[Federal Register Volume 69, Number 3 (Tuesday, January 6, 2004)]
[Notices]
[Pages 638-640]
From the Federal Register Online via the Government Publishing Office [www.gpo.gov]
[FR Doc No: 04-202]


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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: [email protected].
    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: [email protected], 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: 
[email protected].

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 
information in the public domain exists. (See http://

[[Page 639]]

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]
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