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  • 1
    Publication Date: 2016-08-18
    Description: The human genome contains thousands of retrocopies, mostly as processed pseudogenes, which were recently shown to be prevalently transcribed. In particular, those specifically acquired in the human lineage are able to modulate gene expression in a manner that contributed to the evolution of human-specific traits. Therefore, knowledge of the human-specific retrocopies that are transcribed or their full-length transcript structure contributes to better understand human genome evolution. In this study, we identified 16 human-specific retrocopies that harbor 5' CpG islands by in silico analysis and showed that 12 were transcribed in normal tissues and cancer cell lines with a variety of expression patterns, including cancer-specific expression. Determination of the structure of the transcripts associated with the retrocopies revealed that none were transcribed from their 5' CpG islands, but rather, from inside the 3' UTR and the nearby 5' flanking region of the retrocopies as well as the promoter of neighboring genes. The multiple forms of the transcripts, such as chimeric and individual transcripts in both the sense and antisense orientation, might have introduced novel post-transcriptional regulation into the genome during human evolution. These results shed light on the potential role of human-specific retrocopies in the evolution of gene regulation and genomic disorders.
    Electronic ISSN: 1759-6653
    Topics: Biology
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  • 2
    Publication Date: 2012-12-22
    Description: Tertiary dentin is deposited inside teeth after various stimuli and serves as a major defensive wall to preserve pulp cells. However, the molecular mechanisms of the activation of quiescent odontoblasts, immature pulp cells and tertiary dentin formation are still unclear. Therefore, we performed a comprehensive gene expression analysis of pulp cells after cavity preparation of 9-week-old rat molars to clarify the critical molecules in tertiary dentinogenesis. As a result, mRNA expression of various molecules was up- or down-regulated. Notably, several members of the matrix metalloprotease family and their endogenous inhibitors were up-regulated after cavity preparation. In situ hybridization showed that tissue inhibitor of metalloprotease 1 ( Timp1 ) was widely and continuously distributed in the pulp beneath the cavity in vivo . We also observed accumulation of β-catenin in the pulp cells beneath the cavity by fluorescence immunohistochemistry. Furthermore, Timp1 transcription was repressed by a dominant-negative TCF4 in immature undifferentiated mesenchymal cells, but not altered in mature odontoblast-like cells. These results indicate that cavity preparation may activate the Wnt/β-catenin pathway and the Wnt/β-catenin pathway and Timp1 may be correlatively involved in pulp repair. Timp1 might play crucial roles in reactivation of immature pulp cells for tertiary dentinogenesis.
    Print ISSN: 0021-924X
    Electronic ISSN: 1756-2651
    Topics: Biology , Chemistry and Pharmacology
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  • 3
    Publication Date: 2015-09-30
    Description: Sickle cell disease (SCD) is an inherited disorder caused by a point mutation in the β-globin gene, leading to the production of abnormally shaped red blood cells. Sickle cells are prone to hemolysis and thereby release free heme into plasma, causing oxidative stress and inflammation that in turn result in...
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
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  • 4
    Publication Date: 2016-02-02
    Description: We demonstrate experimentally the generation of narrow Fano line shapes in planar multilayer structures. The Fano line shape originates from coupling between a high loss surface plasmon polariton mode with a low loss planar waveguide mode. The line shape is shown to depend strongly on the structural parameters that govern the position of the waveguide mode and the coupling strength, and to be in good agreement with results of electromagnetic calculations.
    Print ISSN: 0003-6951
    Electronic ISSN: 1077-3118
    Topics: Physics
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  • 5
    Publication Date: 2014-10-08
    Description: Autoregulatory negative-feedback loops play important roles in fine-balancing tissue and organ development. Such loops are composed of short-range intercellular signaling pathways via cell–cell communications. On the other hand, leguminous plants use a long-distance negative-feedback system involving root–shoot communication to control the number of root nodules, root lateral organs that harbor...
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
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  • 6
    Publication Date: 2014-08-19
    Description: Two types of DD neutron energy spectrometer (NES) are under development for deuterium plasma operation in KSTAR to understand behavior of beam ions in the plasma. One is based on the state-of-the-art nuclear emulsion technique. The other is based on a coincidence detection of a recoiled proton and a scattered neutron caused by an elastic scattering of an incident DD neutron, which is called an associated particle coincidence counting-NES. The prototype NES systems were installed at J-port in KSTAR in 2012. During the 2012 and 2013 experimental campaigns, multiple shots-integrated neutron spectra were preliminarily obtained by the nuclear emulsion-based NES system.
    Print ISSN: 0034-6748
    Electronic ISSN: 1089-7623
    Topics: Electrical Engineering, Measurement and Control Technology , Physics
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  • 7
    Publication Date: 2011-04-23
    Description: Amination of alkanes has generally required metal catalysts and/or high temperatures. Here we report that simple exposure of a broad range of alkanes to N-triflylimino-lambda(3)-bromane 1 at ambient temperature results in C-H insertion of the nitrogen functionality to afford triflyl-substituted amines in moderate to high yields. Marked selectivity for tertiary over secondary C-H bonds was observed; primary (methyl) C-H bonds were inert. Addition of hexafluoroisopropanol to inhibit decomposition of 1 dramatically improved the C-H amination efficiencies. Second-order kinetics, activation parameters (negative activation entropy), deuterium isotope effects, and theoretical calculations suggest a concerted asynchronous bimolecular transition state for the metal-free C-H amination event.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ochiai, Masahito -- Miyamoto, Kazunori -- Kaneaki, Takao -- Hayashi, Satoko -- Nakanishi, Waro -- New York, N.Y. -- Science. 2011 Apr 22;332(6028):448-51. doi: 10.1126/science.1201686.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Graduate School of Pharmaceutical Sciences, University of Tokushima, 1-78 Shomachi, Tokushima 770-8505, Japan. mochiai@ph.tokushima-u.ac.jp〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21512029" target="_blank"〉PubMed〈/a〉
    Keywords: Adamantane/chemistry ; Alkanes/*chemistry ; Amination ; Amines/*chemistry ; Bromobenzenes/*chemistry ; Carbon/chemistry ; Hydrocarbons, Brominated/*chemistry ; Hydrogen/chemistry ; Kinetics ; Physicochemical Processes ; Stereoisomerism ; Temperature ; Thermodynamics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 8
    Publication Date: 2012-01-24
    Description: Channelrhodopsins (ChRs) are light-gated cation channels derived from algae that have shown experimental utility in optogenetics; for example, neurons expressing ChRs can be optically controlled with high temporal precision within systems as complex as freely moving mammals. Although ChRs have been broadly applied to neuroscience research, little is known about the molecular mechanisms by which these unusual and powerful proteins operate. Here we present the crystal structure of a ChR (a C1C2 chimaera between ChR1 and ChR2 from Chlamydomonas reinhardtii) at 2.3 A resolution. The structure reveals the essential molecular architecture of ChRs, including the retinal-binding pocket and cation conduction pathway. This integration of structural and electrophysiological analyses provides insight into the molecular basis for the remarkable function of ChRs, and paves the way for the precise and principled design of ChR variants with novel properties.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4160518/" 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/PMC4160518/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kato, Hideaki E -- Zhang, Feng -- Yizhar, Ofer -- Ramakrishnan, Charu -- Nishizawa, Tomohiro -- Hirata, Kunio -- Ito, Jumpei -- Aita, Yusuke -- Tsukazaki, Tomoya -- Hayashi, Shigehiko -- Hegemann, Peter -- Maturana, Andres D -- Ishitani, Ryuichiro -- Deisseroth, Karl -- Nureki, Osamu -- Howard Hughes Medical Institute/ -- England -- Nature. 2012 Jan 22;482(7385):369-74. doi: 10.1038/nature10870.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22266941" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Bacteriorhodopsins/chemistry ; Binding Sites ; Cations/*metabolism ; Cattle ; Chlamydomonas reinhardtii/*chemistry/genetics ; Crystallography, X-Ray ; Ion Channel Gating/*radiation effects ; Ion Channels/*chemistry/genetics/radiation effects ; *Light ; Models, Molecular ; Mutation ; Protein Conformation ; Recombinant Fusion Proteins/chemistry/genetics/radiation effects ; Retinaldehyde/metabolism ; Rhodopsin/*chemistry/genetics/radiation effects ; Schiff Bases/chemistry ; Static Electricity
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 9
    Publication Date: 2013-01-22
    Description: Mitotic cells assume a spherical shape by increasing their surface tension and osmotic pressure by extensively reorganizing their interphase actin cytoskeleton into a cortical meshwork and their microtubules into the mitotic spindle. Mitotic entry is known to interfere with tissue morphogenetic events that require cell-shape changes controlled by the interphase cytoskeleton, such as apical constriction. However, here we show that mitosis plays an active role in the epithelial invagination of the Drosophila melanogaster tracheal placode. Invagination begins with a slow phase under the control of epidermal growth factor receptor (EGFR) signalling; in this process, the central apically constricted cells, which are surrounded by intercalating cells, form a shallow pit. This slow phase is followed by a fast phase, in which the pit is rapidly depressed, accompanied by mitotic entry, which leads to the internalization of all the cells in the placode. We found that mitotic cell rounding, but not cell division, of the central cells in the placode is required to accelerate invagination, in conjunction with EGFR-induced myosin II contractility in the surrounding cells. We propose that mitotic cell rounding causes the epithelium to buckle under pressure and acts as a switch for morphogenetic transition at the appropriate time.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kondo, Takefumi -- Hayashi, Shigeo -- England -- Nature. 2013 Feb 7;494(7435):125-9. doi: 10.1038/nature11792. Epub 2013 Jan 13.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory for Morphogenetic Signaling, RIKEN Center for Developmental Biology, 2-2-3, Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23334416" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Division ; Cell Shape/*physiology ; Drosophila melanogaster/anatomy & histology/*cytology/*embryology ; Epidermal Growth Factor/metabolism ; Epithelial Cells/*cytology ; Female ; Fibroblast Growth Factors/metabolism ; *Mitosis ; Myosin Type II/metabolism ; Receptor, Epidermal Growth Factor/metabolism ; Respiratory System/anatomy & histology/cytology/embryology ; Signal Transduction
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 10
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2014-04-26
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hayashi, Shigehiko -- New York, N.Y. -- Science. 2014 Apr 25;344(6182):369-70. doi: 10.1126/science.1253616.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Graduate School of Science, Kyoto University, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24763579" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Chloride Channels/*chemistry/*metabolism ; Chlorides/*metabolism ; Humans ; Neurons/*physiology ; Rhodopsin/*chemistry/*metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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