Effects of Alu elements on global nucleosome positioning in the human genome

<p>Abstract</p> <p>Background</p> <p>Understanding the genome sequence-specific positioning of nucleosomes is essential to understand various cellular processes, such as transcriptional regulation and replication. As a typical example, the 10-bp periodicity of AA/TT and GC dinucleotides has been reported in several species, but it is still unclear whether this feature can be observed in the whole genomes of all eukaryotes.</p> <p>Results</p> <p>With Fourier analysis, we found that this is not the case: 84-bp and 167-bp periodicities are prevalent in primates. The 167-bp periodicity is intriguing because it is almost equal to the sum of the lengths of a nucleosomal unit and its linker region. After masking Alu elements, these periodicities were greatly diminished. Next, using two independent large-scale sets of nucleosome mapping data, we analyzed the distribution of nucleosomes in the vicinity of Alu elements and showed that (1) there are one or two fixed slot(s) for nucleosome positioning within the Alu element and (2) the positioning of neighboring nucleosomes seems to be in phase, more or less, with the presence of Alu elements. Furthermore, (3) these effects of Alu elements on nucleosome positioning are consistent with inactivation of promoter activity in Alu elements.</p> <p>Conclusions</p> <p>Our discoveries suggest that the principle governing nucleosome positioning differs greatly across species and that the Alu family is an important factor in primate genomes.</p

Flow Cytometric Nuclear DNA Analysis in Ulcerative Colitis

The purpose of this study was to assess the usefulness of nuclear DNA analysis in early cancer detection in patients with ulcerative colitis. The results of flow cytometric nuclear DNA anaiysis of tissue specimens from patients with ulcerative colitis, colonic adenoma, and colorectal carcinoma were compared. DNA aneuploidy was observed in 53.1 % of patients with ulcerative colitis and 16.7 % of patients with colonic adenoma. The degree of atypism of the tumor cells was related to the incidence of DNA aneuploidy. DNA aneuploidy was noted in 48.6 % of the patient with ulcerative colitis and coexistent colorectal carcinoma. The degree of dysplasia of the tumor cells was also correlated with the incidence of DNA aneuploidy. DNA aneuploidy was found in 14.3 % of specimens of mucosal tissue that were without cancerous or dysplastic cells. DNA aneuploidy was found in 8.5 % of specimens of mucosal tissue collected from patients with ulcerative colitis alone. Our findings showed that abnormalities in DNA content was closely correlated with histological atypism. In addition, our findings suggested that DNA aneuploidy may precede dysplastic changes in some cases of ulcerative colitis. We concluded that DNA analysis using flow cytometry is a useful method for identification of patients with ulcerative colitis at high risk for the development of cancer

DBTSS: DataBase of Human Transcription Start Sites, progress report 2006

DBTSS was first constructed in 2002 based on precise, experimentally determined 5′ end clones. Several major updates and additions have been made since the last report. First, the number of human clones has drastically increased, going from 190 964 to 1 359 000. Second, information about potential alternative promoters is presented because the number of 5′ end clones is now sufficient to determine several promoters for one gene. Namely, we defined putative promoter groups by clustering transcription start sites (TSSs) separated by <500 bases. A total of 8308 human genes and 4276 mouse genes were found to have putative multiple promoters. Third, DBTSS provides detailed sequence comparisons of user-specified TSSs. Finally, we have added TSS information for zebrafish, malaria and schyzon (a red algae model organism). DBTSS is accessible at

Effect of lymphotoxin-like substance (OH-1) on metastatic tumor proliferation.

The effect of a lymphotoxin-like substance, OH-1, released by human acute lymphatic leukemia BALL-1 cells, on metastatic tumor proliferation was investigated in BDF1 mice with transplanted Lewis lung carcinoma cells. Mitomycin-C, cyclophosphamide and adriamycin were used as control agents. The effect of OH-1 on metastases, as determined by comparison of the numbers of pulmonary nodules and by 3H-thymidine labeling indices, was significant. Also, investigation of the effect of OH-1 on host immunity showed that, while the control preparations had considerable side effects, immunodepression and emaciation were not noted with OH-1. As to direct cytotoxicity, OH-1 is principally cytostatic in activity and effects cell progression delay in both the G1 and G2 phases.</p

マウスガードの自律神経活動への影響 : 瞳孔フラッシュ応答による定量的評価

Background:Recently, it has been reported that mouth guards (MGs), which reduce the incidence and severity of traumatic oral injuries in contact sports, may actually affect sports performance. We have observed that a majority of subjects showed improved dynamic visual acuity during head rotation when using a MG, but subjects who were unwilling to use a MG showed the opposite effect. Thus, we hypothesized that unpleasant sensations due to MGs may decrease sports performance.Methods:In this study, we measured autonomic nervous system activity to evaluate unpleasant sensations objectively and quantitatively by measuring the pupillary flash response (PFR) and heart rate variability (HRV), before, during, and after wearing 3- and 5-mm-thick custom-made MGs in 10 healthy subjects.Results:It was found that the 5-mm MG had a higher incidence of unpleasant sensations (50% of subjects) than did the 3-mm MG (10%). PFR (not HRV) analysis showed that both sympathetic and parasympathetic nervous system activities increased in subjects with unpleasant sensations.Conclusions:We suggest that the unpleasant sensation induced this unusual autonomic nervous system response, which could not be detected by traditional methods such as HRV analysis. By using PFR analysis, it is possible to make MGs without unpleasant sensations for better sports performance.博士（医学）・乙第1306号・平成24年11月27日Copyright © 2012 Japanese Stomatological Society. Published by Elsevier Japan K

Evaluation of fat-free mass by whole-body counter in Japanese healthy young adults

Whole-body counters (WBCs) are special instruments for measuring internal irradiation doses and are usually housed within or around nuclear facilities in the event of unexpected radiation emergencies. As a substantial proportion of total body potassium (TBK) is found in fat-free mass (FFM), FFM volume can be predicted from WBC-measured 40K. We screened TBK in Japanese healthy young adults using a WBC and found strong linear correlations between TBK and lean body mass (LBM) and body mass index (r = 0.97, P < 0.01 and r = 0.47, P < 0.01, respectively). Multiple linear regression analysis, following adjustments for sex, indicates that only LBM has a significant correlation with TBK (P < 0.01). These results strongly support the feasibility of using WBCs for estimating FF

Laparoscopic total colectomy with lymph node dissection for familial adenomatous polyposis with multiple colorectal cancers

　A 49-year-old Japanese man visited our hospital with chief complaints of difficulty with and bleeding during defecation. After a detailed examination, he was diagnosed with familial adenomatous polyposis (FAP) with multiple (five) colorectal cancers. The tumors were located in the right-sided, left-sided, and sigmoid colon, and the lower rectum. Regional lymph node involvement was observed, but no metastasis to other organs was detected. We, therefore, performed a laparoscopic total colectomy with superior mesenteric artery (SMA) and inferior mesenteric artery (IMA) lymph node dissection. We were able to perform minimally invasive and cosmetically acceptable surgery using laparoscopy instead of highly-invasive open abdominal surgery. Our search of the literature revealed no reported cases of laparoscopic total colectomy with lymph node dissection for FAP with multiple colorectal cancers, making the present case the first to be reported in the literature