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Xenbase | Current Xine

Xine Volume 9 - number 2, September 2009



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


A request for letters of support from Enrique Amaya and Jacques Robert



Dear Colleagues,

We are looking for letters of support.

After several informal inquiries, it is apparent that one set of
reagents that are lacking and would be tremendously be useful for many
different types of studies in X. tropicalis, are monoclonal antibodies.
We (Enrique Amaya and myself) are planning to submit a proposal for the
September 30, 2009 deadline that mainly aims to develop of a platform to
generate monoclonal antibodies and monospecific single chain antibodies
(scFv-Abs) using novel technology based on the engineering cDNAs from
any gene of interest identified in the X. tropicalis genome sequence. We
would like also to generate X. tropicalis transgenic lines with cell
type specific fluorescence reporter gene expression.

Although our proposal will focus on the characterization of surface
markers of the myeloid lineage (e.g., macrophages, neutrophils), the
methodology, transgenic lines, cell lines, vectors and antibodies
obtained will be made available to the scientific community. Information
will be made accessible through a web site linked to Xenbase. In
addition, when the platform becomes fully operative, we plan to extend
more widely its use for other investigators. We envision this being done
by establishing collaborations with other researchers, or at least
recovering some of the cost of consumables and labor with interested
investigators. We also propose to establish an advisory committee
composed of internal and external scientific experts, which could help
us in selecting and prioritizing projects, as well as overseeing the
function of the resource. We will also keep connected with the
development of a Xenopus stock center in Woods Hole MA and that of the
established stock centre in Portsmouth, UK. Of course any additional
suggestions are very welcome.

Evidence for a wide interest in the development of such reagents and
resource would strengthen our proposal. Therefore, we need to obtain
letters of supports from interested colleagues. You can send the letters
directly to my email address (Jacques_robert@urmc.rochester.edu) as an
attached pdf. Below are some suggestions concerning the content of the
letters.

Suggestion for the content of a Letter of Support

You should start your letter by stating that you are writing to support
your colleagues' efforts in developing a monoclonal antibody generating
resource center for X. tropicalis. The title of our proposal is:
"Antibodies and transgenesis to study the myeloid lineages in X.
tropicalis" (PAR-09-240).

Your name, title and a brief description of your scientific interest,
including a brief paragraph describing your current position, your
accomplishments in your field and your support (especially if NIH). Any
information relevant regarding your credential with regard to the use of
Xenopus as a model system, would also be helpful.

You may then explain how such new methodologies and resulting reagents
and animals, may benefit your own research project. You may also mention
that, when the platform becomes operational, you would be interested to
suggest other candidate proteins for which generation of monoclonal
antibodies would be beneficial to the community. Thank you for your support,

Jacques ROBERT



Updated information on NCBI resources for Xenopus



The NCBI Xenopus Genome Resources page has links for both X. laevis and
X. tropicalis to NCBI resources as well as resources outside NCBI such
as Xenbase
<http://www.ncbi.nlm.nih.gov/projects/genome/guide/frog/>

The BLAST page for Xenopus has the taxonomy ID for X. tropicalis in the
URL but there are databases choices for both species
<http://www.ncbi.nlm.nih.gov/projects/genome/seq/BlastGen/BlastGen.cgi?ta>
xid=8364


Dear Colleagues,



As recently announced in Xine Volume 9 number 1, a group of Xenopus community representatives has begun to compile a series of recommendations for theDevelopment of Xenopus Resources, which are being summarized in a whitepaper.

Minutes of that meeting held on 6/26/09 at MBL Woods Hole have been posted on Xenbase for community review and input http://www.xenbase.org/other/static/xine/xrd.jsp

Please check this site periodically to see the draft and final versions of the white paper.

Best wishes

Aaron Zorn


Reminder - Deadlines coming up for PAR-09-240, 241, 242 "Genetic and Genomic Analysis of Xenopus.



The next deadline for these award mechanisms is September 30, 2009. See thePAR pages for more details.
http://grants.nih.gov/grants/guide/pa-files/PAR-09-240.html
http://grants.nih.gov/grants/guide/pa-files/PAR-09-241.html
http://grants.nih.gov/grants/guide/pa-files/PAR-09-242.html




Call for content



Xine could be used to disseminate information and
protocols of general utility to the research community. In order for
this to occur, please send any such contributions to the editor who
will include them in a future (or special) issue of Xine.


If you wish to read Xine in html format and/or see back issues,
they are available at the following places

http://blumberg-lab.bio.uci.edu/xine/index.htm
http://blumberg.bio.uci.edu/xine/index.htm
http://www.xenbase.org/xine/xine.html


Links to useful sources of information for Xenopus (in no particular order)



general interest and utility
<http://www.nih.gov/science/models/xenopus/> Trans NIH Xenopus
initiative
<http://tropicalis.berkeley.edu/home/> - Harland lab X. tropicalis site
<http://faculty.virginia.edu/xtropicalis/> - Grainger lab X. tropicalis site
<http://tropmap.biology.uh.edu/> - Amy Sater's X. tropicalis genetic map
<https://list.mail.virginia.edu/mailman/listinfo/troplist> - Information onthe
X. tropicalis listserver
<http://list.mail.virginia.edu/pipermail/troplist/> - Troplist archives.
Lots of good information here.
<http://www.xenbase.org/> - Peter Vize's Xenopus über database
<http://www.nimr.mrc.ac.uk/devbiol/zimmerman/> - Zimmerman Lab
X. tropicalis website, database of mutants

genomic resources
<http://xenopus.nibb.ac.jp/> - XDB at NIBB - Naoto Ueno's
X. laevis EST database <http://xgc.nci.nih.gov/> - Xenopus gene collection
<http://informatics.gurdon.cam.ac.uk/online/xt-fl-db.html> - full length
collection at the Gurdon Institute
<http://genome.jgi-psf.org/Xentr4/Xentr4.home.html> - JGI X. tropicalis
genome site with browser and other info
<http://www.dkfz-heidelberg.de/molecular_embryology/axeldb.htm>
AXELDB - Christof Niehrs' Xenopus database


Subscription information



I have constructed the Xine mailing list from serveral sources. As
always, if you are not on the list and wish to be, want to update your
e-mail address or would rather not receive it at all, please contact
Bruce Blumberg (mailto:blumberg@uci.edu).

Until next time,

Bruce

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