Our proposal for a follow-up project in the 7th Framework Programme, ZF-HEALTH, has been positively evaluated by the European Commission. Please watch this space for more information as it becomes available.
3.5 days 8 – 11 June 2009
Applications are requested from students and post-docs who wish to attend a 3.5 day imaging workshop at UCL focusing on confocal microscopy techniques. The workshop will run from the morning of the 8th June to lunchtime on the 11th June.
Registration and accommodation costs will be covered by the ZF-MODELS Integrated Project (www.zf-models.org).
Day 1 – lectures
Basics of microscopy: setting up Koehler illumination, Phase contrast, DIC. Point spread functions and optical resolution. Objectives – what do all the codes mean? What are the benefits and drawbacks of the different objectives? Which one should I choose for what job?
Introduction to confocal microscopy: Confocal principle, optical paths, signal cross talk. Digital images, optical vs digital resolution, pixels, voxels and grey levels. Digital and physical regions of interest - scanning and analysis. Optical sectioning and 3D reconstruction and rendering methods.
Live cell imaging confocal and multiphoton confocal microscopy: FRET, FRAP, FLIP, FLIM. 2 photon concept, advantages and drawbacks. SHG and THG imaging.
Image analysis and 3D reconstruction: Image composition and properties. Signal co-localization analysis. Deconvolution analysis. Application of algorithms to improve image quality – dangers! 3D reconstruction, volume rendering and visualization. Comparison of software packages available.
Fluorescent probes and cell labeling: Basics of fluorescence, luminescence and spectral properties and consideration. Chemical fluorophores, fluorescent proteins (standard and advanced), FLAsh ReAsh bi-arsinical probes. Labelling techniques, bathing, AM dyes, electroportation, transfection microinjection, gene gun.
Day 2 & 3 & 4 – circus of practical classes to rotate round in groups of 4 (to make sure everyone gets hands on experience).
- Basic microscope set up and alignment for Koehler illumination, Phase contrast, DIC. Alignment of Hg lamps. Confocal basics – image acquisition, correct dynamics range, eliminate cross talk, Z series, lambda scan, image projection and rotation.
- Live cell imaging FRAP and FRET techniques.
- Multiphoton and second harmonic imaging.
- Image analysis and 3D reconstruction practical.
- Zebrafish specific module - high-resolution fish brain imaging, including some detail on transgenics, mounting, imaging, reconstruction and presentation
Deadline for applications: 10th May 2009
To apply, send a CV & cover letter explaining why you would like to attend and a letter of support from your lab to Steve Wilson (email@example.com)
The European working group coordinated by ZF-MODELS Team Leader Uwe Strähle (FZK) will receive funding from the intergovernmental framework for European Cooperation in the field of Scientific and Technical Research (COST). The proposal for a European Network on Fish Biomedical Models (EUFishBioMed) has been finally approved by the COST Committee of Senior Officials on Tuesday 25 November, 2008. COST Action number: BM0804.
The main objective of the Action is to promote research on and use of small fish as models for human diseases via the establishment of a communication platform. This COST Action will coordinate the distribution of these fish models and will disseminate contacts and knowledge to investigate the molecular and genetic basis of the disturbed physiology of these models. The main audience will be the wider biomedical research community and industry for a faster translation of research into medical applications and as in vivo systems for drug development and toxicity testing.
For further information please visit the EUFishBioMed website.
We have received EC approval for the no-cost extension of ZF-MODELS until June 30, 2009 (change of duration to 66 months).
Also approved are the termination of participation of CERBM and the accession of U.Va. (due to the move of Christine Thisse) and the status change of Bergen University to a Joint Research Unit with their spin-off company, Unifob.
The fourth and final ZF-MODELS Consortium meeting was held on March 29 – 30, 2008, attended by approximately 30 scientists representing nearly all members of the ZF-MODELS consortium, Prof. Monte Westerfield representing the Scientific Advisory Committee and
Scientific Officer Dr. Sandra Pinto-Marques, representing the European Commission.
The agenda included workpackage reports and discussions of the Governing Board on the first day, and scientific talks by consortium members on the second day.
At the 2nd Strategic Conference of Zebrafish Researchers held in Asilomar, USA (Feb. 2007) a working group was established to discuss the future of European zebrafish research. This working group, led by Uwe Straehle (FZK), has now released a white paper (PDF).
April 23-29, 2007, SANGER Institute Cambridge
This workshop is aimed at researchers at all levels and will focus on the use of web resources that have been developed in conjunction with the Zebrafish Genome Sequencing Project.
Lectures on a variety of topics, e.g. mapping the zebrafish genome, sequencing techniques and sequence analyses, as well as hands-on exercises to explore bioinformatics resources via the web and via self-written perl scripts have been included in the agenda, a preliminary version of which can be found under http://www.sanger.ac.uk/Projects/D_rerio/zfm_workshop2007.shtml.
Please indicate your intention to attend and accommodation requirements to either Kerstin Howe at firstname.lastname@example.org or Sancha Martin at email@example.com by 23rd of March 2007. Where possible, please indicate whether (and to what level) the attendees are familiar with Perl scripting. Please cascade this message and the poster as appropriate.
The third annual meeting of the ZF-MODELS consortium was held on March 3 - 4, 2007 at the Sanger Institute, hosted by Dr. Jane Rogers. Participating were approximately 40 scientists representing nearly all members of the ZF-MODELS consortium, Prof. Monte Westerfield representing the Scientific Advisory Committee as well as outgoing Scientific Officer Dr. Jacques Remacle and new Scientific Officer Dr. Sandra Pinto-Marques, representing the European Commission.
As this was the project's midterm review meeting, an overview of the workpackage achievements of the past three years was given, followed by dicussions of the Governing Board on the integration of a new commercial partner, and scientific talks by consortium members on the second day. The Governing Board furthermore agreed to hold the 2008 ZF-MODELS annual meeting in Paris, hosted by INSERM.
The 5th European Zebrafish Genetics and Development Meeting will take place from 12-15 July 2007 in Amsterdam, the Netherlands.
- 15 December 2006 – Web site open for registration and abstract submission
- 9 March 2007 – Deadline for abstract submission + early registration
- 30 April 2007 – Notification of acceptance of abstracts
- 12-15 July 2007 – 5th European Zebrafish Meeting in Amsterdam
The meeting will be held at the Amsterdam RAI Convention and Exhibition Centre, ideally located from both the city centre of the Dutch Capital and Amsterdam International Airport Schiphol.
- Ronald Plasterk – Hubrecht Laboratory, Utrecht, NL
- Alexander Schier – Harvard University, Cambridge, US
- Stefan Schulte-Merker – Hubrecht Laboratory, Utrecht, NL
- Jeroen den Hertog – Hubrecht Laboratory, Utrecht, NL
- Dana Zivkovic – Hubrecht Laboratory, Utrecht, NL
- Suresh Jesuthasan – Temasek Life Sciences Laboratory, Singapore
If you would like to receive further information please visit our Meeting site: http://www.zebrafish2007.org/
"ZF-MODELS – Zebrafish Models for Human Development and Disease" is an Integrated Project funded by the European Commission as part of its Sixth Framework Programme (EC Contract LSHG-CT-2003-503496). We aim to exploit the advantages of the zebrafish to produce knowledge, technology and materials in the form of disease models, drug targets and insight into pathways of gene regulation applicable to human development and disease.
The Consortium is seeking a small or medium enterprise (SME) partner with expertise complementing that of the Consortium partners in one or more of the following fields: small-molecule screening; generation of transgenes; microarray services; cryopreservation of embryos; or development of disease models.
The potential partner should propose a specific project that will be integrated with the work performed in the five research-related workpackages of the ZF-MODELS project. The expected duration of participation is from January 2007 to December 2008. Research costs will be supported by Commission funding of up to 50%. A total of €500,000 of Commission funding will be available.
Proposals written in English, not exceeding five pages, should be addressed to the project coordinator: Dr. Robert Geisler, Dept. 3 (Genetics), Max-Planck-Institute for Developmental Biology, Spemannstr. 35, 72076 Tübingen, Germany
The call will close on Wednesday, October 25, 2006, 1700 CET. For further information please refer to our website: http://www.zf-models.org/
This call does not use the EC's Electronic Proposal Submission System. Proposals must be submitted on paper and should address the following points:
- a specific activity or activities by which your company will help the consortium to achieve its goals
- suitable deliverables and milestones
- the strengths of your company complementing the competence of the consortium, and how your company will benefit from its participitation
- personnel that will be involved in or employed for the project
- proposed budget and effort (person-months).
Proposals will be evaluated by the ZF-MODELS Consortium with the aid of an external expert. The highest ranking proposer will be invited to prepare for accession to the consortium, subject to approval by the European Commission. Should negotiations with the highest ranking proposer fail, the Consortium will consider the second ranking proposer, but may also consider other courses of action.
The ZF-MODELS consortium would like to draw attention to its public and free knock-out service for zebrafish, based on the resequencing of mutagenized fish (TILLING). Up to 60 knock-outs will be performed for researchers outside the consortium, whose requests are considered on the basis of their scientific merit. The workload is distributed between the laboratories of Sanger Institute (D. Stemple), Hubrecht Laboratory (E. Cuppen), and TU Dresden (M. Brand). To request a zebrafish KO mutant, please send a brief (approx. one page) summary to Dr. Edwin Cuppen <mailto:firstname.lastname@example.org>. This summary should contain the following information:
Information on the gene to be knocked out: Name of the gene and Ensembl ID. Please note that the ZF-MODELS consortium will only accept requests for KOs based on Ensembl IDs. The requester should also check the Ensembl annotation. In case the annotation is incorrect, the requester has to make sure that it is changed. The ZF-MODELS consortium will not screen for a gene as long as the annotation is not correct.
Scientific relevance: Explain why is it important to knock this gene out.
Zebrafish background of the lab requesting the KO mutant: Explain how any work on the KO mutant provided would be embedded in an environment in your lab where people can actually work with zebrafish mutants.
The summaries received by Dr. Edwin Cuppen form the basis for prioritized lists drafted up by the ZF-MODELS Executive Committee on a regular basis.
Once a request has been accepted, you will be asked to design an amplicon(s) for your region(s) of interest through the LIMSTILL online tool <http://limstill.niob.knaw.nl/>. Oligos will be ordered and tested by the ZF-MODELS consortium. The progress of requests can be tracked through the internal knock-out website of Hubrecht Laboratory (login required).
Information on the knock-out mutants generated by the ZF-MODELS consortium is made publicly available through the knock-out website <http://www.niob.knaw.nl/researchpages/cuppen/zfmodels/> of Hubrecht Laboratory, immediately after a knock-out is generated. Knock-out fish are immediately delivered to the requesters.
"ZF-MODELS - Zebrafish Models for Human Development and Disease" is an Integrated Project funded by the Sixth Framework Programme of the European Commission. For further information please see the project website <http://www.zf-models.org>.
The third annual meeting of the ZF-MODELS consortium was held on March 17 - 18, 2006 at the Lorentz Center of Leiden University, hosted by the group of Prof. Annemarie Meijer. Participating were 40 scientists representing nearly all members of the ZF-MODELS consortium and Prof. Monte Westerfield representing the Scientific Advisory Committee.
The agenda included workpackage reports, discussions of the Governing Board and an invited talk by Prof. Westerfield on the first day, and scientific talks by consortium members on the second day. Among other topics the Governing Board reviewed letters of interest received from potential commercial partners in preparation of a public call, confirmed the consortium's dissemination policy, and accepted an offer of the Sanger Institute to hold the 2007 ZF-MODELS workshop and annual meeting in Hinxton.
The ZF-MODELS consortium is planning an open call to be held in 2006 in order to admit a commercial partner. To help us prepare for such a call, potential commercial partners are invited to submit a letter of interest.
Up to EUR 500,000 in European Commission funding will be available for the new consortium partner in the period from 2006 to 2008. Please be aware that as usual in FP6 projects, only 50 % of eligible cost for research and development will be reimbursed by the EC.
Letters of interest should be informal and not exceed two pages.
- a specific activity or activities by which your company could help the consortium to achieve its goals
- how the strengths of your company will complement the competence of the consortium
- personnel that will be involved in or employed for the project
- how your company will benefit from its participation.
We would appreciate to receive a reply by March 16. The call itself is expected to take place later in spring.
For information about the ZF-MODELS consortium, its activities and goals please refer to our website: http://zf-models.org
Two PIs of the consortium have moved to new organizations on January 1, 2006 and intend to continue with the project tasks assigned to them, necessitating changes in the partnership.
- Termination of the participation of ETH Zurich and addition of Universität Zürich, due to the move of Prof. Stephan Neuhauss.
- Addition of TU Dresden, due to the move of Prof. Michael Brand, who was previously at the MPG (MPI CBG). Carl Philipp Heisenberg's group will remain at MPI CBG.
13 Mar 2006 through 22 Mar 2006
Lorentz Center, Universiteit Leiden, The Netherlands
Description and aim of the workshop
This workshop is organized in the framework of the European ZF-MODELS project: "Zebrafish Models for Human Development and Disease". The workshop will give an introduction to transcriptome microarray analysis and proteomics and is primarily intended for graduate students, postdocs and advanced technicians using zebrafish as research model. The workshop is aimed at providing knowledge on the use of different microarray platforms, RNA labelling techniques, protein extraction methods and 2D-electrophoresis, mass spectrometry, experimental design of genomic studies, statistical analysis of genomic data, linkage of datasets to the zebrafish genome and the use of public databases for storage of genomic data. The practical part will include RNA labeling, quality control and hybridization of oligonucleotide microarrays. Furthermore, the participants will be able to acquire practical experience with bioinformatic methods applied in genomics and proteomics.
Microarray expression profiling
Georg Otto, Max-Planck Institute of Developmental Biology, Germany
Annemarie Meijer and Herman Spaink, Institute of Biology, Leiden University, the Netherlands
Fons Verbeek, Leiden Institute of Advanced Computer Science, Leiden University, the Netherlands
Mario Caccamo, The Wellcome Trust Sanger Institute, Cambridge, United Kingdom
Marc Saric, Max-Planck Institute of Developmental Biology, Germany
Carl-Philipp Heisenberg, Max-Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
Astrid Bruckmann and Enrique Salas, Institute of Biology, Leiden University, the Netherlands
How to apply
Applications must include a short CV including publication list, a brief statement of research interests and motivation for wanting to participate in this workshop and a supervisor's letter of support. The course is limited to a total of 20 participants and half of the places is reserved for ZF-MODELS participants.
There is no registration fee. Accommodation costs will be covered by the workshop organization, but participants are responsible for their own travel expenses.
Application deadline: 1 February, 2006.
Applications should be sent to: Dr. Annemarie H. Meijer <email@example.com>
The Wellcome Trust Sanger Institute leads the world in genomic research, with an expanding scientific programme dedicated to understanding the role of genomes in biological systems.
The genome of the zebrafish (Danio rerio) is an important model organism in understanding vertebrate development and gene function. The ZF-Models project http://www.zf-models.org utilises the advantages of the zebrafish system to produce knowledge and technology in the form of disease models, drug targets and insight into pathways of gene regulation.
We are looking for a bioinformatician to work on this project. Based in the zebrafish genome analysis group at the Sanger Institute http://www.sanger.ac.uk/Projects/D_rerio, your key duties will include the setup and maintenance of a worldwide repository of the resulting data, the integration with existing genome browsers http://www.ensembl.org, http://vega.sanger.ac.uk and the presentation to the community.
Ideally, you will have a degree (preferably a PhD) in a suitable biological or computational discipline and at least three years of programming experience. A knowledge of UNIX, Perl and SQL is essential and familiarity with object-oriented Perl and web-programming would be advantageous. Commitment to science and a team spirit are important.
Benefits include 25 days annual leave, final salary pension scheme, optional private healthcare (on successful completion of probation period), permanent disability insurance, life assurance, childcare voucher scheme, on-site restaurant, café, gym and an active sports and social scene.
To apply for this position please email your CV (including 2 referees) and current salary details, Quoting reference SW1043 to: firstname.lastname@example.org
Or post your application to:
Human Resources Department,
The Wellcome Trust Sanger Institute,
The closing date for applications is 27th January 2006
ZF-ESPRESSO is a new database that aims to give biologists quick access to processed expression profiling data. In particular, it will allow to compare experiments performed by different investigators and to search for genes with similar expression profiles, and provide links to external image databases (such as in situ images at ZFIN and GFP images at CLGY). The eventual aim is to include all zebrafish expression profiling experiments for which raw data are available in public repositories.
The current preview version contains a developmental timecourse of whole embryos of the Tü strain which was generated by Martina Konantz in the Geisler laboratory (unpublished). Two hybridizations on the Affymetrix zebrafish array (biological replicates) were performed for each time point, and the results were normalized to the median of all stages. The raw data and a full description of the experiment are currently being submitted to ArrayExpress.
The zebrafish group at the Sanger Institute is responsible for integrating microarray, enhancer detection, expression pattern and TILLING data with the existing genome sequence. The currently available data has been mapped to the genome sequence and made browsable and searchable. Details can be found here.
The CLGY image database contains images and descriptions of GFP expression patterns generated by the Becker laboratory (Ellingsen et al., Development, in press).
Furthermore, in situ patterns and descriptions of ENU mutations from the ZF-MODELS project will be made available in the coming month through ZFIN.
This 10 day intensive course will introduce graduate students and post-doctoral researchers to recent molecular and embryological technologies that are applicable on a genome-wide scale in this vertebrate model organism. The course combines high throughput transgenesis using retroviral- as well as transposon vectors with the molecular techniques to rapidly isolate genomic sequence flanking these insertions and mapping them onto the zebrafish genome sequence. The program of this course offers mainly hands-on experience ranging from vector design and -construction to generating and isolating insertions by fluorescence microscopy and relevant embryological and live imaging techniques. The laboratory work will be complemented by lectures on these topics as well as bioinformatics and data management. There will be a one-day theoretical course on Targeting Induced Local Lesions IN Genomes (TILLING). Topics are taught and supervised by local and external teachers who have pioneered these technologies.
(text / information from SARS Centre)
Application deadline: April 15th, 2005.
The Organizing Committee of the 4th International European Zebrafish meeting (July, 13-16th 2005) would like to announce the going-live of the conference website: www.zebrafish-dresden.com
We would like to point out the unique opportunity to participate in sizzling hot scientific presentations and discussions, to visit historic Dresden in the heart of Europe, and perhaps to explore a little further afield while you are here - close to Berlin, Prague, Wraclaw, Vienna, Budapest etc.
Registration and abstract submissions can be made immediately, but don't wait for that last in situ to register - let us know you're coming and we will roll out the welcome mat!
Thanks, and best fishes,
Michael Brand, Carl-Philip Heisenberg, Andrew Oates and Makoto Furutani-Seiki and all the fish people from Dresden.
Michael Brand (MPI CBG)
Makoto Furutani-Seiki (MPI CBG)
Carl-Philipp Heisenberg (MPI CBG)
Andrew Oates (MPI CBG)
As part of the ZF-MODELS Integrated Project, there will be a large-scale ENU mutagenesis screen organized by the Max Planck Institute for Developmental Biology starting in January 2005. In addition to the members of the ZF-MODELS Consortium, there will be the possibility for other European scientists to participate in this screen and to employ their own assays. There has been an initial selection of assays at a screen planning meeting held on September 24th, 2004 at the Max Planck Institute for Developmental Biology in Tübingen. However, as there will be more than one round of screening, it is still possible to apply for a screening slot. As the number of screening slots is limited, there will be a review and selection of the assays proposed. Wherever possible, several proposed assays will be combined such that they can be carried out on the same batch of embryos.
Dear European Zebrafish Labs,
with this email, I would like to inform you of the Integrated Project “ZF-MODELS - Zebrafish Models for Human Development and Disease“ - a project funded by the European Commission, which aims to exploit the strengths of the zebrafish to understand the genetic control of development and diseases in vertebrates.
I would like to point out several possibilities for European research groups working with zebrafish to benefit from the project by participating in project activities (e.g. mutagenesis screens, enhancer trap screening, microarray expression analyses) as well as by accessing the projects resources, (zebrafish KO mutants, public databases, workshops etc.). For details on the activities and resources open to European zebrafish groups outside the consortium, please see the attached PDF files ZF-MODELS.pdf and ZF-MODELS_screen_workshop.pdf.
If you have any specific questions concerning the project, please do not hesitate to contact me.
With the best regards,
The Wellcome Trust Sanger Institute in Cambridge, UK, is offering two positions for Computer Biologists. For details, please see below Computer Biologists (Ref: SW781 - 782)
Closing Date: 21st May 2004 Contact: email@example.com
The Wellcome Trust Sanger Institute is one of the leading genomics centres in the world, dedicated to analysing and understanding genomes. With the human genome completed research is now expanding to analyse sequence from other organisms such as zebrafish and support comparative genomics and manual curation. We have exciting opportunities in this area for skilled computer biologists.
The genome of the zebrafish (Danio rerio) is an important model organism in understanding vertebrate development and gene function.
The ZF-Models project (http://www.zf-models.org) utilises the advantages of the zebrafish system to produce knowledge and technology in the form of disease models, drug targets and insight into pathways of gene regulation.
We are looking for two computer biologists to work on this project. Based in the informatics group at the Sanger Institute, your key duties will include the setup and maintenance of a worldwide repository of the resulting data, the integration with existing genome browsers (http://www.ensembl.org, http://vega.sanger.ac.uk) and the presentation to the community.
Ideally, you will have a degree (preferably a PhD) in a suitable biological or computational discipline and at least three years of programming experience. A knowledge of UNIX, Perl and SQL is desirable and familiarity with object-oriented Perl and web-programming would be advantageous. Commitment to science and a team spirit are important.
Benefits include 25 days annual leave, generous non-contributory pension scheme, optional private healthcare (on successful completion of probation period), PHI, life assurance, childcare voucher scheme, on-site restaurant and café, on site gym and an active sports and social scene.
To apply for this position please email your CV (including 2 referees) and current salary details, Quoting reference SW781-782 to: firstname.lastname@example.org
Or post your application to: Human Resources Department, The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA
Internal applicants must complete an internal application form and provide an up-to-date curriculum vitae.
To mark the start of the ZF-MODELS IP, there was a kick-off meeting hosted by the Max Planck Institute for Developmental Biology. The meeting took place at the Tübingen Max Planck Campus from 14th - 15th February 2004.
For further information on the meeting, please contact Dr. Ralf Dahm.
The European Commission has awarded an unprecedented 12 million Euros for zebrafish research to a consortium of 15 European institutions, led by the Max Planck Institute for Developmental Biology. The ZF-MODELS consortium hopes to establish zebrafish models for human diseases, discover genes that will lead to the identification of new drug targets and gain fundamental insights into human development. [read complete article (pdf)]
Europäische Kommission bewilligt 12 Millionen Euro, um am Zebrafisch modellhaft die Entwicklungsbiologie des Menschen und seine Krankheiten zu untersuchen. Ein Konsortium von 15 europäischen Forschungseinrichtungen unter der Leitung des Tübinger Max-Planck-Instituts für Entwicklungsbiologie erhält im Rahmen des 6. Forschungsrahmenprogramms 2004 bis 2009 von der Europäischen Kommission insgesamt 12 Millionen Euro für die weitere Erforschung des Zebrafischs. Es handelt sich um eine der umfangreichsten Bewilligungen für entwicklungs- und zellbiologische Untersuchungen aus Brüssel, die bisher gewährt wurden. Das Forschungskonsortium mit dem Namen "ZF-MODELS" plant, am Zebrafisch Modelle zur Untersuchung wichtiger menschliche Krankheiten zu etablieren, nach neuen und wirkungsvolleren Angriffspunkten für Wirkstoffe (drug targets) zu suchen und grundlegende Erkenntnisse über die Entwicklung des menschlichen Organismus von der Zeugung bis ins Alter zu gewinnen. [den gesamten Artikel lesen (pdf)]