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BACKGROUND: At present, osteoarthritis has become a major disease affecting the quality of life of the elderly, and the therapeutic effect is poor, often focusing on preventing the disease process, and the pathogenesis of osteoarthritis is still not fully understood. Bioinformatics analysis was carried out to explore the main pathogenesis of osteoarthritis and related mechanisms of gene coding regulation. OBJECTIVE: To screen core differential genes with a major role in osteoarthritis by gene expression profiling. METHODS: Datasets were downloaded from the Gene Expression Omnibus (GEO): GSE114007, GSE117999, and GSE129147. Differential genes in the GSE114007 and GSE117999 data collections were screened using R software, performing differential genes to weighted gene co-expression network analysis. The module genes most relevant to osteoarthritis were selected to perform protein interaction analysis. Candidate core genes were selected using the cytocape software. The candidate core genes were subsequently subjected to least absolute shrinkage and selection operator regression and COX analysis to identify the core genes with a key role in osteoarthritis. The accuracy of the core genes was validated using an external dataset, GSE129147. RESULTS AND CONCLUSION: (1) A total of 477 differential genes were identified, 265 differential genes associated with osteoarthritis were obtained by weighted gene co-expression network analysis, and 8 candidate core genes were identified. The least absolute shrinkage and selection operator regression analysis finally yielded a differential gene ASPM with core value that was externally validated. (2) It is concluded that abnormal gene ASPM expression screened by bioinformatics plays a key central role in osteoarthritis. [ABSTRACT FROM AUTHOR]

BACKGROUND: At present, the pathogenesis of osteoarthritis is still unclear, and there is a lack of effective means to control the disease. Research on osteoarthritis is mostly concentrated in the field of immunity, and there are few studies in the field of oxidative stress. OBJECTIVE: To explore the roles of oxidative stress and immune infiltration in osteoarthritis and to predict related miRNAs and therapeutic agents. METHODS: The GSE55235 dataset (10 samples of osteoarthritis and 10 healthy control samples) and the GSE55457 dataset (10 samples of osteoarthritis and 10 healthy control samples) were obtained from the GEO database for merging to obtain their differentially expressed genes that were combined with oxidative stress genes to get the differentially expressed genes of oxidative stress. The differentially expressed genes of oxidative stress were analyzed for KEGG and GO enrichment, and the osteoarthritis pathways and biological processes were evaluated using GSEA enrichment analysis. The protein-protein interaction network was constructed using the STRING online website and Cytoscape software, and the Degree algorithm was run to get the key genes. The GSE1919 dataset was obtained from the GEO database as a validation dataset, and the key genes were analyzed by variance analysis and receiver operating characteristic curve analysis to get the core genes. In addition, immune infiltration was evaluated by CIBERSORT and the correlation between core genes and immune cells was explored. miRNA prediction of core genes was performed using TargetScan and target drugs were predicted using the DSigDB database. RESULTS AND CONCLUSION: Sixty-five differentially expressed genes and five core genes (IL1B, CXCL8, MYC, NFKBIA, JUN) associated with oxidative stress were identified. Enrichment analysis showed that differentially expressed genes associated with oxidative stress were concentrated in the pathways of oxidative stress, interleukin-17, osteoclast differentiation, fluid shear stress and atherosclerosis. The area under the receiver operating characteristic curve for the five core genes exceeded 0.85, indicating their excellent specificity and sensitivity in diagnosing bone and joint conditions, as well as their close association with immune cells. The predicted miRNA was has-miR-3937, and the therapeutic small-molecule drugs were metformin, ionomycin and celecoxib. To conclude, oxidative stress and immune infiltration exist in osteoarthritis, and immune infiltration is involved in activating oxidative stress. The core genes and predicted miRNAs can be used as novel markers for the diagnosis of osteoarthritis, and small molecule drugs are predicted to treat osteoarthritis. [ABSTRACT FROM AUTHOR]

BACKGROUND: m6 A modification has been confirmed to play an important role in the occurrence and development of osteonecrosis of the femoral head; however, the role of m6 A modification patterns in steroid-induced osteonecrosis of the femoral head remains unknown. OBJECTIVE: Bioinformatics analysis was performed based on the Gene Expression Omnibus (GEO) database to analyze the differential expression of the m6 A gene in steroid-induced osteonecrosis of the femoral head, predict the downstream targeted miRNAs, and investigate the potential pathogenesis. METHODS: Expressing profiles of mRNA data of steroid-induced osteonecrosis of the femoral head were downloaded from GEO database (GSE123568). Differentially expressed genes (DEGs), Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were performed using the R software. After obtaining these differentially methylated m6 A genes (m6 A-DEGs), we analyzed GO function and KEGG pathway enrichment and compared the correlation among the m6 A-DEGs typing according to gene expression. The protein-protein interaction network and core gene subnetwork of m6 A-DEGs were constructed using Cytoscape software. The m6 A-DEGs-associated potential miRNAs were predicted using the TargetScan, miRTarBase, and miRBD databases. Simultaneously, ChIPBase and hTFtarget databases were used to predict potential transcription factors of seven core genes, then m6 A-miRNA and transcription factor-m6 A regulatory networks were constructed separately. Finally, the expression levels of the seven core m6 A-DEGs were verified by using the GSE74089 dataset. RESULTS AND CONCLUSION: (1) A total of 2 460 common DEGs were screened out from datasets, among which 1 455 genes were upregulated and 1 005 genes were downregulated. (2) A total of 14 m6 A-DEGs were identified in the datasets. Among them, 11 m6 A-DEGs were up-regulated and 3 m6 A-DEGs were down-regulated. Differential gene expression was considered significant for m6 A-DEGs in steroid-induced osteonecrosis of the femoral head (P < 0.05). Spearman correlation analysis showed a significant correlation between m6 A-DEGs. (3) GO and KEGG enrichment analysis showed that m6 A-DEGs were mainly enriched in myeloid cell differentiation and development, immune and cytokine receptor activity, osteoclast differentiation, AMPK signaling pathway and interleukin-17 signaling pathway. (4) The seven core genes of m6 A-DEGs contained YTHDF3, YTHDF1, YTHDF2, ALKBH5, METTL3, HNRNPA2B1, and HNRNPC. A total of 44 miRNAs overlapping were detected in the miRTarBase, miRDB, and TargetScan databases. Totally 79 transcription factors overlapping were found in the ChIPBase and hTFtarget databases. (5) The expression levels of six core m6 A-DEGs in the GSE74089 dataset were consistent with those in the GSE123568 dataset. (6) These findings confirm that the seven m6 A-DEGs identified through bioinformatics techniques play a regulatory role in the expression of various miRNAs, transcription factors, AMPK, and interleukin-17 signaling pathways, and these genes have a significant impact on the differentiation and development of bone marrow cells as well as osteoclast differentiation in steroid-induced osteonecrosis of the femoral head. Consequently, these findings offer data support and establish a research direction for future investigations into the pathogenesis and targeted therapeutic strategies for steroid-induced osteonecrosis of the femoral head. [ABSTRACT FROM AUTHOR]

BACKGROUND: Cannabidiol is effective in ameliorating the body’s inflammatory response, but no clear mechanistic studies have been conducted to ameliorate skeletal muscle inflammation induced by exhaustive exercise. OBJECTIVE: To explore the mechanism by which cannabidiol improves skeletal muscle inflammation during exhaustive exercise by using transcriptome sequencing technology. METHODS: Thirty-six Sprague-Dawley rats were randomly divided into six groups: blank control group, exercise coconut oil group, exercise control group, 50 mg/kg cannabidiol group, 60 mg/kg cannabidiol group, and 70 mg/kg cannabidiol group, with six rats in each group. Except for rats in the blank control group, rats in each group were subjected to swimming exercise for 9 days to produce the exhaustive exercise model. At the end of each swimming exercise, rats in the cannabidiol groups were given 2 mL of fat-soluble cannabidiol at different concentrations (50, 60, and 70 mg/kg) by gavage; rats in the exercise coconut oil group were given the same volume of coconut oil by gavage until the end of the exercise on the 9th day; and rats in the blank control group and the exercise control group were not given any special treatment. The levels of inflammatory factors and differentially expressed genes in the skeletal muscle of rats in each group were determined using ELISA and transcriptome sequencing techniques. Differentially expressed genes obtained were subjected to KEGG analysis, and the accuracy of the sequencing data was verified by fluorescence quantitative PCR. RESULTS AND CONCLUSION: The results of ELISA showed that the contents of interleukin-6 (P < 0.05), tumor necrosis factor-α (P < 0.01), interleukin-10 and other inflammatory factors in the exercise group increased significantly compared with the blank control group and the coconut oil group. After cannabidiol intervention, the mass concentrations of interleukin-6 and tumor necrosis factor-α showed a sequential decrease with increasing cannabidiol concentration. By comparing GO and KEGG databases, the functional properties of differentially expressed genes were analyzed, and the results showed that the differentially expressed genes were mainly involved in the tumor necrosis factor signaling pathway and the Toll-like receptor signaling pathway. RT-qPCR results showed that the trends of five randomly selected differentially expressed genes were in agreement with the transcriptome sequencing results. To conclude, cannabidiol can improve skeletal muscle inflammation caused by exhaustive exercise. [ABSTRACT FROM AUTHOR]

BACKGROUND: Rheumatoid arthritis is a chronic autoimmune disease. Early diagnosis is crucial for preventing disease progression and for effective treatment. Therefore, it is of significance to investigate the diagnostic characteristics and immune cell infiltration of rheumatoid arthritis. OBJECTIVE: Based on the Gene Expression Omnibus (GEO) database, to screen potential diagnostic markers of rheumatoid arthritis using machine learning algorithms and to investigate the relationship between the diagnostic characteristics of rheumatoid arthritis and immune cell infiltration in this pathology. METHODS: The gene expression datasets of synovial tissues related to rheumatoid arthritis were obtained from the GEO database. The data sets were merged using a batch effect removal method. Differential expression analysis and functional correlation analysis of genes were performed using R software. Bioinformatics analysis and three machine learning algorithms were used for the extraction of disease signature genes, and key genes related to rheumatoid arthritis were screened. Furthermore, we analyzed immune cell infiltration on all differentially expressed genes to examine the inflammatory state of rheumatoid arthritis and investigate the correlation between their diagnostic characteristics and infiltrating immune cells. RESULTS AND CONCLUSION: In both rheumatoid arthritis and normal synovial tissues, we identified 179 differentially expressed genes, with 124 genes upregulated and 55 genes down-regulated. Enrichment analysis revealed a significant correlation between rheumatoid arthritis and immune response. Three machine learning algorithms identified LRRC15 and MICB as potential biomarkers of rheumatoid arthritis. LRRC15 (area under the curve=0.964, 95% confidence interval: 0.924-0.992) and MICB (area under the curve=0.961, 95% confidence interval: 0.923-0.990) demonstrated strong diagnostic performance on the validation dataset. The infiltration of 13 types of immune cells was altered, with macrophages being the most affected. In rheumatoid arthritis, the majority of proinflammatory pathways in immune cell function were activated. Immunocorrelation analysis revealed that LRRC15 and MICB had the strongest correlation with M1 macrophages. To conclude, this study identified LRRC15 and MICB as potential diagnostic markers for rheumatoid arthritis, with strong diagnostic performance and significant correlation with immune cell infiltration. Machine learning and bioinformatics analysis deepened the understanding of immune infiltration in rheumatoid arthritis and provided new ideas for the diagnosis and treatment of rheumatoid arthritis. [ABSTRACT FROM AUTHOR]

BACKGROUND: Endometrial receptivity is a key factor in embryo implantation in northwest Tibetan cashmere goats, and the expression of genes related to endometrial receptivity and their variable splicing are still unclear. OBJECTIVE: To analyze and explore genes and variable splicing events related to endometrial receptivity in northwest Tibetan cashmere goats. METHODS: On days 5 and 15 of pregnancy (representing pre receptive endometrium group and receptive endometrium group), three northwest Tibetan cashmere goats were randomly selected. Endometrial tissue was collected and stained with hematoxylin and eosin to observe tissue morphology. Immunohistochemical staining was used to detect the expression of endometrial receptive marker proteins leukemia inhibitory factor and vascular endothelial growth factor. After the total RNA was extracted and the quality test was qualified, transcriptome sequencing was performed to search differentially expressed mRNAs, lncRNAs, circRNAs, and miRNAs, perform functional prediction, and analyze alternative splicing mRNAs and lncRNAs related to endometrial receptivity. RESULTS AND CONCLUSION: (1) Compared with the pre receptive endometrium group, the expression levels of leukemia inhibitory factor and vascular endothelial growth factor proteins in the endometrial tissue of the receptive endometrium group were significantly increased. (2) The sequencing results showed that the differentially expressed genes were mostly mRNA and lncRNA genes, including 250 upregulated mRNAs, 193 upregulated lncRNAs, 135 downregulated mRNAs, and 123 downregulated lncRNAs, which were significantly enriched in the Wnt, Hedgehog, and Hippo signaling pathways. (3) Alternative splicing event analysis uncovered 8 differentially expressed variable splicing transcripts, which were all mRNA transcripts, including 2 downregulated and 6 upregulated, and were significantly associated with vascular endothelial growth factor receptor signaling, cell motility, and embryonic development. [ABSTRACT FROM AUTHOR]

【Objective】Oryza officinalis belongs to the CC chromosome group of rice genus, and it had accumulated a large number of resistance genes that adapt to harsh environments during long-term natural survival. Based on transcriptome sequencing (RNA-seq), disease resistance related genes could be discovered, laying a foundation for researches on gene function and regulatory mechanisms.【Methods】Two isolates of Xanthomonas oryzae pv. oryzae CX28-3 and PXO99 were inoculated to 38 O. officinalis wild rice materials of 6 populations (Ⅰ-Ⅵ) from Yunnan Province, and different resistance phenotypes were evaluated. The highly resistant and susceptible populations were selected for transcriptome sequencing. The transcriptome sequencing data of O. officinalis 36 (resistant) and O. officinalis 37 (susceptible) plants after PXO99 inoculation stress at 0, 24, and 48 h were analyzed. And genes related to resistance to bacterial leaf blight in O. officinalis wild rice were predicted.【Results】The 38 O. officinalis wild rice materials from 6 populations showed different disease resistance to 2 strains (CX28-3 and PXO99), and the overall resistance rate was medium or above, among which the highest resistance rate was 93.50% in Ⅴ population and the lowest rate was 62.50% in Ⅲ population. Among them, it was found that 5 accessions of O.officinalis were susceptible to CX28-3 isolate, with a disease infection rate of 13.15%, and 42.10% to PXO99 strain, indicating that PXO99 had strong pathogenicity. There were 20 O. officinalis materials resistant to two strains simultaneously, accounting for 66.67% of all materials. O. officinalis 37 showed moderate susceptibility to both strains, while O. officinalis 36 showed resistance to both strains. Through transcriptome sequencing of O. officinalis 36 and 37 plants, a total of 75 650 differentially expressed genes (DEGs) were identified. GO functional enrichment analysis revealed that PXO99 treatment resulted in a total of 45 significantly enriched GO categories in biological processes. Among them, the most enriched DEGs were concentrated in cellular processes, metabolic processes, cellular anatomical entities, binding, catalytic activity, etc. KEGG enrichment analysis showed that 19 KEGG pathways were significantly enriched in the resistant and susceptible O. officinalis materials, among which KEGG pathways related to disease resistance to proteins were significantly enriched and increased. This further clarified that the resistance to disease of the O. officinalis 36 was significantly stimulated by the Xanthomonas oryzae pv. oryzae. A total of 256 common DEGs were screened, and 11 genes were closely related to the resistance to bacterial leaf blight in O. officinalis; Unigene1184, Unigene15669, CL1239, CL1421, CL4899, CL660, and CL7463 genes were up-regulated in resistant materials and down-regulated in susceptible materials. Unigene18206, CL210, CL3554, and CL9248 genes were down-regulated in resistant materials and up-regulated in susceptible materials.【Conclusion】38 accessions of O. officinalis of 6 populations from Yunnan showed different disease resistances to two strains (CX-28 and PXO99), but overall resistance was moderate or above. By using transcriptome sequencing technology, 11 genes related to resistance to bacterial leaf blight in O. officinalis were obtained. The research results will provide references for the exploration and functional study of genes related to resistance to bacterial leaf blight in O. officinalis.

BACKGROUND: Research has shown that fatty acid metabolism genes are closely related to the development of rheumatoid arthritis. Therefore, exploring the progression of rheumatoid arthritis based on fatty acid metabolism genes is of clinical significance. OBJECTIVE: To investigate whether fatty acid metabolism genes can serve as reliable biomarkers for predicting the progression of rheumatoid arthritis. METHODS: Gene data related to synovial tissue were downloaded from the Gene Expression Comprehensive Database (GEO). STRING was used to construct the protein-protein interaction network analysis. Cytoscape was utilized for biological annotation (gene ontology) and signaling pathway enrichment analysis (Kyoto Encyclopedia of Genes and Genomes). Fatty acid metabolism related genes were screened from the molecular feature database (MSigDB). Least absolute shrinkage and selection operator and support vector machine recursive feature elimination feature were used to screen for potential biomarkers. Immune cell infiltration levels in normal individuals and rheumatoid arthritis patients were assessed using the CIBERSORT algorithm. Finally, the expression levels of fatty acid metabolism related genes were verified using the receiver operating characteristic curve in GSE77298. RESULTS AND CONCLUSION: 361 differentially expressed genes in rheumatoid arthritis were identified, of which 13 overlapped with the reported fatty acid metabolism related genes. Based on machine learning algorithms, five genes were selected, and the receiver operating characteristic curve showed that five genes (PCK1, PDK1, PTGS2, PLA2G2D, and DPEP2) could predict the development of rheumatoid arthritis. The CIBERSORT algorithm results showed that five genes were associated with activated mast cells, neutrophils, resting mast cells, and memory resting CD4+ T cells. The receiver operating characteristic curve showed that PLA2G2D and PCK1 have high diagnostic value. To conclude, the expression characteristics of fatty acid metabolism related genes can serve as potential biomarkers for predicting clinical outcomes, which can further improve the accuracy of prediction in RA patients. [ABSTRACT FROM AUTHOR]

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Copyright of Journal of Dalian Ocean University is the property of Journal of Dalian Ocean University Editorial Office and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Thamnaconus septentrionali has excellent breeding characteristics, is omnivorous, easy to domesticate, is especially suitable for netting, cleans the netting, and effectively reduces labor-costs. T. septentrionali is available in various sizes and is raised in the market at 100 g. Under water temperature of 18–25 ℃, after 5–6 months of breeding, it reaches commercial size. As the Yellow Sea and Bohai Sea are cold in winter, a suitable breeding cycle for green fins is from May to November annually. Under natural conditions, the spawning period of T. septentrionali in the Yellow Sea and Bohai Sea is from early May to early June, making good use of the suitable breeding cycle of net box culture. Therefore, reproductive regulation is required to advance the reproductive period of T. septentrionali. Previous studies have primarily focused on the expression and functional analysis of individual genes. In contrast, no studies exist on the overall expression analysis of gonad-related genes based on histology. Herein, we conducted the first transcriptome sequencing analysis of the spermatophores and ovaries of T. septentrionali using an Illumina high-throughput sequencing platform. Overall, 165, 981, 523 raw reads were sequenced from the cDNA, and 161, 234, 846 clean reads were obtained after quality control. The Q20 of each sample was > 98.43%, Q30 was > 95.25%, and GC content of the sample bases was greater than 52.31%. Our findings indicate that the sequencing data are accurate, of good quality, and were used for subsequent analyses. The obtained unigenes were annotated in the NR (NCBI non-redundant protein sequences), NT (NCBI nucleotide sequences), PFAM (protein family), KOG (euKaryotic Ortholog Groups), SwissProt (a manually annotated and reviewed protein sequence database), GO (Gene Ontology), and KO (KEGG Orthology) databases, and 24, 009, 35, 057, 18, 453, 26, 971, 30, 294, 11, 420, and 21, 613 unigenes were annotated, respectively. The KEGG annotation results were divided into five major categories: organic systems, with 2, 115 genes in nine pathways; metabolism, with 1, 444 genes in 12 pathways; environmental information processing, with 1, 200 genes in three pathways; and genetic information processing, with 1, 128 genes in four pathways. Environmental information processing (1, 200 genes in three pathways), genetic information processing (1, 128 genes in four pathways), and cellular processes (1, 128 genes in four pathways). The number of genes enriched in cellular process-related pathways was 927 distributed in four related pathways. The signal transduction pathway was the most annotated KEGG pathway with 804 genes. The experiment used 24, 546 unigenes annotated in the KOG database, which were then classified into 26 categories based on their function. The largest number of unigenes were annotated in the signal transduction mechanism category (5, 411), followed by the general function prediction-only category (4, 252 unigenes), and posttranslational modification, protein folding and chaperone category (1, 713 unigenes). Unigene posttranslational modification, protein turnover, chaperones; transcription, 1, 613; and other related functions. There were 18, 954 differentially expressed genes (DEGs) in the spermatophore and ovary transcriptomes of the T. septentrionali, with 11, 265 genes up-regulated and 7, 689 down-regulated in the ovary relative to the spermatophore. The GO functional enrichment analysis revealed that DEGs were most enriched in the cellular component of biological processes, intracellular component of the cellular component subclass, and nucleic acid binding of the molecular functional subclass. GO analysis of the DEGs in males and females provided a partial list of genes associated with the reproductive process (GO: 0022414), sexual reproduction (GO: 0019953), gamete formation (GO: 0007276,), sex differentiation (GO: 0007548), and gonad development (GO: 00084060). To further characterize the specific functions of the DEGs in the spermatophores and ovaries of T. septentrionali, the enriched signaling pathways were further analyzed using the KEGG database. In total, 154 KEGG pathways were included, of which the top 30 were selected. The functional pathways with the highest number of expressed genes were closely associated with gonadal sex differentiation and development, including the insulin signaling pathway, steroid hormone biosynthesis, FoxO signaling pathway, M-TOR signaling pathway, and progesterone-mediated oocyte maturation. Among these, the FoxO signaling pathway regulatory genes are expressed in multiple processes, such as cell cycle control, apoptosis, and gluconeogenesis. The insulin signaling pathway plays an important role in regulating developmental, metabolic, and lifespan physiological processes, and the insulin signaling pathway is involved in gonadal development and maturation. Nine DEGs, bmp2, sox3, figla, hsd17b1, cyp19a, cyp17, foxl2, star, and amh, were selected for real-time fluorescence quantitative PCR (qRT-PCR) validation. The qPCR results were consistent with those of RNA-seq analysis. GO and KEGG enrichment results were analyzed and revealed that amh, cyp17, and star are imperative in male spermatogenesis of T. septentrionali; bmp2, foxl2, cyp19a, figla, and hsd17b1 are essential in female oogenesis and ovarian steroidogenesis. By comparing the transcriptome expression differences between the spermatophore and ovary of T. septentrionali, we elucidated the gene expression characteristics of the spermatophore and ovary, laying the foundation for future research on the mechanism of reproductive development of T. septentrionali and providing theoretical support for optimizing reproductive regulation techniques.

[Objective] To explore the molecular mechanism involved in anthocyanin biosynthesis during the fruit development of Lycium ruthenicum Murr. is important for deeply understanding the regulatory network of anthocyanin biosynthesis. [Method] Transcriptome sequencing was performed on the samples at the five stages of fruit development: green fruit, early color-changing, late color-changing, ripeness, and complete ripeness. The candidate genes related to anthocyanin biosynthesis were mined. [Result] With the development of L. ruthenicum Murr. fruit, the anthocyanin content gradually increased. The anthocyanin content in the fruits at the ripeness and complete ripeness stages were significantly higher than that at the green fruit, early color-changing, and late color-changing stages. A total of 13 540 differentially expressed genes (DEGs) were identified from the five stages of fruit development. Using the green fruit stage as a control, the number of DEGs gradually increased with the development of the fruit. GO analysis showed that DEGs were co-enriched GO terms including phenylpropanoid metabolic process, polysaccharide catabolic process, phenylpropanoid biosynthetic process, flavonoid biosynthetic process, cell wall macromolecule metabolic process, anchored component of membrane, and nutrient reservoir activity. KEGG analysis indicated the significant enrichment of DEGs in flavonoid biosynthesis, phenylpropanoid biosynthesis, plant hormone signal transduction, stilbenoid, diarylheptanoid and gingerol biosynthesis, as well as cutin, suberine, and wax biosynthesis. The correlation between DEGs expression and anthocyanin content was performed and 36 candidate genes involved in anthocyanin biosynthesis during the L. ruthenicum fruit development were screened, including ten structural genes of anthocyanin biosynthesis pathway, four genes of transcription factors, nine, eight, and five genes of ABA, GA, and JA signal transduction pathway. Ten DEGs were selected for RT-qPCR analysis, and the results were consistent with RNA-seq data. [Conclusion] DEGs related to structural genes and transcription factors involved in anthocyanin biosynthesis, as well as genes involved in the ABA, GA, and JA signal transduction pathways, affect fruit coloration during the development of L. ruthenicum Murr. fruit. [ABSTRACT FROM AUTHOR]

[Objective] The“three line”method is the main way to breed hybrid soybeans. At present, only a few soybean restoration genes have been cloned. Thus it will be helpful in the breeding strong restorer lines with multi genes aggregation, thereby improving the fertility stability of hybrid F1, if more new Rf genes can be discovered. [Method] Using soybean cytoplasmic male sterile line JLCMS5A and its restorer line JLR2 as materials, transcriptome sequencing technology was used to analyze the transcriptional level changes of JLCMS5A and JLR2 flower buds at different stages, and to explore the relevant genes and pathways regulating restorer of fertility and flower bud development processes. Further gene annotation, sequence difference analysis, RT-qPCR validation, phylogenetic analysis, and protein structure prediction were performed on differentially expressed genes（DEGs） with Rf gene features encoding PPR（pentatrioptide repeat）proteins to explore Rf related genes. [Result] Transcriptome sequencing identified 17 181 DEGs, of which 3 856 were related to developmental stage and 2 808 were related to fertility. GO（gene ontology）functional annotation indicated that fertility-related DEGs were mainly enriched in functional categories such as ADP binding, nucleic acid binding transcription factor activity, and protein kinase activity, while developmental stage-related DEGs were mainly enriched in functional categories such as protein heterodimerization activity, DNA replication, and DNA binding. KEGG（kyoto encyclopedia of genes and genes）enrichment analysis showed that fertility-related DEGs mainly participate in metabolic pathways closely related to protein, carbohydrates, and signal transduction, such as endoplasmic reticulum protein processing, glucoside biosynthesis, and plant hormone signal transduction. Development-related DEGs mainly participated in metabolic pathways closely related to DNA replication, mismatch repair, starch and sucrose metabolism, and cell division and energy degradation. Analysis of candidate Rf genes revealed that the Glyma.09G176400 in JLR2 may play a certain role in regulating the restorer-of-fertility process of soybean cytoplasmic male sterility. [Conclusion] 3 856 DEGs and 2 808 DEGs which respectively related to developmental stage and fertility were identified by transcriptomic techniques and molecular biological methods. Whereafter, a total of 15 DEGs encoding PPR protein were identified, which had the characteristics of restorer-of-fertility gene. Finally, a restorer-of-fertility related gene Glyma.09G176400 was excavated [ABSTRACT FROM AUTHOR]

Objective To evaluate differentially expressed genes with correlation of gene body methylation. Methods The lingual carcinogenesis was induced through the delivery of drinking water of 4-nitroquinoline-1- oxide (4NQO) with a density of 50 mg/L. The lingual mucosae specimens were harvested at 0, 12, 28 weeks, which represented normal, pre-cancer, and cancer individually. The microarray and methylated DNA immunoprecipitation sequencing (MeDIP-Seq) were used for the evaluation of gene expression and global DNA methylation in these specimens. The mRNA expression of Ubiquitin carboxyl-terminal hydrolase CYLD was tested with qRT-PCR in human normal and dysplasia mucosa. Results There were no statistical differences in gene body methylation among normal (C), pre-cancer (M), and cancer (E) (mean±sofMeDIP-score were 5.58±14.80, 5.79±13.35, 5.83±17.25 individually, H = 100.75, P > 0.05) There presented 145 differentially expressed genes with positive correlation to gene body methylation changes.The expression of CYLD mRNA was decreased in human dysplasia compared to normal mucosa with downregulation of gene body methylation. Conclusions There are many differentially expressed genes with a positive correlation to gene body methylations. The expression of CYLD is downregulated with the downregulation of gene body methylation in earlier stage during tongue carcinogenesis. [ABSTRACT FROM AUTHOR]

【Objective】The effects of different altitudinal gradients on gene expression in Sichuan pepper（Zanthoxylum bungeanum Maxim.） were investigated to provide the basis for studying the genetic diversity and metabolic regulation of Sichuan pepper and its molecular mechanisms adapting to different altitudinal habitats stress.【Method】Using the leaves of Sichuan pepper from different altitudes（1054, 821 and 645 meters） in Banguixiang of Zhenfeng county in Guizhou province as test materials, we employed bioinformatics methods of transcriptome sequencing to analyze alternative splicing（AS） and SNP/InDel variant sites of differentially expressed genes, thereby uncovering novel transcripts involved in the adaptation of Sichuan pepper to its environment. 【Result】In the leaves of Sichuan pepper plants from three different altitudes, a total of 2619 genes underwent alternative splicing events, mainly consisting of two types of skipped exon（SE） and mutually exclusive exons（MXE） with SE being the most abundant. Additionally, a significant increase in alternative splicing events was observed in the high-altitude comparison group. Furthermore, a total of 748 331 SNPs and 87 402 InDel loci were identified, with a higher occurrence of SNP transitions than the transversion and a distribution of exonic SNPs accounting for 40.0%.InDel loci were predominantly found in intronic regions, reaching 28.6%. Moreover, 9363 novel transcripts were discovered, with 5648 of them being annotated in 7 major databases. KEGG metabolic pathway analysis revealed that functional genes undergoing alternative splicing in Sichuan pepper leaves were mainly involved in metabolic pathways, biosynthesis of secondary metabolites and biosynthesis pathways of cofactors. On the other hand, novel transcripts were mainly enriched in pathways such as photosynthesis, phenylpropanoid biosynthesis, isoflavonoid biosynthesis, flavonoid biosynthesis and terpenoid biosynthesis.【Conclusion】The study enriches understanding of genetic structural variations of Sichuan pepper under different altitudinal conditions and lays the foundation for subsequent research on genetic diversity, metabolic regulation and molecular mechanisms in response to environmental stress. [ABSTRACT FROM AUTHOR]

Aim To reveal the mechanism of cross-species ischemic heart failure from the perspective of spatial and gene co-expression networks. Methods GSE210374 and GSE57338 high-throughput sequencing datas were retrieved from the national center for biotechnology information gene expression database (NCBI-GEO), and R language software packages was used to analyze and screen differentially expressed genes (DEG) in different myocardial regions of myocardial infarction rats, as well as DEG of myocardial samples from patients with ischemic heart failure and healthy controls, and the regional expression of common genes was analyzed. Weighted gene co-expression network analysis (WGCNA) was used to screen the genes related to myocardial infarction and to carry out enrichment analysis, protein-protein interaction network (PPI) was constructed to screen core genes (HG). Results A total of 4 835 differentially expressed genes were screened out in myocardial infarction rats and normal controls, and 51 differentially expressed genes were screened out in ischemic heart failure patients and normal control samples, which revealed representative gene sets in the left ventricular myocardial infarction area (I area), border area (BZ area), and remote area (R area) after myocardial infarction. Spatial expression analysis revealed that there were 20 co-expressed genes in each myocardial region, 16 of which were expressed in all three regions, the number of genes specifically expressed in I, BZ and R regions were 2, 0 and 2, respectively. Enrichment analysis showed that the functions of co-expressed genes were different in different region. The I and BZ regions were related to collagen fiber assembly, stress-induced cardiomyocyte hypertrophy, down-regulation of c-Jun amino terminal kinase (JNK signal) and cell proliferation, and complement signaling pathways; The I and R regions were enriched in the binding of Wnt and collagen; As a non-ischemic distal R region, the co-expressed genes were significantly enriched in the extracellular matrix for functions such as compressive resistance, cytolysis and inhibition of T cell proliferation. Furthermore, it was worth noting that the products of co-expressed genes in the three regions were mostly located in the extracellular space and extracellular matrix, suggesting that there may be active cellular secretion and interaction regulation. Further PPI analysis suggested that asporin (ASPN), osteoglycin (OGN) and collagentype ⅩⅣ alpha chain (COL14A1) gene might be the core genes of the mechanism mentioned above. Conclusions The common mechanism of ischemic heart failure in rats and human involves multiple signaling pathways such as complement and coagulation cascade signaling and Wnt; which may be closely related to cell apoptosis mediated by extracellular matrix and exosomes; ASPN, OGN, and COL14A1 may be the core genes. This work is expected to provide spatial and pathway reference for the selection of intervention targets and pathway in the transformation research related to ischemic heart failure. [ABSTRACT FROM AUTHOR]

Objective: To discuss the differentially expressed genes in severe bronchial asthma [severe asthma (SA)] by bioinformatics methods and analyze their mechanisms, and to screen the traditional Chinese medicines and their active components with potential therapeutic effects. Methods: The GSE136587 and GSE158752 datasets were selected from the Gene Expression Omnibus (GEO)Database; R software was used for the differential analysis to obtain the differentially expressed gene; the proteinprotein interaction (PPI)network analysis was used to screen the core genes, and the key pathways and hub genes were identified. The core genes were uploaded to the Coremine Database to screen for the traditional Chinese medicines with the potential therapeutic effects, and the relevant Chinese herbal prescriptions were searched in Chinese Medical Dictionary. Results: A total of 466 differentially expressed genes were screened. The PPI network constructed through the STRING platform led to the selection of synaptosomal associated protein 25 kDa (SNAP25), glutamate ionotropic receptor AMPA type subunit 2 (GRIA2), neurexin 1 (NRXN1), potassium voltage-gated channel subfamily a member 1 (KCNA1), synaptotagmin 1 (SYT1), and chromogranin A (CHGA). The Gene Ontology (GO) functional enrichment analysis results showed that the biological processes of SA were significantly related to the cellular chemotaxis and leukocyte migration. The Kyoto Encyclopedia of Genes and Genomes (KEGG) signaling pathways enrichment mainly involve bone marrow leukocyte migration, leukocyte chemotaxis, cell chemotaxis, leukocyte migaration, up-regulation of outside stimulus, and bone marrow leukocyte activation signaling pathways. Network pharmacology was applied to screen for 367 traditional Chinese medicines with potential therapeutic effects based on the core targets. Among them, ginseng, water buffalo horn, scorpio, and astragalus, which involve multiple core targets, were highly related to SA. A total of 17 potential Chinese herbal prescriptions with therapeutic effects were retrieved from Chinese Medical Dictionary. Conclusion: The bioinformatics screening of potential biomarkers and traditional Chinese medicines with therapeutic effects for SA provides the new targets for the early diagnosis and research on the pathogenesis of SA, and offers new insights into the development of herbal prescriptions for its treatment. [ABSTRACT FROM AUTHOR]

[Objective] The present paper aims to investigate the molecular mechanisms and associated regulatory networks involved in endo- sperm development for the tropical maize inbred line. (Method) The study employed high-throughput RNA-Seq sequencing technology to compare the endosperm transcriptome of the tropical inbred maize line ZOL-1 at six stages after pollination, including 5 (day after pollination), 10, 15, 20, 25 and 30 days. Differentially expressed genes were annotated with KEGG and GO functions, and time-series analysis was conducted on genes with an average FPKM value greater than 1. [Result] The endosperm development of the maize inbred line ZOL-1 exhibited the fastest growth rate in grain length, width, and thickness at 25-30 days after pollination, with growth rates reaching 15.9%, 16.1% and 10.2%, respectively. Following transcriptome sequencing and comparison with the reference genome, the percentage of filtered reads was at least 83.99%, indicating good sequencing quality and assembly. A total of 7129, 5252, 4254, 775 and 312 differentially ex- pressed genes were identified between 10 d_VS_5 d, 15 d_VS_10 d, 20 d_VS_15 d, 25 d_VS_20 d and 30 d_VS_25 d, based on the sequential comparison system approach. GO functional annotation indicated that the differentially expressed genes were mainly involved in cell differentiation process, metabolic process, catalytic activity and organelles. KEGG functional enrichment analysis revealed that differentially expressed genes were mainly enriched in pathways related to energy metabolism, carbohydrate metabolism, carbon metabolism, amino acid metabolism, signal transduction, and other processes associated with endosperm development. Through time-series analysis of genes with an FPKM mean greater than 1, 19 554 genes were classified into 10 clusters. In Cluster 7, eight starch synthase-related genes were identified, showing a significant increase in expression starting at the 15-day period and maintaining a high expression level thereafter. (Conclusion] The regulation of endosperm development in maize self-incompatible lines appears to be primarily governed by the expression of down-regulated genes. The developmental pattern of the endosperm undergoes a significant change before and after 15 days, indicating a transcriptome reprogramming. Additionally, the study identifies eight genes associated with maize starch biosynthesis, providing valuable insights into the molecular regulatory mechanisms of endosperm development. [ABSTRACT FROM AUTHOR]

【Objective】Excessive deposition of abdominal fat reduces disease resistance and slaughter rate of broilers. RNA alternative splicing is an important regulatory modality that affects gene function. Systematic analysis of RNA alternative splicing events during broiler abdominal fat deposition contributes to further understanding of the molecular regulation mechanism of broiler abdominal fat deposition.【Method】The transcriptome sequencing results of liver and abdominal fat tissues in high-fat-fed and normal-fed broilers were used to identify the differentially expressed and alternative spliced genes in abdominal fat and liver tissues during high-fat feeding. Significantly differentially spliced genes were analyzed by GO functional annotation, KEGG pathway enrichment analysis and Metascape enrichment analysis, and visualization processing was conducted for the significantly differential alternative splicing events, then splicing factors regulating these differential splicing events were analyzed.【Result】Transcriptome sequencing was performed on the abdominal fat and liver tissues of high-fat-fed broilers and normal-fed broilers. 233 significantly differentially expressed genes and 349 significantly differentially alternative spliced genes were found in the abdominal fat tissues. It was found that the significantly differential spliced genes were mainly enriched in cell proliferation, such as cell division and cell growth, as well as in pathways related to adipogenesis, such as glycerophospholipid metabolism and insulin signaling pathway. In liver tissues, 276 significantly differentially expressed genes and 224 significantly differential spliced genes were found, and the enrichment analysis of the significantly differential spliced genes revealed that these genes were mainly enriched in biological processes related to cellular metabolism such as protein acetylation, intra-protein amino acid acetylation and mRNA processing and also enriched in adipogenesis-related pathways such as insulin signaling pathway, glucagon signaling pathway and AMPK signaling pathway. Among the significantly differential spliced genes in abdominal fat and liver, a total of four candidate genes related to influencing abdominal fat deposition traits in broiler were screened, including GPAT4, RELCH, CYP39A1, and PPARA.【Conclusion】The results preliminarily revealed the patterns of RNA alternative splicing regulation in abdominal fat and liver tissues of broilers under high-fat feeding. It was inferred that high-fat feeding may lead to abdominal fat deposition in broilers by affecting the alternative splicing process of genes, which may activate the proliferation of preadipocytes and the metabolism of adipogenesis-related cells. Regulation of target genes by splicing factors was significantly involved in influencing the process of abdominal fat deposition in broilers.

[Objective] Excessive deposition of abdominal fat reduces disease resistance and slaughter rate of broilers. RNA alternative splicing is an important regulatory modality that affects gene function. Systematic analysis of RNA alternative splicing events during broiler abdominal fat deposition contributes to further understanding of the molecular regulation mechanism of broiler abdominal fat deposition. [Method] The transcriptome sequencing results of liver and abdominal fat tissues in high-fat-fed and normal-fed broilers were used to identify the differentially expressed and alternative spliced genes in abdominal fat and liver tissues during high-fat feeding. Significantly differentially spliced genes were analyzed by GO functional annotation, KEGG pathway enrichment analysis and Metascape enrichment analysis, and visualization processing was conducted for the significantly differential alternative splicing events, then splicing factors regulating these differential splicing events were analyzed. [Result] Transcriptome sequencing was performed on the abdominal fat and liver tissues of highfat-fed broilers and normal-fed broilers. 233 significantly differentially expressed genes and 349 significantly differentially alternative spliced genes were found in the abdominal fat tissues. It was found that the significantly differential spliced genes were mainly enriched in cell proliferation, such as cell division and cell growth, as well as in pathways related to adipogenesis, such as glycerophospholipid metabolism and insulin signaling pathway. In liver tissues, 276 significantly differentially expressed genes and 224 significantly differential spliced genes were found, and the enrichment analysis of the significantly differential spliced genes revealed that these genes were mainly enriched in biological processes related to cellular metabolism such as protein acetylation, intra-protein amino acid acetylation and mRNA processing and also enriched in adipogenesisrelated pathways such as insulin signaling pathway, glucagon signaling pathway and AMPK signaling pathway. Among the significantly differential spliced genes in abdominal fat and liver, a total of four candidate genes related to influencing abdominal fat deposition traits in broiler were screened, including GPAT4, RELCH, CYP39A1, and PPARA. [Conclusion] The results preliminarily revealed the patterns of RNA alternative splicing regulation in abdominal fat and liver tissues of broilers under high-fat feeding. It was inferred that high-fat feeding may lead to abdominal fat deposition in broilers by affecting the alternative splicing process of genes, which may activate the proliferation of preadipocytes and the metabolism of adipogenesisrelated cells. Regulation of target genes by splicing factors was significantly involved in influencing the process of abdominal fat deposition in broilers. [ABSTRACT FROM AUTHOR]

Copyright of Modern Food Science & Technology is the property of Editorial Office of Modern Food Science & Technology and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

BACKGROUND: Pueraria decoction is a famous prescription of traditional Chinese medicine, which has good anti-inflammatory and analgesic effects. The mechanism of Pueraria decoction in osteoarthritis was analyzed using network pharmacology to obtain the main therapeutic components of Pueraria decoction. OBJECTIVE: To analyze the mechanism of Pueraria decoction in the treatment of osteoarthritis through network pharmacology and animal experiments. METHODS: First, the active ingredients of Pueraria decoction were screened through the Chinese Herbal Medicine Analysis platform (TCMSP) and the genes related to osteoarthritis were collected in the GeneCards database. Second, Cytoscape software was used to construct the “active ingredient-target-disease” network diagram, explore hub genes and analyze gene expression differences. Subsequently, the therapeutic effect of luteolin, one of the main components of Pueraria decoction, was verified in a mouse model of osteoarthritis. Finally, the Kyoto Encyclopedia of Genes and Genomes (KEGG) and the gene ontology (GO) enrichment analyses of the target genes were conducted to further explore the relevant mechanisms. RESULTS AND CONCLUSION: 115 active ingredients and 147 target genes related to osteoarthritis were identified. GO and KEGG analyses found that Pueraria decoction could affect osteoarthritis through a variety of reaction mechanisms and metabolic pathways. Six hub genes and compounds acting on these genes were determined. Luteolin, the main component of Pueraria decoction, could better promote cartilage repair, accelerate the decrease of typy II collagen and inhibit the expression of matrix metalloproteinase 1 and cyclooxygenase 2 in animal experiments. To conclude, Pueraria decoction contains various active ingredients to prevent the progression of osteoarthritis through oxidative stress and metabolic pathways. [ABSTRACT FROM AUTHOR]

To explore the molecular mechanism of fungal elicitors regulating shikonin synthesis, RNA sequencing and analysis were performed on the roots of Arnebia euchroma sterile seedlings after bio-induction by elicitors prepared from Fusarium oxysporum and Rhizoctonia solani. The results showed that, compared with the control group, the Fusarium oxysporum experimental group differentially expressed 1 735 genes; the Rhizoctonia solani experimental group differentially expressed 1 043 genes. GO (gene ontology) analysis revealed that the differentially expressed genes of 2 experimental groups were mainly enriched in cellular processes in biological processes, membrane in cellular components, and catalytic activity in molecular functions. KEGG (kyoto encyclopedia of genes and genomes) analysis revealed that 2 experimental groups were enriched in a large number of differentially expressed genes in the pathways of plant-pathogen interaction, phytohormone signaling pathways and phenylpropanoid synthesis. The same transcription factors were differentially expressed in 2 experimental groups, mainly including bHLH, AP2/ERF-ERF and LOB. The expression of AeGHQH, AeDSH1, AeAP, AePAL, AeDI2, AePGT, AeHMGR and AeG10H genes, which were involved in the synthesis and positive regulation of shikonin, were found to be up-regulated in 2 experimental groups, with more significant up-regulation in the Fusarium oxysporum experimental group. Above results elaborated the response mechanism of Arnebia euchroma in the biological induction of fungal elicitors at the molecular level, which laid a theoretical foundation for the future application of fungal elicitors in the cultivation and production of Arnebia euchroma. [ABSTRACT FROM AUTHOR]

Copyright of Journal of South China Agricultural University is the property of Gai Kan Bian Wei Hui and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

To study the genes regulating the synthesis of sugar esters in tobacco, transcriptome sequencing analysis was performed on tobacco glandular hair cells and bundle sheath cells, and RT-qPCR was used for verification. The results showed that 11 962 differentially expressed genes were obtained, of which 5145 were up-regulated and 6817 were down-regulated. GO annotation of differentially expressed genes showed that the up-regulated genes mainly included biological processes (2265), molecular functions (1169), and cellular components (363), with a total of 3793 GO terms. Based on the assignment of KEGG pathway, the sequence was mapped to 122 metabolic pathways. Glycolysis/gluconeogenesis, starch and sucrose metabolism, phenylpropanoid biosynthesis related to glycoester synthesis were highly enriched, and acyl sugar pathway in glandular hairs was significantly up-regulated. By comparing with the tobacco reference genome, 12 up-regulated acyltransferase genes were identified in glandular hair cells. RT-qPCR results showed that the expression of 11 genes was higher than that of the control. The expression of gene 63826, gene 16194 and gene 37511 increased by 195.79 times, 166.23 times and 132.65 times, respectively. The above 11 genes may be involved in regulating the synthesis of sugar esters in glandular hair cells, providing a basis for further verification of gene function. [ABSTRACT FROM AUTHOR]

The objective of this study is to explore the molecular mechanism of carotenoid metabolism and color mutation of sweetpotato and to study the carotenoid metabolism related genes by RNA-seq technology. Zheshu 81 and its mutant line with color mutation in root skin (from red to yellow) and leaf vein base (from purple to green) were used as the experimental materials. Bioinformatics analysis showed that the carotenoid biosynthesis (ko00906) pathway was significantly enriched in root skin and leaf vein base. The 24 differentially expressed genes (DEGs) and 10 DEGs in the ko00906 were screened from root skin and vein base, among which four were screened in both two parts, respectively. In the upstream pathway of carotenoid anabolism, compared with Zheshu 81, the geranylgeranyl pyrophosphate synthase gene GGDPS (g29773, g38646), lycopene synthase gene PSY (g11630) and Z-carotene isomerase gene Z-ISO (g42608) were significantly up-regulated in mutant line, and GGDPS (g29773) was only expressed in mutant lines. DEGs were not screened in the upstream metabolic pathway of carotenoids in vein base. After the branching point of lycopene cyclization, two ζ-carotene hydroxylase genes CHYB (g33351, g953) were screened in root skin, one up-regulated and the other down-regulated. Two zeaxanthin epoxidase gene ZEP (g41700, g1103) were detected in root skin and vein base, respectively. And g41700 in root skin was significantly down-regulated, and g1103 in vein base was significantly up-regulated. In carotenoid catabolism, CCD8 (g21348), a carotenoid cleavage dioxygenase gene, was significantly up-regulated in root skin of mutant line. Two 9-cis epoxide carotenoid oxygenase genes NCED (g30636, g43412) were down-regulated in root skin and vein base of the mutant line. In addition, ten xanthoxin dehydrogenase ABA2 genes were detected in root skin and vein base, and nine of them were up-regulated. The relative expression levels of some genes by qRT-PCR were highly consistent with those of RNA-seq data. This study provides an important reference for the molecular mechanism of carotenoid metabolism and the analysis of different color mutations in root skin and vein base of sweetpotato. [ABSTRACT FROM AUTHOR]

Copyright of Acta Edulis Fungi is the property of Acta Edulis Fungi and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

BACKGROUND: The granulosa cell state greatly affects the quality of oocytes. As the increased proportion of aged women in assisted reproduction, granulosa cells from patients of different ages are examined at transcript levels in order to better assess oocyte quality. OBJECTIVE: To investigate the expression changes of mRNA and long non-coding RNA in granulosa cells from the young and aged patients. METHODS: Waste cumulus granulosa cells obtained during the assisted reproductive cycle. Young group was in 25-35 years old, and the aged group was in 38- 45 years old. Granulosa cells collected from the young and aged females were analyzed using RNA sequencing, three replications for each group. RESULTS AND CONCLUSION: (1) The RNA sequencing analysis results showed that the average sequencing volume of samples was more than 14 G; the data quality Q30 after quality control was more than 93%; the average mapping rate of data was 98.4%, which indicates that the data had good quality. (2) The results of principal component analysis and correlation analysis showed that the samples of the aged group and the young group could be clearly distinguished. (3) The difference analysis results showed that compared with the young group, a total of 410 differentially expressed mRNAs were detected in the aged group (167 up-regulated and 243 down-regulated). GO analysis results showed that the down-regulated genes were mainly enriched in regulatedexocytosis and the emetabolicprocess. GSEA analysis results showed that secretion-related pathways in the aged group were down-regulated. (4) Compared with the young group, 662 differentially expressed long non-coding RNAs were detected in the aged group, and 1 772 protein-coding genes were directly regulated by these long non-coding RNAs, among which 59 genes overlaped with differentially expressed genes. The results showed that the expression of secretion-related genes and pathways in granulosa cells of the aged group was down-regulated, thus affecting oocyte quality. At the same time, these down-regulated genes were regulated by long non-coding RNA. Therefore, the expression of long non-coding RNA might be related to age. [ABSTRACT FROM AUTHOR]

BACKGROUND: Osteoarthritis is inseparable from synovitis, so it has important clinical significance to explore osteoarthritis pathogenesis based on synovial tissue. OBJECTIVE: To explore the diagnosis and therapeutic targets of osteoarthritis from the perspective of synovium through analyzing the transcriptome data of synovial tissues between patients with osteoarthritis and healthy controls based on bioinformatics methods, as well as to provide follow-up research ideas for osteoarthritis. METHODS: Datasets containing normal and osteoarthritis synovial tissues were screened from Gene Expression Omnibus (GEO) database. GSE55457 and GSE55235 were selected, both of which contained 10 synovial tissue samples of osteoarthritis and 10 synovial tissue samples of healthy controls. GEO2R was utilized to perform differential gene expression analysis of GSE55457 and GSE55235 datasets, and genes with adjusted P values (adj.P) < 0.05 were collected. The online tool Xiantao Academy was used to obtained common up-regulated and down-regulated differentially expressed genes in the two datasets. GO functional annotation and KEGG pathway enrichment analysis for differentially expressed genes were performed. The STRING database was used to perform protein-protein interaction analysis. The results were visualized in Cytoscape software through CytoHubba App by 7 algorithms (BottleNeck, Clossness, Degree, DNNC, EPC, NNC and MCC). The top 10 genes with the highest scores were picked out for each algorithm, and the intersected genes of 7 algorithms were selected as the hub genes of osteoarthritis. RESULTS AND CONCLUSION: 200 common up-regulated differential genes and 124 common down-regulated differential genes were gained from the above two datasets. The results of GO analysis for the 324 differential genes showed that these genes were mainly associated with the DNA-binding transcription factor binding, RNA polymerase II specific DNA-binding transcription factor binding, poly(A) binding, platelets-derived growth factor receptor binding, glucocorticoid receptor binding, etc. KEGG analysis showed that the differential genes were mainly enriched in MAPK signaling pathway, insulin signaling pathway, osteoclast differentiation as well as parathyroid hormone synthesis, secretion and action pathways. Protein-protein interaction network analysis screened two hub genes of osteoarthritis, namely heat shock protein 90α class A member 1 (HSP90AA1) and suppressors of cytokine signaling 3 (SOCS3). These findings confirm that HSP90AA1 and SOCS3 are differentially expressed in synovial tissue of patients with osteoarthritis and healthy subjects, and may serve as surveillance markers and therapeutic target, which provide sound ideas for further study of molecular mechanisms of osteoarthritis. [ABSTRACT FROM AUTHOR]

Copyright of Journal of Henan Agricultural Sciences is the property of Editorial Board of Journal of Henan Agricultural Sciences and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

BackgroundThe rise of single cell RNA sequencing (scRNA-seq) and spatial transcriptome sequencing technologies has allowed for intensive study of lung diseases, but both have been poorly studied in silicosis. ObjectiveTo explore differentially expressed genes DEGs in silicosis macrophages by scRNA-seq combined with spatial transcriptome sequencing and analyze the potential diagnostic genes.MethodsMale C57BL/6 mice (5-6 weeks old, 22-30 g) were randomly divided into 4 groups: normal saline (NS) group for 7 d, NS group for 56 d, SiO2 group for 7 d, and SiO2 group for 56 d, with 1 mouse in each group. A silicosis model was constructed by tracheal drip injection of SiO2 suspension (0.2 g·kg−1, 50 g·cm−2), and the control mice were given the same volume of NS. The right lung was removed for scRNA-seq and the left lung for spatial transcriptome sequencing on day 7 and day 56, respectively. Cell populations were captured using principal component analysis techniques and dimensionality reduction of uniform manifold approximation and projection. The Find Markers function in R language was applied to analyze the DEGs changes of macrophages in two groups of lung tissues, and the corresponding DEGs were subjected to Gene Ontology enrichment analysis and Kyoto Encyclopedia of Genes and Genomes signaling pathway analysis, while STRING and CytoHubba plug-ins of Cytoscape software were applied to protein-protein interaction network analysis to screen out key (Hub) genes. Spatial transcriptome sequencing was used to explore the original location of Hub genes on lung tissue sections and their mapping in lung macrophages. Finally, the correlation of Hub gene expression levels in lung tissues of silicosis patients and mouse silicosis models was verified, the diagnostic efficacy of Hub gene using subject operating characteristic curves (ROC). In vitro experiments by applying cell viability assay were conducted to verify the changes in viability of mouse macrophages (RAW264.7) under SiO2 stimulation. ResultsThe scRNA-seq revealed a total of 20 clusters captured and defined. The results of scRNA-seq and spatial transcriptome sequencing showed an increased number of macrophages in the lung tissue of the SiO2 group compared to the NS group and clustered in the focal areas. Among the 97 macrophage DEGs screened out, 75 were up-regulated genes, and mainly enriched in chemotaxis and migration of neutrophils, chemokine receptor binding, tumor necrosis factor signaling pathway, cytokine-cytokine receptor interaction pathway, and interleukin-17 signaling pathway; and 22 were down-regulated genes, and mainly enriched in late endosomes, peroxisome proliferator-activated receptors signaling pathway, and alcoholic liver disease signaling pathway. A total of 2 core modules and 3 Hub genes were screened out, including Ccl2, Ccl7, and Ptgs2. The scRNA-seq showed that they were expressed at elevated levels in the SiO2 group compared to the NS group and clustered in additional macrophages, and the spatial transcriptome sequencing showed that they clustered in inflammatory areas with nodular lesions. The CCL7 and PTGS2 expressions were increased in the lung tissue of SiO2 patients compared with the healthy subjects, and the areas under the working curve of the subjects were 0.850 and 0.786, respectively. The viability of RAW264.7 cells was enhanced under SiO2 stimulation at 3 h, 6 h, and 12 h compared to those without the stimulation (P

BACKGROUND: In some preclinical and clinical studies, human umbilical cord mesenchymal stem cells have shown promising therapeutic results but limited efficacy. Therefore, enhancing the function of human umbilical cord mesenchymal stem cells by priming provides a new idea for the development of stem cell culture technology. OBJECTIVE: To explore the changes of biological properties and mechanism of human umbilical cord mesenchymal stem cells primed with inflammatory factor tumor necrosis factor-α. METHODS: The human umbilical cord mesenchymal stem cells were cultured to the sixth generation and primed with inflammatory factor tumor necrosis factor-α. The changes of immunomodulatory ability, anti-inflammatory function, surface markers, doubling time, and adipogenesis and osteogenesis ability were evaluated in control group and tumor necrosis factor-α-primed group of human umbilical cord mesenchymal stem cells. In addition, the transcriptome analysis of the two groups was compared to illustrate the precise mechanism. RESULTS AND CONCLUSION: (1) Compared with the control group, different mass concentrations of tumor necrosis factor-α-primed human umbilical cord mesenchymal stem cells inhibited T cell proliferation and promoted Treg cell proliferation significantly. The effect of 1 ng/mL tumor necrosis factor-α was the most significant. (2) Compared with the control group, different mass concentrations of tumor necrosis factor-α-primed human umbilical cord mesenchymal stem cells released lower levels of tumor necrosis factor-α and higher levels of interleukin-10 in inflammatory model in vitro, and their anti-inflammatory ability was significantly enhanced. (3) There was no significant difference in cell multiplication time and surface marker expression between the control group and tumor necrosis factor-α-primed group, and both groups had strong osteogenic and lipogenic differentiation abilities. (4) Transcriptome changes between control group and tumor necrosis factor-α-primed group were mainly reflected in the activation of nuclear factor-κB signaling pathway and tumor necrosis factor-α signaling pathway. (5) These results indicated that tumor necrosis factor-α-primed human umbilical cord mesenchymal stem cells significantly enhanced their immunomodulatory and anti-inflammatory functions. [ABSTRACT FROM AUTHOR]

BACKGROUND: Rheumatoid arthritis is an autoimmune disease. Research on rheumatoid arthritis mainly focuses on its pathogenesis and target therapy. OBJECTIVE: To search for differential genes by bioinformatics analysis of rheumatoid arthritis synovitis gene chip datasets, and to establish and improve the gene regulation network of rheumatoid arthritis. METHODS: GEO2R was used to analyze the differential expression of rheumatoid arthritis chips screened from the database. R language and DAVID were used for gene ontology enrichment analysis and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis of differentially expressed genes. String database was used for protein-protein interaction network analysis. Cystoscape software was used to obtain key genes. qPCR and western blot were used for experimental verification of some key target genes. RESULTS AND CONCLUSION: There were 2 064 differentially expressed genes in the synovial tissue of patients with rheumatoid arthritis, including 625 upregulated genes and 1 439 down-regulated genes. Differentially expressed genes are mainly involved in immune response-activated cell surface receptor signaling pathway, antigen receptor mediated signaling pathway and other biological responses. Ten key target genes, including epidermal growth factor receptor (EGFR), MYC, RELA, ITGB2, LCK, EPHB2, IRF4, NRAS, FN1, and MAPK1, were identified by the protein-protein interaction network analysis. The number of protein interaction lines based on the protein-protein interaction network and Cystoscape algorithm score were used to obtain five genes with high significance, including EGFR, MYC, RELA, ITGB2, and LCK, and the experimental verification of these genes was carried out by qPCR and western blot experiments. The mRNA and protein expression levels of EGFR, MYC, RELA, ITGB2, and LCK genes in the synovial tissue of patients with rheumatoid arthritis were significantly higher than those of the control group, and the expression of EGFR changed most significantly. To conclude, there are distinct gene expression characteristics in the synovial tissue of knee joint after rheumatoid arthritis, and EGFR is the most valuable differentially expressed gene in the synovium of rheumatoid arthritis. [ABSTRACT FROM AUTHOR]

Objective To screen for differentially expressed genes( DEGs) involved in the development of spinal cord injury using bioinformatics methods, and to explore the changes of lipopolysaccharide( LPS) activated BV2 cells DEGs in vitro, in order to provide a new target for the treatment of spinal cord injury. Methods The gene-chip data were downloaded from GEO database, and the samples in the data set were divided into the spinal cord injury Day 2 group and the Day 5 group. R software was used to process the batch effect between the samples from different data sets, and the expression data of the gene-chip was standardized. R software was used to analyze the standardized gene expression matrix to obtain the differential genes. The differential genes were imported into the DAVID database for gene ontology( GO) analysis, and the pathway analysis was performed through the KEGG database. The protein-protein interactions( PPI) network was constructed using STRING protein database, and 10 Hub genes were analyzed by Cystoscope software. Real-time fluorescence quantitative polymerase chain reaction( RT-qPCR) was used to analyze the top two genes with high scores in the Hub gene of BV2 microglia activated by LPS. Results Compared with the Day 2 group, there were 340 DEGs in the Day 5 group. Analysis of the bioinformation showed that DEGs were enriched in cell inflammatory response and substance metabolism. A total of 10 central nodes were obtained through module analysis with STRING software. KEGG re-analysis of 10 genes revealed that CXCL10,CCR3,CCR10 and CCL2 genes were significantly enriched in chemokine signaling pathway and cytokine-cytokine receptor interaction. In vitro experiment, compared with normal group, the expression levels of inflammatory cytokines [interleukin-1β( IL-1β),IL-6 and tumor necrosis factor α( TNF-α) ] and mRNA expressions of chemokines CXCL10,CCR9/10 and CCL2 were increased in the LPS group, with statistical significance( P＜0.05) .Conclusion CXCL10,CCR3,CCR10 and CCL2 chemokine signaling pathways and cytokine-cytokine receptor interactions may be closely related to the development mechanism of spinal cord injury.CXCL10,CCR9/10 and CCL2 mediate the inflammatory responses of BV2 cells. [ABSTRACT FROM AUTHOR]

The experiment was to study the effect of dietary chromium yeast on sheep liver transcriptional group. Fourteen Duhu hybrid sheep with similar body weight and good health from 5 to 6 months old were randomly divided into two groups, which were control group and the yeast chromium group, with seven sheep in each group. In the experiment, 147 348 445 and 148 419 153 data obtained from yeast chromium treatment group and control group were screened respectively, the selected differential genes were analyzed by GO functional annotation and KEGG enrichment analysis, and the differentially expressed genes were verified by real-time fluorescence quantitative PCR. The results showed that dietary chromium yeast could improve the slaughtering performance of sheep. Chromium yeast can regulate T cells by upregulating CD80 and inhibiting CD86. Chromium yeast can improve the body's ability to adapt to heat stress. The study indicates that the addition of yeast chromium in sheep diet can protect the body liver of sheep from damage. [ABSTRACT FROM AUTHOR]

Objective: To screen the differentially expressed genes in type 2 diabetes mellitus model rats by transcriptomics sequencing, and to preliminarily explore the relationship between the differentially expressed genes and the syndrome manifestations of deficiency of both Qi and Yin. Methods: Eighteen male SD rats were randomly selected as control group, and the other rats were fed with high-fat and high-sugar diet and injected with streptozotocin (STZ) in the abdomen to establish the type 2 diabetes models. On the 6th week, 31 successfully modeling rats were divided into model group (n=14) and drug evidence group (n=17) according to the principle of blood glucose and body mass balance. The rats in model group were fed with high sugar and high fat diet sequentially. The rats in drug evidence group were given Xiaokeling 2. 2 g·kg-1·d-1 by gavage; the experiment last for 21 weeks. The body masses, food intakes, water intakes, mental state scores, sport scores, foot temperatures, grasping force, pulse amplitudes, respiratory rates, and tongue image integral of the rats were detected and the physiological signs of the rats during model preparation were evaluated. The fasting blood glucose (FBG) levels of the rats in various groups were detected by blood glucose meter. After the last administration, the rats were anesthetized, the blood samples were collected and the serum samples were separated. The levels of triglyceride (TG) and total cholesterol (TC) of the rats were detected by oxidase method. The levels of high density lipoprotein cholesterol (HDL-c) and low density lipoprotein cholesterol (LDL-c) of the rats were detected by direct method, and the levels of CD4, CD8, cyclic adenosine monophosphate (cAMP), and cyclic guanosine monophosphate (cGMP) of the rats were detected by enzyme-linked immunosorbent assay (ELISA) method. The liver tissue of the rats was obtained, and the differentially expressed genes between model group and control group and between model group and drug evidence group were screened by transcriptomic sequencing. Results: Compared with blank group, the physiological signs of the rats in model group were basically consistent with the syndrome manifestations of Qi and Yin deficiency; compared with model group, the some physiological signs of Qi and Yin deficiency of the rats in drug evidence group were significantly improved. Compared with blank group, the FBG, serum TC, TG and LDL-c levels of the rats in model group were significantly increased (P<0. 01), and the serum HDL-c level had no significant difference (P>0. 05); compared with model group, there were no significant differences in the above indexes of the rats in drug evidence group (P>0. 05). Compared with blank group, the level of serum CD4 and the CD4/CD8 ratio of the rats in model group were significantly decreased (P<0. 01), while the level of serum CD8 had no significant difference (P>0. 05); the cAMP level in serum and the ratio of cAMP/ cGMP were obviously increased (P<0. 01), while the cGMP level in serum was significantly decreased (P<0. 01); compared with model group, the level of serum CD4 and the CD4/CD8 ratio of the rats in drug evidence group were remarkably increased (P<0. 01), the cGMP level in serum was increased (P< 0. 01) and the cAMP/cGMP ratio was significantly decreased (P<0. 01), the cAMP level in serum had no significant difference (P>0. 05). Compared with blank group, the up-regulated expressed genes of the rats in model group mainly included early growth response factor 2 (Egr2), insulin-like growth factor binding protein 1 (Igfbp1) and a disintegrin and metallopeptidase with thrombospondin motifs 4 (Adamts4); the down-regulated expressed genes mainly included G0/G1 switch 2 (G0s2), midline 1 interaction protein 1 (Mid1ip1), and basic helix-loop-helix family e40 (Bhlhe40); compared with model group, the levels of the above differentially expressed genes in drug evidence group showed the opposite trend. Conclusion: The syndrome of type 2 diabetes mellitus combined with deficiency of Qi and Yin is associated with up-regulation of Egr2, Igfbp1 and Adamts4 and down-regulation of G0s2, Mid1ip1, and Bhlhe40 [ABSTRACT FROM AUTHOR]

【Objective】The present study aimed to screen the key genes regulating back fat deposition of large Diqing Tibetan pigs(TPs) at different growth stages and analyze their regulatory pathway.【Method】Transcriptome sequencing of back fat tissues of TPs with body weight up to 40, 80 and 120 kg was performed, and 3 pigs as a group. The sequencing data were spliced, compared, annotated and analyzed. Differential genes related to back fat deposition were screened by functional enrichment analysis, STEM analysis and differential gene interaction network analysis.【Result】There were 845 and 558 significantly differentially expressed genes(DEGs) in 10-40 kg(stage 1) vs. 40-80 kg(stage 2), 40-80 kg vs. 80-120 kg(stage 3), respectively. STEM analysis of differential genes showed that the genes of modules 0,3 and 4 were down-regulated with increasing body weight of TPs, and the genes of modules 14 were up-regulated firstly and then slightly down-regulated. Differential gene interaction network analysis showed that PTGER3, CPT1B and LPIN3 genes were located in the core of the gene interaction network constructed by genes in modules 0,3 and 4. The down-regulation of PTGER3 inhibited lipolysis and promoted adipocyte enlargement, the down-regulation of CPT1B reduced fatty acid oxidation and increased triglycerides, and the down-regulation of LPIN3 maintained lipid homeostasis. AACS, SOCS3, AQP3 and RPS6KA1 were located at the core of gene interaction network constructed by genes in module 14. The up-regulation of AACS promoted adipocyte differentiation and the increase in number of adipocytes, the up-regulation of SOCS3 and RPS6KA1 promoted adipogenesis, and the up-regulation of AQP3 promoted the increase of triglycerides in adipocytes. This was consistent with the result that backfat thickness of TPs increased significantly with the increase of body weight, but the increase of backfat thickness at stage 1 vs. stage 2 was greater than that at stage 2 vs. stage 3. There were 15 differential genes such as PTGER3 and AACS were selected for qPCR verification, and the quantitative verification results of 15 genes were consistent with the transcriptome sequencing results.【Conclusion】In the study, 15 potential candidate genes that regulate backfat thickness of TPs are screened to provide reference for the genetic improvement of TPs [ABSTRACT FROM AUTHOR]

Copyright of Journal of China Medical University is the property of Journal of China Medical University Editorial Office and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Objective To identify the key genes and targeted protection methods affecting the survival of human islets. Methods Using bioinformatics method, the gene expression profile (GSE53454) was selected through screening and comparison from Gene Expression Omnibus(GEO) database. GEO2R tool was employed to screen the differentially expressed gene(DEG) between the human islets exposed (exposure group) and non-exposed (non-exposure group) to interleukin (IL)-1β and interferon (IFN)-γ for 24, 48 and 72 h, respectively. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed by DAVID. Protein-protein interaction (PPI) network was constructed by STRING and Cytoscape apps. Results A total of 69 up-regulated DEGs and 2 downregulated DEGs were identified. GO analysis showed that during the biological process, DEGs were enriched in the aspects of virus defense and inflammatory response. In cellular components, DEGs were significantly enriched in extracellular space, outside plasma membrane and extracellular regions. Regarding molecular functions, DEGs were significantly enriched in chemokine activity and cytokine activity. KEGG analysis revealed that DEGs were mainly enriched in multiple signaling pathways, such as cytokine-cytokine receptor interaction, virus protein-cytokine and cytokine-receptor interaction, etc. Ten key genes (STAT1, CXCL10, IRF1, IL6, CXCL9, CCL5, CXCL11, ISG15, CD274, IFIT3) with high connectivity were selected by STRING analysis, all of which were significantly up-regulated in human islets exposed to IL-1β and IFN-γ. Six genes (STAT1, CXCL10, CXCL9, CXCL11, CCL5, IL6) were screened by KEGG enrichment analysis, mainly in Toll-like receptor signaling pathway. Conclusions STAT1, CXCL10, CXCL9, CXCL11, CCL5 and IL6 are the key genes affecting the survival of human islets, which are mainly enriched in Toll-like receptor signaling pathway and act as important targets for islet protection. [ABSTRACT FROM AUTHOR]

Copyright of Journal of South China Agricultural University is the property of Gai Kan Bian Wei Hui and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

ObjectiveTo explore the differential expression of messenger RNA （mRNA） in myocardial tissues of rats with sudden coronary death （SCD）, and to provide ideas for the forensic identification of SCD.MethodsThe rat SCD model was established, and the transcriptome sequencing was performed by next-generation sequencing technology. Differentially expressed genes （DEGs） in myocardial tissues of SCD rats were screened by using the R package limma. A protein-protein interaction （PPI） network was constructed by using the STRING database and Cytoscape 3.8.2 on DEG, and hub genes were screened based on cytoHubba plug-in. Finally, the R package clusterProfiler was used to analyze the biological function and signal pathway enrichment of the selected DEG.ResultsA total of 177 DEGs were associated with SCD and were mainly involved in the renin-angiotensin system and PI3K-Akt signaling pathway. The genes including angiotensinogen （AGT）, complement component 4a （C4a）, Fos proto-oncogene （FOS） and others played key roles in the development of SCD.ConclusionGenes such as AGT, C4a, FOS and other genes are expected to be potential biomarkers for forensic identification of SCD. The study based on mRNA expression profile can provide a reference for forensic identification of SCD.

Copyright of Journal of China Medical University is the property of Journal of China Medical University Editorial Office and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Objective To identify M1 macrophage-related genes in rejection after kidney transplantation and construct a risk prediction model for renal allograft survival. Methods GSE36059 and GSE21374 datasets after kidney transplantation were downloaded from Gene Expression Omnibus (GEO) database. GSE36059 dataset included the samples from the recipients with rejection and stable allografts. Using this dataset, weighted gene co-expression network analysis (WGCNA) and differential analysis were conducted to screen the M1 macrophage-related differentially expressed gene (M1-DEG). Then, GSE21374 dataset (including the follow-up data of graft loss) was divided into the training set and validation set according to a ratio of 7∶3. In the training set, a multivariate Cox’s model was constructed using the variables screened by least absolute shrinkage and selection operator (LASSO), and the ability of this model to predict allograft survival was evaluated. CIBERSORT was employed to analyze the differences of infiltrated immune cells between the high-risk group and low-risk group, and the distribution of human leukocyte antigen (HLA)-related genes was analyzed between two groups. Gene set enrichment analysis (GSEA) was used to further clarify the biological process and pathway enrichment in the high-risk group. Finally, the database was employed to predict the microRNA (miRNA) interacting with the prognostic genes. Results In the GSE36059 dataset, 14 M1-DEG were screened. In the GSE21374 dataset, Toll-like receptor 8 (TLR8), Fc gamma receptor 1B (FCGR1B), BCL2 related protein A1 (BCL2A1), cathepsin S (CTSS), guanylate binding protein 2(GBP2) and caspase recruitment domain family member 16 (CARD16) were screened by LASSO-Cox regression analysis, and a multivariate Cox’s model was constructed based on these 6 M1-DEG. The area under curve (AUC) of receiver operating characteristic of this model for predicting the 1- and 3-year graft survival was 0.918 and 0.877 in the training set, and 0.765 and 0.736 in the validation set, respectively. Immune cell infiltration analysis showed that the infiltration of rest and activated CD4+ memory T cells, γδT cells and M1 macrophages were increased in the high-risk group (all P<0.05). The expression level of HLA I gene was up-regulated in the high-risk group. GSEA analysis suggested that immune response and graft rejection were enriched in the high-risk group. CTSS interacted with 8 miRNA, BCL2A1 and GBP2 interacted with 3 miRNA, and FCGR1B interacted with 1 miRNA. Conclusions The prognostic risk model based on 6 M1-DEG has high performance in predicting graft survival, which may provide evidence for early interventions for high-risk recipients. [ABSTRACT FROM AUTHOR]

Copyright of Forest Research is the property of Forest Research Editorial Office and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Objective To screen the differentially expressed genes of Xuling Jiangu Prescription in osteoporosis model rats by gene expression profile chip. Methods 15 rats were divided into three groups according to random number method : sham operation group, model group and Xuling Jiangu Fang group, with 5 rats in each group.The experimental group was given Xuling Jiangu Prescription according to body weight, and the other two groups were given the same volume of normal saline by intragastric administration, once a day, for 13 consecutive weeks. After 13 weeks, the femur of the left leg of the rat was taken for gene expression profile microarray detection, and the differentially expressed genes between groups were obtained by microarray analysis, and their functions and pathways were analyzed. Results Ten genes with significantly decreased expression after modeling but significantly increased expression after medication were screened, and 218 genes with significantly increased expression after modeling but significantly decreased expression after medication were screened under the conditions of | log2 Fold change | ≥ 1, Q < 0. 05). Enrichment analysis of KEGG signaling pathway revealed that PI3K/Akt pathway was one of the key pathways. The differential genes RplpO and Cnpy2 were further screened under the following conditions; | log2 Fold change | ≥ 2, q < 0. 01). Conclusion The therapeutic mechanism of Xuling Jiangu Prescription may be related to PI3K/AKT signaling pathway, RplpO and Cnpy2 genes. [ABSTRACT FROM AUTHOR]

Copyright of Journal of Henan Agricultural Sciences is the property of Editorial Board of Journal of Henan Agricultural Sciences and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Copyright of Acta Edulis Fungi is the property of Acta Edulis Fungi and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Objective To screen and analyze the differentially expressed genes(DEGs)between human lung adenocarcinoma tissues and normal adjacent tissues by bioinformatics methods, and to screen the key genes———Hub genes in the occurrence and development of lung adenocarcinoma, and to provide candidate genes for the follow-up study. Methods The lung adenocarcinoma gene chip datasets———GSE63459 and GSE27262 were downloaded from the GEO database. The DEGs of human lung adenocarcinoma tissues and normal adjacent tissues were screened by GEO2R. Then DAVID database was used for gene ontology enrichment analysis of DEGs and KOBAS database was used for pathway enrichment analysis of KEGG. The protein interaction network was constructed and Hub genes were screened by STRING database and Cytoscape software, and then Hub genes were further screened by Oncomine database. Kaplan-Meier plotter was used for survival analysis. Results A total of 22 significantly up-regulated DEGs were screened out. And three Hub genes, E-cadherin 1, human epidermal growth factor receptor and cell tyrosine kinase were identified. The three Hub genes were significantly associated with the overall survival of lung adenocarcinoma patients. Conclusion The three Hub genes, E-cadherin 1, human epidermal growth factor receptor and cell tyrosine kinase may be closely related to the occurrence and development of human lung adenocarcinoma. It may be a new target for the pathogenesis, prognosis and treatment of lung adenocarcinoma. [ABSTRACT FROM AUTHOR]

BACKGROUND: The incidence of osteoarthritis is increasing as the population ages, and there is still no effective treatment. Gene chip technology has been widely used in the diagnosis and treatment of diseases. OBJECTIVE: To identify the key genes in osteoarthritis by using integrative bioinformatics and weighted gene co-expression network analysis (WGCNA) and to investigate its mechanism. METHODS: Four original data sets of synovial tissue chips in osteoarthritis patients were downloaded from Gene Expression Omnibus database, and the immune infiltration was analyzed by CIBERSORT algorithm. Differentially expressed genes were screened by R-language software. Gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) were used to analyze the selected differentially expressed genes. The text files of these differentially expressed genes were obtained through the online tool STRING (http://string-db.org/) and were imported into the Cytoscape software to edit the visual protein-protein interaction network. R-language software was used to build a bar chart of differentially expressed genes to obtain the top 10 differentially expressed genes in degree values. The four chip data sets were integrated to screen out the genes with the highest correlation of gene co-expression module by WGCNA algorithm, and the intersection genes were screened by Venn analysis method. The synovial tissues of four patients with osteoarthritis and four patients with joint trauma were collected for quantitative real-time PCR verification. RESULTS AND CONCLUSION: (1)A total of 107 differentially expressed genes were screened out, including 46 up-regulated genes and 61 down-regulated genes. (2)The gene ontology enrichment results showed that differentially expressed genes were mainly involved in biological processes such as positive regulation of ossification and cell adhesion. KEGG pathways were mainly enriched in rheumatoid arthritis pathways, nuclear factor-κB signaling pathways, and receptor protein tyrosine kinase B signaling pathways. Immune infiltration results indicated that the contents of M0 macrophages and M2 macrophages were relatively high in the synovial tissue of patients with osteoarthritis. (3)The obtained intersection genes included matrix metalloproteinase 1, tissue inhibitor of metalloproteinase 4, laminin subunit alpha 3, and follistatin 3. The results of quantitative real-time PCR confirmed that there were significant differences in the expression levels of tissue inhibitor of metalloproteinase 4, laminin subunit alpha 3, and follistatin 3 between the synovial tissue samples from patients with osteoarthritis and those with joint trauma. (4)Therefore, tissue inhibitor of metalloproteinase 4, laminin subunit alpha 3, and follistatin 3 may be therapeutic targets for osteoarthritis. [ABSTRACT FROM AUTHOR]

BACKGROUND: MicroRNAs (miRNAs) have been confirmed to be involved in the pathogenesis, prevention, and treatment of osteonecrosis of the femoral head. However, the mechanism is not yet elucidated. OBJECTIVE: To screen miRNA-mRNA regulatory pairs related to osteonecrosis of the femoral head, to explain its potential mechanism, based on microarray data in the GEO database. METHODS: The miRNA microarray dataset (GSE89587) and mRNA microarray dataset (GSE74089) were retrieved from NCBI GEO database. Then, we identified the differentially expressed miRNAs and mRNAs for each dataset by the Limma package in R software. Potential downstream targets of these differentially expressed miRNAs were predicted using miRDB, miRTarbase, and TargetScan databases. Based on the relationship among miRNA and mRNA, the miRNA- mRNA regulatory network was visualized using Cytoscape. Next, gene ontology function and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses of target genes in the regulatory network were carried out by clusterProfiler package in R software. Protein-protein interaction network was constructed by using the Search Tool for the Retrival of Interacting Genes/Protein (STRING) database. RESULTS AND CONCLUSION: In total, 23 differentially expressed miRNAs, including 10 upregulated (e.g., hsa-miR-4325, hsa-miR-3654) and 13 downregulated miRNAs (e.g., hsa-miR-4680-5p, hsa-miR-4711-3p), were identified. Totally 3992 differentially expressed mRNAs, including 2503 upregulated (e.g., TGFBI, AMTN) and 1489 downregulated (e.g., MSMP, FLJ35424) mRNAs, were screened by the Limma package in R software. 255 miRNA downstream target genes predicted co-existed in miRDB, miRTarbase, and TargetScan databases, and 10 miRNAs (e.g., hsa-miR-3920, hsa-miR-3675-5p) and 34 mRNAs (e.g., MAPK6, SP1 ) were sorted out to construct regulatory networks. These screened targets mainly were significantly enriched in the regulation of mRNA stability and transforming growth factor-β signaling pathway and autophagy. DDX3X, HNRNPC, and SP1 were analyzed as the hub genes in protein-protein interactions, which may be the target genes for osteonecrosis of the femoral head. In summary, the miRNA-mRNA regulatory network constructed in this study clarifies that miR-4725-3p may target ONFH by inhibiting SP1-mediated transforming growth factor-β signaling pathway, providing a strong data support and research direction for the prevention and treatment of ONFH [ABSTRACT FROM AUTHOR]