Zebrafish News

The Sanger Institute has released the ninth zebrafish genome assembly, Zv9, on 22nd July 2010. This assembly comprises 1.41 Gbp in 4560 scaffolds. It was generated starting with 1.18 Gbp from 11,099 BAC clones ordered with SATMAP, a new high-density meiotic map. The resulting genome sequence was supplemented with a new whole genome shotgun assembly WGS31, based on a combination of Illumina and capillary reads from double-haploid Tuebingen individuals. More information can be found at http://www.sanger.ac.uk/Projects/D_rerio/Zv9_assembly_information.shtml and http://www.sanger.ac.uk/Projects/D_rerio/assembly_details.shtml.

Zv9 has been used to generate a pre-ensembl database available at http://pre.ensembl.org/Danio_rerio featuring sequence, automated feature annotation and first-pass gene models plus search and download facilities. A full Ensembl site, providing a gene build and comparative genomic and data mining tools, will be available in winter 2010/11.

Please send your questions/comments to zfish-help@sanger.ac.uk.

The NIH has issued two Notices in the NIH Guide clarifying that the existing PARs that support the development of genetic screens (PAR-08-138: Genetic Screens to Enhance Zebrafish Research (R01) ) and of tools for zebrafish research (http://grants.nih.gov/grants/guide/pa-files/PAR-08-139.html) will also accept relevant applications related to phenotyping of mutant lines generated through high-throughput mutagenesis efforts. Please read the Notices (http://grants.nih.gov/grants/guide/notice-files/NOT-HD-10-015.html and http://grants.nih.gov/grants/guide/notice-files/NOT-DK-10-009.html) carefully before submitting your Letter of Intent and application.

National Institutes of Health Program Announcements with Review (PAR-010-221, PAR-10-222) Biophysical and Biomechanical Aspects of Embryonic Development (RO1, R21)

The purpose of these announcements is to solicit applications designed to exploit innovative ideas for studying biophysical and mechanical processes contributing to embryonic development. An additional goal is to promote studies conducted in vivo.

Letter of Intent (non-binding): August 20, 2010

Application Receipt Date: September 20, 2010

For more information,
http://grants.nih.gov/grants/guide/pa-files/PAR-10-221.html
http://grants.nih.gov/grants/guide/pa-files/PAR-10-222.html

Questions may be directed to
Mahua Mukhopadhyay, Ph.D.
Developmental Biology, Genetics and Teratology Branch
Center for Developmental Biology and Perinatal Medicine
Eunice Kennedy Shriver National Institute of Child Health and Human Development
(NICHD)
Telephone: (301) 435-6886
Email: mukhopam@mail.nih.gov

Ensembl release 58 contains a new set of gene models using Illumina RNAseq data from 9 zebrafish tissues and developmental stages. Fragmented polyA+ RNA was paired end sequenced to read lengths of 37, 54 or 76 bases at the Wellcome Trust Sanger Institute as part of the Zebrafish Transcriptome Sequencing Project, European Read Archive ERP000016. Gene models have been automatically produced by an initial local alignment to Zv8 to identify exons, then read pair information was used to call adjacent exons and approximate transcripts were assembled. Reads were realigned to these transcripts with a splice model. Reads which splice relative to the genomic reference sequence defined canonical and non-canonical intron. All variants were called using the approximate transcripts and spliced read information and Ensembl displays the gene models with the most supporting reads. For further details see

http://www.ensembl.org/info/docs/genebuild/zebrafish_rnaseq_annotation.html

http://ensembl.blogspot.com/2010/06/zebrafish-rna-seq-gene-models.html

GBrowse at ZFIN

The zebrafish genomic sequence and annotated data can now be explored at ZFIN using the Generic Genome Browser, or GBrowse. GBrowse at ZFIN hosts the Sanger Institute's genome assembly, based on fully sequenced BAC and PAC clones from the Tuebingen strain with Vega gene and transcript annotation. The data in the tracks show genome annotation, including the position of genes on the linkage groups, alternatively spliced transcripts, BACs used as assembly components, and genes that have expression and/or phenotype data stored in ZFIN.

ZFIN will continue to add tracks to GBrowse incrementally, based on availability of data and community interest.

GBrowse at ZFIN can be launched by clicking on the GBrowse link on the ZFIN home page (http://zfin.org) or directly at http://zfin.org/genome-browser . GBrowse can also be accessed by clicking on the image on ZFIN transcript pages, and on assembly BAC pages. A link to a GBrowse tutorial from Open Helix is available on the ZFIN GBrowse page.

The process of literature curation is described in Hirschman, et al., A MOD(ern) perspective on literature curation, Mol Genet Genomics (2010), written by four curators from SGD (The Saccharomyces Genome Database), TAIR (The Arabidopsis Information Resource), ZFIN (The Zebrafish Information Network), and MGI (Mouse Genome Informatics). This perspective discusses how papers are identified and prioritized for curation, some of the challenges MOD curators face, and ways in which researchers and publishers can support and facilitate the work of curators.

ZFIN will experience periods of downtime next Saturday, March 20. Interruptions in service can be expected between the hours of 2 pm and 10 pm, PST. We apologize for the inconvenience.

The Sanger Institute has released a Vega update on the 17th of December 2009. The Vega database contains finished clone sequence with manual annotation, placed on chromosomes according to data from the physical mapping project. The current release features 10,755 clones with 15,761 manually annotated genes.

You can browse/search Vega at http://vega.sanger.ac.uk/Danio_rerio. If you have comments on the annotation or arrangements of clones, or want a clone to be annotated, please let us know at zfish-help@sanger.ac.uk

We were very excited by the large number of people who attended the Chemical Biology session in Rome, and want to follow up on the idea of an on-line discussion group. We hope this forum may provide an opportunity to discuss chemical biology techniques, to help each other develop the field, share ideas, and identify unmet needs in the community.

We would like to invite you to join the next Chemical Biology discussion using free broadcasting (http://www.ustream.tv/) on January 20 at 11:00 am EST.

You will need to login, and then join Len Zon's "Chemical Biology Zebrafish" sessions. We recommend signing up a few days before, so that you are able to be sure to be able to access the live broadcast. For this broadcast Len Zon and Randy Peterson will host the video, and we can join in for the discussion via the "chat room". This provides a rapid way to ask questions, to which Len and Randy can respond.

The Ustream technology will allow us to ask questions live. However, please also feel free to send Liz Patton (epatton@staffmail.ed.ac.uk) some questions before the broadcast, and she can send them on to Len and Randy in advance.

The broadcast will be at 11am from Boston (EST). This is 8am for the West Coast (California), 4pm for the UK, and 5pm for Holland, France and Germany.

Reactome is committed to providing access to high-quality pathway information and helpful data analysis tools. With this in mind, we are actively soliciting comments from the research community in order to assess community needs. We are interested to hear about your experience with Reactome, and would like to know a bit about your background and research interests so that we can continue to improve the Reactome site and tools.

You can access the survey at: http://tinyurl.com/l48zzq

Revised Resource Sharing Plan Instructions for PAR-08-138 and PAR-08-139, Genetic Screens to Enhance Zebrafish Research and Enhancing Zebrafish Research with Research Tools and Techniques (R01) (NOT-HD-09-019) Eunice Kennedy Shriver National Institute of Child Health and Human Development National Institute of Diabetes and Digestive and Kidney Diseases http://grants.nih.gov/grants/guide/notice-files/NOT-HD-09-019.html

Notice Number: NOT-HD-09-019

Key Dates

Release Date: August 7, 2009

Issued by Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD) (http://www.nichd.nih.gov) National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), (http://www2.niddk.nih.gov)

Purpose

Applicants responding to PAR-08-138 (http://grants.nih.gov/grants/ guide/pa-files/PAR-08-138.html), Genetic Screens to Enhance Zebrafish Research, and/or PAR-08-139 (http://grants.nih.gov/grants/guide/pa- files/PAR-08-139.html), Enhancing Zebrafish Research with Research Tools and Techniques, when preparing their Resource Sharing Plan are strongly encouraged to contact the Zebrafish International Resource Center (ZIRC, http://zfin.org/zirc/home/stckctr.php) to discuss their plans for sharing resources created under their proposed application and to receive a cost estimate for deposition of materials at ZIRC. As per NOT-OD-04-042 (http://grants.nih.gov/grants/guide/notice-files/ NOT-OD-04-042.html), investigators may request funds in their application to defray reasonable costs associated with sharing materials or data or transfer of model organisms and associated data to appropriate repositories. These costs should be considered in developing the budget for the project. For applications with modular budgets, this cost estimate should be included as part of the resource sharing plan. For non-modular applications with detailed budgets, the cost estimate should be justified as part of the requested budget.

All other aspects of these FOAs remain the same.

Inquiries

Questions about this Notice should be directed to:

Lorette C. Javois, Ph.D.
Eunice Kennedy Shriver National Institute of Child Health and Human Development
National Institutes of Health
Building 6100, Room 4B01, MSC 7500
Bethesda, Maryland 20892-7500
Phone: 301-496-5541
Email: lj89j@nih.gov (e-mail is the strongly preferred method for inquiries)

WikiPathways has recently quadrupled its zebrafish pathway collection, which now totals over 100 pathways representing over 2,400 unique genes. At WikiPathways, you can browse, edit, download and publish pathways that are annotated for computational analysis and illustrated for human consumption. Check out the new pathways here.

WikiPathways has also recently published an article describing the new web service API, which allows programmatic access to search, download, and data mapping functions. Check out the PLoS One article here.

The Sanger Institute has released a Vega update on the 30th of March 2009. The Vega database contains finished clone sequence with manual annotation, placed on chromosomes according to data from the physical mapping project. The current release features 8,954 clones with 14,707 manually annotated genes.

You can browse/search Vega at http://vega.sanger.ac.uk/Danio_rerio. If you have comments on the annotation or arrangements of clones, or want a clone to be annotated, please let us know at zfish-help@sanger.ac.uk

Dear Zebrafish researchers,

The need for more anti-zebrafish antibodies was again highlighted at the recent conference of zebrafish investigators at Asilomar. To facilitate the involvement of the commercial sector in addressing this problem, I am conducting another community poll to identify the most popular antibody targets. AnaSpec, a commercial antibody manufacturer has committed to producing 100 rabbit anti-peptide polyclonal antibodies with some level of validation.

Email me: gw2@sanger.ac.uk by Monday 6th April, with a list of preferred targets unambiguously identified by a GenBank accession number. Please forward this message to your local mailing lists.

Thanks,

Gavin

Gavin J. Wright
Cell Surface Signalling Laboratory
Wellcome Trust Sanger Institute
Cambridge CB10 1HH
T: 01223 496852

The LN54 panel interactive mapping service can be accessed through ZFIN by following the "Interactive Mapping" link at http://zfin.org/cgi-bin/webdriver?MIval=aa-crossview.apg&OID=ZDB-REFCROSS-990426-6 Every attempt will be made to return a mapping location to you within 2 business days. Graphics will not be available.

The Zebrafish TILLING Consortium is pleased to announce the launch of a submission site for TILLING requests. TILLING is a method for finding unique ENU-induced mutations in specific genes in a library of mutagenized fish. This project is a joint effort of the Moens lab at the Fred Hutchinson Cancer Research Center, the Solnica-Krezel lab at Vanderbilt University, and the Postlethwait lab at the University of Oregon. The goal of the project is to generate and distribute loss-of-function mutations in genes of interest to the zebrafish community. Our labs have established large cryopreserved libraries of ENU-mutagenized zebrafish and have identified loss-of-function mutations in over 70 zebrafish genes to date. Our consortium-based approach will be to screen genes of interest sequentially at the three locations. This work is supported by a multi-PI NIH Grant HG002995-04, which provides salary support for TILLING personnel. The cost of TILLING consumables is passed on to the requesters.

To learn more about the project and to submit your requests online, go to:

http://www.fhcrc.org/tilling

Zv8 Assembly and Pre Ensembl

The Sanger Institute has released the eighth zebrafish genome assembly, Zv8, on the 11th of December 2008. This assembly comprises 1.48 Gbp in 11,623 scaffolds. It was generated starting with 1.1 Gbp from 9,816 BAC clones and supplemented with a 7x whole genome shotgun assembly. Particular attention has been paid to sort the clone and contig order according to the genetic and radiation hybrid maps as explained in detail at http://www.sanger.ac.uk/Projects/D_rerio/assembly_notes/Zv8_assembly_notes.shtml.

More information is available from http://www.sanger.ac.uk/Projects/D_rerio/wgs.shtml.

The Zv8 sequence has been used to generate an Ensembl database available at http://pre.ensembl.org/Danio_rerio featuring sequence and automated feature annotation plus search and download facilities. A full Ensembl site, providing a gene build and comparative genomic and data mining tools, will be available in spring 2009.

Community Annotation Tool

If you want to comment on certain regions in the Zv8 assembly, you can do so now using the webform at http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/Annotation/submitAnnotation.pl. Your report will be automatically saved to a database and the comments can be viewed as a feature track on the Zv8 pre-ensembl web site at http://www.pre-ensembl.org/Danio_rerio and later in the full Ensembl release. Please follow the instructions on the community annotation web site. Your annotation is visible to the public to inform them about issues with the assembly. We will be using your information to improve the clone path and the next assembly Zv9.

Please send your questions/comments to zfish-help@sanger.ac.uk.

We would like to let the zebrafish community know about the availability of reagents and resources relating to our recent paper describing the use of zinc finger nucleases to generate targeted mutations in zebrafish. These tools will enable labs to perform bacterial 1-hybrid selections to make zinc finger proteins against a particular target site of interest. These resources include the plasmids and the bacterial selection strain that are now available through www.addgene.org, along with an on-line tool that will help identify good sites and generate libraries for screening.

To download a PDF that includes a list of plasmids and strains, go to: http://lawsonlab.umassmed.edu/PDFs/B1Hrec.pdf

For tips getting started with the bacterial 1-hybrid: http://lawsonlab.umassmed.edu/PDFs/B1HStart.pdf

For the on-line search tool to identify target sites and design library oligos, go to: http://pgfe.umassmed.edu/ZFPsearch.html

Related references:
Noyes et al. (2008) Nucleic Acids Res. 36(8):2547-60
Meng et al. (2008) Nat Biotechnol. 26(6):695-701

We will try to make additional documentation on these available as soon as possible. Check back at the Lawson (http://lawsonlab.umassmed.edu) and Wolfe Lab (http://labs.umassmed.edu/WolfeLab) websites for updates.

Finding an antibody that works on zebrafish is about to get easier. The new antibody search page lets you search for antibodies by name or labeling pattern. Antibody marker pages show a summary of labeling in wild-type fish along with other useful data. We are starting with the full set of antibodies available at ZIRC, and will be adding many more antibodies described in the literature. You can help by telling us which antibodies are most useful to you.

ZGC has added 1819 full length ZGC clones recloned into a Gateway Entry vector (pENTR223.1; http://mgc.nci.nih.gov/Vectors/prot_pENTR223.1) for expression analysis and other applications.

These clones can be found by searching Entrez nucleotide for "NIH_ZGC_36".

Zebrafish SNPs can be retrieved in ZFIN. This is the first phase of implementation. We provide the ability to access SNPs mapped to a genomic clone. Options are provided to retrieve a text file or conduct a Batch Query at NCBI. For example, see: BAC DKEY-5N18

and

the SNP retrieval page for DKEY-5N18.

The full implementation including the ability to search for and retrieve SNP information directly as well as association between SNPs and genes will happen after the implementation of a Genome Browser in ZFIN. This will allow the SNP information to be placed in a genomic context.

NIH and the Trans-NIH Coordinating Committee have published two new Program Announcements with special Receipt dates (PARs) soliciting R01 applications for research using zebrafish. Please note that not all NIH Institutes and Centers are participating in both of these solicitations; therefore, only applications relevant to the missions of participating Institutes and Centers will be considered responsive to the announcements. These two new PAR's can be found in the NIH Guide at the following urls:

http://grants.nih.gov/grants/guide/pa-files/PAR-08-138.html

Genetic Screens to Enhance Zebrafish Research (R01)

http://grants.nih.gov/grants/guide/pa-files/PAR-08-139.html

Enhancing Zebrafish Research with Research Tools and Techniques (R01)

Maximizing Data Impact
Anatomy Pages Expanded
Full Text publications
Morpholino Database (MODB) and ZFIN
Microarray Data at ZFIN
Nomenclature Guidelines Updated

Click here for our ZFIN Newsletter Archive.

We are pleased to announce that the meeting website for the 2008 International Zebrafish meeting has now gone live:

http://www.union.wisc.edu/zebrafish/index.html

A description of the meeting follows below, and more information is available on the website. Important deadlines: Abstract submission, April 14, 2008; Lodging reservations, May 19, 2008.

8th International Meeting on Zebrafish Development and Genetics
June 25-29, 2008 - Madison, WI, USA
The organizers of the 2008 International Zebrafish Development and Genetics Conference welcome all interested scientists to join us for discussion of their latest results and ideas. The schedule will feature a variety of oral sessions, posters, and vendors, as well as opportunities to socialize on the shores of Lake Mendota.

This year's schedule will feature extra time for free discussion, as well as a workshop format featuring topics suggested by the community. (Thanks to all of those who wrote in to suggest workshop topics.) We have also provided extra information about bus connections, as an alternate way to reach Madison from Chicago or Milwaukee airports.

Planners are working hard on the 2008 international zebrafish meeting (June 25-29, Madison), and would like to solicit your help. This year's meeting will introduce workshops on specialized topics proposed by the community. These will be organized in two sessions, each with up to 5 workshops running concurrently. Workshops will last two hours, and might consist of 3 or 4 short ( e.g. 15 min) talks, with extensive time for discussion.

We are now asking for the community to propose the topics for these workshops. Topics will be posted on a blog: http://zf2008workshops.blogspot.com/ and we encourage everyone in the community to visit this blog and comment on proposals. To propose a topic, email zfmeeting@gmail.com. Please include your name and institution. We will invite you to be a blog author so that you can describe your proposal in a new post. If you want to comment on a topic, or propose a change, simply comment on the relevant post (please include your name and institution in your comment).

The Sanger Institute has released a Vega update on the 27th of September 2007. The Vega database contains finished clone sequence with manual annotation, placed on chromosomes according to data from the physical mapping project. The current release features 9,535 clones, 2,800 of which have been annotated. 11,115 genes have been manually annotated on over 415 Mb of annotated sequence.

You can browse/search Vega at http://vega.sanger.ac.uk/Danio_rerio. If you have comments on the annotation or arrangement of clones, or would like a particular clone to be annotated, please contact zfish-help@sanger.ac.uk.

The ZFIQ (Zebrafish Image Quantitator) software toolkit provides a set of image analysis tools for quantitative, reproducible and accurate interpretation of zebrafish imaging data.

We are pleased to announce that FishNet, an interactive database of zebrafish anatomy, is now available at www.FishNet.org.au. FishNet contains more than 36,000 images of zebrafish development, with more than 1.500 of these being annotated. The 3D models can be manipulated on screen or virtually sectioned. A detailed description of the database is available at http://www.biomedcentral.com/1741-7007/5/34/ Comment and suggestions can be submitted via the website or to fishnet@victorchang.edu.au

The Sanger Institute has released the seventh zebrafish genome assembly, Zv7, in Ensembl on the 16th of August 2007. The database features repeatmasking, marker placement, alignments with cDNAs, ESTs and peptides, mapped BAC ends, expression patterns, as well as comparative genomics data and data mining tools. The gene build resulted in 21,322 genes, 98 pseudogenes and 4,053 non-coding genes.

Please note that previous Ensembl data built on assembly Zv6 are still available in the Ensembl archives.

The assembly can be downloaded at ftp://ftp.ensembl.org/pub/assembly/zebrafish/Zv7release and more information can be found at http://www.sanger.ac.uk/Projects/D_rerio/Zv7_assembly_information.shtml.

The Sanger Institute has released a Vega update on the 12th of July 2007. The Vega database contains finished clone sequence with manual annotation, placed on chromosomes according to data from the physical mapping project. The current release features 9,254 clones, 2,411 of which have been annotated. 10,374 genes have been manually annotated on over 370 Mb of annotated sequence.

You can browse/search Vega at http://vega.sanger.ac.uk/Danio_rerio. If you have comments on the annotation or arrangements of clones, or want a clone to be annotated, please contact zfish-help@sanger.ac.uk.

The Sanger Institute has released the seventh zebrafish genome assembly, Zv7, on the 13th of July 2007. This assembly comprises 1.44 Gbp in 5,036 scaffolds. It was generated starting with 1.02 Gbp from 7,823 BAC clones and supplemented with a 5.5x whole genome shotgun assembly. The sequences were integrated using alignments as well as BAC end and marker placement. Over 200 Mbp of duplicated sequence has been removed compared to Zv6. The assembly can be downloaded at ftp://ftp.ensembl.org/pub/assembly/zebrafish/Zv7release and more information can be found at http://www.sanger.ac.uk/Projects/D_rerio/Zv7_assembly_information.shtml.

The Zv7 sequence has been used to generate an Ensembl database available at http://pre.ensembl.org/Danio_rerio/index.html. This is an extended Pre Ensembl site, providing a full Ensembl gene set for Zv7. A full Ensembl site, providing comparative genomic and data mining tools, will be available for the next Ensembl release in August.

We would like to request a call for papers concerning a disease-based review to the American Journal of Medical Genetics. The focus of this manuscript is understanding human malformation phenotypes using the zebrafish model. We believe such a review, written for an audience of primarily non-zebrafish scientists, would be helpful in communicating the value of this model organism for scientists and policy-makers considering alternate vertebrate model systems. We had started the process of drafting this review late last year, and at the Investigator's Workshop, several members of the community expressed interest in such a document for the whole community.

We would like to make this review as comprehensive as possible and don't want to miss any of the great papers that have come out in this area. If you have a publication that is out or about to be out (i.e. in press), we would love to receive the citation and/or preprint so we can include your science in this review. All materials received prior to publication release will be held in strict confidence until the appropriate paper has come out in the respective journal.

Sincerely, Shelly Myers, Genetics, Cell Biology and Genetics - University of Minnesota Lisa Schimmenti, MD, Pediatrics- University of Minnesota Stephen C. Ekker, Genetics, Cell Biology and Genetics - University of Minnesota

Please send your information to:

Stephen C. Ekker ekker001@umn.edu
Lisa Schimmenti las@umn.edu

Thanks!

The need for more anti-zebrafish antibodies was highlighted at the recent conference of zebrafish investigators at Asilomar. To try and address this, I have made some preliminary enquiries to an antibody supplier to see if this niche market would be commercially viable. The company that has shown some interest has expertise in making polyclonal affinity-purified anti-peptide antibodies in goats. To make the most of this opportunity, I need to know which antibodies would initially be the most useful to the zebrafish community as a whole.

To obtain these data, please email me, gw2@sanger.ac.uk, by Friday 6th April with a list of preferred targets identified by a GenBank or ENSembl accession number. Preference would be given according to the following criteria:

1. Popularity (number of requests for a particular antibody);
2. Willingness of the requestor to test a small aliquot of the antibody and provide these data *quickly* to the company so that they can show it works; please indicate in your reply if you'd be willing to do this.
   

Please note that the abstract submission deadline for the 5th European Zebrafish Genetics and Development Meeting is March 9th, 2007. Also, March 9th is the deadline for early registrations, which are somewhat cheaper than later registrations.

For more information, see the official Meeting website: http://www.zebrafish2007.org/

Efficacy Test of Chordin Morpholinos

Zebrafish genes have been added to the HGNC HCOP search tool (http://www.gene.ucl.ac.uk/hcop) which compares orthology assertions from different databases.