Leung Lab Blog

Nature Special Issue on “The Future of Publishing“

Neuroscience

1. Horikawa T, Tamaki M, Miyawaki Y, Kamitani Y. Neural Decoding of Visual Imagery During Sleep. Science. 2013 Apr 4. [Epub ahead of print] PubMed PMID: 23558170.
2. Chung K, Wallace J, Kim SY, Kalyanasundaram S, Andalman AS, Davidson TJ, Mirzabekov JJ, Zalocusky KA, Mattis J, Denisin AK, Pak S, Bernstein H, Ramakrishnan C, Grosenick L, Gradinaru V, Deisseroth K. Structural and molecular interrogation of intact biological systems. Nature. 2013 Apr 10. doi: 10.1038/nature12107. [Epub ahead of print]
   • A new way of clearing tissue for imaging!
   • Commentary: Shen H. See-through brains clarify connections. Nature. 2013 Apr 11;496(7444):151. doi: 10.1038/496151a. PubMed PMID: 23579658.
   • From the New York Times: Brains as Clear as Jell-O for Scientists to Explore

Genomics

Zebrafish genome sequencing

1. Howe K, et al. The zebrafish reference genome sequence and its relationship to the human genome. Nature. 2013 Apr 17. doi: 10.1038/nature12111. [Epub ahead of print] PubMed PMID: 23594743.
2. Schier AF. Genomics: Zebrafish earns its stripes. Nature. 2013 Apr 17. doi: 10.1038/nature12094. [Epub ahead of print] PubMed PMID: 23594741.
3. Kettleborough RN, Busch-Nentwich EM, Harvey SA, Dooley CM, de Bruijn E, van Eeden F, Sealy I, White RJ, Herd C, Nijman IJ, Fényes F, Mehroke S, Scahill C, Gibbons R, Wali N, Carruthers S, Hall A, Yen J, Cuppen E, Stemple DL. A
   systematic genome-wide analysis of zebrafish protein-coding gene function. Nature. 2013 Apr 17. doi: 10.1038/nature11992. [Epub ahead of print] PubMed PMID: 23594742.

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.

Gene Therapy/Retinal degeneration

1. Cideciyan AV, Jacobson SG, Beltran WA, Sumaroka A, Swider M, Iwabe S, Roman AJ, Olivares MB, Schwartz SB, Komáromy AM, Hauswirth WW, Aguirre GD. Human retinal gene therapy for Leber congenital amaurosis shows advancing retinal degeneration despite enduring visual improvement. Proc Natl Acad Sci U S A. 2013 Jan 22. [Epub ahead of print] PubMed PMID: 23341635.
   • News coverage: Another Bump in the Road to Gene Therapy?

Neuroscience

1. Muto A, Ohkura M, Abe G, Nakai J, Kawakami K. Real-Time Visualization of Neuronal Activity during Perception. Curr Biol. 2013 Jan 29. doi:pii: S0960-9822(13)00002-X. 10.1016/j.cub.2012.12.040. [Epub ahead of print] PubMed PMID: 23375894.
   • News coverage: See a Thought Move Through a Living Fish’s Brain
   • News coverage: Fluorescent protein lets us read a fish’s thoughts
   • More videos by the authors:

Genetics

1. Hwang WY, Fu Y, Reyon D, Maeder ML, Tsai SQ, Sander JD, Peterson RT, Yeh JR, Joung JK. Efficient genome editing in zebrafish using a CRISPR-Cas system. Nat Biotechnol. 2013 Jan 29. doi: 10.1038/nbt.2501. [Epub ahead of print] PubMed PMID: 23360964.
2. Bedell VM, Wang Y, Campbell JM, Poshusta TL, Starker CG, Krug RG 2nd, Tan W, Penheiter SG, Ma AC, Leung AY, Fahrenkrug SC, Carlson DF, Voytas DF, Clark KJ, Essner JJ, Ekker SC. In vivo genome editing using a high-efficiency TALEN system. Nature. 2012 Nov 1;491(7422):114-8. doi: 10.1038/nature11537. Epub 2012 Sep 23. PubMed PMID: 23000899; PubMed Central PMCID: PMC3491146.

Evolution

1. Feuda R, Hamilton SC, McInerney JO, Pisani D. Metazoan opsin evolution reveals a simple route to animal vision. Proc Natl Acad Sci U S A. 2012 Nov 13;109(46):18868-72. doi: 10.1073/pnas.1204609109. Epub 2012 Oct 29. PubMed PMID: 23112152; PubMed Central PMCID: PMC3503164.
   • News article:  Vision evolved 700 million years ago

Genetics

1. Cong L, Ran FA, Cox D, Lin S, Barretto R, Habib N, Hsu PD, Wu X, Jiang W, Marraffini LA, Zhang F. Multiplex Genome Engineering Using CRISPR/Cas Systems. Science. 2013 Jan 3. [Epub ahead of print] PubMed PMID: 23287718.
2. Mali P, Yang L, Esvelt KM, Aach J, Guell M, Dicarlo JE, Norville JE, Church GM. RNA-Guided Human Genome Engineering via Cas9. Science. 2013 Jan 3. [Epub ahead of print] PubMed PMID: 23287722.
   • News coverage: Cheap, easy technique to snip DNA could revolutionize gene therapy
   • News coverage: Editing the genome with high precision

Science special section - Forces in Development

1. Purnell BA. Forces in development. Forceful thinking. Introduction. Science. 2012 Oct 12;338(6104):209. doi: 10.1126/science.338.6104.209. PubMed PMID: 23066070.
2. Kicheva A, Cohen M, Briscoe J. Developmental pattern formation: insights from physics and biology. Science. 2012 Oct 12;338(6104):210-2. doi: 10.1126/science.1225182. Review. PubMed PMID: 23066071.
3. Furusawa C, Kaneko K. A dynamical-systems view of stem cell biology. Science.  2012 Oct 12;338(6104):215-7. doi: 10.1126/science.1224311. Review. PubMed PMID: 23066073.
4. Newman SA. Physico-genetic determinants in the evolution of development. Science. 2012 Oct 12;338(6104):217-9. doi: 10.1126/science.1222003. PubMed PMID: 23066074.
5. Behrndt M, Salbreux G, Campinho P, Hauschild R, Oswald F, Roensch J, Grill SW, Heisenberg CP. Forces driving epithelial spreading in zebrafish gastrulation. Science. 2012 Oct 12;338(6104):257-60. doi: 10.1126/science.1224143. PubMed PMID: 23066079.

Visual sciences

1. Hardie RC, Franze K. Photomechanical responses in Drosophila photoreceptors. Science. 2012 Oct 12;338(6104):260-3. doi: 10.1126/science.1222376. PubMed PMID: 23066080.

Neural behaviour

1. Fernandes AM, Fero K, Arrenberg AB, Bergeron SA, Driever W, Burgess HA. Deep Brain Photoreceptors Control Light-Seeking Behavior in Zebrafish Larvae. Curr Biol. 2012 Sep 18. pii: S0960-9822(12)00944-X. doi: 10.1016/j.cub.2012.08.016. [Epub ahead of print] PubMed PMID: 23000151.

Retinal development

1. Xiang M. Intrinsic control of mammalian retinogenesis. Cell Mol Life Sci. 2012 Oct 12. [Epub ahead of print] PubMed PMID: 23064704.

Eye diseases

1. Sahly I, Dufour E, Schietroma C, Michel V, Bahloul A, Perfettini I, Pepermans E, Estivalet A, Carette D, Aghaie A, Ebermann I, Lelli A, Iribarne M, Hardelin JP, Weil D, Sahel JA, El-Amraoui A, Petit C. Localization of Usher 1 proteins to the photoreceptor calyceal processes, which are absent from mice. J Cell Biol. 2012 Oct 15;199(2):381-99. doi: 10.1083/jcb.201202012. Epub 2012 Oct 8. PubMed PMID: 23045546; PubMed Central PMCID: PMC3471240.

Medicine

1. Krogsbøll LT, Jørgensen KJ, Grønhøj Larsen C, Gøtzsche PC. General health checks in adults for reducing morbidity and mortality from disease. Cochrane Database Syst Rev. 2012 Oct 17;10:CD009009. doi: 10.1002/14651858.CD009009.pub2. PubMed PMID: 23076952.
   • News coverage:
     • BBC news: “General health check-ups ‘offer no benefit‘”
     • Time: “Are Health Check-Ups Necessary? Study Says Not So Much“

Retinal Development

1. Salbreux G, Barthel LK, Raymond PA, Lubensky DK. Coupling mechanical deformations and planar cell polarity to create regular patterns in the zebrafish retina. PLoS Comput Biol. 2012 Aug;8(8):e1002618. Epub 2012 Aug 23. PubMed PMID: 22936893; PubMed Central PMCID: PMC3426565.
2. Chen M, Wang K, Lin B. Development and degeneration of cone bipolar cells are  independent of cone photoreceptors in a mouse model of retinitis pigmentosa. PLoS One. 2012;7(8):e44036. Epub 2012 Aug 31. PubMed PMID: 22952865.
3. He J, Zhang G, Almeida AD, Cayouette M, Simons BD, Harris WA. How variable clones build an invariant retina. Neuron. 2012 Sep 6;75(5):786-98. PubMed PMID: 22958820.
   • Commentary: Chen Z, Li X, Desplan C. Deterministic or stochastic choices in retinal neuron specification. Neuron. 2012 Sep 6;75(5):739-42. PubMed PMID: 22958814.

Eye disease

1. Murakami Y, Matsumoto H, Roh M, Suzuki J, Hisatomi T, Ikeda Y, Miller JW, Vavvas DG. Receptor interacting protein kinase mediates necrotic cone but not rod cell death in a mouse model of inherited degeneration. Proc Natl Acad Sci U S A. 2012 Sep 4;109(36):14598-603. Epub 2012 Aug 20. PubMed PMID: 22908283.
2. Kohl S, Coppieters F, Meire F, Schaich S, Roosing S, Brennenstuhl C, Bolz S, van Genderen MM, Riemslag FC; the European Retinal Disease Consortium, Lukowski R, den Hollander AI, Cremers FP, De Baere E, Hoyng CB, Wissinger B. A Nonsense Mutation in PDE6H Causes Autosomal-Recessive Incomplete Achromatopsia. Am J Hum Genet. 2012 Sep 7;91(3):527-532. Epub 2012 Aug 16. PubMed PMID: 22901948.
3. Manzini MC, Tambunan DE, Hill RS, Yu TW, Maynard TM, Heinzen EL, Shianna KV, Stevens CR, Partlow JN, Barry BJ, Rodriguez J, Gupta VA, Al-Qudah AK, Eyaid WM, Friedman JM, Salih MA, Clark R, Moroni I, Mora M, Beggs AH, Gabriel SB, Walsh CA. Exome Sequencing and Functional Validation in Zebrafish Identify GTDC2 Mutations as a Cause of Walker-Warburg Syndrome. Am J Hum Genet. 2012 Sep 7;91(3):541-7. PubMed PMID: 22958903.

Genetics

1. Schmitt MW, Kennedy SR, Salk JJ, Fox EJ, Hiatt JB, Loeb LA. Detection of ultra-rare mutations by next-generation sequencing. Proc Natl Acad Sci U S A. 2012 Sep 4;109(36):14508-13. Epub 2012 Aug 1. PubMed PMID: 22853953.
2. Papers related to ENCODE
   • Genome Research
   1. Schaub MA, Boyle AP, Kundaje A, Batzoglou S, Snyder M. Linking disease associations with regulatory information in the human genome. Genome Res. 2012 Sep;22(9):1748-59. PubMed PMID: 22955986.
   2. Stamatoyannopoulos JA. What does our genome encode? Genome Res. 2012 Sep;22(9):1602-11. PubMed PMID: 22955972.
   3. Frazer KA. Decoding the human genome. Genome Res. 2012 Sep;22(9):1599-601. PubMed PMID: 22955971.
   1. Nature (with links to Genome Research papers)
      1. Skipper M, Dhand R, Campbell P. Presenting ENCODE. Nature. 2012 Sep6;489(7414):45. doi: 10.1038/489045a. PubMed PMID: 22955612.
      2. Ecker JR, Bickmore WA, Barroso I, Pritchard JK, Gilad Y, Segal E. Genomics: ENCODE explained. Nature. 2012 Sep 6;489(7414):52-5. doi: 10.1038/489052a. PubMed PMID: 22955614.
      3. ENCODE Project Consortium, Bernstein BE, Birney E, Dunham I, Green ED, Gunter C, Snyder M. An integrated encyclopedia of DNA elements in the human genome.Nature. 2012 Sep 6;489(7414):57-74. doi: 10.1038/nature11247. PubMed PMID: 22955616.
      4. Thurman RE, et al., The accessible chromatin landscape of the human genome. Nature. 2012 Sep 6;489(7414):75-82. doi: 10.1038/nature11232. PubMed PMID: 22955617.
      5. Neph S, et al., An expansive human regulatory lexicon encoded in transcription factor footprints. Nature. 2012 Sep 6;489(7414):83-90. doi: 10.1038/nature11212. PubMed PMID:22955618.
      6. Gerstein MB, et al., Architecture of the human regulatory network derived from ENCODE data. Nature. 2012 Sep 6;489(7414):91-100. doi: 10.1038/nature11245. PubMed PMID: 22955619.
      7. Djebali S, et al., Landscape of transcription in human cells. Nature. 2012 Sep 6;489(7414):101-8. doi: 10.1038/nature11233. PubMed PMID: 22955620.

Oxidative Stress

1. Mukaigasa K, Nguyen LT, Li L, Nakajima H, Yamamoto M, Kobayashi M. Genetic Evidence of an Evolutionarily Conserved Role for Nrf2 in the Protection against Oxidative Stress. Mol Cell Biol. 2012 Sep 4. [Epub ahead of print] PubMed PMID: 22949501.

Stem cells

1. Sancho-Martinez I, Baek SH, Izpisua Belmonte JC. Lineage conversion methodologies meet the reprogramming toolbox. Nat Cell Biol. 2012 Sep 3;14(9):892-9. doi: 10.1038/ncb2567. PubMed PMID: 22945254.
2. Loh KM, Lim B. Epigenetics: Actors in the cell reprogramming drama. Nature. 2012 Aug 30;488(7413):599-600. doi: 10.1038/488599a. PubMed PMID: 22932382.

Medicine

1. Asch DA, Volpp KG. What business are we in? The emergence of health as the business of health care. N Engl J Med. 2012 Sep 6;367(10):888-9. Epub 2012 Aug 30. PubMed PMID: 22931228.
2. Fani Marvasti F, Stafford RS. From sick care to health care–reengineering prevention into the U.S. system. N Engl J Med. 2012 Sep 6;367(10):889-91. PubMed PMID: 22931257.
3. Barnes KA, Kroening-Roche JC, Comfort BW. The developing vision of primary care. N Engl J Med. 2012 Sep 6;367(10):891-3. PubMed PMID: 22931258.
4. Baker M. Doctors back circumcision. Nature. 2012 Aug 30;488(7413):568. doi: 10.1038/488568a. PubMed PMID: 22932355.
5. Nature Outlook HPV
   1. Crow JM. HPV: The global burden. Nature. 2012 Aug 30;488(7413):S2-3. doi: 10.1038/488S2a. PubMed PMID: 22932437.

Nutrition

1. Maxmen A. Calorie restriction falters in the long run. Nature. 2012 Aug 30;488(7413):569. doi: 10.1038/488569a. PubMed PMID: 22932356.

Ethics, Social and Legal Issues

1. Greenland P, Fontanarosa PB. Ending honorary authorship. Science. 2012 Aug 31;337(6098):1019. PubMed PMID: 22936744.

Stem cells

1. Nakano T, Ando S, Takata N, Kawada M, Muguruma K, Sekiguchi K, Saito K, Yonemura S, Eiraku M, Sasai Y. Self-formation of optic cups and storable stratified neural retina from human ESCs. Cell Stem Cell. 2012 Jun 14;10(6):771-85. PubMed PMID: 22704518.
2. Cyranoski D. Tissue engineering: The brainmaker. Nature. 2012 Aug 23;488(7412):444-6. doi: 10.1038/488444a. PubMed PMID: 22914148.
   • An interesting article about Dr. Sasai who leads the team to make the eye cup from human ESCs as described above and from mouse ESCs, among many other interesting discoveries!

Imaging

1. Small A. Faster and more versatile tools for super-resolution fluorescence microscopy. Nat Methods. 2012 Jun 28;9(7):655-6. doi: 10.1038/nmeth.2079. PubMed PMID: 22743767.
2. Weber M, Huisken J. Omnidirectional microscopy. Nat Methods. 2012 Jun 28;9(7):656-7. doi: 10.1038/nmeth.2022. PubMed PMID: 22743768.
3. Schindelin J, Arganda-Carreras I, Frise E, Kaynig V, Longair M, Pietzsch T, Preibisch S, Rueden C, Saalfeld S, Schmid B, Tinevez JY, White DJ, Hartenstein V, Eliceiri K, Tomancak P, Cardona A. Fiji: an open-source platform for biological-image analysis. Nat Methods. 2012 Jun 28;9(7):676-82. doi: 10.1038/nmeth.2019. PubMed PMID: 22743772.
4. Kankaanpää P, Paavolainen L, Tiitta S, Karjalainen M, Päivärinne J, Nieminen J, Marjomäki V, Heino J, White DJ. BioImageXD: an open, general-purpose and high-throughput image-processing platform. Nat Methods. 2012 Jun 28;9(7):683-9.doi: 10.1038/nmeth.2047. PubMed PMID: 22743773.
5. de Chaumont F, Dallongeville S, Chenouard N, Hervé N, Pop S, Provoost T, Meas-Yedid V, Pankajakshan P, Lecomte T, Le Montagner Y, Lagache T, Dufour A, Olivo-Marin JC. Icy: an open bioimage informatics platform for extended reproducible research. Nat Methods. 2012 Jun 28;9(7):690-6. doi: 10.1038/nmeth.2075. PubMed PMID: 22743774.
6. Eliceiri KW, Berthold MR, Goldberg IG, Ibáñez L, Manjunath BS, Martone ME, Murphy RF, Peng H, Plant AL, Roysam B, Stuurmann N, Swedlow JR, Tomancak P, Carpenter AE. Biological imaging software tools. Nat Methods. 2012 Jun 28;9(7):697-710. doi: 10.1038/nmeth.2084. PubMed PMID: 22743775.
7. Ronneberger O, Liu K, Rath M, Rueß D, Mueller T, Skibbe H, Drayer B, Schmidt T, Filippi A, Nitschke R, Brox T, Burkhardt H, Driever W. ViBE-Z: a framework for 3D virtual colocalization analysis in zebrafish larval brains. Nat Methods. 2012  Jun 17;9(7):735-42. doi: 10.1038/nmeth.2076. PubMed PMID: 22706672.
8. Lubeck E, Cai L. Single-cell systems biology by super-resolution imaging and combinatorial labeling. Nat Methods. 2012 Jun 3;9(7):743-8. doi: 10.1038/nmeth.2069. PubMed PMID: 22660740; PubMed Central PMCID: PMC3418883.
9. Tomer R, Khairy K, Amat F, Keller PJ. Quantitative high-speed imaging of entire developing embryos with simultaneous multiview light-sheet microscopy. Nat Methods. 2012 Jun 3;9(7):755-63. doi: 10.1038/nmeth.2062. PubMed PMID: 22660741.
10. The quest for quantitative microscopy. Nat Methods. 2012 Jul;9(7):627. PubMed PMID: 22930824.
11. Schneider CA, Rasband WS, Eliceiri KW. NIH Image to ImageJ: 25 years of image analysis. Nat Methods. 2012 Jul;9(7):671-5. PubMed PMID: 22930834.

Systems Biology

1. Karr JR, Sanghvi JC, Macklin DN, Gutschow MV, Jacobs JM, Bolival B Jr, Assad-Garcia N, Glass JI, Covert MW. A whole-cell computational model predicts phenotype from genotype. Cell. 2012 Jul 20;150(2):389-401. PubMed PMID: 22817898; PubMed Central PMCID: PMC3413483.
   • Commentary: Freddolino PL, Tavazoie S. The dawn of virtual cell biology. Cell. 2012 Jul 20;150(2):248-50. PubMed PMID: 22817888.

Genomics/Genetics

1. Kong A, Frigge ML, Masson G, Besenbacher S, Sulem P, Magnusson G, Gudjonsson SA, Sigurdsson A, Jonasdottir A, Jonasdottir A, Wong WS, Sigurdsson G, Walters GB, Steinberg S, Helgason H, Thorleifsson G, Gudbjartsson DF, Helgason A, Magnusson OT, Thorsteinsdottir U, Stefansson K. Rate of de novo mutations and the importance of father’s age to disease risk. Nature. 2012 Aug 23;488(7412):471-5. doi: 10.1038/nature11396. PubMed PMID: 22914163.
   • A new study that shows the older the father is, the more the mutations that he will pass to the next generation!
   • News: Callaway E. Fathers bequeath more mutations as they age. Nature. 2012 Aug 23;488(7412):439. doi: 10.1038/488439a. PubMed PMID: 22914142.
   • Commentary: Kondrashov A. Genetics: The rate of human mutation. Nature. 2012 Aug 23;488(7412):467-8. doi: 10.1038/488467a. PubMed PMID: 22914161.
2. Schuster-Böckler B, Lehner B. Chromatin organization is a major influence on regional mutation rates in human cancer cells. Nature. 2012 Aug 23;488(7412):504-7. PubMed PMID: 22820252.

Development

1. Lefebvre JL, Kostadinov D, Chen WV, Maniatis T, Sanes JR. Protocadherins mediate dendritic self-avoidance in the mammalian nervous system. Nature. 2012 Aug 23;488(7412):517-21. PubMed PMID: 22842903; PubMed Central PMCID: PMC3427422.

Development

1. Nancy P, Tagliani E, Tay CS, Asp P, Levy DE, Erlebacher A.  Chemokine gene silencing in decidual stromal cells limits T cell access to the maternal-fetal interface. Science. 2012 Jun 8;336(6086):1317-21. PubMed PMID: 22679098.
• News coverage: New Discovery Provides Insight on Long-Standing Pregnancy Mystery.

Behaviour

1. Polverino G, Abaid N, Kopman V, Macrì S, Porfiri M. Zebrafish response to robotic fish: preference experiments on isolated individuals and small shoals. Bioinspir Biomim. 2012 Jun 8;7(3):036019. [Epub ahead of print] PubMed PMID: 22677608.
• News coverage: Zebrafish Like their Robots Striped, Female and Fertile.

Systems Biology

1. Ku CJ, Wang Y, Weiner OD, Altschuler SJ, Wu LF. Network Crosstalk Dynamically Changes during Neutrophil Polarization. Cell. 2012 May 25;149(5):1073-83. PubMed PMID: 22632971.

Human Microbiome

1. Human Microbiome Project Consortium. Structure, function and diversity of the healthy human microbiome. Nature. 2012 Jun 13;486(7402):207-14. doi:10.1038/nature11234. PubMed PMID: 22699609.
2. Human Microbiome Project Consortium. A framework for human microbiome research. Nature. 2012 Jun 13;486(7402):215-21. doi: 10.1038/nature11209. PubMed PMID: 22699610.
• Commentary: Relman DA. Microbiology: Learning about who we are. Nature. 2012 Jun 13;486(7402):194-5. doi: 10.1038/486194a. PubMed PMID: 22699602.
• News coverage: Microbe census maps out human body’s bacteria, viruses, other bugs
• News coverage: Bacteria, viruses and fungi (oh my!) on the human body

Retinal degeneration

1. Taylor S, Chen J, Luo J, Hitchcock P. Light-induced photoreceptor degeneration in the retina of the zebrafish. Methods Mol Biol. 2012;884:247-54. PubMed PMID: 22688711.

Neuroscience

1. Cyranoski D. Neuroscience: The mind reader. Nature. 2012 Jun 13;486(7402):178-80. doi: 10.1038/486178a. PubMed PMID: 22699592.
2. Van Horn JD, Irimia A, Torgerson CM, Chambers MC, Kikinis R, Toga AW. Mapping connectivity damage in the case of phineas gage. PLoS One. 2012;7(5):e37454. Epub 2012 May 16. PubMed PMID: 22616011; PubMed Central PMCID: PMC3353935.
• News coverage: Phineas Gage’s connectome
• I wonder if mapping of the connectome can also help us understand how Derek Amato acquires his music talent after head injury.

Retinal development

1. Stacher Hörndli C, Chien CB. Sonic hedgehog is indirectly required for intraretinal axon pathfinding by regulating chemokine expression in the optic stalk. Development. 2012 Jun 13. [Epub ahead of print] PubMed PMID: 22696293.

An interesting study have reported a way that may potential help people who suffer from spinal cord injury.

From the New York Times, “In Rat Experiment, New Hope for Spine Injuries“:

Rats with a spinal cord injury that left their hind legs completely paralyzed learned to walk again on their own after an intensive training course that included electrical stimulation of the brain and the spine, scientists reported on Thursday.

Adopted from the New York Times; Source: École Polytechnique Fédérale de Lausanne

Reference

van den Brand R, Heutschi J, Barraud Q, DiGiovanna J, Bartholdi K, Huerlimann M, Friedli L, Vollenweider I, Moraud EM, Duis S, Dominici N, Micera S, Musienko P, Courtine G. Restoring voluntary control of locomotion after paralyzing spinal cord injury. Science. 2012 Jun 1;336(6085):1182-5. PubMed PMID: 22654062.

Stem cells

1. Chen J, Pei D. Reprogramming in suspension. Nat Methods. 2012 Apr 27;9(5):449-51. doi: 10.1038/nmeth.1989. PubMed PMID: 22543375.

Genomics

1. Clarke L, Zheng-Bradley X, Smith R, Kulesha E, Xiao C, Toneva I, Vaughan B, Preuss D, Leinonen R, Shumway M, Sherry S, Flicek P; The 1000 Genomes Project Consortium. The 1000 Genomes Project: data management and community access. Nat Methods. 2012 Apr 27;9(5):459-462. doi: 10.1038/nmeth.1974. PubMed PMID: 22543379; PubMed Central PMCID: PMC3340611.

Eye disease

1. Pearson RA, Barber AC, Rizzi M, Hippert C, Xue T, West EL, Duran Y, Smith AJ, Chuang JZ, Azam SA, Luhmann UF, Benucci A, Sung CH, Bainbridge JW, Carandini M,Yau KW, Sowden JC, Ali RR. Restoration of vision after transplantation of photoreceptors. Nature. 2012 May 3;485(7396):99-103. PubMed PMID: 22522934.

Genetic disease

1. Whalley K. Neurodevelopmental disorders: Reversing the fragile X phenotype. Nat Rev Neurosci. 2012 May 3. doi: 10.1038/nrn3255. [Epub ahead of print] PubMed PMID: 22551664.

Systems biology

1. Zhu J, Sova P, Xu Q, Dombek KM, Xu EY, Vu H, Tu Z, Brem RB, Bumgarner RE, Schadt EE. Stitching together Multiple Data Dimensions Reveals Interacting Metabolomic and Transcriptomic Networks That Modulate Cell Regulation. PLoS Biol. 2012 Apr;10(4):e1001301. Epub 2012 Apr 3. PubMed PMID: 22509135; PubMed Central PMCID: PMC3317911.

Medicine

1. Freedman ND, Park Y, Abnet CC, Hollenbeck AR, Sinha R. Association of coffee drinking with total and cause-specific mortality. N Engl J Med. 2012 May 17;366(20):1891-904. PubMed PMID: 22591295.
• The more the coffee you drink, the longer you live!
• News coverage, from Huffington Post: “Coffee Drinkers Live Longer, Claim Scientists (Although They’re Not Quite Sure Why…) “