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Hand, foot and mouth disease caused by Coxsackievirus Group B5 is one of the most common herpetic disorders in infants and children. In the present study, we investigated the expression of circRNAs using RNA sequencing techniques in CVB5-infected and mock-infected human rhabdomyosarcoma cells. The differentially expressed circRNAs were primarily involved in specific signaling pathways related to ErbB, TNF, and innate immunity, according to a detailed review of genes and Genomes enrichment. Novel_circ_0000566 could act as a molecular sponge for miR-152-3p through the IFN-I pathway to reduce CVB5 replication, and it may also be a molecular sponge for miR-29b-3p through the NF-B pathway and for CVB5 inhibition. These results will help to clarify the biological roles of circRNAs in the development of CVB5-related HFMD and identify potential biomarkers and therapeutic targets for this disease.
Source link: https://doi.org/10.3390/ijms23094628
By spongy microRNA-144COX-2 axis, we analyzed long-coding RNA HCG11 regulates proliferation, apoptosis, and drug resistance of glioma cells. The proliferation rate of glioma cells in the down-regulated group was up in comparison to the unregulated group; In the up-regulated group, the proliferation rate of glioma cells in the down-regulated group was reduced; Compared to the up-regulated group, the emergence rate of glioma cells in the down-regulated group was reduced; Compared to the up-regulated group's up-regulated group was reduced; In general, down-regulation of long-coding RNA-HCG11 in glioma can influence the microRNA-144COX-2 axis in glioma, thus lowering the proliferation of glioma cells and raising the apoptosis rate of glioma cells.
Source link: https://doi.org/10.14715/cmb/2021.67.9
Abstract Microglia, a class of immune effector cells present in the central nervous system, plays a major role in brain formation and neurodegenerative diseases; however, the extent of human microglia heterogeneity and complex molecular functions are still unclear. Cell subsets' functions are solely determined by high/low gene expression levels, effectively ignoring gene linkages between genes. We constructed gene regulatory networks of each microglia subtype based on single-cell RNA sequencing and then identified key genes in each network using graph theory techniques. In a word, the strategy that gene regulatory network coupled with graph theory to determine the function of microglia subtypes compensates for differential expression's deficiency of differential expression and provides new insight into AD cell type therapies related to AD.
Source link: https://doi.org/10.21203/rs.3.rs-1411661/v1
Abstract: Although the field of microbiology has adapted to the study of complex microbiomes using advanced meta-omics techniques, we have yet to update our basic knowledge about the quantitative properties of DNA, RNA, and protein molecules in a microbial cell's cells, which ultimately determine cell function. Within a mixed bacterial-archaeal group, we present temporal results of absolute RNA and protein levels per gene. Our results show that upgrading multi-omic toolkits with traditional absolute measurements reduces core biological studies' scaling to dynamic and complex microbiomes, providing greater insight into inter-organismal relationships that fuel greater community function.
Source link: https://doi.org/10.1038/s41467-020-18543-0
Microbiota profiling using NGS technologies is common for microbiota profiling. Sequencing the full-length 16S RNA gene is impractical since the majority of NGS platforms produce short reads. Both nine 16S rRNA hypervariable regions are taxonomically useful, but choosing the right 16S rRNA hypervariable region will depend on the habitat under study's bacterial composition. Uro tract microbes were discovered by NGS, and urinary microbiota has emerged as an important research field. We obtained urine samples from male participants and analyzed their urinary microbiota by sequencing a panel of six amplicons representative of all nine 16S rRNA hypervariable regions. V1V2 hypervariable regions help identify the taxa commonly present in male urine samples, which may indicate that V1V2 amplicon sequencing is more appropriate for male urinary microbiota profiling.
Source link: https://doi.org/10.3389/fcimb.2022.862338
Abstract Background The tumor microenvironment plays a role in tumor formation, development, invasion, and metastasis. The tumor microenvironment is heterogeneous in cellular and acellular components, with particular physical appearances and gene expression at the inter- and intra-tumor levels. Although spatial details are lacking, single-cell transcriptome sequencing results cell proportions and trajectories to reveal cell numbers and trajectories. Conclusion The integration of two techniques may help to crack the bottlenecks in the spatial resolution of neighboring cell subpopulations of cancer, as well as help to define the signaling circuitry that leads to the discovery of various types and malignant tumor types.
Source link: https://doi.org/10.1186/s12935-022-02580-4
Using bioinformatics techniques, we investigated the probable molecular functions related to microRNA-802 and determined its prognostic value in breast cancer. Methods: To find hub genes among overlapping genes of four miRNA target prediction databases, PPI network, pathway enrichment, and transcription factor analysis were used. Our findings: The miR-802 overexpression was found to be correlated with poor patient survival rates, which was inexorable. We found 247 target genes that were relevant for both GO and KEGG terms. RUNX3, FOXO3, and E2F1 were potential TFs that could influence the miR-802 expression and target gene network, according to TRUST's review of TFs. Conclusion: The comprehensive bioinformatics report on miR-802 target genes provided insight into miR-802-mediated pathways and processes. In addition, presenting candidate target genes by prognostic measurements suggests the possibility of clinical use of miR-802 in breast cancer.
Source link: https://doi.org/10.18502/ajmb.v14i2.8882
Mycobacterium bovis Bacille Calmette-Guérin is the only available tuberculosis vaccine currently available at vivo, and it is the only recognized tuberculosis vaccine available. The vaccine's protection against Pulmonary tuberculosis differs based on the strain, the patient's age, and the sampled population. Although the adaptive immune responses induced by various BCG strains have been widely researched, no conclusive evidence is available on innate immune responses, especially in macrophages. We analyzed the mRNA expression profiles and pathway enrichment analysis using RNA microarrays after a brief in vitro investigation of the bacterial strains and the innate immune responses, including nitric oxide production and cytokine profiles. Despite this, four DEGs were found in macrophages infected with M. BCG compared to P. BCG. Both BCG strains were found to proinflammatory stimulation of macrophages, both on the cytokine level and in terms of gene expression, suggesting a varying expression pattern of innate immune transcripts depending on the mycobacterial species.
Source link: https://doi.org/10.3390/ijms23094525
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