TOOLS FOR GENETIC AND GENOMIC STUDIES IN EMERGING MODEL ORGANISMS RELEASE DATE: July 28, 2004 PA NUMBER: PA-04-135 - September 29, 2007 (Reissued as PA-07-457) September 17, 2007 - Expiration Date adjusted to accommodate recent changes to standing submission deadlines, per NOT-OD-07-093. May 10, 2006 (NOT-GM-06-010) - See this notice for Changes in Program Announcement PA-04-135: Tools for Genetic and Genomic Studies in Emerging Model Organisms EXPIRATION DATE: November 2, 2007, unless reissued (September 28, 2007 per PA-07-457) (January 8, 2008 per NOT-OD-07-093) Department of Health and Human Services (DHHS) PARTICIPATING ORGANIZATION: National Institutes of Health (NIH) ( COMPONENT OF PARTICIPATING ORGANIZATION: National Institute of General Medical Sciences (NIGMS) ( CATALOG OF FEDERAL DOMESTIC ASSISTANCE NUMBER(S): 93.859 THIS PA CONTAINS THE FOLLOWING INFORMATION o Purpose of the PA o Research Objectives o Mechanism(s) of Support o Eligible Institutions o Individuals Eligible to Become Principal Investigators o Special Requirements o Where to Send Inquiries o Submitting an Application o Supplementary Instructions o Peer Review Process o Review Criteria o Award Criteria o Required Federal Citations PURPOSE OF THIS PA This Program Announcement (PA) is to encourage investigator-initiated applications for research designed to generate genetic tools and genomic resources that will enable researchers to exploit the full potential of novel or developing model systems for comparative and functional genomic studies. The typical model organism to be considered should have a publicly available draft of the genomic DNA sequence with a minimum of 5X coverage. In addition, it should have at least one of the following characteristics: (1) shows promise as, or is, a model for basic biological or behavioral mechanisms; (2) occupies an important evolutionary niche that may yield novel insights in comparative studies; or (3) has potential as, or is, a model for developmental or disease processes. Applicants are expected to ensure that reagents, technologies, and resources developed under this initiative are made widely available to the research community. This PA is not intended to encourage genome sequencing projects or studies of model organisms for which there are well-established databases and other genome-related resources e.g. mouse, Drosophila, C. elegans, S. cerevisiae. In general, resources to study organisms that fit primarily within the mission of another NIH Institute or Center, such as, pathogenic microorganisms, are not encouraged through this PA. RESEARCH OBJECTIVES The advent of the genomic era has been a boon for the investigation of a growing number of model organisms. Completion of DNA sequencing of each genome presents opportunities for novel insights into genomic function, the regulation of gene expression, and evolutionary processes. Yet, the large scale of many sequencing projects and the sheer volume of sequence data create a considerable challenge for the individual investigator as well as consortia of researchers to obtain the resources and tools required to make maximal use of genomic information for comparative or functional studies. The major goal of this PA is to support research that will enhance the usefulness of DNA sequence information for newly emerging or developing model organisms for which there are limited genomic resources. Objectives to be addressed in applications submitted in response to this PA include, but are not limited to, the following: o Improvements in tools for mining of data for genomes having unique composition or structure o Improved database management and integration with other databases (Requests for the maintenance of databases alone are not encouraged.) o Generation of comprehensive cDNA libraries o Development of microarray reagents and/or services o Improved methods for linking expression arrays with standard phenotypes or with specific biological or behavioral outcomes o Development of novel approaches for mutagenesis and for rapid identification and characterization of point mutations o Development of novel transposable element-based techniques for the generation of knockouts or other mutations o Improvements in gene transfer technology and in vectors for genomic manipulation o Generation of sets of gene knockouts or knock-downs MECHANISM(S) OF SUPPORT This PA will use the National Institutes of Health (NIH) research resource grant (R24) mechanism. Responsibility for the planning, direction, and execution of the proposed project will be solely that of the applicant. The total project period for an application submitted in response to this PA may not exceed four years. A maximum of $250,000 direct costs (exclusive of subcontractual indirect costs) per year will be provided. This PA uses just-in-time concepts. It uses the non-modular budgeting format. Follow the instructions for non-modular budget research grant applications. This program does not require cost sharing as defined in the current NIH Grants Policy Statement at ELIGIBLE INSTITUTIONS You may submit (an) application(s) if your institution has any of the following characteristics: o For-profit or non-profit organizations o Public or private institutions, such as universities, colleges, hospitals, and laboratories o Units of State and local governments o Eligible agencies of the Federal government o Domestic or foreign institutions/organizations INDIVIDUALS ELIGIBLE TO BECOME PRINCIPAL INVESTIGATORS Any individual with the skills, knowledge, and resources necessary to carry out the proposed research is invited to work with their institution to develop an application for support. Individuals from underrepresented racial and ethnic groups as well as individuals with disabilities are always encouraged to apply for NIH programs. SPECIAL REQUIREMENTS The NIH is interested in ensuring that the research resources (constructs, reagents, cell lines, software tools, expression data, methods, etc.) developed through this PA become readily available to the research community for further research, development, and application, in the expectation that this will lead to products and knowledge of benefit to the public. At the same time, NIH recognizes the rights of grantees to elect and retain title to subject inventions developed under federal funding under the provision of the Bayh-Dole Act. This PA has two special requirements regarding research resources produced in proposed projects: (1) Applicants are required to include in their applications a specific plan by which they will share research resources with the wider scientific community. A reasonable time frame for periodic deposition of mutants, reagents, and data should be specified in the application. (2) Applicants are required to include a plan addressing if, or how, they will exercise their intellectual property rights while making available to the broader scientific community patentable research resources. The plan should address the following questions: o Will material transfers be made with no more restrictive terms than in the Simple Letter Material Transfer Agreement or the Uniform Biological Material Transfer Agreement? o Will there be reach-through requirements on materials transferred? o Should any intellectual property arise that requires a patent, will the technology remain widely available to the research community? Both the sharing and intellectual property plans should, at a minimum, address these elements in a clear and concise manner. Applicants are encouraged to inform and/or confer with their institutional offices of technology transfer to develop plans for addressing these requirements. Applicants are reminded that the grantee institution is required to disclose each subject invention to NIH within two months after the inventor discloses it in writing to grantee institutional personnel responsible for patent matters. The awarding Institute reserves the right to monitor awardee activity in this area to ascertain if patents or patent applications are adversely affecting the goals of this PA. WHERE TO SEND INQUIRIES We encourage your inquiries concerning this PA and welcome the opportunity to answer questions from potential applicants. Inquiries may fall into two areas: scientific/research and financial or grants management issues: o Direct your questions about scientific/research issues to: Anthony Carter, Ph.D. Division of Genetics and Developmental Biology National Institute of General Medical Sciences Building 45, Room 2AS-25R, MSC 6200 Bethesda, MD 20892-6200 Telephone: 301-594-0943 FAX: 301-480-2228 Email: o Direct inquiries about financial or grants management matters to: Ms. Marcia Cohn Grants Administration Branch National Institute of General Medical Sciences Building 45, Room 2AN50E, MSC 6200 Bethesda, MD 20892-6200 Telephone: 301-594-3918 FAX: 301-480-2554 Email: SUBMITTING AN APPLICATION Applications must be prepared using the PHS 398 research grant application instructions and forms (rev. 5/2001). Applications must have a Dun and Bradstreet (D&B) Data Universal Numbering System (DUNS) number as the Universal Identifier when applying for Federal grants or cooperative agreements. The DUNS number can be obtained by calling (866) 705-5711 or through the web site at The DUNS number should be entered on line 11 of the face page of the PHS 398 form. The PHS 398 is available at in an interactive format. For further assistance contact GrantsInfo, Telephone (301) 710-0267, Email: The title and number of this program announcement must be typed on line 2 of the face page of the application form and the YES box must be checked. SUPPLEMENTARY INSTRUCTIONS APPLICATION CONTENTS: In the Background section, the applicant should include a description of existing publicly available resources for the model organism being studied. The applicant should define how the proposal will enhance available resources and provide evidence of research community consultation and consensus regarding the potential value of the resource. In a brief section following the research plan, the applicant must describe plans to share research resources and to exercise intellectual property rights (see SPECIAL REQUIREMENTS). APPLICATION RECEIPT DATES: Applications submitted in response to this program announcement will be accepted at the standard application deadlines, which are available at Application deadlines are also indicated in the PHS 398 application kit. SENDING AN APPLICATION TO THE NIH: Submit a signed, typewritten original of the application, including the checklist, and five signed photocopies in one package to: Center for Scientific Review National Institutes of Health 6701 Rockledge Drive, Room 1040, MSC 7710 Bethesda, MD 20892-7710 Bethesda, MD 20817 (for express/courier service) APPLICATION PROCESSING: Applications must be mailed on or before the receipt dates described at The CSR will not accept any application in response to this PA that is essentially the same as one currently pending initial review unless the applicant withdraws the pending application. The CSR will not accept any application that is essentially the same as one already reviewed. This does not preclude the submission of a substantial revision of an unfunded version of an application already reviewed, but such application must include an Introduction addressing the previous critique. Although there is no immediate acknowledgement of the receipt of an application, applicants are generally notified of the review and funding assignment within 8 weeks. PEER REVIEW PROCESS Applications submitted for this PA will be assigned on the basis of established PHS referral guidelines. Appropriate scientific review groups convened in accordance with the standard NIH peer review procedures ( will evaluate applications for scientific and technical merit. As part of the initial merit review, all applications will: o Undergo a selection process in which only those applications deemed to have the highest scientific merit, generally the top half of applications under review, will be discussed and assigned a priority score o Receive a written critique o Receive a second level review by the National Advisory General Medical Sciences Council. REVIEW CRITERIA The goals of NIH-supported research are to advance our understanding of biological systems, improve the control of disease, and enhance health. In the written comments, reviewers will be asked to evaluate application in order to judge the likelihood that the proposed research will have a substantial impact on the pursuit of these goals. The scientific review group will address and consider each of the following criteria in assigning the application’s overall score, weighting them as appropriate for each application. o Significance o Approach o Innovation o Investigator o Environment The application does not need to be strong in all categories to be judged likely to have major scientific impact and thus deserve a high priority score. For example, an investigator may propose to carry out important work that by its nature is not innovative but is essential to move a field forward. SIGNIFICANCE: Does the proposed resource or technology development address an important problem or need? If the aims of the application are achieved, how will scientific knowledge be advanced? What will be the effect of this project on the concepts or methods that drive the field? Will this project enhance the usefulness of the model organism being studied? APPROACH: Are the conceptual framework, design, methods, and analyses adequately developed, well-integrated, and appropriate to the aims of the project? Does the applicant acknowledge potential problem areas and consider alternative tactics? INNOVATION: Does the project employ novel concepts, approaches or methods? INVESTIGATOR: Is the investigator appropriately trained and well suited to carry out this work? Is the work proposed appropriate to the experience level of the principal investigator and other researchers (if any)? ENVIRONMENT: Does the scientific environment in which the work will be done contribute to the probability of success? Do the proposed experiments take advantage of unique features of the scientific environment or employ useful collaborative arrangements? Is there evidence of institutional support? ADDITIONAL REVIEW CRITERION: In addition to the above criteria, the following item will be considered in the determination of scientific merit and the priority score: CARE AND USE OF VERTEBRATE ANIMALS IN RESEARCH: If vertebrate animals are to be used in the project, the five items described under Section f of the PHS 398 research grant application instructions (rev. 5/2001) will be assessed. ADDITIONAL REVIEW CONSIDERATIONS DATA SHARING: Reviewers will evaluate the reasonableness of the data sharing plan. However, reviewers will not factor the proposed data sharing plan into the determination of scientific merit or priority score. BUDGET: The reasonableness of the proposed budget and the requested period of support in relation to the proposed research. AWARD CRITERIA Applications submitted in response to a PA will compete for available funds with all other recommended applications. The following will be considered in making funding decisions: o Scientific merit of the proposed project as determined by peer review o Availability of funds o Relevance to program priorities REQUIRED FEDERAL CITATIONS PUBLIC ACCESS TO RESEARCH DATA THROUGH THE FREEDOM OF INFORMATION ACT: The Office of Management and Budget (OMB) Circular A-110 has been revised to provide public access to research data through the Freedom of Information Act (FOIA) under some circumstances. Data that are (1) first produced in a project that is supported in whole or in part with Federal funds and (2) cited publicly and officially by a Federal agency in support of an action that has the force and effect of law (i.e., a regulation) may be accessed through FOIA. It is important for applicants to understand the basic scope of this amendment. NIH has provided guidance at Applicants may wish to place data collected under this PA in a public archive, which can provide protections for the data and manage the distribution for an indefinite period of time. If so, the application should include a description of the archiving plan in the study design and include information about this in the budget justification section of the application. In addition, applicants should think about how to structure informed consent statements and other human subjects procedures given the potential for wider use of data collected under this award. URLs IN NIH GRANT APPLICATIONS OR APPENDICES: All applications and proposals for NIH funding must be self-contained within specified page limitations. Unless otherwise specified in an NIH solicitation, Internet addresses (URLs) should not be used to provide information necessary to the review because reviewers are under no obligation to view the Internet sites. Furthermore, we caution reviewers that their anonymity may be compromised when they directly access an Internet site. HEALTHY PEOPLE 2010: The Public Health Service (PHS) is committed to achieving the health promotion and disease prevention objectives of "Healthy People 2010," a PHS-led national activity for setting priority areas. This PA is related to one or more of the priority areas. Potential applicants may obtain a copy of "Healthy People 2010" at AUTHORITY AND REGULATIONS: This program is described in the Catalog of Federal Domestic Assistance at and is not subject to the intergovernmental review requirements of Executive Order 12372 or Health Systems Agency review. Awards are made under the authorization of Sections 301 and 405 of the Public Health Service Act as amended (42 USC 241 and 284) and under Federal Regulations 42 CFR 52 and 45 CFR Parts 74 and 92. All awards are subject to the terms and conditions, cost principles, and other considerations described in the NIH Grants Policy Statement. The NIH Grants Policy Statement can be found at The PHS strongly encourages all grant recipients to provide a smoke- free workplace and discourage the use of all tobacco products. In addition, Public Law 103-227, the Pro-Children Act of 1994, prohibits smoking in certain facilities (or in some cases, any portion of a facility) in which regular or routine education, library, day care, health care, or early childhood development services are provided to children. This is consistent with the PHS mission to protect and advance the physical and mental health of the American people.

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