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  • 1
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    All-atom molecular dynamics calculation study of entire poliovirus empty capsids in solution (2014)
    American Institute of Physics (AIP)
    Details
    Publication Date: 2014-10-23
    Description: Small viruses that belong, for example, to the Picornaviridae , such as poliovirus and foot-and-mouth disease virus, consist simply of capsid proteins and a single-stranded RNA (ssRNA) genome. The capsids are quite stable in solution to protect the genome from the environment. Here, based on long-time and large-scale 6.5 × 10 6 all-atom molecular dynamics calculations for the Mahoney strain of poliovirus, we show microscopic properties of the viral capsids at a molecular level. First, we found equilibrium rapid exchange of water molecules across the capsid. The exchange rate is so high that all water molecules inside the capsid (about 200 000) can leave the capsid and be replaced by water molecules from the outside in about 25 μs. This explains the capsid's tolerance to high pressures and deactivation by exsiccation. In contrast, the capsid did not exchange ions, at least within the present simulation time of 200 ns. This implies that the capsid can function, in principle, as a semipermeable membrane. We also found that, similar to the xylem of trees, the pressure of the solution inside the capsid without the genome was negative. This is caused by coulombic interaction of the solution inside the capsid with the capsid excess charges. The negative pressure may be compensated by positive osmotic pressure by the solution-soluble ssRNA and the counter ions introduced into it.
    Electronic ISSN: 1931-9223
    Topics: Chemistry and Pharmacology , Physics
    Published by American Institute of Physics (AIP)
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  • 2
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    All-atom molecular dynamics calculation study of entire poliovirus empty capsids in solution (2014)
    American Institute of Physics (AIP)
    Details
    Publication Date: 2014-10-23
    Description: Small viruses that belong, for example, to the Picornaviridae , such as poliovirus and foot-and-mouth disease virus, consist simply of capsid proteins and a single-stranded RNA (ssRNA) genome. The capsids are quite stable in solution to protect the genome from the environment. Here, based on long-time and large-scale 6.5 × 10 6 all-atom molecular dynamics calculations for the Mahoney strain of poliovirus, we show microscopic properties of the viral capsids at a molecular level. First, we found equilibrium rapid exchange of water molecules across the capsid. The exchange rate is so high that all water molecules inside the capsid (about 200 000) can leave the capsid and be replaced by water molecules from the outside in about 25 μs. This explains the capsid's tolerance to high pressures and deactivation by exsiccation. In contrast, the capsid did not exchange ions, at least within the present simulation time of 200 ns. This implies that the capsid can function, in principle, as a semipermeable membrane. We also found that, similar to the xylem of trees, the pressure of the solution inside the capsid without the genome was negative. This is caused by coulombic interaction of the solution inside the capsid with the capsid excess charges. The negative pressure may be compensated by positive osmotic pressure by the solution-soluble ssRNA and the counter ions introduced into it.
    Print ISSN: 0021-9606
    Electronic ISSN: 1089-7690
    Topics: Chemistry and Pharmacology , Physics
    Published by American Institute of Physics (AIP)
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  • 3
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    Mechanics of the injected pulsejet into gelatin gel and evaluation of the effect by puncture and crack generation and growth (2014)
    American Institute of Physics (AIP)
    Details
    Publication Date: 2014-08-16
    Description: Recently, fluid jets have become widely used in medical devices and have been created and evaluated in clinical environments. Such devices are classified into two broad groups; those adopting continuous jets and those adopting discrete (or pulsed) jets. We developed a discrete jet device for brain cancer treatment, called a laser-induced liquid jet (LILJ) system. Although several studies have evaluated the availability and described the treatment mechanisms of fluid jet devices, the mechanisms of the fluid and injected material remain under-investigated. In this paper, we report the mechanism of frequent pulsejet injections into a viscoelastic biological material; namely, simulated gelatin brain tissue. The mechanism is evaluated by the injection depth, an easily measured parameter. To explain the injection mechanism, we propose that the pulsejet is pressured by forces introduced by resistance on the side surface of the hole and the reaction force proportionate to the injection depth. The pulsejet generated and propagated cracks in the gelatin, and the resistance eventually fractured the side surface of the hole. We evaluated the proposed model by measuring the behavior of pulsejets injected into gelatin by the LILJ. From the results, the following conclusions were obtained. First, the proposed model accurately describes the behavior of the injected pulsejet. Second, whether the hole or crack growth largely increases the final injection depth can be evaluated from differences in the decay constant. Finally, crack growth increases the final injection depth when the number of the injected pulsejets is greater than the inverse of the decay constant.
    Print ISSN: 0021-8979
    Electronic ISSN: 1089-7550
    Topics: Physics
    Published by American Institute of Physics (AIP)
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  • 4
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    Caspase-dependent conversion of Dicer ribonuclease into a death-promoting deoxyribonuclease (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-03-13
    Description: Chromosome fragmentation is a hallmark of apoptosis, conserved in diverse organisms. In mammals, caspases activate apoptotic chromosome fragmentation by cleaving and inactivating an apoptotic nuclease inhibitor. We report that inactivation of the Caenorhabditis elegans dcr-1 gene, which encodes the Dicer ribonuclease important for processing of small RNAs, compromises apoptosis and blocks apoptotic chromosome fragmentation. DCR-1 was cleaved by the CED-3 caspase to generate a C-terminal fragment with deoxyribonuclease activity, which produced 3' hydroxyl DNA breaks on chromosomes and promoted apoptosis. Thus, caspase-mediated activation of apoptotic DNA degradation is conserved. DCR-1 functions in fragmenting chromosomal DNA during apoptosis, in addition to processing of small RNAs, and undergoes a protease-mediated conversion from a ribonuclease to a deoxyribonuclease.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4313557/" 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/PMC4313557/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nakagawa, Akihisa -- Shi, Yong -- Kage-Nakadai, Eriko -- Mitani, Shohei -- Xue, Ding -- R01 GM059083/GM/NIGMS NIH HHS/ -- R01 GM079097/GM/NIGMS NIH HHS/ -- R01 GM59083/GM/NIGMS NIH HHS/ -- R01 GM79097/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2010 Apr 16;328(5976):327-34. doi: 10.1126/science.1182374. Epub 2010 Mar 11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20223951" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Animals, Genetically Modified ; *Apoptosis ; Caenorhabditis elegans/cytology/*enzymology/genetics/physiology ; Caenorhabditis elegans Proteins/chemistry/genetics/*metabolism ; Caspases/genetics/*metabolism ; Catalytic Domain ; *DNA Fragmentation ; DNA, Helminth/*metabolism ; Deoxyribonucleases/*metabolism ; In Situ Nick-End Labeling ; RNA Interference ; RNA, Double-Stranded/metabolism ; RNA, Helminth/metabolism ; Recombinant Fusion Proteins/metabolism ; Ribonuclease III/chemistry/genetics/*metabolism
    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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    The structure of importin-beta bound to SREBP-2: nuclear import of a transcription factor (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-12-03
    Description: The sterol regulatory element-binding protein 2 (SREBP-2), a nuclear transcription factor that is essential for cholesterol metabolism, enters the nucleus through a direct interaction of its helix-loop-helix leucine zipper domain with importin-beta. We show the crystal structure of importin-beta complexed with the active form of SREBP-2. Importin-beta uses characteristic long helices like a pair of chopsticks to interact with an SREBP-2 dimer. Importin-beta changes its conformation to reveal a pseudo-twofold symmetry on its surface structure so that it can accommodate a symmetric dimer molecule. Importin-beta may use a similar strategy to recognize other dimeric cargoes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lee, Soo Jae -- Sekimoto, Toshihiro -- Yamashita, Eiki -- Nagoshi, Emi -- Nakagawa, Atsushi -- Imamoto, Naoko -- Yoshimura, Masato -- Sakai, Hiroaki -- Chong, Khoon Tee -- Tsukihara, Tomitake -- Yoneda, Yoshihiro -- New York, N.Y. -- Science. 2003 Nov 28;302(5650):1571-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Protein Research, Graduate School of Frontier Biosciences, Osaka University, Yamadaoka 2-2, Suita, Osaka 565-0871, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14645851" target="_blank"〉PubMed〈/a〉
    Keywords: *Active Transport, Cell Nucleus ; Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Binding Sites ; Cell Nucleus/metabolism ; Crystallography, X-Ray ; DNA-Binding Proteins/*chemistry/*metabolism ; Dimerization ; Helix-Loop-Helix Motifs ; Humans ; Hydrophobic and Hydrophilic Interactions ; Mice ; Models, Molecular ; Molecular Sequence Data ; Nuclear Localization Signals ; Nuclear Pore/metabolism ; Protein Binding ; *Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Sterol Regulatory Element Binding Protein 2 ; Transcription Factors/*chemistry/*metabolism ; beta Karyopherins/*chemistry/*metabolism ; ran GTP-Binding Protein/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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  • 6
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    EFF-1-mediated regenerative axonal fusion requires components of the apoptotic pathway (2015)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2015-01-09
    Description: Functional regeneration after nervous system injury requires transected axons to reconnect with their original target tissue. Axonal fusion, a spontaneous regenerative mechanism identified in several species, provides an efficient means of achieving target reconnection as a regrowing axon is able to contact and fuse with its own separated axon fragment, thereby re-establishing the original axonal tract. Here we report a molecular characterization of this process in Caenorhabditis elegans, revealing dynamic changes in the subcellular localization of the EFF-1 fusogen after axotomy, and establishing phosphatidylserine (PS) and the PS receptor (PSR-1) as critical components for axonal fusion. PSR-1 functions cell-autonomously in the regrowing neuron and, instead of acting in its canonical signalling pathway, acts in a parallel phagocytic pathway that includes the transthyretin protein TTR-52, as well as CED-7, NRF-5 and CED-6 (refs 9, 10, 11, 12). We show that TTR-52 binds to PS exposed on the injured axon, and can restore fusion several hours after injury. We propose that PS functions as a 'save-me' signal for the distal fragment, allowing conserved apoptotic cell clearance molecules to function in re-establishing axonal integrity during regeneration of the nervous system.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Neumann, Brent -- Coakley, Sean -- Giordano-Santini, Rosina -- Linton, Casey -- Lee, Eui Seung -- Nakagawa, Akihisa -- Xue, Ding -- Hilliard, Massimo A -- GM059083/GM/NIGMS NIH HHS/ -- GM079097/GM/NIGMS NIH HHS/ -- GM088241/GM/NIGMS NIH HHS/ -- P40 OD010440/OD/NIH HHS/ -- R01 NS060129/NS/NINDS NIH HHS/ -- England -- Nature. 2015 Jan 8;517(7533):219-22. doi: 10.1038/nature14102.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉CJCADR, Queensland Brain Institute, The University of Queensland, Brisbane QLD 4072, Australia. ; Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado 80309, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25567286" target="_blank"〉PubMed〈/a〉
    Keywords: ATP-Binding Cassette Transporters/metabolism ; Animals ; Apoptosis/*physiology ; Axons/*metabolism/pathology ; Caenorhabditis elegans/*cytology/*metabolism ; Caenorhabditis elegans Proteins/genetics/*metabolism ; Carrier Proteins/metabolism ; Growth Cones/metabolism ; Membrane Glycoproteins/*metabolism ; Mutation ; Nerve Regeneration/*physiology ; Phagocytes/metabolism ; Phagocytosis ; Phosphatidylserines/metabolism ; Phosphoproteins/metabolism ; Receptors, Cell Surface/metabolism ; Signal Transduction ; Spectrin/genetics/metabolism
    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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    14-3-3 proteins act as intracellular receptors for rice Hd3a florigen (2011)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2011-08-02
    Description: 'Florigen' was proposed 75 years ago to be synthesized in the leaf and transported to the shoot apex, where it induces flowering. Only recently have genetic and biochemical studies established that florigen is encoded by FLOWERING LOCUS T (FT), a gene that is universally conserved in higher plants. Nonetheless, the exact function of florigen during floral induction remains poorly understood and receptors for florigen have not been identified. Here we show that the rice FT homologue Hd3a interacts with 14-3-3 proteins in the apical cells of shoots, yielding a complex that translocates to the nucleus and binds to the Oryza sativa (Os)FD1 transcription factor, a rice homologue of Arabidopsis thaliana FD. The resultant ternary 'florigen activation complex' (FAC) induces transcription of OsMADS15, a homologue of A. thaliana APETALA1 (AP1), which leads to flowering. We have determined the 2.4 A crystal structure of rice FAC, which provides a mechanistic basis for florigen function in flowering. Our results indicate that 14-3-3 proteins act as intracellular receptors for florigen in shoot apical cells, and offer new approaches to manipulate flowering in various crops and trees.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Taoka, Ken-ichiro -- Ohki, Izuru -- Tsuji, Hiroyuki -- Furuita, Kyoko -- Hayashi, Kokoro -- Yanase, Tomoko -- Yamaguchi, Midori -- Nakashima, Chika -- Purwestri, Yekti Asih -- Tamaki, Shojiro -- Ogaki, Yuka -- Shimada, Chihiro -- Nakagawa, Atsushi -- Kojima, Chojiro -- Shimamoto, Ko -- England -- Nature. 2011 Jul 31;476(7360):332-5. doi: 10.1038/nature10272.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Plant Molecular Genetics, Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21804566" target="_blank"〉PubMed〈/a〉
    Keywords: 14-3-3 Proteins/*metabolism ; *Arabidopsis Proteins/chemistry ; Calcium-Binding Proteins/chemistry ; Cell Nucleus/metabolism ; Flowers/*growth & development/*metabolism ; Gene Expression Regulation, Plant ; MADS Domain Proteins/chemistry ; Models, Molecular ; Multiprotein Complexes/chemistry/metabolism ; Oryza/genetics/growth & development/*metabolism ; Plant Proteins/chemistry/genetics/*metabolism ; Plant Shoots/cytology ; Protein Binding ; Sequence Homology, Amino Acid ; Transcription Factors/chemistry ; Two-Hybrid System Techniques
    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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  • 8
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    Utilization of Bark Condensed Tannin as Natural Preservatives Against Subterranean Termite (2018)
    Institute of Physics (IOP)
    Details
    Publication Date: 2018-06-30
    Description: Extractive-based preservative has been isolated from many parts of plant to protect wood from fungi or pest. This is due to the presence of bioactive chemical as a natural preservative. Present study, the condensed tannin was isolated from bark-waste of Acacia crassicarpa and Acacia mearnsii . The yield of the extracts obtained from A. crassicarpa using a 70% acetone aqueous solution (7% based on bark weight) is less than that obtained from A. mearnsii (34%). To evaluate the termiticidal activity of condensed tannin from both extracts, no-choice tests were conducted using Reticulitermes speratus . After 14 days, mass loss of the dimmer condensed tannin treated was less than 50%, significantly different with control. In addition, a monomer condensed tannin, catechin was presented the similar result. Meanwhile, the termite mortality of catechin is slightly higher than the dimmer. According to both parameter, the medium level of mass loss and termit...
    Print ISSN: 1755-1307
    Electronic ISSN: 1755-1315
    Topics: Geography , Geosciences , Physics
    Published by Institute of Physics (IOP)
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  • 9
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    A high-resolution structure of the pre-microRNA nuclear export machinery (2009)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2009-12-08
    Description: Nuclear export of microRNAs (miRNAs) by exportin-5 (Exp-5) is an essential step in miRNA biogenesis. Here, we present the 2.9 angstrom structure of the pre-miRNA nuclear export machinery formed by pre-miRNA complexed with Exp-5 and a guanine triphosphate (GTP)-bound form of the small nuclear guanine triphosphatase (GTPase) Ran (RanGTP). The x-ray structure shows that Exp-5:RanGTP recognizes the 2-nucleotide 3' overhang structure and the double-stranded stem of the pre-miRNA. Exp-5:RanGTP shields the pre-miRNA stem from degradation in a baseball mitt-like structure where it is held by broadly distributed weak interactions, whereas a tunnel-like structure of Exp-5 interacts strongly with the 2-nucleotide 3' overhang through hydrogen bonds and ionic interactions. RNA recognition by Exp-5:RanGTP does not depend on RNA sequence, implying that Exp-5:RanGTP can recognize a variety of pre-miRNAs.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Okada, Chimari -- Yamashita, Eiki -- Lee, Soo Jae -- Shibata, Satoshi -- Katahira, Jun -- Nakagawa, Atsushi -- Yoneda, Yoshihiro -- Tsukihara, Tomitake -- New York, N.Y. -- Science. 2009 Nov 27;326(5957):1275-9. doi: 10.1126/science.1178705.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Protein Research, Osaka University, 3-2 Yamada-oka, Suita, Osaka 565-0871, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19965479" target="_blank"〉PubMed〈/a〉
    Keywords: Active Transport, Cell Nucleus ; Animals ; Binding Sites ; Crystallization ; Crystallography, X-Ray ; Dogs ; Humans ; Hydrogen Bonding ; Karyopherins/*chemistry/metabolism ; MicroRNAs/*chemistry/metabolism ; Models, Molecular ; Nucleic Acid Conformation ; Physicochemical Processes ; Protein Conformation ; ran GTP-Binding Protein/chemistry/metabolism
    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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  • 10
    Electronic Resource
    Electronic Resource
    Structure-activity relations among the O-acyl derivatives of leucomycin. Correlation of minimal inhibitory concentrations with binding to Escherichia coli ribosomes (1977)
    s.l. : American Chemical Society
    Journal of medicinal chemistry 20 (1977), S. 732-736 
    Details
    ISSN: 1520-4804
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/jm00215a025
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