Deciphering the role of rapidly evolving conserved elements in primate brain development and exploring their potential involvement in Alzheimer's Disease

Although previous studies have identified human-specific accelerated regions as playing a key role in the recent evolution of the human brain, the characteristics and cellular functions of rapidly evolving conserved elements (RECEs) in ancestral primate lineages remain largely unexplored. Here, based on large-scale primate genome assemblies, we identify 888 RECEs that have been highly conserved in primates that exhibit significantly accelerated substitution rates in the ancestor of the Simiiformes. This primate lineage exhibits remarkable morphological innovations, including an expanded brain mass. Integrative multiomic analyses reveal that RECEs harbor sequences with potential cis-regulatory functions that are activated in the adult human brain. Importantly, genes linked to RECEs exhibit pronounced expression trajectories in the adult brain relative to the fetal stage. Furthermore, we observed an increase in the chromatin accessibility of RECEs in oligodendrocytes from individuals with Alzheimer's disease (AD) compared to that of a control group, indicating that these RECEs may contribute to brain aging and AD. Our findings serve to expand our knowledge of the genetic underpinnings of brain function during primate evolution

NextDenovo: an efficient error correction and accurate assembly tool for noisy long reads

Long-read sequencing data, particularly those derived from the Oxford Nanopore sequencing platform, tend to exhibit high error rates. Here, we present NextDenovo, an efficient error correction and assembly tool for noisy long reads, which achieves a high level of accuracy in genome assembly. We apply NextDenovo to assemble 35 diverse human genomes from around the world using Nanopore long-read data. These genomes allow us to identify the landscape of segmental duplication and gene copy number variation in modern human populations. The use of NextDenovo should pave the way for population-scale long-read assembly using Nanopore long-read data

ZIKV infection effects changes in gene splicing, isoform composition and lncRNA expression in human neural progenitor cells

Abstract Background The Zika virus (ZIKV) is a mosquito-borne flavivirus that causes microcephaly and Guillain-Barré syndrome in infected individuals. To obtain insights into the mechanism of ZIKV infection and pathogenesis, we analyzed the transcriptome of ZIKV infected human neural progenitor cells (hNPCs) for changes in alternative splicing (AS), gene isoform (ISO) composition and long noncoding RNAs (lncRNAs) expression. Methods We analyzed differentially expressed lncRNAs, AS, ISO from RNA-seq data in ZIKV infected hNPCs. Results We obtained 149 differentially expressed lncRNAs, including potential viral targets to modulate cellular processes such as cell cycle, apoptosis and immune response. The infection induced 262 cases of AS occurring in 229 genes, which were enriched in cell death, RNA processing, transport, and neuron development. Among 691 differentially expressed ISOs, upregulated ISOs were enriched in signaling, regulation of transcription, and amino acid biosynthesis, while downregulated ISOs were mostly enriched in cell cycle. Importantly, these analyses revealed specific links between ZIKV induced changes in cellular pathways and the type of changes in the host transcriptome, suggesting important regulatory mechanisms. Conclusions Our analyses revealed candidate lncRNAs, AS events and ISOs which may function in ZIKV infection induced cell cycle disruption, apoptosis and attenuation of neurogenesis, and shed light on the roles of lncRNAs, AS and ISOs in virus-host interactions, and would facilitate future studies of ZIKV infection and pathogenesis

Additional file 1: Figure S1. of Functional prediction of differentially expressed lncRNAs in HSV-1 infected human foreskin fibroblasts

Computational prediction of lncRNAs in HSV-1 infected HFF cells. The computational strategy of predicting of function of lncRNAs in HSV-1 infected HFF cells. Figure S2 The predicted function of lncRNAs based on co-expressed modules in cis. a. there were 5 significant co-expressed modules in positive regulatory model, p value ≤ 0.05. b-c. GO analysis and pathway analysis of PCGss co-expressed with lncRNAs, p value ≤ 0.05; d. there were 4 significant co-expressed modules in negative regulatory model, p value ≤ 0.05. e-f. GO analysis and pathway analysis of PCGs co-expressed with lncRNAs, p value ≤ 0.05. Figure S3 The predicted function of lncRNAs based on co-expressed modules in trans. a. there were 8 significant co-expressed modules in positive regulatory model, p value ≤ 0.05. b-c. GO analysis and pathway analysis of PCGss co-expressed with lncRNAs, p value ≤ 0.05; d. there were 6 significant co-expressed modules in negative regulatory model, p value ≤ 0.05. e-f. GO analysis and pathway analysis of PCGs co-expressed with lncRNAs, p value ≤ 0.05. (DOCX 653 kb

Additional file 2: of ZIKV infection effects changes in gene splicing, isoform composition and lncRNA expression in human neural progenitor cells

Differential gene expression between Zike Virus infection and control. (XLSX 5758 kb

Highly Selective Ethylene Production from Solar-Driven CO₂ Reduction on the Bi₂S₃@In₂S₃ Catalyst with In–S_V–Bi Active Sites

Photothermal catalysis that utilizes solar energy to not only generate charge carriers but also supply heat input represents a potentially sustainable strategy for the efficient conversion of CO2 to valuable chemicals. It is highly desirable to develop photothermal catalysts with broadband light absorption across the whole solar spectrum, efficient photothermal conversion, and appropriate active sites. In this work, the Bi2S3@In2S3 heterostructure catalyst is fabricated via one-step solvothermal synthesis, where Bi2S3 serves as a photothermal material and synchronously affords photoexcited charge carriers. Experimental results indicate that the photoinduced charge carriers trigger H2O-assisted CO2 reduction and the elevated temperature kinetically accelerates the reaction. Furthermore, the tightly bonded heterointerfaces provide unique In–SV–Bi active centers consisting of adjacent Bi and In atoms coupled with sulfur vacancies, which reduces the energy barriers of CO2 activation and C–C coupling, facilitating the generation and dimerization of CO intermediates for highly selective C2H4 production. The integration of In–SV–Bi active sites and the photothermal effect into the Bi2S3@In2S3 catalyst induces a high rate of 11.81 μmol gcat–1 h–1 and near 90% selectivity for CO2 conversion to C2H4 under simulated sunlight without extra heat input. The catalytic mechanism is expounded by in situ characterizations and theoretical calculations. This work would provide some enlightening guidance to construct efficient photothermal catalysts for the direct transformation of CO2 to multicarbon (C2+) products with solar energy