Dear  Ciliate Researcher:

        A number of members of the Tetrahymena research community have
indicated that they would be happy if we submitted a proposal in
response to NIH's request for applications to build upon the genome
sequences of emerging model organisms. Drafts of the abstract and of
the specific aims are included below (feel free to comment on them).

        If you support this effort, we propose to submit a proposal for the
Feb. 1 deadline. An essential component of this program is
demonstration of widespread community involvement and support for the
effort. So, what we need from you to make this application as strong as
possible is at least the first item below, and hopefully both.

        As you can imagine, with a Feb.1 deadline, a rapid response will be
greatly
appreciated. We also need to know if anyone else is submitting a
proposal to the same program, since NIH has indicated that  it is very
important to demonstrate that the community is fully aware of all
proposals being submitted.

1) A letter indicating your enthusiastic support for the effort.

2) A brief description of how you would use genome-wide microarrays in
your work. This description should list your name and institution, a
title for the project, and an estimate of the number of whole-genome
arrays you would need.

Thanks for your cooperation.

Kathy Collins & Marty Gorovsky
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Abstract

Funds are requested in response to PA-040135 to enable genome wide
analysis of gene expression in the eukaryotic model organism
Tetrahymena thermophila using microarrays. T. thermophila is a widely
distributed,  easily grown,  genetically tractable freshwater ciliate
protozoan that is related to Apicomplexans,  a group made up
exclusively of parasitic protozoans that includes Plasmodium
falciparum, the cause of malaria. Data obtained using the resources
provided will be made publicly available via the recently established
Tetrahymena Genome Database (OR OTHER WEB BASED SYSTEM).  This resource
will greatly expand the usefulness of the recently sequenced
macronuclear genome of T. thermophila, which contains ~27,000 predicted
open reading frames, including many that are homologous to those of
humans, greatly facilitating the work of the Tetrahymena community and
making this model system more accessible and attractive to other
investigators.

A. Specific Aims

1. To develop a user-friendly, microarray system for genome-wide
analysis of gene expression by the community of scientists using the
eukaryotic model Tetrahymena thermophila.

2. To establish a web-based system where all Tetrahymena microarray
data supported by this proposal (and any other that community members
wish to submit) will be publicly available to anyone wishing to use it.

3. To provide baseline data for expression of all predicted Tetrahymena
open reading frames during growth, starvation and conjugation and to
assess the variability in gene expression that exists in different
inbred strains.

4. To partially defray the costs of genome wide microarray analyses in
order to encourage projects initiated by current and future members of
the research community using Tetrahymena.

5. When sufficient microarray data are available, to initiate
mechanisms that make available to Tetrahymena researchers a web-based
system that facilitates  cluster analyses of gene expression patterns
and preliminary genome-wide information about regulatory networks and
developmental pathways.