Development of a Novel Output Value for Quantitative Assessment in Methylated DNA Immunoprecipitation-CpG Island Microarray Analysis

In DNA methylation microarray analysis, quantitative assessment of intermediate methylation levels in samples with various global methylation levels is still difficult. Here, specifically for methylated DNA immunoprecipitation-CpG island (CGI) microarray analysis, we developed a new output value. The signal log ratio reflected the global methylation levels, but had only moderate linear correlation (r = 0.72) with the fraction of DNA molecules immunoprecipitated. By multiplying the signal log ratio using a coefficient obtained from the probability value that took account of signals in neighbouring probes, its linearity was markedly improved (r = 0.94). The new output value, Me value, reflected the global methylation level, had a strong correlation also with the fraction of methylated CpG sites obtained by bisulphite sequencing (r = 0.88), and had an accuracy of 71.8 and 83.8% in detecting completely methylated and unmethylated CGIs. Analysis of gastric cancer cell lines using the Me value showed that methylation of CGIs in promoters and gene bodies was associated with low and high, respectively, gene expression. The degree of demethylation of promoter CGIs after 5-aza-2'-deoxycytidine treatment had no association with that of induction of gene expression. The Me value was considered to be useful for analysis of intermediate methylation levels of CGIs

Transcriptional repression by MYB3R proteins regulates plant organ growth

In multicellular organisms, temporal and spatial regulation of cell proliferation is central for generating organs with defined sizes and morphologies. For establishing and maintaining the post-mitotic quiescent state during cell differentiation, it is important to repress genes with mitotic functions. We found that three of the Arabidopsis MYB3R transcription factors synergistically maintain G2/M-specific genes repressed in post-mitotic cells and restrict the time window of mitotic gene expression in proliferating cells. The combined mutants of the three repressor-type MYB3R genes displayed long roots, enlarged leaves, embryos, and seeds. Genome-wide chromatin immunoprecipitation revealed that MYB3R3 binds to the promoters of G2/M-specific genes and to E2F target genes. MYB3R3 associates with the repressor-type E2F, E2FC, and the RETINOBLASTOMA RELATED proteins. In contrast, the activator MYB3R4 was in complex with E2FB in proliferating cells. With mass spectrometry and pairwise interaction assays, we identified some of the other conserved components of the multiprotein complexes, known as DREAM/dREAM in human and flies. In plants, these repressor complexes are important for periodic expression during cell cycle and to establish a post-mitotic quiescent state determining organ size

Clinicopathological characteristics and treatment strategies in early gastric cancer: a retrospective cohort study

<p>Abstract</p> <p>Background</p> <p>Both endoscopic and surgical approaches are employed in the treatment of early gastric cancer (EGC). The aim of this study was to establish appropriate treatment strategies for early gastric cancer.</p> <p>Methods</p> <p>We retrospectively examined clinicopathological data of EGC patients who had undergone surgery.</p> <p>Results</p> <p>A total of 327 patients (204 males and 123 females, mean age 63.2 years) were eligible for inclusion in the study. The median follow-up period was 31 months. Of 161 mucosal (pT1a) tumors, 87 were mainly undifferentiated and 110 had an undifferentiated component. Four patients with pT1a tumors had lymph node metastases; all these tumors were signet-ring cell carcinomas and were macroscopic type 0-IIc with ulceration, and only one of them had lymphatic invasion. Among patients with submucosal tumors, four of 43 patients with pT1b1 tumors and 37 of 123 patients with pT1b2 tumors had nodal metastases. Lymph node metastases were significantly higher in mixed undifferentiated type group than differentiated type group for both groups, pT1a-pT1b1 (p = 0.0251) and pT1b2 (p = 0.0430) subgroups. Only four of 45 patients with nodal metastases were diagnosed preoperatively by computed tomography (sensitivity 8.9%, specificity 96.2%). Nine patients with pT1b tumors had recurrence after surgery, and died. The sites of initial recurrence were liver, bone, peritoneum, distant nodes, and the surgical anastomosis.</p> <p>Conclusions</p> <p>The incidence of nodal metastases was approximately 5% in undifferentiated type mucosal (pT1a) tumors, and higher in submucosal (pT1b) tumors. The sensitivity of preoperative diagnosis of nodal metastases in EGC using computed tomography was relatively low in this study. Therefore at present surgery with adequate lymphadenectomy should be performed as curative treatment for undifferentiated type EGC.</p

Characterizing interdependencies of multiple time series: theory and applications

This book introduces academic researchers and professionals to the basic concepts and methods for characterizing interdependencies of multiple time series in the frequency domain. Detecting causal directions between a pair of time series and the extent of their effects, as well as testing the non existence of a feedback relation between them, have constituted major focal points in multiple time series analysis since Granger introduced the celebrated definition of causality in view of prediction improvement. Causality analysis has since been widely applied in many disciplines. Although most analyses are conducted from the perspective of the time domain, a frequency domain method introduced in this book sheds new light on another aspect that disentangles the interdependencies between multiple time series in terms of long-term or short-term effects, quantitatively characterizing them. The frequency domain method includes the Granger noncausality test as a special case. Chapters 2 and 3 of the book introduce an improved version of the basic concepts for measuring the one-way effect, reciprocity, and association of multiple time series, which were originally proposed by Hosoya. Then the statistical inferences of these measures are presented, with a focus on the stationary multivariate autoregressive moving-average processes, which include the estimation and test of causality change. Empirical analyses are provided to illustrate what alternative aspects are detected and how the methods introduced here can be conveniently applied. Most of the materials in Chapters 4 and 5 are based on the authors' latest research work. Subsidiary items are collected in the Appendix

Large-scale hybridization of Japanese populations of Hinamoroko, Aphyocypris chinensis, with A. kikuchii introduced from Taiwan

Aphyocypris chinensis is a small cyprinid that is widely distributed in lowland areas of continental China, the Korean Peninsula, and the northwestern part of Kyushu, Japan. However, this species is severely threatened in Japan due to human impacts; thus, several facilities and citizen groups implemented captive breeding and reintroduction/reinforcement programs using several dozen founder fish collected from Tanushimaru, the location with the only known natural population, in the 1980s and 1990s. To determine the phylogenetic position and genetic authenticity of Japanese populations of A. chinensis, we conducted mtDNA and genome-wide SNP analyses using a total of 254 specimens from 31 wild and captive samples, including specimens of Chinese and Korean A. chinensis and the close relative A. kikuchii from Taiwan. The mtDNA divergence and phylogeny indicated that the haplotypes found exclusively in Japan were differentiated from the Chinese/Korean haplotypes (uncorrected p = 2.6% in the cytochrome b gene) to the same extent as they were from A. kikuchii haplotypes (p = 2.9%). Results from mtDNA sequences and 47–359 SNPs, obtained using the MIG-seq method with different parameter sets, revealed that the initial captive populations and an extinct wild population in Ukiha, adjacent to Tanushimaru, were genuine Japanese populations, whereas all extant captive and wild populations in Japan are hybrids between Japanese A. chinensis and A. kikuchii, or A. kikuchii itself. The details of the captive breeding and exchange programs, as well as evidence for the aquarium trade of A. kikuchii since the 1990s, strongly suggest that the mixture of A. kikuchii into Japanese populations occurred within the first several years of the establishment of captive populations in 1994. The present case of the highly probable extinction of genuine Japanese populations of A. chinensis emphasizes the importance of confirmation and management of the genetic authenticity of conservation-targeted species

Semi-automated algorithm for calculating heart-to-mediastinum ratio in cardiac Iodine-123 MIBG imaging

金沢大学医薬保健研究域医学系Background: We have developed novel software for semi-automatically measuring heart-to-mediastinum (H/M) ratio in cardiac Iodine-123 (123I)-labeled meta-iodobenzylguanidine (MIBG) imaging. Our aim is to improve the reproducibility of the H/M ratio using the semi-automated method as opposed to the manual method. Methods and Results: The software algorithm automatically determined the mediastinal region of interest (ROI) using information from 123I-MIBG uptake of the heart, lung, liver, and thyroid after a cardiac circular ROI was manually set. A total of 37 patients who underwent both early and delayed 123I-MIBG imaging was retrospectively selected. The heart-to-mediastinum (H/M) ratios were calculated by both semi-automated and manual methods and assessed for the intra- and inter-observer variability. All H/M ratios were classified into three groups: normal, slight abnormality, and severe abnormality. The H/M ratios with the new method were higher than those obtained manually (P<.001). In the test-retest reliability, the intra-class correlation coefficient from the semi-automated method showed excellent reproducibility for early (0.99) and delayed (0.99) imaging. The Bland-Altman plots demonstrated better agreement using the semi-automated method (a range of 95% limits -0.11 to 0.10) than that in the manual method (-0.34 to 0.27). The inter-observer agreement was also good using the semi-automated method (κ = 0.866). Conclusions: The H/M ratio using the semi-automated method showed high reproducibility in both early and delayed imaging. © 2010 American Society of Nuclear Cardiology

Endless loop tachycardia below the upper tracking rate of a pacemaker: A case report

An 82-year-old female with a history of hypertrophic cardiomyopathy (HCM), sick sinus syndrome (SSS), and an implanted DDD pacemaker was admitted to our hospital for congestive heart failure caused by rapid atrial fibrillation. After administration of amiodarone, atrial fibrillation (AF) became atrial flutter (AFL). Electrophysiological investigation revealed counterclockwise AFL. Catheter ablation of the cavotricuspid isthmus was performed. Burst pacing from the coronary sinus ostium to confirm the block line of the isthmus induced rapid, regular, ventricular pacing at a rate of 110 bpm. The differential diagnosis of this tachycardia included ectopic atrial tachycardia and pacemaker-mediated, endless loop tachycardia (ELT). We diagnosed this arrhythmia as ELT, because temporary reprogramming of the pacemaker mode from DDD to VVI terminated the tachycardia. In this patient, pacing parameters favored ELT (long atrioventricular delay [AVD] and short postventricular atrial refractory period [PVARP]), and atrioventricular and ventriculoatrial conduction time was prolonged as a result of amiodarone administration. The ELT continued because the rate was lower than the programmed upper tracking rate. Reprogramming the parameter (decreasing AVD and increasing PVARP) resulted in termination of ELT