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  • 1
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    "Newton's cradle" proton relay with amide-imidic acid tautomerization in inverting cellulase visualized by neutron crystallography (2015)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2015-08-23
    Description: Hydrolysis of carbohydrates is a major bioreaction in nature, catalyzed by glycoside hydrolases (GHs). We used neutron diffraction and high-resolution x-ray diffraction analyses to investigate the hydrogen bond network in inverting cellulase Pc Cel45A, which is an endoglucanase belonging to subfamily C of GH family 45, isolated from the basidiomycete Phanerochaete chrysosporium . Examination of the enzyme and enzyme-ligand structures indicates a key role of multiple tautomerizations of asparagine residues and peptide bonds, which are finally connected to the other catalytic residue via typical side-chain hydrogen bonds, in forming the "Newton’s cradle"–like proton relay pathway of the catalytic cycle. Amide–imidic acid tautomerization of asparagine has not been taken into account in recent molecular dynamics simulations of not only cellulases but also general enzyme catalysis, and it may be necessary to reconsider our interpretation of many enzymatic reactions.
    Electronic ISSN: 2375-2548
    Topics: Natural Sciences in General
    Published by American Association for the Advancement of Science (AAAS)
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  • 2
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    The slow earthquake spectrum in the Japan Trench illuminated by the S-net seafloor observatories (2019)
    American Association for the Advancement of Science (AAAS)
    In: Science
    Details
    Publication Date: 2019
    Description: 〈p〉Investigating slow earthquake activity in subduction zones provides insight into the slip behavior of megathrusts, which can provide important clues about the rupture extent of future great earthquakes. Using the S-net ocean-bottom seismograph network along the Japan Trench, we mapped a detailed distribution of tectonic tremors, which coincided with very-low-frequency earthquakes and a slow slip event. Compiling these and other related observations, including repeating earthquakes and earthquake swarms, we found that the slow earthquake distribution is complementary to the Tohoku-Oki earthquake rupture. We used our observations to divide the megathrust in the Japan Trench into three along-strike segments characterized by different slip behaviors. We found that the rupture of the Tohoku-Oki earthquake, which nucleated in the central segment, was terminated by the two adjacent segments.〈/p〉
    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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  • 3
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    The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-12-14
    Description: The first chordates appear in the fossil record at the time of the Cambrian explosion, nearly 550 million years ago. The modern ascidian tadpole represents a plausible approximation to these ancestral chordates. To illuminate the origins of chordate and vertebrates, we generated a draft of the protein-coding portion of the genome of the most studied ascidian, Ciona intestinalis. The Ciona genome contains approximately 16,000 protein-coding genes, similar to the number in other invertebrates, but only half that found in vertebrates. Vertebrate gene families are typically found in simplified form in Ciona, suggesting that ascidians contain the basic ancestral complement of genes involved in cell signaling and development. The ascidian genome has also acquired a number of lineage-specific innovations, including a group of genes engaged in cellulose metabolism that are related to those in bacteria and fungi.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dehal, Paramvir -- Satou, Yutaka -- Campbell, Robert K -- Chapman, Jarrod -- Degnan, Bernard -- De Tomaso, Anthony -- Davidson, Brad -- Di Gregorio, Anna -- Gelpke, Maarten -- Goodstein, David M -- Harafuji, Naoe -- Hastings, Kenneth E M -- Ho, Isaac -- Hotta, Kohji -- Huang, Wayne -- Kawashima, Takeshi -- Lemaire, Patrick -- Martinez, Diego -- Meinertzhagen, Ian A -- Necula, Simona -- Nonaka, Masaru -- Putnam, Nik -- Rash, Sam -- Saiga, Hidetoshi -- Satake, Masanobu -- Terry, Astrid -- Yamada, Lixy -- Wang, Hong-Gang -- Awazu, Satoko -- Azumi, Kaoru -- Boore, Jeffrey -- Branno, Margherita -- Chin-Bow, Stephen -- DeSantis, Rosaria -- Doyle, Sharon -- Francino, Pilar -- Keys, David N -- Haga, Shinobu -- Hayashi, Hiroko -- Hino, Kyosuke -- Imai, Kaoru S -- Inaba, Kazuo -- Kano, Shungo -- Kobayashi, Kenji -- Kobayashi, Mari -- Lee, Byung-In -- Makabe, Kazuhiro W -- Manohar, Chitra -- Matassi, Giorgio -- Medina, Monica -- Mochizuki, Yasuaki -- Mount, Steve -- Morishita, Tomomi -- Miura, Sachiko -- Nakayama, Akie -- Nishizaka, Satoko -- Nomoto, Hisayo -- Ohta, Fumiko -- Oishi, Kazuko -- Rigoutsos, Isidore -- Sano, Masako -- Sasaki, Akane -- Sasakura, Yasunori -- Shoguchi, Eiichi -- Shin-i, Tadasu -- Spagnuolo, Antoinetta -- Stainier, Didier -- Suzuki, Miho M -- Tassy, Olivier -- Takatori, Naohito -- Tokuoka, Miki -- Yagi, Kasumi -- Yoshizaki, Fumiko -- Wada, Shuichi -- Zhang, Cindy -- Hyatt, P Douglas -- Larimer, Frank -- Detter, Chris -- Doggett, Norman -- Glavina, Tijana -- Hawkins, Trevor -- Richardson, Paul -- Lucas, Susan -- Kohara, Yuji -- Levine, Michael -- Satoh, Nori -- Rokhsar, Daniel S -- HD-37105/HD/NICHD NIH HHS/ -- New York, N.Y. -- Science. 2002 Dec 13;298(5601):2157-67.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉U.S. Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12481130" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Animals ; Apoptosis ; Base Sequence ; Cellulose/metabolism ; Central Nervous System/physiology ; Ciona intestinalis/anatomy & histology/classification/*genetics/physiology ; Computational Biology ; Endocrine System/physiology ; Gene Dosage ; Gene Duplication ; Genes ; Genes, Homeobox ; *Genome ; Heart/embryology/physiology ; Immunity/genetics ; Molecular Sequence Data ; Multigene Family ; Muscle Proteins/genetics ; Organizers, Embryonic/physiology ; Phylogeny ; Polymorphism, Genetic ; Proteins/genetics/physiology ; *Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Species Specificity ; Thyroid Gland/physiology ; Urochordata/genetics ; Vertebrates/anatomy & histology/classification/genetics/physiology
    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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  • 4
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    Cold acclimation via the KQT-2 potassium channel is modulated by oxygen in Caenorhabditis elegans (2019)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2019
    Description: 〈p〉Adaptive responses to external temperatures are essential for survival in changing environments. We show here that environmental oxygen concentration affects cold acclimation in 〈i〉Caenorhabditis elegans〈/i〉 and that this response is regulated by a KCNQ-type potassium channel, KQT-2. Depending on culture conditions, 〈i〉kqt-2〈/i〉 mutants showed supranormal cold acclimation, caused by abnormal thermosensation in ADL chemosensory neurons. ADL neurons are responsive to temperature via transient receptor potential channels—OSM-9, OCR-2, and OCR-1—with OCR-1 negatively regulating ADL function. Similarly, KQT-2 and KQT-3 regulate ADL activity, with KQT-2 positively regulating ADL function. Abnormal cold acclimation and acute temperature responses of ADL neurons in 〈i〉kqt-2〈/i〉 mutants were suppressed by an oxygen-receptor mutation in URX coelomic sensory neurons, which are electrically connected to ADL via RMG interneurons. Likewise, low oxygen suppressed supranormal 〈i〉kqt-2〈/i〉 cold acclimation. These data thus demonstrate a simple neuronal circuit integrating two different sensory modalities, temperature and oxygen, that determines cold acclimation.〈/p〉
    Electronic ISSN: 2375-2548
    Topics: Natural Sciences in General
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  • 5
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    Anisotropy and corotation of galactic cosmic rays (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-10-21
    Description: The intensity of Galactic cosmic rays is nearly isotropic because of the influence of magnetic fields in the Milky Way. Here, we present two-dimensional high-precision anisotropy measurement for energies from a few to several hundred teraelectronvolts (TeV), using the large data sample of the Tibet Air Shower Arrays. Besides revealing finer details of the known anisotropies, a new component of Galactic cosmic ray anisotropy in sidereal time is uncovered around the Cygnus region direction. For cosmic-ray energies up to a few hundred TeV, all components of anisotropies fade away, showing a corotation of Galactic cosmic rays with the local Galactic magnetic environment. These results have broad implications for a comprehensive understanding of cosmic rays, supernovae, magnetic fields, and heliospheric and Galactic dynamic environments.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Amenomori, M -- Ayabe, S -- Bi, X J -- Chen, D -- Cui, S W -- Danzengluobu -- Ding, L K -- Ding, X H -- Feng, C F -- Feng, Zhaoyang -- Feng, Z Y -- Gao, X Y -- Geng, Q X -- Guo, H W -- He, H H -- He, M -- Hibino, K -- Hotta, N -- Hu, Haibing -- Hu, H B -- Huang, J -- Huang, Q -- Jia, H Y -- Kajino, F -- Kasahara, K -- Katayose, Y -- Kato, C -- Kawata, K -- Labaciren -- Le, G M -- Li, A F -- Li, J Y -- Lou, Y-Q -- Lu, H -- Lu, S L -- Meng, X R -- Mizutani, K -- Mu, J -- Munakata, K -- Nagai, A -- Nanjo, H -- Nishizawa, M -- Ohnishi, M -- Ohta, I -- Onuma, H -- Ouchi, T -- Ozawa, S -- Ren, J R -- Saito, T -- Saito, T Y -- Sakata, M -- Sako, T K -- Sasaki, T -- Shibata, M -- Shiomi, A -- Shirai, T -- Sugimoto, H -- Takita, M -- Tan, Y H -- Tateyama, N -- Torii, S -- Tsuchiya, H -- Udo, S -- Wang, B -- Wang, H -- Wang, X -- Wang, Y G -- Wu, H R -- Xue, L -- Yamamoto, Y -- Yan, C T -- Yang, X C -- Yasue, S -- Ye, Z H -- Yu, G C -- Yuan, A F -- Yuda, T -- Zhang, H M -- Zhang, J L -- Zhang, N J -- Zhang, X Y -- Zhang, Y -- Zhang, Yi -- Zhaxisangzhu -- Zhou, X X -- Tibet ASgamma Collaboration -- New York, N.Y. -- Science. 2006 Oct 20;314(5798):439-43.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physics, Hirosaki University, Hirosaki 036-8561, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17053141" target="_blank"〉PubMed〈/a〉
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
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  • 6
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    Draxin, a repulsive guidance protein for spinal cord and forebrain commissures (2009)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2009-01-20
    Description: Axon guidance proteins are critical for the correct wiring of the nervous system during development. Several axon guidance cues and their family members have been well characterized. More unidentified axon guidance cues are assumed to participate in the formation of the extremely complex nervous system. We identified a secreted protein, draxin, that shares no homology with known guidance cues. Draxin inhibited or repelled neurite outgrowth from dorsal spinal cord and cortical explants in vitro. Ectopically expressed draxin inhibited growth or caused misrouting of chick spinal cord commissural axons in vivo. draxin knockout mice showed defasciculation of spinal cord commissural axons and absence of all forebrain commissures. Thus, draxin is a previously unknown chemorepulsive axon guidance molecule required for the development of spinal cord and forebrain commissures.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Islam, Shahidul M -- Shinmyo, Yohei -- Okafuji, Tatsuya -- Su, Yuhong -- Naser, Iftekhar Bin -- Ahmed, Giasuddin -- Zhang, Sanbing -- Chen, Sandy -- Ohta, Kunimasa -- Kiyonari, Hiroshi -- Abe, Takaya -- Tanaka, Satomi -- Nishinakamura, Ryuichi -- Terashima, Toshio -- Kitamura, Toshio -- Tanaka, Hideaki -- New York, N.Y. -- Science. 2009 Jan 16;323(5912):388-93. doi: 10.1126/science.1165187.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Developmental Neurobiology, Graduate School of Medical Sciences, Kumamoto University, 1-1-1 Honjo, Kumamoto 860-8556, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19150847" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Axons/*physiology ; COS Cells ; Cercopithecus aethiops ; Chick Embryo ; Coculture Techniques ; Corpus Callosum/embryology/metabolism ; Electroporation ; Growth Cones/metabolism/physiology ; Intercellular Signaling Peptides and ; Proteins/chemistry/genetics/metabolism/*physiology ; Mice ; Mice, Knockout ; Molecular Sequence Data ; Neurites/metabolism/*physiology ; Neurogenesis ; Neuroglia/metabolism ; Prosencephalon/abnormalities/*embryology/metabolism ; Recombinant Proteins/metabolism ; Spinal Cord/*embryology/metabolism ; Tissue Culture Techniques
    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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  • 7
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    Thin-film transistor fabricated in single-crystalline transparent oxide semiconductor (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-05-24
    Description: We report the fabrication of transparent field-effect transistors using a single-crystalline thin-film transparent oxide semiconductor, InGaO3(ZnO)5, as an electron channel and amorphous hafnium oxide as a gate insulator. The device exhibits an on-to-off current ratio of approximately 106 and a field-effect mobility of approximately 80 square centimeters per volt per second at room temperature, with operation insensitive to visible light irradiation. The result provides a step toward the realization of transparent electronics for next-generation optoelectronics.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nomura, Kenji -- Ohta, Hiromichi -- Ueda, Kazushige -- Kamiya, Toshio -- Hirano, Masahiro -- Hosono, Hideo -- New York, N.Y. -- Science. 2003 May 23;300(5623):1269-72.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Hosono Transparent ElectroActive Materials, Exploratory Research for Advanced Technology (ERATO), Japan Science and Technology (JST), 3-2-1 Sakado, Takatsu, Kawasaki 213-0012, Japan. nomura@lucid.msl.titech.ac.jp〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12764192" target="_blank"〉PubMed〈/a〉
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
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  • 8
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    Nuclear encoding of a chloroplast RNA polymerase sigma subunit in a red alga (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-06-28
    Description: A chloroplast RNA polymerase sigma factor is encoded by a nuclear gene, sigA, in the red alga Cyanidium caldarium RK-1. The encoded protein functions as an RNA polymerase sigma factor in vitro and it is localized to the chloroplast in vivo. SigA shows high sequence similarity to the sigma factors of cyanobacteria, which is indicative of the ancestral endosymbiotic event and subsequent transfer of the sigA gene to the nuclear genome.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tanaka, K -- Oikawa, K -- Ohta, N -- Kuroiwa, H -- Kuroiwa, T -- Takahashi, H -- New York, N.Y. -- Science. 1996 Jun 28;272(5270):1932-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Molecular and Cellular Biosciences, University of Tokyo, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8658165" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Base Sequence ; Blotting, Southern ; Cell Nucleus/genetics ; Chloroplasts/*enzymology/genetics ; DNA-Directed RNA Polymerases/chemistry/*genetics/isolation & ; purification/metabolism ; Molecular Sequence Data ; Recombinant Proteins/isolation & purification/metabolism ; Rhodophyta/enzymology/*genetics/ultrastructure ; Sequence Alignment ; Sigma Factor/chemistry/*genetics/isolation & purification/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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  • 9
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    Population biology of antigen presentation by MHC class I molecules (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-04-05
    Description: In principle, the function of major histocompatibility complex (MHC) molecules is simple: to bind a peptide and engage a T cell. In practice, placing this function within the context of the immune response begs questions of population biology; How does the immune response emerge from the interactions among populations of peptides, T cells and MHC molecules? Within a population of vertebrates, how does MHC polymorphism stamp individuality on the response? Does polymorphism confer differential advantages in responding to parasites? How are the pressures on the MHC reflected in turnover of alleles? The role of mutation, recombination, selection, and drift in the generation and maintenance of MHC class 1 polymorphism are considered.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Parham, P -- Ohta, T -- New York, N.Y. -- Science. 1996 Apr 5;272(5258):67-74.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Structural Biology, Stanford University, CA 94305 USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8600539" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; *Antigen Presentation ; Antigens/immunology ; Evolution, Molecular ; Gene Frequency ; *Genes, MHC Class I ; Genetic Variation ; *Genetics, Population ; Histocompatibility Antigens Class I/genetics/*immunology ; Humans ; Indians, North American/genetics ; Indians, South American/genetics ; Infection/immunology ; Molecular Sequence Data ; Polymorphism, Genetic ; Recombination, Genetic ; Selection, Genetic
    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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    Controlling the electronic structure of bilayer graphene (2006)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2006-08-19
    Description: We describe the synthesis of bilayer graphene thin films deposited on insulating silicon carbide and report the characterization of their electronic band structure using angle-resolved photoemission. By selectively adjusting the carrier concentration in each layer, changes in the Coulomb potential led to control of the gap between valence and conduction bands. This control over the band structure suggests the potential application of bilayer graphene to switching functions in atomic-scale electronic devices.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ohta, Taisuke -- Bostwick, Aaron -- Seyller, Thomas -- Horn, Karsten -- Rotenberg, Eli -- New York, N.Y. -- Science. 2006 Aug 18;313(5789):951-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Advanced Light Source, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16917057" target="_blank"〉PubMed〈/a〉
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
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