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The correlations between oxidative stress markers and indoor volatile organic compounds among the general population in Ansan and Incheon cities, Korea

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Toxicology and Environmental Health Sciences 2009年第1期1卷 37-48页

作者： Hong, Eunyoung Lee, Eunil Kim, Yanghee Oh, Eunha Kim, Young Whan Moon, Kyoung Whan Choi, Jae Wook Lee, Junghwa Roh, JooYoung Dept. of Preventive Med. and Medical Res. Center for Environmental Toxico-Genomics and Proteomics Korea University Seoul South Korea Department of Public Health School of Medicine Graduate School of Medicine Korea University Seoul South Korea Cellular and Developmental Biology Division of Brain Korea 21 Program for Biomedical Science Graduate School Korea University Seoul South Korea Department of Environmental Health Science School of Public Health Korea University Seoul South Korea Department of Environmental Health Science College of Health Sciences Korea University Seoul South Korea Department of Pediatrics College of Medicine Korea University Seoul South Korea Department of Dermatology Gachon Univeristy of Medicine Gil Medical Center Incheon South Korea

Indoor VOC and aldehydes may increase oxidative stress for home dwellers. Our study aim was to determine the correlations between oxidative stress markers in subjects and exposure to VOC and aldehydes in homes. Among ninety five control subjects in Ansan and Incheon (South Korea), blood samples were collected for evaluation of total antioxidant capacity, malondialdehyde (MDA) in plasma, protein carbonyl, and DNA damage of lymphocytes. Indoor VOC and aldehydes were measured in the homes of the subjects. A partial correlation analysis was performed to assess the association between oxidative stress markers and VOC/aldehydes with adjustment for formaldehyde levels. There were significant correlations between the total antioxidant capacity and some chemicals, including heptanes, α-pinene, β-pinene, and decanal in the young age (10-19 years) group. The many correlations between VOC/aldehydes and DNA damage expressed as the Olive tail moment showed statistically significant in the middle (20-39 years) and older age (40-59 years) groups, but not in the young age group. These correlation could not account for the exposure to specific chemicals being related to an increase in DNA damage because most VOC/aldehydes were highly correlate exac other except some chemicals. In conclusion, we found that DNA damage of T- and B-lymphocytes evaluated by the Comet assay could be sensitive oxidative stress markers to evaluate the human response to VOC/ aldehydes exposure in middle and older age groups. Our study also showed that age affected the association between VOC/aldehydes exposure and oxidative stress markers including DNA damage and antioxidants. However, further studies are needed to confirm these correlations in a larger number of subjects because of limitations of this study, including a lack of personal exposure. © 2009 The Korean Society of Environmental Risk Assessment and Health Science and Springer.

关键词： Comet assay DNA damage Formaldehyde Indoor air pollution Organic compounds Oxidative stress

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Identification of microRNA in the protist Trichomonas vaginalis

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genomics 2009年第5期93卷 487-493页

作者： Lin, Wei-Chen Li, Sung-Chou Lin, Wen-Chang Shin, Jyh-Wei Hu, Song-Nian Yu, Xiao-Min Huang, Ting-Yun Chen, Shih-Chieh Chen, Hua-Chien Chen, Shu-Jen Huang, Po-Jung Ruei-Chi Gan, Richie Chiu, Cheng-Hsun Tang, Petrus Molecular Regulation and Bioinformatics Laboratory Chang Gung University Taoyuan 333 Taiwan Division of Microbiology Graduate Institute of Biomedical Sciences Chang Gung University Taoyuan 333 Taiwan Institute of Biomedical Informatics National Yang-Ming University Taipei 112 Taiwan Taiwan International Graduate Program in Bioinformatics Academia Sinica Taipei 115 Taiwan Institute of Biomedical Sciences Academia Sinica Taipei 115 Taiwan Department of Parasitology National Cheng Kung University Tainan 701 Taiwan Key Laboratory of Genome Sciences and Information Beijing Institute of Genomics Chinese Academy of Sciences Beijing China Graduate University Chinese Academy of Sciences Beijing China Department of Life Sciences Chang Gung University Taoyuan 333 Taiwan Molecular Medicine Research Center Chang Gung University Taoyuan 333 Taiwan Bioinformatics Center Chang Gung University Tao-Yuan 333 Taiwan Chang Gung Molecular Infectious Diseases Research Center Chang Gung Memorial Hospital Taoyuan 333 Taiwan

MicroRNAs (miRNAs) are a class of small noncoding RNAs that have important regulatory roles in multicellular organisms. However, miRNA has never been identified experimentally in protist. Direct cloning of 438 expressed miRNA tags by microRNA serial analysis of gene expression from the parasitic protist Trichomonas vaginalis identified nine candidate miRNAs. bioinformatics analysis of the corresponding genomic region revealed that these miRNA candidates contain a classical stem-loop-stem structure of pre-microRNAs. Analysis of the 20 nt long mature tva-miR-001 showed that it is an intergenic miRNA located at the scaffold DS113596. Tva-miR-001 was differentially expressed in the trophozoite, pseudocyst and amoeboid stages. Based on the experimental results of the present study, we provided solid evidence that protist possesses a miRNA regulating network comparable with multicellular organisms for the first time. © 2009 Elsevier Inc. All rights reserved.

关键词： MicroRNA Protist Trichomonas vaginalis

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The Alternative Splicing Mutation Database: A hub for investigations of alternative splicing using mutational evidence

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BMC Research Notes 2008年第1期1卷 1-7页

作者： Bechtel, Jason M. Rajesh, Preeti Ilikchyan, Irina Deng, Ying Mishra, Pankaj K. Wang, Qi Wu, Xiaochun Afonin, Kirill A. Grose, William E. Wang, Ye Khuder, Sadik Fedorov, Alexei Program in Bioinformatics and Proteomics/Genomics University of Toledo Health Science Campus Toledo OH 43614 United States Dept. of Medical Microbiology and Immunology University of Toledo Health Science Campus Toledo OH 43614 United States Dept. of Basic Pharmaceutical Sciences South Carolina College of Pharmacy University of South Carolina Columbia SC 29208 United States Department of Biological Sciences Bowling Green State University Bowling Green OH 43403 United States College of Engineering University of Toledo Toledo OH 43606 United States Dept. of Medicine University of Toledo Health Science Campus Toledo OH 43614 United States

Background. Some mutations in the internal regions of exons occur within splicing enhancers and silencers, influencing the pattern of alternative splicing in the corresponding genes. To understand how these sequence changes affect splicing, we created a database of these mutations. Findings. The Alternative Splicing Mutation Database (ASMD) serves as a repository for all exonic mutations not associated with splicing junctions that measurably change the pattern of alternative splicing. In this initial published release (version 1.2), only human sequences are present, but the ASMD will grow to include other organisms, (see Availability and requirements section for the ASMD web address). This relational database allows users to investigate connections between mutations and features of the surrounding sequences, including flanking sequences, RNA secondary structures and strengths of splice junctions. Splicing effects of the mutations are quantified by the relative presence of alternative mRNA isoforms with and without a given mutation. This measure is further categorized by the accuracy of the experimental methods employed. The database currently contains 170 mutations in 66 exons, yet these numbers increase regularly. We developed an algorithm to derive a table of oligonucleotide Splicing Potential (SP) values from the ASMD dataset. We present the SP concept and tools in detail in our corresponding article. Conclusion. The current data set demonstrates that mutations affecting splicing are located throughout exons and might be enriched within local RNA secondary structures. Exons from the ASMD have below average splicing junction strength scores, but the difference is small and is judged not to be significant. © 2008 Bechtel et al;licensee BioMed Central Ltd.

关键词： Alternative Splice Splice Effect Splice Junction Alternative Splice Effect mRNA Isoforms

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Calculation of splicing potential from the alternative splicing mutation database

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BMC Research Notes 2008年第1期1卷 1-6页

Background. The Alternative Splicing Mutation Database (ASMD) presents a collection of all known mutations inside human exons which affect splicing enhancers and silencers and cause changes in the alternative splicing pattern of the corresponding genes. Findings. An algorithm was developed to derive a Splicing Potential (SP) table from the ASMD information. This table characterizes the influence of each oligonucleotide on the splicing effectiveness of the exon containing it. If the SP value for an oligonucleotide is positive, it promotes exon retention, while negative SP values mean the sequence favors exon skipping. The merit of the SP approach is the ability to separate splicing signals from a wide range of sequence motifs enriched in exonic sequences that are attributed to protein-coding properties and/or translation efficiency. Due to its direct derivation from observed splice site selection, SP has an advantage over other computational approaches for predicting alternative splicing. Conclusion. We show that a vast majority of known exonic splicing enhancers have highly positive cumulative SP values, while known splicing silencers have core motifs with strongly negative cumulative SP values. Our approach allows for computation of the cumulative SP value of any sequence segment and, thus, gives researchers the ability to measure the possible contribution of any sequence to the pattern of splicing. © 2008 Bechtel et al;licensee BioMed Central Ltd.

关键词： Splice Enhancer Exonic Splice Enhancer Code Potential Constitutive Exon 14th Exon

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Involvement of Rho-associated kinase in neurite sprouting and amyloid beta production of rat cortical neurons cultured in insulin-free medium

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Psychogeriatrics 2003年第1期3卷

作者： Naohiko Matsumoto Yu Nakamura Yujiro Kashiwagi Ryota Hashimoto Takashi Kudo Toshihisa Tanaka Kazuhiro Shinosaki Masatoshi Takeda Division of Psychiatry and Behavioral Proteomics Department of Post-Genomics and Diseases Course of Advanced Medicine Osaka University Graduate School of Medicine Osaka Department of Psychiatry Nara Medical University Nara Department of Psychosomatic Medicine and Psychiatry Kansai Rosai Hospital Hyogo Japan and Section on Molecular Neurobiology Mood and Anxiety Disorder Program National Institute of Mental Health National Institutes of Health Bethesda MD USA

Background: Abnormal sprouting of neurites is one of the neuropathological features of Alzheimer's disease. The mechanism of neurite sprouting of cultured neurons remains unknown. Among small guanosine triphosphate binding proteins, participation of the Rho family has been speculated. Methods: The involvement of Rho-associated kinase in neurite sprouting and in amyloid beta (Αβ) production was investigated in primary cultured rat cortical neurons using morphometric analysis, immunohistochemistry and ELISA assay. Results: In a serum-free medium, Y-27632, a Rho-associated kinase specific inhibitor, was found on the neurite outgrowth; however, there was no effect of Y-27632 on Neurobasal/B27. A custom medium without insulin was prepared because insulin potentially influences neurite formation. In the insulin-free medium, 10 µmol/L Y-27632 appeared to promote neurite outgrowth, showing significant increases in neurite length and in the number of neurite terminals. Y-27632 generated abnormal neurites, which were positively stained by both MAP2 and neurofilament-L. Furthermore, the effect of Y-27632 on Αβ production in primary cultured rat cortical neurons was investigated. Inhibition of Rho-associated kinase increased the ratio of Αβ 42 /40+42. Conclusion: Our findings indicated that Rho-associated kinase might be involved not only in neurite sprouting, but also in Αβ production in primary cultured neurons. Considering these two effects, inhibition of Rho-associated kinase activity might be involved in the pathology of Alzheimer's disease.

关键词： Alzheimer's disease amyloid beta insulin neurite sprouting primary cultured neurons Rho

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Contributory presentations/posters

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Journal of Biosciences 1999年第1期24卷 33-198页

作者： N. Manoj V. R. Srinivas A. Surolia M. Vijayan K. Suguna R. Ravishankar R. Schwarzenbacher K. Zeth Diederichs G. M. Kostner A. Gries P. Laggner R. Prassl Madhusudan Pearl Akamine Nguyen-huu Xuong Susan S. Taylor M. Bidva Sagar K. Saikrishnan S. Roy K. Purnapatre P. Handa U. Varshney B. K. Biswal N. Sukumar J. K. Mohana Rao A. Johnson Vasantha Pattabhi S. Sri Krishna Mira Sastri H. S. Savithri M. R. N. Murthy Bindu Pillai Kannan M. V. Hosur Mukesh Kumar Swati Patwardhan K. K. Kannan B. Padmanabhaa S. Sasaki-Sugio M. Nukaga T. Matsuzaki S. Karthikevan S. Sharma A. K. Sharma M. Paramasivam P. Kumar J. A. Khan S. Yadav A. Srinivasan T. P. Singh S. Gourinath Neelima Alam A. Srintvasan Vikas Chandra Punit Kaur Ch. Betzel S. Ghosh A. K. Bera S. Bhattacharya S. Chakraborty A. K. Pal B. P. Mukhopadhyay I. Dey U. Haldar Asok Baneriee Jozef Sevcik Adriana Solovicova K. Sekar M. Sundaralingam N. Genov Dong-cai Liang Tao Jiang Ji-ping Zhang Wen-rui Chang Wolfgang Jahnke Marcel Blommers S. C. Panchal R. V. Hosur Bindu Pillay Puniti Mathur S. Srivatsun Ratan Mani Joshi N. R. Jaganathan V. S. Chauhan H. S. Atreya S. C. Sahu K. V. R. Chary Girjesh Govil Elisabeth Adjadj Éric Quinjou Nadia Izadi-Pruneyre Yves Blouquit Joël Mispelter Bernadette Heyd Guilhem Lerat Philippe Milnard Michel Desmadreil Y. Lin B. D. Nageswara Rao Vidva Raghunathan Mei H. Chau Prashant Pesais Sudha Srivastava Evans Coutinho Anil Saran Leizl F. Sapico Jayson Gesme Herbert Lijima Raymond Paxton Thamarapu Srikrishnan C. R. Grace G. Nagenagowda A. M. Lynn Sudha M. Cowsik Sarata C. Sahu S. Chauhan A. Bhattacharya G. Govil Anil Kumar Maurizio Pellecchia Erik R. P. Zuiderweg Keiichi Kawano Tomoyasu Aizawa Naoki Fujitani Yoichi Hayakawa Atsushi Ohnishi Tadayasu Ohkubo Yasuhiro Kumaki Kunio Hikichi Katsutoshi Nitta V. Rani Parvathy R. M. Kini Takumi Koshiba Yoshihiro Kobashigawa Min Yao Makoto Demura Astushi Nakagawa Isao Tanaka Kunihiro Kuwajima Jens Linge Seán O. Donoghue Michael Nilges G. Chakshusmathi Girish S. Ratnaparkhi P. K. Madhu R. Varadarajan C. Tetreau Molecular Biophysics Unit Indian Institute of Science Bangalore India Austrian Academy of Sciences Institute of Biophysics and X-ray Structure Research Graz Austria Faculty of Biology University of Konstanz Germany Institute of Medical Biochemistry University of Graz Austria Howard Huges Medical Institute Department of Chemistry & Biochemistry University of California La Jolla USA Department of Chemistry & Biochemistry University of California San Diego La Jolla USA Molecular Biophysics Unit India Department of Microbiology &Cell Biology Indian Institute of Science Bangalore India Macromolecular Structure Laboratory NCI - Frederick Cancer Research and Development Center ABL - Basic Research Program Frederick USA Department of Crystallography and Biophysics University of Madras Chennai Biochemistry Department Indian Institute of Science Bangalore India Condensed Matter Physics Division B.A.R.C. Trombay Mumbai Condensed Matter Physics Division Bhabha Atomic Research Centre Trombay Mumbai IMCB The University of Tokyo Tokyo Japan Mitsubishi Chemical Corporation Yokohama Research Center Yokohama Japan Faculty of Pharmaceutical Sciences Chiba University Chiba Japan Department of Biophysics All India Institute of Medical Sciences New Delhi India Department of Biophysics All India Institute of Medical sciences New Delhi India Institüt Physiologische Chemie Hamburg Germany Biophysics Department Bose Institute Calcutta India Slovak Academy of Sciences Institute of Molecular Biology Bratislava Slovakia Indian Institute of Science Bioinformatics Centre Bangalore Departments of Chemistry and Biochemistry Biological Macromolecular Structure Center USA Bulgarian Academy of Sciences Institute of Organic Chemistry Sofia Bulgaria Chinese Academy of Sciences Institute of Biophysics Beijing China Novartis Pharma AG Preclinical Research Basel Switzerland Department of Chemical Sciences Tata Institute of Fundamental Research Mumbai India Solid State Physics Div

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