Posts tagged ‘imaging’

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.

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.

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.

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. Vogel G. Reproductive biology. Potential egg stem cells reignite debate. Science. 2012 Mar 2;335(6072):1029-30. PubMed PMID: 22383817.

Scientific career

  1. Mervis J. Scientific careers. Is motherhood the biggest reason for academia’s gender imbalance? Science. 2012 Mar 2;335(6072):1030-1. PubMed PMID: 22383818.

Genomics

  1. Xu X, Hou Y, Yin X, Bao L, Tang A, Song L, Li F, Tsang S, Wu K, Wu H, He W, Zeng L, Xing M, Wu R, Jiang H, Liu X, Cao D, Guo G, Hu X, Gui Y, Li Z, Xie W, Sun X, Shi M, Cai Z, Wang B, Zhong M, Li J, Lu Z, Gu N, Zhang X, Goodman L, Bolund L, Wang J, Yang H, Kristiansen K, Dean M, Li Y, Wang J. Single-cell exome sequencing reveals single-nucleotide mutation characteristics of a kidney tumor. Cell. 2012 Mar 2;148(5):886-95. PubMed PMID: 22385958.
  2. Hou Y, Song L, Zhu P, Zhang B, Tao Y, Xu X, Li F, Wu K, Liang J, Shao D, Wu H, Ye X, Ye C, Wu R, Jian M, Chen Y, Xie W, Zhang R, Chen L, Liu X, Yao X, Zheng H, Yu C, Li Q, Gong Z, Mao M, Yang X, Yang L, Li J, Wang W, Lu Z, Gu N, Laurie G, Bolund L, Kristiansen K, Wang J, Yang H, Li Y, Zhang X, Wang J. Single-Cell ExomeSequencing and Monoclonal Evolution of a JAK2-Negative Myeloproliferative Neoplasm. Cell. 2012 Mar 2;148(5):873-85. PubMed PMID: 22385957.

Systems biology

  1. Angermann BR, Klauschen F, Garcia AD, Prustel T, Zhang F, Germain RN, Meier-Schellersheim M. Computational modeling of cellular signaling processes embedded into dynamic spatial contexts. Nat Methods. 2012 Jan 29;9(3):283-9. doi: 10.1038/nmeth.1861. PubMed PMID: 22286385.
    • Commentary: Sneddon MW, Emonet T. Modeling cellular signaling: taking space into the computation. Nat Methods. 2012 Feb 28;9(3):239-42. doi: 10.1038/nmeth.1900. PubMed PMID: 22373909.

Imaging

  1. Allan C, Burel JM, Moore J, Blackburn C, Linkert M, Loynton S, Macdonald D, Moore WJ, Neves C, Patterson A, Porter M, Tarkowska A, Loranger B, Avondo J, Lagerstedt I, Lianas L, Leo S, Hands K, Hay RT, Patwardhan A, Best C, Kleywegt GJ, Zanetti G, Swedlow JR. OMERO: flexible, model-driven data management for experimental biology. Nat Methods. 2012 Feb 28;9(3):245-53. doi: 10.1038/nmeth.1896. PubMed PMID: 22373911.
  2. Ragan T, Kadiri LR, Venkataraju KU, Bahlmann K, Sutin J, Taranda J, Arganda-Carreras I, Kim Y, Seung HS, Osten P. Serial two-photon tomography for automated ex vivo mouse brain imaging. Nat Methods. 2012 Jan 15;9(3):255-8. doi:  10.1038/nmeth.1854. PubMed PMID: 22245809; PubMed Central PMCID: PMC3297424

Genetics

  1. Wang X, Chen X, Yang Y. Spatiotemporal control of gene expression by a light-switchable transgene system. Nat Methods. 2012 Feb 12;9(3):266-9. doi: 10.1038/nmeth.1892. PubMed PMID: 22327833.

 

Delta-Notch

  1. Luo H, Jin K, Xie Z, Qiu F, Li S, Zou M, Cai L, Hozumi K, Shima DT, Xiang M. Forkhead box N4 (Foxn4) activates Dll4-Notch signaling to suppress photoreceptor cell fates of early retinal progenitors. Proc Natl Acad Sci U S A. 2012 Feb 8. [Epub ahead of print] PubMed PMID: 22323600.

Stem Cells

  1. Robinton DA, Daley GQ. The promise of induced pluripotent stem cells in research and therapy. Nature. 2012 Jan 18;481(7381):295-305. doi: 10.1038/nature10761. PubMed PMID: 22258608.

Imaging

  1. Miller EW, Lin JY, Frady EP, Steinbach PA, Kristan WB Jr, Tsien RY. Optically monitoring voltage in neurons by photo-induced electron transfer through molecular wires. Proc Natl Acad Sci U S A. 2012 Feb 7;109(6):2114-9. Epub 2012 Jan 24. PubMed PMID: 22308458.

Eye Disease

  1. Beltran WA, Cideciyan AV, Lewin AS, Iwabe S, Khanna H, Sumaroka A, Chiodo VA, Fajardo DS, Román AJ, Deng WT, Swider M, Alemán TS, Boye SL, Genini S, Swaroop A, Hauswirth WW, Jacobson SG, Aguirre GD. Gene therapy rescues photoreceptor blindness in dogs and paves the way for treating human X-linked retinitis pigmentosa. Proc Natl Acad Sci U S A. 2012 Feb 7;109(6):2132-7. Epub 2012 Jan 23. PubMed PMID: 22308428.

Genomics

  1. Kaiser J. Cell biology. Donation spurs a cell observatory–and bigger plans. Science. 2012 Feb 3;335(6068):514. PubMed PMID: 22301289.
  2. Normile D. Genomics. China’s sequencing powerhouse comes of age. Science. 2012 Feb 3;335(6068):516-9. PubMed PMID: 22301291.
  3. Brar GA, Yassour M, Friedman N, Regev A, Ingolia NT, Weissman JS. High-resolution view of the yeast meiotic program revealed by ribosome profiling. Science. 2012 Feb 3;335(6068):552-7. Epub 2011 Dec 22. PubMed PMID: 22194413.
  4. Iverson V, Morris RM, Frazar CD, Berthiaume CT, Morales RL, Armbrust EV. Untangling genomes from metagenomes: revealing an uncultured class of marine Euryarchaeota. Science. 2012 Feb 3;335(6068):587-90. PubMed PMID: 22301318.

Development

  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.

Genetics

  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.

Genomics

  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.

Imaging

  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.

Ageing

  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.

Brg1

  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.

Funding

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