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Identification of the interactive region by the homology of the sequence spectrum

Journal of Biomedical Science and Engineering 2010年第9期3卷 868-883页

作者： masatoshi nakahara Masaharu Takeda 不详

The base sequence in genome was governed by some fundamental principles such as reverse-complement symmetry, multiple fractality and so on, and the analytical method of the genome structure, the “Sequence Spectrum Method (SSM)”, based on the structural features of genomic DNA faithfully visualized these principles. This paper reported that the sequence spectrum in SSM closely reflected the biological phenomena of protein and DNA, and SSM could identify the interactive region of protein-protein and DNA-protein uniformly. In order to investigate the effectiveness of SSM we analyzed the several protein-protein and DNA-protein interaction published primarily in the genome of Saccharomyces cerevisiae. The method proposed here was based on the homology of sequence spectrum, and it advantageously and surprisingly used only base sequence of genome and did not require any other information, even information about the amino-acid sequence of protein. Eventually it was concluded that the fundamental principles in genome governed not only the static base sequence but also the dynamic function of protein and DNA.

关键词： Spectrum of Genome Base Sequence Homology of Sequence Spectrum Interactive Region Reverse-Complement Symmetry Multiple Fractality Analytical Method Of Genome

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Characterization of the sequence spectrum of DNA based on the appearance frequency of the nucleotide sequences of the genome——A new method for analysis of genome structure

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Journal of Biomedical Science and Engineering 2010年第4期3卷 340-350页

作者： masatoshi nakahara Masaharu Takeda 不详

The nucleotide (base) sequence of the genome might reflect biological information beyond the coding sequences. The appearance frequencies of successive base sequences (key sequences) were calculated for entire genomes. Based on the appearance frequency of the key sequences of the genome, any DNA sequences on the genome could be expressed as a sequence spectrum with the adjoining base sequences, which could be used to study the corresponding biological phenomena. In this paper, we used 64 successive three- base sequences (triplets) as the key sequences, and determined and compared the spectra of specific genes to the chromosome, or specific genes to tRNA genes in Saccharomyces cerevisiae, Schizosaccharomyces pombe and Escherichia coli. Based on these analyses, a gene and its corresponding position on the chromosome showed highly similar spectra with the same fold enlargement (approximately 400-fold) in the S. cerevisiae, S. pombe and E. coli genomes. In addition, the homologous structure of genes that encode proteins was also observed with appropriate tRNA gene(s) in the genome. This analytical method might faithfully reflect the encoded biological information, that is, the conservation of the base sequences was to make sense the conservation of the translated amino acids sequence in the coding region, and might be universally applicable to other genomes, even those that consisted of multiple chromosomes.

关键词： Appearance Frequency of Triplet in Genome Base Sequence Self-Similarity Analytical Method of Genome Structure

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Impact of lipoprotein lipase gene polymorphisms on ulcerative colitis

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World Journal of Gastroenterology 2006年第39期12卷 6325-6330页

作者： Toshihito Kosaka Junji Yoshino Kazuo Inui Takao Wakabayashi Kazumu Okushima Takashi Kobayashi Hironao Miyoshi Yuta Nakamura Shigekazu Hayashi Taizou Shiraishi masatoshi Watanabe Takayuki Yamamoto Ai nakahara Takahiko Katoh Department of Internal Medicine Second Teaching Hospital Fujita Health University School of Medicine 3-6-10 Otobashi Nakagawaku Nagoya 454-8509 Japan Department of Gastroenterology Nagoya Ekisaikai Hospital 4-66 Shounencho Nakagawaku Nagoya 454-8502 Japan Department of Pathologic Oncology Mie University Graduate School of Medicine 2-174 Edobashi Tsu Mie 514-8507 Japan School of Engineering Yokohama National University 79-5 Tokiwadai Hodogaya-ku Yokohama 240-8501 Japan Inflammatory bowel disease centre and department of surgery Yokkaichi Social Insulance Hospital 10-8 Hazuyamacho Yokkaichi Mie Japan Department of Public Health Miyazaki Medical College University of Miyazaki 5200 Kihara Miyazaki 889-1692 Japan

AIM： To examine the influence of lipoprotein lipase （LPL） gene polymorphism in ulcerative colitis （UC） patients.METHODS： Peripheral blood was obtained from 131 patients with UC and 106 healthy controls for DNA extraction. We determined LPL gene polymorphisms affecting the enzyme at Ser447stop, as well as Hind Ⅲ and Pvu Ⅱ polymorphisms using PCR techniques. PCR products were characterized by PCR-RFLP and direct sequencing. Polymorphisms were examined for association with clinical features in UC patients. Genotype frequencies for LPL polymorphisms were also compared between UC patients and controls.RESULTS： In patients with onset at age 20 years or younger, C/G and G/G genotypes for Ser447stop polymorphism were more prevalent than C/C genotype （OR = 3.13, 95% CI = 0.95-10.33）. Patients with H^＋/- or H^-/- genotype for Hind Ⅲ polymorphism also were more nu merous than those with H^＋/＋ genotype （OR = 2.51, 95% CI = 0.85-7.45）. In the group with H^＋/＋ genotype for Hind Ⅲ polymorphism, more patients had serum triglyceride concentrations over 150 mg/dL than patients with H^＋/- or H^- genotype （P 〈 0.01, OR = 6.46, 95% CI = 1.39-30.12）. Hypertriglycemia was also more prevalent in patients with P^＋/＋ genotypes for Pvu Ⅱ polymorphism （P 〈 0.05, OR = 3.0, 95% CI = 1.06-8.50）. Genotype frequency for LPL polymorphism did not differ significantly between UC patients and controls.

关键词： Ulcerative colitis Lipoprotein lipase Lipid metabolism Triglyceride

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Dosimetric Comparison between Bone and Target Matching Considering Interfractional Prostate Motion in Volumetric Modulated Arc Therapy

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International Journal of Medical Physics, Clinical Engineering and Radiation Oncology 2018年第1期7卷 47-60页

作者： Ryuta nakahara Kentaro Ishii Nobuhide Wakai Ryu Kawamorita Wataru Okada Shun Kishimoto Kazuki Kubo Toshifumi Nakajima masatoshi Hasegawa Department of Radiation Oncology Tane General Hospital Osaka Japan Department of Radiation Oncology Nara Medical University Kashihara Japan

Adequate matching methods are critical for accurate volumetric-modulated arc therapy (VMAT). We investigated the dosimetric differences in the target and organs at risk (OARs) between bone matching and target matching in patients with prostate cancer treated with VMAT. The relationship between the dosimetric differences and interfractional motion of the prostate was also evaluated. Forty patients with prostate cancer classified as intermediate risk were enrolled in a study to assess the differences in dosimetry between two matching methods. These patients were treated with VMAT and prescribed dose was 78 Gy. The dose distribution was calculated using cone-beam computed tomography (CBCT) for this study. We selected clinical target volume (CTV) as the target, and the rectum and bladder as the OARs. The Dmean, D98, D95, and D2 to the target and V10-V70 to the OARs were calculated as different dose from target matching value minus bone matching value. Multiple regression analysis was used to evaluate the effect of interfractional motion of the prostate on the differences in dose. The CTV D95 values differed by -0.22 ± 1.01 Gy (mean ± standard deviation). Rectum and bladder V70 values differed by 4.6% ± 7.2% and -2.6% ± 7.2%, respectively. There was a correlation between interfractional motion of the prostate and the dose differences to OARs (R2 = 0.73 - 0.94). The dose differences to OARs also varied depending on the direction of the prostate’s motion. We found that bone matching resulted in an increased rectal dose and high risk of decreasing dose to the CTV.

关键词： Radiotherapy Image-Guided Radiation Dosage Prostate

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