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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 acidbased 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 bacteriaa
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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