著者

Norihito Kawashita Hiroyuki Yamasaki Tomoyuki Miyao Kentaro Kawai Yoshitake Sakae Takeshi Ishikawa Kenichi Mori Shinya Nakamura Hiromasa Kaneko

出版者

公益社団法人 日本化学会・情報化学部会

雑誌

Journal of Computer Aided Chemistry (ISSN:13458647)

巻号頁・発行日

vol.16, pp.15-29, 2015 (Released:2015-10-29)

参考文献数

192

被引用文献数

3 6

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We have reviewed chemoinformatics approaches for drug discovery such as aromatic interactions, aromatic clusters, structure generation, virtual screening, de novo design, evolutionary algorithm, inverse-QSPR/QSAR, Monte Carlo, molecular dynamics, fragment molecular orbital method and matched molecular pair analysis from the viewpoint of young researchers. We intend to introduce various fields of chemoinformatics for non-expert researchers. The structure of this review is given as follows: 1. Introduction, 2. Analysis of Aromatic Interactions, 2.1 Aromatic Interactions, 2.2 Aromatic Clusters, 3. Ligand Based Structure Generation, 3.1 Virtual Screening, 3.2 De Novo Ligand Design, 3.3 Combinatorial Explosion, 3.4 Inverse-QSPR/QSAR, 4. Trends in Chemoinformatics-Based De Novo Drug Design, 5. Conformational Search Method Using Genetic Crossover for Bimolecular Systems, 6. Interaction Analysis using Fragment Molecular Orbital Method for Drug Discovery, 7. Matched Molecular Pair Analysis and SAR Analysis by Fragment Molecular Orbital Method, 8. Chemoinformatics Approach in Pharmaceutical Processes, 9. Conclusion.

著者

Chiaki KITA James K. CHAMBERS Mika TANABE Mitsuhiro IRIE Hiroyuki YAMASAKI Kazuyuki UCHIDA

出版者

JAPANESE SOCIETY OF VETERINARY SCIENCE

雑誌

Journal of Veterinary Medical Science (ISSN:09167250)

巻号頁・発行日

vol.84, no.3, pp.406-413, 2022 (Released:2022-03-15)

参考文献数

29

被引用文献数

4

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Dogs with ovarian papillary adenocarcinoma occasionally present with ascites and/or pleural effusion. These aspirated fluids often contain a large number of cells, and distinction between neoplastic cells and activated mesothelial cells can be difficult. In this study, 7 cases of canine ovarian papillary adenocarcinoma, including 3 with ascites and pleural effusion, were immunohistochemically examined. Ovarian tumor cells were positive for cytokeratin CAM5.2 (CAM5.2), Wilms’ tumor 1 (WT-1) and progesterone receptor (PR) in all 7 cases. A metastatic lesion of the mediastinum in one case was also positive for CAM5.2, WT-1 and PR. Immunohistochemistry on cell blocks obtained from ascites and/or pleural effusion of 2 cases revealed the presence of PR-positive epithelial cells. Whereas, activated mesothelial cells in ascites or pleural effusion collected from dogs without neoplastic lesions were negative for PR. In addition, surface epithelium and subsurface epithelial structures (SES) of normal canine ovaries, that are considered to be the cell of origin for ovarian papillary adenocarcinoma, were also positive for CAM5.2, WT-1 and PR. These results indicate that, together with CAM5.2, WT-1 and PR is a useful diagnostic marker for canine ovarian papillary adenocarcinoma. Expression of PR may be associated with progesterone-dependent nature of canine ovarian papillary adenocarcinoma.

著者

Satoshi WATANABE Naofumi YOSHIDA Kairi BABA Hiroyuki YAMASAKI Natsuko O. SHINOZAKI Masato OGAWA Tomoya YAMASHITA Aya K. TAKEDA

出版者

BMFH Press

雑誌

Bioscience of Microbiota, Food and Health (ISSN:21863342)

巻号頁・発行日

pp.2022-047, (Released:2023-10-18)

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Gut microbiota imbalance plays an important role in the pathogenesis of various diseases. Here, we determined microbe–microbe interactions and gut microbiome stability in a Japanese population with varying body mass indices (BMIs) and enterotypes. Using 16S ribosomal RNA gene sequencing, we analyzed gut microbial data from fecal samples obtained from 3,365 older Japanese individuals. The individuals were divided into lean, normal, and obese groups based on their BMIs. They were further categorized according to their gut microbiota enterotypes: Bacteroides (enterotype B), Prevotella (enterotype P), and Ruminococcus (enterotype R). We obtained data on different host factors, such as age, BMI, and disease status, using a survey questionnaire evaluated by the Mykinso gut microbiome testing service. Subsequently, we evaluated the co-occurrence network. Individual differences in BMI were associated with differences in co-occurrence networks. By exploring the network topology based on BMI status , we observed that the network density was lower in the lean group than that in the normal group. Furthermore, a simulation-based stability analysis revealed a lower resistance index in the lean group than those in the other two groups. Our results provide insights into various microbe–microbe interactions and gut microbial stability and could aid in developing appropriate therapeutic strategies targeting gut microbiota modulation to manage frailty.

著者

Naofumi YOSHIDA Satoshi WATANABE Hiroyuki YAMASAKI Hajime SAKUMA Aya K. TAKEDA Tomoya YAMASHITA Ken-ichi HIRATA

出版者

BMFH Press

雑誌

Bioscience of Microbiota, Food and Health (ISSN:21863342)

巻号頁・発行日

pp.2021-056, (Released:2021-12-07)

被引用文献数

13

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Imbalance of the gut microbiota plays an important role in the pathogenesis of various diseases. Although many clinical studies have analyzed the gut microbiota, the definition of normal gut microbiota remains unclear. In this study, we aim to establish the average gut microbiota in the healthy Japanese population. Using 16S ribosomal RNA gene sequencing, we analyzed gut microbial data from fecal samples obtained from 6,101 healthy Japanese individuals. Based on their ages, the individuals were divided into three groups: young, middle-age, and old. Individuals were further categorized according to body mass index (BMI) into lean, normal, and obese groups. The α and β diversities in the old group were significantly higher than those in the young and middle-age groups. The Firmicutes/Bacteroidetes ratio of subjects in the obese category was significantly lower compared with those of subjects in the lean and normal categories in the young and middle-age groups. Genus Bacteroides was the dominant gut microbiota across all the BMI categories in all the age groups. Among the top ten genera, the abundances of Bacteroides, Bifidobacterium, Anaerostipes, Blautia, Dorea, Fusicatenibacter, Lachnoclostridium, and Parabacteroides were significantly lower in the old group than in the young and middle-age groups. The correlation network at the genus level revealed different microbe-microbe interactions associated with age and BMI. We determined the average Japanese gut microbiota, and this information could be used as a reference. The gut microbiota greatly differs based on the life stage and metabolic status of the host, and this gives rise to a variety of host–gut microbe interactions that can lead to an increased susceptibility to disease.