The entire organization of transcription units on the Bacillus subtilis genome

<p>Abstract</p> <p>Background</p> <p>In the post-genomic era, comprehension of cellular processes and systems requires global and non-targeted approaches to handle vast amounts of biological information.</p> <p>Results</p> <p>The present study predicts transcription units (TUs) in <it>Bacillus subtilis</it>, based on an integrated approach involving DNA sequence and transcriptome analyses. First, co-expressed gene clusters are predicted by calculating the Pearson correlation coefficients of adjacent genes for all the genes in a series that are transcribed in the same direction with no intervening gene transcribed in the opposite direction. Transcription factor (TF) binding sites are then predicted by detecting statistically significant TF binding sequences on the genome using a position weight matrix. This matrix is a convenient way to identify sites that are more highly conserved than others in the entire genome because any sequence that differs from a consensus sequence has a lower score. We identify genes regulated by each of the TFs by comparing gene expression between wild-type and TF mutants using a one-sided test. By applying the integrated approach to 11 σ factors and 17 TFs of <it>B. subtilis</it>, we are able to identify fewer candidates for genes regulated by the TFs than were identified using any single approach, and also detect the known TUs efficiently.</p> <p>Conclusion</p> <p>This integrated approach is, therefore, an efficient tool for narrowing searches for candidate genes regulated by TFs, identifying TUs, and estimating roles of the σ factors and TFs in cellular processes and functions of genes composing the TUs.</p

Ischemic enteritis with intestinal stenosis

A 75-year-old man was admitted to our hospital with sudden onset of vomiting and abdominal distension. The patient was taking medication for arrhythmia. Computed tomography showed stenosis of the ileum and a small bowel dilatation on the oral side from the region of stenosis. A transnasal ileus tube was placed. Enteroclysis using contrast medium revealed an approximately 6-cm afferent tubular stenosis 10 cm from the terminal ileum and thumbprinting in the proximal bowel. Transanal double-balloon enteroscopy showed a circumferential shallow ulcer with a smooth margin and edema of the surrounding mucosa. The stenosis was so extensive that we could not perform endoscopic balloon dilation therapy. During hospitalization, the patient's nutritional status deteriorated. In response, we surgically resected the region of stenosis. Histologic examination revealed disappearance of the mucosal layer and transmural ulceration with marked fibrosis, especially in the submucosal layer. Hemosiderin staining revealed sideroferous cells in the submucosal layers. Based on the pathologic findings, the patient was diagnosed with ischemic enteritis. The patient's postoperative course was uneventful

Prediction of POPF using CRP after LG

Purpose : Postoperative pancreatic fistula (POPF) is a serious complication after gastrectomy for gastric cancer. The purpose of this study is to identify the risk factor of POPF and evaluate C-reactive protein on postoperative day 1 (POD1) as the predictor for POPF after laparoscopic gastrectomy (LG). Methods : Between May 2013 and September 2016, 226 patients who underwent LG for gastric cancer were investigated. Patients were divided into 2 groups; POPF group (n = 17) and control group (n = 209). Clinicopathological factors were compared between 2 groups. Results : In POPF group, there are more male patients (p = 0.003) compared with control group. Preoperative factors, such as age, BMI, and prevalence of previous operation and comorbidity showed no significant difference between 2 groups. Regarding tumor factors and perioperative data such as blood loss and operative time, there were also no significant difference between 2 groups. POPF group showed longer postoperative hospital stay, and higher serum CRP level on POD1 (p < 0.0001). Multivariate analysis revealed that high CRP level on POD1 ( ≥ 3mg/dl) was independent risk factor of POPF. Conclusions : High serum CRP level on POD1 can predict the occurrence of POPF

Pathological Approach for Surveillance of Ulcerative Colitis-associated cancer:Usefulness of Immunohistochemistry for p53

The patients with long-standing ulcerative colitis( UC) have a high-risk of neoplastic lesions in the colonicmucosa. The UC-associated neoplastic lesion is difficult to detect by endoscopic examination or diagnosehistologically. In the present study, we aimed to clarify whether immunohistochemistry for p53 is useful todiscriminate the UC-associated neoplasia from inflammed regenerating epithelium. Tissue samples were obtainedfrom colorectomy specimens from 20 patients with long-standing UC (range 6-29 years). The surfaceof microstructure of the tissues was observed by stereomicroscopy, and the sections were examined usingimmunohistochemistry for p53. All of T2-4 carcinomas were detectable by endoscopic examination beforesurgery, whereas considerable number of dysplasias (52.5%), Tis carcinomas (33.3%), and T1 carcinomas(60.0%) were undetectable. Fifty-three of 67 UC-associated neoplastic lesions (79.1%) were of flat-typemacroscopically. The detection rate of flat-type neoplasias( 45.3%) was significantly lower than that of protrudingones (100%). The positivity of p53 overexpression was 0 % in UC-II, 52.5 % in UC-III, and 70.4 %in UC-IV, respectively. UC-II lesions had lower positivity of p53 overexpression than UC-III( P=0.027) or-IV lesions( P=0.003). Immunohistochemical analysis of p53 protein is useful to discriminate the UC-associatedneoplasia from inflammed regenerating epithelium

Immunohistochemical Localization of REG Ia Protein in Salivary Gland Tumors

The regenerating gene( Reg) Ia protein has a trophic effect on gastric epithelial cells, and its overexpressionis reported in gastrointestinal cancers. The salivary gland is a component of the digestive system, andtherefore, REG Ia protein may play some role in the pathophysiology of salivary gland tumors. In the presentstudy, we determined the immunohistochemical localization of REG Ia protein in salivary gland tumorsand moreover investigated its relationship to clinicopathological features. Twenty-eight patients with salivarygland tumor were enrolled. The specimens resected by surgery from those patients were examinedusing immunohistochemistry for REG Ia protein and Ki67. Five of the 16 pleomorphic adenomas (31.3%)were positive for REG Ia protein. Regarding salivary gland carcinomas, four of five mucoepidermoid carcinomas(80%), three of five adenoid cystic carcinomas (60%), one of two polymorphous low-grade adenocarcinomas(50%) were also positive for REG Ia protein. However, no relationships were found betweenREG Ia protein expression and clinicopathological features. Regarding the Ki67 expression, strong signalwas observed in the tumor cells of patients with salivary gland adenoma as well as carcinoma. REG Ia proteinis expressed not only in adenocarcinoma but also precancerous adenoma cells proliferating actively,suggesting that REG Ia protein may play a role at least in part in the development of salivary gland tumors

Stretching Actin Filaments within Cells Enhances their Affinity for the Myosin II Motor Domain

To test the hypothesis that the myosin II motor domain (S1) preferentially binds to specific subsets of actin filaments in vivo, we expressed GFP-fused S1 with mutations that enhanced its affinity for actin in Dictyostelium cells. Consistent with the hypothesis, the GFP-S1 mutants were localized along specific portions of the cell cortex. Comparison with rhodamine-phalloidin staining in fixed cells demonstrated that the GFP-S1 probes preferentially bound to actin filaments in the rear cortex and cleavage furrows, where actin filaments are stretched by interaction with endogenous myosin II filaments. The GFP-S1 probes were similarly enriched in the cortex stretched passively by traction forces in the absence of myosin II or by external forces using a microcapillary. The preferential binding of GFP-S1 mutants to stretched actin filaments did not depend on cortexillin I or PTEN, two proteins previously implicated in the recruitment of myosin II filaments to stretched cortex. These results suggested that it is the stretching of the actin filaments itself that increases their affinity for the myosin II motor domain. In contrast, the GFP-fused myosin I motor domain did not localize to stretched actin filaments, which suggests different preferences of the motor domains for different structures of actin filaments play a role in distinct intracellular localizations of myosin I and II. We propose a scheme in which the stretching of actin filaments, the preferential binding of myosin II filaments to stretched actin filaments, and myosin II-dependent contraction form a positive feedback loop that contributes to the stabilization of cell polarity and to the responsiveness of the cells to external mechanical stimuli

p53 ノックアウト マウス オ モチイタ デキストラン リュウサン ナトリウム ニ ヨル ダイチョウエンショウセイ ハツガン ニ カンスル ケンキュウ

京都大学0048新制・課程博士博士(医学)甲第10750号医博第2734号新制||医||863(附属図書館)UT51-2004-G597京都大学大学院医学研究科内科系専攻(主査)教授 武藤 誠, 教授 今村 正之, 教授 千葉 勉学位規則第4条第1項該当Doctor of Medical ScienceKyoto UniversityDA