DNA methylation patterns of protein-coding genes and long non-coding RNAs in males with schizophrenia

Schizophrenia (SCZ) is one of the most complex mental illnesses affecting 1% of the population worldwide. SCZ pathogenesis is considered to be a result of genetic as well as epigenetic alterations. Previous studies have aimed to identify the causative genes of SCZ. However, DNA methylation of long non-coding RNAs (lncRNAs) involved in SCZ has not been fully elucidated. In the present study, a comprehensive genome-wide analysis of DNA methylation was conducted using samples from two Male patients with paranoid and undifferentiated SCZ, respectively. Methyl-CpG binding domain protein-enriched genome sequencing was used. In the two patients with paranoid and undifferentiated SCZ, 1,397 and 1,437 peaks were identified, respectively. Bioinformatic analysis demonstrated that peaks were enriched in protein-coding genes, which exhibited nervous system and brain functions. A number of these peaks in gene promoter regions may affect gene expression and, therefore, influence SCZ-associated pathways. Furthermore, 7 and 20 lncRNAs, respectively, in the Refseq database were hypermethylated. According to the lncRNA dataset in the NONCODE database, similar to 30% of intergenic peaks overlapped with novel lncRNA loci. The results of the present study demonstrated that aberrant hypermethylation of lncRNA genes may be an important epigenetic factor associated with SCZ. However, further studies using larger sample sizes are required

Distribution Dynamics of Macroinvertebrates in the Source Water Areas of the South-water-to-north Project

A field investigation was made from July 2007 to May 2008 to study the distribution dynamics of macroinvertbrates in several streams that flow to the Danjiangkou Reservoir. The results showed that Baetis spp., Heptagenia spp., Caenis spp., Ceratopsyche spp, Parakiefferiella spp. and Eukiefferiella spp. were dominant groups in the study period, and their relative abundances were 20.4%, 11.5%, 9.1%, 5.9%, 11.6% and 5.0%, respectively. The difference in macroinvertbrates density was significant, but the differences in macroinvertbrate biomass, Shannon-Wiener index and Margalef index were not significant. Canonical correspondence analysis showed that the influence on the macroinvertbrates varied in different seasons. Fig 4, Tab 3, Ref 2

Characterizing macroinvertebrate communities across China: Large-scale implementation of a self-organizing map

Understanding the geographical patterns and divisions of communities is a fundamental step in achieving the sustainable management of ecosystems, especially in deteriorating global and local environments. The idea of geographical division has been applied on all continents but Antarctica, but it has never been rigorously tested for stream ecosystems in China, leaving a gap in knowledge for many basic and applied research questions regarding, for example, diversity patterns, conservation issues or climate change effects. To fill this gap, we aimed to (1) evaluate the geographical divisions of the macroinvertebrate communities in Chinese streams using the self-organizing map (SUM) method and (2) to characterize the distribution patterns in relation to different environmental variables. Macroinvertebrates were collected from 57 relatively clean stream sites covering a south-north gradient along the boundary of the geographic ladder (or altitudinal divide) in China. SUM was used to analyze large-scale biogeographical divisions of the macroinvertebrate communities. The sampling sites were divided into six clusters, distinguishing the samples from northern, central, and southern China. This pattern was also reflected by biotic metrics (abundance, biomass, taxa and sum of Ephemeroptera, Plecoptera, and Trichoptera richness, and diversity). The gradient of environmental variables, particularly water quality variables, was similar between the clusters, with the exceptions of two clusters from southwestern China when considering altitude and one cluster from northern China when considering conductivity and TN. The different clusters from the SUM were associated with indicator species, with clean-water adapted species dominating in southwestern China and pollution tolerant species in northern China. However, there were no significant correlations between environmental variables and biotic metrics. The overall combination of environmental variables and organism data suggests that spatial variation was the main predictor determining the composition of the macroinvertebrate communities on a large-scale, and the trained SUM appeared to be efficient at classifying streams on a broad geographic scale. (C) 2012 Elsevier Ltd. All rights reserved.Understanding the geographical patterns and divisions of communities is a fundamental step in achieving the sustainable management of ecosystems, especially in deteriorating global and local environments. The idea of geographical division has been applied on all continents but Antarctica, but it has never been rigorously tested for stream ecosystems in China, leaving a gap in knowledge for many basic and applied research questions regarding, for example, diversity patterns, conservation issues or climate change effects. To fill this gap, we aimed to (1) evaluate the geographical divisions of the macroinvertebrate communities in Chinese streams using the self-organizing map (SUM) method and (2) to characterize the distribution patterns in relation to different environmental variables. Macroinvertebrates were collected from 57 relatively clean stream sites covering a south-north gradient along the boundary of the geographic ladder (or altitudinal divide) in China. SUM was used to analyze large-scale biogeographical divisions of the macroinvertebrate communities. The sampling sites were divided into six clusters, distinguishing the samples from northern, central, and southern China. This pattern was also reflected by biotic metrics (abundance, biomass, taxa and sum of Ephemeroptera, Plecoptera, and Trichoptera richness, and diversity). The gradient of environmental variables, particularly water quality variables, was similar between the clusters, with the exceptions of two clusters from southwestern China when considering altitude and one cluster from northern China when considering conductivity and TN. The different clusters from the SUM were associated with indicator species, with clean-water adapted species dominating in southwestern China and pollution tolerant species in northern China. However, there were no significant correlations between environmental variables and biotic metrics. The overall combination of environmental variables and organism data suggests that spatial variation was the main predictor determining the composition of the macroinvertebrate communities on a large-scale, and the trained SUM appeared to be efficient at classifying streams on a broad geographic scale. (C) 2012 Elsevier Ltd. All rights reserved

Male-Specific Association between Dopamine Receptor D4 Gene Methylation and Schizophrenia

<div><p>Objective</p><p>The goal of our study was to investigate whether <i>DRD4</i> gene DNA methylation played an important role in the susceptibility of Han Chinese SCZ.</p><p>Methods</p><p>Using the bisulphite pyrosequencing technology, DNA methylation levels of 6 CpG dinucleotides in <i>DRD4</i> CpG island were measured among 30 paranoid SCZ patients, 30 undifferentiated SCZ patients, and 30 age- and gender-matched healthy controls.</p><p>Results</p><p>Strong correlation was observed among the six CpG sites (r>0.5, P<0.01), thus average methylation levels were applied thereafter. Our results indicated that there was a significant association between <i>DRD4</i> methylation and the risk of SCZ (P = 0.003), although there was no significant difference in <i>DRD4</i> methylation between the two SCZ subtypes (P = 0.670). A breakdown analysis by gender showed that the significant association of <i>DRD4</i> methylation and SCZ was driven by males (P<0.001) but not by females (P = 0.835). <i>DRD4</i> methylation was significantly associated with p300 in male SCZ patients (r = −0.543, P = 0.005) but not in female SCZ patients (r = 0.110, P = 0.599). Moreover, receiver operating characteristic (ROC) curves showed <i>DRD4</i> methylation was able to predict the status of SCZ in males [area under curve (AUC) = 0.832, P = 0.002] but not in females (AUC = 0.483, P = 0.876). Finally, a further expression experiment showed that <i>DRD4</i> methylation in the gene body was positively associated with gene expression, although the exact mechanism of gene regulation remained unknown for this interesting <i>DRD4</i> methylation.</p><p>Conclusion</p><p>The gender disparity in the <i>DRD4</i> DNA methylation provides novel insights into the pathogenesis of SCZ.</p></div

Male specific correlation between <i>DRD4</i> methylation and p300 in SCZ patients.

<p>Male specific correlation between <i>DRD4</i> methylation and p300 in SCZ patients.</p

Male specific prediction of SCZ using <i>DRD4</i> methylation as a diagnostic marker.

<p>Male specific prediction of SCZ using <i>DRD4</i> methylation as a diagnostic marker.</p

Male specific association of <i>DRD4</i> methylation with the susceptibility of SCZ.

<p>Male specific association of <i>DRD4</i> methylation with the susceptibility of SCZ.</p