ZFIN groups reagents that target a specific nucleotide sequence, Morpholinos (MOs), CRISPRs and TALENs together and calls them sequence targeting reagents (STR). When one of these reagents is published, ZFIN staff checks that the published sequence matches the genome and contacts authors if there are any questions about either the MO sequence or the target sequences of TALENs and CRISPRs. The most common issues are: sequences that aren’t reported in the paper or sequences that don’t match the current genome build. Once the sequences are checked they are added to ZFIN, and are incorporated into reagent specific BLAST databases (https://zfin.org/action/blast/blast ) and where possible mapped onto the genome.
To map the STR targets in the genome the sequences are analyzed using Bowtie (http://bowtie-bio.sourceforge.net/index.shtml) and mapped onto the genome for display on the ZFIN GBrowse map (http://zfin.org/gb2/gbrowse/zfin_ensembl/?label=knockdown_reagent). This mapping location is displayed on the individual data pages as thumbnails of the genomic region. If a sequence doesn’t match the genome sequence an image doesn’t appear on the reagent page. When a STR hits multiple places exactly the locations are all shown on the page as an example MO1-mir375-1,mir375-2 targets both mir375 genes (https://zfin.org/ZDB-MRPHLNO-071106-1). Many Morpholinos don’t match the genome because they were either targeted to an older version of the genome, or they cross a splice site so there isn’t an uninterrupted genome match. Multiple equivalent genome matches occur for several reasons; in some cases the reagents were designed to hit multiple genes in the same family but many other cases exist where multiple target sites seems to have been unintentional.
We always recommend double checking the target of a knockdown reagent. If there is no image on a page it is a sign that reagent might not target as expected.
The Alliance of Genome Resources, With ZFIN as a Founding Member, Opening Doors with Version 1.0 Website Release
For the past year, ZFIN has been working with members of the other major National Institutes of Health NHGRI-funded Model Organism Database (MOD) groups, and the Gene Ontology Consortium, to establish The Alliance of Genome Resources (The Alliance; www.alliancegenome.org). The Alliance now announces the release of the Alliance of Genome Resources website 1.0 - providing unified access to comparative genetics and genomics data from the Alliance data resources (www.alliancegenome.org). The MODs currently included in the Alliance in addition to ZFIN are the Saccharomyces Genome Database (SGD), FlyBase, WormBase, Mouse Genome Database (MGD), and Rat Genome Database (RGD). In addition, the Alliance includes the Gene Ontology (GO) Consortium. These groups will merge key activities and data representations, coordinating data retrieval and analysis, within a comparative perspective. The Alliance aims to provide a synergistic integration of expertly-curated information about the functioning of cellular systems from model organisms, including zebrafish, and humans to facilitate better understanding of human biology and disease. Other MODs and related resources will be added to the Alliance going forward.
As part of the initial 1.0 website release, Alliance working groups have focused on the ability to easily access pages that summarize details of Genes and Diseases, with extensive representation of orthology data, and with access to multi-track JBrowse capabilities primarily for visualization of sequence data. Gene details, functional information, and disease associations are provided with a comparative perspective. As the MOD and GO teams make progress with inclusion of additional data types, the vision going forward includes the incorporation of other model organism information resources and bioinformatic tools within a common data platform, facilitating data access, comparative analyses, and cross-species data integration.
If you have questions about The Alliance in general or the Alliance website contact email@example.com. ZFIN provides all the zebrafish data found at the alliancegenome.org website, so if you have questions about zebrafish data specifically, feel free to contact us directly at firstname.lastname@example.org.
19th Australia and New Zealand Zebrafish Meeting (Jan 29 - Feb 1, 2018; Sydney, Australia)
The annual Australia-New Zealand Zebrafish Meeting will be held at North Wollongong, NSW from Monday Jan 29 to Thursday Feb 1. Our meeting has a strong emphasis on trainee presentations but international visitors are welcome.
Please see the meeting website for further details including keynote speakers, travel and accommodation information, and a preliminary timetable: https://www.garvan.org.au/symposium/anzzebrafish
Registration and abstract submission close December 15th.
Dear zebrafish researchers,
My lab has generated more than 1,500 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 on the web database (http://kawakami.lab.nig.ac.jp/ztrap/). However, the database contain 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.
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 18th December, 2017.
If you are interested in this, please contact me (email@example.com).
We are very pleased to draw your attention to a session at SETAC Europe 2018 with the title: Fish model species in human and environmental toxicology. The session is part of the main track: Ecotoxicology and human toxicology: from molecules to organism, from omics to in vivo. The meeting is held in Brussels, Rome, Italy 13-17 May 2018. Details about submitting a proposal are available on the meeting website https://rome.setac.org/. The deadline for abstract submission is 29 November 2017. We hope to receive many fascinating abstracts and are looking forward to a fruitful meeting in Rome.
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
NCBI webinar Disambiguating common author names Wed, Oct 4 12 noon EDT http://bit.ly/2wq0dE8 get an ORCiD to help link papers to your ZFIN record.
On October 4, 2017, NCBI staff will present a webinar on author disambiguation and the advantages of using an ORCID ID.
Disambiguating common author names is tough in any field, but if your published research is cited in PubMed, we can help you find your citations, create a bibliography, and share your publication list with others.
In this webinar, we'll also talk about the advantage of quickly registering for a free, unique identifier that will remain constant - even if your name changes.
Date & time: Wednesday, October 4, 2017 12:00 PM - 12:30 PM EDT
Register here: http://bit.ly/2wq0dE8
After registering, you will receive a confirmation email with information about attending the webinar. After the live presentation, the webinar will be uploaded to the NCBI YouTube channel. You can learn about future webinars on the Webinars and Courses page.
* NCBI YouTube channel: https://www.youtube.com/user/NCBINLM
* Webinars and Courses: https://www.ncbi.nlm.nih.gov/home/coursesandwebinars.shtml
Between approximately 7:55am and 8:50am PDT today, http://zfin.org and affiliated sites such as wiki.zfin.org, zebrafishmine.org, and ftp.zfin.org were unavailable due to a widespread network outage at the University of Oregon. We believe all network services have now been restored. If you experience any further problems or have any questions, please contact us (firstname.lastname@example.org). Our apologies for any inconvenience.
Keynote Speaker: Randall Peterson, University of Utah, USA
Young FishMed Keynote Speaker: Benoit Vanhollebeke, Université libre de Bruxelles, Belgium
Catherina G. Becker, University of Edinburgh, UK
Filippo del Bene, Institut Curie - Centre de Recherche, France
Peter Currie, Monash University, Australia
Carl-Philipp Heisenberg, Institute of Science and Technology, Austria
Corinne Houart, Kings College London, UK
Adam Hurlstone, University of Manchester, UK
Anna Huttenlocher, University of Madison, USA
Hernan Lopez-Schier, Helmholtz Zentrum München, Germany
Ferdinand le Noble, Max Delbrück Center for Molecular Medicine, Germany
Paul Martin, University of Bristol, UK
Annemarie Meijer, Leiden University, The Netherlands
Marina Mione, University of Trento, Italy
Claire Russell, University of London, UK
Karuna Sampath, University of Warwick, UK
Stefan Schulte-Merker, University of Münster, Germany
Kristin Tessmar-Raible, University of Vienna, Austria
Tanya Whitfield, University of Sheffield, UK
Cecilia L. Winata, International Institute of Molecular and Cell Biology in Warsaw, Poland
Mehmet Fatih Yanik, ETH Zurich, Switzerland
Lilianna Solnica-Krezel, Washington University School of Medicine, USA
Steve Wilson, University College London, UK
Ewa Snaar-Jagalska, Leiden University, The Netherlands
Uwe Strähle, Karlsruhe Institute of Technology, Germany
Vladimir Korzh, International Institute of Molecular and Cell Biology in Warsaw, Poland
Jacek Kuźnicki, International Institute of Molecular and Cell Biology in Warsaw, Poland
Registration starts on October 1, 2017.
Additional information including preliminary program are available at the conference website: http://fishmed2018.pl/
The 2017 Fall MARZ (Mid Atlantic Region Zebrafish) meeting will take place on Friday, Sep 22/2017
at NYU Langone Medical Center (550 First Avenue between E 30th St and E 33th St), New York City
(550 First Avenue between E 30th St and E 33th St), New York City.
REGISTRATION LINK (TO BE FILLED BY ONE PERSON PER LAB)
The meeting starts at 12:30 pm and ends with closing dinner (over by 8 pm).
NYU Langone Medical Center at Farkas Auditorium (The Ruth & George Farkas Auditorium).
DIRECTIONS TO NYU LANGONE MEDICAL CENTER:
DIRECTIONS TO FARKAS AUDITORIUM:
Enter the NYU Langone Medical Center through the revolving doors. Once inside you will see the lobby's security desk facing you. Turn right immediately and walk a few steps. You will see on your left a breezeway marked as "Yellow Pathway." Walk through the breezeway via the double doors (as you do this you will see on either side courtyards with grass and statues of white lions). The Farkas Auditorium is just past the double doors on the right-hand side.
Dear Zebrafish Community members,
This summer marks the 20th Anniversary of the MBL Zebrafish Genetics and Development summer course. Over the last 20 years, this course has trained over 350 students, postdocs, and faculty.
To mark the 20th anniversary, we are holding an all-day symposium on the last day of the course, Friday, August 18th. The symposium will bring together course participants (alumni and faculty) from the past two decades, as well as other community members, for synergistic and networking interactions, to acknowledge the contributions of the zebrafish model to modern developmental biology and biomedical research, and to highlight the positive impact of the zebrafish course on the research of course alumni, their institutions, and the greater scientific community. Please check the schedule for details.
We have a limited number of spots left for this event and would like to open registration to others who would like to learn more about zebrafish, the course, and/or the MBL. A registration fee is required: $30 to attend talks and coffee breaks only OR $100 to attend talks, coffee breaks, AND the mixer/poster session and banquet. All attendees are responsible for arranging their own travel and lodging. If you would like to attend, please register here to reserve your spot.
Sharon Amacher, Corinne Houart, and Erez Raz
2017 Zebrafish Genetics and Development course co-directors
**If the registration link above doesn’t work, please paste the following into your browser:
The 5th European Zebrafish Principal Investigators Meeting brings together principal investigators working at the forefront of zebrafish research.
The meeting will feature plenary symposia of general interest and specialised workshops, providing unique opportunities for discussions, networking and creative thinking. EZPM 2018 is co-organized by the University of Trento and EuFishbiomed and is set in the beautiful surroundings of the Dolomites, providing an idyllic environment to combine mental stimulation and nature exploration.
The Meeting will take place in Trento (Italy), March 20 to 23, 2018.
In association with the 14th Transgenic Technology Meeting we are pleased to invite participants to the Zebrafish Workshop : An introduction to genome modification methods in the zebrafish
Organised by Timothy Dahlem and David Grunwald
Assisted by Rich Dorsky, Kristen Kwan, Maureen Hobbs, Grunwald Lab, Kwan Lab
Date: September 28, 1pm – October 1, 11am
Location: University of Utah
Applications still accepted up to July 31st, for further information please see:
Registration deadline: Augus 31, 2017
Presented by a distinguished panel of leaders in the Zebrafish Community. Presentations will be given by facility managers and vets who are advancing zebrafish husbandry in their facilities and in the zebrafish community. Attendees will get firsthand knowledge on how to improve their current facilities from speakers who have greatly improved the normal levels of zebrafish breeding, fry growth and facility management.
This course is limited to 35 attendees.
Participants in the USA contact
Lance Squires email: email@example.com
Eric Smith email firstname.lastname@example.org
Dear Zebrafish Community:
The International Zebrafish Society (IZFS) is currently hosting an election. If you are interested in voting and are not an IZFS member, click here to join. Ballots close on Friday, June 23, 2017 at 11:59pm EST. For questions email the IZFS Administrator, Monika Dezhbod at email@example.com. We look forward to your participation.
After 2.5 years of assembly curation, the GRC presents the new zebrafish reference genome assembly, GRCz11 (https://www.ncbi.nlm.nih.gov/assembly/GCA_000002035.4/). This latest assembly has been refined by the addition of nearly 1000 finished clone sequences and the resolution of more than 400 genome issues. GRCz11 shows a significant reduction in scaffold numbers and increase in scaffold N50 whilst the overall genome size was not affected. For the first time in a zebrafish assembly, GRCz11 also features alternate loci scaffolds (ALT_REF_LOCI) for representations of variant sequences. The alignments of the alternate loci scaffolds to the primary chromosomal path are also included in the GRCz11 assembly to provide the chromosome context for these alternate sequences.
For more details, please have a look at http://genomeref.blogspot.co.uk/2017/05/grcz11-latest-zebrafish-reference.html