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2016-08-10 new articles we read this week

Wednesday, August 10, 2016

Genome editing

  1. Braun CJ, Bruno PM, Horlbeck MA, Gilbert LA, Weissman JS, Hemann MT. Versatile in vivo regulation of tumor phenotypes by dCas9-mediated transcriptional perturbation. Proc Natl Acad Sci U S A. 2016 Jun 20. pii: 201600582. [Epub ahead of print] PubMed PMID: 27325776.

Regeneration

  1. Neves J, Zhu J, Sousa-Victor P, Konjikusic M, Riley R, Chew S, Qi Y, Jasper H, Lamba DA. Immune modulation by MANF promotes tissue repair and regenerative success in the retina. Science. 2016 Jul 1;353(6294):aaf3646. doi: 10.1126/science.aaf3646. PubMed PMID: 27365452.

Genomics

  1. Ståhl PL, Salmén F, Vickovic S, Lundmark A, Navarro JF, Magnusson J, Giacomello S, Asp M, Westholm JO, Huss M, Mollbrink A, Linnarsson S, Codeluppi S, Borg Å, Pontén F, Costea PI, Sahlén P, Mulder J, Bergmann O, Lundeberg J, Frisén J. Visualization and analysis of gene expression in tissue sections by spatial transcriptomics. Science. 2016 Jul 1;353(6294):78-82. doi: 10.1126/science.aaf2403. PubMed PMID: 27365449.
  2. Wu J, Huang B, Chen H, Yin Q, Liu Y, Xiang Y, Zhang B, Liu B, Wang Q, Xia W, Li W, Li Y, Ma J, Peng X, Zheng H, Ming J, Zhang W, Zhang J, Tian G, Xu F, Chang Z, Na J, Yang X, Xie W. The landscape of accessible chromatin in mammalian preimplantation embryos. Nature. 2016 Jun 15;534(7609):652-657. doi: 10.1038/nature18606. [Epub ahead of print] PubMed PMID: 27309802.

Development

  1. Wu J, Huang B, Chen H, Yin Q, Liu Y, Xiang Y, Zhang B, Liu B, Wang Q, Xia W, Li W, Li Y, Ma J, Peng X, Zheng H, Ming J, Zhang W, Zhang J, Tian G, Xu F, Chang Z, Na J, Yang X, Xie W. The landscape of accessible chromatin in mammalian preimplantation embryos. Nature. 2016 Jun 15;534(7609):652-657. doi: 10.1038/nature18606. [Epub ahead of print] PubMed PMID: 27309802.

Funding

  1. von Hippel T, von Hippel C. To apply or not to apply: a survey analysis of grant writing costs and benefits. PLoS One. 2015 Mar 4;10(3):e0118494. doi: 10.1371/journal.pone.0118494. eCollection 2015. PubMed PMID: 25738742; PubMed Central PMCID: PMC4349454.


				

				

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My visit to the School of Optometry of the Hong Kong Polytechnic University.

				
Saturday, August 6, 2016

				


On July 20th 2016, I was invited by Dr. Chi-ho To, Professor and Head, and Dr. Chi-wai Do to visit the School of Optometry of the Hong Kong Polytechnic University. This is the leading Optometry school in Hong Kong and Asia. They have also been conducting many research programs that lead to translational products that help eye-disease patients. Their cohesive and collegial team great enhances efficiency and contributes to their success in research. During my visit, I gave a seminar on “Discover New Drugs for Retinal Degeneration by Zebrafish Research” and shared our vision on using this research platform to help patients with this great research team.


Yuk Fai Leung with the Professors from the School of Optometry at the Hong Kong Polytechnic University.


Yuk Fai Leung shared his vision on zebrafish research.


Yuk Fai Leung shared his vision on zebrafish research.


				

				

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My visit to Dr. Zi-Bing Jin’s group at the Eye Hospital of Wenzhou Medical University

				
Saturday, August 6, 2016

				


On July 18th and 19th of 2016, I was invited by Dr. Zi-Bing Jin to visit his research group at the Eye Hospital of Wenzhou Medical University in Wenzhou, China again. They are doing amazing work on various aspects of ophthalmology, from human genetics, stem cells, microRNAs to zebrafish. We have been working together on the zebrafish platform for years, and it is gratifying to see Dr. Jin’s group’s development over the years. When I visited them every time, I was always impressed by how enthusiastic and hard working the Wenzhou students are. Dr. Jin’s group probably has 30 to 40 students. Most of them work at least 12 hours in the lab every day! With this dedication, no wonder many Chinese students are making a big contribution to science these days.


A few pictures of my visit:


Yuk Fai Leung gave a research talk on using zebrafish to discover new drugs for rod degeneration to the students at Wenzhou Medical University.


 


Dr. Zi-Bing Jin at Wenzhou Medical University shared his research vision with Yuk Fai Leung.


Yuk Fai Leung gave a workshop on “Effective Scientific Communication”. In this workshop, I shared with the enthusiastic students many writing tricks and communication skills that I learned through experience over the years. These skills are particularly suitable for those of us who speak English as a second language and want to effectively communicate our findings to the research community.


				

				

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2016-07-06 new articles we read this week

				
Wednesday, July 6, 2016

				


Development


    

  1. Baxendale S, Whitfield TT. Methods to study the development, anatomy, and function of the zebrafish inner ear across the life course. Methods Cell Biol. 2016;134:165-209. doi: 10.1016/bs.mcb.2016.02.007. Epub 2016 Mar 9. PubMed PMID: 27312494.
    2. 

  2. Simoes-Costa M, Bronner ME. Reprogramming of avian neural crest axial identity and cell fate. Science. 2016 Jun 24;352(6293):1570-3. doi: 10.1126/science.aaf2729. PubMed PMID: 27339986.
    3. 



Genetics


    

  1. Birney E, Smith GD, Greally JM. Epigenome-wide Association Studies and the Interpretation of Disease -Omics. PLoS Genet. 2016 Jun 23;12(6):e1006105. doi: 10.1371/journal.pgen.1006105. eCollection 2016 Jun. Review. PubMed PMID: 27336614.
    2. 



Molecular Biology


    

  1. Ellefson JW, Gollihar J, Shroff R, Shivram H, Iyer VR, Ellington AD. Synthetic evolutionary origin of a proofreading reverse transcriptase. Science. 2016 Jun 24;352(6293):1590-3. doi: 10.1126/science.aaf5409. PubMed PMID: 27339990.
    2. 



Genome Editing


    

  1. Feng Y, Chen C, Han Y, Chen Z, Lu X, Liang F, Li S, Qin W, Lin S. Expanding CRISPR/Cas9 Genome Editing Capacity in Zebrafish Using SaCas9. G3 (Bethesda). 2016 Jun 17. pii: g3.116.031914. doi: 10.1534/g3.116.031914. [Epub ahead of print] PubMed PMID: 27317783.
    2. 



Behaviour 


    

  1. Peeters BW, Moeskops M, Veenvliet AR. Color Preference in Danio rerio: Effects of Age and Anxiolytic Treatments. Zebrafish. 2016 Aug;13(4):330-4. doi: 10.1089/zeb.2015.1150. PubMed PMID: 27333080.
    2. 



Stem cells 


    

  1. Clevers H. Modeling Development and Disease with Organoids. Cell. 2016 Jun 16;165(7):1586-97. doi: 10.1016/j.cell.2016.05.082. Review. PubMed PMID: 27315476.
    2. 



Retina


    

  1. Malicki J, Pooranachandran N, Nikolaev A, Fang X, Avanesov A. Analysis of the retina in the zebrafish model. Methods Cell Biol. 2016;134:257-334. doi: 10.1016/bs.mcb.2016.04.017. Epub 2016 Jun 2. PubMed PMID: 27312496.
    2. 

  2. Kim JW, Yang HJ, Oel AP, Brooks MJ, Jia L, Plachetzki DC, Li W, Allison WT, Swaroop A. Recruitment of Rod Photoreceptors from Short-Wavelength-Sensitive Cones during the Evolution of Nocturnal Vision in Mammals. Dev Cell. 2016 Jun 20;37(6):520-32. doi: 10.1016/j.devcel.2016.05.023. PubMed PMID: 27326930; PubMed Central PMCID: PMC4918105.
    3. 







				

				

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2016-06-07 new articles we read this week

				
Tuesday, June 7, 2016

				


Retinal development


    

  1. Tian C, Zou S, Hu B. Extraocular Source of Oligodendrocytes Contribute to Retinal Myelination and Optokinetic Responses in Zebrafish. Invest Ophthalmol Vis Sci. 2016 Apr 1;57(4):2129-38. doi: 10.1167/iovs.15-17675. PubMed PMID: 27100159.
    2. 

  2. Riesenberg AN, Brown NL. Cell autonomous and nonautonomous requirements for Delltalike1 during early mouse retinal neurogenesis. Dev Dyn. 2016 Jun;245(6):631-40. doi: 10.1002/dvdy.24402. Epub 2016 Apr 4. PubMed PMID: 26947267; PubMed Central PMCID: PMC4873400.
    3. 



Scientific Career


    

  1. Mervis J. BEHIND THE NUMBERS. ‘Employment crisis’ for new Ph.D.s is an illusion. Science. 2016 May 20;352(6288):880. doi: 10.1126/science.352.6288.880. PubMed PMID: 27199396.


    2. 



Evolution


    

  1. Karnkowska A, Vacek V, Zubáčová Z, Treitli SC, Petrželková R, Eme L, Novák L, Žárský V, Barlow LD, Herman EK, Soukal P, Hroudová M, Doležal P, Stairs CW, Roger AJ, Eliáš M, Dacks JB, Vlček Č, Hampl V. A Eukaryote without a Mitochondrial Organelle. Curr Biol. 2016 May 23;26(10):1274-84. doi: 10.1016/j.cub.2016.03.053. Epub 2016 May 12. PubMed PMID: 27185558.


    2. 



Visual behaviour


    

  1. Orger MB. The Cellular Organization of Zebrafish Visuomotor Circuits. Curr Biol. 2016 May 9;26(9):R377-85. doi: 10.1016/j.cub.2016.03.054. Review. PubMed PMID: 27166700.
    2. 

  2. Currie SP, Doherty GH, Sillar KT. Deep-brain photoreception links luminance detection to motor output in Xenopus frog tadpoles. Proc Natl Acad Sci U S A. 2016 May 24;113(21):6053-8. doi: 10.1073/pnas.1515516113. Epub 2016 May 10. PubMed PMID: 27166423.
    3. 



Scientific publishing 


    

  1. Berg JM, Bhalla N, Bourne PE, Chalfie M, Drubin DG, Fraser JS, Greider CW, Hendricks M, Jones C, Kiley R, King S, Kirschner MW, Krumholz HM, Lehmann R, Leptin M, Pulverer B, Rosenzweig B, Spiro JE, Stebbins M, Strasser C, Swaminathan S, Turner P, Vale RD, VijayRaghavan K, Wolberger C. SCIENTIFIC COMMUNITY. Preprints for the life sciences. Science. 2016 May 20;352(6288):899-901. doi: 10.1126/science.aaf9133. PubMed PMID: 27199406.
    2. 

  2. Sarewitz D. The pressure to publish pushes down quality. Nature. 2016 May 11;533(7602):147. doi: 10.1038/533147a. PubMed PMID: 27172010.
    3. 



Genome editing


    

  1. Abudayyeh OO, Gootenberg JS, Konermann S, Joung J, Slaymaker IM, Cox DB, Shmakov S, Makarova KS, Semenova E, Minakhin L, Severinov K, Regev A, Lander ES, Koonin EV, Zhang F. C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector. Science. 2016 Jun 2. pii: aaf5573. [Epub ahead of print] PubMed PMID: 27256883.


    2. 



				

				

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2016-05-15 new articles we read this week

				
Sunday, May 15, 2016

				


Zebrafish


    

  1. Sotolongo-Lopez M, Alvarez-Delfin K, Saade CJ, Vera DL, Fadool JM. Genetic Dissection of Dual Roles for the Transcription Factor six7 in Photoreceptor Development and Patterning in Zebrafish. PLoS Genet. 2016 Apr 8;12(4):e1005968. doi: 10.1371/journal.pgen.1005968. eCollection 2016 Apr. PubMed PMID: 27058886.
    2. 



Genome editing


    

  1. Nelles DA, Fang MY, O’Connell MR, Xu JL, Markmiller SJ, Doudna JA, Yeo GW. Programmable RNA Tracking in Live Cells with CRISPR/Cas9. Cell. 2016 Mar 16. pii: S0092-8674(16)30204-5. doi: 10.1016/j.cell.2016.02.054. [Epub ahead of print] PubMed PMID: 26997482.
    2. 

  2. Anders C, Bargsten K, Jinek M. Structural Plasticity of PAM Recognition by Engineered Variants of the RNA-Guided Endonuclease Cas9. Mol Cell. 2016 Mar 17;61(6):895-902. doi: 10.1016/j.molcel.2016.02.020. PubMed PMID: 26990992.
    3. 

  3. Hirano S, Nishimasu H, Ishitani R, Nureki O. Structural Basis for the Altered PAM Specificities of Engineered CRISPR-Cas9. Mol Cell. 2016 Mar 17;61(6):886-94. doi: 10.1016/j.molcel.2016.02.018. PubMed PMID: 26990991.
    4. 

  4. Kamiyama D, Sekine S, Barsi-Rhyne B, Hu J, Chen B, Gilbert LA, Ishikawa H, Leonetti MD, Marshall WF, Weissman JS, Huang B. Versatile protein tagging in cells with split fluorescent protein. Nat Commun. 2016 Mar 18;7:11046. doi: 10.1038/ncomms11046. PubMed PMID: 26988139; PubMed Central PMCID: PMC4802074.
    5. 

  5. Horlbeck MA, Witkowsky LB, Guglielmi B, Replogle JM, Gilbert LA, Villalta JE, Torigoe SE, Tijan R, Weissman JS. Nucleosomes impede Cas9 access to DNA in vivo and in vitro. Elife. 2016 Mar 17;5. pii: e12677. doi: 10.7554/eLife.12677. [Epub ahead of print] PubMed PMID: 26987018.
    6. 

  6. Kang X, He W, Huang Y, Yu Q, Chen Y, Gao X, Sun X, Fan Y. Introducing precise genetic modifications into human 3PN embryos by CRISPR/Cas-mediated genome editing. J Assist Reprod Genet. 2016 Apr 6. [Epub ahead of print] PubMed PMID: 27052831.
    7. 

  7. Gao F, Shen XZ, Jiang F, Wu Y, Han C. DNA-guided genome editing using the Natronobacterium gregoryi Argonaute. Nat Biotechnol. 2016 May 2. doi: 10.1038/nbt.3547. [Epub ahead of print] PubMed PMID: 27136078.
    8. 



Genetics


    

  1. Chen R, Shi L, Hakenberg J, Naughton B, Sklar P, Zhang J, Zhou H, Tian L, Prakash O, Lemire M, Sleiman P, Cheng WY, Chen W, Shah H, Shen Y, Fromer M, Omberg L, Deardorff MA, Zackai E, Bobe JR, Levin E, Hudson TJ, Groop L, Wang J, Hakonarson H, Wojcicki A, Diaz GA, Edelmann L, Schadt EE, Friend SH. Analysis of 589,306 genomes identifies individuals resilient to severe Mendelian childhood diseases. Nat Biotechnol. 2016 Apr 11. doi: 10.1038/nbt.3514. [Epub ahead of print] PubMed PMID: 27065010.
    2. 



				

				

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Leung Lab participated at the 2016 Purdue Spring Fest

				
Saturday, April 23, 2016

				


On 2016-04-16 – 17, Prahatha Venkatraman, Logan Ganzen, Paige Cassidy, Khaled Noui-Mehidi and Menna Hassan demonstrated zebrafish research in 2016 Purdue Spring Fest.


Purdue Spring Fest at Department of Biological Sciences.


Paige Cassidy and Logan Ganzen demonstrating zebrafish research to the public.


Logan Ganzen demonstrating how to measure zebrafish vision.


Paige Cassidy showing zebrafish embryos to the public.


Prahatha Venkatraman, Khaled Noui-Mehidi and Menna Hassan demonstrated zebrafish research to the public.


Khaled Noui-Mehidi showing zebrafish embryos to the public.


 




 


				

				

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Purdue University Undergraduate Research Symposium

				
Saturday, April 23, 2016

				


On 2016-04-12, Paige Cassidy presented her research work at the Purdue University Undergraduate Research Symposium. She was supervised by Prahatha Venkatraman, a graduate student in the laboratory and a Schlumberger Foundation Faculty for Future Fellow.


Paige Cassidy and her poster.


				

				

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Sylvia Bonilla’s defense and celebration party

				
Saturday, April 23, 2016

				


On 2016-04-11, Sylvia Bonilla defended her thesis and graduated.


Fai introducing Sylvia.


Sylvia presenting her research work.


Celebration party.


A zebrafish cake!


One more fin clipping!


Congratulations!


 


				

				

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Leung Lab presented at the 131st Annual Academy Meeting of the Indiana Academy of Science

				
Saturday, April 23, 2016

				


On 2016-03-26, Menna Hassan, Patrick Tiffany, Ryan Wyer and Khaled Noui-Mehidi presented their research at the 131st Annual Academy Meeting of the Indiana Academy of Science. They were supervised by graduate students Prahatha Venkatraman and Logan Ganzen.


Menna Hassan and her graduate mentor Prahatha Venkatraman.


Menna Hassan presenting her poster.


Khaled Noui-Mehidi and his graduate mentor Logan Ganzen.


Khaled Noui-Mehidi presenting his poster.


Patrick Tiffany and his poster.


 


Patrick Tiffany presenting his poster.


Ryan Wyer and his poster.


Ryan Wyer presenting his poster.


 


				

				

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