**Critical Issues: Emerging and New Plant and Animal Pests and
Diseases**

***[FY 2008 Request for Applications #2]{.underline}***

**APPLICATION DEADLINE: June 18, 2008**

![](media/image1.png) **U.S. Department of Agriculture**

![](media/image2.png){width="0.47708333333333336in"
height="0.5923611111111111in"} **Cooperative State Research, Education,
and Extension Service**

**COOPERATIVE STATE RESEARCH, EDUCATION, AND EXTENSION SERVICE; U.S.
DEPARTMENT OF AGRICULTURE**

**CRITICAL ISSUES: EMERGING AND NEW PLANT AND ANIMAL PESTS AND
DISEASES**

**INITIAL ANNOUNCEMENT**

**CATALOG OF FEDERAL DOMESTIC ASSISTANCE:** This program is listed in
the Catalog of Federal Domestic Assistance under 10.200 (Special
Research Grants).

**DATES:** Applications must be received by close of business (COB) on
June 18, **2008** (5:00 p.m. Eastern Time). Applications received after
this deadline will normally not be considered for funding. Comments
regarding this request for applications (RFA) are requested within six
months from the issuance of this notice. Comments received after that
date will be considered to the extent practicable.

**STAKEHOLDER INPUT:** The Cooperative State Research, Education, and
Extension Service (CSREES) is requesting comments regarding this RFA
from any interested party. These comments will be considered in the
development of the next RFA for the program, if applicable, and will be
used to meet the requirements of section 103(c)(2) of the Agricultural
Research, Extension, and Education Reform Act of 1998 (7 U.S.C.
7613(c)(2)). This section requires the Secretary to solicit and consider
input on a current RFA from persons who conduct or use agricultural
research, education and extension for use in formulating future RFAs for
competitive programs. Written stakeholder comments on this RFA should be
submitted in accordance with the deadline set forth in the DATES portion
of this Notice.

Written stakeholder comments should be submitted by mail to: Policy,
Oversight, and Funds Management Staff; Office of Extramural Programs;
Cooperative State Research, Education, and Extension Service; USDA; STOP
2299; 1400 Independence Avenue, SW; Washington, DC 20250-2299; or via
e-mail to: <RFP-OEP@csrees.usda.gov> (This e-mail address is intended
only for receiving comments regarding this RFA and not requesting
information or forms.) In your comments, please state that you are
responding to the Critical Issues: Emerging and New Plant and Animal
Pests and Diseases RFA.

**EXECUTIVE SUMMARY:** CSREES announces the availability of grant funds
and requests applications for the Critical Issues program to perform
critical research activities related to time-critical, emerging plant
and animal pest and disease issues. The amount of funds available for
support of this particular solicitation is approximately \$500,000.
CSREES anticipates funding critical research projects in Johne's Disease
Vaccination Modeling and Porcine High Fever Disease (PHFD). The program
is designed to provide one-time seed funding to help initiate work
requiring immediate attention until other longer-term resources can be
secured to address the issue. CSREES intends to solicit applications
multiple times during FY 2008 and FY 2009 to address specific new or
emerging issues.

**Table of Contents**

[PART I---FUNDING OPPORTUNITY DESCRIPTION
4](#__RefHeading___Toc196116173)

[A. Legislative Authority and Background
4](#__RefHeading___Toc196116174)

[B. Purpose and Priorities 4](#__RefHeading___Toc196116175)

[PART II---AWARD INFORMATION 5](#__RefHeading___Toc196116176)

[A. Available Funding 5](#__RefHeading___Toc196116177)

[B. Types of Applications 5](#__RefHeading___Toc196116178)

[C. Project Types 5](#__RefHeading___Toc196116179)

[D. Scientific Peer Review 8](#__RefHeading___Toc196116180)

[PART III---ELIGIBILITY INFORMATION 9](#__RefHeading___Toc196116181)

[A. Eligible Applicants 9](#__RefHeading___Toc196116182)

[B. Cost Sharing or Matching 9](#__RefHeading___Toc196116183)

[PART IV---APPLICATION AND SUBMISSION INFORMATION
10](#__RefHeading___Toc196116184)

[A. Address to Request Application Package
10](#__RefHeading___Toc196116185)

[B. Content and Form of Application Submission
11](#__RefHeading___Toc196116186)

[C. Submission Dates and Times 13](#__RefHeading___Toc196116187)

[D. Funding Restrictions 14](#__RefHeading___Toc196116188)

[E. Other Submission Requirements 14](#__RefHeading___Toc196116189)

[PART V--- APPLICATION REVIEW REQUIREMENTS
15](#__RefHeading___Toc196116190)

[A. General 15](#__RefHeading___Toc196116191)

[B. Evaluation Criteria 15](#__RefHeading___Toc196116192)

[C. Conflicts of Interest and Confidentiality
16](#__RefHeading___Toc196116193)

[D. Organizational Management Information
16](#__RefHeading___Toc196116194)

[PART VI---AWARD ADMINISTRATION 17](#__RefHeading___Toc196116195)

[A. General 17](#__RefHeading___Toc196116196)

[B. Award Notice 17](#__RefHeading___Toc196116197)

[C. Administrative and National Policy Requirements
18](#__RefHeading___Toc196116198)

[D. Expected Program Outputs and Reporting Requirements
19](#__RefHeading___Toc196116199)

[PART VII---AGENCY CONTACT 20](#__RefHeading___Toc196116200)

[PART VIII---OTHER INFORMATION 21](#__RefHeading___Toc196116201)

[A. Access to Review Information 21](#__RefHeading___Toc196116202)

[B. Use of Funds; Changes 21](#__RefHeading___Toc196116203)

[C. Confidential Aspects of Applications and Awards
22](#__RefHeading___Toc196116204)

[D. Regulatory Information 22](#__RefHeading___Toc196116205)

[E. Definitions 22](#__RefHeading___Toc196116206)

[]{#__RefHeading___Toc196116173 .anchor}**PART I---FUNDING OPPORTUNITY
DESCRIPTION**

[]{#__RefHeading___Toc196116174 .anchor}A. Legislative Authority and
Background

The authority for this program is contained in Section 2(c)(1)(B) of the
Act of August 4, 1965, Public Law No. 89-106, as amended (7 U.S.C. 450i
(c)(1)(B)). This program supports critical research activities related
to time-critical, emerging plant and animal pest and disease issues.

[]{#__RefHeading___Toc196116175 .anchor}B. Purpose and Priorities

CSREES announces the availability of grant funds and requests
applications for the Critical Issues program to perform critical
research activities related to time-critical, emerging plant and animal
pest and disease issues. The program is designed to provide one-time
seed funding to help initiate work requiring immediate attention until
other longer-term resources can be secured to address the issue. CSREES
intends to solicit applications multiple times during FY 2008 and FY
2009 to address specific new or emerging issues. For this particular
solicitation, CSREES is requesting applications that address specific
aspects of the following issues:

-   **Johne's Disease Vaccination Modeling**

-   **Porcine High Fever Disease (PHFD)**

**Priority will be given to proposed projects that:**

1)  Are staffed by collaborative teams who document their experience in
    making optimal use of existing local, regional, and national
    capabilities and capacities; and

2)  Demonstrate their experience in conducting time-critical research.

This notice identifies the objectives for Critical Issues projects, the
eligibility criteria for projects and applicants, and the application
forms and associated instructions needed to apply for a Critical Issues
grant. CSREES additionally requests stakeholder input about emerging
plant and/or animal pests and diseases from any interested party for use
in the development of the next RFA for this program.

[]{#__RefHeading___Toc196116176 .anchor}PART II---AWARD INFORMATION

[]{#__RefHeading___Toc196116177 .anchor}A. Available Funding

There is no commitment by USDA to fund any particular application or to
make a specific number of awards. Approximately \$500,000 will be
available to support Critical Issues applications submitted in response
to this solicitation for project periods of up to 2 years with the
option for a 1 year no cost extension.

[]{#__RefHeading___Toc196116178 .anchor}B. Types of Applications

Only **new applications** are to be submitted in response to this RFA. A
**new application** is a project application that has not been
previously submitted to the Critical Issues Program. All new
applications will be reviewed competitively using the selection process
and evaluation criteria described in Part V---Application Review
Requirements.

[]{#__RefHeading___Toc196116179 .anchor}C. Project Types

**Johne's Disease Vaccination Modeling: Impacts on the Bovine
Tuberculosis (TB) Eradication and the Voluntary Bovine Johne's Disease
Control Programs -- CSREES anticipates funding up to 2 applications for
up to \$200,000 each**.

Current estimates indicate that up to 70 percent of U.S. dairy herds,
and a smaller percent of beef herds, are infected with Johne's disease.
The economic impact to the dairy industry varies widely but Animal and
Plant Health Inspection Service
([APHIS](http://www.aphis.usda.gov/animal_health/animal_diseases/johnes/index.shtml))
estimates are around \$200,000,000/year based on collaborative research
conducted by the [Centers for Epidemiology and Animal
Health](http://www.aphis.usda.gov/vs/ceah), USDA-APHIS, and the
Department of Clinical Sciences and Population Sciences, College of
Veterinary Medicine, University of Minnesota. Economic impact data from
this research, first published as "[Herd-level economic losses
associated with Johne\'s disease on US dairy
operations](http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TBK-47YY8RP-4&_user=6128582&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000052423&_version=1&_urlVersion=0&_userid=6128582&md5=a6b5d13327d3f74ded5e9616069317fb)"
[Preventive Veterinary
Medicine](http://www.sciencedirect.com/science/journal/01675877) /
[Volume 40, Issues
3-4](http://www.sciencedirect.com/science?_ob=PublicationURL&_tockey=%23TOC%235145%231999%23999599996%23392672%23FLA%23&_cdi=5145&_pubType=J&_auth=y&_acct=C000052423&_version=1&_urlVersion=0&_userid=6128582&md5=93ed4054d9b4bdd043e42e979a18f5b1),
11 June 1999, Pages 179-192, has been utilized in several subsequent
USDA publications and Fact Sheets on Johne's Disease.

There is a growing consensus among U.S. and international Johne's
disease subject matter experts that vaccination may be a cost-effective
way to control the spread of Johne's disease. However, there is
uncertainty with respect to the potential impacts Johne's vaccination
may have on the TB Eradication Program given the phylogenetic
relatedness of the two causative mycobacterial agents. The [Committee on
Johne's Disease of the United States Animal Health
Association](http://www.usaha.org/committees/jd/jd.shtml) (USAHA)
specifically identified this concern in its "Knowledge Gaps Report"
published in the Proceedings of the 109th Annual Meeting of the [United
States Animal Health Association](http://www.usaha.org/) (2005, p: 416).
The ability to take into account the impact of Johne's vaccination on
the TB Eradication Program, as well as the Voluntary Bovine Johne's
Disease Control Program, will be critical for the USDA -- APHIS to
respond to the growing stakeholder desire to allow unrestricted vaccine
use.

The [Voluntary Bovine Johne's Disease Control
Program](http://www.aphis.usda.gov/animal_health/animal_diseases/johnes/downloads/johnes-umr.pdf)
seeks tools that can be used to help predict whether widespread use of
Johne's vaccination would have a significant effect on the reduction of
Johne's disease infected animals/herds, and what the impacts of
vaccination would be on the [TB Eradication
Program](http://nsu.aphis.usda.gov/inventory/activity.faces?INVENTORY_NUMBER=163).
Furthermore, if there is potential negative impact on the TB Eradication
Program, the Voluntary Bovine Johne's Disease Control Program must be
able to evaluate alternative criteria for new vaccination products or to
develop new vaccine use protocols that would mitigate negative impacts
to the Program(s).

Critical Issues applications addressing Johne's Disease Vaccination
Modeling should propose to develop predictive model(s) based on
currently available information and data pertaining to a variety of
relevant parameters. Examples of such parameters are: 1) efficacy of the
approved killed vaccine, 2) Caudal Fold TB Test reactor rates and costs
with and without vaccination, 3) Comparative Cervical TB Test reactor
rates with and without vaccination, and 4) cross-reactivity rates with
respect to age of vaccine administration.

Optimally, cost-benefit model(s) developed under this RFA would be
flexible enough to enable comparison of a variety of current and
hypothetical Johne's disease vaccine management strategies. Model(s)
should enable predictive comparative analyses of the impact(s) on the
Voluntary Bovine Johne's Disease Control and TB Eradication Programs,
for example: 1) using the current licensed vaccine product only, 2)
using a new vaccine product that does interfere with TB and Johne's
disease testing but prevents or significantly reduces shedding, and 3)
using a new product that does not interfere with TB testing but may not
be 100% effective in reducing shedding or reducing clinical signs.

The principal research objective will be development of predictive tools
using, as appropriate, scientific principals and methodologies derived
from the fields of epidemiology, risk analysis, systems modeling,
veterinary microbiology and immunology, and agricultural economics.
Strategies for validation of model(s) should be included in the proposed
plan of work, and full characterization of limitations of the model(s)
should be provided. It is understood that the model development process
could lead to a first-generation tool that may or may not be
sufficiently robust to effectively guide decision-making with respect to
developing control program policies. In this regard, it is expected that
work products from the funded project may ultimately serve as
foundational or pilot studies that will in turn underpin future
development of a fully functional model.

Johne's Disease Vaccination Modeling applicants should assemble from the
literature, and from existing programs devoted to Johne's Disease
management and research (e.g., [Johne's Disease Integrated
Program](http://www.jdip.org/) (JDIP) and the Voluntary Bovine Johne's
Disease Control Program), relevant information, methodologies, and data
required to construct and validate a predictive model enabling
comparative cost-benefit analysis of implementation of candidate Johne's
vaccination strategies. Applications demonstrating evidence of
collaboration and communication with existing major programs and
initiatives within the at-large Johne's disease scientific community are
desirable. Additionally, applications for Critical Issues funding should
be innovative and inspire other sources of public and/or private funding
to enhance prospects for project success.

**Porcine High Fever Disease (PHFD) -- CSREES anticipates funding up to
two applications for up to \$200,000 each.**

Beginning in 2006, epidemics of severe swine disease, termed "Porcine
High Fever Disease (PHFD)", have been reported in Southeast Asia
([American Association of Swine
Veterinarians](http://www.aasv.org/shap/issues/v15n6/v15n6letter.htm)).
Data from research conducted by Chinese scientists Guang-Zhi Tong,
Yan-Jun Zhou, Xiao-Fang Hao, Zhi-Jun Tian, Tong-Qing An, Hua-Ji Qiu
resulted in the article "[Highly pathogenic porcine reproductive and
respiratory syndrome,
China](http://findarticles.com/p/articles/mi_m0GVK/is_9_13/ai_n19505903)",
and was first published online in [Emerging Infectious
Diseases](http://findarticles.com/p/articles/mi_m0GVK), [Sept,
2007](http://findarticles.com/p/articles/mi_m0GVK/is_9_13).
Investigations into these cases consistently identified porcine
reproductive and respiratory syndrome virus (PRRSV). This virus has been
implicated as the primary cause of these epidemics ([USDA -- APHIS:
Veterinary Services -- Centers for Epidemiology and Animal Health,
August
2007](http://www.aphis.usda.gov/vs/ceah/cei/taf/emergingdiseasenotice_files/prrschinavietnam2007.pdf)).

Although PRRSV is known to contribute to the disease, in the United
States it has not been associated with such severe diseases as have been
officially reported in China, Vietnam, and informally in other
neighboring countries. Applicants should propose to study tissue samples
recovered from a Vietnam epidemic of PHFD using animal infection models
and perform genetic analyses of the swine pathogen(s) identified. Due to
the potential for previously unidentified or unknown pathogens to have a
role in the PHFD syndrome, the live-animal infection work is to be done
in a laboratory that can ensure biosecurity, can prevent accidental
release of pathogens and can protect the U.S. swine herd from infection.

These studies are expected to provide insight into the contributing role
of PRRSV and other pathogens in the Southeast Asia epidemics and into
the epidemiology of PHFD. Insights gleaned from this research will
benefit the U.S. pork industry by providing advance knowledge about the
contribution of possible new virulence features of the PRRSV isolate
that has emerged in swine in SE Asia, but has yet to appear in North
America; and about other pathogens that may be identified in the course
of this research.

PHFD applicants should propose collaborative research activities
designed to determine the mechanisms of pathogenesis and the etiologic
agents responsible for the syndrome identified as PHFD. Using archived
or newly collected tissue samples recovered from foreign-source pigs
known to be positive for PHFD, studies should be conducted that focus
on 1) isolation of unknown disease agent(s) that could be interacting
and/or synergizing with PRRSV to cause PHFD, 2) descriptive, functional
and comparative molecular genetic analyses of PRRSV and other identified
potential disease agents, 3) development of a model of pathogenesis, and
4) assessment of the threat PHFD poses to the U.S. national porcine
population by evaluation of relative host strain susceptibility,
characterization of the role of environment in PHFD ecology, and
characterization of the dynamics of disease spread. Applicants must
describe specialized facilities and collaborations necessary for work
that may involve select agents or other high-consequence foreign animal
disease agents. **Investigators must stipulate that work will be carried
out in accordance with all relevant APHIS policies, regulations and
guidance pertaining to foreign animal disease agents.** For example,
plans for access to appropriate bio-safety level laboratory space,
technical staff trained in the safe use of highly infectious agents, and
collaborations with DHS and/or ARS scientists at the Foreign Animal
Disease Diagnostic Laboratory (FADDL) at Plum Island should be clearly
described in the application. Applications demonstrating assembly of
collaborative teams that make optimal use of existing local, regional,
and national capabilities and capacity are desirable. Additionally,
applications for Critical Issues funding should be innovative and
inspire other sources of public and/or private funding to enhance
prospects for project success.

[]{#__RefHeading___Toc196116180 .anchor}D. Scientific Peer Review

Subsection (c)(5) of the Competitive, Special, and Facilities Research
Grant Act, as amended (7 U.S.C. 450i(c)(5)) requires applicants to
conduct scientific peer review of their proposed research activities in
accordance with regulations promulgated by the Secretary prior to the
Secretary making a grant award under this authority.  Regulations
implementing this requirement are set forth in 7 CFR part 3400.20.  The
regulations impose the following requirements:

\(1\) Scientific peer review.  Prior to the award of a standard or
continuation grant by CSREES, any proposed project shall have undergone
a review arranged by the grantee.  For research projects, the review
arranged by the grantee must be a scientific peer review conducted in
accordance with 7 CFR 3400.21.

\(2\) Credible and independent review.  A review arranged by the grantee
must provide for a credible and independent assessment of the proposed
project.  A credible review is one that provides an appraisal of
technical quality and relevance sufficient for an organizational
representative to make an informed judgment as to whether the
applications is appropriate for submission for Federal support.  To
provide for an independent review, such review may include USDA
employees, but should not be conducted solely by USDA employees.

\(3\) Notice of completion and retention of records.  **A notice of
completion of the review shall be conveyed in writing to CSREES as part
of the Other Attachments (Field 11. of the R&R Other Project Information
Form).**  The written notice constitutes certification by the applicant
that a review in compliance with these regulations has occurred. 
Applicants are not required to submit results of the review to CSREES;
however, proper documentation of the review process and results should
be retained by the applicant.  **Please note: award funds cannot be
released until the Scientific Peer Review Certification is received**.

[]{#__RefHeading___Toc196116181 .anchor}PART III---ELIGIBILITY
INFORMATION

[]{#__RefHeading___Toc196116182 .anchor}A. Eligible Applicants

Applications may be submitted by State agricultural experiment stations,
land-grant colleges and universities, research foundations established
by land-grant colleges and universities, colleges and universities
receiving funds under the Act of October 10, 1962 (16 U.S.C. 582a et
seq.) McIntire-Stennis Cooperative Forestry Research Act, and accredited
schools or colleges of veterinary medicine for the purpose of
facilitating or expanding ongoing State-Federal food and agricultural
research programs that:

\(i\) promote excellence in research on a regional and national level;

\(ii\) promote the development of regional research centers;

\(iii\) promote the research partnership between the Department of
Agriculture, colleges and universities, research foundations, and State
agricultural experiment stations for regional research efforts; and

\(iv\) facilitate coordination and cooperation of research among States
through regional research grants.

Award recipients may subcontract to organizations not eligible to apply
provided such organizations are necessary for the conduct of the
project. An applicant's failure to meet an eligibility criterion by the
time of an application deadline will result in CSREES returning the
application without review or, even though an application may be
reviewed, will preclude CSREES from making an award.

[]{#__RefHeading___Toc196116183 .anchor}B. Cost Sharing or Matching

CSREES does not require matching support for this program and matching
resources will not be factored into the review process as evaluation
criteria.

[]{#__RefHeading___Toc196116184 .anchor}PART IV---APPLICATION AND
SUBMISSION INFORMATION

[]{#__RefHeading___Toc196116185 .anchor}A. Address to Request
Application Package

Only electronic applications may be submitted via Grants.gov to CSREES
in response to this RFA.

Prior to preparing an application, it is suggested that the PD/PI first
contact an Authorized Organizational Representative (AOR) to determine
if the organization is prepared to submit electronic applications
through Grant.gov. If the organization is not prepared, the AOR should
see <http://www.grants.gov/applicants/get_registered.jsp> for steps for
preparing to submit applications through Grants.gov.

The steps to access application materials are as follows:

1.  Download and install PureEdge Viewer, a small, free program that
    provides access to the grant application. See
    <http://www.grants.gov/help/help.jsp#pureedge>.

```{=html}
<!-- -->
```
2.  The application package must be obtained via Grants.gov, go to
    <http://www.grants.gov/>, click on "Apply for Grants" in the
    left-hand column, click on "**Step 1:**
    <https://apply.grants.gov/forms_apps_idx.html>**,"** enter the
    funding opportunity number **USDA-CSREES-OP-001054** in the
    appropriate box and click "Download Package." From the search
    results, click "Download" to access the application package.

> Contained within the application package is the
> "<http://www.csrees.usda.gov/funding/grant_forms/electronic_app_guide.pdf>"
>
> This Guide contains an introduction and general Grants.gov
> instructions, information about how to use a Grant Application Package
> in Grants.gov, and instructions on how to complete the application
> forms.
>
> **If assistance is needed to access the application package** (e.g.,
> downloading or navigating PureEdge forms, using PureEdge with a
> Macintosh computer), refer to resources available on the Grants.gov
> Web site first (<http://grants.gov/>). Grants.gov assistance is also
> available as follows:

-   Grants.gov customer support\
    Toll Free: 1-800-518-4726\
    Business Hours: M-F 7:00 am -- 9 pm Eastern Standard Time\
    Email: <support@grants.gov>

See <http://www.csrees.usda.gov/funding/electronic.html> for additional
resources for applying electronically.

[]{#__RefHeading___Toc196116186 .anchor}B. Content and Form of
Application Submission

::: Definition-Term
Electronic applications should be prepared following Part V and VI of
the document entitled "[A Guide for Preparation and Submission of CSREES
Applications via
Grants.gov](http://www.csrees.usda.gov/funding/grant_forms/electronic_app_guide.pdf)."
This guide is part of the corresponding application package (see Section
A. of this Part). The following is **additional information** needed in
order to prepare an application in response to this RFA. If there is
discrepancy between the two documents, the information contained in this
RFA is overriding.
:::

Note the attachment requirements (e.g., portable document format) in
Part III section 3. of the CSREES Grants.gov Application Guide available
with the Application Package at Grants.gov. **[Any APPLICATIONS
containing non-PDF documents will be at risk of being excluded from
CSREES review.]{.underline}** Partial applications will be excluded from
consideration. With documented prior approval, resubmitted applications
will be accepted until close of business (COB) on the closing date in
the RFA.

If you do not own PDF generating software, Grants.gov provides online
tools to assist applicants. Users will find PDF Conversion programs at
the following link:
[http://www.grants.gov/help/help.jsp#pdf_conversion_programs#pdf_conversion_programs](http://www.grants.gov/help/help.jsp#pdf_conversion_programs%23pdf_conversion_programs).

**1. [R&R Other Project Information Form]{.underline}**

Information related to the questions on this form is dealt with in
detail in Part V, 3. of the CSREES Grants.gov Application Guide.

a\. Project Summary/Abstract (Field 6. on the Form). The summary should
also include the relevance of the project to the goals of the Critical
Issues Program and to performing critical research activities related to
time-critical, emerging plant and animal pest and disease issues.

b\. Project Narrative (Field 7. on the Form).

PLEASE NOTE: The Project Narrative shall not exceed **25** pages of
written text and up to **5** additional pages for figures and tables.
This maximum **30** pages has been established to ensure fair and
equitable competition. The Project Narrative must include all of the
following:

\(1\) Objectives. Clear, concise, complete, and logically arranged
statement(s) of the specific aims of the proposed effort to the segment
of the time critical research activities contained in the application
must be included.

\(2\) Procedures. The procedures or methodology to be applied to the
proposed effort should be explicitly stated. This section should include
but not necessarily be limited to: (i) a description of the proposed
investigations and/or experiments in the sequence in which it is planned
to carry them out; (ii) techniques to be employed, including their
feasibility; (iii) kinds of results expected; (iv) means by which data
will be analyzed or interpreted; (v) pitfalls which might be
encountered; and (vi) limitations to proposed procedures.

\(3\) Justification. This section should include in‑depth information on
the following, when applicable: (i) estimates of the magnitude of the
problem and its relevance to ongoing State-Federal food and agricultural
research programs; (ii) importance of starting the work during the
current FY; and (iii) reasons for having the work performed by the
proposing institution; (iv) evidence of collaboration and experience in
making optimal use of existing local, regional, and national
capabilities and capacities; (v) level of innovation; and (vi)
demonstrated experience in conducting time-critical research.

\(4\) Literature Review. A summary of pertinent publications with
emphasis on their relationship to the effort being proposed should be
provided and should include all important and recent publications from
other institutions, as well as those from your institution. The
citations themselves should be accurate, complete, and written in an
acceptable journal format.

\(5\) Current Work. Current unpublished institutional activities to date
in the program area under which the application is being submitted
should be described.

\(6\) Project Timetable. The application should outline all important
phases as a function of time for the entire project period.

\(7\) Demonstrate assembly of collaborative teams that make optimal use
of existing local, regional, and national capabilities and capacity.

\(8\) Demonstrate experience in conducting time-critical research

\(9\) Additional Project Specific Information:

**[Information for Inclusion Specific to Johne's Disease Vaccination
Modeling Applications:]{.underline}**

a.  Clearly describe development of predictive model(s) based on
    currently available information and data pertaining to a variety of
    relevant parameters (as described in Part IIC).

b.  Describe level and method(s) of proposed collaboration and
    communication with existing major programs and initiatives within
    the at-large Johne's Disease scientific community.

**[Information for Inclusion Specific to PHFD
Applications:]{.underline}**

a.  Clearly describe proposed collaborative research activities designed
    to determine the mechanisms of pathogenesis and the etiologic agents
    responsible for the syndrome identified as PHFD (as described in
    Part IIC).

b.  Provide a comprehensive description of specialized facilities and
    collaborations necessary for work that may involve select agents or
    other high-consequence foreign animal disease agents.

c.  Describe research and oversight protocols to ensure that work will
    be carried out in accordance with all relevant APHIS policies,
    regulations and guidance pertaining to foreign animal disease
    agents.

**2. [R&R Senior/Key Person Profile (Expanded)]{.underline}**

Information related to the questions on this form is dealt with in
detail in Part V, 4. of the CSREES Grants.gov Application Guide.

Also, you must attach "Current and Pending Support" information. See
CSREES Grants.gov Application Guide, Part 4.3 for guidelines and
information format for each senior/key person identified. Note: Even if
no funding is currently reported under the "Active" section of this
attachment, you must still list information for this grant application
under the "Pending" section of this attachment for each senior/key
person identified.

**3. [R&R Personal Data]{.underline} --** As noted in Part V, 5., the
submission of this information

is voluntary and is not a precondition of award. **PLEASE DO NOT PROVIDE
THE SOCIAL SECURITY NUMBER OF PROJECT DIRECTOR / PRINCIPAL
INVESTIGATOR**.

::: Definition-Term
**4. [R&R Budget]{.underline}**
:::

Information related to the questions on this form is dealt with in
detail in Part V, 6. of the CSREES Grants.gov Application Guide.

5\. [Supplemental Information Form]{.underline}

Information related to the questions on this form is dealt with in
detail in Part VI, 1. of the CSREES Grants.gov Application Guide.

a\. Program Code (Field 2. on the Form). Enter the program code name
"**Critical Issues: Emerging and New Plant and Animal Pests and
Diseases**" and the program code "**NI**".

b\. Conflict of Interest List (Field 8. on the Form). A conflict of
interest list is required under this announcement.

[]{#__RefHeading___Toc196116187 .anchor}C. Submission Dates and Times

**Instructions for submitting an application are included in Part IV,
Section 1.9 of the CSREES Grants.gov Application Guide.**

Applications must be received by Grants.gov by COB on June 18, **2008**
(5:00 p.m. Eastern Time). Applications received after this deadline will
normally not be considered for funding.

Correspondence regarding submitted applications will be sent using
e-mail. Therefore, applicants are strongly encouraged to provide
accurate e-mail addresses, where designated, on the SF-424 R&R
Application for Federal Assistance.

If the AR has not received correspondence **from CSREES** regarding a
submitted application within 30 days of submission of the application,
please contact the Program Contact identified in Part VII of the RFA and
request the proposal number assigned to the application. **Failure to do
so may result in (for competitive programs) the application not being
considered for funding by the peer review panel.   Once the application
has been assigned a proposal number, this number should be cited on all
future correspondence.**

[]{#__RefHeading___Toc196116188 .anchor}D. Funding Restrictions

1\. Indirect Costs

Pursuant to Section 1473 of the National Agricultural Research,
Extension, and Teaching Policy Act of 1977, as amended, 7 U.S.C. 3319,
**indirect costs are not allowable costs under Section 2(c)(1)(B)
Special Grant projects,** and no funds will be approved for this
purpose. Further, costs that are a part of the institution\'s indirect
cost pool, (e.g., administrative or clerical salaries), may not be
reclassified as direct costs for the purpose of making them allowable.

2\. Building Construction or Renovation

No funds will be awarded for the renovation or refurbishment of research
spaces; the purchase or installation of fixed equipment in such spaces;
or for the planning, repair, rehabilitation, acquisition, or
construction of a building or facility.

3\. Tuition Remission

In accordance with Section 1473 of the National Agricultural Research,
Extension, and Teaching Policy Act of 1977 (91 Stat. 981), as amended,
**tuition remission is not an allowable cost under Section 2(c)(1)(B)
projects**, and no funds will be approved for this purpose.

[]{#__RefHeading___Toc196116189 .anchor}E. Other Submission Requirements

The applicant should follow the submission requirements noted in the
document entitled "A Guide for Preparation and Submission of CSREES
Applications via Grants.gov."

[]{#__RefHeading___Toc196116190 .anchor}PART V--- APPLICATION REVIEW
REQUIREMENTS

[]{#__RefHeading___Toc196116191 .anchor}A. General

Each application will be evaluated in a 2-part process. First, each
application will be screened to ensure that it meets the administrative
requirements as set forth in this RFA. Second, applications that meet
these requirements will be technically evaluated by a review panel.

Reviewers will be selected based upon training and experience in
relevant scientific, extension, or education fields, taking into account
the following factors: (a) The level of relevant formal scientific,
technical education, or extension experience of the individual, as well
as the extent to which an individual is engaged in relevant research,
education, or extension activities; (b) the need to include as reviewers
experts from various areas of specialization within relevant scientific,
education, or extension fields; (c) the need to include as reviewers
other experts (e.g., producers, range or forest managers/operators, and
consumers) who can assess relevance of the applications to targeted
audiences and to program needs; (d) the need to include as reviewers
experts from a variety of organizational types (e.g., colleges,
universities, industry, state and Federal agencies, private profit and
non-profit organizations) and geographic locations; (e) the need to
maintain a balanced composition of reviewers with regard to minority and
female representation and an equitable age distribution; and (f) the
need to include reviewers who can judge the effective usefulness to
producers and the general public of each application.

[]{#__RefHeading___Toc196116192 .anchor}B. Evaluation Criteria

The evaluation criteria and weights below will be used in reviewing
applications submitted in response to this RFA:

**[General Evaluation Criteria: (40 Points total)]{.underline}**

1.  Feasibility of attaining objectives (10 points);

2.  Relevance and importance of the proposed research to achieving the
    program objectives (as described in Part IIC) (15 points);

3.  Professional training and experience of key project personnel (5
    points);

4.  Adequacy of facilities and equipment (5 points)(NOTE: for PHFD
    applications, this 5points will be in addition to the consideration
    of Specific Criteria for PHFD Applications -- #2., as listed below);
    and

5.  Appropriateness of budget request to attaining project objectives (5
    points).

**[Specific Criteria for Johne's Disease Vaccination Modeling
Applications (60 Points total):]{.underline}**

1.  Technical merit of proposed predictive model(s) based on currently
    available information and data pertaining to a variety of relevant
    parameters (as described in Part IIC) (40 points).

2.  Clarity and quality of proposed collaboration and communication with
    existing major programs and initiatives within the at-large Johne's
    Disease scientific community (20 points).

**[Specific Criteria for PHFD Applications (60 Points
total):]{.underline}**

1.  Technical merit of proposed collaborative research activities
    designed to determine the mechanisms of pathogenesis and the
    etiologic agents responsible for the syndrome identified as PHFD (as
    described in Part IIC) (15 points).

2.  Capacity of proposed specialized facilities and collaborations to
    conduct work that may involve select agents or other
    high-consequence foreign animal disease agents (25 points).

3.  Adequacy of proposed research and oversight protocols to ensure that
    work will be carried out in accordance with all relevant APHIS
    policies, regulations and guidance pertaining to foreign animal
    disease agents (20 points).

[]{#__RefHeading___Toc196116193 .anchor}C. Conflicts of Interest and
Confidentiality

During the peer evaluation process, extreme care will be taken to
prevent any actual or perceived conflicts of interest that may impact
review or evaluation. For the purpose of determining conflicts of
interest, the academic and administrative autonomy of an institution
shall be determined by reference to the current Higher Education
Directory, published by Higher Education Publications, Inc., 6400
Arlington Boulevard, Suite 648, Falls Church, Virginia 22042. Phone:
(703) 532-2300. Web site: <http://www.hepinc.com/>.

Names of submitting institutions and individuals, as well as application
content and peer evaluations, will be kept confidential, except to those
involved in the review process, to the extent permitted by law. In
addition, the identities of peer reviewers will remain confidential
throughout the entire review process. Therefore, the names of the
reviewers will not be released to applicants.

[]{#__RefHeading___Toc196116194 .anchor}D. Organizational Management
Information

Specific management information relating to an applicant shall be
submitted on a one time basis, with updates on an as needed basis, as
part of the responsibility determination prior to the award of a grant
identified under this RFA, if such information has not been provided
previously under this or another CSREES program. CSREES will provide
copies of forms recommended for use in fulfilling these requirements as
part of the preaward process. Although an applicant may be eligible
based on its status as one of these entities, there are factors which
may exclude an applicant from receiving Federal financial and
nonfinancial assistance and benefits under this program (e.g., debarment
or suspension of an individual involved or a determination that an
applicant is not responsible based on submitted organizational
management information).

[]{#__RefHeading___Toc196116195 .anchor}PART VI---AWARD ADMINISTRATION

[]{#__RefHeading___Toc196116196 .anchor}A. General

Within the limit of funds available for such purpose, the awarding
official of CSREES shall make grants to those responsible, eligible
applicants whose applications are judged most meritorious under the
procedures set forth in this RFA. The date specified by the awarding
official of CSREES as the effective date of the grant shall be no later
than September 30 of the Federal fiscal year in which the project is
approved for support and funds are appropriated for such purpose, unless
otherwise permitted by law. It should be noted that the project need not
be initiated on the grant effective date, but as soon thereafter as
practical so that project goals may be attained within the funded
project period. All funds granted by CSREES under this RFA shall be
expended solely for the purpose for which the funds are granted in
accordance with the approved application and budget, the regulations,
the terms and conditions of the award, the applicable Federal cost
principles, and the Department\'s assistance regulations (parts 3015 and
3019 of 7 CFR).

[]{#__RefHeading___Toc196116197 .anchor}B. Award Notice

The award document will provide pertinent instructions and information
including, at a minimum, the following:

\(1\) Legal name and address of performing organization or institution
to which the Administrator has issued an award under the terms of this
request for applications;

\(2\) Title of project;

\(3\) Name(s) and institution(s) of PDs chosen to direct and control
approved activities;

\(4\) Identifying award number assigned by the Department;

\(5\) Project period, specifying the amount of time the Department
intends to support the project without requiring recompetition for
funds;

\(6\) Total amount of Departmental financial assistance approved by the
Administrator during the project period;

\(7\) Legal authority(ies) under which the award is issued;

\(8\) Appropriate Catalog of Federal Domestic Assistance (CFDA) number;

\(9\) Applicable award terms and conditions
<http://www.csrees.usda.gov/business/awards/awardterms.html> to view
CSREES award terms and conditions;

\(10\) Approved budget plan for categorizing allocable project funds to
accomplish the stated purpose of the award; and

\(11\) Other information or provisions deemed necessary by CSREES to
carry out its respective awarding activities or to accomplish the
purpose of a particular award.

[]{#__RefHeading___Toc196116198 .anchor}C. Administrative and National
Policy Requirements

Several Federal statutes and regulations apply to grant applications
considered for review and to project grants awarded under this program.
These include, but are not limited to:

7 CFR Part 1, subpart A**---**USDA implementation of the Freedom of
Information Act.

7 CFR Part 3**---**USDA implementation of OMB Circular No. A-129
regarding debt collection.

7 CFR Part 15, subpart A**---**USDA implementation of Title VI of the
Civil Rights Act of 1964, as amended.

7 CFR Part 331 and 9 CFR Part 121**---**USDA implementation of the
Agricultural Bioterrorism Protection Act of 2002.

7 CFR Part 3015**---**USDA Uniform Federal Assistance Regulations,
implementing OMB directives (i.e., OMB Circular Nos. A-21 and A-122, now
codified at 2 CFR Parts 220 and 230) and incorporating provisions of 31
U.S.C. 6301-6308 (formerly the Federal Grant and Cooperative Agreement
Act of 1977, Pub. L. No. 95-224), as well as general policy requirements
applicable to recipients of Departmental financial assistance.

7 CFR Part 3017**---**USDA implementation of Governmentwide Debarment
and Suspension (Nonprocurement) and 7 CFR Part 3021**---**Governmentwide
Requirements for Drug Free Workplace (Grants).

7 CFR Part 3018**---**USDA implementation of Restrictions on Lobbying.
Imposes prohibitions and requirements for disclosure and certification
related to lobbying on recipients of Federal contracts, grants,
cooperative agreements, and loans.

7 CFR Part 3019**---**USDA implementation of OMB Circular A-110, Uniform
Administrative Requirements for Grants and Other Agreements With
Institutions of Higher Education, Hospitals, and Other Nonprofit
Organizations.

7 CFR Part 3052**---**USDA implementation of OMB Circular No. A-133,
Audits of States, Local Governments, and Non profit Organizations.

7 CFR Part 3407**---**CSREES procedures to implement the National
Environmental Policy Act of 1969, as amended.

29 U.S.C. 794 (section 504, Rehabilitation Act of 1973) and 7 CFR Part
15b (USDA implementation of statute) **---**prohibiting discrimination
based upon physical or mental handicap in Federally assisted programs.

35 U.S.C. 200 et seq. **---**Bayh Dole Act, controlling allocation of
rights to inventions made by employees of small business firms and
domestic nonprofit organizations, including universities, in Federally
assisted programs (implementing regulations are contained in 37 CFR Part
401).

[]{#__RefHeading___Toc196116199 .anchor}D. Expected Program Outputs and
Reporting Requirements

Grantees are also required to submit initial project information and
annual and summary reports to CSREES\' Current Research Information
System (CRIS). The CRIS database contains narrative project information,
progress/impact statements, and final technical reports that are made
available to the public. For applications recommended for funding,
instructions on preparation and submission of project documentation
will be provided to the applicant by the agency contact. Documentation
must be submitted to CRIS before CSREES funds will be released. Project
reports will be requested by the CRIS office when required. For more
information about CRIS, visit the [USDA/Current Research Information
System](http://cris.csrees.usda.gov/) (<http://cris.csrees.usda.gov/>). 

[]{#__RefHeading___Toc196116200 .anchor}PART VII---AGENCY CONTACT

Applicants and other interested parties are encouraged to contact [Dr.
Gary B.
Sherman](http://www.csrees.usda.gov/about/AllUnits/staff_view.cfm?record_id=1680&CFID=6941711&CFTOKEN=23065061);
telephone: (202) 401 - 4952; fax: (202) 401 - 6156; e-mail:
<gsherman@csrees.usda.gov>; or [Dr. Peter
Johnson](http://www.csrees.usda.gov/about/AllUnits/staff_view.cfm?record_id=73);
telephone: (202) 401 - 1896; fax: (202) 205 - 3641; e-mail:
<pjohnson@csrees.usda.gov>.

[]{#__RefHeading___Toc196116201 .anchor}PART VIII---OTHER INFORMATION

[]{#__RefHeading___Toc196116202 .anchor}A. Access to Review Information

Copies of reviews, not including the identity of reviewers, and a
summary of the panel comments will be sent to the applicant PD after the
review process has been completed.

[]{#__RefHeading___Toc196116203 .anchor}B. Use of Funds; Changes

**1. [Delegation of Fiscal Responsibility]{.underline}**

Unless the terms and conditions of the award state otherwise, the
awardee may not in whole or in part delegate or transfer to another
person, institution, or organization the responsibility for use or
expenditure of award funds.

**2. [Changes in Project Plans]{.underline}**\
\
a. The permissible changes by the awardee, PD(s), or other key project
personnel in the approved project shall be limited to changes in
methodology, techniques, or other similar aspects of the project to
expedite achievement of the project\'s approved goals. If the awardee or
the PD(s) is uncertain as to whether a change complies with this
provision, the question must be referred to the Authorized Departmental
Officer (ADO) for a final determination. The ADO is the signatory of the
award document, not the program contact.

b\. Changes in approved goals or objectives shall be requested by the
awardee and approved in writing by the ADO prior to effecting such
changes. In no event shall requests for such changes be approved which
are outside the scope of the original approved project.

c\. Changes in approved project leadership or the replacement or
reassignment of other key project personnel shall be requested by the
awardee and approved in writing by the ADO prior to effecting such
changes.

d\. Transfers of actual performance of the substantive programmatic work
in whole or in part and provisions for payment of funds, whether or not
Federal funds are involved, shall be requested by the awardee and
approved in writing by the ADO prior to effecting such transfers, unless
prescribed otherwise in the terms and conditions of the award.

e\. The project period may be extended by CSREES without additional
financial support, for such additional period(s) as the ADO determines
may be necessary to complete or fulfill the purposes of an approved
project, but in no case shall the total project period exceed three
years. Any extension of time shall be conditioned upon prior request by
the awardee and approval in writing by the ADO, unless prescribed
otherwise in the terms and conditions of award.

f\. Changes in Approved Budget: Unless stated otherwise in the terms and
conditions of award, changes in an approved budget must be requested by
the awardee and approved in writing by the ADO prior to instituting such
changes if the revision will involve transfers or expenditures of
amounts requiring prior approval as set forth in the applicable Federal
cost principles, Departmental regulations, or award.

[]{#__RefHeading___Toc196116204 .anchor}C. Confidential Aspects of
Applications and Awards

When an application results in an award, it becomes a part of the record
of CSREES transactions, available to the public upon specific request.
Information that the Secretary determines to be of a confidential,
privileged, or proprietary nature will be held in confidence to the
extent permitted by law. Therefore, any information that the applicant
wishes to have considered as confidential, privileged, or proprietary
should be clearly marked within the application. The original copy of an
application that does not result in an award will be retained by the
Agency for a period of three years. Other copies will be destroyed. Such
an application will be released only with the consent of the applicant
or to the extent required by law. An application may be withdrawn at any
time prior to the final action thereon.

[]{#__RefHeading___Toc196116205 .anchor}D. Regulatory Information

For the reasons set forth in the final Rule related Notice to 7 CFR part
3015, subpart V (48 FR 29114, June 24, 1983), this program is excluded
from the scope of the Executive Order 12372 which requires
intergovernmental consultation with State and local officials. Under the
provisions of the Paperwork Reduction Act of 1995 (44 U.S.C. chapter
35), the collection of information requirements contained in this Notice
have been approved under OMB Document No. 0524-0039.

[]{#__RefHeading___Toc196116206 .anchor}E. Definitions

For the purpose of this program, the following definitions are
applicable:

For the purpose of this program, the following definitions are
applicable:

[Administrator]{.underline} means the Administrator of the Cooperative
State Research, Education, and Extension Service (CSREES) and any other
officer or employee of the Department to whom the authority involved is
delegated.

[Authorized departmental officer]{.underline} means the Secretary or any
employee of the Department who has the authority to issue or modify
grant instruments on behalf of the Secretary.

[Authorized representative]{.underline} means the president, director,
or chief executive officer or other designated official of the applicant
organization who has the authority to commit the resources of the
organization.

[Budget period]{.underline} means the interval of time (usually 12
months) into which the project period is divided for budgetary and
reporting purposes.

[Department or USDA]{.underline} means the United States Department of
Agriculture.

[Grant]{.underline} means the award by the Secretary of funds to an
eligible organization or individual to assist in meeting the costs of
conducting, for the benefit of the public, an identified project which
is intended and designed to accomplish the purpose of the program as
identified in these guidelines.

[Grantee]{.underline} means an organization designated in the grant
award document as the responsible legal entity to which a grant is
awarded.

[Peer review]{.underline} means an evaluation of a proposed project for
scientific or technical quality and relevance performed by experts with
the scientific knowledge and technical skills to conduct the proposed
work or to give expert advice on the merits of an application.\
\
[Prior approval]{.underline} means written approval evidencing prior
consent by an authorized departmental officer.

[Project]{.underline} means the particular activity within the scope of
the program supported by a grant award.

[Project director]{.underline} means the single individual designated in
the grant application and approved by the Secretary who is responsible
for the direction and management of the project.

[Project period]{.underline} means the period, as stated in the award
document, during which Federal sponsorship begins and ends.

[Research activity]{.underline} means a scientific investigation or
inquiry that results in the generation of knowledge.

[Secretary]{.underline} means the Secretary of Agriculture and any other
officer or employee of the Department to whom the authority involved is
delegated.