Targeted and conditional gene expression

Posted for Koichi Kawakami:

I would like to suggest a workshop “Targeted and conditional gene expression”. These days several groups developed various types of targeted or conditional gene expression systems in zebrafish by using Gal4-UAS, Cre-loxP, etc. Although these systems should be powerful for genetic studies, they all still have some weaknesses, for instance, mosaic expression, background, low efficiencies etc... The aim of this workshop is to present newly developed methods related to this issue and also unspoken disadvantages, and to discuss how we can improve these methods. If many of you think this topic is important, I will find and ask someone to organize this workshop (since I will probably too busy as an organizer).

regeneration

It would be interesting to have a workshop on regeneration studies in zebrafish. There could be a small number of talks from those looking at different organs (e.g. spinal cord, fins, heart, retina...). Also, there could be talks describing progress of technology that will move this field forward, such as new ablation technology, genetic screens, inducible ectopic gene expression, transplantation, etc. In thinking about this, though, there might well be enough interest and abstracts for the organizers to consider choosing Stem cells/Regeneration as a session topic. If so, many of the relevant topics could be included within several of the good ideas for workshops proposed by others (adult zebrafish work, targeted mutations, disease models, transplantation).
Ken Poss
Duke University

Live Imaging

Posted on behalf of Karuna Sampath:

I would like to suggest "Live Imaging" as a possible workshop topic.
Given that high resolution imaging in vivo is one of the biggest
strengths of zebrafish , this session could highlight some of the
significant advances that have come from using imaging approaches and
also show the applications of newer techniques like TIRF. I think
the community would benefit from such a session.

The Standardization of Husbandry in Zebrafish

I propose a workshop on the standardization of husbandry in zebrafish. Currently protocols for husbandry issues such as stocking densities, feeding, water quality control, breeding, fry rearing etc. appear to differ, sometimes widely, from institution to institution. These differences certainly may affect the efficiency and cost of research, and may in some instances influence the consistency and reproducibility of experiments. Further, the increased usage of the zebrafish in biomedical research is likely to prompt an increase in the rigor and complexity of regulatory oversight. These changes are imminent in the E.U., and are on certainly on the horizon in the U.S. and beyond. Given these and other, related issues, it would be beneficial for the zebrafish research community to begin discussions on how best to develop scientifically based husbandry protocols (best practices) that can be adopted by all current and future users of the model.

Carole Wilson

Fish Facility Manager, Zebrafish Group
Department of Anatomy and Developmental Biology
University College London, Gower Street, London WC1E 6BT
UK
Tel: +44 207 679 3338

ucgahar@ucl.ac.uk

Zebrafish in the Undergraduate Classroom

The same characteristics that make zebrafish a powerful system for basic research also make it excellent for giving undergraduate students hands-on experience with experimental science. As the field of zebrafish biology grows, there is an increasing number of researchers using zebrafish for undergraduate teaching. The goal of this workshop is to develop methods for sharing protocols, teaching tools, and ideas for using zebrafish in education.

At the last meeting in Madison this workshop gave an introduction to selected undergraduate zebrafish courses that have already been created, and discuss how ideas and protocols for using zebrafish in the classroom can be shared. Provide ideas for discussion topics or volunteer to present your experiences in undergraduate teaching. Additionally discussion on undergraduate research in zebrafish laboratories could be presented during this workshop. Any ideas on amount of discussion time, topics to be discussed, or volunteers to present are welcome!

Germ line development

I would like to propose a workshop on germ line development, which would also include maternal and paternal regulation of embryonic development. One possible format would be 7, 10-minute talks each with 5-minute discussion, followed by a 15-minute general discussion of the field. There are a growing number of us working in this area. Such a workshop would allow us to see where this field currently stands in the zebrafish as a whole, where it is going, and what are the stumbling blocks. The general discussion would include, for example, the techniques and tools needed to move studies specifically in this area more rapidly forward over the next 5 years and what major contributions zebrafish studies can make to this field more broadly in the future.

Mary Mullins
University of Pennsylvania
Dept. of Cell and Developmental Biology
1211 BRB II/III
421 Curie Blvd
Philadelphia, PA 19104-6058
USA
email: mullins@mail.med.upenn.edu

FGF signaling in Zebrafish development

I propose a workshop topic on FGF signaling. FGFs are important signaling molecules controlling many aspects of development and many labs study the roles of FGF activity. Several tools are available for the study of FGF signaling including a FGFR inhibitor SU5402. However, discussion about FGF signaling is generally very limited, mostly likely due to the redundancy and confusing nature of FGF activity. A workshop focusing on FGF signaling will hopefully bring more lively discussion about a very intriguing pathway.

Judith Neugebauer
Graduate Student
Neurobiology and Anatomy
University of Utah

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

****************************************************

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.


************************************************
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

**************************************
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

Morphogenesis workshop

I would like to propose a workshop on morphogenesis. I am particularly interested in early development/gastrulation but later evens such as organ morphogenesis could also be included. I envision both technical and conceptual aspects of morphogenesis being addressed. Possibilities include: in vivo vs. in vitro assays, methods/software/microscopy techniques, defining the open questions/burning issues in the field and how best to approach them.

Ashley Bruce
Assistant Professor
Department of Cell & Systems Biology
University of Toronto
25 Harbord Street, Room 615
Toronto, ON M5S 3G5

Tools for assessing infection and immune response

I propose a workshop on "Molecular tools for assessing infection and immune response". Such a workshop could focus on recently developed "lineage tracer" transgenic lines, antibodies and/or flow cytometry sorting strategies for identifying and purifying hematopoietic lineages. The workshop could also include the development of new pathogen models as well as recent advancements in established pathogens.

Jeff

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Jeffrey A. Yoder, Ph.D.
Assistant Professor
Department of Molecular Biomedical Sciences
College of Veterinary Medicine
North Carolina State University
4700 Hillsborough Street
Raleigh, NC 27606
E-mail: Jeff_Yoder@ncsu.edu
Internet: www4.ncsu.edu/~jayoder/

emerging Gene Knockout technology

I would propose a Zebrafish meeting Workshop on emerging Gene Knockout technology. My lab and at least two other labs are using engineered Zinc Finger Nucleases to perform targeted gene knock out and eventually gene knock-in in zebrafish, and it would be good to compare the various things we’ve tried, as well as other related technologies.

Regards,
Joe

*****
H. Joseph Yost, Ph.D.
Professor of Neurobiology & Anatomy
University of Utah School of Medicine
Eccles Institute of Human Genetics
Bldg. 533, Room 3160
15 North 2030 East
Salt Lake City, UT 84112-5330

Hematopoiesis in zebrafish

Type your suggestion for a workshop topic here.

I propose a workshop on hematopoiesis in the zebrafish. There have been a
number of papers published in high-profile journals (Nature, Immunity,
Development) in the last 1-2 years on the lineage relationships and genetic
regulations of hematopoiesis in the zebrafish. There have been novel
findings, new genetic models, and new hypotheses that may significantly
advance the field (both mouse and zebrafish). The different findings from
several groups may need to be reconciled as well.

Paul Liu
--
NIH
pliu@mail.nih.gov
http://www.genome.gov/Staff/Liu/