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DEPARTMENT OF ENERGY For more information about the Office of Science, go to Office of Science |
To DOE National Laboratories LAB 07-12 New Analytical and Imaging Technologies for Lignocellulosic Material Degradation, and for Multiplexed Screening for Plant Phenotypes
SUMMARY: The Office of Biological and Environmental Research (BER) of the Office of
Science (SC), U.S. Department of Energy (DOE), hereby announces its interest in receiving
proposals for research that supports the Genomics: GTL research program
(
http://www.genomicsGTL.energy.gov). In the first part of this notice, proposals are solicited for
the development of technologies for studying lignocellulosic systems, real-time characterization
of such systems in the course of processing, and other innovative techniques that could facilitate
lignocellulosic material degradation. The second part of this notice solicits the development of
improved methods leading to high-throughput, sensitive, and selective phenotypic screening of
plant feedstocks.
DATES: Potential researchers are required to submit a brief preproposal, referencing
LAB 07-12 for receipt by DOE by 4:30 p.m., Eastern Time, January 4, 2007. Preproposals
will be reviewed for conformance with the guidelines presented in this Notice and suitability in
the technical areas specified in this Notice. A response to the preproposals encouraging or
discouraging formal proposals will be communicated to the researchers by January 12, 2007.
Researchers who have not received a response regarding the status of their preproposal by this
date are responsible for contacting the program to confirm this status.
Only those researchers that receive notification from DOE encouraging a formal proposal may
submit a full proposal. No other formal proposals will be considered.
Potential researchers must submit a brief preproposal that consists of no more than three pages
of narrative stating the research objectives, describing the technical approach(s), and identifying
the proposed team members and their expertise. The intent in requesting a preproposal is to save
the time and effort of researchers in preparing and submitting a formal project proposal that may
be inappropriate for the program. Preproposals will be reviewed relative to the scope and
research needs as outlined in the summary paragraph and in the SUPPLEMENTARY
INFORMATION. The preproposal should identify, on the cover sheet, the title of the project, the
institution or organization, principal investigator name, telephone number, fax number, and
e-mail address. No budget information or biographical data need be included, nor is an
institutional endorsement necessary.
Preproposals referencing the first aim in LAB 07-12 should be sent as a text file without
attachments or a single PDF file attachment via e-mail to: genomicsGTL@science.doe.gov with
"Preproposal LAB 07-12 Lignocellulose Lastname Institution" as the subject. Preproposals
referencing the second aim in LAB 07-12 should be sent as a text file without attachments or a
single PDF file attachment via e-mail to: genomicsGTL@science.doe.gov with "Preproposal
LAB 07-12 Phenotyping Lastname Institution" as the subject. No FAX or mail submission of
preproposals will be accepted.
Eligibility: Researchers from FFRDCs (Federally Funded Research and Development Centers)
or DOE National Laboratories. BER reserves the right to encourage, in whole or in part, any, all,
or none of the preproposals submitted, and may issue further guidance on the scope of the full
proposal submissions of those encouraged.
Formal proposals in response to this Notice should be submitted via ePMA and must be
received by 8:00 pm Eastern Time, March 6, 2007.
This section pertains only to those proposers that have been encouraged to submit a full
proposal. A complete formal FWP in a single Portable Document Format (PDF) file must be
submitted through the DOE ePMA system (
https://epma.doe.gov) as an attachment. To identify
that the FWP is responding to this program announcement, please fill in the following fields in
the "ePMA Create Proposal Admin Information" screen as shown:
* Please use the wording shown when filling in these fields to identify that the FWP is
responding to this Program Announcement.
In order to expedite the review process, please submit a CD and three copies of the
proposal using the following, by U.S. Postal Service Express Mail, any commercial mail
delivery service, or when hand-carried to:
FOR FURTHER INFORMATION CONTACT:
Aim One: New Analytical and Imaging Technologies for Studying Lignocellulosic Material
Degradation
Dr. John Houghton, phone: (301) 903-8288; E-mail: john.houghton@science.doe.gov
Aim Two: New Technologies for Multiplexed Screening for Plant Phenotypes
Dr. Sharlene Weatherwax, phone: (301) 903-6165; E-mail:
sharlene.weatherwax@science.doe.gov
SUPPLEMENTARY INFORMATION:
Introduction:
The conversion of lignocellulosic biomass to liquid fuels may have the promise to significantly
substitute biofuels for petroleum on a domestic scale. Biofuels may successfully compete
economically as well as improve energy security, reduce greenhouse gas emissions, improve
balance of trade, provide jobs in rural America, and achieve other ancillary benefits. Although
pilot scale biorefineries convert lignocellulosic material to ethanol today, the efficiencies are not
yet as high as would be desirable for a major shift in energy use.
One of the pivotal issues for successful economic utilization of biomass for biofuels is
developing an effective strategy to overcome the defenses that plants have evolved against the
degradation of lignocellulose - the major component of plant cell walls. Plant cell walls are
made up of celluloses, hemicelluloses, pectins, lignins, proteoglycans, and other organic
molecules. Each plays a distinct role in both the structural integrity of the plant as well as in the
recalcitrance of conversion and the ultimate energy content of the energy products.
Fundamental scientific understanding of the biology of cell wall degradation by bacteria, fungi,
microbial communities, or symbiotic associations between microbes and animals, as well as
processes that alter plant cell wall composition and morphology, will promote effective options
to modify and/or decompose the complicated mixture of recalcitrant materials. This knowledge
of the underlying mechanisms of cell wall deconstruction to sugars and other energy-containing
substrates will enable development of conversion processes with increased yields and reaction
rates and decreased creation and/or impact of inhibitory byproducts.
New and innovative applications of technologies are needed to understand the properties of these
materials and to relate these properties to the behavior of the materials under a large variety of
treatment conditions. The scientific community will require these technologies to develop new
strategies for handling and pretreating the feedstock, and converting it into products suitable for
fermentation or other downstream processes. Research using the new technologies will enable
better understanding of how feedstock material is altered during different treatment options with
consequent changes in the accessibility of the material to microbes or enzymes used for
processing into fuels. For example, dehydrating biomass as it is stored may inhibit later
saccharification. Certain chemical or heat pretreatments may cause the cellulose or lignin to re-
anneal over the lignocellulosic material and reduce subsequent enzymatic access. A deeper
understanding at a molecular scale of the external surface properties of the lignocellulosic
material may enable better treatment options that facilitate hydration and enzymatic
effectiveness.
Research Topics:
Research and technology development is invited that will result in new capabilities for
characterizing the lignocellulosic material in plants, the changes undergone by lignocellulosic
material during the stages of pretreatment, the effects of enzymes and chemical reagents that
deconstruct the lignocellulosic material into saccharides and other products, and the cell wall
degradative strategies of microbes, fungi, etc. Techniques for characterizing these materials
either non-invasively or with minimal requirements for sampling are of particular interest.
Techniques for characterizing and/or imaging treatment processes in real time are also of high
interest.
Proposed research should seek resolution in space and time sufficient to understand the materials
and processes under study at the molecular level. For instance, the morphological fate of the
lignin or cellulose portions that are altered through the addition of heat, acid, base, or pressure
may hinder further accessibility by downstream processes.
Development of computational techniques for analyzing data produced using these new
technologies is also of interest. Proposals may include objectives that focus on the computational
tools needed to make optimal use of the new analytical technology that is the main focus of the
proposed project. Computational research should support the proposed research into
characterization and imaging technologies.
A comprehensive description of the major research and development needs for converting
lignocellulosic materials to fuels is given in "Breaking the Biological Barriers to Cellulosic
Ethanol",
http://genomicsgtl.energy.gov/biofuels/b2bworkshop.shtml. The Genomics: GTL
Roadmap includes discussions of the basic research goals of the program,
http://genomicsgtl.energy.gov/roadmap/index.shtml.
A. Analytical and Imaging Technologies for Lignocellulosic Material Degradation
Research funded through this component of the solicitation will support the development of
technologies for studying lignocellulosic systems, real-time characterization of such systems in
the course of processing, and other innovative techniques that could enable progress in the
biomass research program described above.
Potential approaches include but are not limited to:
B. Improved technologies for multiplexed screening for plant phenotypes
Another prerequisite for a competitive biofuel industry is the development of plant feedstocks
that exhibit both desirable cell-wall traits and high biomass productivity under sustainable low-
input conditions. Full leveraging of plant genome sequence information against advances in
conventional breeding requires robust functional genomic tools and high throughput phenotyping
platforms for identification and characterization of improved plant feedstock species. Such
optimization might include decreasing the lignin content or changing the lignin cross-linked
structure in plant feedstocks, to facilitate access of degradative enzymes to cellulosic substrates.
Similarly, improved microscreens or high-throughput screens for specific alterations in defined
cellular targets or molecular metabolites may result in more rapid identification of potentially
interesting plant mutants exhibiting desired changes in metabolic reactions resulting from
introduced genetic modifications. This information may contribute to testable models of the
genes and regulatory mechanisms that control plant growth, increase net photosynthetic CO2
fixation and direct carbon flux to cell wall polysaccharides and storage polymers. The resulting
fundamental knowledge will lead to the accelerated development of a suite of new crops and new
varieties of existing crops specifically bred for biofuels and adapted to a range of different soil
types and climatic conditions.
In this second component of this solicitation, proposals are sought for the development of
improved methods leading to high-throughput, sensitive, and selective phenotypic screening of
plant feedstocks. These screening methodologies will be used to identify quantitative and
qualitative differences in plant cell wall phenotypes of major cell wall biopolymers (lignin,
cellulose, hemicellulose, and others), net photosynthetic efficiency and CO2 fixation, and
morphometric traits. Researchers must describe how their proposed method will result in a
significant improvement with respect to accuracy, dynamic range, or throughput over existing
phenotyping methods. The proposed method must permit recovery of the individual from the
screening population subsequent to analysis, either through low materials-input requirements that
do not consume the entire test sample or using nondestructive sampling techniques.
Examples of current analytical technologies that may be optimized for high throughput screening
platforms include:
Data and results that are generated through these investigations that are appropriate to share with
the broader community should be provided in timely, open, and machine-readable format where
possible. Funded investigators are expected to contribute to and participate with the GTL
working group on data management, and to adhere to the group's consensus on data sharing.
The Genomics:GTL program supports a combination of large, well integrated, multidisciplinary
research teams and smaller, focused research projects. This solicitation will support smaller,
focused research projects to develop new technologies, research strategies, or research resources
needed by the Genomics:GTL program.
Information on the research projects currently funded by the Genomics: GTL program and a
description of project goals and overall program organization can be found at:
http://genomicsgtl.energy.gov/).
Program Funding: It is anticipated that up to $4 million total will be available for multiple
awards to be made in FY 2007 for New Analytical and Imaging Technologies for
Lignocellulosic Material Degradation, and for Multiplexed Screening for Plant Phenotypes. The
number of awards will be contingent on satisfactory peer review, the availability of appropriated
funds, and the size of the awards. Multiple year funding is expected. Proposals may request
project support for up to three years, with out-year support contingent on the availability of
funds, progress of the research, and programmatic needs. Annual budgets are expected to range
from $250,000 to $1,000,000 total costs. DOE is under no obligation to pay for any costs
associated with the preparation or submission of a proposal. DOE reserves the right to fund, in
whole or in part, any, all, or none of the proposals submitted in response to this Notice.
Submission Information
The Department of Energy will accept Full Proposals by invitation only, based upon the
evaluation of the preproposals. After receiving notification from DOE concerning successful
preproposals, researchers may prepare formal proposals. The Project Description must not
exceed 20 pages, including tables and figures, but exclusive of attachments. The proposal must
contain an abstract or project summary, short vitae, and letters of intent from collaborators if
appropriate.
Full proposals adhering to DOE Field Work Proposal format (Reference DOE Order 412.1) are
to be prepared and submitted consistent with policies of the investigator's laboratory and the
local DOE Operations Office. Laboratories may submit proposals directly to the SC Program
Office listed above. A copy should also be provided to the appropriate DOE Operations Office.
The instructions and format described below should be followed. You must reference Program
Announcement LAB 07-12 on all submissions and inquiries about this program.
GUIDE FOR PREPARATION OF SCIENTIFIC/TECHNICAL PROPOSALS TO BE SUBMITTED BY NATIONAL LABORATORIES Proposals from National Laboratories submitted to the Office of Science (SC) as a result of this program announcement will follow the Department of Energy Field Work Proposal process with additional information requested to allow for scientific/technical merit review. The following guidelines for content and format are intended to facilitate an understanding of the requirements necessary for SC to conduct a merit review of a proposal. Please follow the guidelines carefully, as deviations could be cause for declination of a proposal without merit review. 1. Evaluation Criteria Proposals will be subjected to formal merit review (peer review) and will be evaluated against the following criteria which are listed in descending order of importance:
Appropriateness of the proposed method or approach Competency of the personnel and adequacy of the proposed resources Reasonableness and appropriateness of the proposed budget 2. Summary of Proposal Contents
2.1 Number of Copies to Submit This section pertains only to those proposers that have been encouraged to submit a full proposal. A complete formal FWP in a single Portable Document Format (PDF) file must be submitted through the DOE ePMA system ( https://epma.doe.gov) as an attachment. To identify that the FWP is responding to this program announcement, please fill in the following fields in the "ePMA Create Proposal Admin Information" screen as shown:
Fiscal Year: Proposal Reason: Program Announcement Number: Lab 07-12 * Program announcement Title: New Analytical and Imaging Technologies for Lignocellulosic Material Degradation, and for Multiplexed Screening for Plant Phenotypes * Proposal Purpose: Estimated Proposal Begin Date: HQ Program Manager Organization: * Please use the wording shown when filling in these fields to identify that the FWP is responding to this Program Announcement. In order to expedite the review process, please submit a CD and three copies of the proposal using the following, by U.S. Postal Service Express Mail, any commercial mail delivery service, or when hand-carried to:
U.S. Department of Energy Office of Biological and Environmental Research, SC-23.2 19901 Germantown Road Germantown, MD 20874-1290 ATTN: Program Announcement LAB 07-12 3. Detailed Contents of the Proposal Adherence to type size and line spacing requirements is necessary for several reasons. No researcher should have the advantage, or by using small type, of providing more text in their proposals. Small type may also make it difficult for reviewers to read the proposal. Proposals must have 1-inch margins at the top, bottom, and on each side. Type sizes must be 10 point or larger. Line spacing is at the discretion of the researcher but there must be no more than 6 lines per vertical inch of text. Pages should be standard 8 1/2" x 11" (or metric A4, i.e., 210 mm x 297 mm). 3.1 Field Work Proposal Format (Reference DOE O 412.1A) (DOE ONLY) The Field Work Proposal (FWP) is to be prepared and submitted consistent with policies of the investigator's laboratory and the local DOE Operations Office. Additional information is also requested to allow for scientific/technical merit review. Laboratories may submit proposals directly to ePMA. 3.2 Proposal Cover Page The following proposal cover page information may be placed on plain paper. No form is required.
SC Program announcement title Name of laboratory Name of principal investigator (PI) Position title of PI Mailing address of PI Telephone of PI Fax number of PI Electronic mail address of PI Name of official signing for laboratory* Title of official Fax number of official Telephone of official Electronic mail address of official Requested funding for each year; total request Use of human subjects in proposed project:
Signature of official, date of signature* *The signature certifies that personnel and facilities are available as stated in the proposal, if the project is funded.
Provide the initial page number for each of the sections of the proposal. Number pages consecutively at the bottom of each page throughout the proposal. Start each major section at the top of a new page. Do not use unnumbered pages and do not use suffices, such as 5a, 5b. 3.4 Budget and Budget Explanation A detailed budget is required for the entire project period and for each fiscal year. It is preferred that DOE's budget page, Form 4620.1 be used for providing budget information*. Modifications of categories are permissible to comply with institutional practices, for example with regard to overhead costs. A written justification of each budget item is to follow the budget pages. For personnel this should take the form of a one-sentence statement of the role of the person in the project. Provide a detailed justification of the need for each item of permanent equipment. Explain each of the other direct costs in sufficient detail for reviewers to be able to judge the appropriateness of the amount requested. Further instructions regarding the budget are given in section 4 of this guide. * Form 4620.1 is available at web site: http://www.science.doe.gov/grants/budgetform.pdf 3.5 Abstract Provide an abstract of less than 400 words. Give the project objectives (in broad scientific terms), the approach to be used, and what the research is intended to accomplish. State the hypotheses to be tested (if any). At the top of the abstract give the project title, names of all the investigators and their institutions, and contact information for the principal investigator, including e-mail address. 3.6 Narrative (main technical portion of the proposal, including background/introduction, proposed research and methods, timetable of activities, and responsibilities of key project personnel) The narrative comprises the research plan for the project and is limited to 20 pages (maximum). It should contain enough background material in the Introduction, including review of the relevant literature, to demonstrate sufficient knowledge of the state of the science. The major part of the narrative should be devoted to a description and justification of the proposed project, including details of the methods to be used. It should also include a timeline for the major activities of the proposed project, and should indicate which project personnel will be responsible for which activities. If any portion of the project is to be done in collaboration with another institution (or institutions), provide information on the institution(s) and what part of the project it will carry out. Further information on any such arrangements is to be given in the sections "Budget and Budget Explanation", "Biographical Sketches", and "Description of Facilities and Resources". 3.7 Literature Cited Give full bibliographic entries for each publication cited in the narrative. 3.8 Biographical Sketches This information is required for senior personnel at the institution submitting the proposal and at all subcontracting institutions (if any). The biographical sketch is limited to a maximum of two pages for each investigator. To assist in the identification of potential conflicts of interest or bias in the selection of reviewers, the following information must be provided in each biographical sketch.
Graduate and Postdoctoral Advisors and Advisees: A list of the names of the individual's own graduate advisor(s) and principal postdoctoral sponsor(s), and their current organizational affiliations. A list of the names of the individual's graduate students and postdoctoral associates during the past 5 years, and their current organizational affiliations. 3.9 Description of Facilities and Resources Facilities to be used for the conduct of the proposed research should be briefly described. Indicate the pertinent capabilities of the institution, including support facilities (such as machine shops), that will be used during the project. List the most important equipment items already available for the project and their pertinent capabilities. Include this information for each subcontracting institution (if any). 3.10 Other Support of Investigators Other support is defined as all financial resources, whether Federal, non-Federal, commercial, or institutional, available in direct support of an individual's research endeavors. Information on active and pending other support is required for all senior personnel, including investigators at collaborating institutions to be funded by a subcontract. For each item of other support, give the organization or agency, inclusive dates of the project or proposed project, annual funding, and level of effort (months per year or percentage of the year) devoted to the project. 3.11 Appendix Information not easily accessible to a reviewer may be included in an appendix, but do not use the appendix to circumvent the page limitations of the proposal. Reviewers are not required to consider information in an appendix, and reviewers may not have time to read extensive appendix materials with the same care they would use with the proposal proper. The appendix may contain the following items: up to five publications, manuscripts accepted for publication, abstracts, patents, or other printed materials directly relevant to this project, but not generally available to the scientific community; and letters from investigators at other institutions stating their agreement to participate in the project (do not include letters of endorsement of the project).
4. Detailed Instructions for the Budget 4.1 Salaries and Wages List the names of the principal investigator and other key personnel and the estimated number of person-months for which DOE funding is requested. Proposers should list the number of postdoctoral associates and other professional positions included in the proposal and indicate the number of full-time-equivalent (FTE) person-months and rate of pay (hourly, monthly or annually). For graduate and undergraduate students and all other personnel categories such as secretarial, clerical, technical, etc., show the total number of people needed in each job title and total salaries needed. Salaries requested must be consistent with the institution's regular practices. The budget explanation should define concisely the role of each position in the overall project. 4.2 Equipment DOE defines equipment as "an item of tangible personal property that has a useful life of more than two years and an acquisition cost of $25,000 or more." Special purpose equipment means equipment which is used only for research, scientific or other technical activities. Items of needed equipment should be individually listed by description and estimated cost, including tax, and adequately justified. Allowable items ordinarily will be limited to scientific equipment that is not already available for the conduct of the work. General purpose office equipment normally will not be considered eligible for support. 4.3 Domestic Travel The type and extent of travel and its relation to the research should be specified. Funds may be requested for attendance at meetings and conferences, other travel associated with the work and subsistence. In order to qualify for support, attendance at meetings or conferences must enhance the investigator's capability to perform the research, plan extensions of it, or disseminate its results. Consultant's travel costs also may be requested. 4.4 Foreign Travel Foreign travel is any travel outside Canada and the United States and its territories and possessions. Foreign travel may be approved only if it is directly related to project objectives. 4.5 Other Direct Costs The budget should itemize other anticipated direct costs not included under the headings above, including materials and supplies, publication costs, computer services, and consultant services (which are discussed below). Other examples are: aircraft rental, space rental at research establishments away from the institution, minor building alterations, service charges, and fabrication of equipment or systems not available off- the-shelf. Reference books and periodicals may be charged to the project only if they are specifically related to the research. a. Materials and Supplies The budget should indicate in general terms the type of required expendable materials and supplies with their estimated costs. The breakdown should be more detailed when the cost is substantial. b. Publication Costs/Page Charges The budget may request funds for the costs of preparing and publishing the results of research, including costs of reports, reprints page charges, or other journal costs (except costs for prior or early publication), and necessary illustrations. c. Consultant Services Anticipated consultant services should be justified and information furnished on each individual's expertise, primary organizational affiliation, daily compensation rate and number of days expected service. Consultant's travel costs should be listed separately under travel in the budget. d. Computer Services The cost of computer services, including computer-based retrieval of scientific and technical information, may be requested. A justification based on the established computer service rates should be included. e. Subcontracts Subcontracts should be listed so that they can be properly evaluated. There should be an anticipated cost and an explanation of that cost for each subcontract. The total amount of each subcontract should also appear as a budget item. 4.6 Indirect Costs Explain the basis for each overhead and indirect cost. Include the current rates.
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