Coordinated evolution of co-expressed gene clusters in the Drosophila transcriptome

Abstract Background Co-expression of genes that physically cluster together is a common characteristic of eukaryotic transcriptomes. This organization of transcriptomes suggests that coordinated evolution of gene expression for clustered genes may also be common. Clusters where expression evolution of each gene is not independent of their neighbors are important units for understanding transcriptome evolution. Results We used a common microarray platform to measure gene expression in seven closely related species in the Drosophila melanogaster subgroup, accounting for confounding effects of sequence divergence. To summarize the correlation structure among genes in a chromosomal region, we analyzed the fraction of variation along the first principal component of the correlation matrix. We analyzed the correlation for blocks of consecutive genes to assess patterns of correlation that may be manifest at different scales of coordinated expression. We find that expression of physically clustered genes does evolve in a coordinated manner in many locations throughout the genome. Our analysis shows that relatively few of these clusters are near heterochromatin regions and that these clusters tend to be over-dispersed relative to the rest of the genome. This suggests that these clusters are not the byproduct of local gene clustering. We also analyzed the pattern of co-expression among neighboring genes within a single Drosophila species: D. simulans. For the co-expression clusters identified within this species, we find an under-representation of genes displaying a signature of recurrent adaptive amino acid evolution consistent with previous findings. However, clusters displaying co-evolution of expression among species are enriched for adaptively evolving genes. This finding points to a tie between adaptive sequence evolution and evolution of the transcriptome. Conclusion Our results demonstrate that co-evolution of expression in gene clusters is relatively common among species in the D. melanogaster subgroup. We consider the possibility that local regulation of expression in gene clusters may drive the connection between adaptive sequence and coordinated gene expression evolution

Inequalities in the Access to Health Services Among Older Migrants: Evidence From the China Migrant Dynamic Monitoring Survey

Objectives: To identify differences in healthcare use between older migrant workers (OMWs) and older migrants (OMs) and explore associated factors and paths of healthcare use.Methods: The data came from the 2015 China Migrant Dynamic Monitoring Survey (CMDMS). CMDMS used a multi-stage stratified probability proportionate to size method as the sampling technique and conducted a desk review. The samples include OMWs, OMs for caring offspring (N = 4,439), and OMs for receiving care from family (N = 4,184). We built logistic regression and path analysis models to analyze the data.Results: Social health insurance (SHI) in current place of residence is associated with less expenditure among all subgroups. OMWs and OMs for receiving care from family with SHI in current place of residence are more likely to use healthcare.Conclusion: OMWs are particularly vulnerable in healthcare use and socioeconomic status. Having SHI registered in current place of residence helps decrease expenditure among OMs. We urge policymakers to consider a united health financing scheme across OMWs and other urban employees and streamline policies for migrants to enroll in SHI in current place of residence

Plumbagin Enhances the Anticancer Efficacy of Cisplatin by Increasing Intracellular ROS in Human Tongue Squamous Cell Carcinoma

Cisplatin is widely used in the treatment of tongue squamous cell carcinoma (TSCC), but its clinical efficacy is limited by drug resistance and toxic side effects. Hence, a novel compound capable of enhancing the anticancer effect of cisplatin while reducing the side effects is urgently needed. We have previously shown that plumbagin (PLB), an anticancer phytochemical, is able to inhibit the growth of TSCC in vitro and in vivo. The objective of this study was to investigate the effect of PLB in reversing the resistance of TSCC to cisplatin as well as its molecular mechanisms. Here, we found that PLB enhances cisplatin-induced cytotoxicity, apoptosis, and autophagy in CAL27 and cisplatin-resistant CAL27/CDDP cells. PLB could inhibit the viability and growth of TSCC cells by increasing the production of intracellular reactive oxygen species (ROS). In addition, the combination treatment of PLB and cisplatin resulted in a synergistic inhibition of TSCC viability, apoptosis, and autophagy by increasing intracellular ROS, which may be achieved by activating JNK and inhibiting AKT/mTOR signaling pathways. Finally, the synergistic treatment was also demonstrated in vivo. Therefore, PLB combined with cisplatin is a potential therapeutic strategy against therapy TSCC cisplatin resistance

Characteristics of ginsenoside Rd-induced effects on rat intestinal contractility with irritable bowel syndrome

Irritable bowel syndrome (IBS) is a very common refractory disease. Its exact pathophysiological mechanism is still unclear. Despite the availability of plentiful drugs to control IBS, most patients do not respond well. Ginsenoside Rd is one of the major active components of Panax ginseng, which has been verified to produce various pharmacological actions. However, the role of ginsenoside Rd in modulating smooth muscle contractility is still undefined. The aim of this study is to investigate the effects of ginsenoside Rd on intestinal contractility and related mechanisms in IBS.</p

Temporal Changes of Fish Diversity and Driver Factors in a National Nature Reserve, China

Freshwater-fish diversity declined rapidly due to multiple anthropogenic disturbances. The loss of fish diversity often manifested itself in taxonomic homogenization over time. Knowledge of multi-faceted diversity (i.e., species, functional, and phylogenetic diversity) perspectives is important for biodiversity assessment and conservation planning. Here, we analyzed the change of the species diversity and phylogenetic diversity of fish in 2008 and 2021 as well as explored the driver factors of the biodiversity patterns in the Lushan National Nature Reserve. The results showed that the species diversity and phylogenetic diversity of fish have declined from 2008 to 2021, with five species lost over time. We found an overall homogenization trend in the fish fauna of the study area, with a 4% increase in taxonomic similarity among the rivers. Additionally, we found that community structure of fish was significantly different among the rivers, and environmental filtering was the main contributor to the phylogenetic diversity of fish in 2008 and 2021. This study provides new insight into the patterns and drivers of fish-biodiversity change in the broader Yangtze River basin and informs management efforts

Dear-DIAXMBD: Deep Autoencoder Enables Deconvolution of Data-Independent Acquisition Proteomics

Data-independent acquisition (DIA) technology for protein identification from mass spectrometry and related algorithms is developing rapidly. The spectrum-centric analysis of DIA data without the use of spectra library from data-dependent acquisition data represents a promising direction. In this paper, we proposed an untargeted analysis method, Dear-DIAXMBD, for direct analysis of DIA data. Dear-DIAXMBD first integrates the deep variational autoencoder and triplet loss to learn the representations of the extracted fragment ion chromatograms, then uses the k-means clustering algorithm to aggregate fragments with similar representations into the same classes, and finally establishes the inverted index tables to determine the precursors of fragment clusters between precursors and peptides and between fragments and peptides. We show that Dear-DIAXMBD performs superiorly with the highly complicated DIA data of different species obtained by different instrument platforms. Dear-DIAXMBD is publicly available at https://github.com/jianweishuai/Dear-DIA-XMBD