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Xenbase | Current Xine

Xine Volume 9 - number 4, November 2009


Dear ,

Welcome to Xine, the source for Xenopus news and information. Here's
what's happening...
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Here are the draft letters of support mentioned in Mustafa and John's message.....

November 10, 2009

Dr. James Coulombe
Program Director, Developmental Genetics and Immunology
Developmental Biology, Genetics and Teratology Branch
Center for Developmental Biology and Pediatric Medicine
Eunice Kennedy Shriver National Institute of Child Health and Human Development
RM 4B01, MSC 7510
6100 Executive Blvd
Bethesda, MD 20892-7510
CoulombeJ@mail.nih.gov <mailto:CoulombeJ@mail.nih.gov>

Dear Dr. Coulombe:
    I would like to take this opportunity to write a letter of support for the Xenopus Resource Center (XRC) to be built in the Loeb building at the Marine Biological Laboratory.  The XRC has two main goals: 1) to generate, house, distribute transgenic lines of X. laevis and X. tropicalis and 2) to provide mini-courses to educate Xenopus researchers on the latest techniques across the broad disciplines that use Xenopus including cell, molecular and developmental biology.
    For my lab, the XRC would be particularly useful for providing transgenic lines ..  I would also be happy to participate in courses relating to cell/developmental biology and anticipate that members of my lab would greatly benefit from courses in cell/developmental biology..
    Currently, a proposal to fund the establishment of the XRC has been submitted to the NIH (1P40RR025867) and received an excellent Impact/Priority score (17) when reviewed in June.  The MBL has gone ahead and initiated plans to completely remodel the space in Loeb for the XRC which will be purpose built specifically for housing frogs.  Gary Borisy met us at this meeting and reiterated the MBL's commitment to this endeavor.  In addition, Josh Hamilton along with members of the Xenopus Community submitted a G20 application to facilitate this remodeling.  At our meeting last week at the MBL, we reiterated strong support for this endeavor, and we review here some of the key reasons why this proposed Center is such a high priority for our research community.
    First, there is an urgent need for a site to house and generate animal lines for the research community.  A centralized facility to house critical lines is a vital resource for us, as it is for researchers using other model systems (e.g. mouse, zebrafish and Drosophila).  The vast majority of Xenopus users employ Xenopus laevis for their scientific studies.  Their research will be greatly facilitated by ready access to existing or newly-developed transgenic lines.  However, because X. laevis has a long generation time, it is simply not practical for most X. laevis users to raise their own transgenic animals in sufficient numbers.  Therefore, there is a community-wide need for a stock center that can:  1) acquire the large number of transgenic lines that have already been generated, propagate these lines, and distribute them and 2) generate and distribute new transgenic lines that are needed by the Community.  The XRC funding proposed in 1P40RR025867 and the G20 application will provide the resources to do both.  Transgenic technologies are very inexpensive in Xenopus, and the XRC will have a majority of its space allocated to X. laevis for acquiring and propagating these lines.
    In addition to X. laevis, space in the XRC will be allocated to X. tropicalis as well, which will allow a large collection of X. tropicalis to be housed.  Due to its shorter generation time and diploid genome, X. tropicalis allows for genetic analysis in addition to the embryological and cell biological tools of X. laevis, adding a powerful new dimension to Xenopus research.  A large number of genetic lines (transgenic animals as well as mutants) are already available for this species and collecting and housing these animals is essential for developing this new direction for Xenopus research.  In addition, developing new lines including null mutations will be a critical resource for the Xenopus genetics community.
    It is worth noting that while a Xenopus stock center exists in the UK, it is essential for US investigators that a US Xenopus stock center be opened.  Shipping animals internationally is incredibly costly (recently an NIH-funded investigator requested a line from the UK stock centre only to discover a shipping cost in excess of $2000) and complex shipping regulations make routine shipments prohibitive.  The proposed US Xenopus stock center will house and consolidate the many lines available across the US and also capitalize on the lines in the UK stock center, and once established, the two facilities would provide a backup store of critical stocks and would coordinate the exchange of animals for US researchers.
    A third important function of the XRC is to develop a training core.  Technologies for applying Xenopus in biomedical research are advancing rapidly, in large part due to the investment made by the Trans-NIH Xenopus initiative.  In order for the entire spectrum of Xenopus investigators to capitalize on these advances in imaging, proteomics, cell extracts, transgenesis, genetic manipulation, in vitro assays, genomics, and animal husbandry, there is an urgent need for a Center that would serve as a site for researchers to learn new methods.  The XRC proposed in 1P40RR025867 and the G20 application would serve this function by offering both minicourses and opportunities for informal visits by individual researchers to learn cutting edge technology.  We strongly believe that it is this function which will make the Xenopus stock center a standout amongst other stock centers and leave a legacy for the next generation of Xenopus investigators.
    Finally, this is an exceptionally opportune time for such a Center to be established.  Not only is the need high, but there is an outstanding opportunity available to house the proposed XRC at the Marine Biological Laboratory at Woods Hole, a leading research institution and the site of many notable advanced research courses.  The Loeb building at the MBL is undergoing renovation, and the Director of the MBL, Gary Borisy, has enthusiastically offered the Xenopus research community a newly renovated space to house the proposed Center.  The MBL has also offered to provide a research laboratory and set up funds for the proposed Director of the Center.  In addition to providing the site for the XRC, the MBL has extensive resources that greatly augment the value of this particular location.  For example, the MBL has outstanding imaging and genomic facilities located proximally to the proposed XRC.  The Loeb building hosts a number of exceptional courses including the venerable physiology and embryology courses, both of which make extensive use of Xenopus.  The remodeling of Loeb will create impressive teaching facilities, which would be available for our training courses as part of the XRC mission.
    In summary, the Xenopus Community feels strongly that the time is right for establishing the XRC and that the MBL in Woods Hole, MA is the ideal place.  The need for the XRC is immediate and would benefit the entire Community of Xenopus researchers, facilitating their efforts to use Xenopus to better understand human health.
Sincerely,

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Dr. James Coulombe
Program Director, Developmental Genetics and Immunology
Developmental Biology, Genetics and Teratology Branch
Center for Developmental Biology and Pediatric Medicine
Eunice Kennedy Shriver National Institute of Child Health and Human Development
RM 4B01, MSC 7510
6100 Executive Blvd
Bethesda, MD 20892-7510
CoulombeJ@mail.nih.gov <mailto:CoulombeJ@mail.nih.gov>

Dear Dr. Coulombe,

I am writing in support of the P41 grant application for Xenbase, the Xenopus community database, which is currently being considered for funding by NICHD.

Xenbase is an essential resource to the entire biomedical community that uses Xenopus as a model system. Xenbase is an efficiently organized central database and community web site that gives me access to many diverse types of data including gene sequence, expression and function. It has become the first place I go to for all my bioinformatic analyses. It provides a number of unique search tools tailored to the Xenopus specific information that I need and allows me to efficiently navigate to many other web sites. Another important role of Xenbase is making Xenopus data visible to other model systems and contributing to both basic science and to understanding human health and development.

My colleagues and I wrote letters of support for the initial application, as this resource is an essential part of our daily research. A gap in funding of this critical resource would be a significant setback for the entire research community and researchers would waste an enormous amount of time constantly searching for information at many unlinked databases. In recent Xenopus community meetings there was a consensus that maintaining and expanding Xenabse is a top priority that will accelerate the research capability of the entire community. If funded the proposal to curate gene expression, gene function and proteomics data will make this an even more powerful resource.

I understand that the P41 application received an excellent score of 20 in recent review and is awaiting a funding decision. I very strongly urge NICHD to support this essential Xenopus community resource and to ensure that this excellent score is matched by strong funding.









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protocols of general utility to the research community. In order for
this to occur, please send any such contributions to the editor who
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If you wish to read Xine in html format and/or see back issues,
they are available at the following places

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http://blumberg.bio.uci.edu/xine/index.htm
static-xenbase/xine/xine.html
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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 �ber 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
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