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Genomics, Proteomics & Bioinformatics 2016年第2期14卷 103-112页

作者： Yusei Kobori satoshi mizuta Graduate School of Science and Technology Hirosaki University

Graphical representation of DNA sequences is one of the most popular techniques for alignment-free sequence comparison. Here, we propose a new method for the feature extraction of DNA sequences represented by binary images, by estimating the similarity between DNA sequences using the frequency histograms of local bitmap patterns of images. Our method shows linear time complexity for the length of DNA sequences, which is practical even when long sequences, such as whole genome sequences, are compared. We tested five distance measures for the estimation of sequence similarities, and found that the histogram intersection and Manhattan distance are the most appropriate ones for phylogenetic analyses.

关键词： Genome sequence Mitochondria Bitmap image Occurrence frequency Distance measure

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Significant Deviations in the Configurations of Homologous Tandem Repeats in Prokaryotic Genomes

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Genomics, Proteomics & Bioinformatics 2009年第4期7卷 163-174页

作者： Shintaro Hirayama satoshi mizuta Graduate School of Science and Technology Hirosaki University

We explored the possibilities of whole-genome duplication （WGD） in prokaryotic species, where we performed statistical analyses of the configurations of the central angles between homologous tandem repeats （TRs） on the circular chromosomes. At first, we detected TRs on their chromosomes and identified equivalent tandem repeat pairs （ETRPs）; here, an ETRP is defined as a pair of tandem repeats sequentially similar to each other. Then we carried out statistical analyses of the central angle distributions of the detected ETRPs on each circular chromosome by way of comparisons between the detected distributions and those generated by null models. In the analyses, we estimated a P value by a simulation using the Kullback-Leibler divergence as a distance measure between two distributions. As a result, the central angle distributions for 8 out of the 203 prokaryotic species showed statistically significant deviations （P〈0.05）. In particular, we found out the characteristic feature of one round of WGD in Photorhabdus luminescens genome and that of two rounds of WGD in Escherichia coli K12.

关键词： whole-genome duplication statistical analysis tandem repeat Kullback-Leibler divergence prokaryote

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Mucosa-associated lymphoid tissue lymphoma of the transverse colon: A case report

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World Journal of Gastroenterology 2006年第34期12卷 5573-5576页

作者： Shigetoshi Matsuo Yohei mizuta Tomayoshi Hayashi Seiya Susumu Ryuji Tsutsumi Takashi Azuma satoshi Yamaguchi Department of Surgery Nagasaki Prefectural Shimabara Hospital Shimabara Nagasaki Japan Second department of Internal medicine Nagasaki University School of Medicine Nagasaki Japan Department of Pathology Nagasaki Prefectural Shimabara Hospital Shimabara Nagasaki Japan

We herein present a case of a 75-year-old female with mucosa-associated lymphoid tissue （MALT） lymphoma of the transverse colon with the stage IE （Ann Arbor classification）. Colonoscopy revealed the tumor＇s appearance as a IIa plus Ⅱ c-like early colon cancer as defined according to the macroscopic classification of the Japanese Research Society for Cancer of Colon, Rectum and Anus, measuring less than 2 cm in diameter. Histologically, the tumor was diagnosed as MALT lymphoma because of the presence of lymphoepithelial lesions consisting of diffuse proliferation of atypical lymphocytes and glandular destruction. The majority of these lymphocytes immunohistochemically stained for the B-lymphocyte marker. The patient first underwent H pylori eradication therapy with Lansap. However, the tumor size gradually increased over the next 4 mo and the patient eventually underwent surgical resection. The operative procedure included a partial colectomy with dissection of the paracolic lymph nodes. The tumor measured 45 mm × 30 mm in diameter and histological examination showed that the lymphoma cells had infiltrated the muscle layer of the colon without nodal involvement. The patient has had no recurrence postoperatively without any chemotherapy.

关键词： Mucosa-associated lymphoid tissue Malignant lymphoma

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