High throughput methods for behavioral video analysis

Automatic behavior studies offers new possibilities for phenotype characterization and pharmacology studies.

Audience : Researchers working on zebrafish and willing to analyze behavior by mean of imaging techniques.

This workshop will show a state of the art based on the past 4 years behavioral studies, focusing on Movement characterization (Locomotor activity), Behavioral stereotypes (C shape, S shape) and other Behavioral tests (Mirror test, T maze,Place preference test).

We will then discuss on new challenges for those methods. Especially focusing on High throughput applications : Larvae behavior analysis, Adult schooling analysis, Chronobiology and circadian rhythms, Group screening ...

Contact:

Yann CHOMIS

ViewPoint Life Sciences Inc.
2550 Bates St. Suite 404,
Montreal, QC H3S 1A7
Canada

Email : pub@viewpoint.fr

Phone :(514) 343 5003

Use of adult zebrafish

I would like to see a general workshop on use of adult zebrafish (either in conjunction with or separate from Disease Models, suggested by Steve and/or transplantations into adults, suggested by Jill). This might include one or more of the following: methods for fixation and processing of adults in whole or in part, histological methods, surgical manipulations, nerve crush (or similarly 'compromising' of other tissues) to analyze regeneration, drawing blood, testing effects of alternative housing arrangements, behavior...

Lara Hutson, PhD
Assistant Professor
Department of Biology
59 Lab Campus Drive
Williams College
Williamstown, MA 01267
office: (413) 597-4508
lab: (413) 597-3550
fax: (413) 597-3495

Disease Models

I would like to prose a workshop on disease models that may have a focus on developmental stages later than 3 dpf. For many organs, it is not until these later stages that they more closely resemble the adult form and/or begin to function in a more adult like manner. Further, these later stages have been more difficult to study because of the limitations of morpholinos. What kind of tools are available and what tools do we need (tissue specific KO etc.)? Tilling can be useful but, as is often the case, a gene can have an early developmental role that when lost alters subsequent development at these later stages.

steve

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Steven Farber Ph.D.
Carnegie Institution of Washington
Department of Embryology
3520 San Martin Drive
Baltimore, MD 21218
farber@ciwemb.edu
http://www.ciwemb.edu/labs/farber/index.php

Improving K-12 Science Education Using Zebrafish

I would like to propose a workshop on improving K-12 science education through the use of the zebrafish. This past year, the National Academy released a report, "Rising Above the Gathering Storm" that was the work of the Committee on Prospering in the Global Economy of the 21st Century. The 1st of 4 recommendations was to, "Increase America's talent pool by vastly improving K–12 science and mathematics education." This distinguished panel rightly concluded that the quality of life and standard of living in the US hinges on our ability to educate our young specifically in math and science. While this report was focused on the US economy, the issues still apply worldwide. There is clearly a growing movement that scientists need to care about the educational pipeline. Why is this relevant to a zebrafish meeting? Well, we have found that the same features that excite our research community about the benefits of using the zebrafish for our research, also excites children and interests them in science. Our efforts have been growing with Project BioEYES zebrafish units expanding across the country (over 10,000 kids have participated) and it is useful to hear what others our doing in this area. I think the workshop format is ideal for this type of discussion.


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Steven Farber Ph.D.
Carnegie Institution of Washington
Department of Embryology
3520 San Martin Drive
Baltimore, MD 21218
farber@ciwemb.edu
http://www.ciwemb.edu/labs/farber/index.php

Zebrafish transplantation methods, advances and challenges

I propose a workshop on advances and challenges in transplantation biology in zebrafish, emphasizing transplants into adult recipients, as opposed to embryonic and blastula transplants. This could encompass a wide range of transplantation issues including hematopoietic stem cell transplantation, tumor transplantation models, immunologic issues related to MHC-matching of donors and recipients (or lack thereof), quantitation of chimerism in engrafted recipients, immune suppression of recipients with drugs and/or radiation treatment, etc. The methods published to date have shown promise, but are not optimized. Our group (in Len Zon's lab) and others have made recent advances with our transplant methods, and I believe a community discussion would facilitate improved communication to disseminate the challenges and improvements.

Jill

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Jill de Jong, M.D., Ph.D.
Division of Hematology/Oncology
Children's Hospital Boston
300 Longwood Avenue, Karp 7
Boston, MA 02115
phone: 617-919-2077
jill.dejong@childrens.harvard.edu

Zebrafish Microarray Platforms

I would like to propose a workshop on zebrafish microarray
platforms. Microarray has been used to profile Gene
expressions for characterizing and studying genes that
control interesting biological phenotypes. We have primarily
been using Affymetrix Zebrafish Genome Array for studying
gene expression profiles in mutants and treated zebrafish.
As we know, this platform is outdated and covers about 50%
of zebrafish genes. We have worked with Sanger, UCSC, ZFIN,
and Nimblegen to design a next generation microarray chip
covering 37,177 transcripts including 12,694 alternative
transcript seqences. It is important to inform the community
about the strategies and tools we used to collect zebrafish
gene transcripts for the probe design and selection, the
informatic pipeline for analyzing data generated on this new
array, and results from experiments designed to access the
quality of the chip design. In addition, it is important to
discuss the gene annotation strategies that will expedite the
use of microarray technology. Agilent microarray platform is
used by the zf-model project in Europe. There are long-oligo
probes available from Compugen, MWG, and Operon for producing
spotted arrays. A cDNA platform has also been developed in
Singapore. This workshop will try to include information from
all platforms in presentations and discussions. Microarray
technology is complimentary to the next generation sequencing
technologies for analyzing gene transcription regulations,
which is a topic of the workshop titled as Use of High-
throughput Sequencing Approaches for Problems in Zebrafish
Biology.

Use of high-throuput sequencing approaches for problems in zebrafish biology

I would like to propose a workshop on the application of high-throughput sequencing technologies (i.e. 454, Solexa/Illumina, ABI) to problems in zebrafish biology. There are a wide variety of new possibilities that emerge with these high throughput sequencers that could be explored both as individual projects and community efforts. For example there is the Mouse Transcriptome Project done by Massively Parallel Signature Sequencing (MPSS) (see project here) that could be replicated in zebrafish using a platform superior to the one used for the mouse project. Possible uses for TILLING or cSNP detection, etc. could be discussed. Forum would be open to participants and possibly bringing in presentations from the main, commercially available, high-throughput sequencing platforms.

Shawn Burgess
Developmental Genomics Section
Genome Technology Branch
National Human Genome Research Institute
Bldg 50, Rm. 5537, MSC 8004
50 South Dr.
National Institutes of Health
Bethesda, MD 20892

ph: 301-594-8224
Fax: 301-496-0474
burgess@mail.nih.gov

http://genome.gov/staff/burgess