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2013-07-13 Articles we read this week

Saturday, July 13, 2013

Neuroscience

  1. Cai D, Cohen KB, Luo T, Lichtman JW, Sanes JR. Improved tools for the Brainbow toolbox. Nat Methods. 2013 May 5;10(6):540-7. doi: 10.1038/nmeth.2450. Epub 2013 May 5. PubMed PMID: 23817127.
  2. Pan YA, Freundlich T, Weissman TA, Schoppik D, Wang XC, Zimmerman S, Ciruna B, Sanes JR, Lichtman JW, Schier AF. Zebrabow: multispectral cell labeling for cell tracing and lineage analysis in zebrafish. Development. 2013 Jul;140(13):2835-46. doi: 10.1242/dev.094631. PubMed PMID: 23757414; PubMed Central PMCID: PMC3678346.
    1. Blog post by the first author: Red fish, blue fish, Brainbow fish!

Eye disease

  1. Berger W, Kloeckener-Gruissem B, Neidhardt J. The molecular basis of human retinal and vitreoretinal diseases. Prog Retin Eye Res. 2010 Sep;29(5):335-75. doi: 10.1016/j.preteyeres.2010.03.004. Epub 2010 Mar 31. Review. PubMed PMID: 20362068.
  2. Dalkara D, Byrne LC, Klimczak RR, Visel M, Yin L, Merigan WH, Flannery JG, Schaffer DV. In vivo-directed evolution of a new adeno-associated virus for therapeutic outer retinal gene delivery from the vitreous. Sci Transl Med. 2013 Jun 12;5(189):189ra76. doi: 10.1126/scitranslmed.3005708. PubMed PMID: 23761039.
    1. News coverage: Genes Get in Your Eye.

Genetics

  1. A collection of seminal papers on CRISPR-CAS
    1. Qi LS, Larson MH, Gilbert LA, Doudna JA, Weissman JS, Arkin AP, Lim WA. Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell. 2013 Feb 28;152(5):1173-83. doi: 10.1016/j.cell.2013.02.022. PubMed PMID: 23452860; PubMed Central PMCID:PMC3664290.
    2. Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA, Charpentier E. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science. 2012 Aug 17;337(6096):816-21. doi: 10.1126/science.1225829. Epub 2012 Jun 28. PubMed PMID: 22745249.
    3. Horvath P, Barrangou R. CRISPR/Cas, the immune system of bacteria and archaea. Science. 2010 Jan 8;327(5962):167-70. doi: 10.1126/science.1179555. Review. PubMed PMID: 20056882.
    4. Sampson TR, Saroj SD, Llewellyn AC, Tzeng YL, Weiss DS. A CRISPR/Cas system mediates bacterial innate immune evasion and virulence. Nature. 2013 May 9;497(7448):254-7. doi: 10.1038/nature12048. Epub 2013 Apr 14. PubMed PMID: 23584588; PubMed Central PMCID: PMC3651764.
  2. Ma AC, Lee HB, Clark KJ, Ekker SC. High Efficiency In Vivo Genome Engineering with a Simplified 15-RVD GoldyTALEN Design. PLoS One. 2013 May 29;8(5):e65259.doi: 10.1371/journal.pone.0065259. Print 2013. PubMed PMID: 23734242.
  3. Lim S, Wang Y, Yu X, Huang Y, Featherstone MS, Sampath K. A simple strategy for heritable chromosomal deletions in zebrafish via the combinatorial action of  targeting nucleases. Genome Biol. 2013 Jul 1;14(7):R69. [Epub ahead of print] PubMed PMID: 23815890.

Funding

  1. Fortin JM, Currie DJ. Big Science vs. Little Science: How Scientific Impact Scales with Funding. PLoS One. 2013 Jun 19;8(6):e65263. Print 2013. PubMed PMID: 23840323; PubMed Central PMCID: PMC3686789.

Philosophy of science

  1. Biesecker LG. Hypothesis-generating research and predictive medicine. Genome Res. 2013 Jul;23(7):1051-3. doi: 10.1101/gr.157826.113. PubMed PMID: 23817045; PubMed Central PMCID: PMC3698497.

Stem cells

  1. Tachibana M, Amato P, Sparman M, Gutierrez NM, Tippner-Hedges R, Ma H, Kang E, Fulati A, Lee HS, Sritanaudomchai H, Masterson K, Larson J, Eaton D, Sadler-Fredd K, Battaglia D, Lee D, Wu D, Jensen J, Patton P, Gokhale S, Stouffer RL, Wolf D,  Mitalipov S. Human embryonic stem cells derived by somatic cell nuclear transfer. Cell. 2013 Jun 6;153(6):1228-38. doi: 10.1016/j.cell.2013.05.006. Epub 2013 May 15. PubMed PMID: 23683578
    1. News coverage: Scientists create human embryos to make stem cells
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My visit to the Shenyang Eye Research Institute

Saturday, July 13, 2013

On 6/24-25, I visited Shenyang Eye Research Institute, a growing eye research institute in the Fourth People’s Hospital, Shenyang, China. During my visit, I shared our vision on using zebrafish to screen traditional Chinese medicines for better vision with the local eye doctors and research students. I am very impressed with the dedication of the students and leadership team in establishing a competitive research program. To improve their English skill, they have established a regular English debate on non-scientific subjects! I enjoyed participating in their lively discussion. I look forward to interact more with this enthusiastic group in the future!

With Drs Yang Qu and Shaodan Zhang, and the enthusiastic research students.

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Summer research project promotes collaboration between Statistics and Biological Sciences

Tuesday, July 2, 2013

Robert Carmer, an HHMI Summer Undergrate Student, was featured in the press releases of the College of Science and Department of Biological Sciences.

Robert Carmer presenting the research work that he conducted with the other lab members, including Gaonan Zhang and Prahatha Venkatraman

Also see him describing his research experience in this video.

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2013-05-19 New articles we read this week

Monday, May 20, 2013

Neuroscience

  1. Kabra M, Robie AA, Rivera-Alba M, Branson S, Branson K. JAABA: interactive machine learning for automatic annotation of animal behavior. Nat Methods. 2013 Jan;10(1):64-7. doi: 10.1038/nmeth.2281. Epub 2012 Dec 2. PubMed PMID: 23202433.
  2. Koch KW. The guanylate cyclase signaling system in zebrafish photoreceptors. FEBS Lett. 2013 May 6. doi:pii: S0014-5793(13)00318-9. 10.1016/j.febslet.2013.04.023. [Epub ahead of print] PubMed PMID: 23660405.

Genetics

  1. Potok ME, Nix DA, Parnell TJ, Cairns BR. Reprogramming the maternal zebrafish genome after fertilization to match the paternal methylation pattern. Cell. 2013 May 9;153(4):759-72. doi: 10.1016/j.cell.2013.04.030. PubMed PMID: 23663776.
  2. Jiang L, Zhang J, Wang JJ, Wang L, Zhang L, Li G, Yang X, Ma X, Sun X, Cai J, Zhang J, Huang X, Yu M, Wang X, Liu F, Wu CI, He C, Zhang B, Ci W, Liu J. Sperm, but not oocyte, DNA methylome is inherited by zebrafish early embryos. Cell. 2013 May 9;153(4):773-84. doi: 10.1016/j.cell.2013.04.041. PubMed PMID: 23663777.
    1. Commentary for #1 & 2: Hackett JA, Surani MA. Beyond DNA: Programming and Inheritance of Parental Methylomes. Cell. 2013 May 9;153(4):737-9. doi: 10.1016/j.cell.2013.04.044. PubMed PMID: 23663772.
  3. Wang H, Yang H, Shivalila CS, Dawlaty MM, Cheng AW, Zhang F, Jaenisch R. One-Step Generation of Mice Carrying Mutations in Multiple Genes by CRISPR/Cas-Mediated Genome Engineering. Cell. 2013 May 9;153(4):910-8. doi: 10.1016/j.cell.2013.04.025. Epub 2013 May 2. PubMed PMID: 23643243.
  4. Qi LS, Larson MH, Gilbert LA, Doudna JA, Weissman JS, Arkin AP, Lim WA. Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell. 2013 Feb 28;152(5):1173-83. doi: 10.1016/j.cell.2013.02.022. PubMed PMID: 23452860.
  5. Gerety SS, Breau MA, Sasai N, Xu Q, Briscoe J, Wilkinson DG. An inducible transgene expression system for zebrafish and chick. Development. 2013 May;140(10):2235-43. doi: 10.1242/dev.091520. PubMed PMID: 23633515.
  6. Ibarra-Laclette E, Lyons E, Hernández-Guzmán G, Pérez-Torres CA, Carretero-Paulet L, Chang TH, Lan T, Welch AJ, Juárez MJ, Simpson J, Fernández-Cortés A, Arteaga-Vázquez M, Góngora-Castillo E, Acevedo-Hernández G, Schuster SC, Himmelbauer H, Minoche AE, Xu S, Lynch M, Oropeza-Aburto A, Cervantes-Pérez SA, de Jesús Ortega-Estrada M, Cervantes-Luevano JI, Michael TP, Mockler T, Bryant D, Herrera-Estrella A, Albert VA, Herrera-Estrella L. Architecture and evolution of a minute plant genome. Nature. 2013 May 12. doi: 10.1038/nature12132. [Epub ahead of print] PubMed PMID: 23665961.

Development

  1. Yi P, Park JS, Melton DA. Betatrophin: A Hormone that Controls Pancreatic β Cell Proliferation. Cell. 2013 May 9;153(4):747-58. doi: 10.1016/j.cell.2013.04.008. Epub 2013 Apr 25. PubMed PMID: 23623304.
  2. Mongera A, Nüsslein-Volhard C. Scales of fish arise from mesoderm. Curr Biol. 2013 May 6;23(9):R338-9. doi: 10.1016/j.cub.2013.02.056. PubMed PMID: 23660349.

Systems Biology

  1. Fisher JK, Bourniquel A, Witz G, Weiner B, Prentiss M, Kleckner N. Four-Dimensional Imaging of E. coli Nucleoid Organization and Dynamics in Living Cells. Cell. 2013 May 9;153(4):882-95. doi: 10.1016/j.cell.2013.04.006. Epub 2013 Apr 25. PubMed PMID: 23623305.
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Leung Lab @ ARVO 2013

Friday, May 10, 2013

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.

Sylvia and Fai in front of Sylvia’s poster

Picture opportunity with the hosts of ARVO CUHK-JSIEC Research Networking Evening
From Left to Right: Yuk Fai Leung (Purdue), Prof. Mingzhi Zhang (Joint Shantou International Eye Center), and Prof. Calvin Pang (Chinese University of Hong Kong)

We have got an opportunity to share the vision on using zebrafish for screening eye drugs in our JSIEC-Purdue Joint Laboratory with many distinguished guests from all over the world, including Dr. Mansoor Sarfarazi (U Conn), Dr. G Kumaramanickavel (Narayana Nethralaya), Dr. John Prakash (Associate Director, NEI), Dr. Martine Jager (Former ARVO president, Leiden University), Dr. Motokazu Tsujikawa (Osaka), Dr.Vincent Raymond (U Laval) , Dr. Kanxing Zhao (Zhongshan) and many more.

Fai and Sylvia with Dr. Mingzhi Zhang (JSIEC), Dr. Haoyu Chen (JSIEC), Dr. John Prakash (NEI) and Mrs. Prakash.

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2013-04-21 New articles we read this week

Sunday, April 21, 2013

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.

 

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My visit to Ho Yu College in Hong Kong

Friday, April 12, 2013

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!

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2013-04-07 Articles we read this week

Sunday, April 7, 2013

Genetics

  1. Zu Y, Tong X, Wang Z, Liu D, Pan R, Li Z, Hu Y, Luo Z, Huang P, Wu Q, Zhu Z, Zhang B, Lin S. TALEN-mediated precise genome modification by homologous recombination in zebrafish. Nat Methods. 2013 Feb 24. doi: 10.1038/nmeth.2374. [Epub ahead of print] PubMed PMID: 23435258.
  2. Chang N, Sun C, Gao L, Zhu D, Xu X, Zhu X, Xiong JW, Xi JJ. Genome editing with RNA-guided Cas9 nuclease in Zebrafish embryos. Cell Res. 2013 Apr;23(4):465-72. doi: 10.1038/cr.2013.45. Epub 2013 Mar 26. PubMed PMID: 23528705; PubMed Central PMCID: PMC3616424.

Retinal development

  1. Chiodini F, Matter-Sadzinski L, Rodrigues T, Skowronska-Krawczyk D, Brodier L, Schaad O, Bauer C, Ballivet M, Matter JM. A Positive Feedback Loop between ATOH7 and a Notch Effector Regulates Cell-Cycle Progression and Neurogenesis in the Retina. Cell Rep. 2013 Mar 28;3(3):796-807. doi: 10.1016/j.celrep.2013.01.035. Epub 2013 Feb 21. PubMed PMID: 23434507.

Eye diseases

  1. From the Telegraph: Eye drops could treat macular degeneration. Original article in Cell Metabolism: Impaired Cholesterol Efflux in Senescent Macrophages Promotes Age-Related Macular Degeneration.
  2. From the Washington Post: First U.S. artificial retina approved; device could restore some sight to blind. FDA’s news release.

Neuroscience

  1. Blackiston DJ, Levin M. Ectopic eyes outside the head in Xenopus tadpoles provide sensory data for light-mediated learning. J Exp Biol. 2013 Mar 15;216(Pt 6):1031-40. doi: 10.1242/jeb.074963. PubMed PMID: 23447666.
    • Commentary: Tadpoles See with Extra Eyes
    • Very interesting article. It demonstrates how tadpole can sense light by the innervation from an ectopic eye.

 

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Has education destroyed our creativity?

Monday, March 25, 2013

Recently I have got the privilege to share my research work with secondary school students. During the talk, it was obvious to me  that the younger the students were, the more imaginative the questions that they could come up with and the more fearless they were in asking questions. One reason is that the eduction has often encouraged students to give the “right answer”; otherwise, they will not get good grades. So, when the students are growing up, they quickly learn how to shut up and only seek ways to give the “right answer”. That reminds me of several great talks by Sir Ken Robinson on education, including a TED talk on how schools kill creativity that I shared here before, and an RSA talk on Changing Education Paradigms. The latter is a very thought-provoking talk,  and the RSA has made a nicely animated version of the key part:

 The original talk is equally interesting:

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Issues in scientific communiciation

Saturday, February 16, 2013

Just come across these two great TED talks by Ben Goldacre that talks about how the information in scientific literature can be distorted and why not all information that is essential for medical advance can be found in the literature. It is really a flaw in the research system and human nature that positive and new findings will (preferentially) be rewarded. This has suppressed the appearance of negative findings and solid repeats that would validate ideas that would benefit human kinds. The reason behind this is partially because the scientists who conducted these kinds of studies will often be labeled non-productive (productive = getting positive findings) and non-innovative. Is there a solution to that?

 

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