Logan Ganzen and Yuk Fai Leung attended the 2017 Annual Meeting of the Association for Research in Vision and Ophthalmology (ARVO) in Baltimore, MD from 2017-05-07 to 05-11. Logan presented a poster entitled “Visual Motor Response of a Transgenic Retinitis Pigmentosa Zebrafish Model”. They also attended several events to meet fellow researchers over the world. A few pictures of these events:

Dinner with zebrafish colleagues

 

Dinner with Dr. Mark Tso from the Wilmer Eye Institute.

Fai and Logan with Dr. Mark Tso from the Wilmer Eye Institute.

 

On 2017-04-08, Prahatha Venkatraman, Logan Ganzen, and Khaled Noui-Mehidi demonstrated zebrafish research in the 2017 Purdue Spring Fest.

Prahatha Venkatraman demonstrating zebrafish research to the public.

Logan Ganzen and Khaled Noui-Mehidi demonstrating zebrafish research to the public.

On 2016-03-25, Khaled Noui-Mehidi presented his research at the 131st Annual Academy Meeting of the Indiana Academy of Science. Emre Coskun attended the meeting. They were supervised by graduate student Logan Ganzen.

Khaled Noui-Mehidi presenting his research at the IAS meeting.

 

Neuroscience

  1. Dresler M, Shirer WR, Konrad BN, Müller NC, Wagner IC, Fernández G, Czisch M, Greicius MD. Mnemonic Training Reshapes Brain Networks to Support Superior Memory. Neuron. 2017 Mar 8;93(5):1227-1235.e6. doi: 10.1016/j.neuron.2017.02.003. PubMed PMID: 28279356.
  2. Burton CE, Zhou Y, Bai Q, Burton EA. Spectral properties of the zebrafish visual motor response. Neurosci Lett. 2017 Mar 3. pii: S0304-3940(17)30204-5. doi: 10.1016/j.neulet.2017.03.002. [Epub ahead of print] PubMed PMID: 28267562.

Genome editing

  1. Tang L, Zeng Y, Du H, Gong M, Peng J, Zhang B, Lei M, Zhao F, Wang W, Li X, Liu J. CRISPR/Cas9-mediated gene editing in human zygotes using Cas9 protein. Mol Genet Genomics. 2017 Mar 1. doi: 10.1007/s00438-017-1299-z. [Epub ahead of print] PubMed PMID: 28251317.
  2. Hohmann S. Editor’s comment on “CRISPR/Cas9-mediated gene editing in human zygotes using Cas9 protein”. Mol Genet Genomics. 2017 Mar 1. doi: 10.1007/s00438-017-1300-x. [Epub ahead of print] PubMed PMID: 28251316.

ELSI

  1. Williams WM, Ceci SJ. National hiring experiments reveal 2:1 faculty preference for women on STEM tenure track. Proc Natl Acad Sci U S A. 2015 Apr 28;112(17):5360-5. doi: 10.1073/pnas.1418878112. PubMed PMID: 25870272; PubMed Central PMCID: PMC4418903.

Genome editing

  1. Why the CRISPR patent verdict isn’t the end of the story
  2. Burstein D, Harrington LB, Strutt SC, Probst AJ, Anantharaman K, Thomas BC, Doudna JA, Banfield JF. New CRISPR-Cas systems from uncultivated microbes. Nature. 2017 Feb 9;542(7640):237-241. doi: 10.1038/nature21059. PubMed PMID: 28005056; PubMed Central PMCID: PMC5300952.

Imaging

  1. Pan C, Cai R, Quacquarelli FP, Ghasemigharagoz A, Lourbopoulos A, Matryba P, Plesnila N, Dichgans M, Hellal F, Ertürk A. Shrinkage-mediated imaging of entire organs and organisms using uDISCO. Nat Methods. 2016 Oct;13(10):859-67. doi: 10.1038/nmeth.3964. PubMed PMID: 27548807.

Neuroscience

  1. Krakauer JW, Ghazanfar AA, Gomez-Marin A, MacIver MA, Poeppel D. Neuroscience Needs Behavior: Correcting a Reductionist Bias. Neuron. 2017 Feb 8;93(3):480-490. doi: 10.1016/j.neuron.2016.12.041. Review. PubMed PMID: 28182904.
  2. Jonas E, Kording KP. Could a Neuroscientist Understand a Microprocessor? PLoS Comput Biol. 2017 Jan 12;13(1):e1005268. doi: 10.1371/journal.pcbi.1005268. PubMed PMID: 28081141; PubMed Central PMCID: PMC5230747.

Medicine

  1. Dowdy SF. Overcoming cellular barriers for RNA therapeutics. Nat Biotechnol. 2017 Feb 27. doi: 10.1038/nbt.3802. [Epub ahead of print] PubMed PMID: 28244992.
  2. Khvorova A, Watts JK. The chemical evolution of oligonucleotide therapies of clinical utility. Nat Biotechnol. 2017 Feb 27. doi: 10.1038/nbt.3765. [Epub ahead of print] PubMed PMID: 28244990.

Genomics

  1. Martelotto LG, Baslan T, Kendall J, Geyer FC, Burke KA, Spraggon L, Piscuoglio S, Chadalavada K, Nanjangud G, Ng CK, Moody P, D’Italia S, Rodgers L, Cox H, da Cruz Paula A, Stepansky A, Schizas M, Wen HY, King TA, Norton L, Weigelt B, Hicks JB, Reis-Filho JS. Whole-genome single-cell copy number profiling from formalin-fixed paraffin-embedded samples. Nat Med. 2017 Feb 6. doi: 10.1038/nm.4279. [Epub ahead of print] PubMed PMID: 28165479.

Genetics

  1. Bilow M, Crespo F, Pan Z, Eskin E, Eyheramendy S. Simultaneous Modeling of Disease Status and Clinical Phenotypes to Increase Power in GWAS. Genetics. 2017 Jan 27. pii: genetics.116.198473. doi: 10.1534/genetics.116.198473. [Epub ahead of print] PubMed PMID: 28132020.

				

Genome editing

  1. Park RJ, Wang T, Koundakjian D, Hultquist JF, Lamothe-Molina P, Monel B, Schumann K, Yu H, Krupzcak KM, Garcia-Beltran W, Piechocka-Trocha A, Krogan NJ, Marson A, Sabatini DM, Lander ES, Hacohen N, Walker BD. A genome-wide CRISPR screen identifies a restricted set of HIV host dependency factors. Nat Genet. 2017 Feb;49(2):193-203. doi: 10.1038/ng.3741. PubMed PMID: 27992415.
    • Commentary: Tsui CK, Gupta A, Bassik MC. Finding host targets for HIV therapy. Nat Genet. 2017 Jan 31;49(2):175-176. doi: 10.1038/ng.3777. PubMed PMID: 28138150.
  2. Bengtsson NE, Hall JK, Odom GL, Phelps MP, Andrus CR, Hawkins RD, Hauschka SD, Chamberlain JR, Chamberlain JS. Muscle-specific CRISPR/Cas9 dystrophin gene editing ameliorates pathophysiology in a mouse model for Duchenne muscular dystrophy. Nat Commun. 2017 Feb 14;8:14454. doi: 10.1038/ncomms14454. PubMed PMID: 28195574.

Disease

  1. Leinenga G, Götz J. Scanning ultrasound removes amyloid-β and restores memory in an Alzheimer’s disease mouse model. Sci Transl Med. 2015 Mar 11;7(278):278ra33. doi: 10.1126/scitranslmed.aaa2512. PubMed PMID: 25761889.

Genomics

  1. Li X, Xiong X, Yi C. Epitranscriptome sequencing technologies: decoding RNA modifications. Nat Methods. 2016 Dec 29;14(1):23-31. doi: 10.1038/nmeth.4110. PubMed PMID: 28032622.
  2. Adamson B, Norman TM, Jost M, Cho MY, Nuñez JK, Chen Y, Villalta JE, Gilbert LA, Horlbeck MA, Hein MY, Pak RA, Gray AN, Gross CA, Dixit A, Parnas O, Regev A, Weissman JS. A Multiplexed Single-Cell CRISPR Screening Platform Enables Systematic Dissection of the Unfolded Protein Response. Cell. 2016 Dec 15;167(7):1867-1882.e21. doi: 10.1016/j.cell.2016.11.048. PubMed PMID: 27984733.
  3. Dixit A, Parnas O, Li B, Chen J, Fulco CP, Jerby-Arnon L, Marjanovic ND, Dionne D, Burks T, Raychowdhury R, Adamson B, Norman TM, Lander ES, Weissman JS, Friedman N, Regev A. Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens. Cell. 2016 Dec 15;167(7):1853-1866.e17. doi: 10.1016/j.cell.2016.11.038. PubMed PMID: 27984732; PubMed Central PMCID: PMC5181115.
  4. Jaitin DA, Weiner A, Yofe I, Lara-Astiaso D, Keren-Shaul H, David E, Salame TM, Tanay A, van Oudenaarden A, Amit I. Dissecting Immune Circuits by Linking CRISPR-Pooled Screens with Single-Cell RNA-Seq. Cell. 2016 Dec 15;167(7):1883-1896.e15. doi: 10.1016/j.cell.2016.11.039. PubMed PMID: 27984734.

RNA

  1. Rivas E, Clements J, Eddy SR. A statistical test for conserved RNA structure shows lack of evidence for structure in lncRNAs. Nat Methods. 2017 Jan;14(1):45-48. doi: 10.1038/nmeth.4066. PubMed PMID: 27819659.

Cell cycle

  1. Swaffer MP, Jones AW, Flynn HR, Snijders AP, Nurse P. CDK Substrate Phosphorylation and Ordering the Cell Cycle. Cell. 2016 Dec 15;167(7):1750-1761.e16. doi: 10.1016/j.cell.2016.11.034. PubMed PMID: 27984725; PubMed Central PMCID: PMC5161751.

Genome Editing

  1. Pawluk A, Amrani N, Zhang Y, Garcia B, Hidalgo-Reyes Y, Lee J, Edraki A, Shah M, Sontheimer EJ, Maxwell KL, Davidson AR. Naturally Occurring Off-Switches for CRISPR-Cas9. Cell. 2016 Dec 15;167(7):1829-1838.e9. doi: 10.1016/j.cell.2016.11.017. PubMed PMID: 27984730.
  2. Adamson B, Norman TM, Jost M, Cho MY, Nuñez JK, Chen Y, Villalta JE, Gilbert LA, Horlbeck MA, Hein MY, Pak RA, Gray AN, Gross CA, Dixit A, Parnas O, Regev A, Weissman JS. A Multiplexed Single-Cell CRISPR Screening Platform Enables Systematic Dissection of the Unfolded Protein Response. Cell. 2016 Dec 15;167(7):1867-1882.e21. doi: 10.1016/j.cell.2016.11.048. PubMed PMID: 27984733.
  3. Dixit A, Parnas O, Li B, Chen J, Fulco CP, Jerby-Arnon L, Marjanovic ND, Dionne D, Burks T, Raychowdhury R, Adamson B, Norman TM, Lander ES, Weissman JS, Friedman N, Regev A. Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens. Cell. 2016 Dec 15;167(7):1853-1866.e17. doi: 10.1016/j.cell.2016.11.038. PubMed PMID: 27984732; PubMed Central PMCID: PMC5181115.
  4. Jaitin DA, Weiner A, Yofe I, Lara-Astiaso D, Keren-Shaul H, David E, Salame TM, Tanay A, van Oudenaarden A, Amit I. Dissecting Immune Circuits by Linking CRISPR-Pooled Screens with Single-Cell RNA-Seq. Cell. 2016 Dec 15;167(7):1883-1896.e15. doi: 10.1016/j.cell.2016.11.039. PubMed PMID: 27984734.
  5. Sheridan C. CRISPR therapeutics push into human testing. Nat Biotechnol. 2017 Jan 10;35(1):3-5. doi: 10.1038/nbt0117-3. PubMed PMID: 28072788.

Zebrafish

  1. Reade A, Motta-Mena LB, Gardner KH, Stainier DY, Weiner OD, Woo S. TAEL: A zebrafish-optimized optogenetic gene expression system with fine spatial and temporal control. Development. 2016 Dec 19. pii: dev.139238. [Epub ahead of print] PubMed PMID: 27993986.

Stem Cells

  1. Mandai M, Fujii M, Hashiguchi T, Sunagawa GA, Ito S, Sun J, Kaneko J, Sho J, Yamada C, Takahashi M. iPSC-Derived Retina Transplants Improve Vision in rd1 End-Stage Retinal-Degeneration Mice. Stem Cell Reports. 2017 Jan 10;8(1):69-83. doi: 10.1016/j.stemcr.2016.12.008. PubMed PMID: 28076757.

				

Evolution

  1. Gonzalez P, Uhlinger KR, Lowe CJ. The Adult Body Plan of Indirect Developing Hemichordates Develops by Adding a Hox-Patterned Trunk to an Anterior Larval Territory. Curr Biol. 2016 Dec 7. pii: S0960-9822(16)31273-8. doi: 10.1016/j.cub.2016.10.047. [Epub ahead of print] PubMed PMID: 27939313.
    • Hejnol A, Vellutini BC. Larval Evolution: I’ll Tail You Later…. Curr Biol. 2017 Jan 9;27(1):R21-R24. doi: 10.1016/j.cub.2016.10.057. PubMed PMID: 28073016.

Regeneration

  1. Tornini VA, Puliafito A, Slota LA, Thompson JD, Nachtrab G, Kaushik AL, Kapsimali M, Primo L, Di Talia S, Poss KD. Live Monitoring of Blastemal Cell Contributions during Appendage Regeneration. Curr Biol. 2016 Nov 21;26(22):2981-2991. doi: 10.1016/j.cub.2016.08.072. PubMed PMID: 27839971; PubMed Central PMCID: PMC5121098.
  2. Currie JD, Kawaguchi A, Traspas RM, Schuez M, Chara O, Tanaka EM. Live Imaging of Axolotl Digit Regeneration Reveals Spatiotemporal Choreography of Diverse Connective Tissue Progenitor Pools. Dev Cell. 2016 Nov 21;39(4):411-423. doi: 10.1016/j.devcel.2016.10.013. PubMed PMID: 27840105; PubMed Central PMCID: PMC5127896.
    • Weidinger G. Regeneration: Recorded Live! Curr Biol. 2017 Jan 9;27(1):R30-R33. doi: 10.1016/j.cub.2016.11.022. PubMed PMID: 28073020.

Behaviour

  1. Dreosti E, Lopes G, Kampff AR, Wilson SW. Development of social behavior in young zebrafish. Front Neural Circuits. 2015 Aug 18;9:39. doi: 10.3389/fncir.2015.00039. eCollection 2015. PubMed PMID: 26347614; PubMed Central PMCID: PMC4539524.
  2. Pérez-Escudero A, Vicente-Page J, Hinz RC, Arganda S, de Polavieja GG. idTracker: tracking individuals in a group by automatic identification of unmarked animals. Nat Methods. 2014 Jul;11(7):743-8. doi: 10.1038/nmeth.2994. Epub 2014 Jun 1. PubMed PMID: 24880877.

Genome editing

  1. Kuscu C, Adli M. CRISPR-Cas9-AID base editor is a powerful gain-of-function screening tool. Nat Methods. 2016 Nov 29;13(12):983-984. doi: 10.1038/nmeth.4076. PubMed PMID: 27898061. Ma Y, Zhang J, Yin W, Zhang Z, Song Y, Chang X. Targeted AID-mediated mutagenesis (TAM) enables efficient genomic diversification in mammalian cells. Nat Methods. 2016 Dec;13(12):1029-1035. doi: 10.1038/nmeth.4027. PubMed PMID: 27723754.
  2. Hess GT, Frésard L, Han K, Lee CH, Li A, Cimprich KA, Montgomery SB, Bassik MC. Directed evolution using dCas9-targeted somatic hypermutation in mammalian cells. Nat Methods. 2016 Dec;13(12):1036-1042. doi: 10.1038/nmeth.4038. PubMed PMID: 27798611. Gao Y, Xiong X, Wong S, Charles EJ, Lim WA, Qi LS. Complex transcriptional modulation with orthogonal and inducible dCas9 regulators. Nat Methods. 2016 Dec;13(12):1043-1049. doi: 10.1038/nmeth.4042. PubMed PMID: 27776111.
  3. Nakamura T, Gehrke AR, Lemberg J, Szymaszek J, Shubin NH. Digits and fin rays share common developmental histories. Nature. 2016 Sep 8;537(7619):225-228. doi: 10.1038/nature19322. PubMed PMID: 27533041; PubMed Central PMCID: PMC5161576.
    • CRISPR helps evo-devo scientists to unpick the origins of adaptions. Nature. 2016 Aug 18;536(7616):249. doi: 10.1038/536249b. PubMed PMID: 27535498.
    • Saxena A, Cooper KL. Evolutionary biology: Fin to limb within our grasp. Nature. 2016 Sep 8;537(7619):176-177. doi: 10.1038/nature19425. PubMed PMID: 27533039.

Genetics/Genomics

  1. Lek M, Karczewski KJ, Minikel EV, Samocha KE, Banks E, Fennell T, O’Donnell-Luria AH, Ware JS, Hill AJ, Cummings BB, Tukiainen T, Birnbaum DP, Kosmicki JA, Duncan LE, Estrada K, Zhao F, Zou J, Pierce-Hoffman E, Berghout J, Cooper DN, Deflaux N, DePristo M, Do R, Flannick J, Fromer M, Gauthier L, Goldstein J, Gupta N, Howrigan D, Kiezun A, Kurki MI, Moonshine AL, Natarajan P, Orozco L, Peloso GM, Poplin R, Rivas MA, Ruano-Rubio V, Rose SA, Ruderfer DM, Shakir K, Stenson PD, Stevens C, Thomas BP, Tiao G, Tusie-Luna MT, Weisburd B, Won HH, Yu D, Altshuler DM, Ardissino D, Boehnke M, Danesh J, Donnelly S, Elosua R, Florez JC, Gabriel SB, Getz G, Glatt SJ, Hultman CM, Kathiresan S, Laakso M, McCarroll S, McCarthy MI, McGovern D, McPherson R, Neale BM, Palotie A, Purcell SM, Saleheen D, Scharf JM, Sklar P, Sullivan PF, Tuomilehto J, Tsuang MT, Watkins HC, Wilson JG, Daly MJ, MacArthur DG; Exome Aggregation Consortium.. Analysis of protein-coding genetic variation in 60,706 humans. Nature. 2016 Aug 18;536(7616):285-91. doi: 10.1038/nature19057. PubMed PMID: 27535533; PubMed Central PMCID: PMC5018207.
  2. Shendure J. Human genomics: A deep dive into genetic variation. Nature. 2016 Aug 18;536(7616):277-8. doi: 10.1038/536277a. PubMed PMID: 27535530.
  3. ExAC project pins down rare gene variants. Nature. 2016 Aug 18;536(7616):249. doi: 10.1038/536249a. PubMed PMID: 27535499.
  4. Carss KJ, Arno G, Erwood M, Stephens J, Sanchis-Juan A, Hull S, Megy K, Grozeva D, Dewhurst E, Malka S, Plagnol V, Penkett C, Stirrups K, Rizzo R, Wright G, Josifova D, Bitner-Glindzicz M, Scott RH, Clement E, Allen L, Armstrong R, Brady AF, Carmichael J, Chitre M, Henderson RH, Hurst J, MacLaren RE, Murphy E, Paterson J, Rosser E, Thompson DA, Wakeling E, Ouwehand WH, Michaelides M, Moore AT; NIHR-BioResource Rare Diseases Consortium., Webster AR, Raymond FL. Comprehensive Rare Variant Analysis via Whole-Genome Sequencing to Determine the Molecular Pathology of Inherited Retinal Disease. Am J Hum Genet. 2016 Dec 28. pii: S0002-9297(16)30527-4. doi: 10.1016/j.ajhg.2016.12.003. [Epub ahead of print] PubMed PMID: 28041643.

Evolution

  1. Nakamura T, Gehrke AR, Lemberg J, Szymaszek J, Shubin NH. Digits and fin rays share common developmental histories. Nature. 2016 Sep 8;537(7619):225-228. doi: 10.1038/nature19322. PubMed PMID: 27533041; PubMed Central PMCID: PMC5161576.
  2. CRISPR helps evo-devo scientists to unpick the origins of adaptions. Nature. 2016 Aug 18;536(7616):249. doi: 10.1038/536249b. PubMed PMID: 27535498.
  3. Saxena A, Cooper KL. Evolutionary biology: Fin to limb within our grasp. Nature. 2016 Sep 8;537(7619):176-177. doi: 10.1038/nature19425. PubMed PMID: 27533039.

System biology

  1. Gao Y, Xiong X, Wong S, Charles EJ, Lim WA, Qi LS. Complex transcriptional modulation with orthogonal and inducible dCas9 regulators. Nat Methods. 2016 Dec;13(12):1043-1049. doi: 10.1038/nmeth.4042. PubMed PMID: 27776111.
  2. Frumkin I, Schirman D, Rotman A, Li F, Zahavi L, Mordret E, Asraf O, Wu S, Levy SF, Pilpel Y. Gene Architectures that Minimize Cost of Gene Expression. Mol Cell. 2016 Nov 25. pii: S1097-2765(16)30715-8. doi: 10.1016/j.molcel.2016.11.007. [Epub ahead of print] PubMed PMID: 27989436.


				

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.