[Federal Register Volume 70, Number 53 (Monday, March 21, 2005)]
[Notices]
[Pages 13489-13492]
From the Federal Register Online via the Government Publishing Office [www.gpo.gov]
[FR Doc No: 05-5492]
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DEPARTMENT OF ENERGY
Recommendations for Sequencing Targets in Support of the Science
Missions of the Office of Biological and Environmental Research (BER)
AGENCY: Office of Science; Office of Biological and Environmental
Research; U.S. 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
250Mb-or-less-sized organisms for draft genomic sequencing in support
of Office of Biological and Environmental Research (BER) programs,
among them, the Genomics: GTL Program, the Climate Change Research
Program, the Terrestrial Carbon Processes Program, the Natural and
Accelerated Bioremediation Research (NABIR) Program, the Environmental
Management Science Program (EMSP), the Ocean Science Program, and the
Program for Ecosystem Research. Additional programs of relevance
include the Energy Biosciences, and Nanoscale Science, Engineering and
Technology Programs in the Office of Basic Energy Sciences. 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). A subset of the selected organisms may be
identified for sequence finishing. This announcement is designed to
assist DOE in determining and prioritizing a list of microbes,
microbial consortia, or modest-genome sized (not more than 250Mb)
organisms (including eukaryotes) that address DOE mission needs.
Following merit review, and a determination of satisfactory
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. (e.d.t.), July 14, 2005, to be accepted
for merit review. It is anticipated that review will be completed early
in the fall of 2005 with draft sequencing at the DOE PGF to commence
early in 2006, 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; e-mail is acceptable and
encouraged for submitting nominations using the following addresses:
[email protected] and [email protected].
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, e-mail: [email protected]. The
full text of this notice is available via the Internet using the
following Web site address: http://microbialgenome.org/.
SUPPLEMENTARY INFORMATION: The DOE Office of Biological and
Environmental Research supports fundamental research for a variety of
missions (http://www.science.doe.gov/ober/ober_top.html). Relevant BER
programs may include the the Genomics: GTL Program, the Climate Change
Research Program, the Terrestrial Carbon Processes Program, the Natural
and Accelerated Bioremediation Research (NABIR) Program, the
Environmental Management Science Program (EMSP), the Ocean Science
Program, and the Program for Ecosystem Science. Additional programs of
relevance include the Energy Biosciences, and Nanoscale Science,
Engineering and Technology Programs in the Office of Basic Energy
Sciences. The Genomics:GTL Program, a partnership with the DOE Office
of Advanced Scientific Computing Research, supports research into
systems microbiology towards the comprehensive understanding of
proteins and protein machines, gene regulatory networks, and microbial
communities, and the development of computing and information
infrastructure to enable a predictive understanding of biological
systems. 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 Ocean
[[Page 13490]]
Sciences Program supports research to understand the ocean carbon
cycle. The Program for Ecosystem Science supports research to
understand and predict effects of environmental changes associated with
energy production on the structure and functioning of important
terrestrial ecosystems. In the Office of Basic Energy Sciences, the
Energy Biosciences Program supports fundamental research in molecular-
level studies on solar energy capture through natural photosynthesis;
the mechanisms and regulation of carbon fixation and carbon energy
storage; the synthesis, degradation, and molecular interconversions of
complex hydrocarbons and carbohydrates. Aligned with this, the
Nanoscale Science, Engineering and Technology Program supports studies
of novel biosystems and their potential for materials synthesis,
chemical catalysis, and materials synthesized at the nanoscale needed
to develop future biotechnologies related to energy.
The purpose of this solicitation is to support these key DOE
missions by generating and providing initial analyses of microbial DNA
sequence information to further the understanding and application of
microbiology relating to energy production, biochemical and
biomaterials production, environmental carbon management, and
environmental cleanup. Both terrestrial and ocean environments in which
microbial flora contribute to the sequestration of carbon, particularly
carbon dioxide, are of interest. Within the ocean environment,
microbial flora that sequester or process carbon dioxide in both the
eutrophic and ``twilight'' zones are of interest.
For more than ten years, sequencing of a variety of microorganisms
that live in diverse 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. industry.
(http://www.tigr.org/tdb/mdb/mdbcomplete.html http://microbialgenome.org/organisms.shtml and http://genome.jgi-psf.org/microbial/ microbial/). 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. Little is known of the
organization, membership, or functioning of these consortia, especially
those involved in environmental processes of DOE interest.
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 the 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, or chlorinated
solvents; can potentially generate energy compounds (e.g., hydrogen or
methane); or are involved in carbon sequestration. The candidate(s)
being proposed must mediate or catalyze metabolic events that
contribute to these processes. Priority will be given to studies on
those microbes or microbial consortia that can bioremediate metals and
radionuclides, degrade biomass and 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, protests, and other eukaryotes with
genome sizes not greater than 250 Mbp can be proposed for draft
sequencing. For a current list of microbes that have been and are being
sequenced by the DOE see http://microbialgenome.org/organisms.shtml.
For a more comprehensive list of genomes (including microbes) being
sequenced in the public sector, see http://www.genomesonline.org.
Aims: This request for nominations of candidate sequencing targets
has two broad foci:
(1) Single organisms. These may be bacteria, archaea, fungi,
microalgae or multicellular organisms with genomes not larger than
250Mb. 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) To assess suitability for whole genome shotgun sequencing,
preliminary data on genome size, repeat content, genome structure, GC
content, polymorphism, and other characteristics are provided,
especially for larger genomes;
(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) is 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, although funding will not be provided for these
activities;
(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 scientific user community for the
sequence information, and for the organism in general, is given;
(i) The potential impact on science is large;
(j) Explicit commitment to a data-release schedule, consistent with
the guidelines given below is provided.
(k) Explicit commitment to the deposition of a culture of the
proposed microbe to a publicly accessible repository is made.
(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 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
[[Page 13491]]
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 250Mb,
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, which is provisional and
subject to evolution, is that no more than 3 months from the completion
of a ``first assembly'' 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 3 months will be permitted to elapse before unconditional
release of these data. Proposers should clearly understand that the
priority in the sequencing queue that a selected project is given may
be linked to the willingness of the proposer(s) to shorten this
``embargo'' period. 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. Notification of successful proposals will
take place sometime in November 2005 at which time the successful
proposer is expected to work out a detailed and mutually satisfactory
User Agreement with the JGI. This User Agreement will specify the
expectations of the proposer and the commitment of JGI resources to the
project, including the amount of sequencing capacity or megabases to be
sequenced. Sequencing will NOT begin prior to the finalization of this
User Agreement. Thus proposers are strongly encouraged to begin
preparation of DNA BEFORE notification of successful proposals because
from the date of the conclusion of the User Agreement, the proposer is
expected to furnish the JGI with usable, high quality DNA within 6
months or risk losing her/his place in the sequencing. A separate
communication with the detailed requirements for DNA will be sent to
proposers whose nominations are accepted for sequencing. Following data
acquisition and annotation, DOE expects that Principal Investigators
whose nominations have been sequenced will make good faith efforts to
publish the results of their subsequent work in the open scientific
literature, 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 for a selected subset of proposed
candidates.
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 should be
kept to a minimum) responding to each of the specific criteria set
forth. Electronic submission to ([email protected] and
[email protected]) 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 e-mail. The
nomination should include 2-page curriculum vitae of the key
investigators; letters of intent (or e-mails) 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 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 FY2005: http://microbialgenome.org/.
DOE Joint Genome Institute Microbial Web Page--http://genome.jgi-psf.org/microbial/index.html.
[[Page 13492]]
GenBank Home Page--http://www.ncbi.nlm.nih.gov.
DOE Genomics: GTL--http://DOEGenomestolife.org.
DOE Natural and Accelerated Bioremediation Research (NABIR)
Program--http://www.lbl.gov/nabir.
Climate Change Research Program: http://www.science.doe.gov/ober/CCRD_top.html.
Terrestrial Carbon Processes Program: http://www.science.doe.gov/ober/CCRD/tcp.html.
Environmental Management Science Program (EMSP): http://www.science.doe.gov/ober/ERSD/ersd_emsp.html.
Ocean Science Program: http://www.science.doe.gov/ober/CCRD/oceans.html.
Program for Ecosystem Research: http://www.science.doe.gov/ober/CCRD/per.html.
Ari Patrinos,
Associate Director of Science for Biological and Environmental
Research.
[FR Doc. 05-5492 Filed 3-18-05; 8:45 am]
BILLING CODE 6450-01-P