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  • 1
    Publication Date: 2016-07-22
    Description: The leaf economics spectrum has given us a fundamental understanding of the species variations in leaf variables. Across plant species, tight correlations among leaf mass per area (LMA), mass-based nitrogen ( N m ) and photosynthetic rate ( A m ) and leaf lifespan have been well known as trade-offs in leaf carbon economy. However, the regional or biome-level correlations may not be necessary to correspond with the global-scale analysis. Here, we show that almost all leaf variables in overwintering evergreen oaks in Japan were relatively well included within the evergreen-broadleaved trees in worldwide temperate forests, but N m was more consistent with that in deciduous broadleaved trees. Contrary to the universal correlations, the correlation between A m and N m among the evergreen oaks was negative and the correlation between A m and LMA disappeared. The unique performance was due to specific nitrogen allocation within leaves, i.e. the evergreen oaks with later leaf maturation had lower N m but higher nitrogen allocation to photosynthetic enzymes within leaves, to enhance carbon gain against the delayed leaf maturation and the shortened photosynthetic period due to cold winters. Our data demonstrate that correlations between leaf variables in a local scale are occasionally different from averaged global-scale datasets, because of the constraints in each biome.
    Keywords: plant science, ecology, environmental science
    Electronic ISSN: 2054-5703
    Topics: Natural Sciences in General
    Published by Royal Society
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  • 2
    Publication Date: 2003-07-19
    Description: We collected and completely sequenced 28,469 full-length complementary DNA clones from Oryza sativa L. ssp. japonica cv. Nipponbare. Through homology searches of publicly available sequence data, we assigned tentative protein functions to 21,596 clones (75.86%). Mapping of the cDNA clones to genomic DNA revealed that there are 19,000 to 20,500 transcription units in the rice genome. Protein informatics analysis against the InterPro database revealed the existence of proteins presented in rice but not in Arabidopsis. Sixty-four percent of our cDNAs are homologous to Arabidopsis proteins.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rice Full-Length cDNA Consortium -- National Institute of Agrobiological Sciences Rice Full-Length cDNA Project Team -- Kikuchi, Shoshi -- Satoh, Kouji -- Nagata, Toshifumi -- Kawagashira, Nobuyuki -- Doi, Koji -- Kishimoto, Naoki -- Yazaki, Junshi -- Ishikawa, Masahiro -- Yamada, Hitomi -- Ooka, Hisako -- Hotta, Isamu -- Kojima, Keiichi -- Namiki, Takahiro -- Ohneda, Eisuke -- Yahagi, Wataru -- Suzuki, Kohji -- Li, Chao Jie -- Ohtsuki, Kenji -- Shishiki, Toru -- Foundation of Advancement of International Science Genome Sequencing & Analysis Group -- Otomo, Yasuhiro -- Murakami, Kazuo -- Iida, Yoshiharu -- Sugano, Sumio -- Fujimura, Tatsuto -- Suzuki, Yutaka -- Tsunoda, Yuki -- Kurosaki, Takashi -- Kodama, Takeko -- Masuda, Hiromi -- Kobayashi, Michie -- Xie, Quihong -- Lu, Min -- Narikawa, Ryuya -- Sugiyama, Akio -- Mizuno, Kouichi -- Yokomizo, Satoko -- Niikura, Junko -- Ikeda, Rieko -- Ishibiki, Junya -- Kawamata, Midori -- Yoshimura, Akemi -- Miura, Junichirou -- Kusumegi, Takahiro -- Oka, Mitsuru -- Ryu, Risa -- Ueda, Mariko -- Matsubara, Kenichi -- RIKEN -- Kawai, Jun -- Carninci, Piero -- Adachi, Jun -- Aizawa, Katsunori -- Arakawa, Takahiro -- Fukuda, Shiro -- Hara, Ayako -- Hashizume, Wataru -- Hayatsu, Norihito -- Imotani, Koichi -- Ishii, Yoshiyuki -- Itoh, Masayoshi -- Kagawa, Ikuko -- Kondo, Shinji -- Konno, Hideaki -- Miyazaki, Ai -- Osato, Naoki -- Ota, Yoshimi -- Saito, Rintaro -- Sasaki, Daisuke -- Sato, Kenjiro -- Shibata, Kazuhiro -- Shinagawa, Akira -- Shiraki, Toshiyuki -- Yoshino, Masayasu -- Hayashizaki, Yoshihide -- Yasunishi, Ayako -- New York, N.Y. -- Science. 2003 Jul 18;301(5631):376-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, National Institute of Agrobiological Sciences, 2-1-2 Kannon-dai, Tsukuba, Ibaraki 305-8602, Japan. skikuchi@nias.affrc.go.jp〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12869764" target="_blank"〉PubMed〈/a〉
    Keywords: Alternative Splicing ; Amino Acid Sequence ; Cloning, Molecular ; Computational Biology ; DNA, Complementary ; Databases, Nucleic Acid ; Databases, Protein ; Genes, Plant ; *Genome, Plant ; Molecular Sequence Data ; Open Reading Frames ; Oryza/*genetics ; Plant Proteins/chemistry/genetics/physiology ; Protein Structure, Tertiary ; RNA, Antisense/genetics ; *Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Sequence Homology, Nucleic Acid ; Transcription Factors/chemistry/genetics ; Transcription, 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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  • 3
    Publication Date: 2009-08-21
    Description: Living organisms must acquire new biological functions to adapt to changing and hostile environments. Deepwater rice has evolved and adapted to flooding by acquiring the ability to significantly elongate its internodes, which have hollow structures and function as snorkels to allow gas exchange with the atmosphere, and thus prevent drowning. Many physiological studies have shown that the phytohormones ethylene, gibberellin and abscisic acid are involved in this response, but the gene(s) responsible for this trait has not been identified. Here we show the molecular mechanism of deepwater response through the identification of the genes SNORKEL1 and SNORKEL2, which trigger deepwater response by encoding ethylene response factors involved in ethylene signalling. Under deepwater conditions, ethylene accumulates in the plant and induces expression of these two genes. The products of SNORKEL1 and SNORKEL2 then trigger remarkable internode elongation via gibberellin. We also demonstrate that the introduction of three quantitative trait loci from deepwater rice into non-deepwater rice enabled the latter to become deepwater rice. This discovery will contribute to rice breeding in lowland areas that are frequently flooded during the rainy season.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hattori, Yoko -- Nagai, Keisuke -- Furukawa, Shizuka -- Song, Xian-Jun -- Kawano, Ritsuko -- Sakakibara, Hitoshi -- Wu, Jianzhong -- Matsumoto, Takashi -- Yoshimura, Atsushi -- Kitano, Hidemi -- Matsuoka, Makoto -- Mori, Hitoshi -- Ashikari, Motoyuki -- England -- Nature. 2009 Aug 20;460(7258):1026-30. doi: 10.1038/nature08258.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Bioscience and Biotechnology Center, Nagoya University, Nagoya 464-8601, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19693083" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological/drug effects/genetics/*physiology ; Breeding ; Ethylenes/*metabolism/pharmacology ; *Floods ; Gene Expression Regulation, Plant ; Genes, Plant/genetics/physiology ; Gibberellins/metabolism ; Onions/cytology ; Oryza/drug effects/genetics/*growth & development/*metabolism ; Plant Growth Regulators/*metabolism/pharmacology ; Plant Proteins/genetics/*metabolism ; Quantitative Trait Loci ; Signal Transduction ; Water/metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 4
    Publication Date: 2013-03-12
    Description: CLP1 was the first mammalian RNA kinase to be identified. However, determining its in vivo function has been elusive. Here we generated kinase-dead Clp1 (Clp1(K/K)) mice that show a progressive loss of spinal motor neurons associated with axonal degeneration in the peripheral nerves and denervation of neuromuscular junctions, resulting in impaired motor function, muscle weakness, paralysis and fatal respiratory failure. Transgenic rescue experiments show that CLP1 functions in motor neurons. Mechanistically, loss of CLP1 activity results in accumulation of a novel set of small RNA fragments, derived from aberrant processing of tyrosine pre-transfer RNA. These tRNA fragments sensitize cells to oxidative-stress-induced p53 (also known as TRP53) activation and p53-dependent cell death. Genetic inactivation of p53 rescues Clp1(K/K) mice from the motor neuron loss, muscle denervation and respiratory failure. Our experiments uncover a mechanistic link between tRNA processing, formation of a new RNA species and progressive loss of lower motor neurons regulated by p53.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3674495/" 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/PMC3674495/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hanada, Toshikatsu -- Weitzer, Stefan -- Mair, Barbara -- Bernreuther, Christian -- Wainger, Brian J -- Ichida, Justin -- Hanada, Reiko -- Orthofer, Michael -- Cronin, Shane J -- Komnenovic, Vukoslav -- Minis, Adi -- Sato, Fuminori -- Mimata, Hiromitsu -- Yoshimura, Akihiko -- Tamir, Ido -- Rainer, Johannes -- Kofler, Reinhard -- Yaron, Avraham -- Eggan, Kevin C -- Woolf, Clifford J -- Glatzel, Markus -- Herbst, Ruth -- Martinez, Javier -- Penninger, Josef M -- K99NS077435-01A1/NS/NINDS NIH HHS/ -- NS038253/NS/NINDS NIH HHS/ -- P 19223/Austrian Science Fund FWF/Austria -- P 21667/Austrian Science Fund FWF/Austria -- R00 NS077435/NS/NINDS NIH HHS/ -- R01 NS038253/NS/NINDS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2013 Mar 28;495(7442):474-80. doi: 10.1038/nature11923. Epub 2013 Mar 10.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉IMBA, Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna 1030, Austria.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23474986" target="_blank"〉PubMed〈/a〉
    Keywords: Amyotrophic Lateral Sclerosis ; Animals ; Animals, Newborn ; Axons/metabolism/pathology ; Cell Death ; Diaphragm/innervation ; Embryo Loss ; Embryo, Mammalian/metabolism/pathology ; Exons/genetics ; Female ; Fibroblasts ; Male ; Mice ; Mice, Inbred C57BL ; Mice, Knockout ; Mice, Transgenic ; Motor Neurons/*metabolism/*pathology ; Muscular Atrophy, Spinal ; Neuromuscular Diseases/metabolism/pathology ; Oxidative Stress ; RNA Processing, Post-Transcriptional ; RNA, Transfer, Tyr/genetics/*metabolism ; Respiration ; Spinal Nerves/cytology ; Transcription Factors/deficiency/*metabolism ; Tumor Suppressor Protein p53/metabolism ; Tyrosine/genetics/metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 5
    Publication Date: 2013-06-08
    Description: We studied the seismic structural response of a model of fault-structure system with fine resolution using multiscale analysis with parallel simulation of seismic-wave propagation. Our goal was to generate a numerical model with less geometric approximation for use in fault-structure system analysis that includes the crust, soil, and building structure. In the multiscale analysis, the solution of the fault-structure system was estimated using a two-step process. First, the solution of a low-resolution model (at a geologic-length scale) was computed. Then, this solution was used as an input boundary condition to the high-resolution model (at an engineering-length scale). The final solution from this process is thought to be an acceptable estimate of a direct analysis of a fault-structure system. To reduce the computation time of the simulation from fault to ground surface (at a geologic-length scale), we implemented parallel simulation of seismic-wave propagation based on domain decomposition by a prepartitioning method. This method is based on automated multiresolution (hybrid grid) meshing of subdomains in a distributed-memory computer. We also performed verification and validation tests with application to maximum target frequency of 1.0 Hz. Finally, we computed the dynamic responses of a fault-structure system model that included a nuclear power plant as the building structure using a fine-resolution model based on realistic conditions.
    Print ISSN: 0037-1106
    Electronic ISSN: 1943-3573
    Topics: Geosciences , Physics
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  • 6
    Publication Date: 2015-03-04
    Description: Inflammation promotes regeneration of injured tissues through poorly understood mechanisms, some of which involve interleukin (IL)-6 family members, the expression of which is elevated in many diseases including inflammatory bowel diseases and colorectal cancer. Here we show in mice and human cells that gp130, a co-receptor for IL-6 cytokines, triggers activation of YAP and Notch, transcriptional regulators that control tissue growth and regeneration, independently of the gp130 effector STAT3. Through YAP and Notch, intestinal gp130 signalling stimulates epithelial cell proliferation, causes aberrant differentiation and confers resistance to mucosal erosion. gp130 associates with the related tyrosine kinases Src and Yes, which are activated on receptor engagement to phosphorylate YAP and induce its stabilization and nuclear translocation. This signalling module is strongly activated upon mucosal injury to promote healing and maintain barrier function.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4447318/" 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/PMC4447318/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Taniguchi, Koji -- Wu, Li-Wha -- Grivennikov, Sergei I -- de Jong, Petrus R -- Lian, Ian -- Yu, Fa-Xing -- Wang, Kepeng -- Ho, Samuel B -- Boland, Brigid S -- Chang, John T -- Sandborn, William J -- Hardiman, Gary -- Raz, Eyal -- Maehara, Yoshihiko -- Yoshimura, Akihiko -- Zucman-Rossi, Jessica -- Guan, Kun-Liang -- Karin, Michael -- CA118165-09/CA/NCI NIH HHS/ -- CA132809/CA/NCI NIH HHS/ -- DP2 OD008469/OD/NIH HHS/ -- EY022611/EY/NEI NIH HHS/ -- R00 DK088589/DK/NIDDK NIH HHS/ -- R01 CA118165/CA/NCI NIH HHS/ -- England -- Nature. 2015 Mar 5;519(7541):57-62. doi: 10.1038/nature14228. Epub 2015 Feb 25.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Laboratory of Gene Regulation and Signal Transduction, University of California, San Diego, La Jolla, California 92093, USA [2] Departments of Pharmacology and Pathology, University of California, San Diego, La Jolla, California 92093, USA [3] Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan [4] Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo 160-8582, Japan. ; 1] Laboratory of Gene Regulation and Signal Transduction, University of California, San Diego, La Jolla, California 92093, USA [2] Institute of Molecular Medicine, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan. ; 1] Laboratory of Gene Regulation and Signal Transduction, University of California, San Diego, La Jolla, California 92093, USA [2] Fox Chase Cancer Center, Cancer Prevention and Control Program, Philadelphia, Pennsylvania 19111, USA. ; Department of Medicine, University of California, San Diego, La Jolla, California 92093, USA. ; 1] Departments of Pharmacology and Pathology, University of California, San Diego, La Jolla, California 92093, USA [2] Moores Cancer Center, University of California, San Diego, La Jolla, California 92093, USA [3] Department of Biology, Lamar University, PO Box 10037, Beaumont, Texas 77710, USA. ; 1] Departments of Pharmacology and Pathology, University of California, San Diego, La Jolla, California 92093, USA [2] Moores Cancer Center, University of California, San Diego, La Jolla, California 92093, USA [3] Children's Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China. ; Laboratory of Gene Regulation and Signal Transduction, University of California, San Diego, La Jolla, California 92093, USA. ; Department of Medicine, VA San Diego Healthcare System, San Diego, California 92161, USA. ; Inflammatory Bowel Disease Center, Division of Gastroenterology, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, California 92093, USA. ; 1] Department of Medicine, Medical University of South Carolina, Charleston, South Carolina 29425, USA [2] CSRC and BIMRC, San Diego State University, San Diego, California 92182, USA. ; Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan. ; 1] Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo 160-8582, Japan [2] Japan Science and Technology Agency, CREST, Tokyo 102-0076, Japan. ; 1] Inserm, UMR 1162, Genomique fonctionnelle des tumeurs solides, IUH, Paris 75010, France [2] Universite Paris Descartes, Labex Immuno-oncology, Sorbonne Paris Cite, Faculte de Medicine, Paris 75006, France. ; 1] Departments of Pharmacology and Pathology, University of California, San Diego, La Jolla, California 92093, USA [2] Moores Cancer Center, University of California, San Diego, La Jolla, California 92093, USA. ; 1] Laboratory of Gene Regulation and Signal Transduction, University of California, San Diego, La Jolla, California 92093, USA [2] Departments of Pharmacology and Pathology, University of California, San Diego, La Jolla, California 92093, USA [3] Moores Cancer Center, University of California, San Diego, La Jolla, California 92093, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25731159" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptor Proteins, Signal Transducing/*metabolism ; Animals ; Body Weight ; Cell Differentiation ; Cell Proliferation ; Cytokine Receptor gp130/*metabolism ; Disease Models, Animal ; Enzyme Activation ; Epithelial Cells/*cytology/metabolism/pathology ; HEK293 Cells ; Homeostasis ; Humans ; Inflammation/*metabolism/pathology ; Inflammatory Bowel Diseases/metabolism/pathology ; Intestinal Mucosa/*cytology/metabolism/pathology ; Mice ; Phosphoproteins/*metabolism ; Proto-Oncogene Proteins c-yes/metabolism ; Proto-Oncogene Proteins pp60(c-src)/*metabolism ; Receptors, Notch/metabolism ; *Regeneration ; Signal Transduction ; Up-Regulation
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 7
    Publication Date: 2016-12-03
    Description: d -Aspartate is found in the nervous and reproductive system and participates in various physiological roles. While several lines of evidence suggest that this amino acid has an endogenous origin, the enzyme responsible for mammalian d -Asp biosynthesis has not yet been identified. We show that mammalian serine racemase (SRR), the primary enzyme responsible for brain d -Ser production, catalyses Asp racemization via a two-base mechanism. We observed that overexpression of SRR in rat pheochromocytoma PC12 cells resulted in an increase in intracellular d -Asp compared with control cells, demonstrating that SRR functions as an Asp racemase in the cells. To investigate the impact of endogenous SRR on endogenous d -Asp levels in the cells, we generated SRR-knockout (SRR-KO) PC12 cells. The SRR-KO cells exhibited decreased intracellular d -Ser levels, but production levels of d -Asp were unaffected. In contrast, SRR-KO mice showed significantly decreased d -Asp levels in their frontal cortices and hippocampi, where SRR is normally highly expressed, while d -Asp levels in the cerebellum and testes remained unchanged. Our results indicate that SRR indeed acts as a d -Asp biosynthetic enzyme in some organs and/or tissues, and also provide evidences that there should be some additional enzyme for d -Asp synthesis in mammals.
    Print ISSN: 0021-924X
    Electronic ISSN: 1756-2651
    Topics: Biology , Chemistry and Pharmacology
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  • 8
    Electronic Resource
    Electronic Resource
    Amsterdam : Elsevier
    Biochimica et Biophysica Acta (BBA)/Biomembranes 904 (1987), S. 159-164 
    ISSN: 0005-2736
    Keywords: (Chinese hamster cell) ; Amphotericin B ; Cholesterol synthesis ; Membrane fluidity ; Membrane fusion ; Sendai virus
    Source: Elsevier Journal Backfiles on ScienceDirect 1907 - 2002
    Topics: Biology , Chemistry and Pharmacology , Medicine , Physics
    Type of Medium: Electronic Resource
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  • 9
    Electronic Resource
    Electronic Resource
    Amsterdam : Elsevier
    Journal of Photochemistry and Photobiology A: Chemistry 70 (1993), S. 29-33 
    ISSN: 1010-6030
    Source: Elsevier Journal Backfiles on ScienceDirect 1907 - 2002
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 10
    ISSN: 0020-1693
    Keywords: Charge transfer excited state ; Dinuclear complexes ; Mixed-valence complexes ; Ruthenium complexes ; Spectroelectrochemistry
    Source: Elsevier Journal Backfiles on ScienceDirect 1907 - 2002
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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