the Journal of Clinical Investigation ties a heterozygous missense variant in thrombospondin 1 to childhood glaucoma.

Gene Co-Expression Database for Humans, Model Organisms Gets Update

GeneFriends has been updated to include gene and transcript co-expression networks based on RNA-seq data from 46,475 human and 34,322 mouse samples, a new paper in Nucleic Acids Research says.

New Study Investigates Genomics of Fanconi Anemia Repair Pathway in Cancer

A Rockefeller University team reports in Nature that FA repair deficiency leads to structural variants that can contribute to genomic instability.