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|SCZI 2017 Meeting Report|
The 7th Strategic Conference of Zebrafish Investigators took place January 14-18th at the Asilomar Conference Grounds in Pacific Grove, CA. The PI-only SCZI conferences were initiated in 2005, with the first meeting held at the Mount Desert Island Biological Laboratory in Maine. SCZI meetings have been held at Asilomar every other year since then. These highly interactive meetings include plenary sessions featuring scientific presentations of broad interest, concurrent platform sessions covering a range of research topics, workshops focusing on technical innovations, topics of interest to junior investigators such as grant writing, mentoring, etc., and a variety of other topics, and community sessions for discussion of issues of strong importance to the zebrafish research community. SCZI meetings have become “must-go” meetings for many zebrafish PIs and have had an important role in helping to maintain the cohesion that our community is known for. 204 principal investigators took part in the vibrant and exciting 2017 SCZI meeting. The meeting was covered in real-time on Twitter with the hashtag #SCZI2017. Some of the highlights of this conference are noted below.
The Plenary Sessions:
Keynote speaker Anne Brunet started off the meeting on Saturday evening by introducing the killifish model and its usefulness for studying the genetic and molecular basis for longevity and age –related disorders. This was followed by the first plenary session that highlighted the breadth of science being pursued in the zebrafish community. Alex Schier reported on the Seurat method where single cell RNAseq data is used to map cells back onto the embryo based on genes we already know to be expressed in that area. This allows for the discovery of new regional gene expression patterns. Randy Peterson reported that the small molecule primordaizine, licensed to sterilize salmon and tilapia, eliminates primordial germ cells in part by regulation of translation through a non-canonical polyA-independent mechanism. Mary Mullins shared her group’s computational modeling approach to explore how the BMP morphogen gradient forms during dorsal-ventral axis patterning. Their models suggest that a “source-sink” mechanism, where BMP antagonists act as the sink, drives gradient formation and this model is bolstered by their measurements of Bmp2 diffusion. Antonio Giraldez presented evidence that codons mediate the stability of mRNA, with non-optimal codons enhancing decay in zebrafish and in human tissues. Katie Kindt wrapped up the session by demonstrating that while all neuromasts in the lateral line see an increase in Ca2+ in response to stimulation, only a subset of those go on transmit the signal forward. This was unexpected as all neurons in the field were expected to respond.
Plenary talks continued on Sunday morning with additional interesting presentations on diverse topics. Dan Wagner discussed fusing Cas9 with an endonuclease to take advantage of modifying the free 3’ end produced after Cas9 cleavage and creating larger deletions. Steve Ekker discussed how zebrafish can fill a gap in mitochondrial disease research and discussed progress in directly modifying mitochondrial DNA with TALE proteins. Ken Poss used biotin labeling of histone 3.3 to identify regions of open chromatin in cardiomyocytes. He is using this strategy to identify early enhancers and to find those involved in regeneration. Judith Eisen discussed how germ-free larvae behave differently than conventional larva, further suggesting the role of the microbiome in biology is expanding. New attendee Maggie Dallman is using the zebrafish gill and intestinal mucosa to study inflammation and immunity. She presented evidence that the zebrafish cytokine response to inflammation is similar to the human response, suggesting zebrafish are a good model for further exploration into this mechanism. Shinji Takada demonstrated roles for the nuclear adaptor proteins Ripply1 and 2 in degradation of Tbx6, which is required for somite boundary formation. Philip Washbourne rounded up the second plenary showing that zebrafish orient towards a partner in a social context and this orientation is reciprocal. This behavior requires vision and social feedback, and may serve as a tool for studying social disorders such as autism.
The Monday morning plenary produced actual gasps of delight from the audience. Stephanie Woo described modifications to the blue-light activated EL222 optogenetic system renamed TAEL. TAEL is less toxic than previous systems. She mentioned that activation by light pulsing gives higher levels of expression than constant illumination. Christiane Nüsslein-Volhard discussed the emergence of the adult pigment pattern and showed that stripes form from homotypic competition between pigment cells and not from a prepattern. David Parichy showed amazing movies of xanthoblasts making “airnemes” from blebs on the cell surface. These membrane structures contact, and can stabilize on, newly formed melanophores before they differentiate into stripes and on macrophages. Eliminating the formation of airnemes or macrophages resulted in stripe consolidation defects. Ajay Chitnis followed with additional awe-inspiring movies of cell protrusions from the leading cells towards the trailing cells of lateral line primordia. The leading cells can release a vesicle tip from the extensions that remains associated with the extracellular matrix and can be internalized by the trailing cells. The trailing cells transport the internalized vesicles apically, potentially forming the FGF containing microlumens found in developing rosettes. Brant Weinstein reported on perivascular macrophages or “Mato” cells that reside on the surface of the zebrafish brain. By RNAseq analysis, these cells do not resemble typical macrophages, but instead have lymphatic and endothelial gene expression. He demonstrated that these cells arise by direct transdifferentiation from endothelial cells in the primitive optic choroid vascular plexus.
Didier Stainier used a technique termed Fluorescence Activation after Transgene Coupling (FATC) to explore cell fusion events. They can see these fusion events in skeletal myocytes as expected, but also in cardiomyocytes which has not be recognized before. David Lyons reported on an automated screen using the VAST Bioimager from Union Biometrica integrated with a spinning disk confocal. With this setup, they were able to image whole larvae in a 96-well format to screen for compounds that affect myelinating oligodendrocytes. Adam Miller, 2016 Chi-Bin Chien award winner, wrapped up the session by presenting his work on connexins at the electrical synapse and using CRISPR pools to screen for candidates that effect these synapses in Mauthner neurons.
The final plenary session further showcased beautiful imaging and disease relevance. Tom Look spoke on identifying new drug combinations to treat models of high-risk early thymocyte progenitor (ETP) forms of T-cell leukemia. Cecilia Moens presented a system for visualizing tumor-macrophage interactions by injecting human or zebrafish melanoma cells into the hindbrain ventricle. With this system, they find interaction with macrophages increases metastatic potential. Kristen Kwan showed beautiful time-lapse imaging of optic cup morphogenesis. They find that neural crest cells are critical for proper morphogenesis as in their absence the lens and retina are misshapen. Hitoshi Okamoto continued the theme of morphogenesis demonstrating that oriented cell movement in the olfactory placode are regulated by Neurogenin 1, and provide further evidence that Neurogenin 1 regulates cxcr4b expression in this process. Amin Allalou, stepping in for Mehmet Faith Yanik, showed how VAST Bioimaging of zebrafish can identify potential therapeutic compounds for intractable epilepsies.. In their setup, they scan for brain activity in response to neuroactive compounds. He reports that they can scan an entire brain in 50 milliseconds. Michael Brand described their system for inducing cerebellar injury to study regeneration. They find larval zebrafish can regenerate Purkinje and granular cells, but adults can only regenerate the latter. Lalita Ramakrishnan reported that Myocbacerium leprae, which causes leprosy, appears to cause demyelination through host macrophages that affect the neurons they travel upon. Monte Westerfield spoke about the power of zebrafish genetics to assist with the goals of the Undiagnosed Diseases Network (UDN) to assess causative genes in undiagnosed patients.
In addition to plenary sessions, the 2017 SCZI meeting included ten concurrent platform sessions and two lively poster sessions. Due to the large number of topics and presentations covered in these sessions, we will not go into detail on these presentations here, but information on many of the sessions was tweeted by meeting attendees (see some examples below). You can search Twitter for #sczi2017 to see all the Tweets from the meeting.
Following the second plenary session, the first George Streisinger Award was presented to Dr. Chuck Kimmel from the University of Oregon. This new IZFS “lifetime achievement” award was created to recognize an outstanding zebrafish researcher who in addition to important scientific contributions has also had a key foundational influence on the zebrafish community and its growth and development. Although Dr. Kimmel was unable to attend to receive the award in person, as described in the accompanying piece, Dr. David Grunwald gave an inspiring presentation highlighting Dr Kimmel’s remarkable accomplishments and his profound and lasting influence on and central role in the rise of the zebrafish as one of the top vertebrate animal research models.
Individual concurrent regional community sessions were held for the Americas, Europe, and Asia Pacific on Sunday, followed by a full group Community session the next day with reports from each region. Given the rapidly growing number of zebrafish labs in the Asia-Pacific region, the idea of rotating the International Zebrafish meeting to this region was raised and met with enthusiasm. The community decided to explore this opportunity further.
The top concern of PIs in the European regional meeting was regulations and restrictions affecting their research. SOPs for husbandry have been proposed by a working group including FELASA, EuFishBioMed, and COST, but these have not been officially approved. There was discussion on how to take this forward, perhaps in a central repository on EuFishBioMed. Import of fish into Europe requires patience and you must follow the regulations! ontact ZIRC or EuFishBioMed for assistance on doing this correctly.
The issue of anti-model system bias on grant panels was brought forward. Mary Mullins is working with others to discuss this with NIH leadership and develop a white paper. It was noted that we need community members to serve on study sections when asked. Additionally, if the roster for a study section that is reviewing your grant doesn’t have zebrafish expertise, you can request someone be added to the panel. Clarissa Henry mentioned an effort to publish a review that would discuss cases where zebrafish studies provided answers that were either incorrect or unfeasible in mouse models. This could help counter some of the anti-zebrafish sentiments raised in reviews. The idea that we need more ways to connect clinicians and model organism researchers was also raised.
It has been clear for some time that academia is not the main career pathway for all trainees, and there was a great deal of discussion about how to help our trainees find additional opportunities. Comments were made that US biotech is still strong, but more effort into promoting career paths is needed. Additionally, we need as a group to consider such choices as equal in value. PIs should not be penalized as mentors if they have trainees who do not choose the academic path. This is especially important when trainees apply for grants and fellowships as mentor “success” is considered in these decisions.
A discussion took place on the “absence of phenotypes” in supposed null alleles. Participants cautioned that all alleles must be verified to insure there is an absence of protein. Some have experienced “read through” of stop codons in certain circumstances, thus, relying on the type of lesion without additional controls can be misleading. It was asked that researchers qualify what they mean when they say, “no phenotype”, for example saying, “no morphological phenotype was observed during embryonic stages”, as other phenotypes may be present.
Zoltan Varga updated us on ZIRC. They have worked hard to reduce the time it takes to ship embryos from frozen stocks to a few weeks and have improved their sperm cryopreservation techniques, which are available on the website. Monte Westerfield explained that ZFIN will be part of the new Alliance of Genome Resources (AGR), which will work to integrate databases for model organisms in response to the reduction of funding for these databases by the NIH.
Resources including places to share data were also discussed. The European Bioinformatics Institute (EMBL-EBI) is one useful resources for sharing and accessing datasets (www.ebi.ac.uk). Currently there is only one dataset in the Expression Atlas component of their database and researchers are encouraged to submit their expression datasets. DANIO-CODE is an international effort to provide a centralized resource for zebrafish epigenomics datasets (http://www.birmingham.ac.uk/generic/danio-code/index.aspx).
Diane Slusarski brought forward an offer from the Developmental Studies Hybridoma Bank (DSHB) to work with our community to develop and validate monoclonal antibodies. DSHB distributes validated monoclonal antibodies and hybridoma cells to academic labs at low cost. Contact her if you are interested in helping move this idea forward (email@example.com).
A wide variety of workshops were held throughout the meeting, providing information and support but also generating ideas to benefit the community. In the Diversity workshop organized by Kirsten Sadler Edelphi and Rachel Brewster, the participants discussed increasing the numbers of women and members of underrepresented groups in the zebrafish field. A passionate discussion made it clear that this is a topic or great interest. Several recommendations were put forward including encouraging more participation of these groups in meetings through travel awards and developing a speakers list, like that utilized by the American Society of Cell Biology, to highlight our researchers for meeting and seminar invitations. Finally, there is a proposal to establish a Zebrafish Diversity Committee within IZFS to work on these and other initiatives.
The workshop on Writing High Impact Papers was led by Didier Stainier and Mary Mullins and had over 80 participants. The importance of strong cover letters that convey the significance and novelty of the work was discussed. It was recommended that authors suggest reviewers that are appropriate, and hopefully supportive, as editors often take these recommendations into account. While presubmission inquiries were generally felt to be unhelpful, reviewing for the journals you wish to publish in, and developing good relationships with editors was considered worthwhile.
The Chemical Biology workshop was co-chaired by Randall Peterson and Charles Hong. The discussion, led by Liz Patton and James Chen, covered topics including target identification and translational efforts. Work in the field has identified three repurposed FDA approved compounds in zebrafish disease models that are undergoing clinical trials, and an additional six that are on the path towards clinical trials. Five of these are novel compounds that were first identified in zebrafish. The workshop on Quantitative Biology focused on problems people are having with imaging including how to mount embryos for long time-courses, and how to best balance photobleaching and toxicity with imaging needs in these types of experiments. Making imaging data publicly available for others to analyze was put forth as something to consider.
The Early Career workshop was co-chaired by Tom Schilling and Katie Drerup. Along with panelists Kelly Monk and Patrick Blader, the group discussed funding resources and strategies for early stage investigators. They concluded it is best to apply for funding early to get full benefit of the early investigator status. Attendees were encouraged to reach out of their program officer and to senior colleagues for feedback on their ideas and the grant itself. Other topics of conversation included hiring the right people, and parting ways when necessary, and making sure to network and increase your visibility to help with promotion and tenure. Seeking out senior colleagues for assistance is always strongly encouraged for any issues or questions early career investigators face.
The workshop on Zebrafish in Education discussed existing resources and ways to obtain financing for educational projects. Methods to evaluate outreach programs was considered essential, and participants discussed reaching out to clinicians and educational psychologists and researchers for help with developing tools. The group provided a recommendation for IZFS to create an education page for collecting workshop materials, resources and links.
In the Zebrafish Aquariums Systems and Husbandry workshop issues surrounding feeding and disease were discussed. The group reminds us that there are four scalable measures for colony health programs: 1) Quarantine 2) Detection of existing pathogens 3) Pathogen control and/or elimination, and 4) Disclosure of health statistics when exchanging fish with other facilities. Researchers are encouraged to include nutritional methods, including type of feeding and total amount fed per day, in materials and methods sections of their papers to help control for diet variables. There was discussion about increased concern for environmental enrichment in zebrafish colonies from animal care staff and regulatory groups. Concerns about increasing biofilms and spread of pathogens in such practices were raised. The idea that live feed should be considered for enrichment as they stimulate natural behaviors was put forward. Recommendations included a resource for husbandry and SOPs to be hosted on the IZFS website so researchers can provide a common, international set of accepted standards on this and other husbandry issues to compliance officials.
The workshop on Genome editing also had high attendance. Strategies to improve CRISPR-Cas9 mutagenesis were offered by speakers and participants. Steve Ekker was clear that you have to check cutting efficiency with your designed sgRNA to be sure you will generate mutant alleles using CRISPR. Tissue specific CRISPR knockouts were discussed using a vector to express one or more sgRNAs and Cas9 in regions of interest. The issue of whether or not morpholinos are useful was raised again, especially since mutants are obtainable more readily with CRISPR and TALENs. However, genetic compensation in mutants can obscure phenotypes seen with morpholinos. Genetic compensation refers to the upregulation of paralogs or compensating genes that is observed in mutants, yet does not occur in morphants. In his plenary talk, Didier Stainier mentioned they have multiple cases of this in his group, and it is due to transcriptional upregulation and not RNA stability. Other talks in concurrent sessions found that morpholino phenotypes could be recapitulated in maternal-zygotic mutants, but not zygotic mutants. The fact that reviewers and editors are not sure how to treat morpholino work was also raised. As a community, there is a clear need for additional guidelines on morpholinos in the age of CRISPR. Didier Stainier agreed to lead the efforts to develop these guidelines for publication, and this is currently underway.
Side note – as a member of IZFS, we encourage you to participate in committees and efforts within the society. We will issue calls for volunteers for various projects and would welcome your involvement.
The 8th Strategic Conference of Zebrafish Investigators:
The planning committee for the 2019 meeting includes:
Returning for 2019 New for 2019
Jim Amatruda Florence Marlow
Bon-Chu Chung Kelly Monk
Steve Ekker Elke Ober
Michael Granato Victoria Prince
Stephan Neuhauss Kirsten Sadler-Edelphi
Liz Patton Stefan Schulte-Merker
Tanya Whitfield Thomas Schilling