PhD positions in bioinformatics ("Rapid identification of ENU mutants by HTS sequencing") and molecular biology ("RNA editing in skeletal muscle during development") are currently open in the groups of Robert Geisler and Uwe Strähle as part of the ZENCODE-ITN training network.
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton,
Cambridge, CB10 1SA UK
The Sanger Institute Fellowship provides an opportunity specifically for those who have had a break from research to return to high-quality postdoctoral training at a world-class research institute. The Fellowship will last for three years and can be worked full time, part time or flexibly. The Fellowship includes a salary of £29,829-£37,393 p.a. and research expenses (including consumables and travel costs for conferences and training courses). Applications are invited linked to the following project:
Charting the Zebrafish Immune System One Cell at a Time
Supervisors: Sarah Teichmann and Ana Cvejic
The immune system is one of the fastest-evolving biological processes, and it has become clear that all kingdoms of life, bacteria, plants and animals, have developed their own forms of adaptive immune system. Within the animal kingdom, genome analysis suggests that all vertebrates have rearranging molecules in the form of T- and B-cell receptors. However, the precise nature of the T and B cells in which these receptors are expressed is known only in human and mouse. Using the power of high-throughput single cell transcriptomics, we can now discover the cellular landscape of the adaptive immune system in model organisms ab initio.
Here, we propose to profile T cells in a lower vertebrate, in order to gain insight into the origins of mammalian adaptive immunity. We will begin by profiling T cells in the zebrafish, a genetically tractable vertebrate model organism that is increasingly emerging as a model for immunity and disease (Tobin et al., PLOS Pathog., 2012). Initially, we will focus on CD4+ T helper cells, which are white blood cells that initiate the body's response to infections, and are an essential part of the human immune system. T helper cell subtypes (e.g. Th1, Th2, Th17) have been well characterised in higher vertebrates and can be distinguished by the specific interleukins that serve as activators, repressors or products of these cell types. However, the presence and identity of T helper cell subtypes in bony fish is still an open question. Through computational analysis, we have identified several of the interleukins and their receptors in zebrafish, suggesting that most genes characteristic of T helper cell differentiation are present. In particular, we have compiled evidence of IL1, IL4, IL5, IL6, IL10, IL13, IL17, IL21, IL23 and IL27 based on the literature (Secombes et al., Dev. Comp. Imm., 2011; Laing and Hansen, Dev. Comp. Imm., 2011) and gene prediction. Moreover, synteny and the presence of their receptors indicate that IL2 and IL33 could also be present in zebrafish.
We will answer this intriguing question through massively parallel single cell RNA-sequencing of cells from existing Tg(lck:EGFP) and custom Tg(cd4:EGFP) zebrafish reporter lines, as well as FACS-sorted CD4+ cells with a new commercially available antibody. These experiments will provide a rich data set to mine bioinformatically, and gain unparalleled insights into the evolution of immunity.
The project will benefit from combined expertise of the Teichmann group in single cell RNA-sequencing (Brennecke et al., Nat. Methods, 2013; Mahata et al., Cell Reports, 2014) and the Cvejic group in zebrafish biology (Cvejic et al., Nat. Genet, 2013; Bielczyk-Maczynska, PLOS Genet., 2014, in print). It will involve a combination of in vivo zebrafish experiments, genomics and bioinformatics methods.
The deadline for applications is Friday 15th August 2014. Interviews are likely to be held in late September or early October 2014. The fellow would be expected to start in late 2014 or early 2015.
Applicants should apply at:
Register now for our first International Zebrafish and Medaka Course, July 14 - 18, 2014. It is open to technicians, students, graduates, postgraduates and PIs and will follow the FELASA B concept.
Prof. Dr. Uwe Strähle
Karlsruhe Institute of Technology (KIT)
European Zebrafish Resource Center (EZRC)
76344 Eggenstein- Leopoldshafen
The Institute of Genetics and Toxicology and the European Zebrafish Resource Center at the Karlsruhe Institute of Technology are looking for an outstanding candidate who will develop a PhD research programme in a transdisciplinary team of biologists, engineers and informaticians. The candidate should have an excellent background in molecular cell biology, developmental genetics and have a flair for engineering and computing.
As part of a genome-wide collaborative screen of zebrafish knock-out mutations provided by the Sanger Institute we want to characterize the genes necessary for the earliest behavior of the zebrafish, namely the light-induced motility before hatching and in larval stages up to day 5. We will use a highly automated photomotor response (PMR) assay that is based on the one developed by the laboratory of Randall Peterson (Harvard University) and which we have established at the KIT in collaboration with him. In chemical screens, this assay has allowed to functionally characterize known psychoactive substances and to identify new candidate molecules. In our genetic screen, we will identify genes affecting the photomotor response and compare these responses to those previously observed for particular psychotropic drugs. The candidate shall participate in the screens and develop a PhD programme within this research framework.
The candidate will participate in the BioInterfaces International Graduate School that offers a structured PhD programme with specialized training opportunities including soft skill courses, seminars and summer schools in a highly interdisciplinary environment.
For further information see
The new website of the European Zebrafish Resource Center (EZRC) with a searchable catalog of fish lines is now publicly accessible at http://ezrc.kit.edu.
Our zebrafish stock collection contains several thousand mutations from the laboratory of Christiane Nüsslein-Volhard (Tübingen I, Tübingen 2000 and Tübingen EU screen) and from the Sanger Mutagenesis Project (starting with library SL4) as well as transgenic and wildtype lines. Additionally we offer plasmids, sequencing services, genetic screening of Sanger mutations, and chemical screens.
8-15 September 2013, Karlsruhe, Germany
We would like to welcome applications to the EMBO zebrafish workshop that will take place at KIT, Karlsruhe (Germany) in the fall of 2013. The objective of this EMBO Workshop is to provide theoretical and practical background on the zebrafish model system for direct assessment of open questions using modern microscopy techniques.
We encourage you to share the information on the EMBO course among potential applicants, aiming at experiencing the latest microscopy techniques to study development of nervous system using zebrafish.
For more information on the workshops please visit following webpage:
We look forward to meeting you during the course.
Steffen Scholpp, Lucia Poggi, Mihaela Zigman, Uwe Straehle, Robert Geisler
Registration Submission Deadline: 15th June 2013.
Dear zebrafish researchers,
ZF-HEALTH is proud to announce the workshop on "Zebrafish Models in Translational Medicine" which will take place in Courcelles-sur-Yvette, France, on October 2-4, 2013.
This international meeting is co-organized by the EU FP7 Integrating Project ZF-HEALTH "Zebrafish Regulomics for Human Health" and the European Society for Fish Models in Biology and Medicine “EuFishBioMed”. The aims of the meeting are to provide a stimulating debate on the current knowledge and approaches relevant to long term human pathologies, thanks to the contributions of renowned experts in the medical field; and to pave the way to novel approaches and collaborations using animal models. Within the past decades, advances in understanding the biology of long term human pathologies have been made possible in large part thanks to the development of molecular genetics and cellular biology tools. In a parallel way, the emergence of new animal models, such as zebrafish, has allowed to develop in vivo paradigms for human pathologies, based on the conservation of the genome and the particular technical qualities of the model, including easy in vivo imaging, embryo/genome manipulation and simplified large scale chemical/drug testing.
For more information on the meeting please visit following webpage:
Abstract and registration deadline: 31st July 2013
We look forward to seeing you at the meeting in October.
The scientific organizing committee:
Francesco Argenton (University of Padua)
Laure Bally-Cuif (CNRS, Gif-sur-Yvette)
Marina Mione (KIT, Karlsruhe)
Frederic Rosa (INSERM, Paris)
Freek van Eeden (University of Sheffield)
On behalf of the ZF-HEALTH consortium and EuFishBioMed COST action partners we would like to invite participants to the forthcoming workshop on
Automation methods for zebrafish research
This workshop will be held at the University of Leiden, NL, 18-19 April 2013 (see Invitation attached)
Please register and upload your abstract at: www.lifesciencemethods.com/#menu=workshop
Spaces are limited, so please register soon to avoid disappointment.
Deadline for registration: 18th of March 2013
Herman Spaink (University of Leiden, NL), Uwe Strähle (KIT, Karlsruhe, Germany), Jan de Sonneville (Life Science Methods BV, Leiden, NL), Christian Pylatiuk (KIT, Karlsruhe, Germany).
E-mail contact: firstname.lastname@example.org
Genomics and high throughput sequencing technologies with the zebrafish model
This workshop will be held at the Møller Centre, University of Cambridge, UK between 10-11 December 2012.
Enquiries, registration forms and poster abstracts should be sent to:
Spaces are limited, so please register soon to avoid disappointment.
Please note that the deadline is extended to November 23, 2012!
Press Release 121/2012
Many Findings Can Be Transferred to Humans – Opening of the First Zebrafish Resource Center in Europe and First Screening Center in the World on KIT Campus North
Zebrafish are considered ideal model organisms for biomedical research.
Zebrafish share most organ systems with humans. This makes them ideal model organisms to study the causes of human diseases like cancer or heart diseases. For this purpose, research needs a variety of zebrafish lines. With the European Zebrafish Resource Center (EZRC), Karlsruhe Institute of Technology (KIT) is now opening the first central repository for such lines in Europe. The EZRC is funded jointly by the Biointerfaces programme of the Helmholtz Association and the Klaus Tschira Foundation. The Klaus Tschira foundation provides a funding of 1.5 Million Euro over three years.
Representatives of the media are cordially invited to come to the official opening on Wednesday, July 18, 11 hrs on KIT Campus North.
“Zebrafish are robust, small, and reproduce quickly. Being vertebrates, they share most major organ systems with humans. This makes them ideally suited for biomedical research,” explains Professor Uwe Strähle, Head of the Institute of Toxicology and Genetics (ITG) that operates the Zebrafish Resource Center on KIT’s Campus North. “Zebrafish repair a spinal cord lesion, heart or kidney diseases or a damaged optic nerve all on their own. Their organ function is restored completely.”
Moreover, their eggs are transparent and develop outside of the body of the mother. This allows researchers to observe the development of organs or even individual cells in the embryo as well as in the larva, which is also transparent, without harming adult animals. Such experiments may replace numerous animal experiments with rats or mice. The fish are ideally suited to studying the causes of cancer, heart disease, and behavioral disorders and to evaluating potential drugs. In recent years, laboratories in Europe alone have generated thousands of zebrafish lines, each of which carries either a particular mutation that can serve as a model for human disease, or a fluorescent marker that labels a particular tissue. However, European researchers have been lacking a central repository to store and distribute these fish. The European Zebrafish Resource Center will meet this need in the future. The EZRC has over 3,000 aquaria for keeping live fish as well as freezers capable of holding about 80,000 sperm samples. The EZRC will also be the first zebrafish screening center worldwide, welcoming guest researchers who will perform systematic research on its collection. The scientists will be provided with technologies such as high-throughput synthesis of drug candidates, genome sequencing, and robotics and software developed in-house for sample handling, microscopy, and image analysis. The EZRC will also be the central hub of ZF-HEALTH, a recently started collaborative project funded by the European Commission’s 7th Framework Programme.
For more information, click: www.itg.kit.edu/ezrc
The grand opening ceremony of the EZRC will take place on Wednesday, July 18, 11 hrs, at the Leibniz Saal of the Fachinformationszentrum (FIZ) on KIT Campus North (building 240, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany).
Program of the Opening Ceremony
All presentations will be given in German.
11.00 hrs Welcome addresses
Professor Doris Wedlich, Chief Science Officer, KIT
Professor Christiane Nüsslein-Volhard, Director of the Department of Genetics, Max Planck Institute for Developmental Biology, Tübingen
11.25 hrs “Warum Zebrafische und dann auch noch so viele?“ (“Why zebrafish and why so many?“)
Professor Uwe Strähle, Head of the Institute of Toxicology and Genetics, KIT
11.40 hrs “Zebrafische helfen die Komplexität des Gehirns zu verstehen” (“Zebrafish help understand the complexity of the brain”)
Professor Wolfgang Driever, Head of the Department of Developmental Biology, University of Freiburg
11.55 hrs Opening and opening film of EZRC
12.15 hrs Reception
About the Klaus Tschira Foundation
The Klaus Tschira Foundation (KTS) supports natural sciences, mathematics, and computing and wishes to further promote work in these areas. This is a federal undertaking that starts at the kindergarten level and continues through to schools, universities, and research institutions.
Further information: http://www.klaus-tschira-stiftung.de
“ZF-HEALTH – Zebrafish Regulomics for Human Health” is a large-scale integrating project funded by the European Commission as part of its 7th Framework Programme, encompassing 19 partner organizations in nine countries, and coordinated by Karlsruhe Institute of Technology. The project started on July 01, 2010 and is scheduled to run over a period of five and a half years. Further information: http://zf-health.org
Karlsruhe Institute of Technology (KIT) is a public corporation according to the legislation of the state of Baden-Württemberg. It fulfills the mission of a university and the mission of a national research center of the Helmholtz Association. KIT focuses on a knowledge triangle that links the tasks of research, teaching, and innovation.
For further information, please contact:
Presse, Kommunikation und Marketing
Phone: +49 721 608-48121
Fax: +49 721 608-45681
margarete lehne∂kit edu
The photo of printing quality may be requested by presse∂kit edu or phone: +49 721 608-47414. The press release is available as a PDF file.
Imperial College and MRC Clinical Sciences Centre, London, UK
Boris Lenhard's group: http://www.csc.mrc.ac.uk/Research/Groups/EPI/ComputationalRegulatoryGenomics/
On 01 November 2011 I am moving to Imperial College London (joint position with MRC Clinical Sciences Centre), together with part of my current group. We have four vacant positions in London, all on very exciting projects, and I would be very grateful if you could help me spread the word so I could fill them with the best possible people.
The positions are:
Postdoctoral career development fellow (computational biology)
Closing date: 25 September 2011
Scientific Programmer (Bioinformatics)
Closing date: 25 September 2011
Postdoctoral researcher in computational genomics, on ZF-HEALTH project (EU FP7)
Closing date: 16 October 2011
Senior Research Bioinformatician/Scientific programmer, on ZF-HEALTH project (EU FP7)
Closing date: 16 October 2011
Many thanks for your help,
The BOLD Marie Curie Initial Training Network and the ZF-HEALTH Consortium are co-organizing a workshop for graduate students and junior postdoctoral researchers on "Cutting Edge Technologies in Biomedical Research", to be held on May 4-6, 2011 - Karlsruhe Institute of Technology (KIT), Germany.
Topics will include: High-throughput screening, 3D imaging, next generation sequencing, database resources, zinc finger nuclease knock-out, research management and ethics.
Speakers: Randall Peterson, Cambridge MA; Stefan Schulz, Karlsruhe; Holger Erfle, Heidelberg; Markus Reischl, Karlsruhe; Michael Boutros, Heidelberg; Jochen Wittbrodt, Heidelberg; Lars Hufnagel, Heidelberg; Clemens Grabher, Karlsruhe; Urban Liebel, Karlsruhe; Ferenc Mueller, Birmingham; Uwe Straehle, Karlsruhe; Boris Lenhard, Bergen; Lars Juhl Jensen, Copenhagen; Keith Joung, Cambridge MA; Tim Frayling, Exeter; Didier Stainier, San Francisco.
General information: There is no registration fee. Accommodation costs will be covered by the workshop organization, but participants are responsible for their own travel expenses. 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. Up to 30 participants will be selected by the ZF-HEALTH Consortium, half of these places are reserved for ZF-HEALTH participants.
The deadline is now extended to March 27, 2011.
To mark the start of the ZF-HEALTH project, a kick-off meeting was held in Bad Herrenalb in the Black Forest on July 24 – 25, 2010, hosted by the Karlsruhe Institute of Technology. The meeting was attended by 22 senior scientists reprenting most of the Consortium partners, and Prof. Monte Westerfield representing the Scientific Advisory Board.The agenda included a preview of the work to be performed in each of the work packages and discussions on strategies for mutants selection, phenotyping and chemical screens, as well as on intellectual property issues. The Consortium endorsed proposals to hold the first ZF-HEALTH workshop in Karlsruhe and the next project meeting in Zürich, in the summer of 2011.