Promoter hypermethylation and histone hypoacetylation contribute to pancreatic-duodenal homeobox 1 silencing in gastric cancer

Background and Aims: The expression of pancreatic-duodenal homeobox 1 (PDX1) in gastric cancer is aberrantly reduced. The aim of this study was to elucidate the regulation of DNA methylation and histone acetylation at the promoter for PDX1 silencing in gastric cancer. Methods: PDX1 expression in response to demethylation and acetylation was detected in human gastric cancer cell lines by reverse transcription-polymerase chain reaction (PCR) and western blot. Four CpG islands within the 5#-flanking region of PDX1 gene were analyzed with their transcription activities being detected by dual luciferase assay. Promoter hypermethylation was identified in gastric cancer cell lines and cancer tissues by methylation-specific PCR or bisulfite DNA sequencing PCR analysis. Histone acetylation was determined by chromatin immunoprecipitation (ChIP) assay. Results: Demethylation by 5′-aza-2′-deoxycytidine (5′-aza-dC) and/or acetylation by trichostatin A (TSA) restored PDX1 expression in gastric cancer cells. Hypermethylation was found in four CpG islands in six of seven cancer cell lines. However, only the distal CpG island located in the promoter fragment of PDX1, F383 (c.22063 to 21681 nt upstream of the ATG start codon) displayed significant transcriptional activity that could be suppressed by SssI methylase and increased by 5′-aza-dC and TSA. More than 70% of the single CpG sites in F383 were methylated with hypermethylation of F383 fragment more common in gastric cancerous tissues compared with the paired normal tissues (P < 0.05). ChIP assay showed F383 was also associated with low hypoacetylation level of the histones. Conclusion: Promoter hypermethylation and histone hypoacetylation contribute to PDX1 silencing in gastric cancer. © The Author 2010. Published by Oxford University Press. All rights reserved.postprin

Ezrin interacts with the SARS coronavirus spike protein and restrains infection at the entry stage

© 2012 Millet et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.Background: Entry of Severe Acute Respiratory Syndrome coronavirus (SARS-CoV) and its envelope fusion with host cell membrane are controlled by a series of complex molecular mechanisms, largely dependent on the viral envelope glycoprotein Spike (S). There are still many unknowns on the implication of cellular factors that regulate the entry process. Methodology/Principal Findings: We performed a yeast two-hybrid screen using as bait the carboxy-terminal endodomain of S, which faces the cytosol during and after opening of the fusion pore at early stages of the virus life cycle. Here we show that the ezrin membrane-actin linker interacts with S endodomain through the F1 lobe of its FERM domain and that both the eight carboxy-terminal amino-acids and a membrane-proximal cysteine cluster of S endodomain are important for this interaction in vitro. Interestingly, we found that ezrin is present at the site of entry of S-pseudotyped lentiviral particles in Vero E6 cells. Targeting ezrin function by small interfering RNA increased S-mediated entry of pseudotyped particles in epithelial cells. Furthermore, deletion of the eight carboxy-terminal amino acids of S enhanced S-pseudotyped particles infection. Expression of the ezrin dominant negative FERM domain enhanced cell susceptibility to infection by SARS-CoV and S pseudotyped particles and potentiated S-dependent membrane fusion. Conclusions/Significance: Ezrin interacts with SARS-CoV S endodomain and limits virus entry and fusion. Our data present a novel mechanism involving a cellular factor in the regulation of S-dependent early events of infection.This work was supported by the Research Grant Council of Hong Kong (RGC#760208)and the RESPARI project of the International Network of Pasteur Institutes

High Resolution Detection and Analysis of CpG Dinucleotides Methylation Using MBD-Seq Technology

Methyl-CpG binding domain protein sequencing (MBD-seq) is widely used to survey DNA methylation patterns. However, the optimal experimental parameters for MBD-seq remain unclear and the data analysis remains challenging. In this study, we generated high depth MBD-seq data in MCF-7 cell and developed a bi-asymmetric-Laplace model (BALM) to perform data analysis. We found that optimal efficiency of MBD-seq experiments was achieved by sequencing ∼100 million unique mapped tags from a combination of 500 mM and 1000 mM salt concentration elution in MCF-7 cells. Clonal bisulfite sequencing results showed that the methylation status of each CpG dinucleotides in the tested regions was accurately detected with high resolution using the proposed model. These results demonstrated the combination of MBD-seq and BALM could serve as a useful tool to investigate DNA methylome due to its low cost, high specificity, efficiency and resolution

Functioning styles of personality disorders and five-factor normal personality traits: a correlation study in Chinese students

BACKGROUND: Previous studies show that both the categorical and dimensional descriptors of personality disorders are correlated with normal personality traits. Recently, a 92-item inventory, the Parker Personality Measure (PERM) was designed as a more efficient and precise first-level assessment of personality disorders. Whether the PERM constructs are correlated with those of the five-factor models of personality needs to be clarified. METHODS: We therefore invited 913 students from poly-technical schools and colleges in China to answer the PERM, the Five-Factor Nonverbal Personality Questionnaire (FFNPQ), and the Zuckerman-Kuhlman Personality Questionnaire (ZKPQ). RESULTS: Most personality constructs had satisfactory internal alphas. PERM constructs were loaded with FFNPQ and ZKPQ traits clearly on four factors, which can be labelled as Dissocial, Emotional Dysregulation, Inhibition and Compulsivity, as reported previously. FFNPQ Openness to Experience, Conscientiousness and Extraversion formed another Factor, named Experience Hunting, which was not clearly covered by PERM or ZKPQ. CONCLUSION: The PERM constructs were loaded in a predictable way on the disordered super-traits, suggesting the PERM might offer assistance measuring personality function in clinical practice

In silico prioritisation of candidate genes for prokaryotic gene function discovery: an application of phylogenetic profiles

Background: In silico candidate gene prioritisation (CGP) aids the discovery of gene functions by ranking genes according to an objective relevance score. While several CGP methods have been described for identifying human disease genes, corresponding methods for prokaryotic gene function discovery are lacking. Here we present two prokaryotic CGP methods, based on phylogenetic profiles, to assist with this task. Results: Using gene occurrence patterns in sample genomes, we developed two CGP methods (statistical and inductive CGP) to assist with the discovery of bacterial gene functions. Statistical CGP exploits the differences in gene frequency against phenotypic groups, while inductive CGP applies supervised machine learning to identify gene occurrence pattern across genomes. Three rediscovery experiments were designed to evaluate the CGP frameworks. The first experiment attempted to rediscover peptidoglycan genes with 417 published genome sequences. Both CGP methods achieved best areas under receiver operating characteristic curve (AUC) of 0.911 in Escherichia coli K-12 (EC-K12) and 0.978 Streptococcus agalactiae 2603 (SA-2603) genomes, with an average improvement in precision of >3.2-fold and a maximum of >27-fold using statistical CGP. A median AUC of >0.95 could still be achieved with as few as 10 genome examples in each group of genome examples in the rediscovery of the peptidoglycan metabolism genes. In the second experiment, a maximum of 109-fold improvement in precision was achieved in the rediscovery of anaerobic fermentation genes in EC-K12. The last experiment attempted to rediscover genes from 31 metabolic pathways in SA-2603, where 14 pathways achieved AUC >0.9 and 28 pathways achieved AUC >0.8 with the best inductive CGP algorithms. Conclusion: Our results demonstrate that the two CGP methods can assist with the study of functionally uncategorised genomic regions and discovery of bacterial gene-function relationships. Our rediscovery experiments also provide a set of standard tasks against which future methods may be compared.12 page(s

Physical Confirmation and Mapping of Overlapping Rat Mammary Carcinoma Susceptibility QTLs, Mcs2 and Mcs6

Only a portion of the estimated heritability of breast cancer susceptibility has been explained by individual loci. Comparative genetic approaches that first use an experimental organism to map susceptibility QTLs are unbiased methods to identify human orthologs to target in human population-based genetic association studies. Here, overlapping rat mammary carcinoma susceptibility (Mcs) predicted QTLs, Mcs6 and Mcs2, were physically confirmed and mapped to identify the human orthologous region. To physically confirm Mcs6 and Mcs2, congenic lines were established using the Wistar-Furth (WF) rat strain, which is susceptible to developing mammary carcinomas, as the recipient (genetic background) and either Wistar-Kyoto (WKy, Mcs6) or Copenhagen (COP, Mcs2), which are resistant, as donor strains. By comparing Mcs phenotypes of WF.WKy congenic lines with distinct segments of WKy chromosome 7 we physically confirmed and mapped Mcs6 to ∼33 Mb between markers D7Rat171 and gUwm64-3. The predicted Mcs2 QTL was also physically confirmed using segments of COP chromosome 7 introgressed into a susceptible WF background. The Mcs6 and Mcs2 overlapping genomic regions contain multiple annotated genes, but none have a clear or well established link to breast cancer susceptibility. Igf1 and Socs2 are two of multiple potential candidate genes in Mcs6. The human genomic region orthologous to rat Mcs6 is on chromosome 12 from base positions 71,270,266 to 105,502,699. This region has not shown a genome-wide significant association to breast cancer risk in pun studies of breast cancer susceptibility

Detecting and Characterizing Mg ii Absorption in DESI Survey Validation Quasar Spectra

We present findings of the detection of Magnesium II (Mg ii, λ = 2796, 2803 Å) absorbers from the early data release of the Dark Energy Spectroscopic Instrument (DESI). DESI is projected to obtain spectroscopy of approximately 3 million quasars (QSOs), of which over 99% are anticipated to be at redshifts greater than z > 0.3, such that DESI would be able to observe an associated or intervening Mg ii absorber illuminated by the background QSO. We have developed an autonomous supplementary spectral pipeline that detects these systems through an initial line-fitting process and then confirms the line properties using a Markov Chain Monte Carlo sampler. Based upon a visual inspection of the resulting systems, we estimate that this sample has a purity greater than 99%. We have also investigated the completeness of our sample in regard to both the signal-to-noise properties of the input spectra and the rest-frame equivalent width (W 0) of the absorber systems. From a parent catalog containing 83,207 quasars, we detect a total of 23,921 Mg ii absorption systems following a series of quality cuts. Extrapolating from this occurrence rate of 28.8% implies a catalog at the completion of the five-year DESI survey that will contain over eight hundred thousand Mg ii absorbers. The cataloging of these systems will enable significant further research because they carry information regarding circumgalactic medium environments, the distribution of intervening galaxies, and the growth of metallicity across the redshift range 0.3 ≤ z < 2.5

Trends in healthy life expectancy in Hong Kong SAR 1996–2008

Although Hong Kong has one of the best life expectancy (LE) records in the world, second only to Japan for women, we know very little about the changes in the health status of the older adult population. Our article aims to provide a better understanding of trends in both chronic morbidity and disability for older men and women. The authors compute chronic morbidity-free and disability-free life expectancy and the proportion of both in relation to total LE using the Sullivan method to examine whether Hong Kong older adults are experiencing a compression of morbidity and disability and whether there is any gender difference in relation to mortality and morbidity. The results of this study show that Hong Kong women tend to outlive Hong Kong men but are also more likely to suffer from a ‘double disadvantage’, namely more years of life with more chronic morbidity and disability. There has also been a significant expansion of chronic morbidity, as chronic morbidity-free life expectancy (CMFLE) decreased substantially for both genders from 1996 to 2008. Although disability-free life expectancy (DFLE) increased during this period, it increased at a slower pace compared to LE. The proportion of life without chronic morbidity also declined remarkably during these 12 years. Among the advanced ages, the proportion of remaining life in good health without disability has decreased since 1996, indicating a relative expansion of disability

A Systematic Review of the Effect of Cognitive Strategies on Strength Performance

Background Researchers have tested the beliefs of sportspeople and sports medicine specialists that cognitive strategies influence strength performance. Few investigators have synthesised the literature. Objectives The specific objectives were to review evidence regarding (a) the cognitive strategy–strength performance relationship; (b) participant skill level as a moderator; and (c) cognitive, motivational, biomechanical/physiological, and emotional mediators. Method Studies were sourced via electronic databases, reference lists of retrieved articles, and manual searches of relevant journals. Studies had to be randomised or counterbalanced experiments with a control group or condition, repeated measures, and a quality control score above 0.5 (out of 1). Cognitive strategies included goal setting, imagery, self-talk, preparatory arousal, and free choice. Dependent variables included maximal strength, local muscular endurance, or muscular power. Results Globally, cognitive strategies were reliability associated with increased strength performance (results ranged from 61 to 65 %). Results were mixed when examining the effects of specific strategies on particular dependent variables, although no intervention had an overall negative influence. Indeterminate relationships emerged regarding hypothesised mediators (except cognitive variables) and participant skill level as a moderator. Conclusions Although cognitive strategies influence strength performance, there are knowledge gaps regarding specific types of strength, especially muscular power. Cognitive variables, such as concentration, show promise as possible mediators