270 results match your criteria Advances In Biophysics[Journal]


Molecular mechanism of VDE-initiated intein homing in yeast nuclear genome.

Adv Biophys 2004 ;38:215-32

Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba Prefecture 277-8562, Japan.

In Saccharomyces cerevisiae, VMA1 intein encodes a homing endonuclease termed VDE which is produced by an autocatalytic protein splicing reaction. VDE introduces a DSB at its recognition sequence on intein-minus allele, resulting in the lateral transfer of VMA1 intein. In this review, we summarize a decade of in vitro study on VDE and describe our recent study on the in vivo behavior of both VDE and host proteins involved in intein mobility. Read More

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November 2004

Structure and function of the shufflon in plasmid R64.

Adv Biophys 2004 ;38:183-213

Department of Biology, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan.

Conservative site-specific recombination plays key roles in creating biological diversity in prokaryotes. Most site-specific inversion systems consist of two recombination sites and a recombinase gene. In contrast, the shufflon multiple inversion system of plasmid R64 consists of seven sfx recombination sites, which separate four invertible DNA segments, and the rci gene encoding a site-specific recombinase of the integrase family. Read More

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November 2004

Transposition mechanisms and biotechnology applications of the medaka fish Tol2 transposable element.

Authors:
Akihiko Koga

Adv Biophys 2004 ;38:161-80

Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan.

The Tol2 element of the medaka fish is a member of the hAT (hobo/Activator/ Tam3) transposable element family. About 20 copies are present in the medaka fish genome and, unlike many other hAT family elements, virtually all the copies are autonomous or potentially autonomous, containing an intact transposase gene. Excision of Tol2 is not precise at the nucleotide sequence level, excision foot-prints being heterogeneous. Read More

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November 2004

Genetics and epigenetics in flower pigmentation associated with transposable elements in morning glories.

Adv Biophys 2004 ;38:141-59

National Institute for Basic Biology, Myodaiji, Okazaki, Aichi 444-8585, Japan.

Among the genus Ipomoea, three morning glories, I. nil (the Japanese morning glory), I. purpurea (the common morning glory), and I. Read More

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November 2004

Intermediate molecules generated by transposase in the pathways of transposition of bacterial insertion element IS3.

Adv Biophys 2004 ;38:125-39

Institute of Molecular and Cellular Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan.

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November 2004

Gpt delta transgenic mouse: a novel approach for molecular dissection of deletion mutations in vivo.

Adv Biophys 2004 ;38:97-121

National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo 158-8501, Japan.

Human genome is continuously exposed to various DNA damaging agents including reactive oxygen species. Of various forms of DNA damage, double-strand breaks (DSBs) in DNA are the most detrimental because of the mutagenicity and cytotoxicity. To combat the serious threats posed by DSBs, cells evolved various homologous and non-homologous recombination repair mechanisms. Read More

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November 2004

Cell death promoted by homologous DNA interaction from bacteria to humans.

Authors:
Kohji Kusano

Adv Biophys 2004 ;38:81-96

Department of Biological Functions and Engineering, Graduate School of Life Science and Systems Engineering, Kyushu Institute of Technology, 2-4 Hibikino (Research Park), Wakamatsu-ku, Kitakyushu 808-0196, Japan.

Pairing between homologous DNA controls cellular functions including double-strand break repair, mitotic recombination, and progression of DNA replication forks, as well as chiasma formation during meiosis. Here I summarize that homologous interaction could promote the cell killing in bacteria, yeast, and multicellular organisms. The mechanisms of cell killing are categorized into two types: (1) the killing due to the accumulation of extrachromosomal DNA; (2) the killing induced by Holliday junction structures. Read More

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November 2004

Nijmegen breakage syndrome and DNA double strand break repair by NBS1 complex.

Adv Biophys 2004 ;38:65-80

Department of Radiation Biology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Kasumi 1-2-3, Minami-ku, Hiroshima 734-8553, Japan.

The isolation of the NBS1 gene revealed the molecular mechanisms of DSB repair. In response to DNA damage, histone H2AX in the vicinity of DSBs is phosphorylated by ATM. NBS1 then targets the MRE11/RAD50 complex to the sites of DSBs through interaction of the FHA/BRCT domain with gamma-H2AX. Read More

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November 2004

The function of RecQ helicase gene family (especially BLM) in DNA recombination and joining.

Adv Biophys 2004 ;38:45-64

Department of Pediatrics, Gifu University School of Medicine, 40 Tsukasa-machi, Gifu 500-8705, Japan.

Bloom syndrome is a rare autosomal recessive genetic disorder characterized by lupus-like erythematous telangiectasias of the face, sun sensitivity, stunted growth, and immunodeficiency. Chromosome instability syndromes have a common feature, being associated at high frequency with neoplasia. BS is considered as one of the chromosome instability syndromes since the fibroblasts or lymphocytes of BS patients show excessive spontaneous chromosome instability. Read More

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November 2004

Genetic and physiological regulation of non-homologous end-joining in mammalian cells.

Authors:
Akira Tachibana

Adv Biophys 2004 ;38:21-44

Radiation Biology Center, Kyoto University, Yoshida-Konoecho, Sakyo-ku, Kyoto 606-8501, Japan.

Repair of DSBs is important to prevent chromosomal fragmentation, translocations and deletions. To investigate the process in NHEJ, we have established an in vitro system to clarify the measurement and analysis of the efficiency and the fidelity of rejoining of DSBs, and applied the method to investigate NHEJ in human cells derived from patients suffering from cancer-prone hereditary diseases. A DSB was introduced in plasmid pZErO-2 at a specific site within the ccdB gene that is lethal to E. Read More

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November 2004

Illegitimate recombination mediated by double-strand break and end-joining in Escherichia coli.

Adv Biophys 2004 ;38:3-20

Institute of Molecular Genetics, Medinet Inc, Tamagawadai 2-2-8, Setagaya-ku, Tokyo 158-0096, Japan.

The frequency of illegitimate recombination has been measured by a lambda bio transducing phage assay during the induction of the E. coli lambda cI857 lysogen. Illegitimate recombination falls into two classes, short homology-independent and short homology-dependent illegitimate recombination. Read More

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November 2004

Molecular mechanism of vde-initiated intein homing in yeast nuclear genome.

Adv Biophys 2004 ;38(Complete):215-232

In Saccharomyces cerevisiae, VMAI intein encodes a homing endonuclease termed VDE which is produced by an autocatalytic protein splicing reaction. VDE introduces a DSB at its recognition sequence on intein-minus allele, resulting in the lateral transfer of VMAI intein. In this review, we summarize a decade of in vitro study on VDE and describe our recent study on the in vivo behavior of both VDE and host proteins involved in intein mobility. Read More

View Article and Full-Text PDF
January 2004

Structure and function of the shufflon in plasmid r64.

Adv Biophys 2004 ;38(Complete):183-213

Conservative site-specific recombination plays key roles in creating biological diversity in prokaryotes. Most site-specific inversion systems consist of two recombination sites and a recombinase gene. In contrast, the shufflon multiple inversion system of plasmid R64 consists of seven sfx recombination sites, which separate four invertible DNA segments, and the rci gene encoding a site-specific recombinase of the integrase family. Read More

View Article and Full-Text PDF
January 2004

Transposition mechanisms and biothechnology applications of the medaka fish tol2 transposable element.

Authors:
Akihiko Koga

Adv Biophys 2004 ;38(Complete):161-180

The Tol2 element of the medaka fish is a member of the hAT (hobo/Activator/Tam3) transposable element family. About 20 copies are present in the medaka fish genome and, unlike many other hAT family elements, virtually all the copies are autonomous or potentially autonomous, containing an intact transposase gene. Excision of Tol2 is not precise at the nucleotide sequence level, excision footprints being heterogeneous. Read More

View Article and Full-Text PDF
January 2004

Genetics and epigenetics in flower pigmentation associated with transposable elements in morning glories.

Adv Biophys 2004 ;38(Complete):141-159

Among the genus Ipomoea, three morning glories, I. nil the Japanese morning glory), I. purpurea (the common morning glory), and I. Read More

View Article and Full-Text PDF
January 2004

Gpt delta transgenic mouse: A novel approach for molecular dissection of deletion mutations in vivo.

Adv Biophys 2004 ;38(Complete):97-121

Human genome is continuously exposed to various DNA damaging agents including reactive oxygen species. Of various forms of DNA damage, double-strand breaks (DSBs) in DNA are the most detrimental because of the mutagenicity and cytotoxicity. To combat the serious threats posed by DSBs, cells evolved various homologous and non-homologous recombination repair mechanisms. Read More

View Article and Full-Text PDF
January 2004

Cell death promoted by homologous DNA interaction from bacteria to humans.

Authors:
Kohji Kusano

Adv Biophys 2004 ;38(Complete):81-96

Pairing between homologous DNA controls cellular functions including double-strand break repair, mitotic recombination, and progression of DNA replication forks, as well as chiasma formation during meiosis. Here I summarize that homologous interaction could promote the cell killing in bacteria, yeast, and multicellular organisms. The mechanisms of cell killing are categorized into two types: (1) the killing due to the accumulation of extrachromosomal DNA; (2) the killing induced by Holliday junction structures. Read More

View Article and Full-Text PDF
January 2004

Nijmegen breakage syndrome and DNA double strand break repair by NBS1 complex.

Adv Biophys 2004 ;38(Complete):65-80

Department of Radiation Biology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Kasumi 1-2-3, Minami-ku, Hiroshima 734-8553, Japan.

The isolation of the NBS1 gene revealed the molecular mechanisms of DSB repair. In response to DNA damage, histone H2AX in the vicinity of DSBs is phosphorylated by ATM. NBS1 then targets the MRE11/RAD50 complex to the sites of DSBs through interaction of the FHA/BRCT domain with gamma-H2AX. Read More

View Article and Full-Text PDF
January 2004

The function of RecQ helicase gene family (especially BLM) in DNA recombination and joining.

Adv Biophys 2004 ;38(Complete):45-64

Bloom syndrome is a rare autosomal recessive genetic disorder characterized by lupus-like erythematous telangiectasias of the face, sun sensitivity, stunted growth, and immunodeficiency. Chromosome instability syndromes have a common feature, being associated at high frequency with neoplasia. BS is considered as one of the chromosome instability syndromes since the fibroblasts or lymphocytes of BS patients show excessive spontaneous chromosome instability. Read More

View Article and Full-Text PDF
January 2004

Genetic and physiological regulation of non-homologous end-joining in mammalian cells.

Authors:
Akira Tachibana

Adv Biophys 2004 ;38(Complete):21-44

Radiation Biology Center, Kyoto University, Yoshida-Konoecho, Sakyo-ku, Kyoto 606-8501, Japan.

Repair of DSBs is important to prevent chromosomal fragmentation, translocations and deletions. To investigate the process in NHEJ, we have established an in vitro system to clarify the measurement and analysis of the efficiency and the fidelity of rejoining of DSBs, and applied the method to investigate NHEJ in human cells derived from patients suffering from cancer-prone hereditary diseases. A DSB was introduced in plasmid pZErO-2 at a specific site within the ccdB gene that is lethal to E. Read More

View Article and Full-Text PDF
January 2004

Illegitimate recombination mediated by double-strand break and end-joining in Escherichia coli.

Adv Biophys 2004 ;38(Complete):3-20

Institute of Molecular Genetics, Medinet Inc., Tamagawadai 2-2-8, Setagaya-ku, Tokyo 158-0096, Japan.

The frequency of illegitimate recombination has been measured by a lambdabio transducing phage assay during the induction of the E. coli lambda c1857 lysogen. Illegitimate recombination falls into two classes, short homology-independent and short homology-dependent illegitimate recombination. Read More

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January 2004

Studies and perspectives of calponin in smooth muscle regulation and cancer gene therapy.

Adv Biophys 2003 ;37:91-111

Department of Molecular Medicine & Pathophysiology, Osaka Medical Center for Cancer and Cardiovascular Diseases, The Graduate School of Pharmaceutical Science, Osaka University, Japan.

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Fertilization and development initiation in orthodox and unorthodox ways: from normal fertilization to cloning.

Adv Biophys 2003 ;37:49-89

Institute for Biogenesis Research, Department of Anatomy and Reproductive Biology, John A. Burns School of Medicine, University of Hawaii, Honolulu, Hawaii 96822, USA.

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Brain neurosteroids are 4th generation neuromessengers in the brain: cell biophysical analysis of steroid signal transduction.

Adv Biophys 2003 ;37:1-48

Department of Biophysics and Life Sciences, Graduate School of Arts and Sciences, University of Tokyo, Japan.

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Multiple sequence alignment: algorithms and applications.

Authors:
O Gotoh

Adv Biophys 1999 ;36:159-206

Saitama Cancer Center Research Institute, Japan.

Elucidation of interrelationships among sequence, structure, function, and evolution (FESS relationships) of a family of genes or gene products is a central theme of modern molecular biology. Multiple sequence alignment has been proven to be a powerful tool for many fields of studies such as phylogenetic reconstruction, illumination of functionally important regions, and prediction of higher order structures of proteins and RNAs. However, it is far too trivial to automatically construct a multiple alignment from a set of related sequences. Read More

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September 1999

Induced potential model of muscular contraction mechanism and myosin molecular structure.

Authors:
T Mitsui

Adv Biophys 1999 ;36:107-58

The proposed model is characterized by the constant r (Eq. 2-1), the induced potential (Fig. 1), two attached states of a myosin head (Fig. Read More

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September 1999

Evolution of the carabid ground beetles.

Adv Biophys 1999 ;36:65-106

Institute of Experimental Animal Sciences, Osaka University Medical School, Japan.

The phylogenetic relationships of the carabid ground beetles have been estimated by analysing a large part of the ND5 gene sequences of more than 1,000 specimens consisting of the representative species and geographic races covering most of the genera and subgenera known in the world. From the phylogenetic analyses in conjunction with the mtDNA-based dating, a scenario of the establishment of the present habitats of the respective Japanese carabids has been constructed. The carabid diversification took place ca. Read More

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September 1999

Ryanodine receptor isoforms in excitation-contraction coupling.

Adv Biophys 1999 ;36:27-64

Department of Pharmacology, Juntendo University School of Medicine, Tokyo, Japan.

Three genomically distinct isoforms of RyR are now known. RyR1 homologue is the primary isoform in skeletal muscles, whereas in cardiac muscles it is RyR2 homologue. RyR3 homologue occurs ubiquitously in many cells, but the biological function is little known, partly because of its minuscule amount in mammalian cells. Read More

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September 1999

Biophysical studies on ATP synthase.

Authors:
Y Kagawa

Adv Biophys 1999 ;36:1-25

Graduate School, Women's University of Nutrition, Saitama, Japan.

The isolation of ATP synthase (F0F1) (82) and F0 (83) 34 years ago finally revealed that F0F1 is a motor composed of F0 (ion-motor, abc subunits) and F1 (ATP-motor, alpha 3 beta 3 gamma delta epsilon subunits) (Fig. 1). The single molecule videotape (4, 5, 65, 66) revealed that gamma epsilon axis of F1 rotates counterclockwise, proceeds by each 2 pi/3 step, and is driven by torque of 42 pN. Read More

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September 1999