Posts tagged ‘zebrafish’

Lilly Hall of Science; 2015 Purdue Spring Fest

Prahatha Venkatraman showing the way to measure fish vision to a future scientist.

Martian Tian explaining how to use zebrafish for eye disease research to the Lafayette community.

Cancer

  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.

Zebrafish

  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.

Imaging

  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.

Genetics

  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.

Genome-editing

  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.

Development

  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.

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.

Retina

  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.

Imaging

  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.

Zebrafish

  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.

Genetics

  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.

Medicine

  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.

Evolution

  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.

 

Systems biology

  1. Levo M, Segal E. In pursuit of design principles of regulatory sequences. Nat Rev Genet. 2014 Jul;15(7):453-68. doi: 10.1038/nrg3684. Epub 2014 Jun 10. PubMed PMID: 24913666.
  2. Patel AP, Tirosh I, Trombetta JJ, Shalek AK, Gillespie SM, Wakimoto H, Cahill DP, Nahed BV, Curry WT, Martuza RL, Louis DN, Rozenblatt-Rosen O, Suvà ML, Regev A, Bernstein BE. Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma. Science. 2014 Jun 20;344(6190):1396-401. doi: 10.1126/science.1254257. Epub 2014 Jun 12. PubMed PMID: 24925914.

Stem cells

  1. Cattaneo E, Corbellini G. Stem cells: taking a stand against pseudoscience. Nature. 2014 Jun 19;509(7505):333-5. PubMed PMID: 24955466.
  2. Bertolotti E, Neri A, Camparini M, Macaluso C, Marigo V. Stem cells as source for retinal pigment epithelium transplantation. Prog Retin Eye Res. 2014 Jun 13. pii: S1350-9462(14)00037-8. doi: 10.1016/j.preteyeres.2014.06.002. [Epub ahead of print] Review. PubMed PMID: 24933042.
  3. Ye L, Wang J, Beyer AI, Teque F, Cradick TJ, Qi Z, Chang JC, Bao G, Muench MO, Yu J, Levy JA, Kan YW. Seamless modification of wild-type induced pluripotent stem cells to the natural CCR5?32 mutation confers resistance to HIV infection. Proc Natl Acad Sci U S A. 2014 Jun 9. pii: 201407473. [Epub ahead of print] PubMed PMID: 24927590.
  4. Park CY, Kim J, Kweon J, Son JS, Lee JS, Yoo JE, Cho SR, Kim JH, Kim JS, Kim DW. Targeted inversion and reversion of the blood coagulation factor 8 gene in human iPS cells using TALENs. Proc Natl Acad Sci U S A. 2014 Jun 24;111(25):9253-8. doi: 10.1073/pnas.1323941111. Epub 2014 Jun 9. PubMed PMID: 24927536.

Neuroscience

  1. Rose N. The human brain project: social and ethical challenges. Neuron. 2014 Jun 18;82(6):1212-5. doi: 10.1016/j.neuron.2014.06.001. PubMed PMID: 24945767.
  2. Cohen MA, Konkle T, Rhee JY, Nakayama K, Alvarez GA. Processing multiple visual objects is limited by overlap in neural channels. Proc Natl Acad Sci U S A. 2014 Jun 17;111(24):8955-60. doi: 10.1073/pnas.1317860111. Epub 2014 Jun 2. PubMed PMID: 24889618.
  3. Prevedel R, Yoon YG, Hoffmann M, Pak N, Wetzstein G, Kato S, Schrödel T, Raskar R, Zimmer M, Boyden ES, Vaziri A. Simultaneous whole-animal 3D imaging of neuronal activity using light-field microscopy. Nat Methods. 2014 Jul;11(7):727-30. doi: 10.1038/nmeth.2964. Epub 2014 May 18. PubMed PMID: 24836920.

Neurobehaviour

  1. 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.

Psychology

  1. Jung K, Shavitt S, Viswanathan M, Hilbe JM. Female hurricanes are deadlier than male hurricanes. Proc Natl Acad Sci U S A. 2014 Jun 17;111(24):8782-7. doi: 10.1073/pnas.1402786111. Epub 2014 Jun 2. PubMed PMID: 24889620.

Retinal Development

  1. Laranjeiro R, Whitmore D. Transcription factors involved in retinogenesis are co-opted by the circadian clock following photoreceptor differentiation. Development. 2014 Jun 12. pii: dev.104380. [Epub ahead of print] PubMed PMID: 24924194.

Eye diseases

  1. Huber-Reggi SP, Mueller KP, Straumann D, Huang MY, Neuhauss SC. Individual Larvae of the Zebrafish Mutant belladonna Display Multiple Infantile Nystagmus-Like Waveforms that Are Influenced by Viewing Conditions. Invest Ophthalmol Vis Sci. 2014 May 27;55(6):3971-8. doi: 10.1167/iovs.13-13576. PubMed PMID: 24867578.

Zebrafish

  1. Law SH, Sargent TD. The Serine-Threonine Protein Kinase PAK4 Is Dispensable in Zebrafish: Identification of a Morpholino-Generated Pseudophenotype. PLoS One. 2014 Jun 19;9(6):e100268. doi: 10.1371/journal.pone.0100268. eCollection 2014. PubMed PMID: 24945275.

Genome editing/medicine

  1. Ye L, Wang J, Beyer AI, Teque F, Cradick TJ, Qi Z, Chang JC, Bao G, Muench MO, Yu J, Levy JA, Kan YW. Seamless modification of wild-type induced pluripotent stem cells to the natural CCR5?32 mutation confers resistance to HIV infection. Proc Natl Acad Sci U S A. 2014 Jun 9. pii: 201407473. [Epub ahead of print] PubMed PMID: 24927590.
  2. Park CY, Kim J, Kweon J, Son JS, Lee JS, Yoo JE, Cho SR, Kim JH, Kim JS, Kim DW. Targeted inversion and reversion of the blood coagulation factor 8 gene in human iPS cells using TALENs. Proc Natl Acad Sci U S A. 2014 Jun 24;111(25):9253-8. doi: 10.1073/pnas.1323941111. Epub 2014 Jun 9. PubMed PMID: 24927536.
  3. Kiani S, Beal J, Ebrahimkhani MR, Huh J, Hall RN, Xie Z, Li Y, Weiss R. CRISPR
    transcriptional repression devices and layered circuits in mammalian cells. Nat
    Methods. 2014 Jul;11(7):723-6. doi: 10.1038/nmeth.2969. Epub 2014 May 5. PubMed
    PMID: 24797424.
  4. Nissim L, Perli SD, Fridkin A, Perez-Pinera P, Lu TK. Multiplexed and Programmable Regulation of Gene Networks with an Integrated RNA and CRISPR/Cas Toolkit in Human Cells. Mol Cell. 2014 May 22;54(4):698-710. doi: 10.1016/j.molcel.2014.04.022. Epub 2014 May 15. PubMed PMID: 24837679.

Drug Discovery

  1. Wang YN, Hou YY, Sun MZ, Zhang CY, Bai G, Zhao X, Feng XZ. Behavioural screening of zebrafish using neuroactive traditional Chinese medicine prescriptions and biological targets. Sci Rep. 2014 Jun 16;4:5311. doi: 10.1038/srep05311. PubMed PMID: 24931174; PubMed Central PMCID: PMC4058885.

Science Career

  1. Casadevall A, Fang FC. Causes for the persistence of impact factor mania. MBio. 2014 Mar 18;5(2):e00064-14. doi: 10.1128/mBio.00064-14. PubMed PMID: 24643863; PubMed Central PMCID: PMC3967521.

Development

  1. Nicolas M, Hassan BA. Amyloid precursor protein and neural development. Development. 2014 Jul;141(13):2543-8. doi: 10.1242/dev.108712. PubMed PMID: 24961795.
  2. Deneris ES, Hobert O. Maintenance of postmitotic neuronal cell identity. Nat Neurosci. 2014 Jul;17(7):899-907. doi: 10.1038/nn.3731. Epub 2014 Jun 15. PubMed PMID: 24929660.

Methods

  1. Hughes AJ, Spelke DP, Xu Z, Kang CC, Schaffer DV, Herr AE. Single-cell western blotting. Nat Methods. 2014 Jul;11(7):749-55. doi: 10.1038/nmeth.2992. Epub 2014  Jun 1. PubMed PMID: 24880876.

Stem cells/ regenerative medicine

  1. Zhong X, Gutierrez C, Xue T, Hampton C, Vergara MN, Cao LH, Peters A, Park TS, Zambidis ET, Meyer JS, Gamm DM, Yau KW, Canto-Soler MV. Generation of three-dimensional retinal tissue with functional photoreceptors from human iPSCs. Nat Commun. 2014 Jun 10;5:4047. doi: 10.1038/ncomms5047. PubMed PMID: 24915161.
  2. Reichman S, Terray A, Slembrouck A, Nanteau C, Orieux G, Habeler W, Nandrot EF, Sahel JA, Monville C, Goureau O. From confluent human iPS cells to self-forming neural retina and retinal pigmented epithelium. Proc Natl Acad Sci U S A. 2014 Jun 10;111(23):8518-23. doi: 10.1073/pnas.1324212111. Epub 2014 May 27. PubMed PMID: 24912154.
  3. Chong JJ, Yang X, Don CW, Minami E, Liu YW, Weyers JJ, Mahoney WM, Van Biber B, Cook SM, Palpant NJ, Gantz JA, Fugate JA, Muskheli V, Gough GM, Vogel KW, Astley CA, Hotchkiss CE, Baldessari A, Pabon L, Reinecke H, Gill EA, Nelson V, Kiem HP, Laflamme MA, Murry CE. Human embryonic-stem-cell-derived cardiomyocytes regenerate non-human primate hearts. Nature. 2014 Jun 12;510(7504):273-7. doi: 10.1038/nature13233. Epub 2014 Apr 30. PubMed PMID: 24776797.
  4. Normile D, Vogel G. Cell biology. STAP cells succumb to pressure. Science. 2014 Jun 13;344(6189):1215-6. doi: 10.1126/science.344.6189.1215. PubMed PMID: 24925996.

Eye diseases

  1. Agbaga MP, Tam BM, Wong JS, Yang LL, Anderson RE, Moritz OL. Mutant ELOVL4 That Causes Autosomal Dominant Stargardt-3 Macular Dystrophy Is Misrouted to Rod Outer Segment Disks. Invest Ophthalmol Vis Sci. 2014 May 15;55(6):3669-3680. doi: 10.1167/iovs.13-13099. PubMed PMID: 24833735.

Oxidative stress

  1. Moussavi Nik SH, Croft K, Mori TA, Lardelli M. The comparison of methods for measuring oxidative stress in zebrafish brains. Zebrafish. 2014 Jun;11(3):248-54. doi: 10.1089/zeb.2013.0958. Epub 2014 May 5. PubMed PMID: 24798242.

Molecular Biology

  1. Roberts JW. Molecular biology. Molecular basis of transcription pausing. Science. 2014 Jun 13;344(6189):1226-7. doi: 10.1126/science.1255712. PubMed PMID: 24926002.

Systems Biology

  1. Shalek AK, Satija R, Shuga J, Trombetta JJ, Gennert D, Lu D, Chen P, Gertner RS, Gaublomme JT, Yosef N, Schwartz S, Fowler B, Weaver S, Wang J, Wang X, Ding R, Raychowdhury R, Friedman N, Hacohen N, Park H, May AP, Regev A. Single-cell RNA-seq reveals dynamic paracrine control of cellular variation. Nature. 2014 Jun 11. doi: 10.1038/nature13437. [Epub ahead of print] PubMed PMID: 24919153.

Synthetic Biology/Gene regulatory Network

  1. Attwater J, Holliger P. A synthetic approach to abiogenesis. Nat Methods. 2014 May;11(5):495-8. doi: 10.1038/nmeth.2893. PubMed PMID: 24781322.
  2. Brophy JA, Voigt CA. Principles of genetic circuit design. Nat Methods. 2014 May;11(5):508-20. doi: 10.1038/nmeth.2926. Review. PubMed PMID: 24781324.

Behaviour

  1. Zhou Y, Cattley RT, Cario CL, Bai Q, Burton EA. Quantification of larval zebrafish motor function in multiwell plates using open-source MATLAB applications. Nat Protoc. 2014 Jul;9(7):1533-48. doi: 10.1038/nprot.2014.094. Epub 2014 Jun 5. PubMed PMID: 24901738.

Education

  1. Wieman CE. Large-scale comparison of science teaching methods sends clear message. Proc Natl Acad Sci U S A. 2014 Jun 10;111(23):8319-20. doi: 10.1073/pnas.1407304111. Epub 2014 May 22. PubMed PMID: 24853505.
  2. Zhou M, Lee J. Assessing what is cultural about Asian Americans’ academic advantage. Proc Natl Acad Sci U S A. 2014 Jun 10;111(23):8321-2. doi: 10.1073/pnas.1407309111. Epub 2014 May 29. PubMed PMID: 24876277.
  3. Freeman S, Eddy SL, McDonough M, Smith MK, Okoroafor N, Jordt H, Wenderoth MP. Active learning increases student performance in science, engineering, and mathematics. Proc Natl Acad Sci U S A. 2014 Jun 10;111(23):8410-5. doi: 10.1073/pnas.1319030111. Epub 2014 May 12. PubMed PMID: 24821756.
  4. Hsin A, Xie Y. Explaining Asian Americans’ academic advantage over whites. Proc Natl Acad Sci U S A. 2014 Jun 10;111(23):8416-21. doi: 10.1073/pnas.1406402111. Epub 2014 May 5. PubMed PMID: 24799702.

Scientific Career

  1. van Dijk D, Manor O, Carey LB. Publication metrics and success on the academic job market. Curr Biol. 2014 Jun 2;24(11):R516-7. doi: 10.1016/j.cub.2014.04.039. PubMed PMID: 24892909.

Genomics

  1. Venter’s New Goal: World’s Largest Sequencing Operation
  2. Clinical Whole Genome Sequencing: Not Quite Ready for Prime Time?

Genetics

  1. Vanderperre B, Lucier JF, Bissonnette C, Motard J, Tremblay G, Vanderperre S, Wisztorski M, Salzet M, Boisvert FM, Roucou X. Direct detection of alternative open reading frames translation products in human significantly expands the proteome. PLoS One. 2013 Aug 12;8(8):e70698. doi: 10.1371/journal.pone.0070698. eCollection 2013. PubMed PMID: 23950983; PubMed Central PMCID: PMC3741303.

Stem cells

  1. Acid-bath stem-cell study under investigation.

Genome-editing

  1. Tebas P, Stein D, Tang WW, Frank I, Wang SQ, Lee G, Spratt SK, Surosky RT, Giedlin MA, Nichol G, Holmes MC, Gregory PD, Ando DG, Kalos M, Collman RG, Binder-Scholl G, Plesa G, Hwang WT, Levine BL, June CH. Gene editing of CCR5 in autologous CD4 T cells of persons infected with HIV. N Engl J Med. 2014 Mar 6;370(10):901-10. doi: 10.1056/NEJMoa1300662. PubMed PMID: 24597865.
    • Editorial commentary: Kay MA, Walker BD. Engineering cellular resistance to HIV. N Engl J Med. 2014
      Mar 6;370(10):968-9. doi: 10.1056/NEJMe1400593. PubMed PMID: 24597871.
    • News coverage: Editing Genes May Make Cells Resist HIV.

Philosophy

How Academia and Publishing are Destroying Scientific Innovation: A Conversation with Sydney Brenner

Medicine

  1. Flannick J, Thorleifsson G, Beer NL, Jacobs SB, Grarup N, Burtt NP, Mahajan A, Fuchsberger C, Atzmon G, Benediktsson R, Blangero J, Bowden DW, Brandslund I, Brosnan J, Burslem F, Chambers J, Cho YS, Christensen C, Douglas DA, Duggirala R, Dymek Z, Farjoun Y, Fennell T, Fontanillas P, Forsén T, Gabriel S, Glaser B, Gudbjartsson DF, Hanis C, Hansen T, Hreidarsson AB, Hveem K, Ingelsson E, Isomaa  B, Johansson S, Jørgensen T, Jørgensen ME, Kathiresan S, Kong A, Kooner J, Kravic J, Laakso M, Lee JY, Lind L, Lindgren CM, Linneberg A, Masson G, Meitinger T, Mohlke KL, Molven A, Morris AP, Potluri S, Rauramaa R, Ribel-Madsen R, Richard AM, Rolph T, Salomaa V, Segrè AV, Skärstrand H, Steinthorsdottir V, Stringham HM, Sulem P, Tai ES, Teo YY, Teslovich T, Thorsteinsdottir U, Trimmer JK, Tuomi T, Tuomilehto J, Vaziri-Sani F, Voight BF, Wilson JG, Boehnke M, McCarthy MI, Njølstad PR, Pedersen O, Groop L, Cox DR, Stefansson K, Altshuler D. Loss-of-function mutations in SLC30A8 protect against type 2 diabetes. Nat Genet. 2014 Mar 2. doi: 10.1038/ng.2915. [Epub ahead of print] PubMed PMID: 24584071.
  2. Mapstone M, Cheema AK, Fiandaca MS, Zhong X, Mhyre TR, Macarthur LH, Hall WJ, Fisher SG, Peterson DR, Haley JM, Nazar MD, Rich SA, Berlau DJ, Peltz CB, Tan MT, Kawas CH, Federoff HJ. Plasma phospholipids identify antecedent memory impairment in older adults. Nat Med. 2014 Mar 9. doi: 10.1038/nm.3466. [Epub ahead of print]
    PubMed PMID: 24608097.

Imaging

  1. Foldscope: Origami-based paper microscope

Zebrafish

  1. Cressey D. Fish-kill method questioned. Nature. 2014 Feb 27;506(7489):419-20. doi: 10.1038/506419a. PubMed PMID: 24572404.

 

Eye disease

  1. Fernandez de Castro J, Scott PA, Fransen JW, Demas J, Demarco PJ, Kaplan HJ, McCall MA. Cone Photoreceptors Develop Normally in the Absence of Functional Rod Photoreceptors in a Transgenic Swine Model of Retinitis Pigmentosa. Invest Ophthalmol Vis Sci. 2014 Mar 11. pii: iovs.13-13724v1. doi: 10.1167/iovs.13-13724. [Epub ahead of print] PubMed PMID: 24618325.

Vision

  1. Partridge JC, Douglas RH, Marshall NJ, Chung WS, Jordan TM, Wagner HJ. Reflecting optics in the diverticular eye of a deep-sea barreleye fish (Rhynchohyalus natalensis). Proc Biol Sci. 2014 Mar 19;281(1782):20133223. doi: 10.1098/rspb.2013.3223. Print 2014. PubMed PMID: 24648222.

Evolution

  1. Gassmann AJ, Petzold-Maxwell JL, Clifton EH, Dunbar MW, Hoffmann AM, Ingber DA, Keweshan RS. Field-evolved resistance by western corn rootworm to multiple Bacillus thuringiensis toxins in transgenic maize. Proc Natl Acad Sci U S A. 2014 Mar 17. [Epub ahead of print] PubMed PMID: 24639498.

Neuroscience

  1. Bushdid C, Magnasco MO, Vosshall LB, Keller A. Humans can discriminate more than 1 trillion olfactory stimuli. Science. 2014 Mar 21;343(6177):1370-2. doi: 10.1126/science.1249168. PubMed PMID: 24653035.

Genome editing

  1. Kim JM, Kim D, Kim S, Kim JS. Genotyping with CRISPR-Cas-derived RNA-guided endonucleases. Nat Commun. 2014 Jan 20;5:3157. doi: 10.1038/ncomms4157. PubMed PMID: 24445736.
  2. Bae S, Park J, Kim JS. Cas-OFFinder: A fast and versatile algorithm that searches for potential off-target sites of Cas9 RNA-guided endonucleases. Bioinformatics. 2014 Jan 24. [Epub ahead of print] PubMed PMID: 24463181.
  3. Fu Y, Sander JD, Reyon D, Cascio VM, Joung JK. Improving CRISPR-Cas nuclease specificity using truncated guide RNAs. Nat Biotechnol. 2014 Jan 26. doi: 10.1038/nbt.2808. [Epub ahead of print] PubMed PMID: 24463574.
  4. Jinek M, Jiang F, Taylor DW, Sternberg SH, Kaya E, Ma E, Anders C, Hauer M, Zhou K, Lin S, Kaplan M, Iavarone AT, Charpentier E, Nogales E, Doudna JA. Structures of Cas9 Endonucleases Reveal RNA-Mediated Conformational Activation.
    Science. 2014 Feb 6. [Epub ahead of print] PubMed PMID: 24505130.
  5. Sternberg SH, Redding S, Jinek M, Greene EC, Doudna JA. DNA interrogation by the CRISPR RNA-guided endonuclease Cas9. Nature. 2014 Jan 29. doi: 10.1038/nature13011. [Epub ahead of print] PubMed PMID: 24476820.
  6. Nishimasu H, Ran FA, Hsu PD, Konermann S, Shehata SI, Dohmae N, Ishitani R, Zhang F, Nureki O. Crystal Structure of Cas9 in Complex with Guide RNA and Target DNA. Cell. 2014 Feb 12. pii: S0092-8674(14)00156-1. doi: 10.1016/j.cell.2014.02.001. [Epub ahead of print] PubMed PMID: 24529477.
  7. Niu Y, Shen B, Cui Y, Chen Y, Wang J, Wang L, Kang Y, Zhao X, Si W, Li W, Xiang AP, Zhou J, Guo X, Bi Y, Si C, Hu B, Dong G, Wang H, Zhou Z, Li T, Tan T, Pu X, Wang F, Ji S, Zhou Q, Huang X, Ji W, Sha J. Generation of Gene-Modified Cynomolgus Monkey via Cas9/RNA-Mediated Gene Targeting in One-Cell Embryos. Cell. 2014 Jan 30;. [Epub ahead of print]
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Development

  1. Simões-Costa M, Tan-Cabugao J, Antoshechkin I, Sauka-Spengler T, Bronner ME. Transcriptome analysis reveals novel players in the cranial neural crest gene regulatory network. Genome Res. 2014 Jan 3. [Epub ahead of print] PubMed PMID: 24389048.
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  3. Pauli A, Norris ML, Valen E, Chew GL, Gagnon JA, Zimmerman S, Mitchell A, Ma J, Dubrulle J, Reyon D, Tsai SQ, Joung JK, Saghatelian A, Schier AF. Toddler: An Embryonic Signal That Promotes Cell Movement via Apelin Receptors. Science. 2014 Jan 9. [Epub ahead of print] PubMed PMID: 24407481.
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Genomics

  1. Zhang Y, Vastenhouw NL, Feng J, Fu K, Wang C, Ge Y, Pauli A, van Hummelen P, Schier AF, Liu XS. Canonical nucleosome organization at promoters forms during genome activation. Genome Res. 2014 Jan 8. [Epub ahead of print] PubMed PMID:
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Retinal degeneration/regeneration

  1. Sherpa T, Lankford T, McGinn TE, Hunter SS, Frey RA, Sun C, Ryan M, Robison BD, Stenkamp DL. Retinal regeneration is facilitated by the presence of surviving neurons. Dev Neurobiol. 2014 Feb 1. doi: 10.1002/dneu.22167. [Epub ahead of print] PubMed PMID: 24488694.
  2. Cruz NM, Yuan Y, Leehy BD, Baid R, Kompella U, Deangelis MM, Escher P, Haider NB. Modifier genes as therapeutics: the nuclear hormone receptor rev erb alpha (nr1d1) rescues nr2e3 associated retinal disease. PLoS One. 2014;9(1):e87942.

Zebrafish

  1. Mueller KP, Neuhauss SC. Sunscreen for Fish: Co-Option of UV Light Protection for Camouflage. PLoS One. 2014 Jan 29;9(1):e87372. doi: 10.1371/journal.pone.0087372. eCollection 2014. PubMed PMID: 24489905.

Stem cells

  1. Stress-Induced Stem Cell Method Questioned

 

In January, I visited the Center for Human Molecular Biology & Genetics at the Sichuan Academy of Medical Sciences & Sichuan Provincial People’s Hospital, Chengdu, China [Chinese website of the Institute]. It is a large provincial hospital in Sichuan Province with a population of 80.8 million. The hospital served approximately 3.6 million outpatient and emergency cases, and carried out almost 75,000 surgeries in 2011. With this number of patients, the Center for Human Molecular Biology & Genetics collected extensive human samples and has been a leader in genetics study in China.

Prof. Zhengli Yang, the vice president of the hospital and the director of Center for Human Molecular Biology & Genetics, invited both me and a renowned eye geneticist Prof. Shomi Bhattacharya to discuss our current research on eye disease therapy. I discussed how my lab is setting up the foundation to use zebrafish to screen eye drugs at Purdue. Prof. Bhattacharya discussed his work on gene therapy and stem cell therapy. It was a great experience to interact with a world leader in genetics whom discovered many of the key genes in retinal degeneration, and a top notch research institution in China.

Yuk Fai Leung lectured at the Center for Human Molecular Biology & Genetics, the Sichuan Academy of Medical Sciences & Sichuan Provincial People’s Hospital, Chengdu, China

 

Prof. Shomi Bhattacharya lectured at the Center for Human Molecular Biology & Genetics, the Sichuan Academy of Medical Sciences & Sichuan Provincial People’s Hospital, Chengdu, China. Prof. Zhenglin Yang (right) hosted the symposium.

 

Audience from the Center for Human Molecular Biology & Genetics, the Sichuan Academy of Medical Sciences & Sichuan Provincial People’s Hospital, Chengdu, China.

Image courtesy: Lue Xiang @ Leung lab

We have been hoping to set up the zebrafish electroretinography in the lab to facilitate our drug discovery program for a while. When Prof. Kwoon Wong  from the Kellogg Eye Center at the University of Michigan visited our department in early December, we seized the opportunity to learn from him and asked for his help to put the components together.

Image courtesy: Lue Xiang @ Leung lab

Dr. Don Ready kindly let us used his fly ERG setup for our test. Dr. Wong spent an afternoon trying different parameters and finally we have obtained a very decent ERG trace.  Many more friends and colleagues contributed to this endeavour, including Dr. Woody Walls who gathered a number of components and laid down the foundation over a period of time, lab members Prahatha Venkatraman and Lue Xiang who collected ample healthy embryos for the test, and Lue Xiang as the assistant of Dr. Wong during the course of experimentation. We would like to optimize this system further and are seeking highly motivated students with physiology and/or engineering background. We are particularly interested in the talents who like electrophysiology and would like to contribute their effort to identify new drugs for patients.

Left: Dr. Wong explained various ERG concepts to the lab members. Top right: lab members shared their research with Dr. Wong over lunch. Middle right: Dr. Wong worked on the ERG setup. Bottom right: Dr. Wong and Fai learned from Dr. Ready on several critical components of the ERG setup. Image courtesy: Lue Xiang @ Leung lab

Dr. Woody Walls instructed us on using LabChart for data collection. Image courtesy: Lue Xiang @ Leung lab

Neuroscience

  1. Widmann A, Schröger E. Filter effects and filter artifacts in the analysis of  electrophysiological data. Front Psychol. 2012 Jul 9;3:233. doi: 10.3389/fpsyg.2012.00233. eCollection 2012. PubMed PMID: 22787453; PubMed Central PMCID: PMC3391960.
  2. Hsiao EY, McBride SW, Hsien S, Sharon G, Hyde ER, McCue T, Codelli JA, Chow J, Reisman SE, Petrosino JF, Patterson PH, Mazmanian SK. Microbiota modulate behavioral and physiological abnormalities associated with neurodevelopmental disorders. Cell. 2013 Dec 19;155(7):1451-63. doi: 10.1016/j.cell.2013.11.024. Epub 2013 Dec 5. PubMed PMID: 24315484.
  3. Stern P. The heavily connected brain. Connection, connection, connection… Introduction. Science. 2013 Nov 1;342(6158):577. doi: 10.1126/science.342.6158.577. PubMed PMID: 24179217.
  4. Zatorre RJ. Predispositions and plasticity in music and speech learning: neural correlates and implications. Science. 2013 Nov 1;342(6158):585-9. doi: 10.1126/science.1238414. Review. PubMed PMID: 24179219.
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  6. DeCaen PG, Delling M, Vien TN, Clapham DE. Direct recording and molecular identification of the calcium channel of primary cilia. Nature. 2013 Dec 12;504(7479):315-8. doi: 10.1038/nature12832. PubMed PMID: 24336289.
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Genetics

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  2. Steijger T, Abril JF, Engström PG, Kokocinski F; RGASP Consortium, Abril JF, Akerman M, Alioto T, Ambrosini G, Antonarakis SE, Behr J, Bertone P, Bohnert R, Bucher P, Cloonan N, Derrien T, Djebali S, Du J, Dudoit S, Engström PG, Gerstein M, Gingeras TR, Gonzalez D, Grimmond SM, Guigó R, Habegger L, Harrow J, Hubbard TJ, Iseli C, Jean G, Kahles A, Kokocinski F, Lagarde J, Leng J, Lefebvre G, Lewis S, Mortazavi A, Niermann P, Rätsch G, Reymond A, Ribeca P, Richard H, Rougemont J, Rozowsky J, Sammeth M, Sboner A, Schulz MH, Searle SM, Solorzano ND, Solovyev V, Stanke M, Steijger T, Stevenson BJ, Stockinger H, Valsesia A, Weese D, White S, Wold BJ, Wu J, Wu TD, Zeller G, Zerbino D, Zhang MQ, Hubbard TJ, Guigó R, Harrow J, Bertone P. Assessment of transcript reconstruction methods for RNA-seq. Nat Methods. 2013 Dec;10(12):1177-84. doi: 10.1038/nmeth.2714. Epub 2013 Nov 3. PubMed PMID: 24185837; PubMed Central PMCID: PMC3851240.
  3. Engström PG, Steijger T, Sipos B, Grant GR, Kahles A; RGASP Consortium, Alioto T, Behr J, Bertone P, Bohnert R, Campagna D, Davis CA, Dobin A, Engström PG, Gingeras TR, Goldman N, Grant GR, Guigó R, Harrow J, Hubbard TJ, Jean G, Kahles A, Kosarev P, Li S, Liu J, Mason CE, Molodtsov V, Ning Z, Ponstingl H, Prins JF, Rätsch G, Ribeca P, Seledtsov I, Sipos B, Solovyev V, Steijger T, Valle G, Vitulo N, Wang K, Wu TD, Zeller G, Rätsch G, Goldman N, Hubbard TJ, Harrow J, Guigó R, Bertone P. Systematic evaluation of spliced alignment programs for RNA-seq data.  Nat Methods. 2013 Dec;10(12):1185-91. doi: 10.1038/nmeth.2722. Epub 2013 Nov 3. PubMed PMID: 24185836.
  4. Hnisz D, Abraham BJ, Lee TI, Lau A, Saint-André V, Sigova AA, Hoke HA, Young RA. Super-enhancers in the control of cell identity and disease. Cell. 2013 Nov 7;155(4):934-47. doi: 10.1016/j.cell.2013.09.053. Epub 2013 Oct 10. PubMed PMID: 24119843; PubMed Central PMCID: PMC3841062.
  5. Collins FS, Hamburg MA. First FDA authorization for next-generation sequencer. N Engl J Med. 2013 Dec 19;369(25):2369-71. doi: 10.1056/NEJMp1314561. Epub 2013 Nov 19. PubMed PMID: 24251383.

Imaging

  1. Chen B, Gilbert LA, Cimini BA, Schnitzbauer J, Zhang W, Li GW, Park J, Blackburn EH, Weissman JS, Qi LS, Huang B. Dynamic Imaging of Genomic Loci in Living Human Cells by an Optimized CRISPR/Cas System. Cell. 2013 Dec 19;155(7):1479-91. doi: 10.1016/j.cell.2013.12.001. PubMed PMID: 24360272.
  2. Ma H, Reyes-Gutierrez P, Pederson T. Visualization of repetitive DNA sequences in human chromosomes with transcription activator-like effectors. Proc Natl Acad Sci U S A. 2013 Dec 9. [Epub ahead of print] PubMed PMID: 24324157.
  3. Elia N, Ott C, Lippincott-Schwartz J. Incisive imaging and computation for cellular mysteries: lessons from abscission. Cell. 2013 Dec 5;155(6):1220-31. doi: 10.1016/j.cell.2013.11.011. PubMed PMID: 24315094.
  4. Marx V. Is super-resolution microscopy right for you? Nat Methods. 2013 Nov 26;10(12):1157-63. doi: 10.1038/nmeth.2756. PubMed PMID: 24296472.

Genome editing

  1. Auer TO, Duroure K, De Cian A, Concordet JP, Del Bene F. Highly efficient CRISPR/Cas9-mediated knock-in in zebrafish by homology-independent DNA repair. Genome Res. 2013 Dec 2. [Epub ahead of print] PubMed PMID: 24179142.
  2. Ran FA, Hsu PD, Wright J, Agarwala V, Scott DA, Zhang F. Genome engineering using the CRISPR-Cas9 system. Nat Protoc. 2013 Nov;8(11):2281-308. doi: 10.1038/nprot.2013.143. Epub 2013 Oct 24. PubMed PMID: 24157548.
  3. Cradick TJ, Fine EJ, Antico CJ, Bao G. CRISPR/Cas9 systems targeting ß-globin and CCR5 genes have substantial off-target activity. Nucleic Acids Res. 2013 Nov 1;41(20):9584-92. doi: 10.1093/nar/gkt714. Epub 2013 Aug 11. PubMed PMID: 23939622; PubMed Central PMCID: PMC3814385.
  4. 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 Apr;10(4):329-31. doi: 10.1038/nmeth.2374. Epub 2013 Feb 24. PubMed PMID: 23435258.

Gene regulatory network

  1. Fuxman Bass JI, Diallo A, Nelson J, Soto JM, Myers CL, Walhout AJ. Using networks to measure similarity between genes: association index selection. Nat Methods. 2013 Nov 26;10(12):1169-76. doi: 10.1038/nmeth.2728. PubMed PMID:24296474.

Genomics/Systems biology

  1. Monk JM, Charusanti P, Aziz RK, Lerman JA, Premyodhin N, Orth JD, Feist AM, Palsson BØ. Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments. Proc Natl Acad Sci U S A. 2013 Dec 10;110(50):20338-43. doi: 10.1073/pnas.1307797110. Epub 2013 Nov 25. PubMed PMID: 24277855.
  2. Zhang Y, Wong CH, Birnbaum RY, Li G, Favaro R, Ngan CY, Lim J, Tai E, Poh HM, Wong E, Mulawadi FH, Sung WK, Nicolis S, Ahituv N, Ruan Y, Wei CL. Chromatin connectivity maps reveal dynamic promoter-enhancer long-range associations. Nature. 2013 Dec 12;504(7479):306-10. doi: 10.1038/nature12716. Epub 2013 Nov 10. PubMed PMID: 24213634.
  3. Markson JS, Piechura JR, Puszynska AM, O’Shea EK. Circadian Control of Global Gene Expression by the Cyanobacterial Master Regulator RpaA. Cell. 2013 Dec 5;155(6):1396-408. doi: 10.1016/j.cell.2013.11.005. PubMed PMID: 24315105.

Zebrafish

  1. Xu C, Tabebordbar M, Iovino S, Ciarlo C, Liu J, Castiglioni A, Price E, Liu M, Barton ER, Kahn CR, Wagers AJ, Zon LI. A Zebrafish Embryo Culture System Defines Factors that Promote Vertebrate Myogenesis across Species. Cell. 2013 Nov 7;155(4):909-21. doi: 10.1016/j.cell.2013.10.023. PubMed PMID: 24209627.
  2. Wilkinson RN, Elworthy S, Ingham PW, van Eeden FJ. A method for high-throughput PCR-based genotyping of larval zebrafish tail biopsies. Biotechniques. 2013 Dec;55(6):314-6. doi: 10.2144/000114116. PubMed PMID: 24344681.
  3. Maaswinkel H, Zhu L, Weng W. Using an Automated 3D-tracking System to Record Individual and Shoals of Adult Zebrafish. J Vis Exp. 2013 Dec 5;(82). doi: 10.3791/50681. PubMed PMID: 24336189.

Evolution

  1. Williams TA, Foster PG, Cox CJ, Embley TM. An archaeal origin of eukaryotes supports only two primary domains of life. Nature. 2013 Dec 12;504(7479):231-6. doi: 10.1038/nature12779. PubMed PMID: 24336283.

Development

  1. Kearns NA, Genga RM, Enuameh MS, Garber M, Wolfe SA, Maehr R. Cas9 effector-mediated regulation of transcription and differentiation in human pluripotent stem cells. Development. 2014 Jan;141(1):219-23. doi: 10.1242/dev.103341. PubMed PMID: 24346702.
  2. Koyanagi-Aoi M, Ohnuki M, Takahashi K, Okita K, Noma H, Sawamura Y, Teramoto I, Narita M, Sato Y, Ichisaka T, Amano N, Watanabe A, Morizane A, Yamada Y, Sato T, Takahashi J, Yamanaka S. Differentiation-defective phenotypes revealed by large-scale analyses of human pluripotent stem cells. Proc Natl Acad Sci U S A. 2013 Nov 20. [Epub ahead of print] PubMed PMID: 24259714.
  3. Plouhinec JL, Zakin L, Moriyama Y, De Robertis EM. Chordin forms a self-organizing morphogen gradient in the extracellular space between ectoderm and mesoderm in the Xenopus embryo. Proc Natl Acad Sci U S A. 2013 Nov 27. [Epub ahead of print] PubMed PMID: 24284174.
  4. Tan L, Zong C, Xie XS. Rare event of histone demethylation can initiate singular gene expression of olfactory receptors. Proc Natl Acad Sci U S A. 2013 Dec 16. [Epub ahead of print] PubMed PMID: 24344257.

Retina

  1. Weber A, Hochmann S, Cimalla P, Gärtner M, Kuscha V, Hans S, Geffarth M, Kaslin J, Koch E, Brand M. Characterization of light lesion paradigms and optical coherence tomography as tools to study adult retina regeneration in zebrafish. PLoS One. 2013 Nov 26;8(11):e80483. doi: 10.1371/journal.pone.0080483. PubMed PMID: 24303018; PubMed Central PMCID: PMC3841302.

Funding

  1. Mervis J, Malakoff D. Science funding. U.S. budget deal offers researchers some sequester relief. Science. 2013 Dec 20;342(6165):1426-7. doi: 10.1126/science.342.6165.1426. PubMed PMID: 24357280.

Medicine

  1. Johnson SC, Yanos ME, Kayser EB, Quintana A, Sangesland M, Castanza A, Uhde L, Hui J, Wall VZ, Gagnidze A, Oh K, Wasko BM, Ramos FJ, Palmiter RD, Rabinovitch PS, Morgan PG, Sedensky MM, Kaeberlein M. mTOR inhibition alleviates mitochondrial disease in a mouse model of Leigh syndrome. Science. 2013 Dec 20;342(6165):1524-8. doi: 10.1126/science.1244360. Epub 2013 Nov 14. PubMed PMID: 24231806.
    • Vafai SB, Mootha VK. Medicine. A common pathway for a rare disease? Science. 2013 Dec 20;342(6165):1453-4. doi: 10.1126/science.1248449. PubMed PMID: 24357304.

Biochemistry

  1. Xie XS. Biochemistry. Enzyme kinetics, past and present. Science. 2013 Dec 20;342(6165):1457-9. doi: 10.1126/science.1248859. PubMed PMID: 24357307.