PROTEOMICS: DIABETES, OBESITY, AND ENDOCRINE, DIGESTIVE, KIDNEY, UROLOGIC, AND
HEMATOLOGIC DISEASES
RELEASE DATE: April 1, 2004
PA NUMBER: PA-04-081
March 2, 2006 (NOT-OD-06-046) Effective with the June 1, 2006 submission date,
all R03, R21, R33 and R34 applications must be submitted through Grants.gov using
the electronic SF424 (R&R) application. Accordingly, this funding opportunity
expires on the date indicated below. Replacement R01 (PA-06-184) and R21 (PA-06-185)
funding opportunity announcements have been issued for the submission date
of June 1, 2006 and submission dates thereafter.
See NOT-OD-06-048 for information on May 1, 2006 Submission Date for AIDS and
AIDS-related R03 and R21 Applications.
EXPIRATION DATE: March 2, 2006
Department of Health and Human Services (DHHS)
PARTICIPATING ORGANIZATION:
National Institutes of Health (NIH)
(http://www.nih.gov)
COMPONENT OF PARTICIPATING ORGANIZATION:
National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)
(http://www.niddk.nih.gov)
CATALOG OF FEDERAL DOMESTIC ASSISTANCE NUMBER(S): 93.847 and 93.848
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 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) encourages projects that advance research to
identify and quantitate protein expression patterns, post-translational
modification of proteins, and protein-protein interactions on cells, tissues,
organ systems to diabetes, obesity, endocrine and metabolic diseases,
nutritional function and diseases of the alimentary tract, exocrine pancreas,
liver, kidney, bladder and prostate and normal biological processes related
to the function of these systems. The development and improvement of
innovative proteomic technologies is also encouraged through their
application to relevant biological questions related to the pathophysiology
of endocrine glands, gastrointestinal tract, liver and kidney, bladder and
prostate.
RESEARCH OBJECTIVES
Background
High throughput DNA sequencing has changed biomedical research. The complete
sequence of the genome for more than 100 organisms and the nearly complete
sequence of many others, including the human, are giving a new vision to the
study of biological systems. It is, however, apparent that knowledge of the
genome alone is not sufficient for a complete understanding of complex
biological processes. The genome is the same in different cell types within an
organism and does not change with time while the proteome varies with time and
among different cell types. In view of recent large-scale data showing that
often there is a poor correlation between mRNA quantities and protein
quantities, we cannot limit gene expression studies to the RNA level but must
also investigate biological problems at the protein level. Despite the
significant limitations of using mRNA arrays for studying gene expression,
relatively few investigators have used proteomic approaches. Moreover, post-
translational modifications, regulation of protein function by proteolysis,
and composition of macromolecular complexes or organelles can only be
determined at the protein level, further emphasizing the importance of
studying the proteome.
Proteomic approaches have been successfully used for studying complex
biological problems and for the identification of disease markers. Recent
developments in proteomics indicate that the technologies available are
already sufficiently advanced to approach many biological questions relevant
to the NIDDK mandate. Some of these technologies include: two-dimensional gel
electrophoresis for profiling complex mixtures coupled to mass spectrometry or
other methods for protein identification; isotopically labeled reagents for
the comparison of two different biological states (e.g. disease versus
control) using mass spectrometry; protein or antibody arrays; yeast two-hybrid
systems, phage display or immunoprecipitation coupled to mass spectrometry for
studying protein-protein interactions; characterization of macromolecular
complexes using antibodies, DNA, RNA, or other molecules as bait followed by
identification by mass spectrometry; and computational methods for
structure/function prediction. None of the above technologies is capable of
analyzing the whole proteome at once. However, the study of a subset of the
proteome is feasible, and could be applied to study biological systems and
diseases relevant to NIDDK mission.
There is also a need to further improve the present technologies and develop
novel approaches for studying the proteome that are more sensitive and more
comprehensive. These technology developments would be of particular interest
when accomplished through projects directed at understanding or solving
problems related to organs and/or diseases relevant to the NIDDK mission.
Examples of research areas where the application of proteomics is of interest
include but are not limited to:
o Identification and validation of surrogate markers in bio-fluids (e.g.
plasma, serum, urine, bile, pancreatic and gastrointestinal fluids) or
tissues that correlate with stage, activity or rate of progression, or
complications of diseases, including diabetes and chronic liver diseases,
such as viral hepatitis.
o Identification of novel drug targets, therapeutic agents or diagnostic
tests.
o Elucidation of the molecular basis of normal and abnormal pathways involved
in disease pathogenesis, including signal transduction networks and cell
surface receptors, either in humans or models of diseases.
o Detection, quantification and functional characterization of subset of the
proteome (e.g. phosphoproteome).
o Elucidate the mechanisms of development, differentiation, regeneration and
repair of cells and tissues.
o Development of approaches to better define the functional status and/ or
mass of organs (endocrine glands, liver, pancreas, kidney and bladder) under
normal and pathological conditions.
o Elucidate mechanisms of absorption, transport and metabolism and
disposition of nutrients.
o Characterization of alterations of subsets of the plasma or organ-specific
proteome due to modification by drugs, complementary and alternative
medicines, or other interventions used to treat diseases or environmental
toxins.
o Study carbohydrate, lipid, and protein metabolism, particularly with
respect to diabetes , obesity and its alteration in chronic liver diseases
o Study nuclear receptors and their action.
o Development of computational or bioinformatic tools to analyze and/or
annotate the genome as it might apply to diseases relevant to NIDDK mission.
o Characterization of the mitochondrial proteome as it relates to energy
expenditure, obesity, diabetes and other diseases of interest to NIDDK.
The above examples are illustrative and are not intended to exclude other
disease oriented applications of proteomics to diseases of interest to NIDDK.
It is not the intent of this announcement to solicit clinical trials in
humans. However, costs of collection of samples (e.g. body fluids and
tissues) from clinical research studies can be part of the proposed project.
Research proposals that focus on individual proteins (as opposed to full or
partial proteome studies) will not be considered responsive to this PA.
MECHANISM(S) OF SUPPORT
This PA will use the NIH R01 and R21 award mechanisms. As an applicant, you
will be solely responsible for planning, directing, and executing the
proposed project.
This PA uses just-in-time concepts. It also uses the modular budgeting as
well as the non-modular budgeting formats (see
http://grants.nih.gov/grants/funding/modular/modular.htm). Specifically, if
you are submitting an application with direct costs in each year of $250,000
or less, use the modular budget format. Otherwise, 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
http://grants.nih.gov/grants/policy/nihgps_2001/part_i_1.htm.
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
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:
Salvatore Sechi, Ph.D.
Director, Proteomic Program
National Institute of Diabetes and Digestive and Kidney Diseases
6707 Democracy Blvd. Rm. 611
Bethesda, MD 20892-5460
Telephone: 301-594-8814
FAX: 301-480-2688
Email: ss24q@nih.gov
o Direct your questions about financial or grants management matters to:
Ms. Randi Freundlich
Grants Management Specialist
Division of Extramural Affairs
National Institute of Diabetes and Digestive and Kidney Diseases
6707 Democracy Boulevard, Room 724, MSC 5456
Bethesda, MD 20892-5456
Telephone: (301) 594-8825
FAX: (301) 480-3504
Email: rf160d@nih.gov
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 http://www.dunandbradstreet.com/. The DUNS number
should be entered on line 11 of the face page of the PHS 398 form. The PHS 398
is available at http://grants.nih.gov/grants/funding/phs398/phs398.html in an
interactive format. The title and number of this program announcement must be
typed on line 2 of the application form and the YES box must be checked.
For further assistance contact GrantsInfo, Telephone (301) 710-0267, Email:
GrantsInfo@nih.gov.
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.
APPLICATION RECEIPT DATES: Applications submitted in response to this program
announcement will be accepted at the standard application deadlines, which
are available at http://grants.nih.gov/grants/dates.htm. Application
deadlines are also indicated in the PHS 398 application kit.
SPECIFIC INSTRUCTIONS FOR MODULAR BUDGET GRANT APPLICATIONS: Applications
requesting up to $250,000 per year in direct costs must be submitted in a
modular budget grant format. The modular budget grant format simplifies the
preparation of the budget in these applications by limiting the level of
budgetary detail. Applicants request direct costs in $25,000 modules.
Section C of the research grant application instructions for the PHS 398
(rev. 5/2001) at http://grants.nih.gov/grants/funding/phs398/phs398.html
includes step-by-step guidance for preparing modular grants. Additional
information on modular grants is available at
http://grants.nih.gov/grants/funding/modular/modular.htm.
INSTRUCTIONS FOR R21 APPLICATIONS: This program announcement allows the
submission of R21 (Exploratory/Developmental Research Grant) applications.
R21 applications must adhere to the page and budgetary limitations described
in the trans-NIH R21 program announcement (PA03-107) available at:
http://grants.nih.gov/grants/guide/pa-files/PA-03-107.html.
SPECIFIC INSTRUCTIONS FOR APPLICATIONS REQUESTING $500,000 OR MORE PER YEAR:
Applications requesting $500,000 or more in direct costs for any year must
include a cover letter identifying the NIH staff member within one of NIH
institutes or centers who has agreed to accept assignment of the application.
Applicants requesting more than $500,000 must carry out the following steps:
1) Contact the IC program staff at least 6 weeks before submitting the
application, i.e., as you are developing plans for the study;
2) Obtain agreement from the IC staff that the IC will accept your
application for consideration for award; and,
3) Identify, in a cover letter sent with the application, the staff member
and IC who agreed to accept assignment of the application.
This policy applies to all investigator-initiated new (type 1), competing
continuation (type 2), competing supplement, or any amended or revised
version of these grant application types. Additional information on this
policy is available in the NIH Guide for Grants and Contracts, October 19,
2001 at http://grants.nih.gov/grants/guide/notice-files/NOT-OD-02-004.html.
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
http://grants.nih.gov/grants/funding/submissionschedule.htm. 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
(http://www.csr.nih.gov/refrev.htm) 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 an appropriate national advisory council
or board.
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 this study address an important problem? If the aims of
the application are achieved, how will scientific knowledge be advanced? What
will be the effect of these studies on the concepts or methods that drive
this field?
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?
Are the aims original and innovative? Does the project challenge existing
paradigms or develop new methodologies or technologies?
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?
PROTECTION OF HUMAN SUBJECTS FROM RESEARCH RISK: The involvement of human
subjects and protections from research risk relating to their participation
in the proposed research will be assessed. (See criteria included in the
section on Federal Citations, below).
http://www.hhs.gov/ohrp/humansubjects/guidance/45cfr46.htm
INCLUSION OF WOMEN, MINORITIES AND CHILDREN IN RESEARCH: The adequacy of
plans to include subjects from both genders, all racial and ethnic groups
(and subgroups), and children as appropriate for the scientific goals of the
research will be assessed. Plans for the recruitment and retention of
subjects will also be evaluated. (See Inclusion Criteria in the sections on
Federal Citations, below).
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
Sharing Research Data
Applicants requesting more than $500,000 in direct costs in any year of the
proposed research are expected to include a data sharing plan in their
application. The reasonableness of the data sharing plan or the rationale for
not sharing research data will be assessed by the reviewers. 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
HUMAN SUBJECTS PROTECTION: Federal regulations (45CFR46) require that
applications and proposals involving human subjects must be evaluated with
reference to the risks to the subjects, the adequacy of protection against
these risks, the potential benefits of the research to the subjects and
others, and the importance of the knowledge gained or to be gained.
http://www.hhs.gov/ohrp/humansubjects/guidance/45cfr46.htm
DATA AND SAFETY MONITORING PLAN: Data and safety monitoring is required for
all types of clinical trials, including physiologic, toxicity, and dose-
finding studies (phase I); efficacy studies (phase II), efficacy,
effectiveness and comparative trials (phase III). The establishment of data
and safety monitoring boards (DSMBs) is required for multi-site clinical
trials involving interventions that entail potential risk to the participants.
(NIH Policy for Data and Safety Monitoring, NIH Guide for Grants and
Contracts, June 12, 1998:
http://grants.nih.gov/grants/guide/notice-files/not98-084.html).
SHARING RESEARCH DATA: Starting with the October 1, 2003 receipt date,
investigators submitting an NIH application seeking $500,000 or more in
direct costs in any single year are expected to include a plan for data
sharing or state why this is not possible.
http://grants.nih.gov/grants/policy/data_sharing . Investigators should seek
guidance from their institutions, on issues related to institutional
policies, local IRB rules, as well as local, state and Federal laws and
regulations, including the Privacy Rule. Reviewers will consider the data
sharing plan but will not factor the plan into the determination of the
scientific merit or the priority score.
INCLUSION OF WOMEN AND MINORITIES IN CLINICAL RESEARCH: It is the policy of
the NIH that women and members of minority groups and their sub-populations
must be included in all NIH-supported clinical research projects unless a
clear and compelling justification is provided indicating that inclusion is
inappropriate with respect to the health of the subjects or the purpose of the
research. This policy results from the NIH Revitalization Act of 1993 (Section
492B of Public Law 103-43).
All investigators proposing clinical research should read the "NIH Guidelines
for Inclusion of Women and Minorities as Subjects in Clinical Research -
Amended, October, 2001," published in the NIH Guide for Grants and Contracts
on October 9, 2001
(http://grants.nih.gov/grants/guide/notice-files/NOT-OD-02-001.html);
a complete copy of the updated Guidelines are available at
http://grants.nih.gov/grants/funding/women_min/guidelines_amended_10_2001.htm.
The amended policy incorporates: the use of an NIH definition of clinical
research; updated racial and ethnic categories in compliance with the new OMB
standards; clarification of language governing NIH-defined Phase III clinical
trials consistent with the new PHS Form 398; and updated roles and
responsibilities of NIH staff and the extramural community. The policy
continues to require for all NIH-defined Phase III clinical trials that: a)
all applications or proposals and/or protocols must provide a description of
plans to conduct analyses, as appropriate, to address differences by
sex/gender and/or racial/ethnic groups, including subgroups if applicable;
and b) investigators must report annual accrual and progress in conducting
analyses, as appropriate, by sex/gender and/or racial/ethnic group
differences.
INCLUSION OF CHILDREN AS PARTICIPANTS IN RESEARCH INVOLVING HUMAN SUBJECTS:
The NIH maintains a policy that children (i.e., individuals under the age of
21) must be included in all human subjects research, conducted or supported
by the NIH, unless there are scientific and ethical reasons not to include
them. This policy applies to all initial (Type 1) applications submitted for
receipt dates after October 1, 1998.
All investigators proposing research involving human subjects should read the
"NIH Policy and Guidelines" on the inclusion of children as participants in
research involving human subjects that is available at
http://grants.nih.gov/grants/funding/children/children.htm.
REQUIRED EDUCATION ON THE PROTECTION OF HUMAN SUBJECT PARTICIPANTS: NIH
policy requires education on the protection of human subject participants for
all investigators submitting NIH proposals for research involving human
subjects. You will find this policy announcement in the NIH Guide for Grants
and Contracts Announcement, dated June 5, 2000, at
http://grants.nih.gov/grants/guide/notice-files/NOT-OD-00-039.html.
HUMAN EMBRYONIC STEM CELLS (hESC): Criteria for federal funding of research on
hESCs can be found at http://stemcells.nih.gov/index.asp and at
http://grants.nih.gov/grants/guide/notice-files/NOT-OD-02-005.html. Only
research using hESC lines that are registered in the NIH Human Embryonic Stem
Cell Registry will be eligible for Federal funding (see http://escr.nih.gov).
It is the responsibility of the applicant to provide, in the project
description and elsewhere in the application as appropriate, the official NIH
identifier(s)for the hESC line(s)to be used in the proposed research.
Applications that do not provide this information will be returned without
review.
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
http://grants.nih.gov/grants/policy/a110/a110_guidance_dec1999.htm.
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.
STANDARDS FOR PRIVACY OF INDIVIDUALLY IDENTIFIABLE HEALTH INFORMATION: The
Department of Health and Human Services (DHHS) issued final modification to
the Standards for Privacy of Individually Identifiable Health Information ,
the Privacy Rule, on August 14, 2002. The Privacy Rule is a federal
regulation under the Health Insurance Portability and Accountability Act
(HIPAA) of 1996 that governs the protection of individually identifiable
health information, and is administered and enforced by the DHHS Office for
Civil Rights (OCR). Those who must comply with the Privacy Rule (classified
under the Rule as covered entities ) must do so by April 14, 2003 (with the
exception of small health plans, which have an extra year to comply).
Decisions about applicability and implementation of the Privacy Rule reside
with the researcher and his/her institution. The OCR website
(http://www.hhs.gov/ocr/) provides information on the Privacy Rule, including
a complete Regulation Text and a set of decision tools on Am I a covered
entity? Information on the impact of the HIPAA Privacy Rule on NIH
processes involving the review, funding, and progress monitoring of grants,
cooperative agreements, and research contracts can be found at
http://grants.nih.gov/grants/guide/notice-files/NOT-OD-03-025.html.
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 http://www.healthypeople.gov/.
AUTHORITY AND REGULATIONS: This program is described in the Catalog of
Federal Domestic Assistance at http://www.cfda.gov/ 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
http://grants.nih.gov/grants/policy/policy.htm.
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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