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  • 1
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    Single-cell PTP assay [Biochemistry] (2012)
    National Academy of Sciences
    Details
    Publication Date: 2012-08-29
    Description: Many cellular signaling events are regulated by tyrosine phosphorylation and mediated by the opposing actions of protein tyrosine kinases and phosphatases. Protein tyrosine phosphatases are emerging as drug targets, but poor cell permeability of inhibitors has limited the development of drugs targeting these enzymes [Tautz L, et al. (2006) Expert...
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 2
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    Single molecule profiling of alternative pre-mRNA splicing (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-08-09
    Description: Alternative pre-messenger RNA splicing is an important mechanism for generating protein diversity and may explain in part how mammalian complexity arises from a surprisingly small complement of genes. Here, we describe "digital polony exon profiling,"a single molecule-based technology for studying complex alternative pre-messenger RNA splicing. This technology allows researchers to monitor the combinatorial diversity of exon inclusion in individual transcripts. A minisequencing strategy provides single nucleotide resolution, and the digital nature of the technology allows quantitation of individual splicing variants. Digital polony exon profiling can be used to investigate the physiological and pathological roles of alternately spliced messenger RNAs, as well as the mechanisms by which these messenger RNAs are produced.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhu, Jun -- Shendure, Jay -- Mitra, Robi D -- Church, George M -- 5U54GM62119/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2003 Aug 8;301(5634):836-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genetics, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12907803" target="_blank"〉PubMed〈/a〉
    Keywords: Acrylamide ; *Alternative Splicing ; Animals ; Antigens, CD44/genetics ; Brain/metabolism ; Cell Line ; Cell Line, Transformed ; Cyclic AMP Response Element-Binding Protein ; *Exons ; Humans ; Mice ; Microtubule-Associated Proteins/genetics ; Nerve Tissue Proteins/genetics ; Polymerase Chain Reaction/*methods ; Polymorphism, Single Nucleotide ; Protein Isoforms ; RNA Precursors/*genetics/metabolism ; RNA-Binding Proteins ; SMN Complex Proteins
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 3
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    Global gene deletion analysis exploring yeast filamentous growth (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-09-18
    Description: The dimorphic switch from a single-cell budding yeast to a filamentous form enables Saccharomyces cerevisiae to forage for nutrients and the opportunistic pathogen Candida albicans to invade human tissues and evade the immune system. We constructed a genome-wide set of targeted deletion alleles and introduced them into a filamentous S. cerevisiae strain, Sigma1278b. We identified genes involved in morphologically distinct forms of filamentation: haploid invasive growth, biofilm formation, and diploid pseudohyphal growth. Unique genes appear to underlie each program, but we also found core genes with general roles in filamentous growth, including MFG1 (YDL233w), whose product binds two morphogenetic transcription factors, Flo8 and Mss11, and functions as a critical transcriptional regulator of filamentous growth in both S. cerevisiae and C. albicans.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ryan, Owen -- Shapiro, Rebecca S -- Kurat, Christoph F -- Mayhew, David -- Baryshnikova, Anastasia -- Chin, Brian -- Lin, Zhen-Yuan -- Cox, Michael J -- Vizeacoumar, Frederick -- Cheung, Doris -- Bahr, Sondra -- Tsui, Kyle -- Tebbji, Faiza -- Sellam, Adnane -- Istel, Fabian -- Schwarzmuller, Tobias -- Reynolds, Todd B -- Kuchler, Karl -- Gifford, David K -- Whiteway, Malcolm -- Giaever, Guri -- Nislow, Corey -- Costanzo, Michael -- Gingras, Anne-Claude -- Mitra, Robi David -- Andrews, Brenda -- Fink, Gerald R -- Cowen, Leah E -- Boone, Charles -- 42516-4/Canadian Institutes of Health Research/Canada -- GM035010/GM/NIGMS NIH HHS/ -- GM40266/GM/NIGMS NIH HHS/ -- MOP-97939/Canadian Institutes of Health Research/Canada -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2012 Sep 14;337(6100):1353-6. doi: 10.1126/science.1224339.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Banting and Best Department of Medical Research, University of Toronto, Toronto, ON M5S 3E1, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22984072" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Biofilms/growth & development ; Candida albicans/cytology/*genetics/*growth & development ; DNA Mutational Analysis ; Gene Deletion ; *Gene Expression Regulation, Fungal ; Hyphae/genetics/growth & development ; Nuclear Proteins/genetics ; Saccharomyces cerevisiae/cytology/*genetics/*growth & development ; Saccharomyces cerevisiae Proteins/genetics ; Trans-Activators/genetics ; Transcription Factors/genetics ; Transcription, Genetic
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 4
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    Synchronous x-ray and radio mode switches: a rapid global transformation of the pulsar magnetosphere (2013)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2013-01-26
    Description: Pulsars emit from low-frequency radio waves up to high-energy gamma-rays, generated anywhere from the stellar surface out to the edge of the magnetosphere. Detecting correlated mode changes across the electromagnetic spectrum is therefore key to understanding the physical relationship among the emission sites. Through simultaneous observations, we detected synchronous switching in the radio and x-ray emission properties of PSR B0943+10. When the pulsar is in a sustained radio-"bright" mode, the x-rays show only an unpulsed, nonthermal component. Conversely, when the pulsar is in a radio-"quiet" mode, the x-ray luminosity more than doubles and a 100% pulsed thermal component is observed along with the nonthermal component. This indicates rapid, global changes to the conditions in the magnetosphere, which challenge all proposed pulsar emission theories.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hermsen, W -- Hessels, J W T -- Kuiper, L -- van Leeuwen, J -- Mitra, D -- de Plaa, J -- Rankin, J M -- Stappers, B W -- Wright, G A E -- Basu, R -- Alexov, A -- Coenen, T -- Griessmeier, J-M -- Hassall, T E -- Karastergiou, A -- Keane, E -- Kondratiev, V I -- Kramer, M -- Kuniyoshi, M -- Noutsos, A -- Serylak, M -- Pilia, M -- Sobey, C -- Weltevrede, P -- Zagkouris, K -- Asgekar, A -- Avruch, I M -- Batejat, F -- Bell, M E -- Bell, M R -- Bentum, M J -- Bernardi, G -- Best, P -- Birzan, L -- Bonafede, A -- Breitling, F -- Broderick, J -- Bruggen, M -- Butcher, H R -- Ciardi, B -- Duscha, S -- Eisloffel, J -- Falcke, H -- Fender, R -- Ferrari, C -- Frieswijk, W -- Garrett, M A -- de Gasperin, F -- de Geus, E -- Gunst, A W -- Heald, G -- Hoeft, M -- Horneffer, A -- Iacobelli, M -- Kuper, G -- Maat, P -- Macario, G -- Markoff, S -- McKean, J P -- Mevius, M -- Miller-Jones, J C A -- Morganti, R -- Munk, H -- Orru, E -- Paas, H -- Pandey-Pommier, M -- Pandey, V N -- Pizzo, R -- Polatidis, A G -- Rawlings, S -- Reich, W -- Rottgering, H -- Scaife, A M M -- Schoenmakers, A -- Shulevski, A -- Sluman, J -- Steinmetz, M -- Tagger, M -- Tang, Y -- Tasse, C -- ter Veen, S -- Vermeulen, R -- van de Brink, R H -- van Weeren, R J -- Wijers, R A M J -- Wise, M W -- Wucknitz, O -- Yatawatta, S -- Zarka, P -- New York, N.Y. -- Science. 2013 Jan 25;339(6118):436-9. doi: 10.1126/science.1230960.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉SRON, Netherlands Institute for Space Research, Sorbonnelaan 2, 3584 CA Utrecht, Netherlands. w.hermsen@sron.nl〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23349288" target="_blank"〉PubMed〈/a〉
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 5
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    Accurate multiplex polony sequencing of an evolved bacterial genome (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-08-06
    Description: We describe a DNA sequencing technology in which a commonly available, inexpensive epifluorescence microscope is converted to rapid nonelectrophoretic DNA sequencing automation. We apply this technology to resequence an evolved strain of Escherichia coli at less than one error per million consensus bases. A cell-free, mate-paired library provided single DNA molecules that were amplified in parallel to 1-micrometer beads by emulsion polymerase chain reaction. Millions of beads were immobilized in a polyacrylamide gel and subjected to automated cycles of sequencing by ligation and four-color imaging. Cost per base was roughly one-ninth as much as that of conventional sequencing. Our protocols were implemented with off-the-shelf instrumentation and reagents.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shendure, Jay -- Porreca, Gregory J -- Reppas, Nikos B -- Lin, Xiaoxia -- McCutcheon, John P -- Rosenbaum, Abraham M -- Wang, Michael D -- Zhang, Kun -- Mitra, Robi D -- Church, George M -- New York, N.Y. -- Science. 2005 Sep 9;309(5741):1728-32. Epub 2005 Aug 4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. shendure@alumni.princeton.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16081699" target="_blank"〉PubMed〈/a〉
    Keywords: Acrylic Resins ; Algorithms ; Automation ; Costs and Cost Analysis ; DNA Ligases/metabolism ; DNA Primers ; DNA, Bacterial/*genetics ; Escherichia coli/*genetics ; *Evolution, Molecular ; Fluorescent Dyes ; Gels ; Gene Library ; *Genome, Bacterial ; Microscopy, Fluorescence ; Microspheres ; Mutation ; Nucleic Acid Hybridization ; Point Mutation ; Polymerase Chain Reaction ; Sequence Analysis, DNA/economics/instrumentation/*methods
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 6
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    An ultraviolet-radiation-independent pathway to melanoma carcinogenesis in the red hair/fair skin background (2012)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2012-11-06
    Description: People with pale skin, red hair, freckles and an inability to tan--the 'red hair/fair skin' phenotype--are at highest risk of developing melanoma, compared to all other pigmentation types. Genetically, this phenotype is frequently the product of inactivating polymorphisms in the melanocortin 1 receptor (MC1R) gene. MC1R encodes a cyclic AMP-stimulating G-protein-coupled receptor that controls pigment production. Minimal receptor activity, as in red hair/fair skin polymorphisms, produces the red/yellow pheomelanin pigment, whereas increasing MC1R activity stimulates the production of black/brown eumelanin. Pheomelanin has weak shielding capacity against ultraviolet radiation relative to eumelanin, and has been shown to amplify ultraviolet-A-induced reactive oxygen species. Several observations, however, complicate the assumption that melanoma risk is completely ultraviolet-radiation-dependent. For example, unlike non-melanoma skin cancers, melanoma is not restricted to sun-exposed skin and ultraviolet radiation signature mutations are infrequently oncogenic drivers. Although linkage of melanoma risk to ultraviolet radiation exposure is beyond doubt, ultraviolet-radiation-independent events are likely to have a significant role. Here we introduce a conditional, melanocyte-targeted allele of the most common melanoma oncoprotein, BRAF(V600E), into mice carrying an inactivating mutation in the Mc1r gene (these mice have a phenotype analogous to red hair/fair skin humans). We observed a high incidence of invasive melanomas without providing additional gene aberrations or ultraviolet radiation exposure. To investigate the mechanism of ultraviolet-radiation-independent carcinogenesis, we introduced an albino allele, which ablates all pigment production on the Mc1r(e/e) background. Selective absence of pheomelanin synthesis was protective against melanoma development. In addition, normal Mc1r(e/e) mouse skin was found to have significantly greater oxidative DNA and lipid damage than albino-Mc1r(e/e) mouse skin. These data suggest that the pheomelanin pigment pathway produces ultraviolet-radiation-independent carcinogenic contributions to melanomagenesis by a mechanism of oxidative damage. Although protection from ultraviolet radiation remains important, additional strategies may be required for optimal melanoma prevention.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3521494/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3521494/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mitra, Devarati -- Luo, Xi -- Morgan, Ann -- Wang, Jin -- Hoang, Mai P -- Lo, Jennifer -- Guerrero, Candace R -- Lennerz, Jochen K -- Mihm, Martin C -- Wargo, Jennifer A -- Robinson, Kathleen C -- Devi, Suprabha P -- Vanover, Jillian C -- D'Orazio, John A -- McMahon, Martin -- Bosenberg, Marcus W -- Haigis, Kevin M -- Haber, Daniel A -- Wang, Yinsheng -- Fisher, David E -- 5R01 AR043369-16/AR/NIAMS NIH HHS/ -- F30 ES020663-01/ES/NIEHS NIH HHS/ -- R01 AR043369/AR/NIAMS NIH HHS/ -- R01 CA101864/CA/NCI NIH HHS/ -- R01 CA129933/CA/NCI NIH HHS/ -- R01 CA131075/CA/NCI NIH HHS/ -- R01 CA176839/CA/NCI NIH HHS/ -- R01-CA101864/CA/NCI NIH HHS/ -- T32 GM007753/GM/NIGMS NIH HHS/ -- England -- Nature. 2012 Nov 15;491(7424):449-53. doi: 10.1038/nature11624. Epub 2012 Oct 31.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cutaneous Biology Research Center, Massachusetts General Hospital, Charlestown, Massachusetts 02129, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23123854" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Line, Tumor ; Cell Proliferation/drug effects ; Gene Expression Regulation/drug effects ; Hair Color/*genetics ; Indoles/pharmacology ; Melanins/metabolism ; Melanoma/*genetics ; Mice ; Mice, Inbred C57BL ; Monophenol Monooxygenase/genetics ; Peroxidases/metabolism ; Protein Kinase Inhibitors/pharmacology ; Proto-Oncogene Proteins B-raf/genetics ; Receptor, Melanocortin, Type 1/genetics ; Skin Pigmentation/*genetics ; Sulfonamides/pharmacology ; Survival Analysis ; Tumor Cells, Cultured ; *Ultraviolet Rays
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 7
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    Mitochondria, autophagy, & hepatocyte polarization [Cell Biology] (2013)
    National Academy of Sciences
    Details
    Publication Date: 2013-05-01
    Description: Cell polarization requires increased cellular energy and metabolic output, but how these energetic demands are met by polarizing cells is unclear. To address these issues, we investigated the roles of mitochondrial bioenergetics and autophagy during cell polarization of hepatocytes cultured in a collagen sandwich system. We found that as the...
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 8
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    Ultralow Protein Adsorbing Coatings from Clickable PEG Nanogel Solutions: Benefits of Attachment under Salt-Induced Phase Separation Conditions and Comparison with PEG/Albumin Nanogel Coatings (2013)
    American Chemical Society (ACS)
    In: Langmuir
    Details
    Publication Date: 2013-03-12
    Description: Langmuir DOI: 10.1021/la3051115
    Print ISSN: 0743-7463
    Electronic ISSN: 1520-5827
    Topics: Chemistry and Pharmacology
    Published by American Chemical Society (ACS)
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  • 9
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    Experimental models of transfer zones in rift systems (2013)
    American Association of Petroleum Geologists (AAPG)
    Details
    Publication Date: 2013-05-03
    Description: Transfer zones in rift basins are classified into convergent, divergent, and synthetic, based on the relative dip directions of adjacent faults within the transfer zone. Experimental models were constructed to determine the geometry, evolution, and fault patterns associated with each of these transfer zones. In addition, basement faults with initially approaching, laterally offset, and overlapping geometries were modeled. The models consisted of two layers, with stiff clay representing basement and soft clay representing the sedimentary cover. Laser scanning and three-dimensional surface modeling were used to determine the map geometry to compare the models with examples of natural structures. The experimental models showed many similarities with conceptual models but also showed more details and a few significant differences. Typically, divergent transfer zones are narrower than convergent transfer zones, for the same initial spacing between basement faults. The differences between the different initial fault configurations (approaching, laterally offset, or overlapping) are the degree of interaction of the secondary faults, the amount of overlap between the fault zones, and in some cases, the width of the transfer zone. The main faults propagate laterally and upward and curve in the direction of dip of the faults, so that the faults curve toward each other in convergent transfer zones, away from each other in divergent transfer zones, and in the same direction in synthetic transfer zones. A primary difference with schematic models is the significant component of extensional fault propagation folding (drape folding), accompanied by secondary faulting within the sedimentary cover, especially in the early stages of fault propagation. Therefore, all three types of transfer zones are characterized by significant folding and related variations in the shapes of structures. The transfer zones are marked by a progressive change in relief from the footwall to the hanging wall, resulting in a saddle-shaped geometry. The hanging walls of the faults are marked by a gentle flexure or rollover into the fault, with the amount of flexure increasing with fault throw away from the fault tip. The geometries and fault patterns of the experimental structures match some of the observations in natural structures and also provide predictive analogs for interpretation of surface and subsurface structures and the delineation of structural traps in rift basins.
    Print ISSN: 0149-1423
    Electronic ISSN: 0149-1423
    Topics: Geosciences
    Published by American Association of Petroleum Geologists (AAPG)
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  • 10
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    Determination of subshell-resolved L-shell-ionization cross sections of gold induced by 15–40-keV electrons (2014)
    American Physical Society (APS)
    Details
    Publication Date: 2014-05-15
    Description: Author(s): H. V. Rahangdale, M. Guerra, P. K. Das, S. De, J. P. Santos, D. Mitra, and S. Saha The L-subshell specific electron impact ionization cross sections, near the ionization threshold (15〈E〈40 keV) of gold are calculated from the measured production cross sections in this collaborative work between an experimental and a theoretical group. Calculations are performed using the dis... [Phys. Rev. A 89, 052708] Published Wed May 14, 2014
    Keywords: Atomic and molecular collisions and interactions
    Print ISSN: 1050-2947
    Electronic ISSN: 1094-1622
    Topics: Physics
    Published by American Physical Society (APS)
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