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Differences in dinucleotide frequencies of thermophilic genes encoding water soluble and membrane proteins

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Journal of Zhejiang University-Science B(Biomedicine & Biotechnology) 2011年第6期12卷 419-427页

作者： hiroshi NAKASHIMA Yuka KURODA Department of Clinical Laboratory Science Graduate Course of Medical Science and TechnologySchool of Health SciencesKanazawa University

The occurrence frequencies of the dinucleotides of genes of three thermophilic and three mesophilic species from both archaea and eubacteria were investigated in this study. The genes encoding water soluble proteins were rich in the dinucleotides of purine dimers, whereas the genes encoding membrane proteins were rich in pyrimidine dimers. The dinucleotides of purine dimers are the counterparts of pyrimidine dimers in a double-stranded DNA. The purine/pyrimidine dimers were favored in the thermophiles but not in the mesophiles, based on comparisons of observed and expected frequencies. This finding is in agreement with our previous study which showed that purine/pyrimidine dimers are positive factors that increase the thermal stability of DNA. The dinucleotides AA, AG, and GA are components of the codons of charged residues of Glu, Asp, Lys, and Arg, and the dinucleotides TT, CT, and TC are components of the codons of hydrophobic residues of Leu, Ile, and Phe. This is consistent with the suitabilities of the different amino acid residues for water soluble and membrane proteins. Our analysis provides a picture of how thermophilic species produce water soluble and membrane proteins with distinctive characters: the genes encoding water soluble proteins use DNA sequences rich in purine dimers, and the genes encoding membrane proteins use DNA sequences rich in pyrimidine dimers on the opposite strand.

关键词： Water soluble and membrane proteins Purine/pyrimidine dimers Thermophilic and mesophilic species Dinucleotide frequencies

Network biology approach to epithelial–mesenchymal transition in cancer metastasis: three stage theory

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分子细胞生物学报:英文版 2015年第3期7卷 253-266页

作者： hiroshi Tanaka Soichi Ogishima Department of Bioinformatics Medical Research InstituteTokyo Medical and Dental UniversityTokyoJapan Department of Bioclinical Informatics Tohoku Medical Megabank OrganizationTohoku UniversitySendaiJapan

Epithelial–mesenchymal transition(EMT)plays a critical role in promoting cancer *** this study,cancer EMT is considered as an overall structural change in the gene regulatory network(GRN),and its essential features are elucidated by the network biology *** first defined the state space of GRN as a set of all possible activation patterns of GRN,and then introduced the quasipotential field into this space to show the relative stability distribution of each *** quasi-potential was determined empirically by collecting gene expression profiles from public *** of GRN states during the EMT process were traced in the state space,by using time-course data of gene expression profiles of a cell line inducingEMTfromthe *** wasfound that cancerEMT occurred in three sequential stable stages,each of which formed a potential basin along the EMT *** confirmation,structural changes of GRN were estimated by applying the ARACNe algorithm to the same time-course data,and then applying master regulator analysis to extract the main *** group of master regulators was found to be alternatively active in the subsequent three stages to cause overall structural changes of GRN during cancer EMT.

关键词： epithelial-mesenchymal transition(EMT) Waddington’s epigenetic landscape gene regulatory network GRN network stage space cancer metastasis

Direct observation of the plasmon-enhanced palladium catalysis with single-molecule fluorescence microscopy

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Nano Research 2023年第7期16卷 8817-8826页

作者： Zhuoyao Li Rajkumar Devasenathipathy Junjie Wang Liuyingzi Yu Yan Liang Huixiang Sheng Yameng Zhu Hai Li hiroshi Uji-i Xiao Huang Gang Lu School of Flexible Electronics(Future Technologies) Key Laboratory of Flexible Electronicsand Institute of Advanced MaterialsNanjing Tech University(NanjingTech)Nanjing 211816China Department of Chemistry KU LeuvenCelestijnenlaan 200FLeuven 3001Belgium Research Institute for Electronic Science Hokkaido UniversityN20W10Kita wardSapporoHokkaido 001-0020Japan National Laboratory of Solid State Microstructures Nanjing UniversityNanjing 210093China

Plasmonic nanostructures have been proved effective not only in catalyzing chemical reactions,but also in improving the activity of non-plasmonic *** is essential to reveal the synergy between the plasmonic structure and the non-plasmonic metal photocatalyst for expounding the underlying mechanism of plasmon-enhanced ***,the enhancement of resazurin reduction at the heterostructure of silver nanowire(AgNW)and palladium nanoparticles(PdNPs)is observed in situ by single-molecule fluorescence *** catalysis mapping results around single AgNW suggest that the catalytic activity of PdNPs is enhanced for~20 times due to the excitation of localized surface plasmon resonance(LSPR)in the vicinity of the *** catalysis enhancement is also highly related to the wavelength and polarization of the excitation *** addition,the palladium catalysis is further enhanced by~10 times in the vicinity of a roughened AgNW or a AgNW-AgNW nanogap because of the improvement of catalytic *** findings clarify the contribution of plasmon excitation in palladium catalysis at microscopic scale,which will help to deepen the understanding of the plasmon-enhanced photocatalysis and provide a guideline for developing highly efficient plasmon-based photocatalysts.

关键词： surface plasmon palladium nanoparticles photocatalysis enhancement hot carrier super-resolution fluorescence microscopy

Identification of an intronic enhancer regulating RANKL expression in osteocytic cells

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骨研究:英文版 2023年第3期11卷 607-616页

作者： Minglu Yan Masayuki Tsukasaki Ryunosuke Muro Yutaro Ando Kazutaka Nakamura Noriko Komatsu Takeshi Nitta Tadashi Okamura Kazuo Okamoto hiroshi Takayanagi Department of Immunology Graduate School of Medicine and Faculty of MedicineThe University of TokyoTokyoJapan Department of Osteoimmunology Graduate School of Medicine and Faculty of MedicineThe University of TokyoTokyoJapan Department of Microbiology Tokyo Dental CollegeTokyoJapan Department of Oral and Maxillofacial Surgery Department of Sensory and Motor System MedicineGraduate School of MedicineThe University of TokyoTokyoJapan Department of Laboratory Animal Medicine Research InstituteNational Center for Global Health and MedicineTokyoJapan

The bony skeleton is continuously renewed throughout adult life by the bone remodeling process,in which old or damaged bone is removed by osteoclasts via largely unknown *** regulate bone remodeling by producing the osteoclast differentiation factor RANKL(encoded by the TNFSF11 gene).However,the precise mechanisms underlying RANKL expression in osteocytes are still ***,we explored the epigenomic landscape of osteocytic cells and identified a hitherto-undescribed osteocytic cell-specific intronic enhancer in the TNFSF11 gene *** analyses showed that transcription factors involved in cell death and senescence act on this intronic enhancer ***-cell transcriptomic data analysis demonstrated that cell death signaling increased RANKL expression in osteocytic *** deletion of the intronic enhancer led to a high-bone-mass phenotype with decreased levels of RANKL in osteocytic cells and osteoclastogenesis in the adult stage,while RANKL expression was not affected in osteoblasts or *** data suggest that osteocytes may utilize a specialized regulatory element to facilitate osteoclast formation at the bone surface to be resorbed by linking signals from cellular senescence/death and RANKL expression.

关键词： utilize removed linking

Rough set-based rule generation and Apriori-based rule generation from table data sets: a survey and a combination

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CAAI Transactions on Intelligence Technology 2019年第4期4卷 203-213页

作者： hiroshi Sakai Michinori Nakata Graduate School of Engineering Kyushu Institute of TechnologySensui 1-1TobataKitakyushu 804-8550Japan Faculty of Management and Information Science Josai International UniversityGumyoToganeChiba 283-0002Japan

The authors have been coping with new computational methodologies such as rough sets,information incompleteness,data mining,granular computing,etc.,and developed some software tools on association rules as well as new mathematical *** simply term this research Rough sets Non-deterministic Information Analysis(RNIA).They followed several novel types of research,especially Pawlak’s rough sets,Lipski’s incomplete information databases,Or?owska’s non-deterministic information systems,Agrawal’s Apriori *** are outstanding researches related to information incompleteness,data mining,and rule *** have been trying to combine such novel researches,and they have been trying to realise more intelligent rule generator handling data sets with information *** study surveys the authors’research highlights on rule generators,and considers a combination of them.

关键词： Apriori rule incomplete

Contribution of Cyclic and Pseudo-cyclic Electron Transport to the Formation of Proton Motive Force in Chloroplasts

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Molecular Plant 2017年第1期10卷 20-29页

作者： Toshiharu Shikanai hiroshi Yamamoto Department of Botany Graduate School of Science Kyoto University Oiwake-cho Kitashirakawa Sakyo-ku Kyoto 606-8502 Japan CREST Japan Science and Technology Agency Chiyoda-ku Tokyo 102-0076 Japan

Photosynthetic electron transport is coupled to proton translocation across the thylakoid membrane, re- sulting in the formation of a trans-thylakoid proton gradient （△pH） and membrane potential （△ψ）. Ion trans-porters and channels localized to the thylakoid membrane regulate the contribution of each component to the proton motive force （pmf）. Although both △pH and △ψ contribute to ATP synthesis as pmf, only ~pH downregulates photosynthetic electron transport via the acidification of the thylakoid lumen by inducing thermal dissipation of excessive absorbed light energy from photosystem II antennae and slowing down of the electron transport through the cytochrome bsf complex. To optimize the tradeoff between efficient light energy utilization and protection of both photosystems against photodamage, plants have to regulate the pmf amplitude and its components, △pH and △ψ. Cyclic electron transport around photosystem I （PSI） is a major regulator of the pmf amplitude by generating pmf independently of the net production of NADPH by linear electron transport. Chloroplast ATP synthase relaxes pmf for ATP synthesis, and its activity should be finely tuned for maintaining the size of the pmf during steady-state photosynthesis. Pseudo-cyclic electron transport mediated by flavodiiron protein （FIv） forms a large electron sink, which is essential for PSI photoprotection in fluctuating light in cyanobacteria. FIv is conserved from cyanobacteria to gymno- sperms but not in angiosperms. The Arabidopsis proton gradient regulation 50（pgr5） mutant is defective in the main pathway of PSI cyclic electron transport. By introducing Physcomitrella patens genes encoding Flvs, the function of PSI cyclic electron transport was substituted by that of FIv-dependent pseudo-cyclic electron transport. In transgenic plants, the size of the pmf was complemented to the wild-type level but the contribution of △pH to the total pmf was lower than that in the wild type. In the pgr5 mutant, the size of

关键词： alternative electron transport cyclic electron transport around photosystem I ion channel flavodiironprotein proton motive force pseudo-cyclic electron transport

Revealing the diversity of neutrophil functions and subsets

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Cellular & Molecular Immunology 2021年第4期18卷 781-783页

作者： Kiyoharu Fukushima hiroshi Nabeshima hiroshi Kida Department of Respiratory Medicine National Hospital Organization Osaka Toneyama Medical CenterOsakaJapan Department of Respiratory Medicine and Clinical immunology Osaka University Graduate School of MedicineOsakaJapan Laboratory of Host Defense World Premier Institute Im m unology Frontier Research Center(WPIIFReC)Osaka UniversityOsakaJapan Fujii Memorial Research Institute Otsuka Pharmaceutical CompanyLtdShigaJapan

Several recent studies have shown that diverse neutrophil subsets exhibit distinct phenotypic and functional properties in terms of disease onset and progression.1,2 In a study published in Nature Immunology,Sas et al.3 discovered a new neutrophil subset that promotes neuronal survival and axonal regeneration in the central nervous system(CNS).

关键词： neutrophil Immunology

Endoscopic management of chronic radiation proctitis

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World Journal of Gastroenterology 2011年第41期17卷 4554-4562页

作者： Tarun Rustagi hiroshi Mashimo Department of Internal Medicine University of Connecticut Gastroenterology Section 111 VA Boston Healthcare SystemBrigham and Women’s HospitalHarvard Medical School

Chronic radiation proctopathy occurs in 5%-20% of patients following pelvic radiotherapy. Although many cases resolve spontaneously,some lead to chronic symptoms including diarrhea,tenesmus,urgency and persistent rectal bleeding with iron deficiency anemia requiring blood transfusions. Treatments for chronic radiation proctitis remain unsatisfactory and the basis of evidence for various therapies is generally insuff icient. There are very few controlled or prospective trials,and comparisons between therapies are limited because of different evaluation methods. Medical treatments,including formalin,topical sucralfate,5-amino salicylic acid enemas,and short chain fatty acids have been used with limited *** management is associated with high morbidity and mortality. Endoscopic therapy using modalities such as the heater probe,neodymium:yttrium-aluminium-garnet laser,potassium titanyl phosphate laser and bipolar electrocoagulation has been reported to be of some benef it,but with frequent *** plasma coagulation is touted to be the preferred endoscopic therapy due to its eff icacy and safety *** methods of endoscopic ablation such as radiofrequency ablation and cryotherapy have been recently described which may afford broader areas of treatment per application,with lower rate of *** review will focus on endoscopic ablation therapies,including such newer modalities,for chronic radiation proctitis.

关键词：放射性内镜慢性肠炎钇铝石榴石激光器管理缺铁性贫血氨基水杨酸

SH-wavefield simulation for a laterally heterogeneous whole-Earth model using the pseudospectral method

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Science China Earth Sciences 2011年第12期54卷 1940-1947页

作者： WANG YanBin TAKENAKA hiroshi Department of Geophysics School of Earth and Space Sciences Peking University Beijing 100871 China Department of Earth and Planetary Sciences Kyushu University Hakozaki 6-10-1 Fukuoka 812-8581 Japan

We present a scheme to simulate SH-wave propagation in a whole-Earth model with arbitrary lateral heterogeneities employing the Fourier pseudospectral method. Wave equations are defined in two-dimensional cylindrical coordinates and the model is taken through a great circle of the Earth. Spatial derivatives in the wave equations are calculated in the wavenumber domain by multiplication, and the transformation between spatial and wavenumber domains is performed via fast Fourier transformation. Because of the high accuracy and high speed of the Fourier pseudospectral method, the scheme enables us to calculate a short-wavelength global SH-wavefield with accurate waveforms and arrival times for models with heterogeneities that can be approximated as azimuthally symmetric. Comparing with two-dimensional simulation methods based on an axisymmetric model, implementing the seismic source in the present scheme is more convenient. We calculated the global SH-wavefield for the preliminary reference Earth model to identify the generation, reflection and refraction of various seismic phases propagating in the Earth. Applications to a heterogeneous global model with low-velocity perturbation above the core-mantle boundary were conducted to analyze the effect of lateral heterogeneity on global SH-wave propagation.

关键词：地球模型波场模拟伪谱法异构快速傅立叶变换横向非均质性导数计算横向不均匀性