Blog

ZFIN is a member of the The Genome Reference Consortium (GRC), an international collaboration consisting of NCBI, the Wellcome Trust Sanger Institute, the McDonnell Genome Institute at Washington University, the European Bioinformatics Institute (EBI) and ZFIN. This consortium is tasked with ensuring that the reference assemblies for human, mouse, zebrafish and chicken are updated and improved through new data and analysis from genome centers and the research community.

The zebrafish specific GRC webpage (see Fig. 1) provides an overview of the zebrafish genome including an ideogram of the latest zebrafish assembly (GRCz11) and alternate loci scaffolds, downloadable build and tiling path files as well as links to genome assembly data and genome regions under review.  Zebrafish genome issues (see Fig. 2) can be browsed at the chromosome level, filtered by problem type or status or searched by gene, location, clone name or accession.


If you come across what you suspect is a problem in the build, search the list of genome issues and if it has yet to be reported, select the "Report and Issue" tab in the header (see Fig. 3) to report information about the potential problem in the build.  Be as complete as possible and provide location, flanking sequences and a description of the issue.  Genome annotators will evaluate the region, determine if an update to the genome is needed and submit data to create a new tiling path to improve the build with an update or "patch".


Figure 1



Figure 2


Figure 3

The International Zebrafish Society (IZFS) represents and promotes zebrafish scientific research worldwide, and facilitates the exchange of scientific information and resources within the international zebrafish community.

To promote the latest research approaches, and interaction between leaders in the field and the international zebrafish research community, IZFS will host a series of educational webinars. With kick-off in April 2020, the series is part of our effort to reduce our carbon footprint, and will include a variety of research and professional development topics.

These hour-long webinars will feature an expert or panel of experts who will discuss exciting topics in an interactive online setting. The following topics and faculty have been selected so far:                                             

Date and Time: April 29, 2020 at 5:00 p.m. and 9:00 p.m. ET    
Topic: Use of CRISPR/Cas9 for Targeted Integration in Zebrafish
Presenter: Jeffrey Essner, PhD - Iowa State University         

Date and Time: May 28, 2020 at 11:00 a.m. and 9:00 p.m. ET
Topic: Grant Writing Basics
Presenter: Mary Mullins, PhD - University of Pennsylvania
       
Date and Time: June 23, 2020 at 11:00 a.m. and 3:00 p.m. ET
Topic: Zebrafish Husbandry
Presenter: Christian Lawrence, MS - Boston Children's Hospital                 

IZFS members will have free access to both the live webinars and recordings; non-members will be invited to participate in the live webinars for a fee of $25. Registration opens April 13, 2020.

These webinars will provide attendees with an exclusive opportunity to interact with experts in the field of zebrafish scientific research.

Check out www.izfs.org/education/webinars for more details!

If you have any suggestions for topics or would like to volunteer to present a future webinar, please contact info@izfs.org.



International Zebrafish Society (IZFS)
555 East Wells Street, Suite 1100
Milwaukee, Wisconsin 53202-3823
Phone: (414) 918-9835
Email: info@izfs.org

IZFS 2020 Chi-Bin Chien & George Streisinger Award Winners

Dear Zebrafish Community Members,

On behalf of the International Zebrafish Society (IZFS), we are pleased to announce the 2020 award winners:

Dr. Margot Williams, PhD, Baylor College of Medicine, USA--Chi-Bin Chien Award Winner

Dr. Margot William's outstanding research contributions and dedication to the zebrafish field truly characterize the spirit of Chi-Bin Chien. In November 2019, Dr. Williams started her lab at the Baylor College of Medicine, where she seeks to understand how embryonic cell behaviors are spatiotemporally coordinated to shape the emerging body plan.

Dr. Alexander Schier, PhD, University of Basel, Switzerland--George Streisinger Award Winner

Dr. Alexander Schier has made multiple advancements to the zebrafish field that also characterize the founding father of zebrafish research, George Streisinger. Dr. Schier’s lab at the University of Basel has defined the first morphogen-inhibitor pair for Turing-like pattern formation and discovered the microRNA-induced degradation of maternal mRNAs.

To learn more about IZFS awards, including ways to donate, please visit www.izfs.org/awards.
Follow us on Twitter @InfoIzfs

We would like to thank all of the nominators and high quality nominees for the 2020 IZFS Chi-Bin Chien & George Streisinger Awards. Nominees who were not selected will have their nomination in place for a period of three years starting with the first year of nomination. Individuals can be re-nominated which will start a new three-year period.

Again, congratulations to Dr. Margot Williams and Dr. Alex Schier! IZFS and the zebrafish community are grateful for your tremendous contributions to zebrafish research.


Tatjana Piotrowski, PhD
IZFS Awards Committee Chair


Didier Stainier, PhD
IZFS President
 

ZebraShare

About ZebraShare

ZebraShare is a resource for researchers to share information about and advertise high quality mutant fish lines that they have generated but are not currently studying, such as those with no observed phenotype.

This information will help prevent unnecessary duplication of effort between labs. Understanding which single genes seem dispensable will also help researchers converge on genes or gene combinations which are developmentally important.

We ask that you share well-characterized lines with a confirmed lesion, carried to at minimum the F2 generation.

Contribution via ZebraShare does not constitute a publication, and labs of origination maintain full rights to the lines they generate. After listing fish on ZebraShare, labs may decide to pursue these lines again. If fish lines are shared through ZebraShare, there is an explicit expectation that collaborating labs will discuss appropriate authorship if research culminates in presentations or publications.

All ZebraShare alleles will be publicly visible at ZFIN.

For more details, visit the ZebraShare home page: https://zfin.org/action/zebrashare

How to submit data to ZebraShare:

  1. Go to the ZebraShare home page:
  2. Download the ZebraShare Submission Workbook
    • Click on “Download Submission Workbook” on the ZebraShare page (Fig. 1)
  3. Fill out the ZebraShare Submission Workbook
    • Go to the “Enter Your Data Here” tab in the Workbook and fill out all the details for your alleles (Fig. 2)
    • Details about mutation/variant types and information required for submitting mutant coordinates can be found here
  4. Submit the Submission Workbook to ZFIN
    • Log into ZFIN and return to the ZebraShare page
    • Click on the "Submit Completed Workbook" button (Fig. 3)
    • Fill out the "Submit ZebraShare Workbook" Form:
      1. Your name and e-mail address will be automatically filled in based on your ZFIN login.
      2. Fill in the authors, title, and abstract for your submission
      3. Specify who is authorized to edit the alleles (Fig. 4)
      4. Attach the ZebraShare Submission Workbook and any additional image files to the Form (Fig. 5). Acceptable file formats are png, jpeg, jpg and gif.
      5. Submit the form, which will automatically create a ZFIN submission record.
  5. After your data submission is complete:
    • You will receive a notification that your data was successfully submitted, with a link to your ZebraShare “publication” (Fig. 6)
    • ZFIN curators will process this submission as part of their high priority literature curation workflow.
      • You may be contacted if curators have questions during the processing of your submission.
    • An allele record will be created by ZFIN curators for each allele submitted.
    • The line submitter and others they specify will be able to add/edit some of the details associated with their alleles.
      1. To access your submission, sign in to ZFIN. A user icon will appear on the right-hand side of the ZFIN page. Hover the mouse over the icon to see a menu. Select “Your ZebraShare submissions” from the menu. (Fig. 7)
      2. On the “Your ZebraShare submissions” page, you will see the “publication ID” of your submission, and links to “View” or “Edit” the alleles you submitted (Fig. 8)
      3. Click on “Edit” to edit these fields for your mutant (Fig. 9):
        1. Functional consequence
        2. Adult viable
        3. Maternal zygosity examined
        4. NMD Apparent
        5. Currently available
        6. Other line information (free text)


How to find ZebraShare alleles and submissions in ZFIN:

You can find all ZebraShare alleles in ZFIN using single-box search. In the Mutation/Tg category, select the “Is ZebraShare” option:

https://zfin.org/search?q=&fq=category%3A%22Mutation+%2F+Tg%22&category=Mutation+%2F+Tg&fq=is_zebrashare%3A%22true%22


You can find all ZebraShare submissions in ZFIN using single box search. In the Publication category, go to the Journal option, and select ZebraShare:

https://zfin.org/search?q=&fq=category%3A%22Publication%22&category=Publication&fq=journal:%22ZebraShare%22


ZFIN would like to thank April De Laurier and Jared Talbot for their help in developing ZebraShare.

You can contact us at zfinadmn@zfin.org



Figure 1. Download the Submission Workbook from the ZebraShare home page.


Figure 2. Go to the “Enter Your Data Here” tab in the Submission Workbook and fill out the details for your mutant(s).


Figure 3. When ready to submit your data, return to the ZebraShare page, log in, and click on “Submit Completed Workbook”.


Figure 4. Fill out the “Submit ZebraShare Workbook” form.

  • Your name, e-mail address and lab will be visible in the “Submitter” and “Lab of Origin” sections.
  • Fill in the authors, title, and abstract for your submission.
  • Specify who can edit information about your submission.


Figure 5. Attach your Submission Workbook and images (in png, jpeg, jpg or gif format) in the “Files” section. Click “Submit” to submit your workbook to ZFIN.


Figure 6. You will receive notification that your data submission was received, with a link to your ZebraShare “publication”.


Figure 7. You can access, view and edit your ZebraShare submissions from the ZFIN home page when logged in.


Figure 8. You can View or Edit your submission following the appropriate link.


Figure 9. Click on “Edit” to edit information about your mutant.


Dear Zebrafish Community Members,

Do you have a colleague who is an outstanding leader is the zebrafish community? Are you someone who is passionate about the future of zebrafish research?

The International Zebrafish Society (IZFS) is accepting nominations for the 2020 election for new members of the Board of Directors. The Board acts on the behalf of IZFS to guide the activities and direction of the Society. This is an excellent opportunity to get involved!

Zebrafish community members are invited to submit nominations by Monday, April 13, 2020 for the following positions on the IZFS Board of Directors.

  *  President-Elect

  *  Treasurer

  *  Asia/Pacific Regional Director (1 vacancy)

  *  Europe/Mediterranean Director (1 vacancy)

  *  US/Canada Director (2 vacancies)

Each elected Board member is expected to commit to a 3-year term starting on July 1, 2020.

You may nominate candidates here: https://forms.gle/bibWCiPAMQKnN7MV9 into your browser.

Nominees must be IZFS members in good standing who have paid their 2020 dues. We welcome nominations of individuals who are forward thinkers, strategic planners, and dedicated volunteers active in the zebrafish community. Self-nominations are also welcome. If you have not renewed your membership or are not a member of IZFS, please click below to join today or renew online in order to be considered for Board nomination or to vote in the election!

Join now: https://www.izfs.org/membership/join

Renew now: https://www.izfs.org/membership/renew

Nominations will be reviewed by the IZFS Nominations Committee who will determine the final ballot in accordance with IZFS bylaws. Thank you in advance for your nominations.

Sincerely,

IZFS Nominations Committee

Dear colleagues,

Due to the Covid-19 pandemic, resource distribution and diagnostic health services at the Zebrafish International Resource Center (zebrafish.org) have been suspended until we are able to resume operations again. All requests and inquiries will be logged in the order received, and we will contact you as soon as possible once operations resume. Emergency consultations for health, husbandry, or aquaculture will be addressed as soon as possible.

Your ZIRC team

(zebrafish.org)

Dear colleagues,

Due to the Covid-19 pandemic, resource distribution and diagnostic health services at the Zebrafish International Resource Center (zebrafish.org) may be delayed. All requests and inquiries will be addressed in the order received, and we will contact you when normal operations resume. Emergency consultations for health, husbandry, or aquaculture will be addressed as soon as possible. 


Your ZIRC team


ZFIN Wiki Updates

The ZFIN team has launched a new, easier way to keep up to date with our posts for Jobs, Meetings, News and Protocol on https://wiki.zfin.org.   In the past, users needed accounts on the wiki, and had to login and choose which pages to Watch.    Now, we have created a mailing list that anyone can subscribe to and receive updates.
 
You can subscribe and manage your subscription to the list at  https://lists.uoregon.edu/mailman/listinfo/zfin-posts.
 
Best,
 
The ZFIN technical team

Phenotype annotations in ZFIN include morphological alterations and changes in gene expression in mutant or knockdown fish as well as fish exposed to various experimental treatments.  Often, new insights can come from understanding what genes or treatments modify the phenotype of specific mutants.  ZFIN records phenotypic modification (ie genetic interaction) as either “ameliorated” (partial or complete rescue) or “exacerbated” (made worse).


These genetic interaction annotations are currently best found in ZFIN using the single box search.


Example 1: Filtering approach for ameliorated phenotypes


  1. Go to the ZFIN single box search page (https://zfin.org/search)
  2. Select “Phenotype” from the pulldown menu of data types
  3. Search for “ameliorated”

    At this point all the phenotype results with ameliorated phenotypes are shown.  On 3/5/2020 there are 2470 records.

  4. An example phenotype result showing the ameliorated phenotypes



  5. From there, use the filters on the left side of the search results page to focus the result set on results of interest.
  6. You can filter by:

      a. Phenotypic Gene: the disrupted gene involved in the phenotype


      b. Phenotype Statement: the phenotype trait, like “eye decreased size”

      c. Stage: the developmental stage at which the phenotype was observed

      d. Manifests In:

anatomy: the anatomical structure affected in the phenotype

biological process: the biological process affected in the phenotype

cellular component: the cellular component affected in the phenotype

molecular function: the molecular function affected in the phenotype

misexpressed gene: genes having altered expression as part of the phenotype     


      e. Genotype: the genotype involved in the phenotype

      f. Sequence Targeting Reagent (STR): morpholinos, TALENs or CRISPRs that were involved in the phenotype


      g. Is Monogenic: Yes or No..indicates if there is only one affected gene

      h. Conditions: the experimental treatment involved in the phenotype

      i. Has Image: only include results that have image


The same basic approach can be used for exacerbated phenotypes by searching for “exacerbated” rather than “ameliorated”


Example 2: Searching for ameliorated phenotypes for the fkrp gene

             

  1. Go to the ZFIN single box search page (https://zfin.org/search)
  2. Select “Phenotype” from the pulldown menu of data types
  3. Search for “fkrp ameliorated”
  4. On 3/5/2020 there are 24 ameliorated phenotypes involving the fkrp gene
  5. You can then use the filters on the left side of the results to further focus the result set on records of interest.
    1. The same basic approach can be used for exacerbated phenotypes. Note that fkrp does not have any exacerbated phenotypes.
    2. Example: Search for “atg5 exacerbated”






SAVE THE DATE

2020 Board of Directors Election!

Dear Zebrafish Community Members,

The International Zebrafish Society (IZFS) will be holding Board of Director (BOD) elections in May 2020. We will be electing Officers (President-Elect, Treasurer) and Regional Directors (US/Canada, Asia/Pacific, and Europe/Mediterranean). Regional representation on the IZFS Board is determined by the number of PIs per region who are registered in ZFIN, so we strongly encourage all PIs to register their labs in ZFIN before March 1. You can find details about the BOD positions in the IZFS Bylaws.

Nominations

  • Solicitation for nominations will begin on March 2 and end on March 31.
  • Call for nominations will be sent via email.
  • All nominees must be IZFS members to run for election, and you must be a member to vote.
  • To self-nominate or be considered if nominated, you must become a member before April 1, 2020.

Voting

  • Voting will commence in May for a 2 week period.
  • To cast your vote in the upcoming election, you must be a member by May 2020.
  • A secure, online ballot will be distributed to members in May.

Please click below to join IZFS or renew your membership today! 

Sincerely,

IZFS Nominations Committee


The meeting program will include keynote and plenary talks, short oral presentations, poster sessions and workshops covering a wide range of topics including:

  • Cancer
  • Cell Signaling
  • Chemical Biology and Drug Discovery
  • Circuits and Behavior
  • Disease Models
  • Education and Outreach
  • Emerging Technologies
  • Epigenetics and Gene Regulation
  • Evolution
  • Genomic Resources
  • Germ Line and Early Development
  • Husbandry and Aquaculture
  • Immunity and Infection
  • Metabolism
  • Morphogenesis and Organogenesis
  • Neurobiology
  • Patterning
  • Regeneration
  • Stem Cells
  • Toxicology

Important Dates

  • 12 February, 2020
    Abstract Submission Deadline
  • 23 April, 2020
    Early Bird Registration Deadline
  • 23 June, 2020
    Online Registration Deadline


More information on the Meeting is published on the Meeting webpage: http://www.zebrafish2020.org/

We look forward to meeting you in Prague!


SCZI 2020 - CANCELLED


We have been monitoring closely the outbreak of the coronavirus over this last week.  As you may know, today the World Health Organization has declared the outbreak to be a "Public Health Emergency of International Concern."  

The travel ban preventing Chinese researchers from traveling to Taiwan, together with major airlines cancelling flights to several cities in China that impacts many of our attendees flight plans, have resulted in quite a few cancellations. In addition, several other attendees have also cancelled in recent days, leaving us with a much reduced conference size and a significantly reduced roster of speakers. We are also concerned about a possible expansion of the outbreak that may result in travel restrictions to and from Taiwan, and may develop over the course of the conference.

For those reasons, we have made the difficult decision to cancel the conference. We appreciate the time and effort you have put in to be part of this conference. IZFS staff will be working to refund registration fees over the next couple of weeks.

Please contact us at info@izfs.org with any questions or concerns you may have.

Sincerely,

SCZI 2020 Meeting Organizers:
Bon-chu Chung
Jeff Lee
Didier Stainier

IZFS Executive Committee
Didier Stainier
Mary Mullins
Phil Ingham
Elizabeth Busch-Nentwich
Kate Lewis

SCZI 2020 Information

Registration is still open for the 2020 Strategic Conference of Fish Investigators, Taipei, Taiwan, February 4 – 8, 2020, and we are accepting registrations to the meeting, including walk-in registrations.


The program is now available in several formats including PDF and the mobile application. Here are instruction on how to access the program.


Mobile Application on Smartphones

  1. Download EventMobi in Apple Store (iOS devices) or Google Play Store (Android devices).
  2. Open the EventMobi application after download and the enter the event code: sczi2020
  3. You will be prompted to enter your email address and then enter your first and last name and create a password.

Via Computer Browsers
You can view the program on smartphones, tablets and desktop computers via web browsers athttps://eventmobi.com/sczi2020/.

  1. Visit https://eventmobi.com/sczi2020/
  2. It will prompt you to enter your email address then enter your first and last name and create a password.
  3. Event code: sczi2020

PDFs
Schedule Only (Please cross reference the schedule with the Abstract PDFs) (click to download)

  • Keynote Addresses
  • Plenary and Concurrent Talks
  • Workshops
  • Community Sessions

Plenary and Concurrent Abstracts (click to download)
Poster Abstracts (click to download)

For more meeting information, visit https://www.izfs.org/conferences/9th-sczi-pi-meeting.


Anna Douangphachanh, CMP
Meetings, Membership and Administrative Manager
International Zebrafish Society
555 East Wells Street, Suite 1100

Milwaukee, WI 53202-3823

(414) 918-9835  l adouan@izfs.orgwww.izfs.org 

Gene pages have been quietly spruced up lately, but you might not have noticed all of the changes, so presented below is a list of recent improvements.

First off, we have been reliably informed that tables are easier to read than long, long lists (who knew?), so we’ve been all about tables in these three sections:

— Sequence targeting reagents have been converted from a list to a table that includes alleles created by CRISPRs and direct links to related pubs.

— Antibodies have been updated from a list to a table that includes helpful antibody details such as Type, Isotype, etc.

— Constructs have been updated from a list to a table that includes regulatory regions, coding sequences, species involved, source, and pubs.

On the non-table-related front, we have added some nice things to these sections:

— A link to “multi-species” data at Alliance has been added to the Disease Associated with [gene] Human Ortholog section.

— The Protein domains section now includes domain type and names. We used to show just ID numbers and no names. Not cool. Well, those days are over.

— The Transcripts section now provides a direct link to transcript at Ensembl, as well as links to UCSC, NCBI, Ensembl, and ZFIN genome browsers.

— Links to Expression Atlas now appear in the Expression section.

But wait, there’s more, a LOT more … but not quite yet. A truly epic Gene Page Makeover is in the works. But for now, we hope these various improvements will suffice.

Dear Colleague,


The International Zebrafish Society (IZFS) is pleased to announce the call for nominations for our two prestigious annual awards – The George Streisinger and the Chi-Bin Chien Awards. Members of the zebrafish community are invited to submit nominations by January 27, 2020. Awardees will be recognized and invited to present a plenary lecture during the 11th European Zebrafish Meeting taking place in Prague, Czech June 29-July 2, 2020.

 

About the Awards

The George Streisinger Award recognizes senior investigators in the zebrafish community who have made outstanding and continued contributions to the advancement of the field.


Among the criteria that may be considered:

  • Contributions in the form of conceptual advances that have opened important new research directions
  • Development of tools or resources that have been transformative in enabling new research possibilities
  • Service to the Zebrafish research community


Nominations should be submitted by e-mail with the subject line “George Streisinger Award” toinfo@izfs.org. The email should include a single PDF file that contains:

  1. A statement (up to one page) written by the nominators describing the key contributions of the nominee to the field.
  2. The statement must be co-signed by two or more IZFS members who support the nomination.
  3. 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.


The Chi-Bin Chien Award recognizes outstanding graduate students, postdoctoral trainees, or recently appointed faculty members from any country who have made significant contributions to the field of zebrafish research and have exhibited the generosity and openness that characterized and motivated Chi-Bin Chien.

Mentors of PhD or post-doctoral trainees of the zebrafish community are invited to submit nominations for the Chi-Bin Chien Award.


Nominations should be submitted by e-mail with the subject line “Chi-Bin Chien Award” toinfo@izfs.org. The email should include a single PDF file that contains:

  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 CV
  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


We hope you will submit a nomination and attend the meeting in Prague, Czech Republic.


Sincerely,



Didier Stainier, PhD

IZFS President