Zebrafish are increasingly swimming into the view of large-scale drug screening projects. Behavioral screens can be used as a first-line detection tool for new drug effects, and their popularity continues to grow. Translating results to what we might see in humans requires an appropriate (vertebrate) model suited for large-scale

studies. This is a tall order, but one zebrafish easily fill. Mice and rats are more established model systems, but size and cost are often prohibitive to large-scale analyses. Compromising in favor of size and cost points to an invertebrate model like Drosophila. However, in zebrafish researchers find the economy required for high throughput studies, in a vertebrate model.

Read the rest of this article on the Noldus Blog where it was originally posted.

Writing a thesis, or a paper? Need to get out of the office/house? Here is a work-in-progress collaborative effort to map all thesis writing friendly cafes around the world. Take a look at the map, and maybe contribute your favorite writing friendly cafe in your area.

PennState University has developed a phenomenal resource for zebrafish researchers. It is a web-based anatomical and pathological atlas of the zebrafish. The atlas serves as a resource of reference images of ‘normal’ zebrafish at different stages of development.

The atlas is comprised of two-dimensional histology images taken from serially sectioned specimens, and also includes three-dimensional reconstructions. New additions to the atlas include microCT scans. The atlas can be used as a reference tool, a resource to become more familiar with zebrafish anatomy, and it can serve as a tool for comparing different imaging techniques.

The slides in the Zebrafish Atlas allow the user to choose his or her own field of view and magnification, view labeled sections of the zebrafish, and view sections from different stages of development. The authors report on the Zebrafish Atlas website that they plan to add embryonic, larval, and juvenile sections, as well as comparisons (mutant vs. normal, diseased vs. normal, etc) in the future.

Depending on your area of study, you can select a region of interest to learn more about. For example, the Zebrafish Atlas provides a very useful overview of the (adult) Zebrafish brain in the anatomical reference section.

Credits: http://zfatlas.psu.edu/, NIH grant 5R24 RR01744, Jake Gittlen Cancer Research Foundation, and PA Tobacco Settlement Fund.

Zebrafish are increasing in popularity in countless research areas. Having made its debut in developmental biology, Danio rerio is swimming through research areas spanning from behavioral neuroscience to cardiac or oncological studies. There are few disciplines I can think of where zebrafish have not yet been used, but with the recent surge in zebrafish research there is also a need for good literature on the topic. Here is a brief list of useful resources for zebrafish research:

The Zebrafish Book

Already in its 5th edition, the Zebrafish Book by Westerfield (2007) is certainly not a new kid on the block, but it is by far the most basic and necessary resource for anyone venturing into zebrafish research. You can either purchase a print version of the book, but you can also access all of the content in the 4th edition of the book online (for free!).
The Zebrafish Book covers general methods for zebrafish care, breeding, embryonic and larval culture, cellular and molecular methods, and protocols.

ZFIN Protocol Wiki

ZFIN has built a Wiki with protocols for zebrafish research. Whether you are using Danio rerio for gene cloning, protein analysis, or microscopic observations… ZFIN has a protocol for it.
As it is a wiki, users can load protocols to the site as well. When using protocols, it is worth keeping in mind that although it being a useful resource it is not peer reviewed. Some of the protocols are based on peer reviewed papers.

ZFIN model organism database

ZFIN is a phenomenal database for all things zebrafish. ZFIN has a database with zebrafish lines and also a page with job listings for people in the field.

Zebrafish Neurobehavioral Protocols

Zebrafish are relatively new in behavioral neuroscience. As a consequence, standardized protocols are still in being developed by the different groups in this field. There is a remarkable need for good protocols, and this book covers a number of protocols that have successfully been used in previous studies.

This list is by no means comprehensive, if you know of some other great resources for beginners in zebrafish research, or for those who have used this model organism for decades, feel free to share it in the comments!

Depression affects more than 120 million people world wide (according to the World Health Organization), and the cost of treatment is estimated at 30 billion dollars each year. At this year’s SfN meeting in San Diego, Dr. Herwig Baier presented some very interesting findings:

Dr. Baier and his team found that disrupting the stress response in zebrafish can generate behavioral phenotypes that resemble behaviors characteristic to depression. His work suggests that depression could be linked to a individual’s ability to cope with stress.

The zebrafish displaying depression-like behaviors carried a mutation in the glucocorticoid receptor gene, which is involved in stress management. However, the depression-like behaviors were ameliorated when the fish were given Prozac.

New therapies might be able to play into the activity of the glucocorticoid receptor, and promoting its activity instead of blocking it.

I wanted to take a moment and post an interesting workshop being hosted by AAAS tonight at the Society for Neuroscience annual meeting: Careers Away from the Bench. It will be held from 6:30pm – 8pm at the San Diego Convention Centre, room 4.

The workshop will address career options for PhDs outside of academia or non-academic research. They promise to discuss how to identify opportunities, and how to develop the skills that will help launch a successful career away from (bench) research.

I’d say it is absolutely worth a visit, even if you do want to pursue academia. You never know where a career might take you and being informed of the options will prove valuable at some point in your life.

If you can’t attend, AAAS has a wealth of information available on their outreach website.

One of the funniest things to happen before SfN even started was the realization that all people on my flight but maybe three, were headed to San Diego to attend SfN. We must have left the flight crew a bit confused when one after another passenger brought on board a poster tube. In fact, there were so many that by the end of the flight they made a special announcement:

“…One other thing… we…uhm… noticed very many of you with…uhm… these tubes. I just want to stress for all passengers to make sure they are leaving with their own tube, and not someone else’s because they all look alike so much, and it would be horrible to arrive at your destination with a tube that is not your own.”

Although I arrived yesterday, today was the official start of the conference. This was the first time in my adult life where I can say yet lag is my friend: traveling from Toronto to Southern California gives me the feeling of being a hardcore morning person. I woke up around 5am, truly came to terms with getting up at 6:30 and decided to go for an early morning run. Although I run regularly and I had fully committed to running in San Diego, I certainly had no plans of running before 8am. Somehow, that seemed like the only thing I could do, aside from just walking around the city again (as I already did yesterday). I actively tried to talk myself out of going out that early, but my inner runner won and off I went. My only regret was not being able to take my camera, because the fresh glow the sun left on harbor drive was phenomenal. I’ll have to retrace my steps later and actually take pictures…

Unlike previous years, it feels like SfN is starting off a little bit slow. There was absolutely nothing to do before 11am (another great argument for actually running earlier), but once the conference started it started with a bang! From 11am-1pm Glenn Close spoke to me, and what looked like a few thousand colleagues, about her advocacy through BringChange2Mind.org. You can see a full video of her talk here.

Glenn Close has mental illness in her family, and as it turns out many of us in the audience can identify with that position, or battle some form of mental illness as well. This isn’t that strange, because as Glenn pointed out one in four families has one or more members with mental illness.

Glenn Close shared a portion of her sequenced DNA results

It was interesting that Glenn Close started her talk with a reference to being asked by people “are you who we think you are”, and then those people actually confusing her with Meryl Streep. Glenn then proceeded to say this was an occasion where she could actually show us who she really is, because most of the time she is pretending to be someone else in her career as an actor. She shared a printout of her DNA sequencing data, and in a humourful way referred to her chromosome 1 as “sexy”. I’d like to agree…

Glenn Close pointing at her DNA

The reference to ‘identity’ kept coming back in her talk, and in the talks given by her sister and nephew (both afflicted by mental health disorders), although this did not seem to be intended. Stigma surrounding mental health disorders might have a lot to do with perceived identity. Although never formulated as such, from the discussion I feel it needs to be addressed that others might think of some one’s symptoms as part of their personality. Someone acting out, or showing signs of severe depression are often not recognized as having an illness, they are treated based on how their symptoms appear to the world. Even though it might be difficult to address this because another person might not know to recognize symptoms for what they are, and not attribute it to some one’s personality, if addressed it might help the issue of stigma. It was rightfully pointed out that the same stigma does not exist around other diseases, such as diabetes or even cancer. Most of the time though, the symptoms of other diseases might not be as obvious, or most importantly might not affect some one’s behavior. In terms of behavior that we consider to fit within our “norm”. Whenever people deviate from a norm, others get nervous. As Glenn’s sister Jesse pointed out, perhaps “it is genetically ingrained to be afraid of people who are not like us.” This makes banishing the stigma difficult. After all, even though we know mental illness is not “who” or “what” the person who suffers from it is, we still assess how we treat someone by how they might be behaving.

Glenn’s talk was extraordinarily enlightening, and illustrated how much more needs to be done in the area of advocacy for people with a mental disorder. It also made it clear to me we need to actively think about how to address the stigma that exists, and how important effective treatments are in helping people overcome stigma by addressing their disorder’s symptoms. Basic research can help us find treatments that will brighten another person’s life, in some cases quite literally. This talk highlighted how big a difference we make as a community, even though there is still so far to go.

Anyone who wants to be involved with, or learn more about BringChange2Mind can visit their website. Be sure to check out their videos on youtube, and definitely look out for their PSA. It is a very powerful message, and a fantastic video I encourage everyone to see:

The Society for Neuroscience (SfN) annual meeting is about to kick off on November 13th. Over 30.000 excited neuroscientists will be browsing the poster sessions, attending symposia, and exchanging ideas. At most conferences that are not zebrafish specific, Danio rerio have to battle for some of the attention. Thankfully, this seems to be getting easier every year. One major indication of zebrafish’ increased popularity in (behavioral) research is the remarkable increase in zebrafish studies showcased at SfN.

This year is my third time attending SfN, and I remember the first time I presented my work very clearly: more than one person was surprised to see behavioral work being done on zebrafish. It’s important to remember that these were all scientists, yet some had still not been familiarized yet with danio in research.

This year I am seeing the same thing I noticed last year: an increase in the number of zebrafish presentations. For the zebrafish community, this is a very exciting development. More of us are using Danio rerio in our research, and the benefits are getting us hooked. The community is taking note, and slowly but surely we are taking a significant spot at major conferences.

Here is a list of presentations (posters and symposia) featuring the zebrafish as a model organism at SfN:

Saturday November 13th 2010

1. Poster board: 25.3/OOO19
   Title: Maze tests and pharmacological manipulation of fear and reward-seeking behavior in zebrafish and other teleosts.
   Authors: G. G. Gould, D.J. Echevarria, T.M. Szabo, E.S. Onaivi, T.W. Valenti, and B.W. Brooks.
2. Date and presentation time (NB: Symposia!): 3:00 PM – 3:15 PM, 13.9, Room 7B.
   Title: Expression of a spinocerebellar ataxia type 13 mutant potassium channel subunit in zebrafish impairs execution of the startle response.
   Authors: D. M. Papazian, F. A. Issa, C. Mazzochi, J. L. Richardson, J.-Y. Hsieh, A. F. Mock
3. Poster board: 22.6/NNN28.
   Title: University of utah brain awareness 2010.
   Authors: D. M. Friend, E. Elias, E. Iacob, C. Mencio, W. Oswald, R. Parker, E. Smith, M. Wright
4. Time and poster board: 2:00 PM – 3:00 PM, 26.30/OOO73
   Title: Initiative to link animal models to human disease (LAMHDI).
   Authors: D. Anderson, R. Buccigrossi, M. Ellisman, J. T. Eppig, H. Evans-Kavaldjian, J. S. Grethe, R. Hamel, J. Kemnitz, M. Martone, K. Pohland, N. Preuss, C. L. Smith, M. Sullivan, M. Travers, J. Turner, M. Westerfield, H. Yurt.
5. Time and poster board: 4-5pm 29.4/A4.
   Title: Extracellular nucleotides regulate proliferation of progenitor cells in the adult zebrafish retina during the light:dark cycle.
   Authors: M. Ricatti, A. Battista, M. Faillace
6. Time and poster board: 1-2pm 32.1/D7.
   Title: Optogenetic analysis of correlated spontaneous activity in the developing spinal circuit of zebrafish.
   Authors: E. Warp, C. Wyart, F. Del Bene, H. Baier, E. Y. Isacoff
7. Time and poster board: 3-4pm 37.7/F8.
   Title: Primary motoneuron axonal pathfinding errors guide secondary motoneuron axonal pathfinding in nicotine-exposed zebrafish.
   Authors: K. R. Svoboda, E. Menelaou, L. Paul.
8. Time and poster board: 2-3pm 37.10/F11.
   Title: Expressing alpha7 acetylcholine receptors in a model nicotinic synapse.
   Authors: H. Ikeda, J. Urban, F. Ono.
9. Time and poster board: 3-4pm, 40.23/G32.
   Title: Evidence that position 49 plays a role in transmembrane rearrangement during channel opening in P2X4 receptors.
   Authors: M. Popova, J. R. Trudell, L. Asatryan, R. L. Alkana, D. L. Davies.
10. Time and poster board: 1-2pm 42.9/H5.
    Title: Large myelinated club endings in embryonic zebrafish contain Cx35.
    Authors: C. Yao, S. Nannapaneni, A. E. Pereda.
11. Time and poster board: 4-5pm 65.16/DD2.
    Title: Psychedelic zebrafish: Deconstructing the effects of hallucinogens LSD and MDMA on zebrafish behavior and physiology.
    Authors: J. Cachat, J. Dileo, J. Goodspeed, C. Suciu, T. Gilder, K. Wong, A. Stewart, S. Gaikwad, M. Elegante, D. Tien, A. Kalueff.
12. Time and poster board: 3-4pm 49.7/I36.
    Title: Modulators of Tau induced toxicity in a zebrafish model for FTD.
    Authors: F. Van Bebber, D. Paquet, A. Hruscha, B. Schmid, S. F. Lichtenthaler, C. Haass.

Sunday November 14th 2010

1. Time and poster board: 11:00 AM -12:00 PM, 146.8/H30
   Title: Disruptions of spatacsin and/or spastizin functions lead to motor neuron axonal outgrowth defects in the Danio rerio.
   Authors: E. M. Martin, C. Yanicostas, A. Maouedj, A. Brice, G. Stevanin, N. Soussi-Yanicostas
2. Time and poster board: 8:00 AM – 9:00 AM, 166.13/BB2
   Title: Role of oxytocin/vasopressin system on social behavior and fear response to predator in zebrafish
   Authors: D. Braida, A. Finardi, A. Donzelli, V. Capurro, B. Chini, M. Sala
3. Time and poster board: 4:00 PM – 5:00 PM, 234.16/C38
   Title: Characterization of spontaneous electrical activity in developing spinal motor neurons of zebrafish embryos.
   Authors: P. V. Plazas, N. C. Spritzer
4. Time and poster board: 2:00 PM – 3:00 PM, 240.26/F39
   Title: Identification and modulation of voltage-gated calcium channels in zebrafish Rohon-Beard neurons.
   Authors: Y.-J. Won, F. Ono, S. R. Ikeda
5. Time and board: 2:00 PM – 3:00 PM, 267.10/HH7.
   Title: Effects of ethanol on anxiety-related behaviors in zebrafish (Danio rerio).
   Authors: Y. M. Penalosa, R. Blaser

Monday November 15th 2010

1. Time and poster board: 11:00 AM -12:00 PM, 358.4/V3
   Title: Primary neuronal brainstem culture from adult zebrafish: Interactions with an inhibitory chondroitin sulfate proteoglycan-rich environment
   Authors: A. Tapanes-Castillo, F. Shabazz, K. Vajn, M. Oudega, J. A. Plunkett
2. Time and poster board: 8:00 AM – 9:00 AM, 358.5/V4
   Title: Neurocan mRNA expression following CNS injury in adult zebrafish (Danio rerio).
   Authors: J. A. Plunkett, A. Tapanes-Castillo, F. Shabazz, K. Vajn, M. Oudega
3. Time and poster board: 9:00 AM -10:00 AM, 358.6/V5.
   Title: Molecular and cellular development of scar tissue in the injured spinal cord of adult zebrafish (Danio rerio).
   Authors: K. Vajn, A. Tapanes-Castillo, F. Shabazz, J. A. Plunkett, M. Oudega
4. Time and program (NB: Nanosymposium!): Monday, 2:30 PM – 2:45 PM, 431.7, Room 1B
   Title: Touché: A recessive zebrafish mutation which abolishes generator potentials in cutaneous mechanoreceptors.
   Authors: S. E. Low, J. Ryan, M. Lachance, L. Saint-Amant
5. Time and poster board: 3:00 PM – 4:00 PM, 435.19/B9
   Title: Methylmercury exposure decreases cell proliferation in the zebrafish (Danio rerio) embryonic neural tube
   Authors: E. A. Moussa, S. A. Hassan, L. C. Abbott
6. Time and poster board: 1:00 PM – 2:00 PM, 439.25/E1
   Title: Functional analysis of neuroligin 2 in the developing zebrafish spinal cord
   Authors: J. Fierro, JR, C. Davey, A. Tallafuss, P. Washbourne
7. Time and poster board: 1:00 PM – 2:00 PM, 440.17/E18
   Title: Effects of chlorpyrifos exposure on the development of the cholinergic nervous system of the zebrafish and C. elegans
   Authors: F. Radoniqi, G. Orona, O. Mac, S. Han, D. Bourgaize, E. A. Fradinger
8. Time and poster board: 1:00 PM – 2:00 PM, 446.21/G17
   Title: Voltage activated currents in zebrafish hair cells
   Authors: P. Bravo, B. Escobar, J. Magana, M. Malinao, J. Ngo, O. Sanchez, A. Tucker, M. Valdivia, S. Yaghtin, V. Zeron, B. E. Yazejian
9. Time and poster board: 4:00 PM – 5:00 PM, 464.12/W8
   Title: Behavioral effects of RDX on adult zebrafish
   Authors: K. Wong, L. R. Williams, A. Stewart, J. Goodspeed, C. Suciu, J. Cachat, A. V. Kalueff
10. Time and poster board: 3:00 PM – 4:00 PM, 476.3/MM11
    Title: Modulation of the nicotine response
    Authors: H. Schneider, S. C. Ekker
11. Time and poster board: 4:00 PM – 5:00 PM, 478.8/PP18
    Title: Integrating convergent evidence across species to find QTL candidate genes using the Ontological Discovery Environment
    Authors: V. M. Philip, J. J. Jay, M. A. Langston, E. J. Baker, E. J. Chesler

Tuesday November 16th 2010

1. Time and poster board: 8:00 AM – 9:00 AM, 573.5/II19
   Title: The effects of embryonic etoh exposure on neurochemical and behavioral characteristics of the developing zebrafish
   Authors: C. Buske, R. T. Gerlai
2. Time and poster board: 11:00 AM -12:00 PM, 573.12/JJ6
   Title: Ethanol exposure during gastrulation of zebrafish embryogenesis dysregulates microRNAs and their target genes
   Authors: D. L. Pappalardo, W.-J. A. Chen, R. C. Miranda
3. Time and poster board: 8:00 AM – 9:00 AM, 594.17/HHH30
   Title: Kisspeptin stimulates electrical activity of extra-hypothalamic gonadotropin releasing hormone (GnRH) neurons from transgenic fish
   Authors: Y. Zhao, N. L. Wayne
4. Time and poster board: 11:00 AM -12:00 PM, 614.16/OOO4
   Title: Protein-traps in zebrafish: stressing behavioral genetics
   Authors: K. J. Clark, D. Balciunas, N. J. Boczek, A. M. Petzold, E. W. Klee, H. Schneider, K. J. Skuster, M. D. Urban, T. M. Greenwood, S. C. Ekker
5. Time and poster board: 1:00 PM – 2:00 PM, 636.21/B11
   Title: Enhancer screen reveals complex logic for vertebrate dopamine neuron phenotype specification
   Authors: J. Bonkowsky, E. Fujimoto, C.-B. Chien
6. Time and poster board: 2:00 PM – 3:00 PM, 657.18/P4
   Title: Anxiolytic and anticonvulsant properties of aqueous Valerian extracts
   Authors: L. M. Del Valle-Mojica, B. A. Torres-Hernandez, S. Torres-Rodriguez, C. Rosa-Falero, J. G. Ortiz
7. Time and poster board: 2:00 PM – 3:00 PM, 706.18/LLL66
   Title: Individual differences in zebrafish behavior: Implications for animal models
   Authors: C. Toms, D. J. Jouandot, D. J. Echevarria
8. Time and poster board: 1:00 PM – 2:00 PM, 707.25/MMM27
   Title: Assessing attention in the zebrafish
   Authors: D. J. Jouandot, C. Toms, D. J. Echevarria

Wednesday November 17th 2010

1. Time and poster board: Wednesday, Nov 17, 2010, 8:00 AM – 9:00 AM, 745.13/F8
   Title: Gaba-a receptor mediated spontaneous electrical activity in anterior dorsal and entopenduncular nuclei in adult zebrafish
   Authors: K. Karlsson, Dr., R. A. Vargas

The zebrafish (Danio rerio) belongs to:

Kingdom: Animalia

Phylum: Chordata

Class: Acrinopterygii

Order: Cypriniformes

Family: Cyprinidae

Genus: Danio

Species: Danio rerio

The following phylogenetic tree shows the relationship between Danio rerio and a portion of other Danio and Devario species.

The phylogenetic relationships depicted above were inferred maximum likelihood analyses of 12S and 16S mtDNA. Numbers above branches are support values from Bayesian analysis and nonparametric bootstapping. Figure and analysis by: Parichy, DM. Evolution of danio pigment pattern development. Heredity (2006) 97, 200–210. doi:10.1038/sj.hdy.6800867.

Since I have last posted, there are some new video articles on JoVE involving zebrafish research. A team at MIT published a video protocol showing how to do injections in the zebrafish brain ventricle. This can aid in the study of ventricle formation and morphology. When studying the effect of teratogens, it could also be interesting to look at brain morphology using this technique. Here are some images shown on JoVE from this protocol.

View the video protocol on JoVE here.