On 3/18, students from Jefferson high school in Lafayette visited our department. They were hosted by the Leung Lab. See our departmental news for the details of the visit. Here are several pictures of the event.

Prahatha Venkatraman giving students a lecture on zebrafish research.

Prahatha Venkatraman and Isidore Julien showing students how to observe developing zebrafish embryos.

Dr. Clark Gedney described the research opportunities in our department for high school students.

Yuk Fai Leung showing students how to manipulate lab equipment.

Students studying zebrafish embryos.

Best Advice: What You Want to Do Isn’t Always What You Want to Be


  1. Tomasetti C, Vogelstein B. Cancer etiology. Variation in cancer risk among tissues can be explained by the number of stem cell divisions. Science. 2015 Jan 2;347(6217):78-81. doi: 10.1126/science.1260825. PubMed PMID: 25554788.


  1. Kok FO, Shin M, Ni CW, Gupta A, Grosse AS, van Impel A, Kirchmaier BC, Peterson-Maduro J, Kourkoulis G, Male I, DeSantis DF, Sheppard-Tindell S, Ebarasi L, Betsholtz C, Schulte-Merker S, Wolfe SA, Lawson ND. Reverse Genetic Screening Reveals Poor Correlation between Morpholino-Induced and Mutant Phenotypes in Zebrafish. Dev Cell. 2015 Jan 12;32(1):97-108. doi: 10.1016/j.devcel.2014.11.018. Epub 2014 Dec 18. PubMed PMID: 25533206.


  1. Callaway E. Blown-up brains reveal nanoscale details. Nature. 2015 Jan 15;517(7534):254. doi: 10.1038/nature.2015.16667. PubMed PMID: 25592513.


  1. Gurdasani D, Carstensen T, Tekola-Ayele F, Pagani L, Tachmazidou I, Hatzikotoulas K, Karthikeyan S, Iles L, Pollard MO, Choudhury A, Ritchie GR, Xue Y, Asimit J, Nsubuga RN, Young EH, Pomilla C, Kivinen K, Rockett K, Kamali A, Doumatey AP, Asiki G, Seeley J, Sisay-Joof F, Jallow M, Tollman S, Mekonnen E, Ekong R, Oljira T, Bradman N, Bojang K, Ramsay M, Adeyemo A, Bekele E, Motala A, Norris SA, Pirie F, Kaleebu P, Kwiatkowski D, Tyler-Smith C, Rotimi C, Zeggini E, Sandhu MS. The African Genome Variation Project shapes medical genetics in Africa. Nature. 2015 Jan 15;517(7534):327-32. doi: 10.1038/nature13997. Epub 2014 Dec 3. PubMed PMID: 25470054; PubMed Central PMCID: PMC4297536.
  2. Jens M, Rajewsky N. Competition between target sites of regulators shapes post-transcriptional gene regulation. Nat Rev Genet. 2015 Feb;16(2):113-26. doi: 10.1038/nrg3853. Epub 2014 Dec 9. PubMed PMID: 25488579.
  3. Ritchie MD, Holzinger ER, Li R, Pendergrass SA, Kim D. Methods of integrating data to uncover genotype-phenotype interactions. Nat Rev Genet. 2015 Feb;16(2):85-97. doi: 10.1038/nrg3868. Epub 2015 Jan 13. PubMed PMID: 25582081.


  1. Zalatan JG, Lee ME, Almeida R, Gilbert LA, Whitehead EH, La Russa M, Tsai JC, Weissman JS, Dueber JE, Qi LS, Lim WA. Engineering Complex Synthetic Transcriptional Programs with CRISPR RNA Scaffolds. Cell. 2015 Jan 15;160(1-2):339-50. doi: 10.1016/j.cell.2014.11.052. Epub 2014 Dec 18. PubMed PMID: 25533786; PubMed Central PMCID: PMC4297522.


  1. Singh AP, Nüsslein-Volhard C. Zebrafish Stripes as a Model for Vertebrate Colour Pattern Formation. Curr Biol. 2015 Jan 19;25(2):R81-R92. doi: 10.1016/j.cub.2014.11.013. Review. PubMed PMID: 25602311.
  2. Hiscock TW, Megason SG. Mathematically guided approaches to distinguish models of periodic patterning. Development. 2015 Feb 1;142(3):409-419. Review. PubMed PMID: 25605777; PubMed Central PMCID: PMC4302999.

Interesting discussion about open-access publishing.

Retinal development

  1. Masuda T, Zhang X, Berlinicke C, Wan J, Yerrabelli A, Conner EA, Kjellstrom S, Bush R, Thorgeirsson SS, Swaroop A, Chen S, Zack DJ. The Transcription Factor GTF2IRD1 Regulates the Topology and Function of Photoreceptors by Modulating Photoreceptor Gene Expression across the Retina. J Neurosci. 2014 Nov 12;34(46):15356-68.
  2. Okabe K, Kobayashi S, Yamada T, Kurihara T, Tai-Nagara I, Miyamoto T,
    Mukouyama YS, Sato TN, Suda T, Ema M, Kubota Y. Neurons limit angiogenesis by titrating VEGF in retina. Cell. 2014 Oct 23;159(3):584-96. doi: 10.1016/j.cell.2014.09.025. PubMed PMID: 25417109.


  1. Baehr W. Membrane Protein Transport in Photoreceptors: The Function of PDEd.
    Invest Ophthalmol Vis Sci. 2014 Dec 30;55(12):8653-66. doi: 10.1167/iovs.14-16066. PubMed PMID: 25550383.

Genome editing

  1. Auer TO, Duroure K, Concordet JP, Del Bene F. CRISPR/Cas9-mediated conversion of eGFP- into Gal4-transgenic lines in zebrafish. Nat Protoc. 2014 Dec;9(12):2823-40. doi: 10.1038/nprot.2014.187. Epub 2014 Nov 13. PubMed PMID: 25393779.
  2. Yang L, Grishin D, Wang G, Aach J, Zhang CZ, Chari R, Homsy J, Cai X, Zhao Y, Fan JB, Seidman C, Seidman J, Pu W, Church G. Targeted and genome-wide sequencing reveal single nucleotide variations impacting specificity of Cas9 in human stem cells. Nat Commun. 2014 Nov 26;5:5507. doi: 10.1038/ncomms6507. PubMed PMID: 25425480.
  3. Nielsen AA, Voigt CA. Multi-input CRISPR/Cas genetic circuits that interface host regulatory networks. Mol Syst Biol. 2014 Nov 24;10:763. doi:
    10.15252/msb.20145735. PubMed PMID: 25422271.
  4. Byrne SM, Ortiz L, Mali P, Aach J, Church GM. Multi-kilobase homozygous
    targeted gene replacement in human induced pluripotent stem cells. Nucleic Acids Res. 2014 Nov 20. pii: gku1246. [Epub ahead of print] PubMed PMID: 25414332.
  5. Naito Y, Hino K, Bono H, Ui-Tei K. CRISPRdirect: software for designing
    CRISPR/Cas guide RNA with reduced off-target sites. Bioinformatics. 2014 Nov 20. pii: btu743. [Epub ahead of print] PubMed PMID: 25414360.
  6. Doudna JA, Charpentier E. Genome editing. The new frontier of genome
    engineering with CRISPR-Cas9. Science. 2014 Nov 28;346(6213):1258096. doi: 10.1126/science.1258096. PubMed PMID: 25430774.


  1. Paquet D, Plucinska G, Misgeld T. In vivo imaging of mitochondria in intact
    zebrafish larvae. Methods Enzymol. 2014;547:151-64. PubMed PMID: 25416357.


  1. McCluskey BM, Postlethwait JH. Phylogeny of zebrafish, a ‘model species’, within Danio, a ‘model genus’. Mol Biol Evol. 2014 Nov 20. pii: msu325. [Epub ahead of print] PubMed PMID: 25415969.
  2. Magdeldin S, Blaser RE, Yamamoto T, Yates JR 3rd. Behavioral and Proteomic Analysis of Stress Response in Zebrafish (Danio rerio). J Proteome Res. 2014 Nov 26. [Epub ahead of print] PubMed PMID: 25398274.

Stem cells

  1. Byrne SM, Ortiz L, Mali P, Aach J, Church GM. Multi-kilobase homozygous
    targeted gene replacement in human induced pluripotent stem cells. Nucleic Acids Res. 2014 Nov 20. pii: gku1246. [Epub ahead of print] PubMed PMID: 25414332.

Development & Disease

  1. The Deciphering Developmental Disorders Study; The Deciphering Developmental Disorders Study. Large-scale discovery of novel genetic causes of developmental disorders. Nature. 2014 Dec 24. doi: 10.1038/nature14135. [Epub ahead of print] PubMed PMID: 25533962.


  1. Tan AS, Baty JW, Dong LF, Bezawork-Geleta A, Endaya B, Goodwin J, Bajzikova M, Kovarova J, Peterka M, Yan B, Pesdar EA, Sobol M, Filimonenko A, Stuart S, Vondrusova M, Kluckova K, Sachaphibulkij K, Rohlena J, Hozak P, Truksa J, Eccles D, Haupt LM, Griffiths LR, Neuzil J, Berridge MV. Mitochondrial Genome Acquisition Restores Respiratory Function and Tumorigenic Potential of Cancer Cells without Mitochondrial DNA. Cell Metab. 2015 Jan 6;21(1):81-94. doi: 10.1016/j.cmet.2014.12.003. PubMed PMID: 25565207.


  1. Ling LL, Schneider T, Peoples AJ, Spoering AL, Engels I, Conlon BP, Mueller A, Schäberle TF, Hughes DE, Epstein S, Jones M, Lazarides L, Steadman VA, Cohen DR, Felix CR, Fetterman KA, Millett WP, Nitti AG, Zullo AM, Chen C, Lewis K. A new antibiotic kills pathogens without detectable resistance. Nature. 2015 Jan 7. doi: 10.1038/nature14098. [Epub ahead of print] PubMed PMID: 25561178.


  1. Yoshida MA, Yura K, Ogura A. Cephalopod eye evolution was modulated by the acquisition of Pax-6 splicing variants. Sci Rep. 2014 Mar 5;4:4256. doi: 10.1038/srep04256. PubMed PMID: 24594543; PubMed Central PMCID: PMC3942700.


Prof. Motokazu Tsujikawa from the Department of Ophthalmology and the Department of Visual Regenerative Medicine at the Osaka University Medical School in Japan visited Leung Lab at Purdue, Indiana University School of Medicine – Lafayette, Bindley Bioscience Center and Drug Discovery Center from 10/22 – 24, 2014. He also gave a departmental seminar on  “Retinal degeneration research using zebrafish – from an ophthalmologist’s perspective” during his visit.

Prof. Motokazu Tsuijikawa interacted with Prof. Gordon Coppoc, Director of the Indiana University School of Medicine — Lafayette, the first year medical students, and pre-med students in the Leung lab. They discussed the differences in health care and medical education between US and Japan.

Prof. Motokazu Tsujikawa and students from the Leung Lab visited Bindley Bioscience Center and Drug Discovery Center.

Cell cycle

  1. Malumbres M. Cyclin-dependent kinases. Genome Biol. 2014;15(6):122. PubMed PMID: 25180339; PubMed Central PMCID: PMC4097832.


  1. Gilissen C, Hehir-Kwa JY, Thung DT, van de Vorst M, van Bon BW, Willemsen MH, Kwint M, Janssen IM, Hoischen A, Schenck A, Leach R, Klein R, Tearle R, Bo T, Pfundt R, Yntema HG, de Vries BB, Kleefstra T, Brunner HG, Vissers LE, Veltman JA. Genome sequencing identifies major causes of severe intellectual disability.  Nature. 2014 Jul 17;511(7509):344-7. doi: 10.1038/nature13394. Epub 2014 Jun 4. PubMed PMID: 24896178.


  1. Labin AM, Safuri SK, Ribak EN, Perlman I. Müller cells separate between wavelengths to improve day vision with minimal effect upon night vision. Nat Commun. 2014 Jul 8;5:4319. doi: 10.1038/ncomms5319. PubMed PMID: 25003477.
  2. Busskamp V, Krol J, Nelidova D, Daum J, Szikra T, Tsuda B, Jüttner J, Farrow K, Scherf BG, Alvarez CP, Genoud C, Sothilingam V, Tanimoto N, Stadler M, Seeliger M, Stoffel M, Filipowicz W, Roska B. miRNAs 182 and 183 Are Necessary to Maintain Adult Cone Photoreceptor Outer Segments and Visual Function. Neuron. 2014 Jul 4. pii: S0896-6273(14)00542-X. doi: 10.1016/j.neuron.2014.06.020. [Epub ahead of print] PubMed PMID: 25002228.
  3. Condition Called Tetrachromacy Allows This Artist To See 100 Million Colors


  1. Games D, Valera E, Spencer B, Rockenstein E, Mante M, Adame A, Patrick C, Ubhi K, Nuber S, Sacayon P, Zago W, Seubert P, Barbour R, Schenk D, Masliah E. Reducing C-terminal-truncated alpha-synuclein by immunotherapy attenuates neurodegeneration and propagation in Parkinson’s disease-like models. J Neurosci. 2014 Jul 9;34(28):9441-54. doi: 10.1523/JNEUROSCI.5314-13.2014. PubMed PMID: 25009275.
  2. Schizophrenia Working Group of the Psychiatric Genomics Consortium. Biological insights from 108 schizophrenia-associated genetic loci. Nature. 2014 Jul 24;511(7510):421-7. doi: 10.1038/nature13595. Epub 2014 Jul 22. PubMed PMID:25056061; PubMed Central PMCID: PMC4112379.


  1. Severi KE, Portugues R, Marques JC, O’Malley DM, Orger MB, Engert F. Neural control and modulation of swimming speed in the larval zebrafish. Neuron. 2014 Aug 6;83(3):692-707. doi: 10.1016/j.neuron.2014.06.032. Epub 2014 Jul 24. PubMed PMID: 25066084; PubMed Central PMCID: PMC4126853.
  2. Bruni G, Lakhani P, Kokel D. Discovering novel neuroactive drugs through
    high-throughput behavior-based chemical screening in the zebrafish. Front
    Pharmacol. 2014 Jul 24;5:153. doi: 10.3389/fphar.2014.00153. eCollection 2014. Review. PubMed PMID: 25104936; PubMed Central PMCID: PMC4109429.

Ethical, Social and Legal Issues

  1. Tort AB, Targino ZH, Amaral OB. Rising publication delays inflate journal impact factors. PLoS One. 2012;7(12):e53374. doi: 10.1371/journal.pone.0053374. Epub 2012 Dec 31. PubMed PMID: 23300920; PubMed Central PMCID: PMC3534064.
  2. van Lent M, Overbeke J, Out HJ. Role of editorial and peer review processes in publication bias: analysis of drug trials submitted to eight medical journals. PLoS One. 2014 Aug 12;9(8):e104846. doi: 10.1371/journal.pone.0104846. eCollection 2014. PubMed PMID: 25118182; PubMed Central PMCID: PMC4130599.
  3. Ioannidis JP. How to make more published research true. PLoS Med. 2014 Oct 21;11(10):e1001747. doi: 10.1371/journal.pmed.1001747. eCollection 2014 Oct. PubMed PMID: 25334033; PubMed Central PMCID: PMC4204808.

Stem cells

  1. Pagliuca FW, Millman JR, Gürtler M, Segel M, Van Dervort A, Ryu JH, Peterson QP, Greiner D, Melton DA. Generation of Functional Human Pancreatic β Cells In Vitro. Cell. 2014 Oct 9;159(2):428-39. doi: 10.1016/j.cell.2014.09.040. PubMed PMID: 25303535.
  2. Zhang D, Pekkanen-Mattila M, Shahsavani M, Falk A, Teixeira AI, Herland A. A 3D Alzheimer’s disease culture model and the induction of P21-activated kinase mediated sensing in iPSC derived neurons. Biomaterials. 2014 Feb;35(5):1420-8. doi: 10.1016/j.biomaterials.2013.11.028. Epub 2013 Nov 27. PubMed PMID: 24290439.
  3. Schwartz SD, et al., Human embryonic stem cell-derived retinal pigment
    epithelium in patients with age-related macular degeneration and Stargardt’s macular dystrophy: follow-up of two open-label phase 1/2 studies. Lancet 2014. In press.

Genome editing

  1. Lombardo A, Naldini L. Genome Editing: A Tool For Research and Therapy: Targeted genome editing hits the clinic. Nat Med. 2014 Oct 8;20(10):1101-3. doi: 10.1038/nm.3721. PubMed PMID: 25295939.


  1. Suez J, Korem T, Zeevi D, Zilberman-Schapira G, Thaiss CA, Maza O, Israeli D, Zmora N, Gilad S, Weinberger A, Kuperman Y, Harmelin A, Kolodkin-Gal I, Shapiro H, Halpern Z, Segal E, Elinav E. Artificial sweeteners induce glucose intolerance by altering the gut microbiota. Nature. 2014 Oct 9;514(7521):181-6. doi: 10.1038/nature13793. Epub 2014 Sep 17. PubMed PMID: 25231862.

Molecular biology

  1. Robart AR, Chan RT, Peters JK, Rajashankar KR, Toor N. Crystal structure of a eukaryotic group II intron lariat. Nature. 2014 Oct 9;514(7521):193-7. doi: 10.1038/nature13790. Epub 2014 Sep 24. PubMed PMID: 25252982.


  1. Chen BC, Legant WR, Wang K, Shao L, Milkie DE, Davidson MW, Janetopoulos C, Wu XS, Hammer JA 3rd, Liu Z, English BP, Mimori-Kiyosue Y, Romero DP, Ritter AT, Lippincott-Schwartz J, Fritz-Laylin L, Mullins RD, Mitchell DM, Bembenek JN, Reymann AC, Böhme R, Grill SW, Wang JT, Seydoux G, Tulu US, Kiehart DP, Betzig E. Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution. Science. 2014 Oct 24;346(6208):1257998. doi:
    10.1126/science.1257998. Epub 2014 Oct 23. PubMed PMID: 25342811.
    Wang K, Milkie DE, Saxena A, Engerer P, Misgeld T, Bronner ME, Mumm J, Betzig E. Rapid adaptive optical recovery of optimal resolution over large volumes. Nat Methods. 2014 Jun;11(6):625-8. doi: 10.1038/nmeth.2925. Epub 2014 Apr 13. PubMed PMID: 24727653; PubMed Central PMCID: PMC4069208.
  2. Amat F, Lemon W, Mossing DP, McDole K, Wan Y, Branson K, Myers EW, Keller PJ. Fast, accurate reconstruction of cell lineages from large-scale fluorescence microscopy data. Nat Methods. 2014 Jul 20. doi: 10.1038/nmeth.3036. [Epub ahead of print] PubMed PMID: 25042785.


  1. Rands CM, Meader S, Ponting CP, Lunter G. 8.2% of the Human genome is constrained: variation in rates of turnover across functional element classes in the human lineage. PLoS Genet. 2014 Jul 24;10(7):e1004525. doi:
    10.1371/journal.pgen.1004525. eCollection 2014 Jul. PubMed PMID: 25057982; PubMed Central PMCID: PMC4109858.
  2. News coverage: Only 8.2 % of Human DNA is Functional, Say Genetic Researchers


The thing that ties each of the following links together is a discussion of the need to incorporate equity, affirmation, and continued learning into social, scientific, and political spheres.  And to recognize that the lines between these spaces is a social construct.

This article offers an explanation of how sexism affects both the oppressed and the oppressor.  While they use a binary gender system in their drawings (male vs. female), it  is easy to understand how this could be applied to people in any gender system: http://imgur.com/gallery/n01WW

This article describes the work of Malala Yousafzai and Kailash Satyarthi who were recently awarded the Nobel Peace Prize for their work on expanding women’s and children’s rights in Pakistan and India, respectively.  Their stories highlight how personal identities are political and politics is personal: http://www.nytimes.com/2014/10/11/world/europe/kailash-satyarthi-and-malala-yousafzai-are-awarded-nobel-peace-prize.html?_r=0

This article goes in depth about African American and AfroCarribean identities in the U.S. as part of a larger history of colonization and slavery – how has this history impacted black Americans now and how is this oppression and the struggle for mutual humanization ongoing: http://www.washingtonpost.com/opinions/ferguson-wasnt-black-rage-against-copsit-was-white-rage-against-progress/2014/08/29/3055e3f4-2d75-11e4-bb9b-997ae96fad33_story.html

This article highlights some of the queer and trans* people of color working on gender, race, and sexuality equity in the U.S.  This is especially important given that the U.S. media (news, movies, t.v., radio, etc) predominately rewards and publicizes white, domestic, heterosexual, and cisgender people: http://www.autostraddle.com/22-badass-qtpoc-couples-that-make-our-hearts-flutter-253889/

Lastly, this article shows some really interesting research being done about children’s responsiveness and understanding of human emotions and interactions.  It has incredible implications for understanding the impacts of trauma, domestic violence, and healthy or unhealthy relationships on children as young as 15 months old!  http://www.huffingtonpost.com/2014/10/10/toddlers-angry-behave-study-video_n_5959482.html?ncid=fcbklnkushpmg00000063





Wonderful studies as usual!


The 2014 Ig Nobel Winners: Banana Peels to Nasal Pork