Posts tagged ‘retinal regeneration’


  1. Blomen VA, Májek P, Jae LT, Bigenzahn JW, Nieuwenhuis J, Staring J, Sacco R, van Diemen FR, Olk N, Stukalov A, Marceau C, Janssen H, Carette JE, Bennett KL, Colinge J, Superti-Furga G, Brummelkamp TR. Gene essentiality and synthetic lethality in haploid human cells. Science. 2015 Nov 27;350(6264):1092-6. doi: 10.1126/science.aac7557. Epub 2015 Oct 15. PubMed PMID: 26472760.
  2. Wang T, Birsoy K, Hughes NW, Krupczak KM, Post Y, Wei JJ, Lander ES, Sabatini DM. Identification and characterization of essential genes in the human genome. Science. 2015 Nov 27;350(6264):1096-101. doi: 10.1126/science.aac7041. Epub 2015 Oct 15. PubMed PMID: 26472758; PubMed Central PMCID: PMC4662922.
    • Commentary: Boone C, Andrews BJ. HUMAN GENOME. The indispensable genome. Science. 2015 Nov 27;350(6264):1028-9. doi: 10.1126/science.aad7925. PubMed PMID: 26612934.
  3. Hart T, Chandrashekhar M, Aregger M, Steinhart Z, Brown KR, MacLeod G, Mis M, Zimmermann M, Fradet-Turcotte A, Sun S, Mero P, Dirks P, Sidhu S, Roth FP, Rissland OS, Durocher D, Angers S, Moffat J. High-Resolution CRISPR Screens Reveal Fitness Genes and Genotype-Specific Cancer Liabilities. Cell. 2015 Nov 25. pii: S0092-8674(15)01495-6. doi: 10.1016/j.cell.2015.11.015. [Epub ahead of print] PubMed PMID: 26627737.


  1. Barker AJ, Baier H. Sensorimotor Decision Making in the Zebrafish Tectum. Curr Biol. 2015 Nov 2;25(21):2804-14. doi: 10.1016/j.cub.2015.09.055. Epub 2015 Oct 22. PubMed PMID: 26592341.


  1. Lahne M, Li J, Marton RM, Hyde DR. Actin-Cytoskeleton- and Rock-Mediated INM Are Required for Photoreceptor Regeneration in the Adult Zebrafish Retina. J Neurosci. 2015 Nov 25;35(47):15612-34. doi: 10.1523/JNEUROSCI.5005-14.2015. PubMed PMID: 26609156.
  2. Wilson SG, Wen W, Kastoori LP, Morris AC. Tracking the fate of her4 expressing cells in the regenerating retina using her4:Kaede zebrafish. Exp Eye Res. 2015 Nov 23. pii: S0014-4835(15)30061-0. doi: 10.1016/j.exer.2015.11.002. [Epub ahead of print] PubMed PMID: 26616101.
  3. Aldiri I, Ajioka I, Xu B, Zhang J, Chen X, Benavente C, Finkelstein D, Johnson D, Akiyama J, Pennacchio LA, Dyer MA. Brg1 coordinates multiple processes during retinogenesis and is a tumor suppressor in retinoblastoma. Development. 2015 Dec 1;142(23):4092-106. doi: 10.1242/dev.124800. PubMed PMID: 26628093.

Genome editing

  1. van der Oost J, Brouns SJ. CRISPR sabotage. Genome Biol. 2015 Nov 9;16(1):248. doi: 10.1186/s13059-015-0820-0. PubMed PMID: 26553202; PubMed Central PMCID: PMC4638106.
  2. Kühn R, Chu VT. Pop in, pop out: a novel gene-targeting strategy for use with CRISPR-Cas9. Genome Biol. 2015 Nov 10;16(1):244. doi: 10.1186/s13059-015-0810-2. PubMed PMID: 26553112; PubMed Central PMCID: PMC4640370.
  3. Xi L, Schmidt JC, Zaug AJ, Ascarrunz DR, Cech TR. A novel two-step genome editing strategy with CRISPR-Cas9 provides new insights into telomerase action and TERT gene expression. Genome Biol. 2015 Nov 10;16(1):231. doi: 10.1186/s13059-015-0791-1. PubMed PMID: 26553065; PubMed Central PMCID: PMC4640169.
  4. Graham DB, Root DE. Resources for the design of CRISPR gene editing experiments. Genome Biol. 2015 Nov 27;16(1):260. doi: 10.1186/s13059-015-0823-x. PubMed PMID: 26612492; PubMed Central PMCID: PMC4661947.
  5. Friedland AE, Baral R, Singhal P, Loveluck K, Shen S, Sanchez M, Marco E, Gotta GM, Maeder ML, Kennedy EM, Kornepati AV, Sousa A, Collins MA, Jayaram H, Cullen BR, Bumcrot D. Characterization of Staphylococcus aureus Cas9: a smaller Cas9 for all-in-one adeno-associated virus delivery and paired nickase applications. Genome Biol. 2015 Nov 24;16(1):257. doi: 10.1186/s13059-015-0817-8. PubMed PMID: 26596280; PubMed Central PMCID: PMC4657203.


  1. Briscoe J, Small S. Morphogen rules: design principles of gradient-mediated embryo patterning. Development. 2015 Dec 1;142(23):3996-4009. doi: 10.1242/dev.129452. Review. PubMed PMID: 26628090.


Gene regulatory network

  1. Barsi JC, Tu Q, Davidson E. General approach for in vivo recovery of cell type specific effector gene sets. Genome Res. 2014 Mar 6. [Epub ahead of print] PubMed PMID: 24604781.


  1. Project to Improve Poor Children’s Intellect Led to Better Health, Data Show
  2. Begley CG, Ellis LM. Drug development: Raise standards for preclinical cancer research. Nature. 2012 Mar 28;483(7391):531-3. doi: 10.1038/483531a. PubMed PMID: 22460880.


  1. Portugues R, Feierstein CE, Engert F, Orger MB. Whole-brain activity maps reveal stereotyped, distributed networks for visuomotor behavior. Neuron. 2014 Mar 19;81(6):1328-43. doi: 10.1016/j.neuron.2014.01.019. PubMed PMID: 24656252.
  2. Lancaster MA, Renner M, Martin CA, Wenzel D, Bicknell LS, Hurles ME, Homfray T, Penninger JM, Jackson AP, Knoblich JA. Cerebral organoids model human brain development and microcephaly. Nature. 2013 Sep 19;501(7467):373-9. doi: 10.1038/nature12517. Epub 2013 Aug 28. PubMed PMID: 23995685; PubMed Central
    PMCID: PMC3817409.

    • Brüstle O. Developmental neuroscience: Miniature human brains. Nature. 2013
      Sep 19;501(7467):319-20. doi: 10.1038/nature12552. Epub 2013 Aug 28. PubMed PMID: 23995687.

Genome editing

  1. Auer TO, Del Bene F. CRISPR/Cas9 and TALEN-mediated knock-in approaches in zebrafish. Methods. 2014 Apr 1. pii: S1046-2023(14)00129-7. doi: 10.1016/j.ymeth.2014.03.027. [Epub ahead of print] PubMed PMID: 24704174.
  2. Zhou Y, Zhu S, Cai C, Yuan P, Li C, Huang Y, Wei W. High-throughput screening
    of a CRISPR/Cas9 library for functional genomics in human cells. Nature. 2014 Apr
    9. doi: 10.1038/nature13166. [Epub ahead of print] PubMed PMID: 24717434.
  3. Yin H, Xue W, Chen S, Bogorad RL, Benedetti E, Grompe M, Koteliansky V, Sharp
    PA, Jacks T, Anderson DG. Genome editing with Cas9 in adult mice corrects a disease mutation and phenotype. Nat Biotechnol. 2014 Mar 30. doi: 10.1038/nbt.2884. [Epub ahead of print] PubMed PMID: 24681508.

Stem cells

  1. Becker S, Jayaram H, Limb GA. Recent Advances towards the Clinical Application of Stem Cells for Retinal Regeneration. Cells. 2012 Oct 18;1(4):851-73. doi: 10.3390/cells1040851. PubMed PMID: 24710533.
  2. Assawachananont J et al., Transplantation of Embryonic and Induced Pluripotent Stem Cell-Derived 3D Retinal Sheets into Retinal Degenerative Mice. Stem Cell Reports. 2014; 2: 662-674.

Retinal degeneration

  1. Wasfy MM, Matsui JI, Miller J, Dowling JE, Perkins BD. myosin 7aa(-/-) mutant zebrafish show mild photoreceptor degeneration and reduced electroretinographic responses. Exp Eye Res. 2014 Apr 1. pii: S0014-4835(14)00083-9. doi: 10.1016/j.exer.2014.03.007. [Epub ahead of print] PubMed PMID: 24698764.

Retinal development

  1. Weber IP, Ramos AP, Strzyz PJ, Leung LC, Young S, Norden C. Mitotic Position and Morphology of Committed Precursor Cells in the Zebrafish Retina Adapt to Architectural Changes upon Tissue Maturation. Cell Rep. 2014 Apr 2. pii: S2211-1247(14)00192-2. doi: 10.1016/j.celrep.2014.03.014. [Epub ahead of print] PubMed PMID: 24703843.
  2. Almeida AD, Boije H, Chow RW, He J, Tham J, Suzuki SC, Harris WA. Spectrum of Fates: a new approach to the study of the developing zebrafish retina. Development. 2014 Apr 9. [Epub ahead of print] PubMed PMID: 24718991.
  3. Yoshimatsu T, Williams PR, D’Orazi FD, Suzuki SC, Fadool JM, Allison WT, Raymond PA, Wong RO. Transmission from the dominant input shapes the stereotypic ratio of photoreceptor inputs onto horizontal cells. Nat Commun. 2014 May 15;5:3699. doi: 10.1038/ncomms4699. PubMed PMID: 24832361.


  1. Bianchi E, Doe B, Goulding D, Wright GJ. Juno is the egg Izumo receptor and is essential for mammalian fertilization. Nature. 2014 Apr 24;508(7497):483-7. doi: 10.1038/nature13203. Epub 2014 Apr 16. PubMed PMID: 24739963; PubMed Central PMCID: PMC3998876.

Genetics/Synthetic biology

  1. Malyshev DA, Dhami K, Lavergne T, Chen T, Dai N, Foster JM, Corrêa IR Jr, Romesberg FE. A semi-synthetic organism with an expanded genetic alphabet. Nature. 2014 May 15;509(7500):385-8. doi: 10.1038/nature13314. Epub 2014 May 7. PubMed PMID: 24805238.
    • Commentary: Thyer R, Ellefson J. Synthetic biology: New letters for life’s alphabet. Nature. 2014 May 15;509(7500):291-2. doi: 10.1038/nature13335. Epub 2014 May 7. PubMed PMID: 24805244.

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]
  8. Hai T, Teng F, Guo R, Li W, Zhou Q. One-step generation of knockout pigs by zygote injection of CRISPR/Cas system. Cell Res. 2014 Jan 31;. [Epub ahead of print]
  9. Heigwer F, Kerr G, Boutros M. E-CRISP: fast CRISPR target site identification. Nat Methods. 2014 Jan 30;11(2):122-3.
  10. Nakagawa Y, Yamamoto T, Suzuki K, Araki K, Takeda N, Ohmuraya M, Sakuma T. Screening Methods to Identify TALEN-Mediated Knockout Mice. Exp Anim. 2014;63(1):79-84. PubMed PMID: 24521866.


  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.
  2. Umulis DM, Othmer HG. Mechanisms of scaling in pattern formation. Development. 2013 Dec;140(24):4830-43. doi: 10.1242/dev.100511. Review. PubMed PMID: 24301464; PubMed Central PMCID: PMC3848184.
  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.
  4. Dias AS, de Almeida I, Belmonte JM, Glazier JA, Stern CD. Somites without a clock. Science. 2014 Feb 14;343(6172):791-5. doi: 10.1126/science.1247575. Epub 2014 Jan 9. PubMed PMID: 24407478.
    • Kondo S. Developmental biology. Self-organizing somites. Science. 2014 Feb 14;343(6172):736-7. doi: 10.1126/science.1250245. PubMed PMID: 24531958.


  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:

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.


  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



  1. Balaskas N, Ribeiro A, Panovska J, Dessaud E, Sasai N, Page KM, Briscoe J, Ribes V. Gene regulatory logic for reading the sonic hedgehog signaling gradient in the vertebrate neural tube. Cell. 2012 Jan 20;148(1-2):273-84. PubMed PMID: 22265416; PubMed Central PMCID: PMC3267043.
  2. Lassar A. Finding MyoD with a little help from my friends. Nat Cell Biol. 2012 Feb 2;14(2):116. doi: 10.1038/ncb2421. PubMed PMID: 22298038.
    • An interesting personal account of the discovery of MyoD.

Retinal Regeneration

  1. Qin Z, Kidd AR 3rd, Thomas JL, Poss KD, Hyde DR, Raymond PA, Thummel R. FGF signaling regulates rod photoreceptor cell maintenance and regeneration in zebrafish. Exp Eye Res. 2011 Nov;93(5):726-34. Epub 2011 Sep 17. PubMed PMID: 21945172; PubMed Central PMCID: PMC3243491.
  2. Hochmann S, Kaslin J, Hans S, Weber A, Machate A, Geffarth M, Funk RH, Brand M. Fgf Signaling is Required for Photoreceptor Maintenance in the Adult Zebrafish Retina. PLoS One. 2012;7(1):e30365. Epub 2012 Jan 26. PubMed PMID: 22291943; PubMed Central PMCID: PMC3266925.


  1. Visscher PM, Brown MA, McCarthy MI, Yang J. Five Years of GWAS Discovery. Am J Hum Genet. 2012 Jan 13;90(1):7-24. PubMed PMID: 22243964.


  1. Baker M. Structural variation: the genome’s hidden architecture. Nat Methods. 2012 Jan 30;9(2):133-7. doi: 10.1038/nmeth.1858. PubMed PMID: 22290183.
  2. Xiong Q, Ancona N, Hauser ER, Mukherjee S, Furey TS. Integrating genetic and gene expression evidence into genome-wide association analysis of gene sets. Genome Res. 2012 Feb;22(2):386-97. Epub 2011 Sep 22. PubMed PMID: 21940837.


  1. Cox S, Rosten E, Monypenny J, Jovanovic-Talisman T, Burnette DT, Lippincott-Schwartz J, Jones GE, Heintzmann R. Bayesian localization microscopy reveals nanoscale podosome dynamics. Nat Methods. 2011 Dec 4;9(2):195-200. doi: 10.1038/nmeth.1812. PubMed PMID: 22138825.
    • Commentary: Lidke KA. Super resolution for common probes and common microscopes. Nat Methods. 2012 Jan 30;9(2):139-41. doi: 10.1038/nmeth.1863. PubMed PMID: 22290184.
    • This looks like an interesting article that talks about how to use common fluorescent setup for super-resolution imaging.
  2. Xu K, Babcock HP, Zhuang X. Dual-objective STORM reveals three-dimensional filament organization in the actin cytoskeleton. Nat Methods. 2012 Jan 8;9(2):185-8. doi: 10.1038/nmeth.1841. PubMed PMID: 22231642.

Gene Regulatory Network

  1. Damle SS, Davidson EH. Synthetic in vivo validation of gene network circuitry. Proc Natl Acad Sci U S A. 2012 Jan 11. [Epub ahead of print] PubMed PMID: 22238426.
  2. Weaver J. New signaling chemicals spur worms to seek company. PLoS Biol. 2012 Jan;10(1):e1001240. Epub 2012 Jan 10. PubMed PMID: 22253575; PubMed Central PMCID: PMC3254651.
  3. Gross L. Built-in Timer Delays Differentiation. PLoS Biol. 2012 Jan;10(1):e1001254. Epub 2012 Jan 31. PubMed PMID: 22303284.
  4. van Dijk AD, van Mourik S, van Ham RC. Mutational robustness of gene regulatory networks. PLoS One. 2012;7(1):e30591. Epub 2012 Jan 25. PubMed PMID: 22295094; PubMed Central PMCID: PMC3266278.


  1. Heidinger BJ, Blount JD, Boner W, Griffiths K, Metcalfe NB, Monaghan P. Telomere length in early life predicts lifespan. Proc Natl Acad Sci U S A. 2012 Jan 9. [Epub ahead of print] PubMed PMID: 22232671.


  1. Curtis CD, Griffin CT. The chromatin-remodeling enzymes BRG1 and CHD4 antagonistically regulate vascular Wnt signaling. Mol Cell Biol. 2012 Jan 30. [Epub ahead of print] PubMed PMID: 22290435.


  1. Macilwain C. Funding in 2012: “great recession” starts to bite. Cell. 2012 Jan 20;148(1-2):14-6. PubMed PMID: 22265395.