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Announcements

September 2003

• On September 10, Secretary of Energy Spencer Abraham presented Ari Patrinos and Francis Collins with the Secretary's Gold Award for their leadership of the public Human Genome Project. The Gold Award is DOE's highest honorary award. For more information see the press release.

May 2003

• DOE is seeking nominations of microbes, microbial consortia, and small organisms to be sequenced by the Joint Genome Institute. More. . .
  
  
• JGI and Diversa Announce Collaboration on Microbes
  The U.S. Department of Energy’s Joint Genome Institute and Diversa Corporation are collaborating to discover and sequence novel microbial genomes found in a diverse range of unique habitats. Read more.

April 2003

• First phase of Environmental Genome Project Completed
  The National Institute of Environmental Health Sciences (NIEHS) has announced the completion of the first phase of the Environmental Genome Project, which seeks to characterize genes that confer susceptibility to such leading causes of death and illness as cancer, heart disease, diabetes, and asthma. NIEHS researchers have resequenced and cataloged 200 environmentally responsive genes, identifying links to vascular disease, leukemia, and other conditions that affect the quality and length of life of many Americans.
  
  
• DOE Will Increase Funding to IBEA
  Secretary of Energy Spencer Abraham said that the department will increase its funding to the Institute for Biological Energy Alternatives (IBEA). The money will be used for research to better understand microbial communities and to develop new biological methods for capturing carbon dioxide from the atmosphere and producing hydrogen. Read more.

• Celebration of the Genome

  Fifty years ago this month, researchers Francis Crick and James Watson published their historic paper describing the double-helix structure of DNA. For their achievement, Drs. Watson and Crick were awarded the Nobel Prize in 1962.

  Seventeen years ago this spring, at the recommendation of one of its scientists, the Department of Energy launched the effort to determine the DNA sequence of the human genome. This month, representatives of DOE and the National Institutes of Health will announce the completion of the sequencing of the human genome.

  The 50th anniversary of the Watson-Crick discovery of DNA and the successful completion of the Human Genome Project are being celebrated around the world throughout April 2003 - and in particular, at joint NIH-DOE symposia in Washington, D.C., on April 14-15. There, still another DOE contribution to the advancement of science also will be discussed: the Office of Science's Genomes to Life program. As part of DOE's Celebration of the Genome, Secretary of Energy Spencer Abraham will make a statement.

• "Realizing the Potential of the Genome Revolution: The Genomes to Life Program,"Marvin E. Frazier, Gary M. Johnson, David G. Thomassen, Carl E. Oliver, Aristides Patrinos
  Science 300, 290 (2003)
• 2003: 50 Years of the Double Helix: Celebrating 50 years of the discovery of the double helix DNA structure and the anticipated completion of the Human Genome Project
• Research abstracts from the New Horizons in Genomics meeting held March 30-April 1, 2003, Santa Fe, New Mexico. Prepared for the U.S. Department of Energy Joint Genome Institute.

March 2003

Call for Papers
The IEEE is calling for submission of papers for the 2003 IEEE Computer Society Bioinformatics Conference to be held August 11–13 at Stanford, California. The meeting will cover such topics as machine learning, data mining, robotics, regulatory networks, pattern recognition, Genomes to Life, genomics and proteomics, and gene-expression pathways. Submission date for papers is April 1, 2003. Queries and submissions may be sent to bioinformatics@computer.org. [Information]

Funding Opportunities at NHGRI

• Determination of All Functional Elements in Human DNA: Solicit participants for a Research Network that will conduct a pilot project to test and compare methods for identifying all the functional elements in a limited (~1%) region of the human genome.
• Identification and Verification of Functional Elements: Develop new and improved technologies for the efficient, comprehensive, high-throughput identification and verification of all types of sequence-based functional elements, particularly those other than coding sequences, for which adequate methods do not currently exist. This effort is part of a new public research consortium, the Encylopedia of DNA Elements (ENCODE), the intent of which is eventually to identify all functional elements in the human genome sequence.

Due Dates: Letters of Intent, April 13, 2003; Applications, May 13, 2003

February 2003

BSCS Develops Fifth Module
The Biological Sciences Curriculum Study, with the support of the Department of Energy, has developed a new curriculum for high school biology that explores how scientists extract useful information from the Human Genome Project (HGP). “Bioinformatics and the Human Genome Project,” BSCS's fifth module related to HGP, includes background information for teachers and five classroom lessons. Lessons use both print and Web-based activities to help students learn how computers are used to assemble DNA sequences, locate genes, and obtain clues about gene functions. In this context, the ethical, social, and legal implications of genetic databases and informed consent are considered.

Interested teachers can visit the BSCS Web site to reserve a free copy. The modules are expected to be shipped to requestors the last week of March. After that, the curriculum will be available in PDF on the BSCS Web site or can be obtained from BSCS for $5.00.

January 2003

Eddy Rubin Named JGI Director
Internationally known geneticist and medical researcher Dr. Edward M. (Eddy) Rubin has been named Director of the U.S. Department of Energy's Joint Genome Institute (JGI). Rubin was also named Director of the Genomics Division at Lawrence Berkeley National Laboratory (LBNL). Read more.

Fourth Human Chromosome Finished: Genes Implicated in Immune Response, Ovarian Cancer, Alzheimer’s
Chromosome 14 has been completely sequenced by a team of French and American scientists with the elimination of gaps and inconsistencies present in the draft sequence of the human genome published in February 2001. With more than 87 million nucleotides, this is the fourth and largest human chromosome finished to the high quality specified by the Human Genome Project. Others completed thus far are 22, 21, and 20, which were published in December 1999, May 2000, and December 2001, respectively.

In addition to the 506 genes already known to exist on chromosome 14, the research team at Genoscope, France’s National Sequencing Center, was able to identify 344 more genes. Two genes linked to chromosome 14 play important roles in the immune response. About 60 genes on this chromosome have been associated with a variety of genetic disorders such as early-onset Alzheimer’s, leukemia, Graves disease, spastic paraplegia, and ovarian cancer. A paper reporting the work was published electronically January 1, 2003, by Nature.

December 2002

International Consortium Publishes Draft Sequence of the Mouse Genome
The draft sequence of the mouse genome, completed by the Mouse Genome Sequencing Consortium, was published in the December 5, 2002, issue of Nature and is freely available from public databases. Analysis of similarities and differences between mouse and human genomes is key to understanding how the human genome works. The mouse genome, with 2.5 billion As, Cs, Gs, and Ts, is 14% smaller than the human genome with 2.9 billion. Yet, both genomes contain about 30,000 protein-encoding genes, and about 80% of mouse genes have a single identifiable counterpart in the human genome. In addition to generating a better understanding of gene function, comparative analysis of the noncoding regions of DNA in the mouse and human genomes will help elucidate the role of this so-called junk DNA. In two more years, a finalized, higher-quality version of the mouse genome is expected to be completed.

Our Genes/Our Choices, a DOE HGP-Sponsored PBS Three-Part Series
Coming in January 2003

Our Genes/Our Choices, a three-part television series from the Fred Friendly Seminars (Columbia University School of Journalism), will air on PBS starting December 22nd in New York and nationwide in January. Partly supported by the DOE Office of Science, the series examines the impact of genetics advances on the right to privacy, reproductive choices, and personal responsibility. Local listings, a viewer's guide, and other resources are online at www.pbs.org/fredfriendly/ourgenes.

November 2002

Genomes to Life Program Applications
The DOE Office of Science, Office of Biological and Environmental Research, and Office of Advanced Scientific Computing Research have issued a call for research applications to support the Genomes to Life program (genomicsgtl.energy.gov). The full text of Program Notice 03-05 is at www.er.doe.gov/production/grants/Fr03-05.html. Statements of intent to apply are due January 7, 2003, and formal applications on April 22, 2003.

Human Genome Program ELSI Applications
The Office of Science, Office of Biological and Environmental Research, has announced its interest in receiving proposals in support of the Ethical, Legal, and Social Implications subprogram of the Human Genome Program. Applications, which are due February 13, 2003, should focus on (1) genetics and the workplace and (2) complex or multigenic traits. Preapplications, due November 25, 2002, are strongly encouraged. Complete solicitation text is at www.sc.doe.gov/production/grants/Fr03-06.html.

Student Opportunities to Attend Nobel Laureate Meeting
Each year since 1951, Nobel Prizewinners in Chemistry, Physics, and Physiology or Medicine have met in Lindau, Germany, to discuss major issues of importance to their fields with students from around the world. The DOE Office of Science is sending a group of 25 second-year graduate students to attend the 53rd meeting from June 30 to July 4, 2003. Selected students will attend lectures and small-group meetings with the Nobel laureates. Transportation, lodging, and registration expenses will be arranged and paid for by the Office of Science.

Focus of the 2003 meeting will be on the life sciences, but discussions are sufficiently general that students in related disciplines (e.g., biochemistry, biophysics, computational sciences, biomedical engineering, applications of radiation to imaging, and medical therapy) can benefit from participating. Each institution with Office of Science funding may nominate one student, with nominations due January 23, 2003. Full information and forms are at www.orau.gov/orise/edu/lindau2003/.

October 2002

New NIH Advisory Committee
The National Institutes of Health has established the Secretary's Advisory Committee on Genetics, Health, and Society (SACGHS), which replaces the Secretary's Advisory Committee on Genetic Testing. SACGHS will explore, analyze, deliberate, and make recommendations to the Secretary of Health and Human Services on the broad range of human health and societal issues raised by the development and use or potential misuse of genetic technologies.

JGI and VBI Collaborate on Phytophthora Genome
DOE's Joint Genome Institute is collaborating with the Virginia Bioinformatics Institute to decode and study the genomes of two species of Phytophthora, a fungus-like microbe responsible for a wide variety of destructive plant diseases, including the Irish potato famine in the 1840s. Phytophthora ramorum, the recently identified microbe responsible for Sudden Oak Death Syndrome, and P. sojae, which causes Soybean Root Rot, resemble fungi but are actually Stramenopiles, or "water molds."

Scientists hope to uncover clues leading to the control of virulent diseases that are attacking 17 species of trees on the West Coast, including redwoods, big leaf maples, bay trees, and Douglas firs, and causing serious damage to soybean crops in the Midwest and South. The work is supported by DOE, U. S. Department of Agriculture, and National Science Foundation.

Anopheles gambiae and Plasmodium falciparum Sequenced
A hundred years after the discovery that mosquitoes transmit the malaria parasite, an international consortium of laboratories and funding agencies has announced the sequencing of Anopheles gambiae, the most common mosquito in Africa, and Plasmodium falciparum, the deadliest malaria parasite. A million people, most of them children, are killed by malaria each year, and 90% of all cases occur in sub-Saharan Africa. In addition to causing so many deaths, malaria is considered a huge barrier to economic progress.

Scientists expect that the results of this 6-year project will help to bring malaria under control. Because malarial parasites and mosquitoes have developed resistance to drugs and insecticides, one approach would be to design "malaria-proof" mosquitoes that are unable to carry the parasites. Genetic data for the two organisms were published simultaneously in the journals Nature and Science.

Articles are available from the BBC News , CSMonitor.com, and the Globe and Mail web sites.

August 2002

Sloan Research Fellowships Add Computational and Evolutionary Molecular Biology
(Nominations due Sept. 15, 2002)
Since 1955, Sloan Research Fellowships have provided support and recognition to young scientists, often in their first appointments to university faculties, who were setting up laboratories and establishing independent research projects with little or no outside support. Fellowships have been awarded in physics, chemistry, mathematics, neuroscience, economics, and computer science. Beginning with the 2002 program, awards have been added in computational and evolutionary molecular biology.

Selection procedures are designed to identify the most promising researchers, who, once chosen, are free to pursue lines of inquiry most interesting to them. Their Sloan funds can be applied to a wide variety of uses for which other, more restricted funds such as research project grants cannot usually be employed. This flexibility often gives the fellowships a value well beyond their dollar amounts. Nomination forms are due by September 15 for awards to begin the following September.

For eligibility requirements and nomination forms, see the Sloan Web site or contact Gwen Knowles (Tel: 212/649-1644).

"An Introduction to Issues Underlying Patent Policy for the Emerging Genetic Information and Medical Treatment Industry," a new paper by David J. Bjornstad (Oak Ridge National Laboratory) and Christine Dümmer (Hull, Dümmer, and Garland) is on the Web ( www.jiee.org/pdf/2002_05_patent.pdf ). The paper traces the development of patenting as applied to genomic intellectual property and related public-policy issues since 1998, presents one interpretation of the current state of affairs, and suggests topics worthy of further study.

July 2002

Presidential Early Career Award in Science and Engineering (PECASE) Presented for BER-Funded Research
Jizhong Zhou of the Environmental Sciences Division at Oak Ridge National Laboratory has won the prestigious PECASE award for his leadership in the fields of functional genomics and microbial ecology. In separate ceremonies on June 11 and 12, Zhou received congratulations and citations from Department of Energy Secretary Abraham and President Bush. Zhou, who has made significant contributions to a wide range of Biological and Environmental Research programs, was cited specifically for his "pioneering application of genomic and molecular technologies to environmental studies." Zhou and his research group have developed nucleic acid–based microarrays that can be used to analyze microbial community structure and function at levels of detail never before achieved. In addition to advancing the overall field of biology, their research findings will be critical to a wide range of DOE missions, including bioremediation, carbon sequestration, and biofuel production.

Human cDNA Annotation Jamboree
DOE is contributing to the support of an August 2002 invitational jamboree on cDNA annotation, to be hosted by the newly established Japan Biological Information Research Center. Although interpretation has been ongoing by teams working on particular genes, this will be the first public jamboree for human-genome-scale cDNA annotation. See www.ornl.gov/meetings/wccs/index.html for a concise history of cDNA sequencing and prior workshops.

Energy Department Awards $103 Million for Post-Genomic Research
Secretary of Energy Spencer Abraham today announced five major research awards for post-genomic research. The awards total $103 million over the next five years. Research will be conducted at six national laboratories, 16 universities and research hospitals and four private research institutes. The awards are part of the department's new "Genomes to Life" program.

May 2002

JGI to Sequence Infectious Bacteria
The Department of Energy's Joint Genome Institute in Walnut Creek, California, has been enlisted to determine the whole genome sequences of a variety of infectious bacteria—a first step toward developing tests for rapidly identifying their presence in the environment. The first pathogens to be sequenced under this program at JGI's Production Genomics Facility (PGF) are members of the Bacillus, Brucella, Clostridium, Francisella, Shigella, and Yersinia groups. Several strains or related species will be sequenced in many groups, for example, two strains of Bacillus anthracis (anthrax) and one of the similar species Bacillus thuringiensis.

Sequencing at JGI will not involve actual pathogens but will be done after the DNA of each pathogen is reduced to disassembled fragments at DOE national laboratories equipped with appropriate containment facilities. The completed sequence exists only as a string of letters in a computer's output. Draft sequences will be shared with Los Alamos and Lawrence Livermore national laboratories for finishing and annotation.

One of the largest publicly funded genome-sequencing institutions in the world, JGI has concentrated on organisms of crucial interest to international researchers. For the Human Genome Project, JGI sequenced human chromosomes 5, 16, and 19, which together constitute some 11% of the human genome. JGI sequenced mouse DNA related to human chromosome 19 to illuminate the molecular evolutionary history of the two species and has participated in sequencing more than 50 important microorganisms.

JGI funding is provided predominantly by DOE's Office of Science.

CASP5 Begins
The fifth community-wide experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP) will run from May through August of this year. The goal of CASP is to obtain an in-depth and objective assessment of current abilities and inabilities in the prediction of protein structures. In the competition, each participating team can select targets to predict from a few dozen protein sequences whose structures have been solved experimentally but not published. A group of invited assessors will evaluate how well each predicted structure matches the experimental one. The performance of each team will be ranked at the end of the prediction season, and the results will be announced at a meeting in Asilomar Center, California, at the beginning of December. More than 160 international teams participated in CASP4, which took place in 2000. More information is available on the Web site http://PredictionCenter.llnl.gov/casp5/.

Brookhaven National Laboratory Researcher Wins Award
Richard Setlow (Brookhaven National Laboratory) received the 2002 Environmental Mutagen Society award for his contributions to the scientific understanding of how environmental factors lead to DNA damage and how it is repaired. Setlow, a biophysicist, was honored specifically for his discovery of a DNA repair mechanism and the development of a method to measure this event. He was also cited for his discovery of a crucial link between unrepaired DNA damage and cancer. Among his many honors, Setlow also won the 1988 Enrico Fermi Award, the most prestigious scientific award given by DOE, for contributions to the fields of radiation physics and molecular biology. For more details, see the news release.

April 2002

ELSI-Funded "DNA Files" Radio Shows Win Peabody Award
The DNA Files, a series of PBS radio broadcasts about the science and ethical challenges of the Human Genome Project, was chosen for a coveted Peabody award by the Grady College of Journalism and Mass Communications of the University of Georgia. Produced by SoundVision Productions and narrated by John Hockenberry, The DNA Files was heard on National Public Radio stations in 1998, then augmented with five new programs and presented again in November 2001. The Peabody Award citation stated that the programs are "a vivid, accessible radio series explaining the intricate building blocks of genetic science." Initial funding for this series was provided by the Ethical, Legal, and Social Implications program of the DOE Human Genome Program in the Office of Biological and Environmental Research. Previously, The DNA Files won a Dupont-Columbia University Award for Excellence in Broadcast Journalism. Segments of The DNA Files can be heard on our Web site.

March 2002

Latest issue of Human Genome News Available
The February 2002 Human Genome News, Vol. 12(1-2) is on the HGN Web site.

Mouse Genome Monthly, which will be produced for the next several months by the Mouse Genome Sequencing Consortium, is designed to keep the community of mouse researchers abreast of sequencing progress. The newsletter and related information are on the Web at www.nih.gov/science/models/mouse/genomics/index.html. Click on Mouse Sequencing Liaison Group.

January 2002

Research abstracts from the DOE Genome Program Contractor-Grantee Workshop, held January 27-31, 2002, in Oakland, CA, are available now at www.ornl.gov/sci/techresources/Human_Genome/publicat/02santa/index.shtml.

Office of Science Issues ELSI Call
Program Notice 02-14
The DOE Office of Biological and Environmental Research is receiving applications in support of the Ethical, Legal, and Social Implications (ELSI) component of the Human Genome Program. Applications should focus on issues of genetics and the workplace, storage of genetic information and tissue samples, education, or complex or multigenic traits.

Preapplications referencing Program Notice 02-14 are due January 24, and formal applications are due March 28. More information is on the Web (www.er.doe.gov/production/grants/Fr02-14.html). [Contact: Joanne.Corcoran@science.doe.gov]

Online Sources of Life Science Information
The Human Genome Project Information Web site has added a list of URLs for free online publications containing feature stories on the life sciences (www.ornl.gov/sci/techresources/Human_Genome/resource/urls.shtml). The list emphasizes periodicals from the U.S. Department of Energy, including the Office of Science and national laboratories. Some well-known commercial and nonprofit science organizations also are listed, and most sites comprise current and archived issues.

DOE Seeking Microbial Candidates for Sequencing
DOE is seeking nominations for candidate microbes and microbial communities to sequence in support of the Microbial Genome and Genomes to Life Programs. Candidate microbes should be relevant to DOE missions, such as those involved in environmental processes including waste remediation, carbon management, energy production, and biodefense. Sequencing of the selected microbes will be carried out at the DOE Production Genomics Facility of the Joint Genome Institute (www.jgi.doe.gov). Nominations are due March 28, and review will be completed early in the summer. Draft sequencing will begin later in the year after high-quality DNA has been provided.

NHGRI Initiates New System for Choosing Sequencing Targets
The NIH National Human Genome Research Institute (NHGRI) has developed a new competitive process for selecting genomes to be sequenced with NHGRI support. Based on the submission and review of white papers, the new procedure will apply to all organisms except eubacteria, archaea, and plants, which are more appropriate to the missions of other NIH components or other agencies. Proposals for EST or full-length cDNA sequencing or the development of genomic resources will not be considered through this system. Individual investigators or representatives of scientific communities are encouraged to submit white papers, which will be accepted three times a year on February 10, June 10, and October 10.

Third Human Chromosome Finished
Chromosome 20 Genes Implicated in Diabetes, Obesity
Chromosome 20 is the first to be completed since publication of the working draft in February 2001. Sequenced by the Wellcome Trust Sanger Center (U.K.), this is the third and largest human chromosome finished to the high quality specified by the Human Genome Project. Others completed thus far are 22 and 21, which were published in December 1999 and May 2000, respectively. Some genes linked to chromosome 20 are implicated in Creutzfeldt-Jakob disease, severe combined immunodeficiency, Type 2 diabetes, obesity, cataract, and eczema. A paper reporting the work appeared in the December 20, 2001, issue of Nature.

GTL Program Announcement to National Laboratories
www.sc.doe.gov/production/grants/LAB02_13.html
The offices of Biological and Environmental Research and Advanced Scientific Computing Research of DOE's Office of Science have issued a request for proposals (LAB 02-13) from national laboratories to support the Genomes to Life program (genomicsgtl.energy.gov/). Two or three large, multidisciplinary research teams will be established, preferably including partners from more than one national laboratory, universities, private research institutions, and companies. A similar solicitation for university-initiated Genomes to Life research will be posted in mid-January at the same Web site.
Letter of Intent due: January 31, 2002; Formal Proposal due: April 2, 2002; Contact: Joanne Corcoran (301/903-6488, joanne.corcoran@science.doe.gov)

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