Posts tagged ‘retina’

Stem cells

A young scientist in Japan has found a simple approach to make totipotent stem cells by lowering the pH.

Stimulus-triggered fate conversion of somatic cells into pluripotency. Nature

Bidirectional developmental potential in reprogrammed cells with acquired pluripotency. Nature

Retina

  1. Raymond PA, Colvin SM, Jabeen Z, Nagashima M, Barthel LK, Hadidjojo J, Popova L, Pejaver VR, Lubensky DK. Patterning the cone mosaic array in zebrafish retina requires specification of ultraviolet-sensitive cones. PLoS One. 2014 Jan 21;9(1):e85325. doi: 10.1371/journal.pone.0085325. eCollection 2014 Jan 21. PubMed PMID: 24465536.
  2. Centanin L, Wittbrodt J. Retinal neurogenesis. Development. 2014 Jan;141(2):241-4. doi: 10.1242/dev.083642. PubMed PMID: 24381194.
  3. Lenkowski JR, Raymond PA. Müller glia: Stem cells for generation and regeneration of retinal neurons in teleost fish. Prog Retin Eye Res. 2014 Jan 8.  pii: S1350-9462(14)00002-0. doi: 10.1016/j.preteyeres.2013.12.007. [Epub ahead of
    print] PubMed PMID: 24412518.

Genome-editing

  1. Hruscha A, Krawitz P, Rechenberg A, Heinrich V, Hecht J, Haass C, Schmid B. Efficient CRISPR/Cas9 genome editing with low off-target effects in zebrafish. Development. 2013 Dec;140(24):4982-7. doi: 10.1242/dev.099085. Epub 2013 Nov 20. PubMed PMID: 24257628.
  2. Roberts JA, Miguel-Escalada I, Slovik KJ, Walsh KT, Hadzhiev Y, Sanges R, Stupka E, Marsh EK, Balciuniene J, Balciunas D, Müller F. Targeted transgene integration overcomes variability of position effects in zebrafish. Development. 2014 Feb;141(3):715-24. doi: 10.1242/dev.100347. PubMed PMID: 24449846.
  3. Wang T, Wei JJ, Sabatini DM, Lander ES. Genetic screens in human cells using the CRISPR-Cas9 system. Science. 2014 Jan 3;343(6166):80-4. doi: 10.1126/science.1246981. Epub 2013 Dec 12. PubMed PMID: 24336569.
  4. Shalem O, Sanjana NE, Hartenian E, Shi X, Scott DA, Mikkelsen TS, Heckl D, Ebert BL, Root DE, Doench JG, Zhang F. Genome-scale CRISPR-Cas9 knockout screening in human cells. Science. 2014 Jan 3;343(6166):84-7. doi: 10.1126/science.1247005. Epub 2013 Dec 12. PubMed PMID: 24336571.
  5. Wu Y, Liang D, Wang Y, Bai M, Tang W, Bao S, Yan Z, Li D, Li J. Correction of a genetic disease in mouse via use of CRISPR-Cas9. Cell Stem Cell. 2013 Dec 5;13(6):659-62. doi: 10.1016/j.stem.2013.10.016. PubMed PMID: 24315440.

Neuroscience

  1. Dias BG, Ressler KJ. Parental olfactory experience influences behavior and neural structure in subsequent generations. Nat Neurosci. 2014 Jan;17(1):89-96. doi: 10.1038/nn.3594. Epub 2013 Dec 1. PubMed PMID: 24292232.

Gene therapy

  1. Maclaren RE, Groppe M, Barnard AR, Cottriall CL, Tolmachova T, Seymour L, Clark KR, During MJ, Cremers FP, Black GC, Lotery AJ, Downes SM, Webster AR, Seabra MC. Retinal gene therapy in patients with choroideremia: initial findings from a phase 1/2 clinical trial. Lancet. 2014 Jan 15. pii: S0140-6736(13)62117-0. doi: 10.1016/S0140-6736(13)62117-0. [Epub ahead of print] PubMed PMID: 24439297.

 

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.
  5. Turk-Browne NB. Functional interactions as big data in the human brain.Science. 2013 Nov 1;342(6158):580-4. doi: 10.1126/science.1238409. Review. PubMed PMID: 24179218.
  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.
  7. Delling M, DeCaen PG, Doerner JF, Febvay S, Clapham DE. Primary cilia are specialized calcium signalling organelles. Nature. 2013 Dec 12;504(7479):311-4. doi: 10.1038/nature12833. PubMed PMID: 24336288.

Genetics

  1. Korf I. Genomics: the state of the art in RNA-seq analysis. Nat Methods. 2013 Nov 26;10(12):1165-6. doi: 10.1038/nmeth.2735. PubMed PMID: 24296473.
  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.

Stem cells

  1. Hou P, Li Y, Zhang X, Liu C, Guan J, Li H, Zhao T, Ye J, Yang W, Liu K, Ge J, Xu J, Zhang Q, Zhao Y, Deng H. Pluripotent stem cells induced from mouse somatic cells by small-molecule compounds. Science. 2013 Aug 9;341(6146):651-4. doi: 10.1126/science.1239278. Epub 2013 Jul 18. PubMed PMID: 23868920.

Neuroscience

  1. Shomrat T, Levin M. An automated training paradigm reveals long-term memory in planaria and its persistence through head regeneration. J Exp Biol. 2013 Jul 2. [Epub ahead of print] PubMed PMID: 23821717.
  2. Esposti F, Johnston J, Rosa JM, Leung KM, Lagnado L. Olfactory Stimulation Selectively Modulates the OFF Pathway in the Retina of Zebrafish. Neuron. 2013 Jul 10;79(1):97-110. doi: 10.1016/j.neuron.2013.05.001. PubMed PMID: 23849198.
    • Commentary: “Dowling JE. Olfaction and Vision Meet in the Retina. Neuron. 2013 Jul 10;79(1):1-3. doi: 10.1016/j.neuron.2013.06.024. PubMed PMID: 23849191.

Retina

  1. Endeman D, Klaassen LJ, Kamermans M. Action spectra of zebrafish cone photoreceptors. PLoS One. 2013 Jul 5;8(7):e68540. doi: 10.1371/journal.pone.0068540. Print 2013. PubMed PMID: 23861916; PubMed Central PMCID: PMC3702584.

Genetics

  1. Poznik GD, Henn BM, Yee MC, Sliwerska E, Euskirchen GM, Lin AA, Snyder M, Quintana-Murci L, Kidd JM, Underhill PA, Bustamante CD. Sequencing Y chromosomes resolves discrepancy in time to common ancestor of males versus females. Science. 2013 Aug 2;341(6145):562-5. doi: 10.1126/science.1237619. PubMed PMID: 23908239.
  2. Francalacci P, Morelli L, Angius A, Berutti R, Reinier F, Atzeni R, Pilu R, Busonero F, Maschio A, Zara I, Sanna D, Useli A, Urru MF, Marcelli M, Cusano R, Oppo M, Zoledziewska M, Pitzalis M, Deidda F, Porcu E, Poddie F, Kang HM, Lyons R, Tarrier B, Gresham JB, Li B, Tofanelli S, Alonso S, Dei M, Lai S, Mulas A, Whalen MB, Uzzau S, Jones C, Schlessinger D, Abecasis GR, Sanna S, Sidore C, Cucca F. Low-pass DNA sequencing of 1200 Sardinians reconstructs European Y-chromosome phylogeny. Science. 2013 Aug 2;341(6145):565-9. doi: 10.1126/science.1237947. PubMed PMID: 23908240.
  3. Fu Y, Foden JA, Khayter C, Maeder ML, Reyon D, Joung JK, Sander JD. High-frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells. Nat Biotechnol. 2013 Jun 23. doi: 10.1038/nbt.2623. [Epub ahead of print] PubMed PMID: 23792628.

Genetics

  1. 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 Feb 24. doi: 10.1038/nmeth.2374. [Epub ahead of print] PubMed PMID: 23435258.
  2. Chang N, Sun C, Gao L, Zhu D, Xu X, Zhu X, Xiong JW, Xi JJ. Genome editing with RNA-guided Cas9 nuclease in Zebrafish embryos. Cell Res. 2013 Apr;23(4):465-72. doi: 10.1038/cr.2013.45. Epub 2013 Mar 26. PubMed PMID: 23528705; PubMed Central PMCID: PMC3616424.

Retinal development

  1. Chiodini F, Matter-Sadzinski L, Rodrigues T, Skowronska-Krawczyk D, Brodier L, Schaad O, Bauer C, Ballivet M, Matter JM. A Positive Feedback Loop between ATOH7 and a Notch Effector Regulates Cell-Cycle Progression and Neurogenesis in the Retina. Cell Rep. 2013 Mar 28;3(3):796-807. doi: 10.1016/j.celrep.2013.01.035. Epub 2013 Feb 21. PubMed PMID: 23434507.

Eye diseases

  1. From the Telegraph: Eye drops could treat macular degeneration. Original article in Cell Metabolism: Impaired Cholesterol Efflux in Senescent Macrophages Promotes Age-Related Macular Degeneration.
  2. From the Washington Post: First U.S. artificial retina approved; device could restore some sight to blind. FDA’s news release.

Neuroscience

  1. Blackiston DJ, Levin M. Ectopic eyes outside the head in Xenopus tadpoles provide sensory data for light-mediated learning. J Exp Biol. 2013 Mar 15;216(Pt 6):1031-40. doi: 10.1242/jeb.074963. PubMed PMID: 23447666.
    • Commentary: Tadpoles See with Extra Eyes
    • Very interesting article. It demonstrates how tadpole can sense light by the innervation from an ectopic eye.

 

Since our lab is studying retina, I am intrigued in reading this article about the limitation of retina display by Apple, how we see and the future of developing better displays.

From cultofmac by John Brownlee: Why Retina Isn’t Enough

Apple’s new MacBook Pro follows the fine tradition of the iPhone 4 and third-gen iPad in that it has a super high-resolution Retina display: a 2880 x 1800 panel with an amazing 220 pixels packed in per inch.

It’s an incredible display. In fact, it’s such an incredible display that it actually has about one million, seven hundred thousand pixels more than it needs to satisfy Apple’s definition of Retina, leading some to claim that those pixels are all going to waste.

Nothing could be further from the truth.

Apple’s new MacBook Pros have absolutely great displays, but they need every single pixel they have, because the truth of the matter is that Apple’s got a long way to go before it catches its display tech up to the incredible power of human vision. And that’s a good thing, because it means we’ve got a lot to look forward to.

From http://www.cultofmac.com

I read several classic papers when I am planning projects with some of you. This is a very good review paper on the fundamental architecture of retina. There are a lot useful histological facts and observations. It has great discussions on how the retinal architecture has evolved and in turn provides the necessary visual functions to the animal. I believe you will also find this review paper useful.

Reference

Masland RH. The fundamental plan of the retina. Nat Neurosci. 2001 Sep;4(9):877-86.[PubMed][Nat Neurosci]