[Federal Register: May 21, 2003 (Volume 68, Number 98)]
[Notices]
[Page 27791-27793]
From the Federal Register Online via GPO Access [wais.access.gpo.gov]
[DOCID:fr21my03-29]
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DEPARTMENT OF ENERGY
Office of Science; Office of Biological and Environmental
Research; Recommendations for Sequencing Targets in Support of the
Science Missions of the Office of Biological and Environmental Research
(BER)
AGENCY: Department of Energy (DOE).
ACTION: Notice of recommendations for sequencing targets.
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SUMMARY: This Federal Register notice seeks the input and nominations
of interested parties for candidate microbes, microbial consortia, and
100Mb-or-less-sized organisms for draft genomic sequencing in support
of Office of Biological and Environmental Research (BER) programs,
among them, the Climate Change Research Program, the Natural and
Accelerated Bioremediation Research (NABIR) Program, the Environmental
Management Science Program (EMSP), the Microbial Genome Program (MGP),
and the GTL Program. Nominated candidates should be relevant to DOE
mission needs, e.g., organisms involved in environmental processes,
including waste remediation, carbon management, and energy production.
This announcement is not an offer of direct financial support for
research on these organisms. Those nominations selected will result in
the DNA sequence of selected organisms being determined at a draft
level (6-8 x coverage) at the DOE Production Genomics Facility (PGF) at
the Joint Genome Institute (JGI), (http://www.jgi.doe.gov). This
announcement is designed to assist DOE in determining and prioritizing
a list of microbes, microbial consortia, or modest-genome sized (not
more than 100Mb) organisms (including eukaryotes) that address DOE
mission needs. Following merit review, and subject to the availability
of funding and programmatic relevance, draft sequencing will be carried
out at the PGF.
DATES: To assure consideration, nominations in response to this notice
should be received by 4:30 p.m. (EST), June 26, 2003, to be accepted
for merit review. It is anticipated that review will be completed early
in the fall of 2003 with draft sequencing at the DOE PGF to commence
towards the end of 2003 or early in 2004, conditional upon the
provision of high quality DNA.
ADDRESSES: Nominations responding to this notice should be sent to Dr.
Daniel W. Drell, Office of Biological and Environmental Research, SC-
72, Office of Science, U.S. Department of Energy, 1000 Independence
Ave., SW., Washington, DC 20585-1290; email is acceptable and
encouraged for submitting nominations using the following addresses:
joanne.corcoran@science.doe.gov and daniel.drell@science.doe.gov.
FOR FURTHER INFORMATION CONTACT: Dr. Daniel W. Drell, SC-72, Office of
Biological and Environmental Research, Office of Science, U.S.
Department of Energy, 1000 Independence Ave. SW., Washington, DC 20585-
1290, phone: (301) 903-4742, email: daniel.drell@science.doe.gov. The
full text of this notice is available via the Internet using the
following Web site address: http://www.sc.doe.gov/ober/microbial.html.
SUPPLEMENTARY INFORMATION: The DOE Office of Biological and
Environmental Research supports fundamental research in a variety of
missions (http://www.sc.doe.gov/ober/ober_top.html). Relevant BER
programs may include the Climate Change Research Program, the Natural
and Accelerated Bioremediation Research (NABIR) Program, the
Environmental Management Science Program (EMSP), the Microbial Genome
Program (MGP) and the GTL program. The Climate Change Research Program
supports investigations of microbially-mediated fixation of atmospheric
CO2. The NABIR program supports research on microbial
biotransformations and/or immobilization of metal and radionuclide
wastes. The EMSP supports research into microbially-mediated
biotransformations of DOE-relevant organic wastes such as chlorinated
solvents. The MGP supports key DOE missions by providing and analyzing
microbial DNA sequence information to further the understanding and
application of microbiology relating to energy production, chemical and
materials production, environmental carbon management, and
environmental cleanup. The GTL Program builds on the successes of the
DOE Human Genome Program (HGP) by seeking to understand biological
function in DOE mission relevant microbes with emphases on identifying
the multi-component protein complexes in cells, characterizing gene
regulatory networks, probing the functional capabilities of the
environmental microbial repertoire of genes, and beginning to model
these processes computationally.
Over the last nine years, sequencing of a range of microorganisms
that live in a wide diversity of environments has provided a
considerable information base for scientific research related not only
to DOE missions, but also to other federal agency missions and U.S.
[[Page 27792]]
industry. (http://www.tigr.org/tdb/mdb/mdbcomplete.html, http://www.ornl.gov/microbialgenomes/organisms.html
http://www.jgi.doe.gov/JGI--microbial/html/). Nonetheless, most of our current
knowledge of microbiology still is derived from individual species that
either cause disease or grow easily and readily as monocultures under
laboratory conditions and are thus easy to study. The preponderance of
species in the environment remains largely unknown to science. Many are
thought to grow as part of interdependent consortia in which one
species supplies a nutrient necessary for the growth of another.
Virtually nothing is known of the organization, membership, or
functioning of these consortia, especially those involved in
environmental processes of DOE interest. Fungi and small multicellular
eukaryotes play important roles in the environment as well.
Genomic analyses of sequenced microbes have suggested that
processes such as lateral gene transfers at various times in the
evolutionary history of some microbial lineages may have blurred the
understanding of their phylogenetic relationships. For this notice,
groups of microbes that may have exchanged (or may be exchanging)
genetic information via lateral gene exchange or plasmid mediated
exchanges can be proposed if the processes of genetic exchange result
in functions relevant to DOE missions noted above.
Genomic analyses are badly needed of microbial consortia and
species refractory to laboratory culture that play important roles in
environments challenged with metals, radionuclides, chlorinated
solvents, or are involved in carbon sequestration. The candidate(s)
must mediate or catalyze metabolic events of energy or environmental
importance. Priority will be given to studies on those microbes or
microbial consortia that can bioremediate metals and radionuclides,
degrade significant biopolymers such as celluloses and lignins, produce
potentially useful energy-related materials (H2,
CH4, ethanol, etc.), or fix or sequester CO2.
For this notice, candidate organisms (either individual organisms,
consortia of organisms, or eukaryotes with small genomes) comprised of
archaea, bacteria, fungi, algae, and other eukaryotes with genome sizes
not greater than 100Mbp can be proposed for draft sequencing. For a
current list of microbes that have been and are being sequenced see
http://www.ornl.gov/microbialgenomes/organisms.html and http://www.ornl.gov/microbialgenomes/seq2003.html
Aims: This request for nominations of candidate sequencing targets
has two broad foci:
(1) Single culturable organisms. These may be bacteria, archaea,
fungi, microalgae or multicellular organisms with genomes not larger
than 100Mb. The criteria that will be used to evaluate proposed
candidates for draft sequencing will include:
(a) The candidate has significant relevance to the DOE missions
noted above;
(b) The genome size and structure are known;
(c) The source of genomic DNA (i.e., strain or isolate, and
researcher) is identified, and a clonal sample (or samples with low and
characterized polymorphism) are available;
(d) A brief description of post sequencing follow-up work (e.g., a
data use plan and how will data be annotated to enable rapid and open
use) is included;
(e) The availability of a DNA/gene transfer system supporting
genetic analyses is known;
(f) Biological novelty or uniqueness (i.e., unusual genetically
determined characteristics pertinent to DOE missions) is described;
(g) Place in the currently understood, 16s RNA based, ``Tree of
Life'' is identified, e.g., is the proposed candidate in a sparsely
populated or more heavily populated section of the tree?
(h) A brief description of the user community is given;
(i) The potential impact on the scientific community is large;
(j) Explicit commitment to a data-release schedule, consistent with
the guidelines given below is provided.
(2) Currently unculturable or hard-to-culture organisms and
environmental consortia. The review criteria that will be used to
evaluate proposed candidates for draft sequencing will include most of
the criteria listed above for single culturable organisms (with less
emphasis on genome size/structure, presence/absence of a genetic
system, or position in the ``Tree of Life'' since it is recognized that
few data on these attributes will be available), but in addition, the
following considerations will be included:
(a) Some measure of the ``complexity'' of the target consortium
being proposed, e.g., approximate number of species, size(s) of
genomes, and proportions of different members (it is understood that in
most cases, only estimates of these parameters may be available) is
discussed. When the environmental consortia are complex, approaches
should be described to normalize the DNA libraries in order to reduce
the amount of sequencing required and assure adequate sampling of the
complexity of the consortia. Additionally, the proposer(s) should be
prepared to work together with JGI scientists to optimize the yield
from the sequencing effort required;
(b) Past attempts to cultivate consortium members are described,
e.g., have any members of this consortium been successfully cultured;
(c) Some spatial/temporal/hydrochemical/geochemical or other
characterization of the environment is given, e.g., the physicochemical
parameters of the site from which the selected community is derived; a
description of the site contaminants; the accessibility of the site for
future sampling; the adequacy of site documentation;
(d) If proposed, technical approaches and technology development
specific for defining and isolating members of a given consortium are
described;
(e) Some indication of the biological function of the
relationships, within consortium members, where available along with a
discussion of the scientific and programmatic importance of
understanding these relationships is given;
(f) Information where available is given about the phylogenetic
position(s) of the members of the consortium and what is known about
closely related organisms.
(g) Available informatics tools and annotation plan (e.g., for
annotating genes from a consortium analysis or grouping identified
genes into a putative ``consortium phenotype'' within the chosen
environment) are described;
(h) Explicit commitment to a data-release schedule, consistent with
the guidelines given below is provided.
Scientific community standards regarding access to sequencing data
are evolving. BER conforms to the general guidance contained within the
Draft Rapid Data Release Policy (http://www.genome.gov/page.cfm?pageID=10506537
) for ``community resource projects.'' The
usual and customary practice for the JGI is to put all sequencing data
up on its web site (http://www.jgi.doe.gov/) at frequent and periodic
intervals. However, for the purposes of this notice, BER does not
regard individual genome sequencing efforts involving less than 50Mb,
or microbial community sequencing efforts, as requested herein, as
``community resource projects'' within the definition of the Draft
Rapid Data Release policy. BER's position,
[[Page 27793]]
which is provisional and subject to evolution, is that no more than 6
months from the completion of 6 x coverage of the sequence for a
single-genome project, the data will be released on the JGI web site or
to a publicly accessible database with no use restrictions. For
microbial community projects, the JGI will conduct normal QA/QC
assessments on the sequence output (at approximately 2 x coverage),
then discuss with the proposer(s) and with BER staff the extent to
which sequencing will be continued to achieve a satisfactory genomic
``view'' of the selected microbial community. From the time of
initiation of this discussion, not more than 6 months will be permitted
to elapse before unconditional release of these data. BER is fully
aware that some ambiguity remains in the precise initiation of this
``embargo'' period but stresses its intention and commitment to the
rapid release, without any use restrictions, of this data into publicly
accessible databases.
Upon selection of a nominated microbial sequencing target, BER
expects that Principal Investigators will collaborate with the JGI by
providing high quality, high MW genomic DNA for library construction as
well as assisting in annotating the draft sequence data until a
sufficiently complete annotation is achieved (understanding that this
will be sensitive to hypothetical gene predictions and the usual
uncertainties of annotation). Following data acquisition and
annotation, DOE expects that those whose nominations have been
sequenced will make good faith efforts to publish in the open
scientific literature the results of their subsequent work, including
both the genome sequences of the organisms sequenced under this notice
as well as the annotation. (BER also expects the Principal Investigator
of a selected effort to either deposit a culture of the microbe or
consortium into a publicly accessible collection or repository, or make
it available directly so others can have access). These parties are
encouraged to create process- and cost-effective partnerships that will
maximize data production and analysis, data dissemination, and progress
towards understanding basic biological mechanisms that can further the
aims of this effort. Additionally, it must be explicitly understood
that DOE will provide an assembled and computationally annotated draft
(roughly 6 x; carried out in a paired-end sequencing approach) sequence
of the microbe(s) selected, but that research using that sequence data
should be funded from separate sources and/or separate solicitations.
Finally, there is no commitment to finish a given drafted sequence,
although this option may be considered at a later time.
Submission Information: Interested parties should submit a brief
white paper to either of the foci given above, consisting of not more
than 5 pages of narrative exclusive of attachments (which are
discouraged) responding to each of the specific criteria set forth.
Electronic submission (to joanne.corcoran@science.doe.gov and
daniel.drell@science.doe.gov) is strongly encouraged. It is expected
that the Principal Investigator will serve as the main point of contact
for additional information on the nominated microbe. Nominations must
contain a very short abstract or project summary and a cover page with
the name of the applicant, mailing address, phone, fax, and email. The
nomination should include 2-page curriculum vitae of the key
investigators; letters of intent from collaborators (suggesting the
size of the interested community) are permitted.
Nominations will be reviewed relative to the scope and research
needs of the BER relevant programs cited above. A brief response to
each nomination will be provided electronically following merit and
programmatic reviews.
Other useful Web sites include:
DOE JGI Microbial Sequencing Priorities for FY2003--http://www.ornl.gov/microbialgenomes/seq2003.html
Microbial Genome Program Home Page--http://www.sc.doe.gov/ober/microbial.html
DOE Joint Genome Institute Microbial Web Page--http://www.jgi.doe.gov/JGI_microbial/html/
GenBank Home Page--http://www.ncbi.nlm.nih.gov/ Human Genome Home Page--http://www.ornl.gov/hgmis
DOE Genomes to Life--http://DOEGenomestoLife.org
DOE Natural and Accelerated Bioremediation Research (NABIR)
Program--http://www.lbl.gov/nabir
Biotechnology Investigations--Ocean Margins Program--http://www.sc.doe.gov/ober/GC/omp.html
Issued in Washington, DC, May 14, 2003.
John Rodney Clark,
Associate Director of Science for Resource Management.
[FR Doc. 03-12715 Filed 5-20-03; 8:45 am]
BILLING CODE 6450-01-P