Spatiotemporal specificity of correlated DNA methylation and gene expression pairs across different human tissues and stages of brain development

DNA methylation (DNAm) that occurs on promoter regions is primarily considered to repress gene expression. Previous studies indicated that DNAm could also show positive correlations with gene expression. Both DNAm and gene expression profiles are known to be tissue- and development-specific. This study aims to investigate how DNAm and gene expression are coordinated across different human tissues and developmental stages, as well as the biological significance of such correlations. By analyzing 2,239 samples with both DNAm and gene expression data in the same human subjects obtained from six published datasets, we evaluated the correlations between gene and CpG pairs (GCPs) at cis-regions and compared significantly correlated GCPs (cGCPs) across different tissues and brains at different age groups. A total of 37,363 cGCPs was identified in the six datasets; approximately 38% of the cGCPs were positively correlated. The majority (>90%) of cGCPs was tissue- or development-specific. We also observed that the correlation direction can be opposite in different tissues and ages. Further analysis highlights the importance of cGCPs for their cellular functions and potential roles in complex traits and human diseases. For instance, the early developmental brain possessed a highly unique set of cGCPs that were associated with neurogenesis and psychiatric disorders. By assessing the epigenetic factors involved in cGCPs, we discovered novel regulatory mechanisms of positive cGCPs distinct from negative cGCPs, which were related to multiple factors, such as H3K27me3, CTCF, and JARD2. The catalogue of cGCPs compiled can be used to guide functional interpretation of genetic and epigenetic studies

Relationship between Gingival Crevicular Fluid Microbiota and Cytokine Profile in Periodontal Host Homeostasis

As potential biomarkers in periodontitis, microbiome, and cytokines have recently been extensively investigated, but combined analyses of the variations between the microbial structure and cytokine composition are rare. The present study aimed to investigate whether there are differences in the combined profile of microbiome and cytokines in individuals with or without periodontitis. The microbiome and cytokine composition in gingival crevicular fluid (GCF) from 16 patients and 15 controls from Jishi Shan (Gansu, China) were analyzed using 454 pyrosequencing and RayBio Quantibody Arrays. The results showed that a higher co-occurrence of genera in periodontitis group compared with the healthy group, as evaluated by Schoener's abundance-based co-occurrence index. C-reactive protein (CRP) was significantly (P < 0.05) higher in the GCF of the periodontitis group while interleukin (IL)-8 was significantly (P < 0.01) higher in the GCF of the healthy group. The Mantel test revealed a significant concordance between cytokines and microbiota, in the healthy group (Mantel statistic r = 0.36, P ≤ 0.05) but not in the periodontitis group (Mantel statistic r = 0.013, P = 0.434). The results were further confirmed by the Procrustes test. Matrix metalloproteinase (MMP)-9, osteoactivin, IL-8, and macrophage inflammatory protein (MIP)-1a were significantly associated with bacterial composition at the phylum, class, order, family, and genus levels. CRP was also associated with bacterial composition at the species level. In conclusion, alterations in the polymicrobial community structure leads to disruption in the healthy correlation between cytokines and microbiomes. This dysbiosis between the microbiota and the immune response could be one of the major etiological mechanisms underlying periodontitis

Exploration of Human Salivary Microbiomes—Insights into the Novel Characteristics of Microbial Community Structure in Caries and Caries-Free Subjects

<div><p>Recently, high-throughput sequencing has improved the understanding of the microbiological etiology of caries, but the characteristics of the microbial community structure in the human oral cavity with and without caries are not completely clear. To better understand these characteristics, Illumina MiSeq high-throughput sequencing was utilized to analyze 20 salivary samples (10 caries-free and 10 caries) from subjects from the same town in Dongxiang, Gansu, China. A total of 5,113 OTUs (Operational Taxonomic Units, 97% cutoff) were characterized in all of the salivary samples obtained from the 20 subjects. A comparison of the two groups revealed that (i) the predominant phyla were constant between the two groups; (ii) the relative abundance of the genera <i>Veillonella</i>, <i>Bifidobacterium</i>, <i>Selenomonas</i>, <i>Olsenella</i>, <i>Parascardovia</i>, <i>Scardovia</i>, <i>Chryseobacterium</i>, <i>Terrimonas</i>, <i>Burkholderia</i> and <i>Sporobacter</i> was significantly higher in the group with caries (P < 0.05); and (iii) four genera with low relative abundance (< 0.01% on average), including two characteristic genera in caries (<i>Chryseobacterium</i> and <i>Scardovia</i>), significantly influenced the microbial community structure at the genus and OTU levels. Moreover, via co-occurrence and principal component analyses, the co-prevalence of the pathogenic genera was detected in the caries samples, but in the caries-free samples, the function of clustered genera was more random. This result suggests that a synergistic effect may be influencing the assembly of the caries microbial community, whereas competition may play a more dominant role in governing the microbial community in the caries-free group. Our findings regarding the characteristics of the microbial communities of the groups with and without caries might improve the understanding of the microbiological etiology of caries and might improve the prevention and cure of caries in the future.</p></div

Heatmaps displaying genus distribution patterns within caries-free (a) and caries (b) groups.

<p>The clustering and heatmaps were computed from Schoener’s index matrix. The Schoener’s index matrices calculated from each group are found in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0147039#pone.0147039.s005" target="_blank">S2</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0147039#pone.0147039.s006" target="_blank">S3</a> Tables.</p

The dominant taxa in the caries (C) and caries-free (H) groups were analyzed using LEfSe (P<0.05).

<p>The average relative abundance of each clade was more than 0.05%. (a) Visualization of differential taxa ranked by effect size. (b) Representation of relevant taxa on a phylogenetic tree.</p

Constrained Analysis of Principal Coordinates (CAP) plots (based on weighted UniFrac) estimating the β-diversity variation among the caries and caries-free groups.

<p>Constrained Analysis of Principal Coordinates (CAP) plots (based on weighted UniFrac) estimating the β-diversity variation among the caries and caries-free groups.</p

Study of two-photon decays of pseudoscalar mesons via J/Psi radiative decays

Using a sample of 4.48 x 10(8) Psi(3686) events collected with the BESIII detector at the BEPCII collider, we study the two-photon decays of the pseudoscalar mesons pi(0,) eta , eta' , eta(1405), eta(1475), eta(1760), and X(1835) in J/Psi radiative decays using Psi(3686) -&gt; pi(+) pi(-) J/Psi events. The pi(0), eta, and eta' mesons are clearly observed in the two-photon mass spectra, and the branching fractions are determined to be B(J/Psi -&gt; gamma pi(0) -&gt; 3 gamma) = (3.57 +/- 0.12 +/- 0.16) x 10(-5), B(J/Psi -&gt; gamma eta -&gt; 3 gamma) = (4.42 +/- 0.04 +/- 0.18) x 10(-4), and B(J/Psi -&gt; gamma eta' -&gt; 2 gamma) = (1.26 +/- 0.02 +/- 0.05) x 10(-4), where the first error is statistical and the second is systematic. No clear signal for eta(1405), eta(1475), eta(1760) or X(1835) is observed in the two- photon mass spectra, and upper limits at the 90% confidence level on the product branching fractions are obtained

Dalitz plot analysis of the decay ω→π+π−π0\omega \to \pi^+ \pi⁻ \pi^0

Using a low-background sample of $2.6\times 10^5$ $J/\psi\rightarrow\omega\eta(\omega\rightarrow\pi^{+}\pi^{-}\pi^{0},\eta\rightarrow\gamma\gamma)$ events, about 5 times larger statistics than previous experiments, we present a Dalitz plot analysis of the decay $\omega\rightarrow\pi^{+}\pi^{-}\pi^{0}$. It is found that the Dalitz plot distribution differs from the pure $P$-wave phase space with a statistical significance of $18.9\sigma$. The parameters from the fit to data are in reasonable agreement with those without the cross-channel effect within the dispersive framework, which indicates that the cross-channel effect in $\omega\rightarrow\pi^+\pi^-\pi^0$ is not significant.Comment: 9 pages, 9 figure