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  • 1
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    A primordial and reversible TCA cycle in a facultatively chemolithoautotrophic thermophile (2018)
    American Association for the Advancement of Science (AAAS)
    In: Science
    Details
    Publication Date: 2018-02-03
    Description: Inorganic carbon fixation is essential to sustain life on Earth, and the reductive tricarboxylic acid (rTCA) cycle is one of the most ancient carbon fixation metabolisms. A combination of genomic, enzymatic, and metabolomic analyses of a deeply branching chemolithotrophic Thermosulfidibacter takaii ABI70S6 T revealed a previously unknown reversible TCA cycle whose direction was controlled by the available carbon source(s). Under a chemolithoautotrophic condition, a rTCA cycle occurred with the reverse reaction of citrate synthase (CS) and not with the adenosine 5'-triphosphate–dependent citrate cleavage reactions that had been regarded as essential for the conventional rTCA cycle. Phylometabolic evaluation suggests that the TCA cycle with reversible CS may represent an ancestral mode of the rTCA cycle and raises the possibility of a facultatively chemolithomixotrophic origin of life.
    Keywords: Biochemistry, Microbiology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 2
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    Switching dynamics and linear response spectra of a driven one-dimensional nonlinear lattice containing an intrinsic localized mode (2013)
    American Physical Society (APS)
    Details
    Publication Date: 2013-02-01
    Description: Author(s): M. Sato, S. Imai, N. Fujita, W. Shi, Y. Takao, Y. Sada, B. E. Hubbard, B. Ilic, and A. J. Sievers An intrinsic localized mode (ILM) represents a localized vibrational excitation in a nonlinear lattice. Such a mode will stay in resonance as the driver frequency is changed adiabatically until a bifurcation point is reached, at which point the ILM switches and disappears. The dynamics behind switch... [Phys. Rev. E 87, 012920] Published Thu Jan 31, 2013
    Keywords: Nonlinear Dynamics and Chaos
    Print ISSN: 1539-3755
    Electronic ISSN: 1550-2376
    Topics: Physics
    Published by American Physical Society (APS)
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  • 3
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    ZFN-mediated transgene insertion in sea urchin [Developmental Biology] (2012)
    National Academy of Sciences
    Details
    Publication Date: 2012-07-04
    Description: To understand complex biological systems, such as the development of multicellular organisms, it is important to characterize the gene expression dynamics. However, there is currently no universal technique for targeted insertion of reporter genes and quantitative imaging in multicellular model systems. Recently, genome editing using zinc-finger nucleases (ZFNs) has been reported in several models. ZFNs consist of a zinc-finger DNA-binding array with the nuclease domain of the restriction enzyme FokI and facilitate targeted transgene insertion. In this study, we successfully inserted a GFP reporter cassette into the HpEts1 gene locus of the sea urchin, Hemicentrotus pulcherrimus. We achieved this insertion by injecting eggs with a pair of ZFNs for HpEts1 with a targeting donor construct that contained ∼1-kb homology arms and a 2A-histone H2B–GFP cassette. We increased the efficiency of the ZFN-mediated targeted transgene insertion by in situ linearization of the targeting donor construct and cointroduction of an mRNA for a dominant-negative form of HpLig4, which encodes the H. pulcherrimus homolog of DNA ligase IV required for error-prone nonhomologous end joining. We measured the fluorescence intensity of GFP at the single-cell level in living embryos during development and found that there was variation in HpEts1 expression among the primary mesenchyme cells. These findings demonstrate the feasibility of ZFN-mediated targeted transgene insertion to enable quantification of the expression levels of endogenous genes during development in living sea urchin embryos.
    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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  • 4
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    Experimental Observation of the Bifurcation Dynamics of an Intrinsic Localized Mode in a Driven 1D Nonlinear Lattice (2011)
    American Physical Society (APS)
    Details
    Publication Date: 2011-12-01
    Description: Author(s): M. Sato, S. Imai, N. Fujita, S. Nishimura, Y. Takao, Y. Sada, B. E. Hubbard, B. Ilic, and A. J. Sievers [Phys. Rev. Lett. 107, 234101] Published Wed Nov 30, 2011
    Keywords: Nonlinear Dynamics, Fluid Dynamics, Classical Optics, etc.
    Print ISSN: 0031-9007
    Electronic ISSN: 1079-7114
    Topics: Physics
    Published by American Physical Society (APS)
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  • 5
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    Loss of the autophagy protein Atg16L1 enhances endotoxin-induced IL-1beta production (2008)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2008-10-14
    Description: Systems for protein degradation are essential for tight control of the inflammatory immune response. Autophagy, a bulk degradation system that delivers cytoplasmic constituents into autolysosomes, controls degradation of long-lived proteins, insoluble protein aggregates and invading microbes, and is suggested to be involved in the regulation of inflammation. However, the mechanism underlying the regulation of inflammatory response by autophagy is poorly understood. Here we show that Atg16L1 (autophagy-related 16-like 1), which is implicated in Crohn's disease, regulates endotoxin-induced inflammasome activation in mice. Atg16L1-deficiency disrupts the recruitment of the Atg12-Atg5 conjugate to the isolation membrane, resulting in a loss of microtubule-associated protein 1 light chain 3 (LC3) conjugation to phosphatidylethanolamine. Consequently, both autophagosome formation and degradation of long-lived proteins are severely impaired in Atg16L1-deficient cells. Following stimulation with lipopolysaccharide, a ligand for Toll-like receptor 4 (refs 8, 9), Atg16L1-deficient macrophages produce high amounts of the inflammatory cytokines IL-1beta and IL-18. In lipopolysaccharide-stimulated macrophages, Atg16L1-deficiency causes Toll/IL-1 receptor domain-containing adaptor inducing IFN-beta (TRIF)-dependent activation of caspase-1, leading to increased production of IL-1beta. Mice lacking Atg16L1 in haematopoietic cells are highly susceptible to dextran sulphate sodium-induced acute colitis, which is alleviated by injection of anti-IL-1beta and IL-18 antibodies, indicating the importance of Atg16L1 in the suppression of intestinal inflammation. These results demonstrate that Atg16L1 is an essential component of the autophagic machinery responsible for control of the endotoxin-induced inflammatory immune response.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Saitoh, Tatsuya -- Fujita, Naonobu -- Jang, Myoung Ho -- Uematsu, Satoshi -- Yang, Bo-Gie -- Satoh, Takashi -- Omori, Hiroko -- Noda, Takeshi -- Yamamoto, Naoki -- Komatsu, Masaaki -- Tanaka, Keiji -- Kawai, Taro -- Tsujimura, Tohru -- Takeuchi, Osamu -- Yoshimori, Tamotsu -- Akira, Shizuo -- AI070167/AI/NIAID NIH HHS/ -- England -- Nature. 2008 Nov 13;456(7219):264-8. doi: 10.1038/nature07383. Epub 2008 Oct 5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Host Defense, WPI Immunology Frontier Research Center, Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18849965" target="_blank"〉PubMed〈/a〉
    Keywords: Adenine/analogs & derivatives/pharmacology ; Animals ; Autophagy/*genetics ; Carrier Proteins/*genetics ; Chimera ; Colitis/chemically induced/immunology ; Dextran Sulfate/pharmacology ; Female ; Gene Expression Regulation/*drug effects ; Interleukin-1beta/*biosynthesis/metabolism ; Lipopolysaccharides/*pharmacology ; Macrophages/*drug effects/*metabolism ; Mice ; Mice, Inbred C57BL ; Mutation
    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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  • 6
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    Dodecagonal tiling in mesoporous silica (2012)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2012-07-20
    Description: Recent advances in the fabrication of quasicrystals in soft matter systems have increased the length scales for quasicrystals into the mesoscale range (20 to 500 angstroms). Thus far, dendritic liquid crystals, ABC-star polymers, colloids and inorganic nanoparticles have been reported to yield quasicrystals. These quasicrystals offer larger length scales than intermetallic quasicrystals (a few angstroms), thus potentially leading to optical applications through the realization of a complete photonic bandgap induced via multiple scattering of light waves in virtually all directions. However, the materials remain far from structurally ideal, in contrast to their intermetallic counterparts, and fine control over the structure through a self-organization process has yet to be attained. Here we use the well-established self-assembly of surfactant micelles to produce a new class of mesoporous silicas, which exhibit 12-fold (dodecagonal) symmetry in both electron diffraction and morphology. Each particle reveals, in the 12-fold cross-section, an analogue of dodecagonal quasicrystals in the centre surrounded by 12 fans of crystalline domains in the peripheral part. The quasicrystallinity has been verified by selected-area electron diffraction and quantitative phason strain analyses on transmission electron microscope images obtained from the central region. We argue that the structure forms through a non-equilibrium growth process, wherein the competition between different micellar configurations has a central role in tuning the structure. A simple theoretical model successfully reproduces the observed features and thus establishes a link between the formation process and the resulting structure.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Xiao, Changhong -- Fujita, Nobuhisa -- Miyasaka, Keiichi -- Sakamoto, Yasuhiro -- Terasaki, Osamu -- England -- Nature. 2012 Jul 18;487(7407):349-53. doi: 10.1038/nature11230.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Materials and Environmental Chemistry, Bezelii Center EXSELENT on Porous Materials, Stockholm University, S-10691 Stockholm, Sweden.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22810699" target="_blank"〉PubMed〈/a〉
    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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    Autophagosomes form at ER-mitochondria contact sites (2013)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2013-03-05
    Description: Autophagy is a tightly regulated intracellular bulk degradation/recycling system that has fundamental roles in cellular homeostasis. Autophagy is initiated by isolation membranes, which form and elongate as they engulf portions of the cytoplasm and organelles. Eventually isolation membranes close to form double membrane-bound autophagosomes and fuse with lysosomes to degrade their contents. The physiological role of autophagy has been determined since its discovery, but the origin of autophagosomal membranes has remained unclear. At present, there is much controversy about the organelle from which the membranes originate--the endoplasmic reticulum (ER), mitochondria and plasma membrane. Here we show that autophagosomes form at the ER-mitochondria contact site in mammalian cells. Imaging data reveal that the pre-autophagosome/autophagosome marker ATG14 (also known as ATG14L) relocalizes to the ER-mitochondria contact site after starvation, and the autophagosome-formation marker ATG5 also localizes at the site until formation is complete. Subcellular fractionation showed that ATG14 co-fractionates in the mitochondria-associated ER membrane fraction under starvation conditions. Disruption of the ER-mitochondria contact site prevents the formation of ATG14 puncta. The ER-resident SNARE protein syntaxin 17 (STX17) binds ATG14 and recruits it to the ER-mitochondria contact site. These results provide new insight into organelle biogenesis by demonstrating that the ER-mitochondria contact site is important in autophagosome formation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hamasaki, Maho -- Furuta, Nobumichi -- Matsuda, Atsushi -- Nezu, Akiko -- Yamamoto, Akitsugu -- Fujita, Naonobu -- Oomori, Hiroko -- Noda, Takeshi -- Haraguchi, Tokuko -- Hiraoka, Yasushi -- Amano, Atsuo -- Yoshimori, Tamotsu -- England -- Nature. 2013 Mar 21;495(7441):389-93. doi: 10.1038/nature11910. Epub 2013 Mar 3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genetics, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23455425" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptor Proteins, Vesicular Transport/metabolism ; Animals ; *Autophagy ; COS Cells ; Cercopithecus aethiops ; Endoplasmic Reticulum/*metabolism/ultrastructure ; Gene Knockdown Techniques ; HEK293 Cells ; HeLa Cells ; Humans ; Intracellular Membranes/*metabolism ; Mitochondria/*metabolism/ultrastructure ; Phagosomes/*metabolism/ultrastructure ; Protein Transport ; Qa-SNARE Proteins/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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  • 8
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    Jam1a-Jam2a interactions regulate haematopoietic stem cell fate through Notch signalling (2014)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2014-08-15
    Description: Notch signalling plays a key role in the generation of haematopoietic stem cells (HSCs) during vertebrate development and requires intimate contact between signal-emitting and signal-receiving cells, although little is known regarding when, where and how these intercellular events occur. We previously reported that the somitic Notch ligands, Dlc and Dld, are essential for HSC specification. It has remained unclear, however, how these somitic requirements are connected to the later emergence of HSCs from the dorsal aorta. Here we show in zebrafish that Notch signalling establishes HSC fate as their shared vascular precursors migrate across the ventral face of the somite and that junctional adhesion molecules (JAMs) mediate this required Notch signal transduction. HSC precursors express jam1a (also known as f11r) and migrate axially across the ventral somite, where Jam2a and the Notch ligands Dlc and Dld are expressed. Despite no alteration in the expression of Notch ligand or receptor genes, loss of function of jam1a led to loss of Notch signalling and loss of HSCs. Enforced activation of Notch in shared vascular precursors rescued HSCs in jam1a or jam2a deficient embryos. Together, these results indicate that Jam1a-Jam2a interactions facilitate the transduction of requisite Notch signals from the somite to the precursors of HSCs, and that these events occur well before formation of the dorsal aorta.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4237229/" 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/PMC4237229/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kobayashi, Isao -- Kobayashi-Sun, Jingjing -- Kim, Albert D -- Pouget, Claire -- Fujita, Naonobu -- Suda, Toshio -- Traver, David -- R01 DK074482/DK/NIDDK NIH HHS/ -- R01-DK074482/DK/NIDDK NIH HHS/ -- England -- Nature. 2014 Aug 21;512(7514):319-23. doi: 10.1038/nature13623. Epub 2014 Aug 13.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California 92093-0380, USA. ; Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, California 92093-0380, USA. ; Department of Cell Differentiation, The Sakaguchi Laboratory, School of Medicine, Keio University, Shinjukuku, Tokyo 160-8582, Japan. ; 1] Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California 92093-0380, USA [2] Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, California 92093-0380, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25119047" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Aorta/cytology/growth & development/metabolism ; Cell Differentiation ; Cell Movement ; Hematopoietic Stem Cells/*cytology/*metabolism ; Junctional Adhesion Molecule A/genetics/*metabolism ; Junctional Adhesion Molecule B/genetics/*metabolism ; Phenotype ; Receptors, Cell Surface/genetics/*metabolism ; Receptors, Notch/*metabolism ; *Signal Transduction ; Somites/cytology/embryology/metabolism ; Zebrafish/embryology/*metabolism ; Zebrafish Proteins/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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  • 9
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    Solution structure of the activator contact domain of the RNA polymerase alpha subunit (1995)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1995-12-01
    Description: The structure of the carboxyl-terminal domain of the Escherichia coli RNA polymerase alpha subunit (alpha CTD), which is regarded as the contact site for transcription activator proteins and for the promoter UP element, was determined by nuclear magnetic resonance spectroscopy. Its compact structure of four helices and two long arms enclosing its hydrophobic core shows a folding topology distinct from those of other DNA-binding proteins. The UP element binding site was found on the surface comprising helix 1, the amino-terminal end of helix 4, and the preceding loop. Mutation experiments indicated that the contact sites for transcription activator proteins are also on the same surface.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jeon, Y H -- Negishi, T -- Shirakawa, M -- Yamazaki, T -- Fujita, N -- Ishihama, A -- Kyogoku, Y -- New York, N.Y. -- Science. 1995 Dec 1;270(5241):1495-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Protein Research, Osaka University, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7491496" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Binding Sites ; DNA/metabolism ; DNA-Directed RNA Polymerases/*chemistry/genetics/metabolism ; Escherichia coli/enzymology ; Magnetic Resonance Spectroscopy ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Promoter Regions, Genetic ; Protein Folding ; Protein Structure, Secondary ; Solutions ; Trans-Activators/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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  • 10
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    Manipulation of discrete nanostructures by selective modulation of noncovalent forces (2014)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2014-05-03
    Description: Covalent organic synthesis commonly uses the strategy of selective bond cleavage and formation. If a similar approach can be applied stepwisely to noncovalent synthesis, more exotic or challenging nanostructures might become achievable. Here, we report that ferrocene-based tetratopic pyridyl ligands, which can dynamically change their geometry by means of thermal rotation of their cyclopentadienyl rings in solution, assemble with AgBF4 into discrete metal-organic nanotubes with large and uniform diameters. The nanotubes can be cut into metal-organic nanorings through selective attenuation of the inter-nanoring interaction via ferrocene oxidation. The resultant nanorings can be transferred onto inorganic substrates electrostatically or allowed to reassemble to form the original nanotube by the reductive neutralization of their oxidized ferrocene units.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fukino, Takahiro -- Joo, Hyunho -- Hisada, Yuki -- Obana, Maiko -- Yamagishi, Hiroshi -- Hikima, Takaaki -- Takata, Masaki -- Fujita, Norifumi -- Aida, Takuzo -- New York, N.Y. -- Science. 2014 May 2;344(6183):499-504. doi: 10.1126/science.1252120. Epub 2014 Apr 10.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24786075" 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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