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Case Studies

Image Credit: Greenwood Genetic Center


Hazel and Bill Allin Aquaculture Facility, Greenwood Genetic Center


Duc Dong in his lab  

Dong Lab, Sanford Burnham Prebys Medical Discovery Institute


  Dr Raymond Kwong  

Kwong Lab, York University


Dr Sarah Kucenas in her lab  

Kucenas Lab, University of Virginia


  Dr. Michael Barresi  

Barresi Lab, Smith College


Port Washington High School, Wisconsin  

Port Washington High School, Wisconsin


  Dr. Traver in his lab  

Traver Lab, University of California, San Diego


University of Utah Zebrafish Core Facility  

University of Utah Zebrafish Core Facility


  Dr. Yoot Vin Mount Desert Island Biological Laboratory  

Mount Desert Island Biological Laboratory



Dr. Tamily Weissman-Unni of Lewis & Clark College is lighting up the brains of zebrafish to create maps of their neural networks  

Lewis & Clark College


Visit Lewis & Clark College

  Seattle Children's Research Institute  

Seattle Children's Research Institute


Visit Seattle Children's Research Institute


Hazel and Bill Allin Aquaculture Facility, Greenwood Genetic Center

Greenwood Genetic Center Zebrafish SystemA "powerful new technology' - zebrafish - is unveiled at the Greenwood Genetic Center in Greenwood, South Carolina, and Aquaneering is proud that our equipment supports it! Read all about how the new directors, Richard Steet and Heather Flanagan-Steet, are pursuing zebrafish research at the Hazel and Bill Allin Aquaculture Facility.

Dong Lab, Sanford Burnham Prebys Medical Discovery Institute
  Duc Dong in his lab
  Dr. Duc Dong in his lab

What do you need to know about Dr. Duc Dong of Sanford Burnham Prebys Medical Discovery Institute?
He says, “I love finding answers to fundamental questions that people don't think to ask and to test approaches that they don’t think to try. Our science impacts how we understand biology and treat disease.”

Shape-shifting is not a concept that exists solely within the realm of X-Men any longer. It could happen within our own bodies. It was previously believed that a specialized cell had a very limited ability to change its inherent form and function; once matured, its identity was set, such as an eye or gut cell. Dr. Duc Dong and his research team have discovered that mature cells can indeed be induced to transform into a completely different type of cell. Their research is focusing on developing and optimizing technologies to reprogram a dispensable cell such as skin or fat - who wouldn't want to transform a fat cell into something more useful - into a replacement cell that, for example, produces insulin in a diabetic.
Dr. Dong calls this “hacking a cell”. And he is hacking these cells not in a petri dish, but in vivo - inside a living body - which is believed to be more difficult, but would create safer cells with greater integration and functionality.

A big part for such a little fish

What part does the humble zebrafish play in this innovative scientific research? It is the “in vivo" in question. Because testing transgenes is much easier using zebrafish, compared to the mouse model, Dr. Dong and his team are using them to uncover genes and mechanisms required to reprogram cell identities. They have been able to convert zebrafish muscle and skin cells into pancreatic cells, just one step away from the insulin-producing cells diabetics so lack. They are also close to making neural, liver, and heart cells, all in vivo.

Dr. Dong with a young ALGS patient  

Zebrafish are also playing a critical role in the Dong lab’s research on genetic diseases, including diabetes and Alagille Syndrome. The have generated several zebrafish mutant model of diabetes to investigate the genetic basis of this complex disease. They hope to understand the different subtypes of diabetes so treatments can be better targeted for individual patients.

Alagille Syndrome, or ALGS, is a genetic disorder causing birth defects in many parts of the body, but liver, heart, and blood vessel pathologies are most life threatening. Although this disease has been studied in mouse models for almost two decades, using experimental approaches unique to the zebrafish, Dr. Dong recently uncovered alternative genetic mechanisms for this disease, opening potential new therapeutic avenues. Further, his discoveries suggest that ALGS birth defects may be reversible if the mutated gene JAGGED regains function, implicating regenerative and gene therapy approaches for treating this disease. His lab is now using zebrafish to explore several strategies to functionally restore the JAGGED gene in ALGS patients.

The zebrafish has become an essential model for a rigorous understanding of vertebrate biology and human disease. Further, it provides invaluable alternative perspectives and allows for high risk science for testing outside the box ideas, without the high costs. This model accelerates discoveries, bringing us closer to the next cure,” says Dr. Dong

For further reading:
New Clues to Treat Alagille Syndrome from Zebrafish
Dong Lab Website

Kwong Lab, York University
  Dr Raymond Kwong
  Dr. Raymond Kwong

Degradation of water quality due to anthropogenic contaminants is a pressing problem worldwide, and there is an increasing public concern over the effects of elevated level of metals and metal nanoparticles on aquatic ecosystems. In the Kwong Laboratory at York University in Toronto, Canada, Dr. Raymond Kwong and his research team use zebrafish as a model organism to understand the fundamental mechanisms that regulate ion and metal homeostasis in fish and to identify genes or molecular pathways that underlie the effects of metals/metal nanoparticles on physiological functions.

Transverse section of a zebrafish larvae   Ion-transporting cells in the skin of zebrafish larvae  

The zebrafish provide an excellent model system for integrative physiological and toxicological research. For example, in situ imaging with transgenic zebrafish or mutants can be employed to investigate the etiology and physiological effects in vivo and in real time. The zebrafish also allow high-throughput toxicity screening in combination with forward and reverse genetics approaches to assess direct gene-toxicant relationships.

  Ion transporting cells on larval zebrafish skin


The Kwong Lab hopes that their research will advance fundamental understanding of the mechanisms of toxic action, animal function, and physiological responses to contaminants. They also hope that this information will help to define more specific physiological endpoints for developing more sensitive next-generation biomarkers for environmental monitoring and ecological risk assessment.

Learn more about the research in the Kwong Lab:

Kucenas Lab, University of Virginia
Dr Sarah Kucenas in her lab

Dr. Sarah Kucenas originally became interested in zebrafish when her graduate mentor, Dr. Mark Voigt of Saint Louis University, offered her a choice of two graduate projects:  looking at the role of P2X receptors in neurotransmission using mice/cell culture, which was more typical of his lab, or looking at the role of P2X receptors in development using zebrafish.  Although Dr. Voigt had no experience with zebrafish, Kucenas was intrigued, so she took the plunge.  In retrospect, it was an audacious decision to start a fish project in a non-fish lab as a new graduate student!  But over the course of four years, Kucenas and Voigt not only learned how to keep zebrafish alive, they successfully bred them and nurtured them in their nursery.  The process of using a zebrafish model in a non-fish lab was a challenge; Kucenas and Voigt read research papers and replicated the experimental techniques without any training or help.  But they did it - in situ hybridizations, immunohistochemistry, transgene construction, imaging, etc.!

Glia diversity  
Glial diversity  

Despite tackling some amazing biology with the zebrafish model in Voigt's lab, Dr. Kucenas was uncertain if she wanted to continue with zebrafish for her post-doc, so she interviewed in both fish and mouse labs.  But the science she was after was the same - developmental neuro - and most of these labs were a flavor of neurogenesis/gliogenesis.  Then she read some of Bruce Appel’s papers before applying to his zebrafish lab, and she got hooked.  The beginning imaging he was doing sold his science and his lab to her.  When she interviewed, they were getting long-term in vivo imaging up and running.  She couldn't help but fall in love. The ability to watch the nervous system develop in a vertebrate system while simultaneously manipulating the system either genetically, pharmacologically, or with lasers was exactly the resolution she wanted.  Kucenas saw the potential to tackle some fundamental questions about the nervous system and see things that no one had been able to see before.  Dr. Appel originally hired her to study specification and migration of oligodendrocyte progenitor cells, but while she was learning to in vivo image, she saw something else going on in the developing nervous system.  To her delight, Dr. Appel let her run with it.

Dr. Kucenas is now the head of the Kucenas Lab at the University of Virginia in the Department of Biology.  Her lab studies how glia develop, and how they interact with each other.  And because it is still unknown what some kinds of glial cells do, they also study the functions of different types of glia.  In their zebrafish research models, they watch how the cells develop in zebrafish nervous systems and then manipulate the cells in various ways to observe their behavior and interactions.  The zebrafish knowledge Dr. Kucenas gained by the seat of her pants has been invaluable as she now runs her own zebrafish facility, but did impart some unorthodox techniques:  for example, she dechorionates with two dissecting needles instead of forceps and injects with micromanipulators, not by hand.

  OPC and MEP Glia Characterization

She feels very fortunate that her mentors let her pursue the science she was passionate about.  Zebrafish have allowed her to uncover biology that would have been impossible to discover in any other system.  In her own lab, she mentors the same way she was mentored.  She first lets students and post docs familiarize themselves with the current scientific projects in the lab, and then she has them learn in vivo imaging. From there, they come up with projects that either extend science the lab is already doing, in novel ways, or find totally new areas of biology. For Dr. Kucenas, it’s a win-win. The students and post docs are engaged, excited, and drive the science, and she gets to be a part of their journey and learn alongside them.

Current projects in the Kucenas Lab include:

  • Exploring how one type of glia, motor exit point (MEP) glia, may be used to replace another type called Schwann cells in diseases where Schwann cells are missing or defective.
  • Studying how one type of glial cell called oligodendrocyte progenitor cells (OPCs) move through the body and interact with each other.
  • Learning how perineurial glial develop and what causes them to migrate out of the CNS-PNS transition zone to become the perineurium, a component of the blood-nerve-barrier.
  • Modeling the disease Duchenne Muscular Dystrophy in zebrafish to investigate the neurological component of a disease considered to be primarily muscular
  • Examining the genetic makeup and number of different types of glia
  • Studying glial growth in developing zebrafish

"Learning zebrafish from the ground up I think really set the way I approach science," Dr. Kucenas says. "I’m not afraid. Whether it’s moving into a new biological question or tackling a new technique.  None of that seems scary or hard."

Learn more about the people and the projects in the Kucenas Lab:

Port Washington High School, Wisconsin

Jeff Callies and Sean O'Brien, science teachers at Port Washington High School, share the exciting ways students are using the eRack in the classroom:

Port Washington High School has received a two shelf stand alone education rack from Aquaneering in the fall of 2016 after writing a proposal for an eRack giveaway. The eRack will be used as a cornerstone of research and exploration for the STEM curriculum in Project Lead The Way (PLTW) classes as well as AP Environmental Science and other traditional courses (chemistry, biology, etc.). The high school is itself going under some renovations and next year there will be a new science wing with a separate room designated for using the eRack and an aquaponics tank. Students will have the opportunity to work with zebrafish to study heart and genetic diseases along with other research topics.

Port Washington High School Students record and document temperature and water chemistry in the eRack.

After receiving the eRack, it was set up and cycled to make sure everything was working well. Temperature and water chemistry (pH, hardness, nitrates) were monitored for a stabilized environment to receive zebrafish.

Once the eRack was up and running, Dr. Michael Pickart of Concordia University – Wisconsin was helpful in going over the practical matters of setting up monitoring, schedules and testing to ensure a healthy environment for the zebrafish. Some of the details, such as how to correct water chemistry, establishing feeding schedules, room lighting, water exchanges, and cleaning were discussed. Many of the additional considerations for the eRack (food, water supplies and additives) were purchased and set up to prepare for receiving zebrafish.

Port Washington High School student using their Aquaneering eRack

The zebrafish adapted nicely to our rack set up, and students from PLTW and Ecology were invited to take a look at our system. Students were really excited about this as a functioning education tool. They had many questions for the teachers as to what will be studied, how did we monitor the chemistry, what was the feeding schedule like. Whenever new things happened with the fish, they were very eager to see and participate with what was going on.
Some students who were really engaged by the eRack and what was going on were asked if they liked to help out with monitoring and feeding. This provided those students with authentic record keeping and journaling of the conditions and making observations of the fishes’ behavior. It also provided us with information about the care and maintenance of the system from different points of view. Their concern and ownership of the fish was exciting as a new step into this endeavor.

Zebrafish swimming in tank, Port Washington High School eRackIt was noted that some of the fish were getting larger than the others. Since we had all the tanks occupied with different genders, it was obvious that the fish were spawning. Behaviors such as settling on the bottom or in a corner were good indicators that they were laying embryos. The fish were also consuming the embryos, because we never saw any of the evidence during the day.

It was then that it was decided to separate the fish from one tank from the bottom where the embryos could settle. A tank was chosen that had a fish that was ready to drop embryos and used the insert with grating on the bottom of it. After 2 – 3 days, it was observed that embryo sacks were at the bottom of the tank.

The embryos were moved to one of the smaller tanks at the top. The fish that had been separated using the insert were then moved back into the full tank so they had more room to move.

Using a stereoscope, an image of the larvae and its beating heart was shared with students.

Currently, all the fish we started with are doing well. Water is being turned over regularly and temperature and water chemistry is checked and recorded into a lab notebook. The larvae have grown into tiny fish at this point and although we have had some attrition of the larvae, many of them are doing well and will soon be transferred into a different tank on the system. There are students that are engaged in the care and husbandry of the zebrafish and have inquired about doing further research with them.

This summer will be a time of transition and as the installation of a more permanent location for the eRack at the new building happens, Concordia University – Wisconsin (CUW) will help that transition take place. Many thanks go out to Dr. Michael Pickart and CUW for their time and valuable help in this wonderful opportunity for our students. Also, thanks to Scott Schmutzler of Aquaneering for making the delivery of the eRack easy and quick. Thanks to Beth Freeman and Bobbi Baur of Aquaneering for keeping us in the loop, answering questions and being a valuable resource for novice zebrafish curators.


Barresi Lab, Smith College
Dr. Michael Barresi and graduate student Carla Velez observe zebrafish in a crossing tank

Dr. Michael Barresi is a Renaissance Man in the zebrafish research field. Whether it's research, teaching, student outreach, or art, Dr. Barresi's work seeks the answer to the basic question, why are we the way we are? The desire to find answers to this question led Dr. Barresi to become a developmental neurobiologist using the zebrafish as his model research system. Starting from the tank bottom up, Barresi created Smith College's first zebrafish facility housing to become the director of the Zebrafish Research Center, the largest such facility at a liberal arts school. With the help of a considerable NIH grant, Dr. Barresi plans to expand the facility to house 35,000 fish and transform the facility into a hub of interdisciplinary research for Smith College faculty.

The NIH grant will also fund Dr. Barresi's research on the role of neural stem cells in spinal cord development. Zebrafish have the amazing ability to regenerate their spinal cord, whereas in humans, spinal damage is always permanent and paralyzing. Dr. Barresi wants to find out how this is possible by studying how stem cells affect regeneration. He also plans to investigate how genetic defects can cause brain tumors.

Dr. Barresi's lab investigates the molecular and cellular mechanisms governing how the nervous system is built by delving into three major topics: How are neurons created? How does the nervous system get wired? Which environmental factors impact neural development? In 2011, Dr. Barresi won a National Science Foundation (NSF) CAREER award for his project, "The role of glial cells during commissure formation in the zebrafish forebrain," which provided a "molecular, cellular, and behavioral understanding of how neuron-glial interactions occur in the live developing brain."

As associate professor of biological sciences, Barresi considers teaching and research to go fin-in-fin. His students are encouraged to pursue their own research projects using zebrafish. Zebrafish are ideal for student research projects as the embryos are transparent and mature quickly. But Barresi's interest in cultivating students' passion for science isn't limited to the college level. He also created an outreach program called Student Scientists that introduces zebrafish into the science curriculum at underserved public schools.

Beyond scientific research, Dr. Barresi is also a talented artist and photographer. He graduated from Merrimack College with a major in Biology and a minor in Studio Art in a fusion of art and science. He uses his artistic ability to visually represent his research, such as using discarded slide film from his doctoral research to create a mosaic of an adult zebrafish or illustrating the development of a zebrafish embryo.


University of Utah Zebrafish Core Facility
University of Utah CZAR Central Filtration System

Aquaneering recently installed a 200 GPM Central Filtration System at the University of Utah Zebrafish Core Facility.

The University of Utah Zebrafish Core Facility, under Director Maurine Hobbs, Ph.D., supports the research of 15-20 principal investigators with more than 150 undergraduate students, graduate students, and post-doctoral fellows. Their research interests cover topics as diverse as Developmental Biology, Diabetes, Heart Disease, Muscular Dystrophies, Cancer Biology, Bacterial Pathogenesis, Neurobiology, Behavior, Eye Development and many more.

For more information on CZAR, visit their website.

University of Utah CZAR System Racks

Traver Lab, University of California, San Diego

David Traver, Ph.D., is eminent in the field of zebrafish research and experimental hematology. With fifteen years of experience in the field, Dr. Traver heads his laboratory and acts as Professor of Cellular and Molecular Medicine at the University of California, San Diego. In addition, he is President of the International Society for Experimental Hematology (ISEH) and keynote speaker at many zebrafish research conferences. Dr. Traver was recently the recipient of an LLS Career Development Program (CDP) grant.

Traver Lab Research

Dr. Traver and his research team use the zebrafish as a model to study blood formation in vertebrates. Specifically, the Traver lab is looking for the answer to the question: How are hematopoietic stem cells (HSCs) born in the vertebrate embryo? HSCs are the stem cells that propagate all other blood cells through the lifelong process of haematopoiesis, which literally means "to make blood". Although there are several waves of blood cell formation during the development of all vertebrate animals, HSCs are produced in the final wave and have the unique ability to self-renew for life. Other questions the group seeks to answer are how this self-renewal program is bestowed upon HSCs, and how cancer-initiating cells inappropriately adopt these programs to engender leukemias and other cancers.



The Traver lab also studies how immunity develops in the zebrafish embryo, with a particular emphasis on antigen-presenting cells (APCs). APCs act to orchestrate the immune response to infection, and his group is working to image their behavior in vivo in the translucent zebrafish. In some cases, inappropriate activation of APC subsets, such as microglia present in the brain, has been suggested to underly the etiology of certain neurodegenerative disorders. The Traver lab is thus studying the role of microglia in the development of an autism spectrum disorder termed Rett Syndrome. They hope to help determine the genetic underpinnings of this and other related disorders by utilizing the unique strengths of the zebrafish system.

Using the zebrafish as a research model offers several advantages to study the ontogeny of hematopoiesis and immunity, including easy visualization of blood cells in the translucent embryo and the ability to dissect genetically the pathways important for blood cell specification, maintenance, and function.

Dr. Traver will be chairing several sessions of the ISEH Annual Meeting, held this year in San Diego, California from August 25th to 28th.

For more information on Dr. Traver and his research, visit:

The Traver Lab Homepage
Zebrafish: A New Way to Study Leukemia
Meet Dr. David Traver



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