The role of social support in reducing the impact of violence on adolescents' mental health in São Paulo, Brazil

OBJECTIVES: We investigated whether perceived social support among adolescent students moderated the association between violence exposure and internalising symptoms in São Paulo city, Brazil. METHODS: We tested the stress-buffering model using data from the cross-sectional school-based, survey São Paulo Project on the Social Development of Children and Adolescents. Internalising symptoms were measured using an adapted version of the Social Behaviour Questionnaire; serious victimisation, being bullied once/week, school violence and community violence, friend and teacher support were scales adapted by the research team; the Alabama Parenting Questionnaire measured parenting style. Linear mixed-effects models were used to quantify moderation effects of (i) social support between violence exposure and internalising symptoms and (ii) gender between violence exposure and internalising symptoms across schools. RESULTS: Across schools, being bullied once/week, school violence, and community violence were associated with a significant (p<0.001) increase in internalising symptoms (e.g., bullied b = 5.76, 95% CI 2.26, 9.26; school violence b = 0.48, 95% CI 0.30, 0.67; community violence b = 0.36; 95% CI 0.22, 0.50). Males exposed to all types of violence had significantly lower (p<0.01) internalising symptoms compared to females (e.g., serious victimisation: b = -1.45; 95% CI -2.60, -0.29; school violence b = -0.27; 95% CI -0.30, -0.24; community violence b = -0.23; 95% CI -0.25, -0.20). As a main effect, social support was associated with a significant (p<0.01) decrease in internalising symptoms across schools (e.g., positive parenting b = -2.42; 95% CI -3.12, -1.72; parent involvement b = -2.75; 95% CI -3.32, -2.17; friend support b = -1.05; 95% CI -1.74, -0.34; teacher support b = -0.90; 95% CI -1.58, -0.22). Social support did not moderate the association between violence exposure and internalising symptoms. CONCLUSIONS: Adolescent students in São Paulo exposed to violence have a higher likelihood of internalising symptoms, compared to those who are not. Support from parents, friends, and teachers, independent of violence, appear to be protective against internalising symptoms, pointing to potential programmes that could improve adolescent mental health

Chromosomal-level assembly of the Asian Seabass genome using long sequence reads and multi-layered scaffolding

We report here the ~670 Mb genome assembly of the Asian seabass (Lates calcarifer), a tropical marine teleost. We used long-read sequencing augmented by transcriptomics, optical and genetic mapping along with shared synteny from closely related fish species to derive a chromosome-level assembly with a contig N50 size over 1 Mb and scaffold N50 size over 25 Mb that span ~90% of the genome. The population structure of L. calcarifer species complex was analyzed by re-sequencing 61 individuals representing various regions across the species' native range. SNP analyses identified high levels of genetic diversity and confirmed earlier indications of a population stratification comprising three clades with signs of admixture apparent in the South-East Asian population. The quality of the Asian seabass genome assembly far exceeds that of any other fish species, and will serve as a new standard for fish genomics

Prediction of tissue-specific cis-regulatory modules using Bayesian networks and regression trees

<p>Abstract</p> <p>Background</p> <p>In vertebrates, a large part of gene transcriptional regulation is operated by cis-regulatory modules. These modules are believed to be regulating much of the tissue-specificity of gene expression.</p> <p>Results</p> <p>We develop a Bayesian network approach for identifying cis-regulatory modules likely to regulate tissue-specific expression. The network integrates predicted transcription factor binding site information, transcription factor expression data, and target gene expression data. At its core is a regression tree modeling the effect of combinations of transcription factors bound to a module. A new unsupervised EM-like algorithm is developed to learn the parameters of the network, including the regression tree structure.</p> <p>Conclusion</p> <p>Our approach is shown to accurately identify known human liver and erythroid-specific modules. When applied to the prediction of tissue-specific modules in 10 different tissues, the network predicts a number of important transcription factor combinations whose concerted binding is associated to specific expression.</p

Nuclear Receptor HNF4α Binding Sequences are Widespread in Alu Repeats

<p>Abstract</p> <p>Background</p> <p>Alu repeats, which account for ~10% of the human genome, were originally considered to be junk DNA. Recent studies, however, suggest that they may contain transcription factor binding sites and hence possibly play a role in regulating gene expression.</p> <p>Results</p> <p>Here, we show that binding sites for a highly conserved member of the nuclear receptor superfamily of ligand-dependent transcription factors, hepatocyte nuclear factor 4alpha (HNF4α, NR2A1), are highly prevalent in Alu repeats. We employ high throughput protein binding microarrays (PBMs) to show that HNF4α binds > 66 unique sequences in Alu repeats that are present in ~1.2 million locations in the human genome. We use chromatin immunoprecipitation (ChIP) to demonstrate that HNF4α binds Alu elements in the promoters of target genes (<it>ABCC3, APOA4, APOM, ATPIF1, CANX, FEMT1A, GSTM4, IL32, IP6K2, PRLR, PRODH2, SOCS2, TTR</it>) and luciferase assays to show that at least some of those Alu elements can modulate HNF4α-mediated transactivation <it>in vivo </it>(<it>APOM, PRODH2, TTR, APOA4</it>). HNF4α-Alu elements are enriched in promoters of genes involved in RNA processing and a sizeable fraction are in regions of accessible chromatin. Comparative genomics analysis suggests that there may have been a gain in HNF4α binding sites in Alu elements during evolution and that non Alu repeats, such as Tiggers, also contain HNF4α sites.</p> <p>Conclusions</p> <p>Our findings suggest that HNF4α, in addition to regulating gene expression via high affinity binding sites, may also modulate transcription via low affinity sites in Alu repeats.</p

Spatiotemporal DNA methylome dynamics of the developing mouse fetus

Cytosine DNA methylation is essential for mammalian development but understanding of its spatiotemporal distribution in the developing embryo remains limited. Here, as part of the mouse Encyclopedia of DNA Elements (ENCODE) project, we profiled 168 methylomes from 12 mouse tissues or organs at 9 developmental stages from embryogenesis to adulthood. We identified 1,808,810 genomic regions that showed variations in CG methylation by comparing the methylomes of different tissues or organs from different developmental stages. These DNA elements predominantly lose CG methylation during fetal development, whereas the trend is reversed after birth. During late stages of fetal development, non-CG methylation accumulated within the bodies of key developmental transcription factor genes, coinciding with their transcriptional repression. Integration of genome-wide DNA methylation, histone modification and chromatin accessibility data enabled us to predict 461,141 putative developmental tissue-specific enhancers, the human orthologues of which were enriched for disease-associated genetic variants. These spatiotemporal epigenome maps provide a resource for studies of gene regulation during tissue or organ progression, and a starting point for investigating regulatory elements that are involved in human developmental disorders

Leiomodin-3 dysfunction results in thin filament disorganization and nemaline myopathy

Peer reviewe

Evaluating quality in adolescent mental health services: a systematic review

Objectives To evaluate the quality of adolescent mental health service provision globally, according to the WHO Global Standards of adolescent mental health literacy, appropriate package of services and provider competencies.Design and data sources Systematic review of 5 databases, and screening of eligible articles, from 1 January 2008 to 31 December 2020.Study eligibility criteria We focused on quantitative and mixed-method studies that evaluated adolescent mental health literacy, appropriate package of services and provider competencies in mental health services, and that targeted depression, anxiety and post-traumatic stress disorder among adolescents (10–19 years). This included adolescents exposed to interventions or strategies within mental health services.Study appraisal and synthesis methods Study quality was assessed using the National Institutes for Health Study Quality Assessment Tools. Data were extracted and grouped based on WHO quality Standards.Results Of the 20 104 studies identified, 20 articles were included. The majority of studies came from high-income countries, with one from a low-income country. Most of the studies did not conceptualise quality. Results found that an online decision aid was evaluated to increase adolescent mental health literacy. Studies that targeted an appropriate package of services evaluated the quality of engagement between the therapist and adolescent, patient-centred communication, mental health service use, linkages to mental health services, health facility culture and intensive community treatment. Provider competencies focused on studies that evaluated confidence in managing and referring adolescents, collaboration between health facility levels, evidence-based practices and technology use.Conclusions and implications There is limited evidence on quality measures in adolescent mental health services (as conforms to the WHO Global Standards), pointing to a global evidence gap for adolescent mental health services. There are several challenges to overcome, including a need to develop consensus on quality and methods to measure quality in mental health settings.PROSPERO registration number CRD42020161318