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Xine

Xine Volume 6  - number 2 Feb, 2006

Dear Colleagues:

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

An important notice about Xenopus gene nomenclature from Peter Vize

Dear Members of the Xenopus Community

We are seeking your immediate input on guidelines for Xenopus gene nomenclature. These guidelines will be applied to genes in the new Xenopus community database scheduled for release this summer/fall, and may also be used by other large scale projects such as the JGI trop genome and EST projects in Europe, Japan and the USA. A temporary set of guidelines based on the zebrafish nomenclature system has been used for the past year or so but it is time to forge our own before we start processing data for the community database and before JGI annotates the genome. This is looming and rapid feedback (this week?) is essential.

Your help in letting us know what you think about how genes should be named would be greatly appreciated. This will be relevant to your work as your genes will be renamed (although other names will also be stored) when entered into various databases if the guidelines the community adopts are not followed. A consistent gene naming convention will help us all and make cross-database and cross-species queries easier and more powerful.

If you can spare just a few minutes please complete the online survey at: http://www.xenbase.org/nomenclature_survey.html If you have more detailed comments or suggestions please forward them to pvize@ucalgary.ca

Many thanks in advance,

Peter

Information about Xenopus immune function from Larry Ruben

Recently, we have discovered something that might be of use to others working with Xenopus. Years ago, while studying immune suppressor function, we found that while helper function would not affect cells tht were genetically disparate, suppressor function would. Thus, using comparably immunized allo-thymic and splenic lymphocytes would allow us to monitor immune suppression, as counteracting helper function would not affect antibody production in the allo-combination in vitro. Recently, we have had difficulty reproducing the data on immune suppression. After some investigation, we found that no outbred animals are introduced into the stocks at either NASCO or Xenopus I. Thus, animals derived from their breedings over the years have become more closely related. When, we used lymphocytes from animals from NASCO with those from animals from Xenopus I, immune suppression was observable.

With good wishes,

Larry Ruben

On the lighter side (contributed by Sally Moody)

http://www.newyorker.com/talk/content/articles/060116ta_talk_paumgarten

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.

Links to useful sources of information for Xenopus (in no particular order)
Please let me know if something should be added.

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 site
https://list.mail.virginia.edu/mailman/listinfo/troplist - Information on the X. tropicalis listserver
http://www.xenbase.org/ - Peter Vize's Xenopus �ber database

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

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
static-xenbase/xine/xine.html

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 (blumberg@uci.edu).

Until next time.

Bruce