Interaction Network Analysis Research Articles

Network analysis of interactions of rumination and anxiety on smartphone dependence symptoms

ObjectiveRumination and anxiety have been posited as correlates of smartphone dependence (SPD). However, little is known regarding how the components of both affect SPD symptoms at subtle levels. Therefore, we used the network analysis approach to identify the connections at a micro level to provide possible interventions for reducing SPD symptoms.MethodsUsing symptom-level network analysis, we used the ruminative response scale-10, the generalized anxiety disorder scale-7, and the mobile phone addiction index scale-17 to investigate Chinese preservice teachers (Mage = 21.1, N = 1160). Subsequently, we estimated a graphical lasso correlation network for these teachers, which encompassed rumination components, anxiety components, and SPD symptoms. Specifically, the central and bridge centralities within the network structure were examined for the impacts of rumination and anxiety on SPD symptoms.ResultsThe three intracluster connections of rumination, anxiety, and SPD were tighter than the intercluster, with structural connections in rumination and anxiety networks closer than the triggered SPD symptoms cluster. Importantly, reflection reactions towards “write down what you are thinking and analyze it” (a component of rumination) were identified as a central and bridging node that might be a target for intervention for SPD symptoms.ConclusionWe identify potential edge-bridging rumination and anxiety on SPD and locate highly central components within each cluster via network analysis.

Proteome-Wide Mendelian Randomization Identifies Therapeutic Targets for Abdominal Aortic Aneurysm.

The proteome is a key source of therapeutic targets. We conducted a comprehensive Mendelian randomization analysis across the proteome to identify potential protein markers and therapeutic targets for abdominal aortic aneurysm (AAA). Our study used plasma proteomics data from the UK Biobank, comprising 2923 proteins from 54 219 individuals, and from deCODE Genetics, which measured 4907 proteins across 35 559 individuals. Significant proteomic quantitative trait loci were used as instruments for Mendelian randomization. Genetic associations with AAA were sourced from the AAAgen consortium, a large-scale genome-wide association study meta-analysis involving 37 214 cases and 1 086 107 controls, and the FinnGen study, which included 3869 cases and 381 977 controls. Sequential analyses of colocalization and summary-data-based Mendelian randomization were performed to verify the causal roles of candidate proteins. Additionally, single-cell expression analysis, protein-protein interaction network analysis, pathway enrichment analysis, and druggability assessments were conducted to identify cell types with enriched expression and prioritize potential therapeutic targets. The proteome-wide Mendelian randomization analysis identified 34 proteins associated with AAA risk. Among them, 2 proteins, COL6A3 and PRKD2, were highlighted by colocalization analysis, summary-data-based Mendelian randomization, and the heterogeneity in an independent instrument test, providing the most convincing evidence. These protein-coding genes are primarily expressed in macrophages, smooth muscle cells, and mast cells within abdominal aortic aneurysm tissue. Several causal proteins are involved in pathways regulating lipid metabolism, immune responses, and extracellular matrix organization. Nine proteins have already been targeted for drug development in diabetes and other cardiovascular diseases, presenting opportunities for repurposing as AAA therapeutic targets. This study identifies causal proteins for AAA, enhancing our understanding of its molecular cause and advancing the development of therapeutics.

Comprehensive genome-wide identification and functional characterization of mapk gene family in northern snakeheads (Channa argus)

The mitogen-activated protein kinase (MAPK) signaling cascade, integral to cellular regulation, orchestrates cell growth, differentiation, stress response, and inflammatory reactions to adapt to challenging environments. The northern snakeheads (Channa argus), a valuable freshwater species known for its hypoxia tolerance, rapid growth, and high nutritional value, lacks comprehensive research on its mapk gene family. In this study, we identified 16 mapk genes in northern snakeheads, among which mapk8, mapk12 and mapk14 have duplicate copies. Phylogenetic analysis confirmed the evolutionary conservation of this gene family. Structural and motif analyses further underscored the conserved nature of these genes. Expression pattern analysis under abiotic and biotic stress conditions showed significant differences expression of mapks in the gills and suprabranchial organ (SBO) after air exposure, as well as in the brain following cold stress, highlighting the extensive role of mapks in stress regulation. It was worth noting that the significant expression differences of mapks were also observed in the spleen after N. seriolae infection, implicating that these genes may be involved in the regulation of innate immune responses. Additionally, analysis of protein-protein interaction (PPI) networks suggested that the co-activation of multiple MAPK signaling pathways may play a key role in regulating an organism's response to biotic and abiotic stresses. This study provides a detailed description of the mapk gene family in the northern snakeheads and elucidates its biological functions under various stress conditions, offering valuable insights into the regulatory mechanisms of the mapk gene family.

Recurrent pain in older age: A cross-sectional network analysis of biopsychosocial-existential interactions.

Chronic pain is a prevalent condition in older adults, associated with substantial distress. For many older people, chronic pain interferes with their daily life which is reflected in various life domains. This study aimed to investigate whether interactions among self-reported indicators of biological, psychological, social, and existential life domains differ for older adults with no pain, with non-interfering pain, and with interfering pain. The study was based on the cross-sectional 65+ and Safe Study data (N=622; age range 64-106years; 60.6% women). Network analysis was used to assess the inter-variable associations for older adults reporting no pain, non-interfering pain, and interfering pain separately. Network visualization and centrality tests were performed. Permutation-based analyses were conducted to investigate the connections among variables in three subgroups. We identified a structural difference between the networks of older adults with no pain and interfering pain, suggesting differences in connectivity among the life domains. The strength centrality metrics showed the central role of presence of meaning in the networks of older adults with no pain and with non-interfering pain, while for older adults with interfering pain, anxiety appeared to be dominant. The findings illuminated that anxiety regulation and meaning-enhancement are potentially important intervention targets for older adults with recurrent pain. Overall, the study highlighted the value of a holistic biopsychosocial-existential approach for understanding and managing pain in older adults.

Integrative Analyses of Biomarkers and Pathways in Oxidative Stress-Related Genes for Gestational Diabetes Mellitus.

Oxidative stress (OS) plays a key role in the pathogenesis of gestational diabetes mellitus (GDM), but it was not well understood. We aimed to investigate the biomarkers and underlying mechanisms of OS-related genes in GDM. The GSE103552 and GSE70493 datasets of GDM were acquired from the Gene Expression Omnibus (GEO) database. Then, oxidative stress-related differentially expressed genes (OSDEGs) were screened between GDM and normal samples from these two datasets. Further analyses were conducted by gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene set enrichment analysis (GSEA) for these OSDEGs. Subsequently, protein-protein interaction (PPI) network analyses of these OSDEGs were carried out to screen the hub genes. Eventually, we used single-sample Gene-set enrichment analysis (ssGSEA) to compare the immune cell infiltration between GDM and normal samples. We identified 26 OSDEGs. Enrichment analysis suggested that the OSDEGs enriched in OS and diabetes-related pathways. GSEA revealed that these OSDEGs enriched in sensory perception of taste and negative regulation of notch4 signaling pathways. Moreover, PPI analysis showed that 15 OSDEGs were the hub gene in GDM. A total of 14 hub genes were highly expressed in GDM and might be used as diagnosis biomarkers. Moreover, many potential agents might target 10 hub genes for GDM treatment. In addition, immune infiltrate analyses revealed that expression of 14 hub genes was positively correlated to immune infiltrates in GDM. OSDEGs are significant in GDM and may provide potential diagnostic biomarkers and treatment targets for GDM.

SIV infection induces alterations in gene expression and loss of interneurons in Rhesus Macaque frontal cortex during early systemic infection.

Understanding the neurobiological mechanisms underlying HIV-associated neurocognitive decline in people living with HIV is frequently complicated by an inability to analyze changes across the course of the infection and frequent presence of comorbid psychiatric and substance use disorders. Preclinical non-human primate simian immunodeficiency virus (SIV) models help address these shortcomings. However, SIV studies frequently target protracted endpoints, limiting our understanding of the neuromolecular alterations during the early post-infection window. To begin to address this knowledge gap, we utilized single nuclei transcriptomics to examine frontal cortex samples of rhesus macaques 10- and 20-days post-SIV infection, compared to non-infected controls. We identify and validated a decrease in inhibitory neurons during the early post infection window, representing a potential substrate of longer-term injury and neurocognitive impairment in people living with HIV. Differential expression identified alterations in cellular subtype gene expression that persisted over the 20-day time course and short-lived differences only detected at 10-days post-SIV infection. In silico predicted regulatory mechanisms and dysregulated neural signaling pathways are presented. Analysis of cell-cell interaction networks identify altered signal pathways in the frontal cortex that may represent regional alterations in cell-cell communications. In total, these results identify cell type-specific molecular mechanisms putatively capable of underlying long-term neurocognitive alterations in persons living with HIV.

Bioinformatics analysis combined with experimental validation reveals the biological role of the ILK gene in prostate cancer

BackgroundProstate cancer (PCa) is a prevalent urological malignancy. The integrin-linked kinase (ILK) gene has been identified as an oncogenic driver in hormonal cancers, including PCa.MethodsTo identify key genes in PCa, we utilized differential gene expression analysis and Weighted Gene Co-expression Network Analysis (WGCNA). The ILK gene was silenced using short interfering RNA (siRNA), and subsequent experiments focusing on cellular functionality were conducted to evaluate its impact on cell proliferation, apoptosis, and cell cycle. We examined the expression of autophagy-related and cell cycle-related proteins, including MAP1LC3A, BECN1, C-MYC, TP53, and MDM2. Moreover, we conducted Mfuzz expression pattern clustering analysis, gene set enrichment analysis (GSEA), immune function analysis, transcription factor (TF) analysis, and drug prediction.Results544 significant genes were identified by WGCNA. The protein–protein interaction (PPI) network analysis revealed that MYC was the central regulatory gene, with the intersected genes mainly involved in regulating cell adhesion and drug metabolism in prostate cancer (PCa). Experimental results showed LNCaP cell proliferation was significantly inhibited in the knockdown groups (P < 0.001). Moreover, ILK silencing increased apoptosis in LNCaP cells compared to normal cells and empty vectors, and transfected LNCaP cells were arrested in the S phase of the cell cycle. Notably, C-MYC expression decreased following ILK silencing. Subsequently, we further identified ILK-related regulatory biomarkers.ConclusionsThe ILK is an oncogene mainly through influencing the C-MYC in PCa. Inhibition of ILK expression would be a promising method for treating the development and progression of PCa.

Association between obesity and Bell's palsy by combining Mendelian randomization and network pharmacology.

The issue of obesity has emerged as a significant global health challenge; nevertheless, the association between Bell's palsy (BP) and obesity remains ambiguous. In this study, the Mendelian randomization (MR) approach was employed to investigate their relationship, while network pharmacology methods were utilized to unveil the underlying mechanisms. We utilized single nucleotide polymorphisms closely linked to obesity and BP as instrumental variables for the MR analysis. Four robust bidirectional MR analysis methods, namely inverse variance weighting (IVW), weighted median, weighted mode, and MR-Egger were employed to assess the association between obesity and BP. Additionally, sensitivity analysis was conducted to evaluate levels of heterogeneity, sensitivity, and stability. Furthermore, we identified therapeutic targets associated with obesity and BP. Subsequently, a protein-protein interaction network analysis was conducted. Finally, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were employed to investigate potential mechanisms underlying the relationship between obesity and BP. The IVW analysis demonstrated a significant positive correlation between obesity and BP (odds ratio [OR] = 1.267, 95% confidence interval [95% CI] = 1.049-1.530, P = .013). However, there was no evidence to suggest that BP increased the risk of obesity. Furthermore, network pharmacology analysis revealed that the 2 diseases shared a total of 712 common targets. GO enrichment analysis shows that this process mainly regulates chemical synaptic signal transmission by modulating receptor signaling factor activity, receptor ligand activity, etc. KEGG enrichment analysis shows that the EGFR/PI3K/Akt signaling pathway plays a significant role in this process. Our study findings suggest that obesity may increase the risk of BP, and its underlying mechanism may potentially involve regulating chemical synaptic transmission through the EFGR/PI3K/Akt signaling pathway.

Proteome Analysis Reveals Paraspinal Muscle Fiber Type Changes in Patients with Degenerative Lumbar Scoliosis.

Degenerative lumbar scoliosis (DLS) is a common aging-related spinal deformity. Paraspinal muscle degeneration is highly correlated with the rapid progression of DLS. However, understanding of the role of the degeneration is limited because of a lack of histologic and molecular evidence. Our study profiled the proteomic alteration of paraspinal muscles and investigated the muscle fiber type transition that occurs in DLS, along with its correlation with clinical parameters. Cross-sectional basic science study using clinical data and biological samples. Paraspinal muscle samples were collected intraoperatively from the concave and convex sides of the apex vertrebrae in patients with DLS (n = 10) and either side of L3 level from age- and sex-matched participants without DLS (n = 10). Analysis was perfomed using isobaric tagging for relative and absolute quantitation (iTRAQ) and liquid chromatography with tandem mass spectrometry on muscle tissue from the convex side of spines in patients with DLS and in participants without DLS to identify differentially expressed proteins (DEPs). Western blotting was used to validate the DEPs. The measurement of acidity/basicity of ATPase (pH = 9.4), succinic acid dehydrogenase staining, and real-time quantitative polymerase chain reaction were performed to assess the muscle fiber type change in DLS. The Pearson correlation coefficient was used to analyze the correlation between the myofiber transition and the Cobb angle of the main curve. This study was supported by the National Natural Science Foundation of China (NSFC) (No. 82272545), $ 8,000-10,000 and the Jiangsu Provincial Key Medical Center, and the China Postdoctoral Science Foundation (2021M701677, $ 5,000-7,000). We identified 62 DEPs, of which 16 were downregulated and 46 were upregulated. Gene ontology indicated significant changes in biological processes including muscle contraction. Protein-protein interaction network analysis showed that structural muscle proteins such as MYH1 (myosin heavy chain 1) and TNNT3 (troponin T) were the key nodes. Western blotting further validated the downregulation of MYH1. Histologically, ATPase staining showed a significant reduction of type II muscle fibers in DLS, consistent with the functional changes of the DEPs. Furthermore, we found that the reduction of type II muscle fibers percentage was correlated with the severity of DLS. This study is the first to elucidate the underlying molecular basis and pathways that implicate the paraspinal muscle fiber type transition in DLS. Type II myofiber percentage was diminished both on the concave side and the convex side of the paraspinal muscles in DLS, especially on the convex side, which may play an important role in the onset and/or progression of the disease. This study shows a potential molecular basis for histopathologic change in the paraspinal muscles of DLS and provides a potential tool for assessing paraspinal muscle quality and predicting the poor prognosis of DLS.

The continued evolution of the L2 cephalosporinase in Stenotrophomonas maltophilia: a key driver of beta-lactam resistance.

The Stenotrophomonas maltophilia L2 cephalosporinase is one of two beta-lactamases that afford S. maltophilia beta-lactam resistance. With the overuse of beta-lactams, selective pressures have contributed to the evolution of these proteins, generating proteins with an extended spectrum of activity. Variant L2 cephalosporinases have been detected, as has their distribution into two main clades (clades 1 and 2). Comprehensive analysis of six L2 variants, cloned into pET41a(+) and expressed in Escherichia coli BL21(DE3) cells, revealed that clade 1 variants exhibited higher ceftazidime resistance compared to clade 2. Notably, the Sm5341 L2 variant, carrying a Phe72Ile variation, displayed a significantly reduced resistance profile across all substrates tested, suggesting a key role of Phe72 in enzymatic activity. An Ile72Phe substitution in the pET41a(+) based Sm5341_L2 variant resulted in a gain-of-function for this protein, confirming the role of Phe72 in the activity of L2. Furthermore, residue interaction network analysis elucidated a pi-cation interaction between Tyr272 and Arg244, which may potentially be stabilizing the enzyme and its binding site. The presence of Tyr272 in clade 1 variants correlates with higher ceftazidime affinity, contrasting Asp272 in clade 2 variants. Displaying lower Km values and higher kcat/Km ratios, clade 1 L2 enzymes demonstrated a higher binding efficiency and greater catalytic efficiency for most of the substrates assessed. These results indicate that L2 enzymes are continuing to evolve and adapt to a selective environment fuelled by the overuse of beta-lactams. This adaptation may signal the beginning of an evolutionary process yielding variant L2 cephalosporinases with extended substrate profiles.

Alzheimer's disease may develop from changes in the immune system, cell cycle, and protein processing following alterations in ribosome function.

The prevalence of Alzheimer's disease (AD) is increasing as society ages. The details of AD pathogenesis have not been fully elucidated, and a comprehensive gene expression analysis of the process leading up to the onset of AD would be helpful for understanding the mechanism. We performed an RNA sequencing analysis on a cohort of 1227 Japanese blood samples, representing 424 AD patients, 543 individuals with mild cognitive impairment (MCI), and 260 cognitively normal (CN) individuals. A total of 883 and 1169 statistically significant differentially expressed genes (DEGs) were identified between CN and MCI (CN-MCI) and between MCI and AD (MCI-AD), respectively. Pathway analyses using these DEGs, followed by protein-protein interaction network analysis, revealed key roles of ribosomal function in MCI progression, whereas immune responses, cell cycle, and protein processing in endoplasmic reticulum were involved in AD progression. Our findings indicate that the onset of AD might be associated with gene expression changes in the immune system, cell cycle, and protein processing following alterations in the expression of ribosomal protein genes during the MCI stage, although validation using brain tissue samples will be necessary in the future. Given the known effectiveness of delaying MCI progression in preventing AD, the genes related to ribosomal function might emerge as biomarkers for early diagnosis.

Genome-Wide Characterization of Wholly Disordered Proteins in Arabidopsis

Intrinsically disordered proteins (IDPs) include two types of proteins: partial disordered regions (IDRs) and wholly disordered proteins (WDPs). Extensive studies focused on the proteins with IDRs, but less is known about WDPs because of their difficult-to-form folded tertiary structure. In this study, we developed a bioinformatics method for screening more than 50 amino acids in the genome level and found a total of 27 categories, including 56 WDPs, in Arabidopsis. After comparing with 56 randomly selected structural proteins, we found that WDPs possessed a more wide range of theoretical isoelectric point (PI), a more negative of Grand Average of Hydropathicity (GRAVY), a higher value of Instability Index (II), and lower values of Aliphatic Index (AI). In addition, by calculating the FCR (fraction of charged residue) and NCPR (net charge per residue) values of each WDP, we found 20 WDPs in R1 (FCR &lt; 0.25 and NCPR &lt; 0.25) group, 15 in R2 (0.25 ≤ FCR ≤ 0.35 and NCPR ≤ 0.35), 19 in R3 (FCR &gt; 0.35 and NCPR ≤ 0.35), and two in R4 (FCR &gt; 0.35 and NCPR &gt; 0.35). Moreover, the gene expression and protein-protein interaction (PPI) network analysis showed that WDPs perform different biological functions. We also showed that two WDPs, SIS (Salt Induced Serine rich) and RAB18 (a dehydrin family protein), undergo the in vitro liquid-liquid phase separation (LLPS). Therefore, our results provide insight into understanding the biochemical characters and biological functions of WDPs in plants.

Decoding oral cancer: insights from miRNA expression profiles and their regulatory targets

Oral cancer (OC) is a prevalent malignancy with high mortality rates, largely attributed to late diagnosis and limited therapeutic advancements. MicroRNAs (miRNAs), as critical regulators of gene expression, have emerged as key players in modulating plethora of cellular mechanisms. This study analyzed miRNA and gene expression profiles in OC using publicly available datasets from the Gene Expression Omnibus (GEO) to explore their roles in tumorigenesis. A total of 23 differentially expressed miRNAs (DEmiRs) and 1,233 differentially expressed genes (DEGs) were identified. Functional annotation and pathway enrichment analyses highlighted significant involvement of DEmiRs and their target genes in cell cycle-related processes, including enrichment in the nucleus, transcription factor activity, regulation of nucleosides, nucleotide and nucleic acids, cell growth and/or maintenance, mitotic cell cycle, mitotic M-M/G1 phases an DNA replication. Furthermore, different signaling cascades such as IGF signaling, PDGF signaling and LKB1 signaling and PLK1 signaling pathways were also found associated with DEmiR-related regulation of OC progression. Protein-protein interaction (PPI) network analysis identified key molecular hubs associated with DEmiR and DEGs in OC. Notably, most of these hub genes such as NEK2, NDC80, NUF2, PLK1, SMAD2, TP53, TPX2, TTK, UBE2C, WDHD1, WTAP, YWHAZ are directly or indirectly associated with cell cycle progression, underscoring the role of DEmiRs in driving tumor proliferation and survival in OC via dysregulating cell cycle. This study offers insights into the molecular mechanisms underlying OC and highlights miRNAs as potential biomarkers and therapeutic targets to disrupt the cancerous cell cycle and improve treatment outcomes.

ISG15 promotes M5-induced hacat cell proliferation through Wnt signaling in psoriasis

Abstract Objective Psoriasis is a common chronic, recurrent, immune-mediated inflammatory skin disease, which tends to occur in cold areas. Its pathogenesis is currently unclear. This study aims to screen differentially expressed genes in the psoriasis dataset, identify the central genes, detect the expression of central genes in psoriasis lesions of patients in the cold regions and then conduct further research. Methods Differential genes associated with psoriasis in the GEO database were analyzed, and functional enrichment analysis and protein-protein interaction network analysis. The expression results of the identified genes were validated in psoriasis cell models. The ISG15 gene, which showed the most significant difference in expression, was further studied. The expression level of ISG15 protein in psoriasis was examined. Then, we knocked out ISG15 in psoriasis cell models and detected keratinocyte proliferation by MTT, Real-Time PCR and Western Blot. Western Blot showed the expression of β-catenin after ISG15 gene knockout. Results We detected the protein expression of ISG15 in the cold area of Northeast China, and found that the expression of ISG15 increased in patients with psoriasis, and the proliferation of keratinocytes and the expression of β-catenin decreased in psoriasis cell model after ISG15 was knocked down. ISG15 regulates keratinocyte proliferation through Wnt signaling pathway in psoriasis. Conclusions ISG15 expression is increased in psoriatic cells and skin lesions of patients with psoriasis. In psoriasis, ISG15 promotes keratinocyte proliferation through the Wnt signaling pathway.

Boswellia Extract Promotes Healing and Resolving Inflammation in Oral Ulcers of Rat.

Recurrent aphthous ulcers significantly impact patients' quality of life due to their painful and recurrent nature, necessitating more effective treatments. This study explores the therapeutic potential of Boswellia to treat recurrent aphthous ulcers by its anti-inflammatory and healing promotion effect in a rat oral ulcer model. Network pharmacology techniques were employed to elucidate Boswellia's active components and potential targets. Intersecting targets of Boswellia and oral ulcer-related genes were screened for protein-protein interaction network analysis and functional enrichment. An oral ulcer model in rats was used and rats were treated with Boswellia extract. The healing process was monitored by measuring the ulcer area and body weight changes. Histological analysis was performed, and the role of Boswellia in macrophage polarization was investigated through gene expression analysis and protein array tests. The underlying mechanism involving PPARγ activation was also explored. Network pharmacology analysis revealed Boswellia's interaction with key genes and pathways associated with inflammation and lipid metabolism, such as MAPK3, PPARG, and PTGS2. Boswellia extract significantly accelerated oral ulcer healing and recovered weight loss in rats. Histological examinations revealed reduced tissue swelling and inflammatory cell infiltration in treated groups. Furthermore, Boswellia extract decreased infiltration of M1 macrophage presence while increasing M2 macrophage, indicating an inflammation-resolving effect. Invitro studies showed that Boswellia extract enhanced M2-related gene expression and decreased pro-inflammatory cytokines, which is PPARγ dependent. Boswellia extract promotes oral ulcer healing and resolves inflammation, primarily through the modulation of macrophage polarization via PPARγ activation.

Transcriptome analysis of muscle atrophy in Leizhou black goats: identification of key genes and insights into limb-girdle muscular dystrophy

BackgroundThe Leizhou Black Goat (LZBG), a prominent breed in tropical China’s meat goat industry, frequently exhibits inherent muscle atrophy and malnutrition-related traits. Particularly, muscles critical for support, such as the legs, often display severe symptoms. This study aimed to investigate the differential genes and signaling pathways influencing muscle development and atrophy across various muscle locations in LZBG from a muscular atrophy-affected family.ResultsDifferential expression analysis revealed 536 mRNAs with significant differences across three muscle groups. Marked variations in mRNA expression patterns were observed between leg and back muscles versus abdominal muscles, reflecting characteristics similar to those found in limb-girdle muscular dystrophy. The analysis identified several key differentially expressed genes implicated in muscle development and atrophy, including PITX1, COLQ, ZIC1, SBK2, and TBX1, showed Significant difference expression levels and expression patterns with normal individuals. Functional annotation and protein interaction network analysis indicated enrichment of these genes in muscle-related pathways. Protein interaction network analysis identified five key clusters related to muscle function and development.ConclusionThe mRNA expression patterns of the leg and back muscles in LZBG from a muscular atrophy-affected family differed significantly from those of the abdominal muscle, displaying typical characteristics of limb-girdle muscular dystrophy. Genes such as PITX1, TBX1, SBK2, TCAP, and COLQ were identified as key regulators of muscle development and contributors to muscle atrophy. These findings enhance our understanding of the mechanisms underlying muscular atrophy in LZBGs. The identification of key genes and pathways provides valuable insights for developing future breeding strategies aimed at improving meat production efficiency.

Computational identification of promising genetic markers associated with molecular mechanisms of reduced rice resistance to Rhizoctonia solani under excess nitrogen fertilization using gene network reconstruction and analysis methods

Although nitrogen fertilizers increase rice yield, their excess can impair plant resistance to diseases, particularly sheath blight caused by Rhizoctonia solani. This pathogen can destroy up to 50 % of the crop, but the mechanisms underlying reduced resistance under excess nitrogen remain poorly understood. This study aims to identify potential marker genes to enhance rice resistance to R. solani under excess nitrogen conditions. A comprehensive bioinformatics approach was applied, including differential gene expression analysis, gene network reconstruction, biological process overrepresentation analysis, phylostratigraphic analysis, and non-coding RNA co-expression analysis. The Smart crop cognitive system, ANDSystem, the ncPlantDB database, and other bioinformatics resources were used. Analysis of the molecular genetic interaction network revealed three potential mechanisms explaining reduced resistance of rice to R. solani under excess nitrogen: the OsGSK2-mediated pathway, the OsMYB44-OsWRKY6-OsPR1 pathway, and the SOG1-Rad51-PR1/PR2 pathway. Potential markers for breeding were identified: 7 genes controlling rice responses to various stresses and 11 genes modulating the immune system. Special attention was given to key participants in regulatory pathways under excess nitrogen conditions. Non-coding RNA analysis revealed 30 miRNAs targeting genes of the reconstructed gene network. For two miRNAs (Osa-miR396 and Osa-miR7695), about 7,400 unique long non-coding RNAs (lncRNAs) with various co-expression indices were found. The top 50 lncRNAs with the highest co-expression index for each miRNA were highlighted, opening new perspectives for studying regulatory mechanisms of rice resistance to pathogens. The results provide a theoretical basis for experimental work on creating new rice varieties with increased pathogen resistance under excessive nitrogen nutrition. This study opens prospects for developing innovative strategies in rice breeding aimed at optimizing the balance between yield and disease resistance in modern agrotechnical conditions.

Deciphering the role of metal ion transport-related genes in T2D pathogenesis and immune cell infiltration via scRNA-seq and machine learning

IntroductionType 2 diabetes (T2D) is a complex metabolic disorder with significant global health implications. Understanding the molecular mechanisms underlying T2D is crucial for developing effective therapeutic strategies. This study employs single-cell RNA sequencing (scRNA-seq) and machine learning to explore the the pathogenesis of T2D, with a particular focus on immune cell infiltration.MethodsWe analyzed scRNA-seq data from islet cells of T2D and nondiabetic (ND) patients, identifying differentially expressed genes (DEGs), especially those related to metal ion transport (RMITRGs). We employed 12 machine learning algorithms to develop predictive models and assessed immune cell infiltration using single-sample gene set enrichment analysis (ssGSEA). Correlations between immune cells and key RMITRGs were investigated, and the interactions among these genes were explored through protein-protein interaction (PPI) network analysis. Additionally, we performed a detailed cell-cell communication analysis to identify significant signaling pathways in T2D.ResultsOur analysis identified 1953 DEGs between T2D and ND patients, with the Stepglm[backward] plus GBM model demonstrating high predictive accuracy and identifying 13 hub RMITRGs. Twelve protein structures were predicted using AlphaFold 3, revealing potential functional conformations. We observed a strong correlation between hub RMITRGs and immune cells, and PPI network analysis revealed key interactions. Cell-cell communication analysis highlighted 16 active signaling pathways, with CXCL, MIF, and COMPLEMENT linked to immune and inflammatory responses, and WNT, KIT, LIFR, and HGF pathways uniquely activated in T2D.ConclusionOur analysis identified genes crucial for T2D, emphasizing ion transport, signaling, and immune cell interactions. These findings suggest therapeutic potential to enhance T2D management. The identified pathways and genes provide valuable insights into the disease mechanisms and potential targets for intervention.

Transcriptomic Profiling Highlights Metabolic and Biosynthetic Pathways Involved in In Vitro Flowering in Anoectochilus roxburghii (Wall.) Lindl.

Background: Tissue culture is one of the most important methods for propagating orchids. Notably, many orchid seedlings exhibit autonomous flowering during the cultivation process. To explore the underlying mechanism, Anoectochilus roxburghii (Wall.) Lindl., an orchid that spontaneously forms in vitro flowers, was analyzed in this study. Methods: Bud samples at the early, middle, and fully open stages were collected for transcriptome sequencing, followed by differential expression, trend, enrichment and protein–protein interaction (PPI) network analyses. Results: Differential gene expression analysis identified 2364, 4137, and 6522 differentially expressed genes (DEGs) in the early vs. middle, middle vs. open, and early vs. open comparisons, respectively. These DEGs were significantly enriched in various metabolic and biosynthetic pathways, particularly in ko01100 (metabolic pathways). PPI network analysis further identified hub genes, including MCM3, MCM4, and MCM7, which are associated with DNA replication, and CURL3, which is linked to plant hormone signal transduction pathways. Conclusion: Our findings provide novel insights into the molecular mechanisms driving in vitro flowering in A. roxburghii, highlighting the importance of metabolic and biosynthetic process signaling in this unique developmental transition. These results provide valuable resources for future studies on orchid propagation and floral development.

Qinggan Yipi capsule ameliorates hepatic fibrosis in rats by down-regulating the TGF-β1/Smad2/3 signaling pathway and improving gut microbiota imbalance

Background and objectiveQinggan Yipi Capsule (QgYp) is a hospital preparation that has been used for many years in the treatment of chronic liver diseases. However, the mechanism of QgYp in ameliorating hepatic fibrosis (HF) remains unclear. This study aims to clarify the anti-liver fibrosis effect of QgYp and its mechanism of action.MethodsThis study uses a carbon tetrachloride (CCl4) induced HF rat model and TGF-β1 stimulated HSC-T6 cell line (rat HSCs) as experimental models. The therapeutic effects were evaluated through pathology, biochemical tests, and ELISA. The therapeutic mechanism of QgYp for HF was predicted through network pharmacology. The expression of TGF-β1/Smad2/3 related proteins was detected by qPCR analysis and Western blot analysis. The composition of the gut microbiota was analyzed using 16S rRNA gene sequencing.ResultsHistopathological analysis, serum biochemical tests, and ELISA measurements showed that QgYp effectively decreased the levels of ALT, AST, HA, LN, PCIII, and IV-C while improving collagen deposition and hepatocyte necrosis. Protein-protein interaction (PPI) network analysis screened HF-related genes, including peroxisome proliferator-activated receptor gamma (PPARG), tumor necrosis factor (TNF), and TGF-β1. GO and KEGG analyses indicated that QgYp significantly affects TGF-β signaling pathway. In addition, the results of qPCR and Western blot analysis from both in vitro and in vivo experiments indicated that QgYp significantly downregulated the expression of proteins and mRNA associated with the TGF-β1/Smad2/3 pathway. The 16S rDNA gene sequencing results showed that QgYp can increase the diversity and richness of the gut microbiota in HF rats and alter the composition of the gut microbiota.ConclusionQgYp could effectively ameliorate HF, and this effect might be connected to the downregulation of the TGF-β1/Smad2/3 pathway, the suppression of HSCs activation, and regulation of gut microbiota dysbiosis.