PROTEIN INTERACTIONS IN AUDITORY AND VESTIBULAR BIOLOGY 
 
RELEASE DATE:  June 21, 2004
 
RFA Number:  RFA-DC-04-003  

EXPIRATION DATE:  October 23, 2004

Department of Health and Human Services (DHHS)
 
PARTICIPATING ORGANIZATION:  
National Institutes of Health (NIH)
 (http://www.nih.gov)
 
COMPONENT OF PARTICIPATING ORGANIZATION: 
National Institute on Deafness and Other Communication Disorders (NIDCD) 
 (http://www.nidcd.nih.gov)

CATALOG OF FEDERAL DOMESTIC ASSISTANCE NUMBER(S): 93.173 
 
LETTER OF INTENT RECEIPT DATE: September 24, 2004 
APPLICATION RECEIPT DATE: October 22, 2004 
 
THIS RFA CONTAINS THE FOLLOWING INFORMATION

o Purpose of this RFA
o Research Objectives
o Mechanism(s) of Support 
o Funds Available
o Eligible Institutions
o Individuals Eligible to Become Principal Investigators
o Special Requirements
o Where to Send Inquiries
o Letter of Intent
o Submitting an Application
o Supplementary Instructions
o Peer Review Process
o Review Criteria
o Receipt and Review Schedule
o Award Criteria
o Required Federal Citations

PURPOSE OF THIS RFA 

The National Institute on Deafness and Other Communication Disorders 
(NIDCD) invites applications to study protein interactions involved in 
auditory and vestibular development. Previous decades using molecular 
biology approaches have provided a wealth of molecular tools to dissect 
complex protein interactions involved with numerous molecular pathways.  
While advances in gene identification and regulation have been made in 
the auditory/vestibular systems, understanding how the complex 
orchestration of specific signaling events translates to protein 
function remains elusive.  The availability of molecular technologies 
that allow specific protein targeting and tagging to address function 
provides new opportunities for protein analysis in auditory and 
vestibular function.  The purpose of this RFA is to initiate multi-
faceted approaches to understand protein function important in auditory 
and vestibular biology.

RESEARCH OBJECTIVES

The complex development of auditory and vestibular organs and their 
mechanosensory hair cells involves numerous genes and proteins as the 
molecular drivers for hearing and balance function. Detailed events 
spanning otic placode development have profited from gene and 
phenotypic characterization in powerful model systems such as mouse, 
chick, and zebrafish.  While critically valuable, analyzing targeted 
genetic mutants and mutagenized screens can take several years of 
characterization before forward approaches of interactive protein work 
can be initiated.  Numerous transcription factors and signaling 
molecules participating in otic and vestibular morphogenesis have been 
identified, but a critical gap remains in molecular studies that 
explore the interactive dynamics of these regulatory and signaling 
molecules. 

Protein studies, both in vitro and in vivo, have provided comprehensive 
approaches to identify critical binding partners, domain interactions, 
amino acid mutational effects, and functional oligomerization and 
phosphorylation processes.  These approaches typically encompass both 
binding and cellular protein localization assays, and allow direct 
assessment of individual protein (and domain) interactions with 
putative or unidentified interactive partners, associations which 
provide the connective atlas of cellular function.  Studies commonly 
involve the use of antibodies, and/or combination of both prokaryotic 
and eukaryotic recombinant protein fusion expression systems such as 
glutathione-S-transferase (GST), polyhistidine tags, Flag 
ocatapeptides, and green fluorescent protein (GFP), which can 
facilitate purified reconstitution assays, as well as resolution of 
protein crystal structure.  Even with the onset of powerful high 
throughput proteomics/genomics approaches, the resulting identification 
of protein regulatory networks will require validation using some 
aspect of these approaches.  

The goal of this RFA is to initiate comprehensive approaches using 
multiple molecular techniques to study regulatory and signaling 
proteins important in auditory and vestibular developmental biology.  
Information gained from these approaches will provide insight to 
specific protein regulatory networks important to auditory and 
vestibular function.  Applications using high-throughput proteomics 
approaches are not considered responsive and should apply under PA: 
PROTEOMICS IN AUDITORY DEVELOPMENTAL AND DISEASE PROCESSES 
(http://grants.nih.gov/grants/guide/pa-files/PA-03-151.html).  In 
addition, applications performing microbial/pathogen investigations are 
not considered responsive and are directed to consider the 
appropriateness of  PA: RESEARCH ON MICROBIAL BIOFILMS 
(http://grants.nih.gov/grants/guide/pa-files/PA-03-047.html), or PA: 
NOVEL APPROACHES TO STUDY POLYMICROBIAL DISEASES 
(http://grants.nih.gov/grants/guide/pa-files/PA-04-093.html).

It is anticipated that various combinations of the following examples 
would be proposed.  Studies to be funded in response to this RFA could 
include, but are not limited to:

o Use of auditory/vestibular protein(s) in bacterial or yeast two-
hybrid systems to detect putative protein interactions and 
candidate(s).

o Mutational analysis (single amino acid(s) or domain) of proteins in 
auditory and vestibular biology. 

o Use of purified reconstitution systems to assess protein function, 
either recombinant or natively purified, involved in 
auditory/vestibular biology.  

o Use of fluorescently tagged proteins (either as fusion proteins or 
protein conjugates; purified tagged or labeled proteins delivered using 
microinjection) to monitor in vivo intracellular 
expression/localization and function of auditory/vestibular proteins in 
relative cellular environments (cultured or in ovo).

o Use of single and 2-D SDS/PAGE analysis with auditory and vestibular 
protein assays.

o Use of labeled (radioactive, non-radioactive, quantum dots) proteins 
with in vitro transcription/translation assays to demonstrate binding 
associations of auditory and vestibular proteins.

o Co-precipitation and immunoprecipitations from both native and 
purified reconstitution systems, using various combinations of 
recombinant fusion proteins, such as GST, Myc, etc., immuno-recombinant 
technologies, native immunoreactive antibodies, and native proteins.

o Use of gene/protein knock down technologies, morpholinos or small 
interfering RNA (siRNA).

o Binding assays for determination of direct protein interaction, such 
as overlays, or other purified protein combination systems.

o Use of optical tweezers analyzing proteins important for 
auditory/vestibular function.

o Use of fluorescence resonance energy transfer (FRET) and fluorescence 
recovery after photobleach (FRAP) technologies studying 
auditory/vestibular protein interactions.

o Use of X-ray crystallographic methods to resolve structure of 
proteins important in auditory and vestibular biology.

MECHANISM OF SUPPORT
 
This RFA will use the NIH R01 award mechanism.  As an applicant you will 
be solely responsible for planning, directing, and executing the 
proposed project.  This RFA is a one-time solicitation.  Future 
unsolicited, competing-continuation applications based on this project 
will compete with all investigator-initiated applications and will be 
reviewed according to the customary peer review procedures. The 
anticipated award date is July/August 2005. Applications that are not 
funded in the competition described in this RFA may be resubmitted as 
NEW investigator-initiated applications using the standard receipt dates 
for NEW applications described in the instructions to the PHS 398 
application.   Investigators may submit only a single application for 
this RFA. 
 
This RFA 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_2003/NIHGPS_Part2.htm. 

FUNDS AVAILABLE 
 
The NIDCD intends to commit approximately $1.5 million in FY 05 to fund 
3 to 4 new grants in response to this RFA. An applicant may request a 
project period of up to 5 years and a budget for direct costs of up to 
$250,000 per year. Because the nature and scope of the proposed 
research will vary from application to application, it is anticipated 
that the size and duration of each award will also vary. Although the 
financial plans of the NIDCD provide support for this program, awards 
pursuant to this RFA are contingent upon the availability of funds and 
the receipt of a sufficient number of meritorious applications.  
 
ELIGIBLE INSTITUTIONS
 
An investigator may only submit a single application in response to 
this RFA.  You may submit an application 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 institutions/organizations
o Foreign institutions are not eligible to apply
 
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 

Applications must define the significance of the research to auditory 
and vestibular biology in a separate paragraph titled: Significance to 
Auditory and Vestibular Research.  The paragraph should scientifically 
justify the importance of the proposed experiments, and the value of 
the research to auditory and vestibular biology. Applications without 
this justification paragraph will be determined as non-responsive and 
returned without further consideration.  In addition, it is anticipated 
that successful applications will foster collaborative interactions 
between scientists with signal transduction expertise and with auditory 
and vestibular neurobiologists. 
 
WHERE TO SEND INQUIRIES

We encourage inquiries concerning this RFA and welcome the opportunity 
to answer questions from potential applicants.  Inquiries may fall into 
three areas:  scientific/research, peer review, and financial or grants 
management issues:

o Direct your questions about scientific/research issues to:

Nancy L. Freeman, Ph.D. 
Program Director 
National Institutes of Health 
National Institute on Deafness and Other Communication Disorders 
Executive Plaza South-400C 
6120 Executive Blvd. MSC-7180 
Bethesda, MD 20892-7180 
Tel: (301) 402-3458 
Fax: (301) 402-6251 
Email: FreemanN@mail.NIH.gov 

o Direct your questions about peer review issues to:

Chief, Scientific Review Branch
NIH/NIDCD
Division of Extramural Research
National Institute on Deafness and Other Communication Disorders
6120 Executive Boulevard, EPS Room 400-C, MSC 7180
Bethesda, MD  20892-7180
Rockville, MD  20852 (for express/courier service)
Telephone: (301) 496-8683
Fax: (301) 402-6250

o Direct your questions about financial or grants management matters 
to:

Chief, Grants Management Branch
NIH/NIDCD
Executive Plaza South, Room 400B
6120 Executive Boulevard, MSC-7180
Bethesda, MD 20892
Rockville, MD  20852  (express mail)
Telephone:  (301) 402-0909
FAX:  (301)402-1758
 
LETTER OF INTENT
 
Prospective applicants are strongly encouraged to submit a letter of 
intent that includes the following information:

o Descriptive title of the proposed research
o Name, address, and telephone number of the Principal Investigator
o Names of other key personnel 
o Participating institutions
o Number and title of this RFA 

Although a letter of intent is not required, is not binding, and does 
not enter into the review of a subsequent application, the information 
that it contains allows IC staff to estimate the potential review 
workload and plan the review.
 
The letter of intent is to be sent, either hard copy or electronic 
copy, by the date listed at the beginning of this document.  The letter 
of intent should be sent to:

Nancy L. Freeman, Ph.D. 
Program Director 
National Institutes of Health 
National Institute on Deafness and Other Communication Disorders 
Executive Plaza South-400C 
6120 Executive Blvd. MSC-7180 
Bethesda, MD 20892-7180 
Tel: (301) 402-3458 
Fax: (301) 402-6251 
Email: FreemanN@mail.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 document is 
available at http://grants.nih.gov/grants/funding/phs398/phs398.html in 
an interactive format.  For further assistance contact GrantsInfo, 
Telephone (301) 435-0714, Email: GrantsInfo@nih.gov. 

SPECIFIC INSTRUCTIONS FOR MODULAR GRANT APPLICATIONS: Applications 
requesting up to $250,000 per year in direct costs must be submitted in 
a modular grant format.  The modular 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.

USING THE RFA LABEL: The RFA label available in the PHS 398 (rev. 
5/2001) application form must be affixed to the bottom of the face page 
of the application.  Type the RFA number on the label.  Failure to use 
this label could result in delayed processing of the application such 
that it may not reach the review committee in time for review.  In 
addition, the RFA title and number must be typed on line 2 of the face 
page of the application form and the YES box must be marked. The RFA 
label is also available at: 
http://grants.nih.gov/grants/funding/phs398/labels.pdf.
 
SENDING AN APPLICATION TO THE NIH: Submit a signed, typewritten 
original of the application, including the Checklist, and three 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)
 
At the time of submission, two additional copies of the application and 
all copies of the appendix material must be sent to:
 
Chief, Scientific Review Branch
Division of Extramural Research
National Institute on Deafness and Other Communication Disorders
6120 Executive Boulevard, EPS Room 400-C, MSC 7180
Bethesda, MD  20892-7180
Rockville, MD  20852 (for express/courier service)
Telephone: (301) 496-8683
Fax: (301) 402-6250
 
APPLICATION PROCESSING: Applications must be received on or before the 
application receipt date listed in the heading of this RFA.  If an 
application is received after that date, it will be returned to the 
applicant without review. 

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.
 
The Center for Scientific Review (CSR) will not accept any application 
in response to this RFA that is essentially the same as one currently 
pending initial review, unless the applicant withdraws the pending 
application.  However, when a previously unfunded application, 
originally submitted as an investigator-initiated application, is to be 
submitted in response to an RFA, it is to be prepared as a NEW 
application.  That is, the application for the RFA must not include an 
Introduction describing the changes and improvements made, and the text 
must not be marked to indicate the changes from the previous unfunded 
version of the application.  

PEER REVIEW PROCESS  
 
Upon receipt, applications will be reviewed for completeness by the CSR 
and responsiveness by the NIDCD.  Incomplete and/or nonresponsive 
applications will not be reviewed.  

Applications that are complete and responsive to the RFA will be 
evaluated for scientific and technical merit by an appropriate peer 
review group convened by the NIDCD in accordance with the review 
criteria stated below.  As part of the initial merit review, all 
applications will:

o Undergo a process in which only those applications deemed to have the 
highest scientific merit, generally the top half of the applications 
under review, will be discussed and assigned a priority score
o Receive a written critique
o Receive a second level review by the NDCD National Advisory 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 the 
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?  

ADDITIONAL REVIEW CRITERIA: In addition to the above criteria, the 
following items will be considered in the determination of scientific 
merit and the priority score:

SIGNIFICANCE TO AUDITORY AND VESTIBULAR RESEARCH.  Does the project 
clearly detail the importance of the proposed experiments, and the 
value of the research to auditory and vestibular biology?

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).
 
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.  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.  
 
BUDGET:  The reasonableness of the proposed budget and the requested 
period of support in relation to the proposed research.

RECEIPT AND REVIEW SCHEDULE

Letter of Intent Receipt Date: September 24, 2004
Application Receipt Date: October 22, 2004
Peer Review Date: February/March 2005   
Council Review: May 2005
Earliest Anticipated Start Date: July/August 2005

AWARD CRITERIA

Award criteria that will be used to make award decisions include:

o Scientific merit (as determined by peer review)
o Availability of funds
o Programmatic priorities
 
REQUIRED FEDERAL CITATIONS 

ANIMAL WELFARE PROTECTION:  Recipients of PHS support for activities 
involving live, vertebrate animals must comply with PHS Policy on 
Humane Care and Use of Laboratory Animals 
(http://grants.nih.gov/grants/olaw/references/PHSPolicyLabAnimals.pdf), 
as mandated by the Health Research Extension Act of 1985 
(http://grants.nih.gov/grants/olaw/references/hrea1985.htm), and the 
USDA Animal Welfare Regulations 
(http://www.nal.usda.gov/awic/legislat/usdaleg1.htm), as applicable.

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: 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.

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 RFA 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 RFA 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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