Leung Lab Blog

Sylvia and Fai attended the 2013 Annual Meeting of the Association for Research in Vision and Ophthalmology and presented their work on novel signal transduction for photoreceptor development and using traditional Chinese medicine to treat retinal degeneration. Sylvia received a National Eye Institute Travel Grant and Yeunkyung Woo Achieve Excellence Travel Award to attend the meeting. Sylvia and Fai also interacted with colleagues all over the world during different events including the SERI reception, ARVO dinner with The Eye Hospital of Wenzhou Medical College, and ARVO CUHK-JSIEC Research Networking Evening. More pictures to follow.

Sylvia and Fai in front of Sylvia’s poster

Nature Special Issue on “The Future of Publishing“

Neuroscience

1. Horikawa T, Tamaki M, Miyawaki Y, Kamitani Y. Neural Decoding of Visual Imagery During Sleep. Science. 2013 Apr 4. [Epub ahead of print] PubMed PMID: 23558170.
2. Chung K, Wallace J, Kim SY, Kalyanasundaram S, Andalman AS, Davidson TJ, Mirzabekov JJ, Zalocusky KA, Mattis J, Denisin AK, Pak S, Bernstein H, Ramakrishnan C, Grosenick L, Gradinaru V, Deisseroth K. Structural and molecular interrogation of intact biological systems. Nature. 2013 Apr 10. doi: 10.1038/nature12107. [Epub ahead of print]
   • A new way of clearing tissue for imaging!
   • Commentary: Shen H. See-through brains clarify connections. Nature. 2013 Apr 11;496(7444):151. doi: 10.1038/496151a. PubMed PMID: 23579658.
   • From the New York Times: Brains as Clear as Jell-O for Scientists to Explore

Genomics

Zebrafish genome sequencing

1. Howe K, et al. The zebrafish reference genome sequence and its relationship to the human genome. Nature. 2013 Apr 17. doi: 10.1038/nature12111. [Epub ahead of print] PubMed PMID: 23594743.
2. Schier AF. Genomics: Zebrafish earns its stripes. Nature. 2013 Apr 17. doi: 10.1038/nature12094. [Epub ahead of print] PubMed PMID: 23594741.
3. Kettleborough RN, Busch-Nentwich EM, Harvey SA, Dooley CM, de Bruijn E, van Eeden F, Sealy I, White RJ, Herd C, Nijman IJ, Fényes F, Mehroke S, Scahill C, Gibbons R, Wali N, Carruthers S, Hall A, Yen J, Cuppen E, Stemple DL. A
   systematic genome-wide analysis of zebrafish protein-coding gene function. Nature. 2013 Apr 17. doi: 10.1038/nature11992. [Epub ahead of print] PubMed PMID: 23594742.

I visited Ho Yu College in Hong Kong last month. A good mentor Dr. William Mak has been running a great biotechnology education program for the primary and secondary school students, as well as the public there. See an old post about their outreach program in which they fit a whole research lab into custom-built bus! I shared the research program of our laboratory at Purdue University on using zebrafish to screen drugs for vision benefit.

I outlined our approach on using simple visual behaviour assays to identify positive effects of drugs. I specifically emphasized on the potential to analyze many of traditional Chinese medicines; the treasure that we have been consuming for generations. Some of these possibilities are outlined in our recent review paper:

Zhang LY, Chong L, Cho J, Liao PC, Shen F, Leung YF. Drug Screening to Treat Early-Onset Eye Diseases: Can Zebrafish Expedite the Discovery? Asia-Pac J Ophthalmol 2012; 1:374-383. [Full text][pdf]

The interaction with the students was fantastic. They were very imaginative and eager to ask questions all the time! Their enthusiasm was infectious and is the driving force of scientific progress. That also reminded me of the problem of our education in stifling creativity when students are “educated”, which I wrote in a separate post recently.

This is truly an enjoyable experience and I look forward to visiting them again soon!

Gene Therapy/Retinal degeneration

1. Cideciyan AV, Jacobson SG, Beltran WA, Sumaroka A, Swider M, Iwabe S, Roman AJ, Olivares MB, Schwartz SB, Komáromy AM, Hauswirth WW, Aguirre GD. Human retinal gene therapy for Leber congenital amaurosis shows advancing retinal degeneration despite enduring visual improvement. Proc Natl Acad Sci U S A. 2013 Jan 22. [Epub ahead of print] PubMed PMID: 23341635.
   • News coverage: Another Bump in the Road to Gene Therapy?

Neuroscience

1. Muto A, Ohkura M, Abe G, Nakai J, Kawakami K. Real-Time Visualization of Neuronal Activity during Perception. Curr Biol. 2013 Jan 29. doi:pii: S0960-9822(13)00002-X. 10.1016/j.cub.2012.12.040. [Epub ahead of print] PubMed PMID: 23375894.
   • News coverage: See a Thought Move Through a Living Fish’s Brain
   • News coverage: Fluorescent protein lets us read a fish’s thoughts
   • More videos by the authors:

Genetics

1. Hwang WY, Fu Y, Reyon D, Maeder ML, Tsai SQ, Sander JD, Peterson RT, Yeh JR, Joung JK. Efficient genome editing in zebrafish using a CRISPR-Cas system. Nat Biotechnol. 2013 Jan 29. doi: 10.1038/nbt.2501. [Epub ahead of print] PubMed PMID: 23360964.
2. Bedell VM, Wang Y, Campbell JM, Poshusta TL, Starker CG, Krug RG 2nd, Tan W, Penheiter SG, Ma AC, Leung AY, Fahrenkrug SC, Carlson DF, Voytas DF, Clark KJ, Essner JJ, Ekker SC. In vivo genome editing using a high-efficiency TALEN system. Nature. 2012 Nov 1;491(7422):114-8. doi: 10.1038/nature11537. Epub 2012 Sep 23. PubMed PMID: 23000899; PubMed Central PMCID: PMC3491146.

On 12th November 2012, Prof. Calvin Chi-Pui Pang from the Chinese University of Hong Kong and Prof. Haoyu Chen from the Joint Shantou International Eye Center (JSIEC), Shantou University & the Chinese University of Hong Kong visited the Leung Lab and the research facilities at Purdue University.

Prof Pang and Chen first met with Prof. Marietta Harrison, Associate Vice-President for Research and Dr. Geanie Umberger, Assistant Vice President for Corporate and Foundation Relations to discuss collaborative plans between the Leung Lab, Purdue and JSIEC. Our long-term goal is to explore the opportunities in clinical eye research and drug screening  in China.

From left to right: Dr. Umberger, Prof. Harrison, Prof. Pang, Prof. Leung, and Prof. Chen.

Then, Profs. Pang and Chen visited the Bindley Bioscience Center. Dr. Tommy Sors, the Center Project Manager, showcased the Purdue’s infrastructure for preclinical investigations.

From left to right: Prof. Chen, Prof. Leung, Prof. Pang and Dr. Sors.

Finally, there was a dinner gathering with Prof. Marietta and other distinguished professors from the Department of Biological Sciences to celebrate friendship and new collaborative relationships.

Back row: Prof. Don Ready, Prof. Chen, Prof. Leung and Dr. Liyun Zhang, postdoctoral fellow in the Leung Lab.
Front row: Prof. Bill Pak, Prof. Marietta, Prof. Pang, and Prof. Richard Kuhn.

I was invited and supported by the Purdue Research Foundation (PRF) International Travel Grant to give a Plenary Lecture at the Symposium on Biology of Ophthalmology 2011 which took place in the Hong Kong Eye Hospital from 11-13th December 2011. The event was organized by the Department of Ophthalmology and Visual Sciences at the Chinese University of Hong Kong (CUHK), a leading eye research center in Asia.

Some participants at the Symposium on Biology of Ophthalmology 2011

The symposium covers a wide variety of topics from clinic research, ophthalmic imaging, genetic screen to very basic eye research. Together with Dr. Motokazu Tsujikawa from Osaka University Ophthalmology, we shared our vision on studying  retinal degeneration using zebrafish. Dr. Liyun Zhang, currently a Charles Kelman MD Scholar of the International Retinal Research Foundation whom works in my laboratory, also shared her future plans on studying disease-causing gene network of fish model of human retinal degeneration. It is really impressive that many physicians can perform top clinical service and yet can spare time to do high-quality research.

Both Liyun and I chaired sessions on various aspects of exciting ophthalmic research from different research groups, and through these interactions,  we have met new and old friends, including Dr. Rosa Chan from City University of Hong Kong who is studying computational modeling of brain activity, a group of very dedicated and accomplished scientists including Drs Yan, Hou and Zhou from the Eye Hospital at Wenzhou Medical College where I also visited during the trip, friends from Osaka Ophthalmology including Drs. Kohji Nishida, Yasushi Ikuno and Motokazu Tsujikawa, Dr. Carol Cheung from Singapore, Dr. Richard Choy and Gary Yam, among many others from CUHK and friends from the Joint Shantou International Eye Center (JSIEC) at Shantou University, etc.

Right after the symposium, I led a 2-day workshop on “Frontiers in human genetics and eye research” with about 15 students from several locations. My goal was to help students who have only been focused on a narrow genetic aspect and/or clinical aspects of ophthalmology to put their knowledge on a wider perspective. Each day we read and presented a paper about either human genetics and eye research using zebrafish model in depth. This time we discussed two papers:

1. Zhong Q, Simonis N, Li QR, Charloteaux B, Heuze F, Klitgord N, Tam S, Yu H, Venkatesan K, Mou D, Swearingen V, Yildirim MA, Yan H, Dricot A, Szeto D, Lin C, Hao T, Fan C, Milstein S, Dupuy D, Brasseur R, Hill DE, Cusick ME, Vidal M. Edgetic perturbation models of human inherited disorders. Mol Syst Biol. 2009;5:321. Epub 2009 Nov 3. PubMed PMID: 19888216; PubMed Central PMCID: PMC2795474.
2. Kay JN, Roeser T, Mumm JS, Godinho L, Mrejeru A, Wong RO, Baier H. Transient requirement for ganglion cells during assembly of retinal synaptic layers. Development. 2004 Mar;131(6):1331-42. Epub 2004 Feb 18. PubMed PMID: 14973290.

I was really impressed with many of them who were thinking about the new ideas and tools in a critical manner and was very engaged in a lively discussion.

It was a gratifying experience to interact with and see many students fro the Asia region who are laying down the foundation for and conducting great research! Kudos to the organizers including Drs. Calvin Pang and Chris Leung from the CUHK for putting together an excellent conference program to make the whole trip possible!

Retinal Development

1. Kwan KM, Otsuna H, Kidokoro H, Carney KR, Saijoh Y, Chien CB. A complex choreography of cell movements shapes the vertebrate eye. Development. 2012 Jan;139(2):359-72. PubMed PMID: 22186726.
2. Morgan JL, Soto F, Wong RO, Kerschensteiner D. Development of cell type-specific connectivity patterns of converging excitatory axons in the retina. Neuron. 2011 Sep 22;71(6):1014-21. Epub 2011 Sep 21. PubMed PMID: 21943599; PubMed Central PMCID: PMC3184549.

Stem cells

1. Salero E, Blenkinsop TA, Corneo B, Harris A, Rabin D, Stern JH, Temple S. Adult Human RPE Can Be Activated into a Multipotent Stem Cell that Produces Mesenchymal Derivatives. Cell Stem Cell. 2012 Jan 6;10(1):88-95. PubMed PMID: 22226358.
• Commentary: Trounson A, Grieshammer U. Chimeric Primates: Embryonic Stem Cells Need Not Apply. Cell. 2012 Jan 4. [Epub ahead of print] PubMed PMID: 22225613.
2. Phanstiel DH, Brumbaugh J, Wenger CD, Tian S, Probasco MD, Bailey DJ, Swaney DL, Tervo MA, Bolin JM, Ruotti V, Stewart R, Thomson JA, Coon JJ. Proteomic and phosphoproteomic comparison of human ES and iPS cells. Nat Methods. 2011 Sep 11;8(10):821-7. doi: 10.1038/nmeth.1699. PubMed PMID: 21983960.

Genetics

1. Zhang F, Vierock J, Yizhar O, Fenno LE, Tsunoda S, Kianianmomeni A, Prigge M, Berndt A, Cushman J, Polle J, Magnuson J, Hegemann P, Deisseroth K. The microbial opsin family of optogenetic tools. Cell. 2011 Dec 23;147(7):1446-57. PubMed PMID: 22196724.
2. McMahon MA, Rahdar M, Porteus M. Gene editing: not just for translation anymore. Nat Methods. 2011 Dec 28;9(1):28-31. doi: 10.1038/nmeth.1811. PubMed PMID: 22205513.
3. Zhao S, Ting JT, Atallah HE, Qiu L, Tan J, Gloss B, Augustine GJ, Deisseroth K, Luo M, Graybiel AM, Feng G. Cell  type–specific channelrhodopsin-2 transgenic mice for optogenetic dissection of neural circuitry function. Nat Methods. 2011 Sep;8(9):745-52. PubMed PMID: 21985008; PubMed Central PMCID: PMC3191888.

Genomics

1. Kalhor R, Tjong H, Jayathilaka N, Alber F, Chen L. Genome architectures revealed by tethered chromosome conformation capture and population-based modeling. Nat Biotechnol. 2011 Dec 25;30(1):90-8. doi: 10.1038/nbt.2057. PubMed PMID: 22198700.
• Commentary: Misteli T. Parallel genome universes. Nat Biotechnol. 2012 Jan 9;30(1):55-6. doi: 10.1038/nbt.2085. PubMed PMID: 22231096.
2. Lam HY, Clark MJ, Chen R, Chen R, Natsoulis G, O’Huallachain M, Dewey FE, Habegger L, Ashley EA, Gerstein MB, Butte AJ, Ji HP, Snyder M. Performance comparison of whole-genome sequencing platforms. Nat Biotechnol. 2011 Dec  18;30(1):78-82. doi: 10.1038/nbt.2065. PubMed PMID: 22178993.
3. Mercer TR, Gerhardt DJ, Dinger ME, Crawford J, Trapnell C, Jeddeloh JA, Mattick JS, Rinn JL. Targeted RNA sequencing reveals the deep complexity of the human transcriptome. Nat Biotechnol. 2011 Nov 13;30(1):99-104. doi: 10.1038/nbt.2024. PubMed PMID: 22081020.

Systems Biology

1. Young JW, Locke JC, Altinok A, Rosenfeld N, Bacarian T, Swain PS, Mjolsness E, Elowitz MB. Measuring single-cell gene expression dynamics in bacteria using fluorescence time-lapse microscopy. Nat Protoc. 2011 Dec 15;7(1):80-8. doi: 10.1038/nprot.2011.432. PubMed PMID: 22179594.
2. Dutkowski J, Ideker T. Protein networks as logic functions in development and cancer. PLoS Comput Biol. 2011 Sep;7(9):e1002180. Epub 2011 Sep 29. PubMed PMID: 21980275; PubMed Central PMCID: PMC3182870.

Neuroscience

1. Kralj JM, Douglass AD, Hochbaum DR, Maclaurin D, Cohen AE. Optical recording of action potentials in mammalian neurons using a microbial rhodopsin. Nat Methods. 2011 Nov 27;9(1):90-5. doi: 10.1038/nmeth.1782. PubMed PMID: 22120467; PubMed Central PMCID: PMC3248630.
• Commentary: Looger LL. Running in reverse: rhodopsins sense voltage. Nat Methods. 2011 Dec 28;9(1):43-4. doi: 10.1038/nmeth.1817. PubMed PMID: 22205516.
2. Pan YA, Choy M, Prober DA, Schier AF. Robo2 determines subtype-specific axonal projections of trigeminal sensory neurons. Development. 2012 Feb;139(3):591-600. Epub 2011 Dec 21. PubMed PMID: 22190641; PubMed Central PMCID: PMC3252355.
3. Nishimoto S, Vu AT, Naselaris T, Benjamini Y, Yu B, Gallant JL. Reconstructing visual experiences from brain activity evoked by natural movies. Curr Biol. 2011 Oct 11;21(19):1641-6. Epub 2011 Sep 22. PubMed PMID: 21945275.
4. Cavallari N, Frigato E, Vallone D, Fröhlich N, Lopez-Olmeda JF, Foà A, Berti R, Sánchez-Vázquez FJ, Bertolucci C, Foulkes NS. A blind circadian clock in cavefish reveals that opsins mediate peripheral clock photoreception. PLoS Biol. 2011 Sep;9(9):e1001142. Epub 2011 Sep 6. PubMed PMID: 21909239; PubMed Central PMCID: PMC3167789.

Vision

1. Kingdom FA. Binocular vision: the eyes add and subtract. Curr Biol. 2012 Jan 10;22(1):R22-4. PubMed PMID: 22240475.

Education

1. Vanderford NL. Broadening PhD curricula. Nat Biotechnol. 2012 Jan 9;30(1):113-4. doi: 10.1038/nbt.2091. PubMed PMID: 22231111.

Medical Research

1. Reed JC, White EL, Aubé J, Lindsley C, Li M, Sklar L, Schreiber S. The NIH’s role in accelerating translational sciences. Nat Biotechnol. 2012 Jan 9;30(1):16-9. doi: 10.1038/nbt.2087. PubMed PMID: 22231085.
2. Hudson KL. Genomics, health care, and society. N Engl J Med. 2011 Sep 15;365(11):1033-41. Review. PubMed PMID: 21916641.
3. Devi S. Lasker Foundation honours malaria researcher. Lancet. 2011 Sep 24;378(9797):1129. PubMed PMID: 21969956.

Zebrafish

1. Thummel R, Bailey TJ, Hyde DR. <em>In vivo</em> Electroporation of Morpholinos into the Adult Zebrafish Retina. J Vis Exp. 2011 Dec 27;(58). pii: 3603. doi: 10.3791/3603. PubMed PMID: 22231802.
2. Lawrence C. Advances in zebrafish husbandry and management. Methods Cell Biol. 2011;104:429-51. Review. PubMed PMID: 21924176.

Evolution

1. Pearlman SM, Serber Z, Ferrell JE Jr. A mechanism for the evolution of phosphorylation sites. Cell. 2011 Nov 11;147(4):934-46. PubMed PMID: 22078888; PubMed Central PMCID: PMC3220604.

We have recently begun to work on a project that requires us to find out whether a zebrafish larva can see or not. To this end, we have built a small machine to check whether the larvae show optokinetic response (OKR), a visual behaviour.

This video shows the OKR machine, which is essentially a drum with black and white stripes that the rotating direction is controlled by a motor.

The fish larvae will be immobilized by thick solution in a Petri dish, which will be put inside the drum. The larvae with normal vision will be able to track the rotation and move their eye balls. In this video, the bottom larva shows a normal OKR response, while the top one, a blind larva caused by a genetic mutation, does not show the OKR response. An an bubble is put on the left to reflect the direction of the stripe movement.

During the process of fabricating this machine, we had come across with another cheaper way to do the same thing. There is a type of ancient Chinese lantern that part of outside drum will move due to heat convection generated by the light (A picture can be found in this Chinese article). We bought a contemporary version that the moving drums are driven by motor. The type that we bought has the moving mechanism for rotating in opposite direction. We then took apart the lantern and used the moving mechanism to drive the opposite rotating stripes. See the following video for the moving mechanism of this alternative version of OKR.

Even though it is not perfect, it works! The most amazing part is the difference in the cost of fabrication.

• OKR made from Chinese Lantern: ~ $US 3 (for buying the Chinese Lantern)
• OKR that is properly made as shown in the first video: ~$US 150 (for materials) + ~$600 (for labor) = ~ $800 (and that does not include the controller box) !!!

That is actually another example of the difference in the cost structure in doing research between the East and the West!

I also had a lot of fun sourcing other cheap parts for the final setup. For example, I have bought a very decent eye-piece camera for less than $40 (the price seems to have gone up a bit since then… but is still very cheap) to capture the video of larval eye movement as shown in the second video. I have also bought a very economical ring light from AmScope for less than $60 for illuminating the drum area finally.

We are going to use this assay to identify fish with eye problems and then characterize the underlying molecular defects. That will help us study and find cures for the same diseases in human.

I have requested our library to buy this new book, which contains a lot of useful information (Link to Amazon. Table of contents is available here). This includes several chapters on making transgenic fish (ask me if you need more information) and advanced imaging techniques.