Enhanced single-cell RNA-seq workflow reveals coronary artery disease cellular cross-talk and candidate drug targets

BACKGROUND AND AIMS: The atherosclerotic plaque microenvironment is highly complex, and selective agents that modulate plaque stability are not yet available. We sought to develop a scRNA-seq analysis workflow to investigate this environment and uncover potential therapeutic approaches. We designed a user-friendly, reproducible workflow that will be applicable to other disease-specific scRNA-seq datasets. METHODS: Here we incorporated automated cell labeling, pseudotemporal ordering, ligand-receptor evaluation, and drug-gene interaction analysis into a ready-to-deploy workflow. We applied this pipeline to further investigate a previously published human coronary single-cell dataset by Wirka et al. Notably, we developed an interactive web application to enable further exploration and analysis of this and other cardiovascular single-cell datasets. RESULTS: We revealed distinct derivations of fibroblast-like cells from smooth muscle cells (SMCs), and showed the key changes in gene expression along their de-differentiation path. We highlighted several key ligand-receptor interactions within the atherosclerotic environment through functional expression profiling and revealed several avenues for future pharmacological development for precision medicine. Further, our interactive web application, PlaqView (www.plaqview.com), allows lay scientists to explore this and other datasets and compare scRNA-seq tools without prior coding knowledge. CONCLUSIONS: This publicly available workflow and application will allow for more systematic and user-friendly analysis of scRNA datasets in other disease and developmental systems. Our analysis pipeline provides many hypothesis-generating tools to unravel the etiology of coronary artery disease. We also highlight potential mechanisms for several drugs in the atherosclerotic cellular environment. Future releases of PlaqView will feature more scRNA-seq and scATAC-seq atherosclerosis-related datasets to provide a critical resource for the field, and to promote data harmonization and biological interpretation

Kinematic Simulation and Analysis of Globoidal Indexing Cam

As an important mechanism with intermittent motion, the globoidal indexing cam is always a research hot in the mechanical fields. The working profile of globoidal indexing cam is extremely complicated and undevelopable, which make it quite difficult to be protracted by the conventional drafting method. Aiming at this problem, the working curvilinear equation of the intermittent motion of an indexing cam is derived based on the RPY (Roll-Pitch-Yaw) coordinate transformation method. The 3D model based on the curvilinear equation is built by the Creo2.0 modeling software. The virtual prototype is established based on the ADAMS software, while the kinematics simulation is implemented. The success of virtual simulation verifies the correctness of curvilinear equation. The numerical results, presented and discussed in the paper, indicate that the proposed model is feasible to foresee the kinematic behaviour of an actual system

Kinematic Simulation and Analysis of Globoidal Indexing Cam

As an important mechanism with intermittent motion, the globoidal indexing cam is always a research hot in the mechanical fields. The working profile of globoidal indexing cam is extremely complicated and undevelopable, which make it quite difficult to be protracted by the conventional drafting method. Aiming at this problem, the working curvilinear equation of the intermittent motion of an indexing cam is derived based on the RPY (Roll-Pitch-Yaw) coordinate transformation method. The 3D model based on the curvilinear equation is built by the Creo2.0 modeling software. The virtual prototype is established based on the ADAMS software, while the kinematics simulation is implemented. The success of virtual simulation verifies the correctness of curvilinear equation. The numerical results, presented and discussed in the paper, indicate that the proposed model is feasible to foresee the kinematic behaviour of an actual system

Laser-induced nitrogen fixation

Abstract For decarbonization of ammonia production in industry, alternative methods by exploiting renewable energy sources have recently been explored. Nonetheless, they still lack yield and efficiency to be industrially relevant. Here, we demonstrate an advanced approach of nitrogen fixation to synthesize ammonia at ambient conditions via laser–induced multiphoton dissociation of lithium oxide. Lithium oxide is dissociated under non–equilibrium multiphoton absorption and high temperatures under focused infrared light, and the generated zero–valent metal spontaneously fixes nitrogen and forms a lithium nitride, which upon subsequent hydrolysis generates ammonia. The highest ammonia yield rate of 30.9 micromoles per second per square centimeter is achieved at 25 °C and 1.0 bar nitrogen. This is two orders of magnitude higher than state–of–the–art ammonia synthesis at ambient conditions. The focused infrared light here is produced by a commercial simple CO2 laser, serving as a demonstration of potentially solar pumped lasers for nitrogen fixation and other high excitation chemistry. We anticipate such laser-involved technology will bring unprecedented opportunities to realize not only local ammonia production but also other new chemistries

MicroRNA Transcriptome Profile Analysis in Porcine Muscle and the Effect of miR-143 on the MYH7 Gene and Protein

<div><p>Porcine skeletal muscle fibres are classified based on their different physiological and biochemical properties. Muscle fibre phenotype is regulated by several independent signalling pathways, including the mitogen-activated protein kinase (<i>MAPK</i>), nuclear factor of activated T cells (<i>NFAT</i>), myocyte enhancer factor 2 (<i>MEF2</i>) and peroxisome proliferator-activated receptor (PPAR) signalling pathways. MicroRNAs are non-coding small RNAs that regulate many biological processes. However, their function in muscle fibre type regulation remains unclear. The aim of our study was to identify miRNAs that regulate muscle fibre type during porcine growth to help understand the miRNA regulation mechanism of fibre differentiation. We performed Solexa/Illumina deep sequencing for the microRNAome during 3 muscle growth stages (63, 98 and 161 d). In this study, 271 mature miRNAs and 243 pre-miRNAs were identified. We detected 472 novel miRNAs in the muscle samples. Among the mature miRNAs, there are 23 highest expression miRNAs (over 10000 RPM), account for 85.3% of the total counts of mature miRNAs., including 10 (43.5%) muscle-related miRNAs (ssc-miR-133a-3p, ssc-miR-486, ssc-miR-1, ssc-miR-143-3p, ssc-miR-30a-5p, ssc-miR-181a, ssc-miR-148a-3p, ssc-miR-92a, ssc-miR-21, ssc-miR-126-5p). Particularly, both ssc-miR-1 and ssc-miR-133 belong to the MyomiRs, which control muscle myosin content, myofibre identity and muscle performance. The involvement of these miRNAs in muscle fibre phenotype provides new insight into the mechanism of muscle fibre regulation underlying muscle development. Furthermore, we performed cell transfection experiment. Overexpression/inhibition of ssc-miR-143-3p in porcine skeletal muscle satellite cell induced an/a increase/reduction of the slow muscle fibre gene and protein (<i>MYH7</i>), indicating that miR-143 activity regulated muscle fibre differentiate in skeletal muscle. And it regulate <i>MYH7</i> through the <i>HDAC4-MEF2</i> pathway.</p></div

Potential regulation pathways of muscle fibres by ssc-miR-143-3p.

<p>Potential regulation pathways of muscle fibres by ssc-miR-143-3p.</p

Summary of differential expression miRNAs between the three stages.

<p>DE: differential expression, fold change>2 or fold change<0.5, p<0.05.</p><p>Summary of differential expression miRNAs between the three stages.</p

Basic information from the sequencing data.

<p>(A) Length distribution of the total reads; (B) Length distribution of the unique reads; (C) Length distribution of the unique miRNAs; (D) The numbers of detected miRNAs in the three libraries. (p<0.05).</p

MyHC gene expression in the psoas major muscle at 63, 98 and 161 d.

<p>MyHC gene expression in the psoas major muscle at 63, 98 and 161 d.</p

KEGG pathway analysis of most abundant miRNAs.

<p>KEGG pathway analysis of most abundant miRNAs.</p