Tandem 3′ UTRs produced by alternative polyadenylation (APA) play an important role in gene expression by impacting mRNA stability, translation, and translocation in cells. Several studies have investigated APA site switching in various physiological states; nevertheless, they only focused on either the genes with two known APA sites or several candidate genes. Here, we developed a strategy to study APA sites in a genome-wide fashion with second-generation sequencing technology which could not only identify new polyadenylation sites but also analyze the APA site switching of all genes, especially those with more than two APA sites. We used this strategy to explore the profiling of APA sites in two human breast cancer cell lines, MCF7 and MB231, and one cultured mammary epithelial cell line, MCF10A. More than half of the identified polyadenylation sites are not included in human poly(A) databases. While MCF7 showed shortening 3′ UTRs, more genes in MB231 switched to distal poly(A) sites. Several gene ontology (GO) terms and pathways were enriched in the list of genes with switched APA sites, including cell cycle, apoptosis, and metabolism. These results suggest a more complex regulation of APA sites in cancer cells than previously thought. In short, our novel unbiased method can be a powerful approach to cost-effectively investigate the complex mechanism of 3′ UTR switching in a genome-wide fashion among various physiological processes and diseases.

We identified from suckling piglets with diarrhea in China a new bat-HKU2–like porcine coronavirus (porcine enteric alphacoronavirus). The GDS04 strain of this coronavirus shares high aa identities (>90%) with the reported bat-HKU2 strains in Coronaviridae-wide conserved domains, suggesting that the GDS04 strain belongs to the same species as HKU2.

Care assistant workers as a new pattern of care providers in China play an important role in bridging the mental health treatment gap. Stigma and discrimination against people with mental disorders among care assistant workers is a barrier which adversely influences mental health service delivery. However, programs aimed at reducing stigma among care assistant workers are rare in China. A total of 293 care assistant workers from four districts of Guangzhou, China were randomly divided into an intervention group (n = 139) and a control group (n = 154). The intervention group received anti-stigma training and the control group received traditional mental health training. Both trainings lasted for 3 h. Participants were measured before and after training using Perceived Devaluation and Discrimination Scale (PDD), Mental illness: Clinicians’ Attitudes (MICA) and Mental Health Knowledge Schedule (MAKS). Data were analyzed by descriptive statistics, t-test, Chi square test or Fisher’s exact test. Multilinear regression models were performed to calculate adjusted regression coefficient of the intervention on PPD, MAKS, and MICA. There were significant lower scores on PDD and MICA in the intervention group after training when compared with the control group (both P < 0.001). No significant difference was found on MAKS total score between the two groups after training (P = 0.118). Both groups had better correct identification of schizophrenia, depression and bipolar disorder before and after training. These findings suggest that anti-stigma training may be effective in reducing the perception of devaluation-discrimination against people with mental illness and decreasing the level of negative stigma-related mental health attitudes among care assistant workers.

Vertebrates diverged from other chordates ~500 Myr ago and experienced successful innovations and adaptations, but the genomic basis underlying vertebrate origins are not fully understood. Here we suggest, through comparison with multiple lancelet (amphioxus) genomes, that ancient vertebrates experienced high rates of protein evolution, genome rearrangement and domain shuffling and that these rates greatly slowed down after the divergence of jawed and jawless vertebrates. Compared with lancelets, modern vertebrates retain, at least relatively, less protein diversity, fewer nucleotide polymorphisms, domain combinations and conserved non-coding elements (CNE). Modern vertebrates also lost substantial transposable element (TE) diversity, whereas lancelets preserve high TE diversity that includes even the long-sought RAG transposon. Lancelets also exhibit rapid gene turnover, pervasive transcription, fastest exon shuffling in metazoans and substantial TE methylation not observed in other invertebrates. These new lancelet genome sequences provide new insights into the chordate ancestral state and the vertebrate evolution.

Depression during pregnancy can be detrimental to both maternal and fetal health outcomes. A cross-sectional study was undertaken, with the goal of determining the prevalence and predicting factors associated with antenatal depressive symptoms during late pregnancy among Chinese women. Participants were recruited during bookings for antenatal care at a maternal and child health hospital’s outpatient care clinics. Measurements included the Chinese version of Self-rating Depression Scale, Eysenck Personality Questionnaire, Social Support Rating Scale, and Simplified Coping Strategies Questionnaire. A total of 292 women participated in this study, with 28.5% prevalence of depressive symptoms. Significant protective predictors were: a younger age (OR = 0.85; 95% Confidence Interval-CI 0.76-0.95), good partner relationship (OR = 0.40; 95% CI 0.17-0.93), preparedness for delivery (OR = 0.36; 95% CI 0.20-0.63), active coping (OR = 0.92; 95% CI 0.89-0.96), and social support (OR = 0.92; 95% CI 0.88-0.97). In contrast, significant risk factors were: a history of miscarriage (OR = 1.86; 95% CI 1.30-2.66), irregular menstrual history (OR = 2.98; 95% CI 1.64-5.40), and financial worries (OR = 2.33; 95% CI 1.27-4.30). Psychosocial risk factors include psychoticism and neuroticism personality traits (OR = 1.06; 95% CI 1.02-1.10 and OR = 1.07; 95% CI 1.04-1.10, respectively), and pregnancy pressures (OR = 1.04; 95% CI 1.02-1.07). Depressive symptoms are common in third trimester antenatal clinic attendees. Interventions for early recognition of depression should target older women with a history of miscarriage and financial worries. Intervention strategies could be by providing more social support and promoting active coping strategies. Findings support a recommendation that antenatal services consider integrating screening for depression in routine antenatal care.

Whole-genome shotgun assembly has been a long-standing issue for highly polymorphic genomes, and the advent of next-generation sequencing technologies has made the issue more challenging than ever. Here we present an automated pipeline, HaploMerger, for reconstructing allelic relationships in a diploid assembly. HaploMerger combines a LASTZ-ChainNet alignment approach with a novel graph-based structure, which helps to untangle allelic relationships between two haplotypes and guides the subsequent creation of reference haploid assemblies. The pipeline provides flexible parameters and schemes to improve the contiguity, continuity, and completeness of the reference assemblies. We show that HaploMerger produces efficient and accurate results in simulations and has advantages over manual curation when applied to real polymorphic assemblies (e.g., 4%–5% heterozygosity). We also used HaploMerger to analyze the diploid assembly of a single Chinese amphioxus (Branchiostoma belcheri) and compared the resulting haploid assemblies with EST sequences, which revealed that the two haplotypes are not only divergent but also highly complementary to each other. Taken together, we have demonstrated that HaploMerger is an effective tool for analyzing and exploiting polymorphic genome assemblies.