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Pepper mild mottle virus (PMMoV), a member of the genus Tobamovirus , causes severe damage on pepper worldwide. Despite its impact, the pathogenicity mechanisms of PMMoV and the pepper plant's response to infection remain poorly understood. Here, we compared the transcriptomic changes in a susceptible pepper inbred line 21C241 with a resistant inbred line 21C385 seedlings, following systemic PMMoV infection using RNA sequencing. Our results revealed that PMMoV induced more pronounced mosaic symptoms and higher viral accumulation levels in the susceptible line 21C241 compared to the resistant line 21C385. We identified 462 and 401 differentially expressed genes (DEGs) in the systemically-infected leaves of the susceptible and resistant lines, respectively, when compared to their healthy counterparts. The majority of these DEGs were involved in photosynthesis and the biosynthesis of secondary metabolites, with 28 DEGs exhibiting distinct expression patterns between the two lines. Notably, the expression level of the chlorophyll a-b binding protein 13 (CAB13) was significantly up-regulated in resistant line 21C385 following PMMoV infection. Functional analysis through silencing of CAB13 in pepper and Nicotiana benthamiana demonstrated a reduction in PMMoV accumulation, suggesting that CAB13 plays a positive role in facilitating PMMoV infection in pepper plants. Taken together, our findings highlight the distinct gene expression profiles between susceptible and resistant pepper lines in response to PMMoV infection and confirm the proviral role of CAB13. This study provides valuable insights into the molecular mechanisms underlying resistance and susceptibility in pepper plants and may inform future strategies for disease management. [ABSTRACT FROM AUTHOR]

Objective: Probiotics are living microorganisms that can provide health benefits when consumed. Here, we investigated the effects of probiotics on gene expression in the spleen of mice using RNA-sequencing analysis between negative control and probiotic groups (including 4 Lactobacillus strains: Lactobacillus fermentum, L. casei, L. plantarum, and L. brevis). Methods: Mice exposed with probiotic in 4 weeks by intragastric administration. Then, spleen tissues of the control and probiotics groups were collected on days 14 and 28 for RNA sequencing. Results: In total, 665, 186, and 81 differentially expressed genes (DEGs) were significantly expressed on day 14 vs control, day 28 vs control groups, and probiotics day 28 vs day 14 groups, respectively. On the other hand, 12 toll-like receptor genes underwent additional validation through quantitative real-time polymerase chain reaction (qRT-PCR), affirming the increased alignment between qRT-PCR and RNA-Seq findings. In addition, the Kyoto encyclopedia of genes and genomes and gene ontology analyses revealed that the DEGs were predominantly enriched in defense responses to pathogens, including inflammatory bowel diseases, malaria, leukaemia virus 1, and herpes virus, as well as immune processes related to immune response and signal transduction. This study represents the first investigation into mice's gene expression in the spleen exposed to probiotics using Lactobacillus spp. isolated from a field strain in Vietnam. Conclusion: Our results provide valuable insights into the impacts and functions of probiotics on mammalian development, offering crucial information for the potential therapeutic use of probiotics in defending against pathogens in Vietnam. The findings from this study highlight the potential of probiotics in modulating gene expression in the spleen, which may have implications for immune function and overall health in mice. [ABSTRACT FROM AUTHOR]

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]

With the aim of enhancing plants' ability to respond to pathogenic fungi, this study focuses on disease resistance genes. We commenced a series of investigations by capitalizing on the pronounced differences in resistance to Fusarium wilt between resistant and susceptible varieties. Through an in-depth exploration of the metabolic pathways that bolster this defense, we identified genes associated with resistance to Fusarium oxysporum f. sp. cubense (Foc). For our analysis, root tissues from seedlings that had been in contact with Fusarium oxysporum for four days were harvested, including both infected and uninfected samples, which served as our study specimens. The crude extract treatment led to a significant increase in malondialdehyde (MDA) levels, lignin content, and phenylalanine ammonia lyase (PAL) activity. Conversely, there was a notable decline in protein content, ergosterol levels, and pectinase activity. In the control group, it was observed that 4,474 genes in the resistant varieties were significantly up-regulated compared to the susceptible varieties. The functional annotation of these differentially expressed genes (DEGs) emphasized their predominant participation in biological processes. Further analysis via the KEGG database revealed that 14 DEGs in the susceptible varieties were particularly enriched in pathways related to plant hormone signaling. Through the perspective of transcriptome data, we focused on genes associated with lignin and cell wall development for Q-PCR validation. Notably, the expression levels of Macma4_02_g07840 (COMT) and Macma4_10_g06530 (CCOAOMT) were relatively elevated. Our findings suggest that the resistance of these varieties to wilt infection can be ascribed to the accumulation of lignin metabolites, which inhibits pathogenic fungus growth by restricting the synthesis of cellular metabolites. The evidence documented in our research provides a framework for a deeper understanding of the disease resistance mechanisms in bananas, laying a solid theoretical foundation for future studies in this area. [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]

Objectives: Endometriosis is a common chronic disease in childbearing women and a major cause of infertility. Our study aimed to identify and validate a novel gene signature for diagnosing endometriosis based on histone-related genes (HRGs), and to investigate their biological functions in endometriosis. Material and methods: RNA sequence data were downloaded from the Gene Expression Omnibus database, and HRGs were retrieved from the GeneCards database. We identified differentially expressed genes using the limma package, and constructed a diagnostic model using the rms package. Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) enrichment analyses were performed for visualization, annotation, and integrated discovery. Subsequently, we validated the model using the recall and decision curve analysis (DCA). Additionally, we analyzed the immune microenvironment features using CIBERSORT. Results: A total of 18 differentially expressed HRGs were identified in patients with endometriosis compared with controls. GO and KEGG enrichment was mainly in spindle organization, positive regulation of the cell cycle process, progesterone-mediated oocyte maturation, and cellular senescence and cell cycle. We obtained a signature of four HRGs (JUNB, FRY, LMNB1, and SPAG1). DCA revealed that the diagnostic model benefits patients with endometriosis, regardless of the incidence. CIBERSORT analysis showed that the number of plasma cells increased significantly in endometriosis samples from all four datasets. Conclusions: Our findings provide novel insights into the function of HRGs in the development of endometriosis and identify a new signature of four HRGs that may serve as valuable diagnostic markers and therapeutic targets for this disease. [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]

Objectives: Identifying the specific biomarkers and molecular signatures of MM might provide novel evidence for MM prognosis and targeted therapy. Methods: Bioinformatic analyses were performed through GEO and TCGA datasets. The differential expression of HIST1H2BH in MM sample was validated by the qRT-PCR. And the CCK-8 assay was performed to detect the proliferation activity of HIST1H2BH on MM cell lines. Results: A total of 793 DEGs were identified between bone marrow plasma cells from newly diagnosed myeloma and normal donors in GSE6477. Among them, four vital genes (HIST1H2AC, HIST1H2BH, CCND1 and TCF7L2) modeling were constructed. The increased HIST1H2BH expression was correlated with worse survival of MM based on TCGA datasets. The transcriptional expression of HIST1H2BH was significantly up-regulated in primary MM patients. And knockdown HIST1H2BH decreased the proliferation of MM cell lines. Conclusions: We have identified up-regulated HIST1H2BH in MM patients associated with poor prognosis using integrated bioinformatical methods. [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]

Hypertensive and ischemic heart diseases have high morbidity all over the world, and they primarily contribute to heart failure associated with high mortality. Cardiac remodeling, as a basic pathological process in heart diseases, is mainly comprised of cardiac hypertrophy and fibrosis, as well as cell death which occurs especially in the ischemic cardiomyopathy. Myocardial remodeling has been widely investigated by a variety of animal models, including pressure overload, angiotensin II stimulation, and myocardial infarction. Pressure overload can cause compensatory cardiac hypertrophy at the early stage, followed by decompensatory hypertrophy and heart failure at the end. Recently, RNA sequencing and differentially expressed gene (DEG) analyses have been extensively employed to elucidate the molecular mechanisms of cardiac remodeling and related heart failure, which also provide potential targets for high-throughput drug screenings. In this review, we summarize recent advancements in gene expression profiling, related gene functions, and signaling pathways pertinent to myocardial remodeling induced by pressure overload at distinct stages, ischemia–reperfusion, myocardial infarction, and diabetes. We also discuss the effects of sex differences and inflammation on DEGs and their transcriptional regulatory mechanisms in cardiac remodeling. Additionally, we summarize emerging therapeutic agents and strategies aimed at modulating gene expression profiles during myocardial remodeling. [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.

Abstract The hypothalamus is the coordination center of the sheep (Ovis aries) endocrine system and plays an important role in the reproductive processes of sheep. However, the specific mechanism by which the hypothalamus affects sheep reproductive performance remains unclear. In this study, the hypothalamus tissues of high-reproduction small-tailed Han sheep and low-reproduction Wadi sheep were collected, and full-length transcriptome sequencing by Oxford Nanopore Technologies (ONT) was performed to explore the key functional genes associated with sheep fecundity. The differentially expressed genes (DEGs) were screened and enriched using DESeq2 software through Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). Approximately 41.75 million clean reads were obtained from the hypothalamus tissues of high- and low-reproduction sheep, after quality control, 32,194,872 high-quality full-length sequences and 2,114 DEGs were obtained, including 1,247 upregulated genes and 867 downregulated genes (P adjust 1). Some DEGs were enriched in oocyte meiosis, progesterone-mediated oocyte maturation, estrogen signaling pathway, GnRH signaling pathway and other development-related signaling pathways. The constructed protein-protein interaction (PPI) networks identified the reproduction-related genes, such as GSK3B, PPP2R1B, and PPP2CB. The results of this study will enrich and supplement the genomic information available for small-tailed Han sheep and Wadi sheep, as well as expand the understanding of the molecular mechanisms underlying the regulation of animal reproduction by the hypothalamus, and they also provided reference data for further investigations on the mechanism of high reproduction in sheep.

Abstract To investigate mRNA Expression profile and associated signaling pathways in the treatment of diabetic foot ulcer healing by tibial cortex transverse distraction. Tissue samples were collected from the wound edge before and after the surgery. After reference genome transcriptome sequencing and subsequent bioinformatics analysis, the differentially expressed genes and related pathways were explored, and functional analysis of important genes and pathways was conducted. qRT-PCR was used to verify the significantly expressed genes-HLA-DRB1, HLA-DRB5, CXCL5 and IGFL1. There were 2441 significantly up-regulated and 3904 significantly down-regulated genes in the postoperative group. The qRT-PCR results showed the expression of HLA-DRB1, HLA-DRB5 and CXCL5 was consistent with the transcriptional sequencing results. CXCL5 and CXCL6 differentially up-regulated genes are involved in the process of neovascularization, and HLA-DRB1 is involved in the improvement of the degree of diabetic peripheral nerve degeneration. Pathway analysis showed that differential genes were most significantly enriched in Adherens junction, Inflammatory mediator regulation of TRP channels and Wnt signaling pathway. Inflammatory mediator regulation of TRP channels is involved in the improvement of peripheral neurodegeneration, VEGF signaling pathway is involved in the process of neovascularization, and Wnt signaling pathway is involved in the process of bone healing. Significantly up-regulated CXCL5 and CXCL6 and enriched VEGF signaling pathway analyzed are involved in postoperative lower limb neovascularization. The HLA-DRB1 and the enriched Inflammatory mediator regulation of TRP channels may be related to the improvement of postoperative peripheral neurodegeneration. The differentially expressed genes and related pathways can provide objective basis for further mechanism study.

Abstract Background Koala retrovirus (KoRV), a major pathogen of koalas, exists in both endogenous (KoRV-A) and exogenous forms (KoRV-A to I and K to M) and causes multiple disease phenotypes, including carcinomas and immunosuppression. However, the direct association between the different KoRV subtypes and carcinogenesis remains unknown. Differentially expressed gene (DEG) analysis of peripheral blood mononuclear cells (PBMCs) of koalas carrying both endogenous (KoRV-A) and exogenous (KoRV-A, B, and C) subtypes was performed using a high-throughput RNA-seq approach. PBMCs were obtained from three healthy koalas: one infected with endogenous (KoRV-A; Group I) and two infected with exogenous (KoRV-B and/or KoRV-C; Group II) subtypes. Additionally, spleen samples (n = 6) from six KoRV-infected deceased koalas (K1- K6) and blood samples (n = 1) from a live koala (K7) were collected and examined to validate the findings. Results All koalas were positive for the endogenous KoRV-A subtype, and eight koalas were positive for KoRV-B and/or KoRV-C. Transcription of KoRV gag, pol, and env genes was detected in all koalas. Upregulation of cytokine and immunosuppressive genes was observed in koalas infected with KoRV-B or KoRV-B and -C subtypes, compared to koalas infected with only KoRV-A. We found 550 DEG signatures with significant (absolute p 1.5) dysregulation, out of which 77.6% and 22.4% DEGs were upregulated (log2FC > 1.5) and downregulated (log2FC

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]

The hypothalamus is the coordination center of the sheep (Ovis aries) endocrine system and plays an important role in the reproductive processes of sheep. However, the specific mechanism by which the hypothalamus affects sheep reproductive performance remains unclear. In this study, the hypothalamus tissues of high-reproduction small-tailed Han sheep and low-reproduction Wadi sheep were collected, and full-length transcriptome sequencing by Oxford Nanopore Technologies (ONT) was performed to explore the key functional genes associated with sheep fecundity. The differentially expressed genes (DEGs) were screened and enriched using DESeq2 software through Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). Approximately 41.75 million clean reads were obtained from the hypothalamus tissues of high- and low-reproduction sheep, after quality control, 32,194,872 high-quality full-length sequences and 2,114 DEGs were obtained, including 1,247 upregulated genes and 867 downregulated genes (P adjust < 0.05, |log2FC|>1). Some DEGs were enriched in oocyte meiosis, progesterone-mediated oocyte maturation, estrogen signaling pathway, GnRH signaling pathway and other development-related signaling pathways. The constructed protein-protein interaction (PPI) networks identified the reproduction-related genes, such as GSK3B, PPP2R1B, and PPP2CB. The results of this study will enrich and supplement the genomic information available for small-tailed Han sheep and Wadi sheep, as well as expand the understanding of the molecular mechanisms underlying the regulation of animal reproduction by the hypothalamus, and they also provided reference data for further investigations on the mechanism of high reproduction in sheep. [ABSTRACT FROM AUTHOR]

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Background: Koala retrovirus (KoRV), a major pathogen of koalas, exists in both endogenous (KoRV-A) and exogenous forms (KoRV-A to I and K to M) and causes multiple disease phenotypes, including carcinomas and immunosuppression. However, the direct association between the different KoRV subtypes and carcinogenesis remains unknown. Differentially expressed gene (DEG) analysis of peripheral blood mononuclear cells (PBMCs) of koalas carrying both endogenous (KoRV-A) and exogenous (KoRV-A, B, and C) subtypes was performed using a high-throughput RNA-seq approach. PBMCs were obtained from three healthy koalas: one infected with endogenous (KoRV-A; Group I) and two infected with exogenous (KoRV-B and/or KoRV-C; Group II) subtypes. Additionally, spleen samples (n = 6) from six KoRV-infected deceased koalas (K1- K6) and blood samples (n = 1) from a live koala (K7) were collected and examined to validate the findings. Results: All koalas were positive for the endogenous KoRV-A subtype, and eight koalas were positive for KoRV-B and/or KoRV-C. Transcription of KoRV gag, pol, and env genes was detected in all koalas. Upregulation of cytokine and immunosuppressive genes was observed in koalas infected with KoRV-B or KoRV-B and -C subtypes, compared to koalas infected with only KoRV-A. We found 550 DEG signatures with significant (absolute p < 0.05, and absolute log2 Fold Change (FC) > 1.5) dysregulation, out of which 77.6% and 22.4% DEGs were upregulated (log2FC > 1.5) and downregulated (log2FC < − 1.5), and downregulated (log2 FC < − 1), respectively. We identified 17 unique hub genes (82.3% upregulated and 17.7% down-regulated), with KIF23, CCNB2, POLR3F, and RSL24D1 detected as the potential hub genes modified with KoRV infection. Real-time RT-qPCR was performed on seven koalas to ascertain the expression levels of four potential hub genes, which were subsequently normalized to actin copies. Notably, all seven koalas exhibited distinct expression signatures for the hub genes, especially, KIF23 and CCNB2 show the highest expression in healthy koala PBMC, and POLR3F shows the highest expression in koala with lymphoma (K1). Conclusion: Thus, it can be concluded that multiple KoRV subtypes affect disease progression in koalas and that the predicted hub genes could be promising prognostic biomarkers for pathogenesis. [ABSTRACT FROM AUTHOR]

Cowpea (Vigna unguiculata (L.) Walp.) is appreciated for its suitability for cultivation and obtaining good yields in relatively extreme farming conditions. It is resistant to high temperatures and drought. Moreover, food products prepared from Vigna are rich in many nutrients such as proteins, amino acids, carbohydrates, minerals, fiber, vitamins, and other bioactive compounds. However, in East and Southeast Asia, where the products of this crop are in demand, the climate is characterized by excessive humidity. Under these conditions, the vast majority of cowpea varieties tend to have indeterminate growth (elongated shoot length) and are unsuitable for mechanized harvesting. The molecular mechanisms for tolerance to high relative humidity remain the least studied in comparison with those for other abiotic stress factors (drought, heat, cold, flooding, etc.). The purpose of the work was to reveal and investigate differentially expressed genes in cowpea accessions having contrasting growth habits (determinate and indeterminate) under humid and drought conditions. We performed RNA-seq analysis using selected cowpea accessions from the VIR collection. Among the genotypes used, some have significant changes in their plant architecture in response to high relative humidity, while others were tolerant to these conditions. In total, we detected 1697 upregulated and 1933 downregulated genes. The results showed that phytohormone-related genes are involved in cowpea response to high relative humidity. DEGs associated with jasmonic acid signaling are proposed to be key contributors in the maintenance of compact architecture under humid conditions. [ABSTRACT FROM AUTHOR]

Broomcorn millet (Panicum miliaceum L.) is one of the earliest crops, domesticated nearly 8000 years ago in northern China. It gradually spread across the entire Eurasian continent, as well as to America and Africa, with recent improvement in various reproductive and vegetative traits. To identify the genes that were selected during the domestication and improvement processes, we performed a comparative transcriptome analysis based on wild types, landraces, and improved cultivars of broomcorn millet at both seeding and filling stages. The variations in gene expression patterns between wild types and landraces and between landraces and improved cultivars were further evaluated to explore the molecular mechanisms underlying the domestication and improvement of broomcorn millet. A total of 2155 and 3033 candidate genes involved in domestication and a total of 84 and 180 candidate genes related to improvement were identified at seedling and filling stages of broomcorn millet, respectively. The annotation results suggested that the genes related to metabolites, stress resistance, and plant hormones were widely selected during both domestication and improvement processes, while some genes were exclusively selected in either domestication or improvement stages, with higher selection pressure detected in the domestication process. Furthermore, some domestication- and improvement-related genes involved in stress resistance either lost their functions or reduced their expression levels due to the trade-offs between stress resistance and productivity. This study provided novel genetic materials for further molecular breeding of broomcorn millet varieties with improved agronomic traits. [ABSTRACT FROM AUTHOR]

The heart is the central organ of the circulatory system, and its proper development is vital to maintain human life. As fetal heart development is complex and poorly understood, we use single-cell RNA sequencing to profile the gene expression landscapes of human fetal hearts from the four-time points: 8, 10, 11, 17 gestational weeks (GW8, GW10, GW11, GW17), and identified 11 major types of cells: erythroid cells, fibroblasts, heart endothelial cells, ventricular cardiomyocytes, atrial cardiomyocytes, macrophage, DCs, smooth muscle, pericytes, neural cells, schwann cells. In addition, we identified a series of differentially expressed genes and signaling pathways in each cell type between different gestational weeks. Notably, we found that ANNEXIN, MIF, PTN, GRN signalling pathways were simple and fewer intercellular connections in GW8, however, they were significantly more complex and had more intercellular communication in GW10, GW11, and GW17. Notably, the interaction strength of OSM signalling pathways was gradually decreased during this period of time (from GW8 to GW17). Together, in this study, we presented a comprehensive and clear description of the differentiation processes of all the main cell types in the human fetal hearts, which may provide information and reference data for heart regeneration and heart disease treatment. [Display omitted] • Gene expression map of human fetal hearts from the four-time points were identified. • Dynamic alteration of cell subpopulations and gene expression during heart development. • ANNEXIN, MIF, PTN, GRN, OSM signalling pathways are crucial in heart development. [ABSTRACT FROM AUTHOR]

Septic cardiomyopathy is a secondary myocardial injury caused by sepsis. N6-methyl-adenosine (m6A) modification is involved in the pathological progression of septic cardiomyopathy; however, the pathological mechanism remains unclear. In this study, we identified the overall m6A modification pattern in septic myocardial injury and determined its potential interactions with differentially expressed genes (DEGs). A sepsis mouse model exhibiting septic symptoms and myocardial tissue damage was induced by lipopolysaccharide (LPS). LPS-induced septic myocardial tissues and control myocardial tissues were subjected to methylated RNA immunoprecipitation sequencing and RNA sequencing to screen for differentially expressed m6A peaks and DEGs. We identified 859 significantly m6A-modified genes in septic myocardial tissues, including 432 upregulated and 427 downregulated genes. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses were performed to explore the biological importance of differentially expressed m6A methylated genes and DEGs. Differentially expressed m6A methylated genes were enriched in immune- and inflammation-related pathways. Conjoint analysis revealed co-expression of differentially expressed m6A genes and DEGs, including genes that were upregulated or downregulated and those showing opposite trends. High expression of m6A-related genes (WTAP and IGF2BP2), interleukin-17, and interleukin-17 pathway-related genes (MAPK11 and TRAF3IP2) was verified using reverse transcription-quantitative PCR. We confirmed the presence of m6A modification of the transcriptome and m6A-mediated gene expression in septic myocardial tissues. [ABSTRACT FROM AUTHOR]

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.)

Heat shock transcription factor (HSF) are essential regulators of heat shock protein (HSP) gene expression in plants and algae, contributing to their resilience against biotic and abiotic stresses. However, the localization, structure, phylogenetic relationship, and characteristics of PtHSF genes in microalgae, especially in diatom Phaeodactylum tricornutum, remain largely unexplored. This study presents a comprehensive analysis of the PtHSF gene family in P. tricornutum. A genome-wide analysis identified 68 PtHSF genes, which were classified into two distinct subfamilies: traditional and untraditional. Motif and structure analyses revealed evidence of multiple duplication events within the PtHSF gene family. Expression profiling revealed diurnal patterns, with 34 genes being downregulated during the light period and upregulated during the dark period, while 19 genes exhibited the opposite pattern. These findings suggest that PtHSF genes may have specialized functions during the diurnal cycle and play a crucial role in maintaining cellular homeostasis in response to various stresses. Notably, PtHSF16, 30, and 43 genes exhibited higher expression levels, suggesting their potential importance. This study provides a valuable foundation for future investigations into the specific functions of HSFs under different stress conditions and their regulatory mechanisms in P. tricornutum and other microalgae. [ABSTRACT FROM AUTHOR]

Blister beetles (Coleoptera: Meloidae) produce a natural defensive toxin cantharidin (CTD), which has been used for various cancer treatments and other diseases. Currently, the lack of chromosome‐level reference genomes in Meloidae limits further understanding of the mechanism of CTD biosynthesis and environmental adaptation. In this study, the chromosome‐level genome assembly of Mylabris phalerata was generated based on PacBio and Hi‐C sequencing. This reference genome was about 136.68 Mb in size with contig N50 of 9.17 Mb and composed of 12 chromosomes. In comparison to six other Coleoptera insects, M. phalerata exhibited multiple expanded gene families enriched in juvenile hormone (JH) biosynthetic process pathway, farnesol dehydrogenase activity, and cytochrome P450, which may be related to CTD biosynthesis. Consistently, the transcriptomic analysis suggested the "terpenoid backbone biosynthesis" pathway and "the juvenile hormone" as putative core pathways of CTD biosynthesis and presented eight up‐regulated differential expression genes in male adults as candidate genes. It is possible that the restricted feeding niche and lifestyle of M. phalerata were the cause of the gene family's contraction of odorant binding proteins. The ABC transporters (ABCs) related to exporting bound toxins out of the cell and the resistance to the self‐secreted toxins (e.g. CTD) were also contracted, possibly due to other self‐protection strategies in M. phalerata. A foundation of understanding CTD biosynthesis and environmental adaptation of blister beetles will be established by our reference genome and discoveries. [ABSTRACT FROM AUTHOR]

The aim of this study was to investigate the differentially expressed genes associated with intramuscular fat deposition in the longissimus dorsi muscle of Xinjiang Brown Bulls. The longissimus dorsi muscles of 10 Xinjiang Brown Bulls were selected under the same feeding conditions. The intramuscular fat content of muscle samples was determined by the Soxhlet extraction method, for which 5 samples with high intramuscular fat content (HIMF group) and 5 samples with low intramuscular fat content (LIMF group) were selected. It was found that the intramuscular fat content of the HIMF group was 46.054% higher than that of the LIMF group. Muscle samples produced by paraffin sectioning were selected for morphological observation. It was found that the fat richness of the HIMF group was better than that of the LIMF group. Transcriptome sequencing technology was used to analyze the gene expression differences of longissimus dorsi muscle. Through in-depth analysis of the longissimus dorsi muscle by transcriptome sequencing technology, we screened a total of 165 differentially expressed genes. The results of Gene Ontology (GO) enrichment analysis showed that the differentially expressed genes in the two groups were mainly clustered in biological pathways related to carbohydrate metabolic processes, redox processes and oxidoreductase activities. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that the differentially expressed genes were significantly clustered in 15 metabolic pathways, which mainly covered fatty acid metabolism (related to lipid metabolism and glucose metabolism), the pentose phosphate pathway, the Peroxisome Proliferator-Activated Receptor (PPAR) signaling pathway and other important metabolic processes. The three genes that were predominantly enriched in the glycolipid metabolic pathway by analysis were SCD5, CPT1C and FBP2, all of which directly or indirectly affect intramuscular fat deposition. In summary, the present study investigated the differences in gene expression between high and low intramuscular fat content in the longissimus dorsi muscle of Xinjiang Brown Bulls by transcriptome sequencing technology and revealed the related signaling pathways. Therefore, we hypothesized that SCD5, CPT1C and FBP2 were the key genes responsible for the significant differences in intramuscular fat content of the longissimus dorsi muscles in a population of Xinjiang Brown Bulls. We expect that these findings will provide fundamental support for subsequent studies exploring key genes affecting fat deposition characteristics in Xinjiang Brown Bulls. [ABSTRACT FROM AUTHOR]

Background Olive (Olea europaea L.) oil is well-known commercial product worldwide for its nutritional and therapeutic properties. The molecular mechanisms underlying lipid variations in different olive cultivars remain unclear. Methods To investigate the molecular mechanism involved in lipid synthesis and metabolism, untargeted metabolome and RNA-Seq analyses were performed based on two varieties of olive fruits, i.e., Kalinjot (JZ) with low oil content and Coratina (KLD) with high oil content. Results Totally, 38 lipid compounds of 375 differentially accumulated metabolites (DAMs) were identified in JZ and KLD fruits, with 24 metabolites showing higher contents in KLD than those in JZ. Integrated transcriptome and metabolome analyses identified 48 differentially expressed genes (DEGs) associated with six lipid DAMs from JZ and KLD fruits. The contents of decanoic acid, sphinganine, and leukotriene D4 in KLD fruits were 2.33, 1.91, and 1.53 times greater than that of JZ fruits, respectively. In particular, two BCCP, one ACC, seven KAR, one EAR, one FATA and one SPT genes were observed involving to the content and quality of lipids in olive fruits. These DEGs were associated with the pathways of fatty acid biosynthesis, arachidonic acid metabolism, and limonene degradation. This study provides a strong theoretical and experimental foundation for further revealing the molecular mechanisms regulating lipid synthesis and metabolism in different olive cultivars.

Pepper mild mottle virus (PMMoV), a member of the genus Tobamovirus, causes severe damage on pepper worldwide. Despite its impact, the pathogenicity mechanisms of PMMoV and the pepper plant’s response to infection remain poorly understood. Here, we compared the transcriptomic changes in a susceptible pepper inbred line 21C241 with a resistant inbred line 21C385 seedlings, following systemic PMMoV infection using RNA sequencing. Our results revealed that PMMoV induced more pronounced mosaic symptoms and higher viral accumulation levels in the susceptible line 21C241 compared to the resistant line 21C385. We identified 462 and 401 differentially expressed genes (DEGs) in the systemically-infected leaves of the susceptible and resistant lines, respectively, when compared to their healthy counterparts. The majority of these DEGs were involved in photosynthesis and the biosynthesis of secondary metabolites, with 28 DEGs exhibiting distinct expression patterns between the two lines. Notably, the expression level of the chlorophyll a-b binding protein 13 (CAB13) was significantly up-regulated in resistant line 21C385 following PMMoV infection. Functional analysis through silencing of CAB13 in pepper and Nicotiana benthamiana demonstrated a reduction in PMMoV accumulation, suggesting that CAB13 plays a positive role in facilitating PMMoV infection in pepper plants. Taken together, our findings highlight the distinct gene expression profiles between susceptible and resistant pepper lines in response to PMMoV infection and confirm the proviral role of CAB13. This study provides valuable insights into the molecular mechanisms underlying resistance and susceptibility in pepper plants and may inform future strategies for disease management.

With the aim of enhancing plants’ ability to respond to pathogenic fungi, this study focuses on disease resistance genes. We commenced a series of investigations by capitalizing on the pronounced differences in resistance to Fusarium wilt between resistant and susceptible varieties. Through an in-depth exploration of the metabolic pathways that bolster this defense, we identified genes associated with resistance to Fusarium oxysporum f. sp. cubense (Foc). For our analysis, root tissues from seedlings that had been in contact with Fusarium oxysporum for four days were harvested, including both infected and uninfected samples, which served as our study specimens. The crude extract treatment led to a significant increase in malondialdehyde (MDA) levels, lignin content, and phenylalanine ammonia lyase (PAL) activity. Conversely, there was a notable decline in protein content, ergosterol levels, and pectinase activity. In the control group, it was observed that 4,474 genes in the resistant varieties were significantly up-regulated compared to the susceptible varieties. The functional annotation of these differentially expressed genes (DEGs) emphasized their predominant participation in biological processes. Further analysis via the KEGG database revealed that 14 DEGs in the susceptible varieties were particularly enriched in pathways related to plant hormone signaling. Through the perspective of transcriptome data, we focused on genes associated with lignin and cell wall development for Q-PCR validation. Notably, the expression levels of Macma4_02_g07840 (COMT) and Macma4_10_g06530 (CCOAOMT) were relatively elevated. Our findings suggest that the resistance of these varieties to wilt infection can be ascribed to the accumulation of lignin metabolites, which inhibits pathogenic fungus growth by restricting the synthesis of cellular metabolites. The evidence documented in our research provides a framework for a deeper understanding of the disease resistance mechanisms in bananas, laying a solid theoretical foundation for future studies in this area.

Hypertension (HT) is a major cause of intracerebral hemorrhage (ICH), and hypertensive cerebral hemorrhage (HCH) has a serious impact on life quality of patients and gives society a heavy burden. This study investigated the key genes involved in HT and HCH. Three patients with HT, three with HCH, and three healthy individuals were recruited in the present study. Shared and specific differentially expressed genes (DEGs) in HT and HCH were identified using RNA sequencing and bioinformatics analysis. Functional annotation and protein–protein interaction (PPI) network construction of HT- and HCH-specific DEGs were conducted. Estimation of cell infiltration, drug prediction, and real-time qPCR (RT-qPCR) validation were performed. Compared with the controls, 502 and 1649 DEGs were identified in the HT and HCH groups, respectively. Among them, 378 DEGs were HT-specific and 633 DEGs were HCH-specific, and a total of 1771 DEGs were identified between HT and HCH. In addition, there were fewer immune cell types that differed significantly among the three groups. The RT-qPCR validation results in human subjects and cell models were generally consistent with the sequencing results. Our study may make a contribution for the understanding of the specific mechanisms of HT and HCH. Highlights Hypertension (HT) is a major cause of intracerebral hemorrhage (ICH), and hypertensive cerebral hemorrhage (HCH) has a serious impact on life quality of patients. A total of 502 and 1649 DEGs were obtained in HT and HCH, and 1771 DEGs were obtained between HT and HCH. Doxycycline, fasudil and propylthiouracil were predicted as potential drugs for HT and HCH. Our study may make a contribution for the understanding of the specific mechanisms of HT and HCH and representing a potential novel strategy for HT and HCH treatment.

African swine fever, caused by African swine fever virus (ASFV), is a highly contagious and fatal disease that poses a significant threat to the global pig industry. The limited information on ASFV pathogenesis and ASFV–host interactions has recently prompted numerous transcriptomic studies. However, most of these studies have focused on elucidating the transcriptome profiles of ASFV-infected porcine alveolar macrophages in vitro. Here, we analyzed dynamic transcriptional patterns in vivo in nine organ tissues (spleen, submandibular lymph node, mesenteric lymph node, inguinal lymph node, tonsils, lungs, liver, kidneys, and heart) obtained from pigs in the early stages of ASFV infection (1 and 3 d after viremia). We observed rapid spread of ASFV to the spleen after viremia, followed by broad transmission to the liver and lungs and subsequently, the submandibular and inguinal lymph nodes. Profound variations in gene expression patterns were observed across all organs and at all time-points, providing an understanding of the distinct defence strategies employed by each organ against ASFV infection. All ASFV-infected organs exhibited a collaborative response, activating immune-associated genes such as S100A8, thereby triggering a pro-inflammatory cytokine storm and interferon activation. Functional analysis suggested that ASFV exploits the PI3K-Akt signalling pathway to evade the host immune system. Overall, our findings provide leads into the mechanisms underlying pathogenesis and host immune responses in different organs during the early stages of infection, which can guide further explorations, aid the development of efficacious antiviral strategies against ASFV, and identify valuable candidate gene targets for vaccine development.

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.

Abstract Objective We aimed to investigate key differentially expressed immune related genes in persistent atrial fibrillation. Methods Gene expression profiles were downloaded from Gene Expression Omnibus (GEO) using “GEO query” package. “limma” package and “sva” package were used to conduct normalization and eliminate batch effects, respectively. We screened out differentially expressed genes (DEGs) based on “limma” package with the standard of |log fold change (FC)| ≥ 1.5 and false discovery rate (FDR)

Objective This study was conducted to investigate the differential expression of the major histocompatibility complex (MHC) gene region in Eimeria-infected broiler. Methods We profiled gene expression of Eimeria-infected and uninfected ceca of broilers sampled at 4, 7, and 21 days post-infection (dpi) using RNA sequencing. Differentially expressed genes (DEGs) between two sample groups were identified at each time point. DEGs located on chicken chromosome 16 were used for further analysis. Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis was conducted for the functional annotation of DEGs. Results Fourteen significant (false discovery rate

Simple Summary: The current investigation identifies differentially expressed genes that specifically influence the serous subtype of ovarian cancer. This subtype accounts for around three-quarters of ovarian cancer cases. To identify these genes, transcriptomic profiles of serous ovarian cancer and non-cancerous tissue samples were extracted from the Gene Expression Omnibus. Differentially expressed genes were derived using GEO2R tool analyses; genes consistently found among upregulated genes in these profiles were considered to be a serous gene set. Next, the serous gene set was examined for its ontological function using the Molecular Signatures Database and its mutational impact on the gene expression profile of high-grade serous ovarian (HGSO) adenocarcinoma. Results showed that 26 genes are amplified in over 5% of HGSO cancer patients, and many of these amplified genes are related to the cell cycle. These cell cycle-related genes were also identified as being involved in the recurrence of serous ovarian cancer. Overall, this study identifies genes that are potential prognostic markers for serous ovarian cancer. The objective of this study was to identify differentially expressed genes and their potential influence on the carcinogenesis of serous-type ovarian cancer tumors. Serous cancer is an epithelial ovarian cancer subtype and is the most common type of ovarian cancer. Transcriptomic profiles of serous cancer and non-cancerous datasets were obtained from the Gene Expression Omnibus (GEO-NCBI). Differentially expressed genes were then derived from those profiles; the identified genes were consistently upregulated in three or more transcriptomic profiles. These genes were considered as the serous ovarian cancer gene set for further study. The serous gene set derived from the transcriptomic profiles was then evaluated for ontological functional analysis using the Molecular Signatures Database. Next, we examined the mutational impact of this serous gene set on the transcriptomic profile of high-grade serous ovarian (HGSO) adenocarcinoma using the cBioPortal database. Results from OncoPrint revealed that 26 genes were amplified in more than 5% of HGSO cancer patients. Interestingly, several of these genes are involved in cell cycle processes, including genes ATPase family AAA domain containing 2 (ATAD2), recQ-like helicase 4 (RECQL4), cyclin E1 (CCNE1), anti-silencing function 1B histone chaperone (ASF1B), ribonuclease H2 subunit A (RNASEH2A), structural maintenance of chromosome 4 (SMC4), cell division cycle associated 20 (CDC20), and cell division cycle associated 8 (CDCA8). The receiver operating characteristic (ROC) curve results also revealed higher specificity and sensitivity for this subtype of tumors. Furthermore, these genes may affect the recurrence of serous ovarian carcinogenesis. Overall, our analytical study identifies cell cycle-related genes that can potentially be targeted as diagnostic and prognostic markers for serous ovarian cancer. [ABSTRACT FROM AUTHOR]

[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]

Triadimefon, a type of triazole systemic fungicide, has been extensively used to control various fungal diseases. However, triadimefon could lead to severe environmental pollution, and even threatens human health. To eliminate triadimefon residues, a triadimefon-degrading bacterial strain TY18 was isolated from a long-term polluted site and was identified as Enterobacter hormaechei. Strain TY18 could grow well in a carbon salt medium with triadimefon as the sole nitrogen source, and could efficiently degrade triadimefon. Under triadimefon stress, a total of 430 differentially expressed genes (DEGs), including 197 up-regulated and 233 down-regulated DEGs, were identified in strain TY18 using transcriptome sequencing (RNA-Seq). Functional classification and enrichment analysis revealed that these DEGs were mainly related to amino acid transport and metabolism, carbohydrate transport and metabolism, small molecule and pyrimidine metabolism. Interestingly, the DEGs encoding monooxygenase and hydrolase activity acting on carbon–nitrogen were highly up-regulated, might be mainly responsible for the metabolism in triadimefon. Our findings in this work suggest that strain E. hormaechei TY18 could efficiently degrade triadimefon for the first time. They provide a great potential to manage triadimefon biodegradation in the environment successfully. [ABSTRACT FROM AUTHOR]

N6-methyladenosine (m6A) modification plays a crucial role in thyroid carcinoma (THCA). Insulin-like growth factor 2 binding protein 2 (IGF2BP2) is a m6A-binding protein. We aimed to explore the effect of IGF2BP2 on the development of THCA. Differentially expressed genes (DEGs) were screened from GSE50901 and GSE60542 datasets. LinkedOmics, Genebank, and Sequence-based RNA Adenosine Methylation Site Predictor databases were employed to find potential m6A modification sites. Protein–protein interaction network and receiver-operating characteristic curves were applied to determine hub genes of THCA. ESTIMATE revealed the effect of IGF2BP2 on tumor immunity. The mRNA expression of IGF2BP2 was detected using real-time quantitative polymerase chain reaction. The viability, migration, and invasion were assessed by Cell Counting Kit-8, wound healing, and transwell assays. A total of 166 common DEGs were identified from GSE50901 and GSE60542 datasets. One m6A-related gene, IGF2BP2, was differentially expressed in THCA and selected as the research target. The hub genes (CD44, DCN, CXCL12, ICAM1, SDC4, KIT, CTGF, and FMOD) were identified with high prediction values for THCA. Subsequently, the target genes of IGF2BP2, SDC4, and ICAM1, which had potential m6A modification sites, were screened out based on the hub genes. IGF2BP2 was upregulated in THCA and IGF2BP2 expression was positively correlated with immune infiltration in THCA. Additionally, knockdown of IGF2BP2 inhibited the proliferation, invasion, and migration of THCA cells. IGF2BP2 has a contributory effect on the progression of THCA, which is a novel biomarker and a therapeutic target for THCA. [ABSTRACT FROM AUTHOR]

Senecavirus A (SVA) is an emerging virus that causes the vesicular disease in pigs, clinically indistinguishable from other high consequence vesicular diseases. This virus belongs to the genus Senecavirus in the family Picornaviridae. Its genome is a positive-sense, single-stranded RNA, approximately 7,300 nt in length, with a 3' poly(A) tail but without 5'-end capped structure. SVA can efficiently propagate in different cells, including some non-pig-derived cell lines. A wildtype SVA was previously rescued from its cDNA clone using reverse genetics in our laboratory. In the present study, the BSR-T7/5 cell line was inoculated with the passage-5 SVA. At 12 h post-inoculation, SVA-infected and noninfected cells were independently collected for the analysis on comparative transcriptomics. The results totally showed 628 differentially expressed genes, including 565 upregulated and 63 downregulated ones, suggesting that SVA infection significantly stimulated the transcription initiation in cells. GO and KEGG enrichment analyses demonstrated that SVA exerted multiple effects on immunity-related pathways in cells. Furthermore, the RNA sequencing data were subjected to other in-depth analyses, such as the single-nucleotide polymorphism, transcription factors, and protein-protein interactions. The present study, along with our previous proteomics and metabolomics researches, provides a multi-omics insight into the interaction between SVA and its hosts. [ABSTRACT FROM AUTHOR]