Bioinformatics and machine learning approaches reveal key genes and underlying molecular mechanisms of atherosclerosis: A review.

Atherosclerosis (AS) causes thickening and hardening of the arterial wall due to accumulation of extracellular matrix, cholesterol, and cells. In this study, we used comprehensive bioinformatics tools and machine learning approaches to explore key genes and molecular network mechanisms underlying AS in multiple data sets. Next, we analyzed the correlation between AS and immune fine cell infiltration, and finally performed drug prediction for the disease. We downloaded GSE20129 and GSE90074 datasets from the Gene expression Omnibus database, then employed the Cell-type Identification By Estimating Relative Subsets Of RNA Transcripts algorithm to analyze 22 immune cells. To enrich for functional characteristics, the black module correlated most strongly with T cells was screened with weighted gene co-expression networks analysis. Functional enrichment analysis revealed that the genes were mainly enriched in cell adhesion and T-cell-related pathways, as well as NF-κ B signaling. We employed the Lasso regression and random forest algorithms to screen out 5 intersection genes (CCDC106, RASL11A, RIC3, SPON1, and TMEM144). Pathway analysis in gene set variation analysis and gene set enrichment analysis revealed that the key genes were mainly enriched in inflammation, and immunity, among others. The selected key genes were analyzed by single-cell RNA sequencing technology. We also analyzed differential expression between these 5 key genes and those involved in iron death. We found that ferroptosis genes ACSL4, CBS, FTH1 and TFRC were differentially expressed between AS and the control groups, RIC3 and FTH1 were significantly negatively correlated, whereas SPON1 and VDAC3 were significantly positively correlated. Finally, we used the Connectivity Map database for drug prediction. These results provide new insights into AS genetic regulation.

Response of Carbon-Fixing Bacteria to Patchy Degradation of the Alpine Meadow in the Source Zone of the Yellow River, West China.

This study aims to enlighten our understanding of the distribution of soil carbon-fixing bacteria (cbbL-harboring bacteria) and their community diversity in differently degraded patches at three altitudes. MiSeq high-throughput sequencing technology was used to analyze the soil carbon-fixing bacteria community diversity of degraded patches and healthy meadow at three altitudes. Redundancy analysis (RDA) and structural equation model (SEM) were used to analyze the correlation and influence path between environmental factors and carbon-fixing bacteria. The results showed that degradation reduced the relative abundance of Proteobacteria from 99.67% to 95.57%. Sulfurifustis, Cupriavidus, and Alkalispirillum were the dominant genera at the three altitudes. Hydrogenophaga and Ectothiorhodospira changed significantly with altitude. RDA results confirmed that available phosphorus (AP) was strongly and positively correlated with Proteobacteria. AP and total nitrogen (TN) were strongly and positively correlated with Hydrogenophaga. Grass coverage and sedge aboveground biomass were strongly and positively correlated with Sulfurifustis and Ectothiorhodospira, respectively. Elevation adversely affected the relative abundance of dominant carbon-fixing bacteria and diversity index by reducing the coverage of grass and soil volumetric moisture content (SVMC) indirectly, and also had a direct positive impact on the Chao1 index (path coefficient = 0.800). Therefore, increasing the content of nitrogen, phosphorus and SVMC and vegetation coverage, especially sedge and grass, will be conducive to the recovery of the diversity of soil carbon-fixing bacteria and improve the soil autotrophic microbial carbon sequestration potential in degraded meadows, especially in high-altitude areas.

Expression level and clinical significance of LncRNA PVT1 in the serum of patients with LEASO.

Objective: Our study aims to investigate the long non-coding RNA plasmacytoma variant translocation 1 (lncRNA PVT1) in lower extremity arteriosclerosis obliterans (LEASO) patient serum and its clinical significance in LEASO. Patients and Methods: From July 2021 to April 2022, 133 LEASO patients diagnosed at the Qingdao Municipal Hospital were included. Among them, 44 complicated with coronary artery disease (CAD) were classified as the LEASO with CAD group. The remaining 89 were marked as the LEASO group, which was classified into single (n = 48) and double (n = 41) lower limb groups, with the former being subclassified into the left (n = 28) and right (n = 20) lower limb groups based on the affected sites. Fifty healthy individuals who came to our hospital for physical examination during the same period were randomly included and defined as the Healthy Control group. PVT1 expression was detected in serum samples from each group using a quantitative reverse transcriptase-polymerase chain reaction , and differences in expression levels were calculated. The ankle-brachial index (ABI) of patients in the LEASO group was measured using a sphygmomanometer, and its correlation with PVT1 was analyzed. Clinical data and laboratory test results (including blood routine, liver and renal function, and blood lipids) were collected for all patients upon admission. Logistic regression analyses were performed to determine the influence of PVT1 and laboratory test results on LEASO. The diagnosis and prediction of LEASO were obtained by combing PVT1 with laboratory test indicators. Results: It was found that lncRNA PVT1 expression was the highest in the serum of the LEASO with CAD group, followed by the LEASO and control groups (P < 0.05). Within the LEASO group, no significant difference in PVT1 expression was seen between the left and right limbs (P > 0.05), nor between the single and double lower limb groups. Furthermore, the PVT1 expression increased with the Rutherford grades, indicating a negative correlation between PVT1 and ABI. Logistic regression analysis revealed that triglycerides (OR = 2.972, 95% CI [1.159-7.618]), cholesterol (OR = 6.655, 95% CI [1.490-29.723]), C-reactive protein (OR = 1.686, 95% CI [1.218-2.335]), and PVT1 (OR = 2.885, 95% CI [1.350-6.167]) were independent risk factors for LEASO. Finally, strong sensitivity was observed in the receiver operating characteristic curve when combining PVT1 with meaningful laboratory indicators to diagnose and predict LEASO. Conclusion: lncRNA PVT1 promotes LEASO occurrence and progression and is related to atherosclerosis severity. The expression of PVT1 was negatively correlated with ABI. Logistic regression analysis suggested that blood lipid levels and inflammatory reactions might be related to LEASO occurrence. PVT1 was incorporated into laboratory indicators to predict LEASO. The subject's working curve area was large, and the prediction results were highly sensitive.

Exosomal miR-767 from senescent endothelial-derived accelerating skin fibroblasts aging via inhibiting TAB1.

Skin aging is a complicated physiological process, and microRNA-mediated regulation has been shown to contribute to this process. Exosomes mediate intercellular communication through miRNAs, mRNAs and proteins, and participate in many physiological and pathological processes. Vascular endothelial cell-derived exosomes have been confirmed to be involved in the development of many diseases, however, their effects on skin aging have not been reported. In this study, senescent endothelial cells could regulate skin fibroblast functions and promote cell senescence through exosomal pathway. miR-767 was highly expressed in senescent vascular endothelial cells and their exosomes, and miR-767 is also upregulated in skin fibroblasts after treatment with exosomes derived from senescent vascular endothelial cells. In addition, transfection with miR-767 mimic promoted senescence of skin fibroblasts, while transfection with miR-767 inhibitor reversed the effect of D-galactose. Double luciferase analysis confirmed that TAB1 was a direct target gene of miR-767. Furthermore, miR-767 expression was increased and TAB1 expression was decreased in D-galactose induced aging mice. In mice that overexpressed miR-767, HE staining showed thinning of dermis and senescence appearance. In conclusion, senescent vascular endothelial cell-derived exosome mediated miR-767 regulates skin fibroblasts through the exosome pathway. Our study reveals the role of vascular endothelial cell-derived exosomes in aging in the skin microenvironment and contributes to the discovery of new targets for delaying senescence.

[Effect of Nitrogen Addition on Soil Fungal Diversity in a Degraded Alpine Meadow at Different Slopes].

This study proposed nitrogen addition experiments to analyze the effects of exogenous nitrogen addition on soil fungal diversity in alpine meadow. All the experiments were performed in degraded alpine meadow with two different slopes (gentle slope and steep slope) in Guoluo Prefecture of the Sanjiangyuan Region, and the sequence and analysis of ITS of soil fungi were performed using MiSeq PE250 sequencing technology. Comparative analysis was carried out with three nitrogen addition levels on soil fungal diversity in degraded grassland with different slopes, which included low nitrogen (LN, 2 g·m-2), middle nitrogen (MN, 5 g·m-2), and high nitrogen (HN, 10 g·m-2). The results showed that:① the distribution groups of fungi in the soil were Ascomycota, Basidiomycota, Mortierellomycota, and Glomomycota, and the dominant bacteria was Ascomycota. ② The dominant genera were Mortierella and Archaeorhizomyces, and there were no differences in response to different slopes and nitrogen addition levels. ③ A total of 95 genera (Gibberellum, Preussia, etc.) were identified and significantly differed between two different slopes (P<0.05). ④ Bacteria with a relative abundance less than 1% had significant differences in nitrogen addition at different levels on the same slope (P<0.05). 5 In addition, the analyses of α and ß diversities showed that soil fungal community structure was stable under different slopes and nitrogen addition levels. Exogenous nitrogen supplementation significantly improved the relative abundance of non-dominant fungal communities without destroying soil fungal community structure.

[Changes in Soil Bacterial Community Diversity in Degraded Patches of Alpine Meadow in the Source Area of the Yellow River].

MiSeq sequencing technology was used to investigate the bacterial compositions and diversities of active patch, non-active patch, recovered patch, and healthy alpine meadows so as to understand the changes in soil bacterial community diversity during altitude change and alpine meadow degradation. The relationship between bacterial diversity and environmental factors was analyzed using redundancy analysis (RDA). The results showed that the dominant bacterial phyla in the soil included Proteobacteria, Actinobacteriota, and Acidobacteriota in the study areas. The dominant bacterial genera that were identified via the MiSeq were RB41, Sphingomonas, and Bradyrhizobium. The relative abundance of these genera decreased with altitude increase and increased with the restoration progress of degraded patches but was significantly lower than that in the alpine meadow (P<0.05). The abundance of functional bacteria related to carbon fixation in degraded patches was higher than that in the healthy alpine meadow. The bacterial Chao1 index and species number in different types of degraded patches were significantly higher than those in the alpine meadow (P<0.05). The results of the RDA suggest that biological soil crust coverage and total nitrogen were the main influencing factors on dominant bacterial phyla at the altitude of 4013 m. Biomass, total nitrogen, and pH had a great influence on the dominant bacterial phyla at the altitude of 4224 m. Biomass and total potassium significantly affected the distribution of bacterial genera at the altitude of 4013 m. Sedge coverage and available nitrogen were the main influencing factors on bacterial dominant genera at the altitude of 4224 m. Biological soil crusts and pH had a great influence on bacterial diversities. The bacterial influence factors varied greatly at different altitude areas. Therefore, we should not only pay attention to the effect of alpine meadow degradation but also consider the effect of altitude in the study of bacterial diversity changes.

Endothelial Cell-Derived Extracellular Vesicles Target TLR4 via miRNA-326-3p to Regulate Skin Fibroblasts Senescence.

Backgrounds: Skin aging could be regulated by the aberrant expression of microRNAs. In this manuscript, we explain that endothelial cell-derived extracellular vesicles could act as supporters to deliver exogenous miR-326-3p to accelerate skin fibroblasts senescence. Methods: ß-galactosidase senescence staining assay, Hoechst 33258 apoptosis staining assay, and Ki67 staining assay were used to evaluate the biological function of mouse skin fibroblasts. Real-time PCR was applied to assay miRNAs and mRNAs expressions. Western blot was used to detect TLR4 protein expression. The target gene of miRNA were identified using a double luciferase reporter assay. miR-326-3p mimic/inhibitor and siRNA-TLR4 can demonstrate a nonnegligible link between miR-326-3p-TLR4 and skin aging. Results: In coculture experiment, senescence endothelial cells could promote the skin fibroblasts senescence and apoptosis via extracellular vesicles pathway. In contrast, miR-326-3p mimics accelerated senescence and apoptosis of skin fibroblasts, while miR-326-3p inhibitor could dramatically delay skin fibroblasts senescence and apoptosis. TLR4 was proved to be a miR-326-3p directly target gene via double luciferase assay. After skin fibroblasts transfected with siRNA-TLR4, cellular senescence and apoptosis were significantly increased. Furthermore, the skin tissues of aging mice were shown with overexpression of miR-326-3p and decrease of TLR4 gene and protein expression levels. Conclusions: Endothelial cell-derived extracellular vesicles delivery of miR-326-3p was found to have a function in skin fibroblasts via target TLR4. Therefore, endothelial cell-derived extracellular vesicles in antiaging therapies might be a new treatment way for delaying skin aging.

Infection survey and morphological characteristics of Sarcocystis spp. in naturally infected Tibetan sheep from Qinghai in northwestern China.

Sarcocystosis is a parasitic disease caused by intracellular coccidian protozoans that belong to the genus Sarcocystis. These parasites can cause diseases of the nervous system, abortion and economically significant losses in host animals. Previous studies have reported that Sarcocystis is found in mammals, birds and reptiles, while molecular and morphological studies of infected Tibetan sheep have not been performed in the Qinghai region. The aim of this study was to determine the prevalence of Sarcocystis spp. in Tibetan sheep in Qinghai, northwestern China. The results showed that in 1155 samples, sarcocysts from unspecified species were found in 50% (577/1155) of the sheep tissues by microscopy detection. The positive rates of sarcocysts in the diaphragmatic, esophageal and cardiac muscles were 78.4% (175/223), 29.1% (207/711), and 88.2% (195/221), respectively. Ultrastructural features were exclusively observed in Sarcocystis gigantea in the esophageal tissues. The specific architecture was characterized as a space between the two layers of the original capsule wall, which was filled with fiber bundles and tissue fluid. Cauliflower-like protrusions of the original capsule wall were observed toward the outer surface of the capsule. Prominent protrusions contained fibers and matrix. In addition, the Sarcocystis 18S rRNA genes from 6 esophageal tissue samples were cloned, sequenced, and aligned to related sequences from GenBank. All 5 S. gigantea sequences examined in this study were grouped into the same cluster and belonged to the same genotype. The other 5 Sarcocystis tenella sequences were obtained from cardiac muscle and diaphragm muscle and belonged to the same clade. Overall, this study revealed a high infection rate of Sarcocystis in Tibetan sheep in the region. The results of this study may provide a reference for further research investigating the sarcocystosis epidemic in Qinghai, China.

Direct C4-H phosphonation of 8-hydroxyquinoline derivatives employing photoredox catalysis and silver catalysis.

A simple and efficient protocol for the C4-H phosphonation of 8-hydroxyquinoline derivatives was developed under a photoredox/silver(i) cocatalysis system, providing a new approach to phosphonated 8-hydroxyquinoline derivatives. Note that the reaction did not occur at the C5 site, but regioselectively at an unusual C4 site. Moreover, the reaction proceeded smoothly under mild reaction conditions (a catalytic amount of silver salt and room temperature) with good functional group compatibility.

Ru/Cu Photoredox or Cu/Ag Catalyzed C4-H Sulfonylation of 1-Naphthylamides at Room Temperature.

A mild and efficient protocol for C4-H sulfonylation of 1-naphthylamine derivatives with sodium sulfinates has been described. This C4 sulfonylation proceeded smoothly at room temperature under Ru/Cu photoredox catalysis or Cu/Ag cocatalysis and could tolerate various functional groups. In addition, control experiments suggested that this C4-H sulfonylation reaction might proceed via a single-electron-transfer process.

A Scalable Open-Source Pipeline for Large-Scale Root Phenotyping of Arabidopsis.

Large-scale phenotyping of multicellular organisms is one of the current challenges in biology. We present a comprehensive and scalable pipeline that allows for the efficient phenotyping of root growth traits on a large scale. This includes a high-resolution, low-cost acquisition setup as well as the automated image processing software BRAT. We assess the performance of this pipeline in Arabidopsis thaliana under multiple growth conditions and show its utility by performing genome-wide association studies on 16 root growth traits quantified by BRAT each day during a 5-d time-course experiment. The most significantly associated genome region for root growth rate is a locus encoding a calcium sensing receptor. We find that loss of function and overexpression of this gene can significantly alter root growth in a growth condition dependent manner and that the minor natural allele of the Calcium Sensor Receptor locus is highly significantly enriched in populations in coastal areas, demonstrating the power of our approach to identify regulators of root growth that might have adaptive relevance.

Diindolilmethane (DIM) selectively inhibits cancer stem cells.

Epidemiologic studies repeatedly have shown chemopreventive effects of cruciferous vegetables. Indole-3-carbinol (I3C) and its metabolite diindolylmethane (DIM) were identified in these plants as active ingredients and theirs anti-tumor activities were confirmed in multiple in vitro and in vivo experiments. Here, we demonstrate that DIM is a selective and potent inhibitor of cancer stem cells (CSCs). In several cancer cell lines, DIM inhibited tumor sphere formation at the concentrations 30-300 times lower than concentrations required for growth inhibition of parental cells cultured as adherent culture. We also found that treatment with DIM overcomes chemoresistance of CSCs to cytotoxics, such as paclitaxel, doxorubicin, and SN-38. Pre-treatment of tumor spheres with DIM before implantation to mice significantly retarded the growth of primary tumors compared to tumors formed by untreated tumor spheres. The concentrations of DIM required to suppress CSCs formation are in the close range to those achievable in human plasma after oral dosing of the compound. Therefore, DIM can potentially be used in cancer patients, either alone, or in combinations with existing drugs.