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Dear Colleague:

 

Each year, the International Zebrafish Society (IZFS) presents two prestigious awards at its annual International Zebrafish Conference – the George Streisinger Award and the Chi-Bin Chien Award.

IZFS is currently seeking nominations from the zebrafish community for consideration by our Awards Committee.  We are extending the deadline to February 4 for the Chi-Bin Chien Award.

The Chi-Bin Chien Award will be given to an outstanding graduate student, postdoctoral trainee, or recently appointed faculty member from any country who has made significant contributions to the field of zebrafish research and has exhibited the generosity and openness that characterized and motivated Dr. Chien.   Submit applications to awards@izfs.org in a single PDF file that includes:

  1.  A one-page statement from the nominee describing his/her research and its importance to the advancement of zebrafish research.
  2. The nominee's C.V.
  3. Letter of recommendation from the mentor.
  4. Letter of recommendation from one additional scholar who is familiar with the research being described in the application.


For information about nominating a colleague or to make a donation to this award, please go to https://www.izfs.org/page/CBCAWARDNOM

We hope to see you in Suzhou in June at the 14th IZFC (https://www.izfs.org/page/2019IZFC) as these awards are presented to our honored colleagues.

 

Thank you,
Mary Mullins
IZFS President

We are excited to host the bi-annual 2019 Midwest Zebrafish Meeting at the University of Kentucky on June 7-9. This meeting brings together scientists from all over the Midwest and beyond, whose research utilizes the zebrafish model to study a wide range of biological questions in development, genetics, physiology, and disease. The two-day meeting will include two keynote talks, talks selected from abstract submissions, poster sessions, and a Saturday evening social, all in a friendly and supportive environment. This meeting is a wonderful opportunity for investigators in the region to network with each other, and we especially encourage students, postdocs, and junior investigators to attend and present their research.

The conference website, https://2019midwestzfmeeting.uky.edu/ is now live and additional information will be posted there soon. 

Conference registration and abstract submission will begin in early April.


by Sabrina Toro, on behalf of the ZFIN and Alliance teams

The Zebrafish Information Network (ZFIN; zfin.org) is one of the founding members of the Alliance of Genome Resources (Alliance; alliancegenome.org). The Alliance aims to provide a unified, comparative view of animal model and human data to facilitate foundational and translational biomedical research.

The ambitious effort to unify variant and allele information is currently underway, with the objective to compare human and animal model variants and alleles, their consequences, and the phenotypes they might induce.

Genomic coordinates and nucleotide change(s) of alleles/variations are becoming crucial information in order to make the variants/alleles and associated phenotype data relevant and accessible for display, prediction, cross-species comparison, and translational research application. Genome browsers (such as JBrowse) and tools to predict the effects of variants on transcripts and proteins (such as the Ensembl Variant Effect Predictor) require this genomic coordinate information. Precise genomic coordinate locations must include the genome build, chromosome and base number(s) in order to properly locate any variation. This detailed information is rarely reported in publications and therefore is often unavailable for alleles/variants recorded at ZFIN.

We need the zebrafish community’s help to obtain this missing information, and ultimately make the zebrafish alleles/variants information more relevant and valuable to the research and clinician community. If you have the build version, chromosome, genomic coordinates and nucleotide change of your mutant, or if you have any sequence data which would help us determine the location, please add this information to the genomic coordinates Excel file and submit to Sabrina@zfin.org. Feel free to contact us (sabrina@zfin.org) for more information, or with questions or comments.

Key Dates:  

Abstract submission open: April 1, 2019

Abstract submission deadline: May 15, 2019

Early registration deadline: June 31, 2019

Cover page design competition deadline: July 31, 2019

4th ZPPM Conference: Sept 18 – 20, 2019

3rd Neuroscience Workshop: Sept. 18, 2019 

 

Organizer: Zebrafish Centre for Advanced Drug Discovery (ZCADD), Toronto, Canada

Awards: ZebraPeutics Award X1; Travel Awards x3; Poster Awards x 6; Cover Design Award x1

 

4th ZPPM Conference Organizing Committee:

  • Randall Peterson (Co-Chair, University of Utah, USA)
  • Didier Stainier (Max Planck Institute for Heart and Lung Research, Germany)
  • Han Wang (Soochow University, China)
  • Sarah Childs (University of Calgary, Canada)
  • Xiao-Yan Wen (Chair, ZCADD, St. Michael’s Hospital, Canada)

3rd Z-BRAIN Neuroscience Workshop Organizing Committee:

  • Edward Burton (Co-Chair, University of Pittsburgh, USA)
  • Marika Kapsimali (IBENS, Paris, France)
  • Christopher Barden (Treventis Corp, Toronto, Canada)
  • Kessen Patten (INRS Institut Armand-Frappier, Montreal, Canada)
  • Xiao-Yan Wen (Chair, ZCADD, St. Michael’s Hospital, Toronto, Canada)

 

Conference website: 

https://www.zebrafishcentre.com/conference-2019/

 

Conference e-mails:

zconference@smh.ca

Dear Colleagues:

 

Each year, the International Zebrafish Society (IZFS) presents two prestigious awards at its annual International Zebrafish Conference – the George Streisinger Award and the Chi-Bin Chien Award.  IZFS is currently seeking nominations from the zebrafish community for consideration by our Awards Committee. Nominations are due January 28, 2019.

 

The George Streisinger Award recognizes a senior investigator who has done sustained and foundational work that has opened new possibilities within the zebrafish field that benefit our research today.  Submit applications to awards@izfs.org in a single PDF file that includes:

  1. A statement (up to one page) describing the key contributions of the nominee to the field, co-signed by two or more members of the community who support the nomination.
  2. A list of up to ten publications or links to online resources or databases that illustrate the central contributions of the nominee to the field.

For more information, go to https://www.izfs.org/page/StreisingerAwardNew.

 

The Chi-Bin Chien Award will be given to an outstanding graduate student, postdoctoral trainee, or recently appointed faculty member from any country who has made significant contributions to the field of zebrafish research and has exhibited the generosity that characterized and motivated Dr. Chien.   Submit applications to awards@izfs.org in a single PDF file that includes:

  1.  A one-page statement from the nominee describing his/her research and its importance to the advancement of zebrafish research.
  2. The nominee's C.V.
  3. Letter of recommendation from the mentor.
  4. Letter of recommendation from one additional scholar.


For more information or to make a donation to this award, please go to https://www.izfs.org/page/CBCAWARDNOM

 

We hope to see you in Suzhou, China in June at the 14th International Zebrafish Conference (https://www.izfs.org/page/2019IZFC) where these awards will be presented to our honored colleagues.

 

Thank you,
Mary Mullins
IZFS President


Dear Colleagues:                                                            

As the local organizing committee, we cordially invite you to attend the 14th International Zebrafish Conference (IZFC), which for the first time will be held in the Asia-Pacific region, the Suzhou International Expo Center, Suzhou, China, June 12 (Wednesday) – June 16 (Sunday), 2019. 

Suzhou is well known for its ancient gardens and picturesque scenery. Just like the great traveler Marco Polo described as "Heaven on Earth" and "Venice in Orient", Suzhou features a unique style of “small bridges, running water and households".  Suzhou also is one of the most developed areas in China with a booming economy and highly modernized metropolitan districts. There are two major international airports connecting the world to Suzhou:the Shanghai Pudong International Airport and the Shanghai Hongqiao International Airport, which are approximately 75 miles or 45 miles away from Suzhou, respectively. 

Following the traditions of both the Madison and European Zebrafish Conferences, you will enjoy keynote speeches, awardee lectures, plenary session and concurrent session/workshop talks, and poster sessions, covering all areas of studies using zebrafish and other fish models

To emphasize the importance of trainee and junior faculty professional development, both Trainee Professional Development Workshops and Junior Faculty Workshops will be held on June 12, 2019, the first day of the conference. The Trainee Professional Development Workshops are devoted to scientific and career development activities for trainees (primarily graduate students and postdocs), including a keynote address and a series of workshops on various topics as well as one-on-one blitz discussions, and providing opportunities for the next generation of zebrafish researchers to learn from and interact with faculty members in a more informal and intimate setting. The Junior Faculty Workshops aim to foster the growth and success rate of the next generation of zebrafish researchers by learning from and interacting with established faculty members in a more informal and intimate setting, and a panel of experienced members of the zebrafish field will participate in each meeting, to provide tips and advice to junior faculty members and answer questions.

In addition, the Meet the Professor sessions will provide trainees the opportunity to interact with experienced faculty members in the zebrafish field and to foster scholarly conversation throughout the conference. 

To help us craft the scientific program of the 14th IZFC, we launch Call for Session or Workshop Proposals. Any fish independent investigator will be encouraged to submit a proposal for a plenary session, a concurrent session or a concurrent workshop for our conference, and the Conference Program Committee will select sessions and workshops from these proposals. For those who need financial assistance to attend the Conference, please fill out the Travel Award Application Form. In addition, the Conference Logo Competition is open. 

✔  Please register for the Conference at http://2019IZFC.suzhou.zfish.cn.

 

✔  Please submit your Session or Workshop proposal and/or Conference logo artwork by February 28, 2019.

 

✔  Submit travel award application form by February 28, 2019.

 

✔  Interested sponsors and exhibitors, please contact Dr. Zhaomin Zhong (Tel: +86 15895562190, Email: zhongzhaomin@suda.edu.cn) or Conference Secretariat (the14thIZFC_suzhou@vip.163.com).

We are looking forward to welcoming you in Suzhou, China in June 2019!

Sincerely,

Local Organizing Committee

Han Wang, Feng Liu, Yonghua Sun, Jing-Wei Xiong, Jiu-lin Du, Lingfei Luo, Zilong Wen, Tao Zhong, Bo Zhang, Ying Cao, Jinrong Peng and Anming Meng

 

We are very pleased to draw your attention to a session at SETAC Europe 2019 with the title: Fish model species in human and environmental toxicology. The session is part of the main track 1-Ecotoxicology and human toxicology (from molecules to organisms, from omics to in vivo). The meeting is held in Helsinki, Finland 26-30 May 2019. Details about submitting a proposal are available on the meeting website https://helsinki.setac.org/. The deadline for abstract submission is 28 November 2018.  We hope to receive many fascinating abstracts and are looking forward to a fruitful meeting in Helsinki.

 

Jessica, Riccardo and Jorke

 

 

Fish model species in human and environmental toxicology

  

CHAIRS: Jessica Legradi, Riccardo Massei, Jorke Kamstra

 

Fish models are commonly used in human and ecotoxicological research to investigate the impact of chemicals on whole organisms. In fact, many important biological functions are conserved between fish species and humans. Fish have a wide application domain, spanning from basic developmental biology, neurobiology, endocrinology to immunology. The small size of some available fish species including the zebrafish (Danio rerio) or medaka (Oryzias latipes) and their robust nature makes them ideally suited for application in automated high throughput screening. Furthermore, fish early life stages offer all the key attributes of a complex in vivo system (e.g. including metabolism), as well as the advantages of the in vitro assays, as tests can be conducted in multiwell plate formats with small sample volumes and run in short periods of time. These characteristics make them well suited for toxicity testing of environmental samples and to detect unknown contaminants in effect directed analysis (EDA). Research on fish over the last decade has been greatly facilitated by the increasing number of sequenced genomes, which are available for more than twelve species with more pending. This, together with recent advances in genetic and epigenetic studies, including gene knockout and transgenesis technologies, greatly facilitates the understanding of the molecular mechanisms of toxicity, making fish ideally suited for defining adverse outcome pathways (AOPs). Due to the large similarity with other vertebrates, there is also a growing interest in the application of fish model species in human disease etiology and early development. Fish early life stages have recently been used in several cancer genetics studies and drug discovery tests. In ecotoxicology, fish are also studied outside of the laboratory in their native environment. Prominent models for native fish models are roach (Rutilus rutilus) and rainbow trout (Oncorhynchus mykiss). Studying fish in their natural habitat allows to investigate further than simple dose-effect assessments. Within this session, we intend to show recent developments in toxicological research using a variety of different fish model species, novel systems, endpoints, assays and testing strategies. We will focus on molecular approaches that could lead to new AOPs. Results of toxicity studies of single stressors as well as complex environmental samples are of interest. Molecular effects, multigenerational effects, and population level impacts will be considered. We especially welcome presentations highlighting new Omics approaches for metabolomics, transcriptomics, epigenomics, proteomics and lipidomics, ideally linking these to phenotype for use in AOPs. The session will be interdisciplinary and bring together researchers across a wide range of research areas with the view to enhance approaches for studying adverse effects in human and wildlife.

PRELIM SESSION TYPE:

Platform and Poster

Dear zebrafish researchers,

My lab has generated more than 1,600 transgenic fish lines that express Gal4 in specific organs, tissues and cells, which should be potentially useful for many purposes. You may look at these expression patterns partly on the web database (http://kawakami.lab.nig.ac.jp/ztrap/). However, the database contains only a couple of side-view images that were taken by a stereoscope during our routine screening. If you are interested in particular expression patterns, I recommend for you to visit my lab, perform "shelf-screen", look at them by your eyes more precisely, and find lines that are useful for your research.

Our institute provides an opportunity to support travel expenses from foreign countries to our institute. Please look at the web site of the institute.

https://www.nig.ac.jp/nig/research-infrastructure-collaboration/nig-collaboration-grant-2

There are three systems. You may apply for collaborative research NIG-JOINT A (up to 200,000JPY for travel expense) or NIG-JOINT B (up to 1,000,000JPY for travel expenses and some research money) or NIG-JOINT I (up to 500,000JPY for travel expenses for foreign researchers) (B and I are a bit competitive. You may apply for A simultaneously).


The deadline of the application is 14th December, 2018.

If you are interested in this, please contact me (kokawaka@nig.ac.jp).

Best wishes,
Koichi Kawakami

******************************
Koichi Kawakami, Ph.D.
Professor
Division of Molecular and Developmental Biology
National Institute of Genetics
1111 Yata
Mishima
Shizuoka 411-8540
Japan
Tel: +81-55-981-6740
Fax: +81-55-981-5827
Email: kokawaka@nig.ac.jp
Homepage: http://kawakami.lab.nig.ac.jp
******************************

Scientific Organizers:

Margaret A. Goodell, Baylor College of Medicine

Laura A. Johnston, Columbia University

Thomas P. Zwaka, Icahn School of Medicine at Mount Sinai

 

The four-day conference will:

  1. Bring together, for the first time, researchers from diverse fields who study competitive and cooperative interactions between cells;
  2. Cover recent findings on quality control systems, developing tissues, stem cell populations and tumorigenesis, as well as address important evolutionary aspects of competitive and cooperative behavior in diverse model systems;
  3. Define critical questions shared by the diverse investigators and help shape this exciting and emerging field.

 

Deadlines:

  • Scholarship Applications and Discounted Abstract – October 24, 2018
  • Abstract – November 28, 2018
  • Discounted Registration – January 8, 2019

 

For more information, please visit www.keystonesymposia.org/19B6 and for a flyer, visithttp://www.keystonesymposia.org/index.cfm?e=Web.Meeting.Flyer&MeetingID=1615.

 

The 8th Strategic Conference for Zebrafish Investigators (SCZI/PI meeting) 

Sponsored by the International Zebrafish Society (www.izfs.org

January 12-16, 2019

Asilomar Conference Grounds in Pacific Grove, CA

 

This is the meeting of zebrafish primary investigators and lab heads from around the world.

 

Abstracts are due October 27, 2018.

 

A preliminary program is available at: https://www.izfs.org/page/SCZI2019program

 

Keynote speakers include Ehud Isacoff of the Helen Wills Neuroscience Institute at the University of California-Berkeley and Steven Haddock of the Monterey Bay Aquarium Research Institute

 

Exhibit and sponsorship opportunities are available

https://www.izfs.org/page/sczi_2019

 

Contact: info@izfs.org


The 2nd Italian Zebrafish Meeting will be held in Pisa from January 30th to February 1st 2019, organized by the University of Pisa, the CNR, the Scuola Normale Superiore, the Stella Maris Foundation, ISPRO and the Guido Bernardini Foundation (here the website: https://zfim2019.webs.com/).

The previous edition of this event was attended by about 200 investigators and specialists from Europe and USA.

The conference will be divided into 3 days of study and a poster area; at the end of each day there will be a debate on the topics presented, in particular focusing on the development of the zebrafish model and health issues. In addition an exhibitor area will be organized in parallel so it could be an attractive target for sponsor interaction since participants represent key decision-makers in purchasing decisions. 

Please join us on October 15-18, 2018 at the EMBL-EBI campus in Cambridge/UK to learn how to analyze RNAseq data in zebrafish. 


In this hands-on course, participants will learn how to design functional genomics experiments and how to manage and analyse such datasets from zebrafish and to compare these to other species. The course will be relevant to researchers working on a wide range of topics, but will use a number of cancer datasets as the basis for hands-on analysis. The final day will provide participants with an opportunity to apply the tools and resources introduced during the previous teaching sessions by undertaking a short problem solving session.


Audience: This course is aimed at researchers currently working with zebrafish and generating genomic and functional data. No prior bioinformatics knowledge is required, but knowledge of R and web-based packages would be beneficial. Trainees with limited experience of R will be provided with pre-course preparation materials to increase their R knowledge.  Trainees, junior and senior group leaders are all invited to apply! 

Outcomes

At the end of the course you will be able to:

  • Design and implement RNA-Seq experiments using Zebrafish
  • Know and apply common approaches and tools used in the analysis of zebrafish expression data
  • Undertake basic data visualisation
  • Query RNA-Seq datasets for gene signatures
  • Undertake cross species comparison of gene datasets


https://www.ebi.ac.uk/training/events/2018/bioinformatics-functional-genomics-zebrafish


Space is limited to 30 participants and an application process is required. Deadline is July 27, 2018

Please forward and post. 


Organized by: 

 Elizabeth Busch-Nentwich (Cambridge U), Sarah Morgan (EMBL-EBI) and Kirsten Sadler (NYU Abu Dhabi) 



Dear zebrafish user community, 

we are proud to announce the first release of the DANIO-CODE track hub for zebrafish developmental epigenomics and transcriptomics datasets. It contains almost a 1000 tracks with 17 assay types (ChIP-seq, RNA-seq, ATC-seq, CAGE-seq etc.) from 38 stages of development. The raw data of 30 labs were annotated and reanalyzed by standardised pipelines to create the track hub, which is currently available to upload to UCSC or Ensembl genome browsers at https://danio-code.zfin.org

For information on how to access data, on fair use policy and how to upload new data to the resource, please visit the Data Coordination Centre: https://danio-code.zfin.org.

To learn more about DANIO-CODE visit https://www.birmingham.ac.uk/generic/danio-code/index.aspx.

For enquiries on technical matters contact daniocode@gmail.com.

For general enquiries contact daniocode.enquiries@gmail.com. 

Please spare some time to browse the datasets and to check you favourite gene, to reveal its expression and its true promoter, to predict its enhancers and non-coding RNAs around them and many more…The first release is a beta version, please send feedback to the emails above.

Acknowledgements:

Massive thank you to Matthias Hörtenhuber, Kadir Mukarram, Michael Dong and Carsten Daub at Karolinska Institutet as well as to Damir Baranasic and Boris Lenhard at Imperial College, who have been the main drivers behind the recently achieved DANIO-CODE milestone. 

Thanks extend to Marcus Stoiber at Berkeley and Ben Brown at Berkeley/Birmingham for their work at the early stages of data collecting/processing pipeline development. Anne Eagle, Monte Westerfield and their colleagues at ZFIN for hosting and managing the datasets and WIKI, Matthias Hörtenhuber, Julia Horsefield (Otago), Bernard Peers (Liege) and Shelley Jukes (Birmingham) for helping with management and Fiona Wardle (KCL), Boris Lenhard for their major contributions in lobbying/applying for funds and DANIO-CODE meeting organisations. Further acknowledgements goes to all the data producers (see DCC) particularly those, who submitted unpublished data: Elisabeth Busch-Nentwich (Sanger), Antonio Giraldez (Yale), Tatjana Sauka-Spengler (Oxford), Jose Louis Gomez Skarmeta (UPO Sevilla) and their colleagues. Finally, we need to acknowledge the financial support by the European Commission’s  H2020 Marie Sklodowska-Curie programme to ZENCODE-ITN and the BBSCR, UK. 

We hope this achievement will not only help in learning about the zebrafish genome, it will also motivate all of us to submit additional, published and unpublished datasets to keep this resource growing for the benefit of the user community. 

Again, huge thanks to those who did this great job and wishing you as much fun as we have had with browsing the datasets in their full glory:).  

best wishes, 

Ferenc

On behalf of DANIO-CODE and ZENCODE-ITN partners

Ferenc Mueller f.mueller@bham.ac.uk