Features of Methylation and Gene Expression in the Promoter-Associated CpG Islands Using Human Methylome Data

CpG islands are typically located in the 5′ end of genes and considered as gene markers because they play important roles in gene regulation via epigenetic change. In this study, we compared the features of CpG islands identified by several major algorithms by setting the parameter cutoff values in order to obtain a similar number of CpG islands in a genome. This approach allows us to systematically compare the methylation and gene expression patterns in the identified CpG islands. We found that Takai and Jones' algorithm tends to identify longer CpG islands but with weaker CpG island features (e.g., lower GC content and lower ratio of the observed over expected CpGs) and higher methylation level. Conversely, the CpG clusters identified by Hackenberg et al.'s algorithm using stringent criteria are shorter and have stronger features and lower methylation level. In addition, we used the genome-wide base-resolution methylation profile in two cell lines to show that genes with a lower methylation level at the promoter-associated CpG islands tend to express in more tissues and have stronger expression. Our results validated that the DNA methylation of promoter-associated CpG islands suppresses gene expression at the genome level

A Novel microRNA and transcription factor mediated regulatory network in schizophrenia

<p>Abstract</p> <p>Background</p> <p>Schizophrenia is a complex brain disorder with molecular mechanisms that have yet to be elucidated. Previous studies have suggested that changes in gene expression may play an important role in the etiology of schizophrenia, and that microRNAs (miRNAs) and transcription factors (TFs) are primary regulators of this gene expression. So far, several miRNA-TF mediated regulatory modules have been verified. We hypothesized that miRNAs and TFs might play combinatory regulatory roles for schizophrenia genes and, thus, explored miRNA-TF regulatory networks in schizophrenia.</p> <p>Results</p> <p>We identified 32 feed-forward loops (FFLs) among our compiled schizophrenia-related miRNAs, TFs and genes. Our evaluation revealed that these observed FFLs were significantly enriched in schizophrenia genes. By converging the FFLs and mutual feedback loops, we constructed a novel miRNA-TF regulatory network for schizophrenia. Our analysis revealed EGR3 and hsa-miR-195 were core regulators in this regulatory network. We next proposed a model highlighting EGR3 and miRNAs involved in signaling pathways and regulatory networks in the nervous system. Finally, we suggested several single nucleotide polymorphisms (SNPs) located on miRNAs, their target sites, and TFBSs, which may have an effect in schizophrenia gene regulation.</p> <p>Conclusions</p> <p>This study provides many insights on the regulatory mechanisms of genes involved in schizophrenia. It represents the first investigation of a miRNA-TF regulatory network for a complex disease, as demonstrated in schizophrenia.</p

The single parton fragmentation functions of heavy quarkonium in soft gluon factorization

We study the single parton fragmentation functions (FFs) at the input factorization scale $\mu_0\gtrsim 2m_Q$, with heavy quark mass $m_Q$, in the soft gluon factorization (SGF) approach. We express the FFs in terms of perturbatively calculable short distance hard parts for producing a heavy quark-antiquark pair in all possible states, convoluted with corresponding soft gluon distribution for the hadronization of the pair to a heavy quarkonium. We compute the perturbative short distance hard parts for producing a heavy quark pair in all possible $S$-wave and $P$-wave states up to $O(\alpha_s^2)$. With our results, the SGF can be further used to study the heavy quarkonium production at the hadron colliders and heavy quarkonium production within a jet.Comment: 19 pages, 0 figures. arXiv admin note: text overlap with arXiv:2304.0455

Cell phone–based health education messaging improves health literacy

Background: The ubiquity of cell phones, which allow for short message service (SMS), provides new and innovative opportunities for disease prevention and health education.Objective: To explore the use of cell phone–based health education SMS to improve the health literacy of community residents in China.Methods: A multi-stage random sampling method was used to select representative study communities and participants ≥ 18 years old. Intervention participants were sent health education SMSs once a week for 1 year and controls were sent conventional, basic health education measures. Health literacy levels of the residents before and after the intervention were evaluated between intervention and control groups.Results: Public health literacy scores increased 1.5 points, from 61.8 to 63.3, after SMS intervention for 1 year (P&lt;0.01); the increase was greater for males than females (2.01 vs. 1.03; P&lt;0.01) and for Shenzhen local residents than non permanent residents (2.56 vs. 1.14; P&lt;0.01). The frequency of high health literacy scores was greater for the intervention than control group (22.03% to 30.93% vs. 22.07% to 20.82%). With health literacy as a cost-effective index, the cost-effectiveness per intervention was 0.54.Conclusion: SMS may be a useful tool for improving health literacy.Keywords: Health literacy, intervention, community residents, cell phone, short message servic

Clinical outcomes of osteonecrosis of the femoral head after autologous bone marrow stem cell implantation: a meta-analysis of seven case-control studies

The purpose of this study was to evaluate the clinical outcomes of osteonecrosis of the femoral head after autologous bone marrow stem cell implantation. We searched the PubMed, Embase and Web of Science databases and included all case-control trials that reported on the clinical outcomes of osteonecrosis progression, incidence of total hip arthroplasty and improvement in Harris hip scores. Overall, seven case-control trials were included. Compared with the controls, patients treated with the bone marrow stem cells implantation treatment showed improved clinical outcomes with delayed osteonecrosis progression (odds ratio = 0.17, 95% CI: 0.09 - 0.32;

Overlapping and Distinct Roles of HAM Family Genes in Arabidopsis Shoot Meristems

In Arabidopsis shoot apical meristems (SAMs), a well-characterized regulatory loop between WUSCHEL (WUS) and CLAVATA3 (CLV3) maintains stem cell homeostasis by regulating the balance between cell proliferation and cell differentiation. WUS proteins, translated in deep cell layers, move into the overlaying stem cells to activate CLV3. The secreted peptide CLV3 then regulates WUS levels through a ligand-receptor mediated signaling cascade. CLV3 is specifically expressed in the stem cells and repressed in the deep cell layers despite presence of the WUS activator, forming an apical-basal polarity along the axis of the SAM. Previously, we proposed and validated a hypothesis that the HAIRY MERISTEM (HAM) family genes regulate this polarity, keeping the expression of CLV3 off in interior cells of the SAM. However, the specific role of each individual member of the HAM family in this process remains to be elucidated. Combining live imaging and molecular genetics, we have dissected the conserved and distinct functions of different HAM family members in control of CLV3 patterning in the SAMs and in the de novo shoot stem cell niches as well