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. 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.

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.

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.

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.

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.

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.

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. 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.


				

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. 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.

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.

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.

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. 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.

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

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.

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.

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. 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. 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. 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. 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. 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. 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.

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.

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.

 

 

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.

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!

 

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.

 

Zebrafish

  1. Adatto I, Krug L, Zon LI. The Red Light District and Its Effects on Zebrafish Reproduction. Zebrafish. 2016 Mar 15. [Epub ahead of print] PubMed PMID: 26978703.
  2. Brocal I, White RJ, Dooley CM, Carruthers SN, Clark R, Hall A, Busch-Nentwich EM, Stemple DL, Kettleborough RN. Efficient identification of CRISPR/Cas9-induced insertions/deletions by direct germline screening in zebrafish. BMC Genomics. 2016 Mar 24;17(1):259. doi: 10.1186/s12864-016-2563-z. PubMed PMID: 27009152.
  3. Hoshijima K, Jurynec MJ, Grunwald DJ. Precise Editing of the Zebrafish Genome Made Simple and Efficient. Dev Cell. 2016 Mar 21;36(6):654-67. doi: 10.1016/j.devcel.2016.02.015. PubMed PMID: 27003937.
  4. Varshney GK, Zhang S, Pei W, Adomako-Ankomah A, Fohtung J, Schaffer K, Carrington B, Maskeri A, Slevin C, Wolfsberg T, Ledin J, Sood R, Burgess SM. CRISPRz: a database of zebrafish validated sgRNAs. Nucleic Acids Res. 2016 Jan 4;44(D1):D822-6. doi: 10.1093/nar/gkv998. Epub 2015 Oct 4. PubMed PMID: 26438539; PubMed Central PMCID: PMC4702947.

Retina

  1. Mullally M, Albrecht C, Horton M, Laboissonniere LA, Goetz JJ, Chowdhury R, Manning A, Wester AK, Bose Q, Trimarchi JM. Expression Profiling of Developing Zebrafish Retinal Cells. Zebrafish. 2016 Mar 16. [Epub ahead of print] PubMed PMID: 26982811.

Disease

  1. Roy DS, Arons A, Mitchell TI, Pignatelli M, Ryan TJ, Tonegawa S. Memory retrieval by activating engram cells in mouse models of early Alzheimer’s disease. Nature. 2016 Mar 16. doi: 10.1038/nature17172. [Epub ahead of print] PubMed PMID: 26982728.

Molecular Biology

  1. Louder RK, He Y, López-Blanco JR, Fang J, Chacón P, Nogales E. Structure of promoter-bound TFIID and model of human pre-initiation complex assembly. Nature. 2016 Mar 23. doi: 10.1038/nature17394. [Epub ahead of print] PubMed PMID: 27007846.

Cell Biology

  1. Norris DP, Jackson PK. Cell biology: Calcium contradictions in cilia. Nature. 2016 Mar 23. doi: 10.1038/nature17313. [Epub ahead of print] PubMed PMID: 27007852.

Systems Biology

  1. Hashimoto M, Nozoe T, Nakaoka H, Okura R, Akiyoshi S, Kaneko K, Kussell E, Wakamoto Y. Noise-driven growth rate gain in clonal cellular populations. Proc Natl Acad Sci U S A. 2016 Mar 7. pii: 201519412. [Epub ahead of print] PubMed PMID: 26951676.
  2. Davidi D, Noor E, Liebermeister W, Bar-Even A, Flamholz A, Tummler K, Barenholz U, Goldenfeld M, Shlomi T, Milo R. Global characterization of in vivo enzyme catalytic rates and their correspondence to in vitro kcat measurements. Proc Natl Acad Sci U S A. 2016 Mar 7. pii: 201514240. [Epub ahead of print] PubMed PMID: 26951675.

Genome editing

  1. Hoshijima K, Jurynec MJ, Grunwald DJ. Precise Editing of the Zebrafish Genome Made Simple and Efficient. Dev Cell. 2016 Mar 21;36(6):654-67. doi: 10.1016/j.devcel.2016.02.015. PubMed PMID: 27003937.
  2. Varshney GK, Zhang S, Pei W, Adomako-Ankomah A, Fohtung J, Schaffer K, Carrington B, Maskeri A, Slevin C, Wolfsberg T, Ledin J, Sood R, Burgess SM. CRISPRz: a database of zebrafish validated sgRNAs. Nucleic Acids Res. 2016 Jan 4;44(D1):D822-6. doi: 10.1093/nar/gkv998. Epub 2015 Oct 4. PubMed PMID: 26438539; PubMed Central PMCID: PMC4702947.


				

Several interesting and good discussions on publishing life science articles on BioRxiv, a preprint server based on the arXiv model:

From the New York Times: “Handful of Biologists Went Rogue and Published Directly to Internet“.

From Mike Eisen’s blog.

Eye diseases

  1. Lin H, Ouyang H, Zhu J, Huang S, Liu Z, Chen S, Cao G, Li G, Signer RA, Xu Y, Chung C, Zhang Y, Lin D, Patel S, Wu F, Cai H, Hou J, Wen C, Jafari M, Liu X, Luo L, Zhu J, Qiu A, Hou R, Chen B, Chen J, Granet D, Heichel C, Shang F, Li X, Krawczyk M, Skowronska-Krawczyk D, Wang Y, Shi W, Chen D, Zhong Z, Zhong S, Zhang L, Chen S, Morrison SJ, Maas RL, Zhang K, Liu Y. Lens regeneration using endogenous stem cells with gain of visual function. Nature. 2016 Mar 9. doi: 10.1038/nature17181. [Epub ahead of print] PubMed PMID: 26958831. News release: Stem Cells Regenerate Human Lens After Cataract Surgery, Restoring Vision
  2. Hayashi R, Ishikawa Y, Sasamoto Y, Katori R, Nomura N, Ichikawa T, Araki S, Soma T, Kawasaki S, Sekiguchi K, Quantock AJ, Tsujikawa M, Nishida K. Co-ordinated ocular development from human iPS cells and recovery of corneal function. Nature. 2016 Mar 9. doi: 10.1038/nature17000. [Epub ahead of print] PubMed PMID: 26958835.

Stem cells

  1. Sridhar A, Ohlemacher SK, Langer KB, Meyer JS. Robust Differentiation of mRNA-Reprogrammed Human Induced Pluripotent Stem Cells Toward a Retinal Lineage. Stem Cells Transl Med. 2016 Mar 1. pii: sctm.2015-0093. [Epub ahead of print] PubMed PMID: 26933039.
  2. Sagi I, Chia G, Golan-Lev T, Peretz M, Weissbein U, Sui L, Sauer MV, Yanuka O, Egli D, Benvenisty N. Derivation and differentiation of haploid human embryonic stem cells. Nature. 2016 Mar 16. doi: 10.1038/nature17408. [Epub ahead of print] PubMed PMID: 26982723.

Development

  1. Pueschel R, Coraggio F, Meister P. From single genes to entire genomes: the search for a function of nuclear organization. Development. 2016 Mar 15;143(6):910-23. doi: 10.1242/dev.129007. Review. PubMed PMID: 26980791.
  2. Salomon DR. A CRISPR Way to Block PERVs – Engineering Organs for Transplantation. N Engl J Med. 2016 Mar 17;374(11):1089-1091. PubMed PMID: 26981939.

Neuroscience

  1. Mullins C, Fishell G, Tsien RW. Unifying Views of Autism Spectrum Disorders: A Consideration of Autoregulatory Feedback Loops. Neuron. 2016 Mar 16;89(6):1131-56. doi: 10.1016/j.neuron.2016.02.017. Review. PubMed PMID: 26985722.
  2. Hazen JL, Faust GG, Rodriguez AR, Ferguson WC, Shumilina S, Clark RA, Boland MJ, Martin G, Chubukov P, Tsunemoto RK, Torkamani A, Kupriyanov S, Hall IM, Baldwin KK. The Complete Genome Sequences, Unique Mutational Spectra, and Developmental Potency of Adult Neurons Revealed by Cloning. Neuron. 2016 Mar 16;89(6):1223-36. doi: 10.1016/j.neuron.2016.02.004. Epub 2016 Mar 3. PubMed PMID: 26948891; PubMed Central PMCID: PMC4795965.

Mathematics

  1. Castelvecchi D. Fermat’s last theorem earns Andrew Wiles the Abel Prize. Nature. 2016 Mar 17;531(7594):287. doi: 10.1038/nature.2016.19552. PubMed PMID: 26983518.