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Xenbase | Xine

Xine Volume 8 - number 1 April 2008


_____________________________________________________________

Urgent request for support and input regarding a Xenopus stock
center


U.S. Xenopus Resource Center Proposal-your input needed!

Dear fellow Xenopus researchers,

An extraordinary opportunity has materialized to develop a
Xenopus Stock Center in the US.  In order to realize this
possibility, we need your input and support.

In the past few months the possibility of establishing a stock center
has taken on new life since the administration of the MBL has
endorsed plans to house the Stock Center at Woods Hole.  In order
to pursue that opportunity, we approached officials at the NIH who
expressed enthusiasm and have given the required permission to
apply for a P40 grant to establish such a center.  While not an
assurance that a proposal would be funded, any positive sign from
NIH in these times is encouraging.

In order to take advantage of this prospect, three of us (Richard
Harland, Mustafa Khokha and I) have begun to prepare a P40
application.  A primary aim of course would be to house stocks of
X. laevis and X. tropicalis, including providing healthy wildtype
animals for investigators.  In addition we would like to see this
center become a focus of intellectual activity for the Xenopus
community, including potentially a transgenic facility, where such
animals might be produced, a genetic resource, where mutagenized
animals would be available for both forward and reverse genetic
experiments, and to serve as a training facility where investigators
might learn to apply these new technical approaches/methods in
their own labs; the latter could involve a series of mini-courses.  At
present, many cell biologists use Xenopus laevis at Woods
Hole in the summer, much of this for cell cycle and cytoskeletal
work, and we envision this center as being able to support
increased use.   Also, the Embryology course at Woods Hole
introduces students to Xenopus and would synergize well with the
proposed center.  In addition, we envision a center in which
researchers would be encouraged to visit Woods Hole to undertake
their own experiments and share new developments.

A tentative plan for managing the proposed resource center has
been developed.  A steering committee has been put in place to
oversee the planning process which includes the three of us, Jim
Maller, Rebecca Heald, Chris Wylie and Kris Kroll.  We have
identified a potential director, Dr. Jonathan Henry, Professor of
Cell and Developmental Biology at the University of Illinois.  Jon
has a well-established research program examining lens
development and regeneration in Xenopus, and extensive
experience with both X. laevis and X. tropicalis.  In addition he has
a long-standing connection with Woods Hole which would be very
advantageous in setting up and managing such a facility.  Data
regarding various lines and other resources would be included in
Xenbase, which would be a major portal for information about the
center. Gary Borisy, Director of the MBL, enthusiastically
supports formation of the center and has committed appropriate
space and facilities.

We write today to announce this endeavor and to seek your input
regarding what you would like to see at the proposed center.
During early April, after we hear your responses, a survey will be
distributed to provide detailed data for the grant application
regarding what kinds of lines, facilities and programs should be in
the center, and as the grant deadline nears, letters of support will be
requested from the community.

At this juncture, please send your comments to us at the following
email address:  rmglab@virginia.edu.  Thoughtful and detailed
input and support from the research community will be required to
make this a successful proposal.

Rob Grainger
Richard Harland
Mustafa Khokha
___________________________________________________

Information about Xenopus microarrays


I am pleased to announce the commercial launch of the
GeneChip® Xenopus laevis Genome 2.0 Array
http://www.affymetrix.com/products/arrays/specific/xenopus_2.aff
x.  The Affymetrix GeneChip® Xenopus laevis Genome 2.0 Array
can be used to study the whole genome of Xenopus laevis on a
single array. The array is comprised of more than 32,400 probe
sets representing more than 29,900 X. laevis transcripts, and was
designed in close collaboration with the Xenopus research
community as part of the Affymetrix® GeneChip® Consortia
Program. Sequences used in the design of the array were selected
from the X. laevis UniGene build 69 (July 2006) and GenBank®
mRNAs (through September 12, 2006).

The GeneChip Xenopus laevis Genome 2.0 Array is designed
specifically to monitor gene expression in X. laevis, providing
significant utility in developmental studies, such as induction and
over-expression. The Xenopus laevis 2.0 Array complements the
GeneChip® Xenopus tropicalis Genome Array

http://www.affymetrix.com/products/arrays/specific/x_tropicalis.af
fx, which can be used to combine genetic approaches with the
established strengths of X. laevis.

ORDERING INFORMATION - Arrays now available

Part # 901214  GeneChip® Xenopus laevis Genome 2.0 Array
contains 2 arrays

Part # 901215  GeneChip® Xenopus laevis Genome 2.0 Array
contains 6 arrays

Part # 901216  GeneChip® Xenopus laevis Genome 2.0 Array
contains 30 arrays

Ricardo Mancebo, Ph.D.
Product Manager, Gene Expression Marketing
AFFYMETRIX, INC. |
ricardo_mancebo@affymetrix.com

_______________________________________________

X. tropicalis v2.0 chip


I am pleased to announce the commercial launch of the
GeneChip® Xenopus tropicalis Genome Array.  The new
GeneChip Xenopus tropicalis Genome Array is designed
specifically to monitor gene expression in Xenopus tropicalis, and
was created in close collaboration with many contributors from the
Xenopus Research Community through the Affymetrix
GeneChip® Consortia Program.  The array contains probes to
detect transcripts from X. tropicalis.

The array is comprised of over 58,000 probe sets representing over
51,000 X. tropicalis transcripts.

Sequences used in the design of the array were selected from the
Xenopus tropicalis UniGene database (Build 30, July 2006),
GenBank® mRNAs for Xenopus tropicalis (up to September 12,
2006), and predicted gene sets from both the DOE Joint Genome
Institute (Xentr4 transcripts, file creation date August 17, 2005,
download date May 25, 2006) and Ensembl (release 40, download
date May 2006).

Arrays now available

Part # 901100  GeneChip® Xenopus tropicalis Genome Array
contains 2 arrays

Part # 901101  GeneChip® Xenopus tropicalis Genome Array
contains 6 arrays

Part # 901102  GeneChip® Xenopus tropicalis Genome Array
contains 30 arrays

Sales Support Material

GeneChip Xenopus tropicalis Genome Array web page:

http://www.affymetrix.com/products/arrays/specific/x_tropicalis.af
fx

Xenopus tropicalis Genome Array - Support Materials:

http://www.affymetrix.com/support/technical/byproduct.affx?prod
uct=X_tropicalis

Sincerely,
Ricardo  Mancebo

___________________________________________________
From Mike Gilchrist

New X. tropicalis EST clustering available.

Version Xt7 with 1.22 million ESTs now accessible through the
Gurdon EST database:
http://informatics.gurdon.cam.ac.uk/online/xt-fl-db.html.

Includes all ESTs known to be sequenced to date.

Full-length clones are indicated as before, using an improved
algorithm. The alternative transcript algorithm has also been
significantly improved, and likely alternative transcripts are
elucidated for more highly expressed genes.

The new clustering will now be the default for external linking via
the 'current' mechanism.

Contact Mike Gilchrist (m.gilchrist@gurdon.cam.ac.uk) for more
information.

___________________________________________________

From Peter Vize


Database release, an update on genome annotation, a request for
your  help, and a free tee-shirt


The new Xenbase is now live and can be found at either
xenbase.org It has thousands of gene pages, a genome browser,
community and literature sections and more. If the new site does
not appear with these links try hitting your browser reload button
as the old site may be in cache.

About 2,200 genes have now been annotated by community
members for tropicalis genome release 4.1. The genes are all
named using the human gene nomenclature committee (HGNC)
terms, in response to community surveys we carried out last year.
The exact match between  the Xenopus and human gene symbols
allows us to easily identify human  orthologs, and from the human
records, to pull in data on congenital  diseases, mouse mutants and
much more. Each of the community  annotated genes is now
represented by a gene catalog page at Xenbase.  This page uses
symbol matching to pull in ortholog data from human,  mouse and
zebrafish databases and blast to pull in information on  Xenopus
laevis. If symbols don't match orthologs, OMIM records, mouse
mutants etc. are all missed.

Xenbase curators have gone over the annotated records and entered
an independent Xenbase record for each gene at the JGI. This
secondary annotation serves three purposes:
1. a quality control check
2. an update, as some HGNC names have changed since the
annotations were performed
3. approval of the gene symbol and name. approved names will
appear in NCBI's refseq and Gene records soon.

The original annotator's data is preserved and has not been
touched. We have an automated system that notifies us of new
annotations and we will keep up with additions. As they appear we
will run a secondary annotation on them and submit all confirmed
annotations to Refseq.

If you find a gene missing, please use the "suggest a new gene"
button (in the GENE section) and Xenbase staff will annotate it for
you and a gene page will appear fully populated within a week.

Now that the frog gene set has nice new names, many of which we
don't know, we need your help to give these 2,200 gene records
their old legacy names. This is critical so searches will work using
old names and also to allow automatic matching between the new
gene pages and gene names in the literature, which are mostly old
names. We cannot do this without your help as we simply do not
have the information needed. An example is the brachyury gene.
The new symbol for this is "t" but we all know it as Xbra or bra. If
we don't have Xbra and bra stored as synonyms searches

We have added a tool to the gene page that allows anyone with a
Xenbase account to add Xenopus synonyms, another term for an
old or alternative gene names. If you search for a gene by the old
name and don't find it, please dig a little deeper and when you do
find the record, click on the "add Xenopus synonym" link and add
the old name. Next time somebody looks for this gene, up it will
pop. An automatic system will also match your synonym to the
titles and abstracts stored in the literature database, so you can
jump from gene pages to papers and visa versa. Instructions are
provided once you click on the link and log in. If you have an
account but don't have a password the system should let you add
one, but if it doesn't email us and we will send a pw by return
email.

If you search for a gene symbol and find the right record, but the
symbol isn't visible this is because we are storing the synonym data
in a hidden place and probably means it is used as a synonym in
another organism. If the name you searched with isn't shown as a
Xenopus synonym please add it as one- even though the search
worked. We use only Xenopus names and synonyms for record to
record matching as we can't promote all of these ortholog names as
there are too many and lots are so short they will match dozens of
records and generate collisions.

If a gene has an old X name (Xgsc) please add this also and
include the X, plus if it has a "." or "-" name, like c-myc, once
again add this- a search for cmyc will not find c-myc. As with
anything going into a database it is very important that data entered
is correct. If in doubt, leave it out, as incorrect matches can be a lot
of work to sort out.

We are adding in situ data from the XDB and Axeldb databases
and this should be available from gene pages sometime this year.
Images of expression data from journals are also being added and
will start appearing in a few weeks.


The Xenbase Team

_______________________________________________

Don Brown has made his laboratory's microarray data directed
toward Xenopus laevis metamorphosis available for interested
researchers at the following link

http://www.ciwemb.edu/brownlab/index.html

__________________________________________________

12th International Xenopus Conference 2008


Don't forget, the *12th International Xenopus Conference* will be
held from *Monday, 8th, to Friday, 12th, September 2008*, at
*Leiwen/Trier* in the Mosel-Valley, Germany. The conference
hotel is located nearby the river Mosel in a beautiful landscape
being famous for good wines. A bus service will be organized to
Frankfurt-Main airport (2 h bus ride) and Frankfurt-Hahn (1 h bus
ride). Please note, that these two airports are located at quite
different places, although they share the name Frankfurt. Most
intercontinental flights are destined for Frankfurt-Main, the largest
airport in Germany. Frankfurt-Hahn (a former US military airport
in the Hunsrueck) is used by Ryanair (www.ryanair.com
<http://www.ryanair.com>), a very cheap airline serving various
destinations all over Europe.

The meeting web site is available at http://www.uni-
ulm.de/12thxenopus

Please note that the registration deadline is May 10th, 2008.
_________________________________________________________

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 on the
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

My Xenbase: [ Log-in / Register ]
version: [4.6.0]

Major funding for Xenbase is provided by the National Institute of Child Health and Human Development, grant P41 HD064556