Search Results (61)

Liangshan Yanying chicken is a valuable plateau-adapted indigenous poultry breed in China. The poultry cecum modulates nutrient metabolism, gut microbial colonization and intestinal immune barrier establishment, while the molecular mechanisms driving its age-dependent development during the brooding stage remain unclear. Here, integrated transcriptomic and metabolomic profiling coupled with bioinformatics correlation analysis were conducted on cecal samples collected from chickens at post-hatching days 1, 14 and 28. Significant temporal changes were observed in cecal gene expression and metabolite abundance, and day 14 was identified as a critical window for cecal functional maturation and microbial colonization. In total, 2424 metabolites were annotated, including 600 differentially accumulated metabolites. The cecum exhibited phase-specific metabolic patterns: endogenous energy metabolism dominated at 1–14 d, while lipid biosynthesis prevailed at 14–28 d. The intestinal IgA immune network was verified as the core pathway maintaining cecal immune homeostasis in young chicks. Multi-omics conjoint analysis yielded 53 overlapping KEGG pathways, 14 core pathways, 3 pivotal metabolites and 5 hub genes, based on which three interactive regulatory networks were constructed. Transcriptomic data were validated via qRT-PCR. This study reveals cecal metabolic remodeling and regulatory characteristics during the brooding period, supplementing gut developmental research on plateau indigenous chickens. Notably, these results reflect age-related cecal developmental changes rather than breed-specific high-altitude adaptation mechanisms. Further independent verification is required for metabolomic data and predicted regulatory networks. This finding provides a theoretical basis for scientific breeding and feeding management of Liangshan Yanying chickens. Full article

To elucidate the effects of nitrogen (N) addition on soil carbon (C), N, and phosphorus (P) cycling in high-altitude orchards on the Qinghai–Tibet Plateau, a three-year field experiment was conducted at an altitude of 3000 m with four N application rates (0, 150, 300, and 450 kg N ha⁻¹, designated as CK, N150, N300, and N450, respectively). We determined soil physicochemical properties, 12 soil enzyme activities, and metagenomic characteristics, and further adopted partial least squares path modeling (PLS-PM) for data analysis and mechanism exploration. The results were as follows: (1) The N300 treatment yielded the maximum C-hydrolase activities and soil organic carbon content, with a 40.6% increase in soil organic carbon compared with the CK group. (2) The N450 treatment resulted in a 365.4% increase in soil nitrate content and significantly reduced the soil pH (from 6.32 to 5.86). Such environmental filtering significantly decreased the relative abundance of Nitrospirota and its core denitrification genes, including nosZ and narI. (3) Continuous N input induced secondary soil P limitation, leading to a more than 90% increase in phosphatase activities under the N450 treatment. Pseudomonadota activated soil P sources by enriching the functional potential of the phn gene cluster. Furthermore, the PLS-PM analysis revealed a significant negative statistical association between P-cycling enzymes and N-cycling functional potential (p < 0.01). This statistical linkage supports the observation of divergent metabolic responses among different element cycles. In conclusion, under the specific experimental conditions tested, an optimal N application rate of 300 kg N ha⁻¹ is recommended to balance agricultural productivity and soil ecological health. The microbiome of alpine apple orchards responds to elevated N input through metabolic trade-offs, namely reducing the functional potential for denitrification and enhancing the P recycling system. These findings provide vital molecular evidence to guide fertilizer reduction, optimize nutrient management, and promote the sustainable development of high-altitude agroecosystems. Full article

The rumen epithelium of Tibetan sheep plays a critical role in energy metabolism and immune defense; however, its post-transcriptional regulatory mechanisms under high-altitude hypoxia stress remain unclear. In this study, we employed integrated mRNA and miRNA transcriptome sequencing to analyze the adaptive strategies of the rumen epithelium in Tibetan sheep at different altitudes. A total of 2183 differentially expressed genes (DEGs) and 135 differentially expressed miRNAs (DEmiRNAs) were identified. Functional enrichment analysis revealed that DEGs and their target genes were significantly enriched in immune-related pathways such as the NF-κB signaling pathway and cytokine–cytokine receptor interaction, as well as metabolic pathways including oxidative phosphorylation and branched-chain amino acid degradation. Integrated network analysis highlighted key regulatory pairs, including oar-miR-370-3p targeting PCK2 and IL1R2, and novel-miR-781 regulating PIK3R5, suggesting coordinated modulation between mitochondrial homeostasis and immune responses. Specifically, the upregulation of immune genes (CCL19, MADCAM1) and heat shock proteins at TS4500m indicates enhanced mucosal immunity and stress tolerance, while altered expression of metabolic genes reflects a shift in energy substrate utilization. These findings elucidate a complex mRNA-miRNA regulatory network that enables Tibetan sheep to maintain rumen epithelial integrity and energy balance under extreme high-altitude conditions, providing novel insights into the molecular basis of hypoxia adaptation in ruminants. Full article

High-altitude hypoxic adaptation in mammals involves complex molecular mechanisms, with non-coding RNAs (ncRNAs) increasingly reported to participate in hypoxia-related regulation. However, the contribution of circRNAs in cardiac adaptation to chronic hypoxia remains largely unexplored. This study performed an integrative competitive endogenous RNA (ceRNA) analysis to investigate circRNA-mediated regulatory networks in the hearts of Tibetan pigs and Yorkshire pigs maintained under high- and low-altitude conditions, using four comparison groups (TH, TL, YH, and YL). Using Ribo-Zero RNA sequencing, we identified 961 circRNAs in heart tissues, with 358 differentially expressed circRNAs (DE-circRNAs) detected across the four groups. Functional enrichment analysis revealed that their host genes were associated with hypoxia-related pathways, including HIF-1, VEGF, AMPK, and autophagy, critical for energy metabolism and mitochondrial function. A HIF-1-specific ceRNA network was constructed, identifying key axes including circDUSP16–ssc-miR-671-5p–CAMK2A, circTLK1–ssc-miR-331-3p–SERPINE1, and circTLK1–novel-miR-624–ENO1. JASPAR analysis predicted potential HIF-1α binding sites in the promoters of ENO1, SERPINE1, and CAMK2A, supporting their regulatory roles. These findings provide a transcriptomic overview of circRNA expression patterns in pig heart tissues under different altitude conditions and prioritize candidate ceRNA relationships for further functional investigation. Full article

Background/Objectives: High-altitude exposure represents a complex psychophysiological stressor involving hypoxia, physical effort, sleep disruption and psychological strain. The endocannabinoid system (ECS) plays a key role in stress regulation, yet its epigenetic modulation under extreme environmental conditions remains poorly characterized. This pilot and exploratory study investigated DNA methylation and descriptive microRNA (miRNA) expression patterns of CNR1 and FAAH genes, and their associations with mood and anxiety outcomes, in trekkers exposed to Himalayan high altitude. Methods: Twenty-one healthy lowlanders completed a longitudinal expedition from 2860 m to 5050 m. Psychometric measures (SVARAD, BDI, SAS, SHAPS) and saliva samples were collected at baseline (T0) and at high altitude (T1). DNA methylation of CNR1 and FAAH regulatory regions was quantified by pyrosequencing. Exosomal miRNAs targeting these genes were profiled using qRT-PCR, on pooled samples; results are presented descriptively. Results: DNA methylation analysis revealed heterogeneous, sex-specific epigenetic patterns following high-altitude exposure. A significant increase in CNR1 promoter methylation at CpG4 was observed in males at T1, whereas methylation remained largely stable in females. Descriptive miRNA expression data showed bidirectional differences between groups, consistent with context-dependent stress regulation. Convergent directional patterns between miR-23b-3p expression and CNR1 methylation in males were observed. However, given the descriptive nature of the miRNA data, this observation is purely exploratory and requires replication before any mechanistic conclusions can be drawn. Psychometrically, participants showed a mild mood decline without overt clinical symptoms. Sex-specific differences in the relationship between CNR1 methylation and psychometric outcomes were observed and warrant further investigation in adequately powered cohorts. Conclusions: These preliminary findings suggest that CNR1 epigenetic regulation warrants further investigation as a potential indicator of stress adaptation and psychological responses and underscore the need to consider sex differences when evaluating resilience and vulnerability to extreme environments. Full article

Lactiplantibacillus plantarum EL2, isolated from traditional fermented yak milk in the high-altitude Gannan Tibetan Autonomous Prefecture, produces the class IIb bacteriocin PlnJK. This study established three distinct cultivation models that critically influenced bacteriocin yield. Microbial co-culture was found to enhance the stress tolerance of EL2, significantly boosting PlnJK production. The optimal inducing strain, Enterococcus faecalis MH2, increased the bacteriocin inhibition zone diameter from 15.38 mm to 25.58 mm. Following optimization of key parameters—initial inoculum concentration (10⁷ CFU/mL), inoculation ratio (3:1, EL2:MH2), and initial pH (6.0)—the inhibition zone diameter reached 30.32 mm, representing a 1.97-fold increase over pure culture. Co-culture not only advanced the onset but also extended the duration of bacteriocin synthesis. Throughout the 24 h incubation, cell density, AI-2 autoinducer concentration, and the expression of key regulatory genes were significantly elevated in co-culture compared to monoculture, aligning with a cell-density-dependent, quorum-sensing (QS) regulatory paradigm. Bacteriocin production was co-regulated by two QS pathways: the AI-2/luxS system and the plnA-mediated autoinducing peptide (AIP). Gene expression analysis revealed differential temporal regulation: luxS expression was higher during the exponential phase (2.29 vs. 1.42 in stationary phase), while plnA exhibited the opposite pattern (1.42 in exponential vs. 2.21 in stationary phase). This indicates that the AI-2/luxS pathway drives strong induction during active growth, whereas plnA/AIP-mediated promotion becomes predominant later. The stationary-phase effect is likely triggered by the accumulation of specific MH2 metabolites, which impose an environmental stress on EL2, stimulating the pln-encoded regulatory system and further enhancing bacteriocin yield. This work provides an economically viable strategy and a novel theoretical framework for optimizing microbial cultivation, enhancing bacteriocin production, and elucidating the complex QS-mediated regulatory mechanisms involved. Full article

Corydalis impatiens (Papaveraceae) is a traditional Tibetan medicinal plant (“Pa Xia Ga”) whose mitochondrial genome evolution remains unexplored, particularly in the context of high-altitude adaptation. This study presents the first complete mitochondrial genome sequence of an alpine Corydalis species to establish a comparative framework with the lowland congener C. pauciovulata for investigating environment-associated mitochondrial evolution. Using Illumina sequencing and reference-guided assembly, we characterized a 688,959 bp circular genome containing 74 genes, with GC content variations reflecting functional compartmentalization—elevated in structural RNA genes (tRNAs: 51.24%; rRNAs: 52.79%) versus protein-coding genes (44.19%). We identified 719 RNA editing sites concentrated in NADH dehydrogenase genes, suggesting post-transcriptional optimization of respiratory complex I under hypoxic conditions. The genome harbors 50 dispersed repeats (7.50%) and 67 SSRs with A-rich predominance, providing species-specific markers for authenticating “Pa Xia Ga” in Tibetan medicine quality control. Phylogenomic analysis confirms close affinity with C. pauciovulata while resolving intrageneral relationships within Ranunculales. These findings establish a dual-reference system for distinguishing conserved genus-level features from altitude-associated adaptations, enabling future comparative mitogenomics across the 465-species genus and supporting DNA-based medicinal plant identification. Full article

Glutathione-S-Transferase T1 (GSTT1) and M1 (GSTM1) are key enzymes involved in phase II detoxification. Null genotypes resulting from gene deletions are known to cause a complete loss of enzymatic activity and have been associated with altered xenobiotic metabolism in previous studies. Although genotype frequencies vary across ethnic groups, data from non-European populations, particularly Andean populations, remain limited. In this cross-sectional study, the frequency of GSTM1 and GSTT1 null genotypes was determined in 206 individuals from Cusco and Junín. Genotyping was performed by PCR using genomic DNA extracted from peripheral blood. The frequency of the GSTM1 null genotype was 49.51%, whereas that of GSTT1 was 25.24%. Combined genotype analysis showed that 63.11% of participants carried at least one null genotype and 11.65% carried both null variants. No significant differences were observed between Cusco and Junín. Compared with previously reported data, these frequencies were similar to those observed in Peruvian coastal and several South American populations. At the intercontinental level, frequencies were comparable to Europe, the Middle East, and Asia but differed from Sub-Saharan Africa and Native American populations. This first molecular characterization of GSTM1 and GSTT1 null genotypes in Andean populations provides a population-specific genetic baseline for pharmacogenetics and precision medicine research in high-altitude settings. Full article

Chinese honey bees (Apis cerana cerana Fabricius, 1793) are crucial native pollinators in China, with substantial ecological and economic value. Their morphological traits may vary along altitudinal gradients, particularly in hilly regions such as Wanyuan City, Sichuan Province, which provides typical suitable habitat for a locally thriving ecotype known as the Wanyuan honey bee. To elucidate its adaptive variation across environmental gradients, this study investigated the morphological and genetic diversity of this ecotype along an altitudinal transect in Wanyuan. A total of 656 worker individuals from 15 sampling sites (565–1611 m) were analyzed for 13 morphological traits and mitochondrial DNA (tRNAleu–COII fragment) sequences. Results revealed significant altitudinal clines in morphology: Honey bees from mid-altitude sites exhibited larger body size for several traits, while low-altitude bees possessed a significantly higher number of hindwing hamuli. Key taxonomic indices like the cubital index and proboscis length also varied significantly with altitude. Genetic analysis identified 25 haplotypes with high haplotype diversity and nucleotide diversity, indicating substantial genetic variation. Population differentiation was generally low, with one site (Yinbazhai, 900 m) showing relatively higher distinctiveness. The detected high gene flow suggests frequent genetic exchange among most populations. These findings demonstrate that the Wanyuan honey bee exhibits clear altitudinal adaptation in morphology while maintaining high genetic diversity and connectivity. This study provides a crucial scientific basis for the conservation and sustainable management of this genetic resource by highlighting the importance of its population-specific adaptations and genetic structure. Full article

The Qinghai–Xizang Plateau, known as the “Asian Water Tower”, hosts numerous lakes that are highly sensitive to climate change. Ciliates, key microbial eukaryotes in aquatic ecosystems, play crucial roles in biogeochemical cycling and food web dynamics. However, their community assembly mechanisms in such extreme habitats remain poorly understood. In July 2020, we investigated the ciliate community in Basomtso Lake. A total of 15 sampling sites were established along the horizontal gradient, and 11 vertical depth samples were collected at a central site (B15), resulting in 75 water samples for eDNA analysis. Using 18S rRNA gene high-throughput sequencing, we identified 610 ciliate amplicon sequence variants (ASVs), with the class Spirotrichea being the dominant taxonomic group. Distance–decay relationships indicated a significantly stronger community turnover rate along the vertical gradient compared to the horizontal gradient. Analyses using the neutral community model and null model revealed that community assembly was primarily stochastic. However, increasing vertical environmental heterogeneity enhanced the role of deterministic, niche-based selection. Random forest modeling identified resistivity (RES) and water temperature (WT) as the key predictors for horizontal and vertical community variation, respectively. Furthermore, Threshold Indicator Taxa Analysis (TITAN) detected specific taxa exhibiting pronounced sensitivity to gradients in RES and WT. Our findings demonstrate that horizontal community structure is governed primarily by dispersal limitation, whereas vertical zonation is shaped by environmental filtering driven primarily by RES and WT gradients under extreme plateau conditions. This study provides new insights into the mechanisms sustaining microbial diversity and ecosystem resilience in climatically vulnerable high-altitude lakes. Full article

Cold stress poses a major threat to rice productivity and grain quality. WRKY transcription factors, one of the largest plant-specific gene families, play crucial roles in plant responses to abiotic stress. However, their functions in cold responses and the evolutionary mechanisms underlying cold adaptation during the long-term domestication of cultivated rice remain poorly understood. Here, we identified OsWRKY26 as an important regulator of cold adaptation in japonica subspecies through transcriptome sequencing (RNA-seq). Subcellular localization analysis showed that the OsWRKY26 protein is localized to the nucleus under both normal and cold-stress conditions. Expression analysis indicated that OsWRKY26 is significantly upregulated at low temperature. Moreover, transgenic validation and measurements of multiple physiological traits demonstrated that OsWRKY26 positively regulates seedling cold tolerance in rice. Evolutionary analyses of OsWRKY26 and OsMYB2, a previously reported positive regulator of rice cold tolerance, suggested that these two genes diverged in wild rice and subsequently experienced directional selection in temperate japonica cultivated in high-altitude and high-latitude regions. Together, these findings provide a theoretical foundation for dissecting cold-tolerance mechanisms in rice, as well as promising genetic resources for molecular breeding in low-temperature environments. Full article

The yak represents a distinct domestic animal species that predominantly inhabits the Qinghai–Tibet Plateau and adjacent areas, possessing considerable value in both scientific and economic contexts. Compared to animals that mainly dwell on plains, such as cattle, the sperm maturation process in yak exhibits a certain degree of species specificity to adapt to their unique reproductive needs in high-altitude environments. Serving as the main storage site for functionally competent sperm, the cauda epididymis plays an integral role in mediating their post-testicular maturation. MiRNAs are vital regulatory molecules in the epididymis, influencing sperm maturation by modulating gene expression after transcription. To investigate the unique regulatory mechanisms of sperm maturation in yak, this study compared the miRNA expression profiles in the cauda epididymis of yak and cattle using high-throughput small RNA (sRNA) sequencing. The comparative analysis identified and characterized sRNA populations in the cauda epididymis of yak and cattle, revealing a similar length distribution that peaked at 22 nt and a predominance of known miRNAs. Notably, eight miRNAs were found to be highly expressed in both species. Furthermore, the first-nucleotide bias differed significantly between known and novel miRNAs within each species. A total of 31 differentially expressed (DE) miRNAs were identified, with 11 upregulated and 20 downregulated in yak compared to cattle. Among these, bta-miR-1298 exhibited the most significant upregulation, while bta-miR-2344 displayed the most pronounced downregulation. Bioinformatic analysis linked the predicted target genes of these miRNAs to numerous critical signaling pathways, including calcium signaling, the mitogen-activated protein kinase (MAPK) signaling pathway, the Ras-associated protein 1 (Rap1) signaling pathway, and the cyclic guanosine monophosphate-protein kinase G (cGMP-PKG) signaling pathway. Furthermore, eight significantly DE miRNAs, including bta-miR-2443, bta-miR-503-3p, bta-miR-6517, bta-miR-2440, bta-miR-2431-3p, bta-miR-2436-3p, bta-miR-6523a, and bta-miR-6775, were predicted to target genes involved in various aspects of sperm structural and functional maturation. These aspects include flagellum formation, sperm motility, chromatin remodeling, acrosome reaction, acrosome structure, sperm capacitation, chemotaxis, and nuclear chromatin condensation. Multiple miRNAs and their corresponding predicted target genes were analyzed by quantitative real-time PCR (qPCR), demonstrating an inverse correlation between miRNA expression and target gene levels. These findings reveal a distinct, species-specific miRNA signature in the yak cauda epididymis, which suggests a potential contribution to regulating the epididymal luminal environment and the process of sperm maturation. This study provides preliminary foundational data for elucidating the differences in sperm maturation mechanisms between yak and cattle, and offers potential novel targets for improving reproductive efficiency in plateau livestock. Full article

Cell adhesion molecules (CAMs) are key regulators of tissue structural integrity and functional coordination, yet their specific role in the adaptation of yak lung tissue to high-altitude hypoxia remains unelucidated. Thus, we employed transcriptomic sequencing (RNA-seq), molecular biology assays, and single-cell RNA-seq (scRNA-seq) to analyze the expression characteristics of CAMs in yak lung tissues at high and low altitudes. Trypsin or collagenase digestion showed higher cell counts in high-altitude yak lungs (p < 0.05). RNA-seq analysis revealed significant enrichment of differentially expressed genes (DEGs) in adhesion-related pathways. Inductively coupled plasma mass spectrometry detected elevated Ca²⁺ levels in high-altitude yak lungs (p < 0.05). Quantitative real-time PCR (qRT-PCR) detection of key genes from five major families of CAMs revealed the downregulation of cadherin and integrin family-related genes, and upregulation of immunoglobulin superfamily-related genes, in high-altitude yak lungs (p < 0.05), corroborated by immunohistochemical (IHC) staining. A 10× scRNA-seq revealed adhesion changes in 9 of 15 lung cell subpopulations, with differentially expressed CAMs involving integrins. This study demonstrates that yak lung tissue establishes a sophisticated adhesive homeostasis through differential CAMs regulation. This strategy optimizes pulmonary immune responses and energy allocation, ensures structural integrity and functional coordination, and thereby facilitates superior acclimatization to higher-altitude hypoxia. Full article

Fargesia rufa, one of the main food bamboo species for giant pandas, exhibits significant changes in nutritional composition with altitudinal gradient. However, the molecular mechanisms underlying this adaptation and its impact on the foraging behavior of giant pandas remain unclear. In this study, metabolomic and transcriptomic analyses were integrated to compare gene expression and metabolite profiles in leaves and rhizomes of F. rufa collected from 1000 m and 2000 m altitudes. With increasing altitude, 710 metabolites were up-regulated and 1032 were down-regulated in the leaves of F. rufa, whereas 684 metabolites were up-regulated and 1342 were down-regulated in the rhizomes; only 629 differential metabolites were shared between the two organs. Further analyses revealed that F. rufa responds to altitudinal changes through organ-specific metabolic reprogramming: leaves adopt a “metabolic conservation” strategy, downregulating the majority of flavonoid and phenylpropanoid metabolites, while rhizomes take an “active storage” strategy, significantly enhancing secondary metabolite synthesis and starch accumulation. This functional differentiation is consistent with the biological roles of the organs: the metabolic simplification of leaves may enhance the palatability of high-altitude leaves, while the nutritional reserves in rhizomes support bamboo shoot emergence. This study reveals the molecular mechanisms of bamboo’s altitudinal adaptation at the organ level, clarifies the intrinsic link between plant metabolism and animal diet, and provides a theoretical basis for giant panda habitat conservation. Full article

Squamosa promoter binding protein (SBP) plays a vital role in plant growth, development, and responses to abiotic stresses. The genus Notopterygium is an endangered perennial herbaceous plant mainly distributed in the high-altitude Qinghai–Tibet Plateau and adjacent areas, which possibly occurred the adaptive evolution to the extreme environmental conditions. In this study, we firstly determined the genome-wide structural characteristics, evolutionary history, and expression profiles of the SBP family genes in Notopterygium species by using genome, transcriptome, and DNA resequencing data. We have also investigated the response patterns of SBPs of N. franchetii to the drought and high-temperature stresses. The 21, 18, and 18 SBP family genes of three Notopterygium species, N. incisum, N. franchetii, and N. forrestii, were, respectively, identified and classified into eight subfamilies, with four subfamily members regulated by miR156. The structure analysis showed that the members of the same SBP subfamily had similar structures and conserved motif composition. Cis-element analysis suggested that those SBP genes may have been essential to the growth and environmental adaptation of Notopterygium. The expansion of the SBP gene family was mainly caused by the whole genome duplication/segmental duplication and transposable element duplication. Evolutionary analysis showed the SBP gene family experienced severe contraction events and most of the gene copies underwent purification selection. Population genetics analysis based on SBPs variations suggested that the genus Notopterygium species have obvious genetic structure and interspecific differentiation. RNA-seq and qRT-PCR experiments demonstrated that the expressions of SBPs genes in Notopterygium were not species-specific, but tissue-specific. NinSBP08 and NinSBP10/12 may have played the key roles in heat tolerance and drought resistance, respectively. These results provided novel insights into the evolutionary history of the SBP gene family in the endangered herb Notopterygium species in the high-altitude Qinghai–Tibet Plateau and adjacent areas. Full article