Characterization of viral RNA splicing using whole-transcriptome datasets from host species

RNA alternative splicing (AS) is an important post-transcriptional mechanism enabling single genes to produce multiple proteins. It has been well demonstrated that viruses deploy host AS machinery for viral protein productions. However, knowledge on viral AS is limited to a few disease-causing viruses in model species. Here we report a novel approach to characterizing viral AS using whole transcriptome dataset from host species. Two insect transcriptomes (Acheta domesticus and Planococcus citri) generated in the 1,000 Insect Transcriptome Evolution (1KITE) project were used as a proof of concept using the new pipeline. Two closely related densoviruses (Acheta domesticus densovirus, AdDNV, and Planococcus citri densovirus, PcDNV, Ambidensovirus, Densovirinae, Parvoviridae) were detected and analyzed for AS patterns. The results suggested that although the two viruses shared major AS features, dramatic AS divergences were observed. Detailed analysis of the splicing junctions showed clusters of AS events occurred in two regions of the virus genome, demonstrating that transcriptome analysis could gain valuable insights into viral splicing. When applied to large-scale transcriptomics projects with diverse taxonomic sampling, our new method is expected to rapidly expand our knowledge on RNA splicing mechanisms for a wide range of viruses

Omics-based interpretation of synergism in a soil-derived cellulose-degrading microbial community

Reaching a comprehensive understanding of how nature solves the problem of degrading recalcitrant biomass may eventually allow development of more efficient biorefining processes. Here we interpret genomic and proteomic information generated from a cellulolytic microbial consortium (termed F1RT) enriched from soil. Analyses of reconstructed bacterial draft genomes from all seven uncultured phylotypes in F1RT indicate that its constituent microbes cooperate in both cellulose-degrading and other important metabolic processes. Support for cellulolytic inter-species cooperation came from the discovery of F1RT microbes that encode and express complimentary enzymatic inventories that include both extracellular cellulosomes and secreted free-enzyme systems. Metabolic reconstruction of the seven F1RT phylotypes predicted a wider genomic rationale as to how this particular community functions as well as possible reasons as to why biomass conversion in nature relies on a structured and cooperative microbial community

Proteome wide association studies of LRRK2 variants identify novel causal and druggable proteins for Parkinson\u27s disease

Common and rare variants in the LRRK2 locus are associated with Parkinson\u27s disease (PD) risk, but the downstream effects of these variants on protein levels remain unknown. We performed comprehensive proteogenomic analyses using the largest aptamer-based CSF proteomics study to date (7006 aptamers (6138 unique proteins) in 3107 individuals). The dataset comprised six different and independent cohorts (five using the SomaScan7K (ADNI, DIAN, MAP, Barcelona-1 (Pau), and Fundació ACE (Ruiz)) and the PPMI cohort using the SomaScan5K panel). We identified eleven independent SNPs in the LRRK2 locus associated with the levels of 25 proteins as well as PD risk. Of these, only eleven proteins have been previously associated with PD risk (e.g., GRN or GPNMB). Proteome-wide association study (PWAS) analyses suggested that the levels of ten of those proteins were genetically correlated with PD risk, and seven were validated in the PPMI cohort. Mendelian randomization analyses identified GPNMB, LCT, and CD68 causal for PD and nominate one more (ITGB2). These 25 proteins were enriched for microglia-specific proteins and trafficking pathways (both lysosome and intracellular). This study not only demonstrates that protein phenome-wide association studies (PheWAS) and trans-protein quantitative trail loci (pQTL) analyses are powerful for identifying novel protein interactions in an unbiased manner, but also that LRRK2 is linked with the regulation of PD-associated proteins that are enriched in microglial cells and specific lysosomal pathways

Stroke genetics informs drug discovery and risk prediction across ancestries

Previous genome-wide association studies (GWASs) of stroke — the second leading cause of death worldwide — were conducted predominantly in populations of European ancestry1,2. Here, in cross-ancestry GWAS meta-analyses of 110,182 patients who have had a stroke (five ancestries, 33% non-European) and 1,503,898 control individuals, we identify association signals for stroke and its subtypes at 89 (61 new) independent loci: 60 in primary inverse-variance-weighted analyses and 29 in secondary meta-regression and multitrait analyses. On the basis of internal cross-ancestry validation and an independent follow-up in 89,084 additional cases of stroke (30% non-European) and 1,013,843 control individuals, 87% of the primary stroke risk loci and 60% of the secondary stroke risk loci were replicated (P < 0.05). Effect sizes were highly correlated across ancestries. Cross-ancestry fine-mapping, in silico mutagenesis analysis3, and transcriptome-wide and proteome-wide association analyses revealed putative causal genes (such as SH3PXD2A and FURIN) and variants (such as at GRK5 and NOS3). Using a three-pronged approach4, we provide genetic evidence for putative drug effects, highlighting F11, KLKB1, PROC, GP1BA, LAMC2 and VCAM1 as possible targets, with drugs already under investigation for stroke for F11 and PROC. A polygenic score integrating cross-ancestry and ancestry-specific stroke GWASs with vascular-risk factor GWASs (integrative polygenic scores) strongly predicted ischaemic stroke in populations of European, East Asian and African ancestry5. Stroke genetic risk scores were predictive of ischaemic stroke independent of clinical risk factors in 52,600 clinical-trial participants with cardiometabolic disease. Our results provide insights to inform biology, reveal potential drug targets and derive genetic risk prediction tools across ancestries

Experimental Research on Two-step Cooling Mechanism of the Oxide Film of ELID Grinding Wheel

This paper conducts theoretical analysis on the presence of absorbed water and lattice water in the oxide film of ELID grinding wheel, carries out experimental study by applying X-ray (XRD) diffractometer, infrared spectrometer, and thermal gravimetric analyzer TG-DSC, and further proposes the two-step cooling mechanism of the absorbed water and lattice water in the oxide film of ELID grinding wheel. The study shows that there are adsorbed water and lattice water in ELID oxide film, and the cooling effect of adsorbed water and lattice water makes ELID grinding better cool the grinding zone, and get good grinding surface quality more easily

A Review on Dynamic Recycling of Electric Vehicle Battery: Disassembly and Echelon Utilization

With the growing requirements of retired electric vehicles (EVs), the recycling of EV batteries is being paid more and more attention to regarding its disassembly and echelon utilization to reach highly efficient resource utilization and environmental protection. In order to make full use of the retired EV batteries, we here discuss various possible application methods of echelon utilization, including hierarchical analysis methods based on various battery evaluation index. In addition, retired EV battery disassembly is also reviewed through the entire EV battery recycling based on human–robot collaboration methods. In order to improve the efficiency and reduce the cost of EV recycling, it is necessary to find a suitable recycling mode and disassembly process. This paper discusses the future possibility of echelon utilization and disassembly in retired EV battery recycling from disassembly optimization and human–robot collaboration, facing uncertain disassembly and echelon utilization

Adhesive Hybrid SiO2.01C0.23Hx Nanoparticulate Coating on Polyethylene (PE) Separator by Roll-to-Roll Atmospheric Pressure Plasma

For the ever-increasing demand for highly safe lithium-ion batteries (LIBs), the common sol-gel process provides heat-resistance to separators with an inorganic coating, where the adhesion to the separator is the key to safety and stability. In this paper, we present a SiO2.01C0.23Hx-coated polyethylene (PE) separator through a roll-to-roll atmospheric plasma-enhanced chemical vapor deposition (R2R-APECVD) of hexamethyldisiloxane (HMDSO)/Ar/O2. The adhesion strength of SiO2.01C0.23Hx-coated PE was tested by peel-off test and found to be higher than that of the commercial Al2O3-coated separator (0.28 N/mm vs. 0.06 N/mm). Furthermore, the SiO2.01C0.23Hx-coated PE separator showed better electrochemical performance in C-rate and long term cycle tests. FTIR, SEM, and XPS analysis indicate that the increased adhesion and electrochemical performance are attributed to the inner hybrid SiO2.01C0.23Hx coating with organic and inorganic components

Sorption of tetracycline on biochar derived from rice straw under different temperatures

<div><p>Biochars produced from the pyrolysis of waste biomass under limited oxygen conditions could serve as adsorbents in environmental remediation processes. Biochar samples derived from rice straw that were pyrolyzed at 300 (R300), 500 (R500) and 700°C (R700) were used as adsorbents to remove tetracycline from an aqueous solution. Both the Langmuir and Freundlich models fitted the adsorption data well (R² > 0.919). The adsorption capacity increased with pyrolysis temperature. The R500 and R700 samples exhibited relative high removal efficiencies across a range of initial tetracycline concentrations (0.5mg/L-32mg/L) with the maximum (92.8%–96.7%) found for adsorption on R700 at 35°C. The relatively high surface area of the R700 sample and π–π electron-donor acceptor contributed to the high adsorption capacities. A thermodynamic analysis indicated that the tetracycline adsorption process was spontaneous and endothermic. The pH of solution was also found to influence the adsorption processes; the maximum adsorption capacity occurred at a pH of 5.5. These experimental results highlight that biochar derived from rice straw is a promising candidate for low-cost removal of tetracycline from water.</p></div

Effect of pH on adsorption capacity for tetracycline sorption on biochars.

<p>The concentration of tetracycline solution was 32 mg/L. Values are triplicate means ± SD. Letters indicate significant differences among treatments at a level of p < 0.05(Tukey test).</p

Fourier transform infrared (FTIR) spectroscopic analysis of biochars derived from rice straw.

<p>Fourier transform infrared (FTIR) spectroscopic analysis of biochars derived from rice straw.</p