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Xine Volume 3 Issue 2

Xine Volume 3 Issue 2

Dear Colleagues:

Welcome to Xine, the source for Xenopus news and information. Here’s what’s happening…

From Nancy Papalopulu:

Xenopus tropicalis EST Clones

As part of the Xenopus tropicalis EST Project http://www.sanger.ac.uk/Projects/X_tropicalis/, the Sanger Institute has generated approximately 55,000 5' EST sequences from each of three X.tropicalis cDNA libraries:

X.tropicalis neurula cDNA library - TNeu
X.tropicalis gastrula cDNA library - TGas
X.tropicalis egg cDNA library - TEgg

These sequences can be searched using the Sanger's blast server or downloaded from the Sanger Institute ftp site. The clones can ordered from MRC-geneservice http://www.hgmp.mrc.ac.uk/geneservice/reagents/products/descriptions/XtropEST.shtml

From Steve Klein:

ANNOUNCEMENTS
1) Two Xenopus tropicalis BAC libraries are now available:
75 kb BAC http://www.chori.org/bacpac/ISB1.htm
175 kb BAC http://www.chori.org/bacpac/xenopus216.htm

2) There are now Full-Length sequences for about 1,500 laevis cDNAs in
GenBank. A separate website to search only these entries is under
construction (see question 3, below).

3) dbEST now lists over 260,000 laevis and over 165,000 tropicalis ESTs.
http://www.ncbi.nlm.nih.gov/dbEST/dbEST_summary.html

4) About 19,000 clusters were assembled at UniGene.
http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=Xl. The DDD tool on
the web site allows the comparison of transcript expression levels between
different libraries or combination of libraries.

QUESTIONS
1) Fifty Xenopus cDNA libraries are available at
http://image.llnl.gov/image/html/xenopuslib_info.shtml 44 are laevis
and 6 are trop. Not all can be used for FL sequencing; some are either
short or not very diverse. Sanger is doing 3 more tropicalis libraries,
but they will not sample all the possible tissues. Do we need more
libraries? Which stages, tissues, etc?

2) Full-Length cDNA Sequences
a) How many Xenopus genes are there?
b) What proportion of these should we have a Full-Length cDNA
sequence for?
c) What level of errors can be tolerated in these sequences?
Standard MGC protocol is to do 1 error/ 50,000 - 100,000 bases. Do you
need that level of accuracy, or is 1 error/ 1,000 bases okay? If it costs
less for the lower error rate, we could sequence more cDNAs for the same
money.

3) The NCI is building a Xenopus Website to allow you to analyze the
information obtained from Xenopus cDNA and genome sequences.
What tools do you want on this website? See the NCI's CGAP Website,
http://cgap.nci.nih.gov/Tools for examples of analytic and data mining
tools available for the human genome. Also let us know about other tools
that you may want. Pass this message on to others who may have an opinion.

4) A committee of Xenopus experts, the NCBI, NCI and NICHD is examining
the possibility of designing a Xenopus laevis Affymetrix oligo chip.
However, there may be problems due to the high polymorphism rate among
individuals of this out-bread population. The first step in the process
is to determine the extent of sequence similarity in a gene from
different individuals. Please send your data on full length laevis genes.
Are there any Xenopus population geneticists?

Send your answers to

Steve Klein (NICHD) KleinS@Exchange.NIH.GOV

and Daniela Gerhard. (NCI) gerhardd@mail.nih.gov

From Richard Harland:

Xenopus tropicalis BAC filters are now available from CHORI.

http://bacpac.chori.org/xenopus216.htm

AND

The call for requests to sequence Xenopus tropicalis BACs is posted on the JGI web site

at http://genome.jgi-psf.org/xenopus1/xenopus1.home.html

There will shortly be a meeting of the advisory board to consider the priorities for sequencing.

Following is a request for letters of support from Jacques Robert and Nicholas Cohen to establish a Xenopus stock collection for immunological research. As you may know, letters of support are critical to establish resources of the type. If this resource is something that you think may be useful to the community and your research, please contact Jacques.

Dear Colleagues,

Xenopus is clearly recognized as a unique nonmammalian model system for studying fundamental immunobiological questions. The recent closing of the world's primary Xenopus resource facility at the Basel Institute of Immunology in Switzerland, however, has made the preservation and further development of a widely available Xenopus collection for immunological research problematic. Currently, the Xenopus collection at the University of Rochester School of Medicine and Dentistry is the only one in the world with a large population of different inbred strains of X. laevis, isogenetic clones of laevis-gilli hybrids, and Xenopus subspecies.


Presently, this resource is basically dedicated to providing animals for our own research. If our facility is to serve a larger community of scientists, then its maintenance and future development needs extramural support in addition to that earmarked for our hypothesis-driven research programs. To this end, we are planning to submit an R24 Research Resources grant application to the NIH; NIAID has agreed to consider funding the program if a scientifically strong case can be made to do so. We have attached an RTF version of a prospectus of our plans for this facility that has been submitted to the NIH. If you can not open this attachment please let us know (actually please contact Jacques for the attachment).


The Xenopus facility we envision would not only maintain genetically defined animals, but would also maintain existing, and develop new, immunologically important reagents (e.g., monoclonal antibodies, tumor cell lines, cDNA etc) for Xenopus research. As such, we believe that the proposed facility would be of direct interest and benefit to our scientific colleagues in immunology as well as in other disciplines. As such, would be complementary to, rather than compete with, the NIH-supported Xenopus tropicalis project.


Our R24 application will be stronger if we can demonstrate that our proposed facility will benefit multiple NIH-funded investigators, especially those funded by NIAID. Please let us know your level of enthusiasm for this project. If you think that it would be of benefit to your current and/or future research activities, please indicate whether you would be willing to provide us with a letter of support. We will then get back to you with further details about the nature of your letter. We would also appreciate it if you would forward this email and attachment to other
colleagues who potentially might be interested in endorsing this project.


Thank you for your cooperation.

With best regards,

Jacques Robert, Ph.D. Jacques   robert@uhura.cc.rochester.edu    
Nicholas Cohen, Ph.D.


Jacques ROBERT, Ph. D.
Research Assistant Professor of Microbiology and Immunology
Department of Microbiology & Immunology
Box 672
University of Rochester
Medical Center
Rochester, NY 14642 USA

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Until next time.

Bruce