Search Results (20,482)

Low temperature critically pressures insect pest distributions and population dynamics; however, integrated understanding of cold stress responses in invasive pests, particularly at the adult stage, remains limited. Here, we investigated the integrated physiological, biochemical, metabolomic and transcriptomic responses of Tuta absoluta (Meyrick, 1917) exposed to control (CT: 25 °C), moderate cold stress (MCS: 15 °C) and severe cold stress (SCS: 5 °C) conditions. Our results revealed that low-temperature stress impaired T. absoluta emergence, survival, fecundity and egg hatching in a stress intensity-dependent manner. Also, low temperature reduced the olfactory-mediated host-seeking behaviors of T. absoluta females. The biochemical analyses revealed depletion of triglycerides, glycogen and Na⁺/K⁺-ATPase activity alongside compensatory trehalose accumulations, while antioxidant enzyme activities (SOD, POD, CAT) were differentially modulated indicating progressive oxidative defense impairment under low temperature. Untargeted metabolomic profiling identified extensive differential metabolite accumulations, revealing systematic dysregulation of alkaloid biosynthesis, amino acid metabolism and central carbon metabolic pathways. Transcriptomic analysis identified several differentially expressed genes (DEGs) enriched in thermogenesis, oxidative phosphorylation, MAPK signaling and neurodegeneration-associated pathways. Furthermore, integrative transcriptome–metabolome analysis revealed coordinated gene–metabolite regulatory networks scaling systematically with cold stress intensity. These findings advance our mechanistic understanding of thermal stress adaptations in T. absoluta and may contribute to the development of climate-informed pest management strategies. Full article

Primordial germ cells (PGCs) are the earliest precursors of gametes and essential cellular materials for poultry germplasm conservation and genetic modification. In this study, PGCs isolated from 2.5-day male and female Silkie chicken embryos were defined as circulating PGCs (cPGC_M and cPGC_F), whereas PGCs isolated from 8.5-day male and female embryos were defined as gonad-derived PGCs (gPGC_M and gPGC_F). RNA sequencing with three biological replicates per group was performed to characterize developmental-stage- and sex-associated transcriptional programs. Comparative transcriptomic analyses identified stage-associated differences in pathways related to cell–matrix interaction, focal adhesion, PI3K–Akt signaling, and stem cell pluripotency, with more differentially expressed genes detected in the female than in the male stage comparison. Sex-biased expression was detectable at the circulating stage, mainly reflecting W- and Z-linked expression differences, and the number of sex-biased genes was greater after gonadal colonization, primarily because more autosomal differentially expressed genes were detected. Candidate genes and pathways, including HINTW, DMRT1, SOX2, EDNRB, LPAR4, GFRA3, ECM–receptor interaction, ribosome-related modules, and calcium signaling, were associated with these comparisons and are presented as targets for future validation rather than as confirmed regulators. Because the study used three biological replicates per group, RT-qPCR corroboration was limited to six female stage-associated genes, and no functional perturbation assays were performed, the findings are descriptive and do not establish causal mechanisms of PGC migration, gonadal colonization, or sex differentiation. Within these limitations, the dataset provides an exploratory resource for subsequent studies of chicken PGC biology and biotechnology. Full article

This study aimed to measure mRNA and miRNA expression profile in corneal impression cytology (IC) samples from patients with congenital aniridia (CA) and healthy controls, and to elucidate the key genes and signaling pathways involved in aniridia-associated keratopathy (AAK). Corneal IC samples were collected from 14 patients with CA and 14 healthy controls. RNA sequencing was performed to identify differentially expressed genes (DEGs) and miRNAs. Correlations with age and AAK grade were analyzed, selected miRNAs were validated by RT-qPCR, and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were conducted to characterize biological functions and pathways. A total of 695 DEGs and 19 differentially expressed miRNAs were identified. KRT24 expression was negatively associated with age, whereas LY6D expression positively correlated with AAK grade. Several miRNAs were linked to disease severity, including positive correlations for miR-224-5p, miR-224-3p, and miR-452-5p, and negative correlations for miR-204-3p, miR-181b-5p, and miR-181a-5p. RT-qPCR confirmed significant downregulation of miR-204-5p and miR-138-5p in aniridia samples. Functional enrichment analyses showed that DEGs were mainly involved in cell adhesion, extracellular matrix remodeling, inflammatory and immune responses, and neural-related processes. Target genes of dysregulated miRNAs were enriched in transcriptional regulation, cell proliferation, apoptosis, and migration, with significant involvement of PI3K-Akt, AGE-RAGE, and EGFR signaling pathways. Corneal epithelial cells from patients with CA exhibit coordinated mRNA and miRNA dysregulation associated with extracellular matrix disruption, inflammation, and altered signaling pathways. These findings improve understanding of AAK pathogenesis and identify potential biomarkers and therapeutic targets. Full article

The Activity-Dependent Neuroprotective Protein (ADNP) is an important regulator of early brain development, especially during cortical neurogenesis and neurite formation. De novo point mutations or haploinsufficiency of the ADNP gene result in ADNP syndrome, which is also known as Helsmoortel-Van der Aa syndrome, a complex neurodevelopmental disorder recognized as a leading single-gene cause of syndromic autism spectrum disorder (ASD) and intellectual disability. ADNP works as both a transcription factor and a microtubule (MT) regulator. As a transcription factor, ADNP is a key component of chromatin remodeling complexes such as ChAHP (CHD4 (Chromodomain Helicase DNA-binding Protein 4)-ADNP-HP1 (Heterochromatin Protein 1)) and SWI/SNF (Switch/Sucrose Non-Fermentable), and it tightly regulates the expression of numerous essential developmental genes. ADNP also modulates the Wnt/β-catenin signaling pathway. During neural differentiation, ADNP is redistributed from the nucleus to the cytoplasm, and this redistribution is regulated by binding to 14-3-3 proteins, which are phosphorylated by protein Kinase C (PKC). After relocating to the cytoplasm, ADNP functions as an MT regulator by binding to microtubule end-binding proteins (EB1 and EB3) and Tau to control neurite formation. Previous studies have focused on NAP (also known as Davunetide, a peptide derived from ADNP) in MT regulation and its therapeutic potential for autism spectrum disorder (ASD) and neurodegenerative diseases, such as Alzheimer’s disease. This review highlights the functions of full-length ADNP and NAP in early brain development, particularly in neurogenesis and neurite formation during cortical development. We will also discuss the potential of NAP as a therapeutic medication for neurodevelopmental disorders, especially ASD and ADNP syndrome. Full article

This research evaluated the biocontrol potential of the bacterial flora from cured sugarcane bagasse (SCB) against Fusarium oxysporum f. sp. lycopersici (Fol), the causal agent of tomato Fusarium wilt. Screenings of twenty SCB-derived isolates revealed consistent antagonistic activity, inhibiting mycelial growth from 32.08% to 55.00%. The most effective isolate, 100MTN1, was identified via 16S rRNA sequencing (GenBank: PX506225) as Bacillus atrophaeus. Interaction between B. atrophaeus 100MTN1 and Fol FOLViF has revealed a distinct profile of bioactive metabolites produced specifically during co-cultivation. Transcriptomic profiling of Fol FOLViF exposure to 100MTN1 identified 189 differentially expressed genes, with downregulation of genes involved in DNA replication, translation, and membrane transport, and upregulation of those linked to secondary metabolism and oxidative stress. KEGG pathway mapping further supported the possible causes of disruptions within the pathogen. Molecular docking suggested that the B. atrophaeus 100MTN1 derived metabolite, 6-Hydroxy-3′-methoxyflavone and exhibits binding affinity for key Fol proteins that compares favorably with the commercial fungicides. Greenhouse trials using tomato cv. Kalyan confirmed that treatment with strain 100MTN1 was associated with reduced disease severity and enhanced plant growth. These findings suggest that B. atrophaeus 100MTN1 suppresses Fol FOLViF through a combination of metabolite-driven inhibition and transcriptional interference, signifying its potential as a biological control agent for managing Fusarium wilt. Full article

The sheep Y chromosome encodes genes essential for testicular development and spermatogenesis, yet their transcriptional dynamics across developmental and pathological states remain largely uncharacterized. Here, we profiled Y-linked gene expression using RNA-seq datasets from Hu sheep testes across postnatal development (0, 3, 6, 12 months) and from divergent testicular (large, normal, small, cryptorchid) and epididymal (large, small) weights. Developmental trajectory analysis of 134 expressed Y-linked genes revealed three distinct patterns: progressive activation from birth to sexual maturity (dominated by multicopy families ZNF280BY, HSFY, PRAMEY, TSPY3), progressive decrease, and stage-specific expression. Differential expression identified 41 Y-linked genes consistently downregulated in small, cryptorchid, and pre-pubertal testes compared with normal or large mature testes. Hierarchical clustering showed that 6-month-old small testes transcriptionally clustered with cryptorchid testes, not with immature or normal testes. In the epididymis, only one Y-linked gene was differentially expressed between large and small groups. Among X–Y gametolog pairs, most showed positive expression correlations in testes, whereas DDX3X/DDX3Y exhibited a significant negative correlation (ρ = −0.450, p = 0.0185); strikingly, this pair reversed to a positive correlation in the epididymis (ρ = 0.607, p = 3.29 × 10⁻⁵). In conclusion, Y-linked transcriptional profiles distinguish testicular pathology from normal maturation, and DDX3X/DDX3Y regulation is strictly tissue-specific. Full article

Innate immunity predictors of HIV-1 risk and pathogenesis vary with reproductive hormones, pregnancy, and lactation, yet the underlying mechanisms remain unclear. We hypothesized that pregnancy-associated physiological adaptations alter systemic microRNA (miRNA) expression, thereby regulating immunity, pathogenesis and susceptibility to infection. We analyzed 174 serum samples from 88 participants in a longitudinal cohort from Uganda and Zimbabwe across pre-pregnancy (PP), pregnancy (P), and postpartum breastfeeding (BF). Cell-free peripheral blood miRNAs (n = 2083) were profiled using HTG EdgeSeq. Pregnancy-specific miRNAs were identified by intersecting differentially expressed (DE) miRNAs from P vs. PP and P vs. BF comparisons. miRNA targets and pathways were analyzed using miRWalk, Cytoscape/ClueGO, and cytoHubba. Pregnancy was associated with DE miRNAs (29 upregulated and 131 downregulated) targeting 2733 validated genes. Enriched pathways (FDR < 0.05) included adaptive immune response, Hippo Signaling, Cellular Senescence, HSV-1 infection, and two cancer-related pathways. Pregnancy-enriched targets within each pathway overlapped with the HIV–host interactome by 37–88%. Network analysis identified 47 hub genes interacting with 18 HIV-1 proteins, with Tat and gp120 being most connected viral and HLA-A being the most connected host protein. These findings indicate that pregnancy-driven systemic miRNAs target the HIV–host interactome and specifically identify pregnancy-enriched central hub genes involved in cell cycle control, viral immune evasion and replication to be further investigated for their predictive value in HIV acquisition and pathogenesis in longitudinal cohorts and experimental settings. Full article

Vairimorpha ceranae is a fungal pathogen that infects the honeybee midgut and poses a serious threat to colony health. However, the role of long noncoding RNAs (lncRNAs) of V. ceranae in its infection of the host remains poorly understood. Using lncRNA-seq data from the midguts of Apis mellifera workers at 7 and 10 days post-inoculation with V. ceranae (NcT1L and NcT2L groups), along with controls inoculated with spores (NcCKL group), we performed transcriptome-wide identification and structural characterization of lncRNAs. We identified lncRNAs in V. ceranae and analyzed the regulatory network of the differentially expressed lncRNAs (DElncRNAs). A total of 27 V. ceranae lncRNAs were identified in the midguts. The 19, 21, and 4 DElncRNAs were identified in the NcCKL vs. NcT1L, NcCKL vs. NcT2L, and NcT1L vs. NcT2L comparison groups. These DElncRNAs were predicted to regulate 26, 27, and 2 upstream/downstream genes. Furthermore, 15, 23, and 4 DElncRNAs were found to target 195, 211, and 94 miRNAs, which in turn targeted 204, 216, and 73 mRNAs into the respective comparisons. The ceRNA network prediction revealed that DElncRNAs, miRNAs and mRNAs form a complex regulatory network. This study presents the expression profile of lncRNAs during V. ceranae infection and highlights their potential regulatory functions in pathogenesis. Our findings provide new molecular insights into host–pathogen interactions at the RNA level and establish a foundation for developing targeted strategies to control nosemosis. Full article

Systemic sclerosis (SSc) is a severe autoimmune rheumatic disease with high mortality. Epigenetic factors, particularly micro-RNAs (miRNAs), may contribute to its pathogenesis by regulating gene expression. In this cross-sectional study, we assessed altered miRNA–mRNA regulatory networks in SSc and associated them with disease-related biological processes. We analyzed the miRNA profiles and differentially expressed genes (DEGs) of peripheral blood mononuclear cells (PBMCs) from 52 SSc patients (42 women and 10 men; mean age: 59.1 years) and 24 age- and gender-matched healthy controls. Total RNA was isolated and subjected to high-throughput next-generation sequencing for both miRNA and mRNA profiling. We identified 58 differentially expressed miRNAs (DEMs), 33 upregulated and 25 downregulated in SSc. In parallel, 6610 DEGs were detected (Mann–Whitney U-test, p < 0.05); 31 remained upregulated and nine downregulated after false discovery rate (FDR) correction. Integration of miRNA and mRNA data revealed 180 validated inverse miRNA–mRNA interactions. Notably, 22 of 31 upregulated DEGs corresponded to targets of downregulated miRNAs, indicating coordinated derepression. Functional enrichment analyses highlighted pathways related to extracellular matrix (ECM) remodeling, immune responses, fibrosis, and transcriptional regulation. Our findings suggest that altered miRNA expression contributes to widespread transcriptional dysregulation in SSc, promoting pro-fibrotic and immune-activated molecular pathways through coordinated miRNA–mRNA interactions. Full article

Mandibular condylar cartilage (MCC) exhibits greater susceptibility to mechanical stress-induced degeneration than tibial articular cartilage (TAC). This study investigated whether differential epigenetic regulation of nuclear factor erythroid 2-related factor 2 (Nrf2), a master regulator of antioxidant responses, is associated with distinct antioxidant capacities between these cartilage types. Cartilage tissues from 5-week-old male ICR mice (n = 16 for gene analyses, n = 8 for protein analyses) were obtained using laser microdissection. Gene and protein expression was analyzed by microarray, real-time RT-PCR, and immunohistochemistry. DNA methylation of the Nrf2 promoter was evaluated using pyrosequencing and high-resolution melting analysis. Nrf2 expression in MCC was approximately 1/10 that in TAC at mRNA level and only 5% at protein level. Downstream antioxidant enzymes (NQO1, G6PD, HO-1) showed significantly reduced expression in MCC. Oxidative DNA damage marker 8-OHdG was significantly elevated in MCC compared to TAC (20.0% vs. 10.7%, p < 0.05). The Nrf2 promoter region showed higher DNA methylation levels in MCC, confirmed by high-resolution melting analysis. Higher Nrf2 promoter methylation in MCC is associated with reduced antioxidant capacity and elevated oxidative damage. This epigenetic–antioxidant relationship may contribute to MCC’s vulnerability to mechanical stress-induced degeneration and represents a potential therapeutic target for temporomandibular joint disorders. Full article

Grass carp (Ctenopharyngodon idella) is a major freshwater aquaculture species in China, but its growth is limited under intensive high-density farming. This study aimed to investigate the characteristics of plasma exosomes associated with distinct growth performance by isolating and characterizing exosomes from fast- and slow-growing grass carp after nine months of culture. Exosomes showed typical morphology and expressed characteristic markers (CD63, CD81, TSG101). Small RNA sequencing identified 3325 miRNAs, with 177 highly abundant miRNAs differentially expressed: immune-related miRNAs were upregulated, while development-inhibitory miRNAs were downregulated in fast-growing fish. Target gene enrichment highlighted pathways in neural and skeletal development and amino acid metabolism. Integrative analysis across tissues revealed 26 miRNAs with coordinated expression patterns between plasma exosomes and brain, liver, or muscle, validated by qPCR. DIA proteomics quantified 4203 proteins, identifying 843 differentially enriched proteins linked to immune response, energy metabolism, and endoplasmic reticulum stress. Notably, TYMP was upregulated in muscle and exosomes, while several proteins (e.g., GYG2, BHMT) showed coordinated downregulation across tissues and exosomes in large fish. These results provide comprehensive evidence of exosome-mediated cross-tissue communication in teleosts and suggest a potential role for plasma exosomal miRNAs and proteins as non-invasive biomarkers correlated with growth status in aquaculture. Full article

Objectives: Obesity disrupts adipose and systemic immune–metabolic homeostasis, yet the molecular mechanisms through which exercise restores abnormal tissue function remain incompletely defined. This study aimed to screen cross-tissue candidate genes associated with exercise-mediated correction of obesity-related transcriptional disorders via multi-tissue transcriptome profiling and bioinformatic gene prioritization. Methods: Transcriptomic datasets of mouse visceral white adipose, subcutaneous white adipose and skeletal muscle were downloaded from the public GEO database, covering normal control, high-fat induced obese and post-exercise intervention groups. R programming was applied to complete differential analysis, GO/KEGG enrichment, PPI network, LASSO and GSEA; independent human adipose datasets from GEO validated candidate genes. Results: Exercise reversed obesity-triggered transcriptional changes in adipose tissues. Exercise-responsive genes concentrated on immune inflammation, lipid and energy metabolism. Key hub genes for tissue remodeling were screened, and depot-specific pathway regulation was verified by GSEA. CCL2 showed consistent expression trends across mouse and human adipose data. Conclusions: This study identifies distinct tissue-specific transcriptional responses to exercise: visceral adipose mainly achieves reversal of obesity-induced inflammatory dysregulation, subcutaneous adipose undergoes combined immune–inflammatory and metabolic reprogramming, while skeletal muscle presents only energy-metabolism adaptive remodeling without obvious reversal of obese gene disorders. Immune–metabolic pathways dominate exercise-induced restoration in adipose tissues. Integrated network screening and cross-species validation identified CCL2 as a conserved candidate associated with exercise-responsive immune–metabolic pathways, providing valuable molecular candidates for further anti-obesity research. Full article

The longissimus dorsi (LD) and biceps femoris (BF) muscles are important meat-producing regions in camels. Investigating differences in meat quality and proteomic profiles between the LD and BF muscles in Junggar Bactrian camels can provide a molecular basis for regulating camel meat quality and genetic improvement. In this study, 20 healthy adult male Junggar Bactrian camels were selected. Following slaughter, muscle samples were collected from the splenius (SP), triceps brachii (TB), LD, external oblique (EO), gluteus medius (GM), and BF. Meat quality parameters (pH, meat color, shear force, drip loss, and cooking loss) were measured. The LD exhibited the highest meat quality among the six cuts, in contrast to the BF, which showed the lowest. Proteomic analysis of LD and BF from 6 Junggar Bactrian camels was conducted to identify proteins associated with meat quality, yielding 81 differentially expressed proteins (DEPs). Gene Ontology (GO) enrichment analysis highlighted several significantly enriched terms among the DEPs (p < 0.05), including calcium-dependent phospholipid binding, zinc ion binding, and metal ion binding. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis (p < 0.05) further indicated notable enrichment in cytoskeletal organization, 2-oxocarboxylate metabolism, and the citric acid cycle. DEPs associated with meat quality were identified, including tubulin α-chain-like 3 and synaptic function regulator FMR1 isoform X15, which can serve as candidate DEPs for shear force. Protein phosphatase 1 regulatory subunit 14C isoform X1 can serve as a candidate differentially expressed protein for pH. Protein phosphatase 1 regulatory subunit 14C isoform X and anchoring protein repeat domain 1 can serve as candidate DEPs for cooking loss. Membrane-associated protein A4 and membrane-associated protein A7 isoform X1, as well as the transcriptional activator of cytochrome c oxidase 1, can serve as candidate DEPs for color a*. These data may serve as a reference for further studies on how different cuts affect meat quality and for practical efforts to improve camel meat quality. Full article

Heat stress (HS) is a major issue affecting productivity and physiological responses in dairy cattle. Advances in gene function research have made it possible to identify favorable genotypes for HS tolerance. This study evaluates the combined effects of temperature–humidity index (THI) and genomic load of favorable SNPs in the genes GRM8, SMAD3, and TLR4 on daily milk yield (DMY), rectal temperature (RT), and gene expression in Holstein cows (n = 160). Environmental conditions ranged from thermoneutral to severe HS, allowing the assessment of genotype by environment interactions. A subset of cows (n = 40) was selected based on genomic load to evaluate gene expression under opposite thermal conditions. Results showed that increasing THI was associated with reduced DMY and increased RT, with more pronounced effects in cows carrying fewer favorable genotypes. Slope analyses revealed that cows with higher genomic load exhibited a moderate decline in DMY and lower increase in RT, indicating enhanced resilience to HS. Significant THI × genomic load interactions were detected above a threshold of 79 units (p < 0.05). Gene expression analyses supported these findings, showing differential expressions of GRM8, SMAD3, and TLR4 under HS conditions. The functional and predictive value of these genes as markers of thermotolerance could help producers by supporting their application in genetic selection programs, thus providing another tool to combat HS and improve resilience and productivity in dairy systems. Full article

With the widespread application of microwave technology in communication and medical fields, concerns regarding its biosafety, particularly the effects on the central nervous system, have increased. The brain is considered a sensitive target organ for microwave radiation; however, the molecular mechanisms underlying microwave-induced cognitive impairment remain unclear. The purpose of this study was to evaluate the effects of 4.3 GHz microwave radiation at different power densities on spatial learning and memory in mice, and to identify key molecular changes in the hippocampus associated with cognitive impairment. Mice (male, C57BL/6N) were exposed to 4.3 GHz microwave radiation at power densities of 10 or 30 mW/cm² for 30 min. Spatial learning and memory abilities were assessed using the Morris water maze (MWM). The hippocampal structure was assessed by HE staining at multiple time points following microwave exposure. Integrated RNA-sequencing (RNA-seq) and 4D-data-independent acquisition (4D-DIA) analyses of the hippocampus were performed at 6 h after microwave exposure, and differentially expressed molecules were selected and validated by quantitative polymerase chain reaction (qPCR) and parallel reaction monitoring (PRM). The 4.3 GHz microwave exposure significantly prolonged escape latency in the MWM, indicating impaired spatial learning or navigation ability. Histological examination revealed transient neuronal damage in the hippocampal CA1 and CA3 regions. Multi-omics analysis and subsequent validation revealed molecular alterations. Following microwave radiation, the expression of synaptic plasticity-related genes Arc and Ebf3 was significantly upregulated. At the protein level, significant downregulation was observed for Protein sidekick-2 and IQGAP1, while WNK3 was significantly upregulated. In summary, 4.3 GHz microwave exposure impaired spatial learning or navigation ability, accompanied by structural damage in the hippocampus and molecular alterations in synaptic plasticity-related pathways. Arc, Ebf3, Protein sidekick-2, WNK3, and IQGAP1 might serve as candidate molecules for understanding and mitigating microwave-induced cognitive deficits. Full article