2013 Xenopus PI Meeting Summary

Biomedical researchers from around the world came together to discuss community resource development.

Xenopus PI Meeting held at the Marine Biological Laboratory Woods Hole, MA USA
August 23-25, 2013

Objectives Prior to the Meeting:

There will be updates on the status of numerous Xenopus Resources including:

     Genome Sequencing
     Genome Annotation
     Transgenic Technologies
     Resources Centers
     Proteomics
     RNAseq
     Xenbase (Web Resources)

This will be a great opportunity to connect with other Xenopus researchers and gain valuable insight into emerging technologies that will push your research further.

There will in depth discussions on how to develop and exploit new resources to increase the influence of Xenopus.

Attendees will help define community priorities that will serve to expand the power of Xenopus as a model system.

Discussion Items at 2013 Xenopus PI Meeting Strategy Session (minutes as reported by Mustafa Khokha, Yale University):

White Paper Priorities -
         An important point to weave throughout the white paper:  Xenopus is an excellent sytem to model human disease

Immediate Needs -
         Renewal of NXR
         Renewal of Xenbase

Essential Resources -
         Genome Improvement
               Curation and Annotation of Gene Models - trops and laevis
         Improvement in Xenopus Genome - genome finishing, gap closure
               Functional characterization of Xenopus genomes - XenCODE
         Transgenic Lines
                Identify enhancers
                Employ modular expression system (like gal4-UAS)
                Generate Lines - tissue specific lines
         Antibodies - Llama antibody resource.  Develop for Xenopus
         Mutation Resource
         Generate Community requested knockouts using TALENs or CRISPr
               Opportunity to knockout Disease genes for Disease Modeling
               New Technologies for LOF - inducible LOF (temporal,spatial), Tissue Specific LOF
         Big Data to Knowledge
         Frogbook

Timeline for Xenopus White Paper - 2013 to early 2014
    November - December - DRAFT to circulate to Community
    Jan - Feb - Publish White Paper
    Institute Statements need to be updated as well
    Marko Horb and Aaron Zorn will coordinate writing of White Paper

Discussion Items:

1.  Xenopus needs to be portrayed as an outstanding model to study human diseases

2.  TALENs vs CRISPRs - genetic modification techniques are shown to work well in Xenopus
      Both technologies appear to be working highly efficiently
      Stock Center has designed its TALENs specifically to J strain of X. laevis
      CRISPr appears highly effective with human codon optimized CAS (bacteria didn't work)
      Ira Blitz has a positive control CRISP for X. tropicalis tyrosinase
      Mustafa Khokha/Enrique Amaya/Rob Grainger - has positive control TALEN for X. tropicalis tyrosinase
      Marko Horb has a positive control TALEN for J strain X. laevis tyrosinase
      Protocols need to be posted - please send to Xenbase

3.  Systematic Transgenic Effort

There is a strong and pressing need for additional transgenic lines for Xenopus.  Stock centers are happy and have capacity to both generate lines as well as accept lines for distribution.  Marko Horb will create a working group under the NXR to distribute information and coordinate development of new transgenic lines and technologies.

4.  Xenopus lavis gene nomenclature

Recent results of Xenopus laevis genome assembly and chromosome FISH/cytology reveal that Xenopus homeoalleles can be specifically assigned to particular chromosomes.  In the past, "A" and "B" alleles have been assigned arbitrarily but an opportunity is present to assign names based on chromosome position.  The community agreed that renaming the alleles based on chromosome location would be ideal.  However, an acceptable nomenclature needs to be defined.  The Xenopus laevis genome working group will propose a naming strategy and present this to the Gene Nomenclature Committee at Xenbase.  Publication of the X. laevis genome will provide an opportunity to reassign the allele names.

5.  Big Data to Knowledge

The genomic resources that are being developed for Xenopus are remarkable, temporal expression profiles, proteomics, ribosome profiling, epigenome maps, etc.  Xenopus is at the forefront of Big Data and should play a role in ways to integrate and share this data in ways that are innovative.  

The NIH recognizes the need to move Big Data to Knowledge and has issues notices: RFA-HG-13-009 and Not-HG-13-014

In addition, the NSF has issues interest in Biological Infrastructure.  "Over the past several years, a number of reports on cyberinfrastructure particularly relevant to biological research and biological infrastructure have been issued.  Many of these were supported by the National Science Foundation; others have been supported by other organizations. As an aid to the biological research community, we have compiled a listing of these reports. See http://www.nsf.gov/bio/pubs/bio_ci_workshops.htm  for a compendium posted 6/25/13."  Future meetings of the Xenopus Genome Steering Committee will discuss ways to integrate Xenopus genomics and proteomics data - please contact Mustafa Khokha (mustafa.khokha@yale.edu) if you are interested in participating.

6.  Xenopus Promotion - the frog is an excellent model organism for biomedical research

There were many ideas on how to promote Xenopus as a model system.  It was recognized that there is a lot more thet could be done.  Xenopus should be identified routinely as an excellent model for human disease.  

There were a number of additional ideas:
        A. the community should petition Homologene and NCBI blast to list Xenopus upfront
        B. researchers should promote Xenopus at their institutions via lab websites, PR departments, and local papers
        C. invite Xenopus researchers to give seminars
        D. update wikipedia with images and other information about Xenopus
        E. invite people to create YouTube videos about Xenopus, undergrads other lab members.

Click this link to see previous Xenopus Whitepapers (2011 & 2009)