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Xine Volume 4 issue 5 - December 2004

Xine Volume 4 issue 5 - December 2004

Dear Colleagues:

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

From Janet Heasman and Chris Wylie

Cell and Developmental Biology of Xenopus
APRIL 9-19, 2005

Instructors: Janet Heasman and Chris Wylie
Course Assistants: Bilge Birsoy, Jennifer Taylor and Matt Kofron

Xenopus is the leading vertebrate model for the study of gene function in development. The combination of lineage analysis, gene-knockout strategies, experimental manipulation of the embryo, and genomic/bioinformatic techniques, makes it ideal for studies on the molecular control of embryo patterning, morphogenesis and organogenesis. This course combines intensive laboratory training with daily lectures from recognized experts in the field. Students will learn both emerging technologies and classical techniques to study gene function in Xenopus development. An important element will be the informal interaction between students and course faculty.

Technologies to be covered will include: oocyte and embryo culture, lineage analysis and experimental manipulation of embryos, gain and loss of function analysis using mRNAs and antisense oligos, whole mount in situ hybridization, immunocytochemistry, RT-PCR, and genomic/bioinformatic techniques, preparation of transgenic embryos, use of egg extracts to study the cell cycle and use of Xenopus tropicalis for genetic analyses. Cell and Developmental Biology of Xenopus is designed for those new to the Xenopus field, as well as for those wanting a refresher course in the emerging technologies.

The course is open to investigators from all countries.

Lecturers will include: Chris Wylie, Janet Heasman, Stefano Piccolo, Ray Keller, Aaron Zorn, Kristen Kroll, Betsy Pownall, Matt Kofron, Paul Krieg and Hironori Funabiki.

From Amy Sater

A database of molecular markers for genetic and physical mapping in X. tropicalis is now available at

It includes 500 polymorphic markers representing over 100 scaffolds from JGI tropicalis genome Assembly 2.0, as well as ~300 additional markers. We will add additional markers regularly, and subsequent sets of markers will be distributed more evenly across scaffolds.

We would love to know how to improve our website; please direct feedback regarding the database, etc., to me (

Best wishes,

Amy Sater

From Lynn Schriml

Lynn Schriml at NCBI requests that members of the community send any information about mapped genes/markers to NCBI.

If you only have a small set of markers to submit to UniSTS, the best way
to do that is through the web submission form

Questions regarding these submissions can be directed to the STS person,
Wonhee Jang -

Larger submissions can be processed as one large batch file. Please inquire to Wonhee about the format for doing this.

Lynn also requests a base URL so that these markers could be linked back to your web site, if applicable.

From the Sanger X. tropicalis EST team

Dear Colleagues

An enlarged set of X. tropicalis cDNAs is now available, that were finished at the Sanger Institute. In this release 441 newly-finished sequences have been submitted to public databanks.

The full release note follows, and the files mentioned are available from the Sanger FTP site.

Best regards

Mike Croning, D.Phil. Informatics Team, Sanger Institute 01223 834244 x7282


Release date: 04/11/04

The Sanger Xenopus tropicalis EST/cDNA project are pleased to announce the public availability of an enlarged set of X. tropicalis cDNA sequences finished at the Sanger Institute.

Data are downloadable from:

File : accepted_X_tropicalis_cDNAs_04_11_04.fasta.gz Contents : 3404 cDNA sequences Increase : 441 seqs added to the 13/10/04 release File size : 1669787 bytes MD5 checksum: 2fc3685b98b2b92befd97de3bf19d999

The 3404 cDNA seqs that passed quality control (QC), and accepted by EMBL. This data should also be available from EMBL/GenBank.

In the file, '>' header lines have the format: '> clone_name accession.version'

And also:

File : all_X_tropicalis_cDNAs_04_11_04.fasta.gz Contents : 4115 cDNA sequences Increase : 546 seqs added to the 13/10/04 release File size : 1990618 bytes MD5 checksum: aa3c1ef2e77983854bbad7974e430ab3

All 4115 cDNA sequences finished to date, including the unsubmitted sequences, that did not pass QC.

In the file reason(s) for failure are indicated after the clone_name on '>' header lines. Firstly 'unsubmitted' appears in the place of the accession.version, followed by 'unidentified' and/or 'frameshifted'

Best regards

Mike Croning
D.Phil. Informatics Team
Sanger Institute 01223 834244 x7282

From Steve Klein:

Don't forget about the new Program Announcement from NIGMS that should be very useful for the Xenopus Community.
You can get the whole PA at
The major goal of the PA is to support research to enhance the usefulness of sequence information for newly emerging or developing model organisms for
which there are limited genomic resources. Objectives to be addressed in applications submitted for this PA include, but are not limited to, the
  • Improvements in tools for mining of data for genomes having unique composition or structure
  • Improved database management and integration with other databases (Requests for the maintenance of databases alone are not encouraged.)
  • Generation of comprehensive cDNA libraries
  • Development of microarray reagents and/or services
  • Improved methods for linking expression arrays with standard phenotypes or with specific biological or behavioral outcomes
  • Development of novel approaches for mutagenesis and for rapid identification and characterization of point mutations
  • Development of novel transposable element-based techniques for the generation of knockouts or other mutations
  • Improvements in gene transfer technology and in vectors for genomic manipulation
  • Generation of sets of gene knockouts or knock-downs.

Direct questions to:

Anthony Carter, Ph.D.
Division of Genetics and Developmental Biology
National Institute of General Medical Sciences

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Until next time.