[Federal Register: January 6, 2004 (Volume 69, Number 3)]
[Notices]
[Page 638-640]
From the Federal Register Online via GPO Access [wais.access.gpo.gov]
[DOCID:fr06ja04-72]
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DEPARTMENT OF ENERGY
Office of Science Financial Assistance Program Notice DE-FG01-
04ER04-07; Microbial Genome Program
AGENCY: Department of Energy.
ACTION: Notice inviting grant applications.
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SUMMARY: The Office of Biological and Environmental Research (OBER) of
the Office of Science (SC), U.S. Department of Energy (DOE), hereby
announces its interest in receiving applications for research in
support of the Microbial Genome Program (MGP), focused on microbes of
interest to the DOE, e.g., those involved in environmental processes,
including waste remediation, carbon management, biomass conversion, and
energy production. This announcement is focused on: (1) Whole genome-
based systems or functional biology of DOE mission relevant
microorganisms; (2) bioinformatics tools for high-throughput microbial
genome annotation focused on currently unannotated genes and sequences,
and pathway/function modeling; and (3) technologies and approaches to
assess consortia and environmental diversity of hard-to-culture
microbes. Under this announcement, applications to carry out sequencing
of microbial genomes will be ineligible. A separate process is
available for the nomination and prioritization of sequencing
candidates for the DOE Joint Genome Institute. This announcement
emphasizes the use of already sequenced genomes that address DOE
mission needs.
DATES: Preapplications referencing Program Notice DE-FG01-04ER04-07,
should be received by January 29, 2004.
Formal applications in response to this notice should be received
by 4:30 p.m., e.d.t., April 15, 2004, to be accepted for merit review
and funding in Fiscal Year 2004.
ADDRESSES: Preapplications referencing Program Notice DE-FG01-04ER04-
07, should be sent to Dr. Daniel W. Drell, SC-72/Germantown Building,
U.S. Department of Energy, 1000 Independence Avenue, SW., Washington,
DC 20585-1290. E-mail is strongly encouraged for submitting
preapplications using the following address: kim.laing@science.doe.gov.
Formal applications referencing Program Notice DE-FG01-04ER04-07,
must be sent electronically by an authorized institutional business
official through DOE's Industry Interactive Procurement System (IIPS)
at: http://e-center.doe.gov/. IIPS provides for the posting of
solicitations and receipt of applications in a paperless environment
via the Internet. In order to submit applications through IIPS, your
business official will need to register at the IIPS Web site. IIPS
offers the option of using multiple files; please limit submissions to
one volume and one file if possible, with a maximum of no more than
four PDF files. The Office of Science will include attachments as part
of this notice that provide the appropriate forms in PDF fillable
format that are to be submitted through IIPS. Color images should be
submitted in IIPS as a separate file in PDF format and identified as
such. These images should be kept to a minimum due to the limitations
of reproducing them. They should be numbered and referred to in the
body of the technical scientific grant application as Color image 1,
Color image 2, etc. Questions regarding the operation of IIPS may be e-
mailed to the IIPS Help Desk at: HelpDesk@pr.doe.gov, or you may call
the help desk at: (800) 683-0751. Further information on the use of
IIPS by the Office of Science is available at: http://www.sc.doe.gov/production/
grants/grants.html.
If you are unable to submit an application through IIPS, please
contact the Grants and Contracts Division, Office of Science at: (301)
903-5212 or (301) 903-3604, in order to gain assistance for submission
through IIPS or to receive special approval and instructions on how to
submit printed applications.
FOR FURTHER INFORMATION CONTACT: Dr. Daniel W. Drell, SC-72/Germantown
Building, U.S. Department of Energy, 1000 Independence Avenue, SW.,
Washington, DC 20585-1290, telephone: (301) 903-4742, Email:
daniel.drell@science.doe.gov.
SUPPLEMENTARY INFORMATION: The Microbial Genome Program (MGP), a key
element of the DOE Genomes to Life Program (http://doegenomestolife.org
) supports key DOE missions by leveraging microbial
DNA sequence information to further the understanding and application
of microbiology relating to environmental processes, including waste
remediation, carbon management, biomass conversion, and energy
production. The determination of microbial genome sequences is a
mission of the DOE Joint Genome Institute (JGI) and follows a separate
process independent of this solicitation. Over the last nine years,
sequencing of microorganisms that live in a variety 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. industry. Applications are now being sought in three
complementary areas: Whole-genome based systems and functional
analyses; bioinformatics applied to extracting additional information
from microbial genome sequences; and the characterization of the
diversity of microbial consortia and/or hard-to-culture microbes that
mediate processes of relevance to the DOE. Each application must
clearly state which area is being addressed; if an applicant wishes to
address more than one area, the application must clearly describe the
expected advantages of an integrated approach.
Candidate microorganisms for study can comprise archaea, bacteria,
algae or fungi or communities made up of bacteria, archaea, algae and/
or fungi that mediate or catalyze metabolic events of energy or
environmental importance. Preference will be given to those applicants
using microbes, for which complete or near-complete genomic sequencing
[[Page 639]]
http://www.ornl.gov/microbialgenomes/progress.html for a current list of
microbes that have been and are being sequenced.) Priority will be
given to studies on those microbes or microbial consortia that can
bioremediate metals and radionuclides, generate energy compounds (e.g.,
hydrogen or methane), convert biomass to intermediate or final energy
products, or that are involved in environmental carbon management,
e.g., fix CO2. For studies on microbes that are members of communities,
at least one member should be a fully sequenced microbe. Strict or
opportunistic pathogens or parasites will not be considered.
(1) Systems and Functional Analysis. Even simple microbes are
constituted from thousands of genome-derived proteins. Many of these
proteins do not act alone; rather, they act as parts of protein
complexes that carry out functions not mediated by the individual gene
products themselves. Multi-protein complexes often are not static, they
are dynamic in response to environmental influences, intracellular
conditions and metabolic demands, and whether the cell is responding to
a stress or preparing to divide. The DOE MGP is particularly interested
in improved and high-throughput approaches to functional
characterization (e.g., transporters, environmental sensors, redox
enzymes, cytoskeletal components, DNA repair systems, metal reductases,
biodegradative enzymes, etc.) of the multi-protein complexes within
sequenced microbes participating in processes related to the
aforementioned mission areas. Coordinated expression of pathways and
processes involved in the aforementioned areas of mission interest
(e.g., bioremediation, carbon sequestration, and energy production) in
response to environmental variations or experimental manipulations is
also a priority. It is estimated that between three and six awards for
a total of up to $1 million could be available for this area initiating
in Fiscal Year 2004.
(2) Bioinformatics. By December 2003, completed genomic sequences
of perhaps 145 archaea and bacteria had been completed and published,
many as a direct result of DOE Microbial Genome Program funding. For
several microbes, complete sequences of close evolutionary relatives
now or will soon exist. Computational comparative genomics can
illuminate evolutionary pathways to complement traditional phenotype-
based analyses, provide data for the prediction of gene function
between organisms, and contribute to modeling pathways. The value of
such comparative functional analyses is highlighted by the remarkable
frequency of novel open reading frames in microbial genome sequences
(up to half the predicted genes in many cases) that currently lack any
annotation. The evolutionary conservation of open reading frames and
certain protein functions between microbes and more complex organisms
(including human) emphasizes the value of microbial sequences for
understanding the functions of uncharacterized microbial (and,
potentially, human) genes. To this end, computational methods for high-
throughput interspecies genomic comparisons are an area of particular
interest for this solicitation. Applications are requested that propose
ways in which microbial sequence data from all sources can be analyzed,
compared, annotated, and used to predict the function of homologous
genes in both prokaryotic and eukaryotic organisms. Of particular
interest are those approaches to predicting functions for currently
unannotated open reading frames and approaches to predicting
associations of genes in functional multi-protein complexes. Thus, this
notice solicits applications for research into:
(a) Novel computational tools to increase the value of microbial
genome sequence information, such as improved approaches for
identifying noncoding sequence elements that may participate in
regulatory or genomic management (i.e., binding to intracellular
scaffolding or membrane components) or that affects 3-D structure and
chemistry of the genomic DNA;
(b) Computational tools to identify and model gene expression
networks, or to identify likely participants in higher-order multi-
protein complexes;
(c) Computational analyses to support existing techniques, such as
(but not limited to) adjusting the BAC sequence size or primer walking,
that would enable the more efficient finishing of draft sequences of
microbial genomes. Applications should identify those problems that
require the most resources to finish a sequence and propose
computational steps to reduce the time and effort involved.
Of special interest will be methods that use unique DOE resources
in massively parallel, high-capacity supercomputers (machines in the
multi-teraflop range). It is expected that computational tools
developed under these awards will be widely distributed to the
scientific community (e.g., via a World Wide Web site) and some level
of user support will be available. It is anticipated that between three
and six awards for a total of up to $1 million could be available for
this area initiating in Fiscal Year 2004.
(3) Consortia and Hard-to-Culture Microbes. Most of our current
knowledge of microbiology is derived from individual species that
either cause diseases or grow as monocultures under laboratory
conditions and are thus easy to study. The preponderance of species in
the environment does neither and is thus largely opaque to scientific
study. 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 in which DOE is interested. Technologies and
approaches are sought that will enable genomic analyses of microbial
consortia as well as analyses of the genomic information content and
diversity of those species that have proven refractory to laboratory
culture but are plentiful in environments challenged with metal and
radionuclide wastes, or involved in carbon sequestration. It is
anticipated that between three and six awards totaling up to $1 million
could be available for this area initiating in Fiscal Year 2004.
Preapplicaitons
Potential applicants are strongly encouraged to submit a brief
preapplication that consists of one to two pages of narrative
describing the research objectives and technical approach(es).
Preapplications will be reviewed relative to the scope and research
needs of both the BER Microbial Genome Program, as well as the Genomes
to Life Program into which the Microbial Genome Program will become
fully integrated in Fiscal Year 2008. Preapplication review criteria
are more fully outlined in the summary paragraph and in the
SUPPLEMENTARY INFORMATION. Principal investigator telephone number, Fax
number, and e-mail address are required as part of the preapplication.
A response to each preapplication discussing the potential programmatic
relevance of a formal application will be communicated by e-mail to the
Principal Investigator within 14 to 21 days of receipt. Any renewal
applications must include a list of publications resulting from
previous DOE Microbial Genome Program funding.
Program Funding
It is anticipated that approximately $3 million will be available
for all MGP awards in Fiscal Year 2004, with as
[[Page 640]]
many as 15 awards anticipated, contingent on availability of
appropriated funds in Fiscal Year 2004, and the size of the awards.
Multiple year funding is expected up to a maximum of three years, also
contingent on availability of funds and progress of the research. At
the end of three years, the Microbial Genome Program will transition
fully into the DOE Genomes to Life Program and applications for
continuation of ongoing research started under this Program will not be
accepted. Awards are expected to range from $150,000 to $450,000 per
year, total costs, with terms of one to three years. Reasonable
increases in second and third year budget periods can be requested. DOE
is under no obligation to pay for any costs associated with the
preparation or submission of applications if an award is not made.
Each response to this solicitation will be evaluated for relevance
to: (a) The successful completion of the BER long term measure to
characterize the multiprotein complexes (or the lack thereof) involving
a scientifically significant fraction of microbe proteins; (b) the
development of computational models to direct the use and design of
microbial communities to clean up waste, sequester carbon, or produce
hydrogen; or (c) to develop science-based solutions for the cleanup and
long term monitoring of DOE contaminated sites.
Merit Review
Applications will be subjected to formal merit review (peer review)
and will be evaluated against the following evaluation criteria which
are listed in descending order of importance codified at 10 CFR
605.10(d):
1. Scientific and/or technical merit of the project;
2. Appropriateness of the proposed method or approach;
3. Competency of applicant's personnel and adequacy of proposed
resources;
4. Reasonableness and appropriateness of the proposed budget.
The evaluation will include program policy factors such as the
relevance of the proposed research to the terms of the announcement and
an agency's programmatic needs. Note, external peer reviewers are
selected with regard to both their scientific expertise and the absence
of conflict-of-interest issues. Non-Federal reviewers will often be
used, and submission of an application constitutes agreement that this
is acceptable to the investigator(s) and the submitting institution.
The Office of Science (SC), as part of its grant regulations (10
CFR 605.11(b)) requires that a grantee funded by SC and performing
research involving recombinant DNA molecules shall comply with the
National Institutes of Health ``Guidelines for Research Involving
Recombinant DNA Molecules'' (51 FR 16958, May 7, 1986), or such later
guidelines as may be published in the Federal Register.
The Project Description must be 20 pages or less, exclusive of
attachments. It must contain an abstract or project summary on a
separate page with the name of the applicant, mailing address, phone,
fax and email listed. The application must include letters of intent
from collaborators (briefly describing the intended contribution of
each to the research), and short curriculum vitaes, consistent with the
National Institutes of Health (NIH) guidelines, for the applicant and
any co-PIs. To provide a consistent format for the submission, review
and solicitation of grant applications submitted under this notice, the
preparation and submission of grant applications must follow the
guidelines given in the Application Guide for the Office of Science
Financial Assistance Program 10 CFR part 605. Access to SC's Financial
Assistance Application Guide is possible via the World Wide Web at:
http://www.sc.doe.gov/grants/grants.html.
Other useful Web sites include:
MGP home page--http://www.ornl.gov/sci/microbialgenomes/ DOE Genomes to Life Program: http://DOEGenomestoLife.org.
DOE Joint Genome Institute Microbial Web page: http://www.jgi.doe.gov/JGI_microbial/html/
.
GOLD Microbial Genome Database: http://wit.integratedgenomics.com/GOLD/
.
GenBank home page--http://www.ncbi.nlm.nih.gov/ Human Genome home page--http://www.ornl.gov/hgmis.
The Catalog of Federal Domestic Assistance number for this program
is 81.049, and the solicitation control number is ERFAP 10 CFR part
605.
Issued in Washington, DC on December 23, 2003.
John Rodney Clark,
Associate Director of Science for Resource Management.
[FR Doc. 04-202 Filed 1-5-04; 8:45 am]
BILLING CODE 6450-01-P