Search Results (4,763)

Land use change profoundly impacts the trade-offs and synergies among ecosystem services in ecologically fragile watersheds. Optimizing land use patterns based on ecological function zoning is an important approach to coordinate multiple ecosystem services and promote sustainable watershed management. This study focuses on the Wuding River Basin within the Chinese Loess Plateau, using Self-Organizing Map, multi-objective genetic algorithms, and the Future Land-Use Simulation model to explore land use optimization schemes. The results show that the windbreak and sand fixation service in the Wuding River Basin presents a spatial pattern of higher values in the northwest and lower values in the southeast, while the other six services exhibit a pattern of higher values in the east and lower values in the west. Based on the ecosystem service cluster characteristics, the basin can be divided into soil and water conservation zones, habitat conservation zones, and ecologically fragile zones. The trade-offs and synergies between ecosystem services within different zones differ significantly, with the trade-off between food supply, soil conservation, and habitat quality being particularly prominent. After optimization, the food supply and soil conservation in the soil and water conservation zones increased by an average of 0.63 × 10⁴ t and 1.94 × 10⁵ t, respectively. The food supply in the habitat conservation zones increased by 0.11 × 10⁴ t, while habitat quality remained stable. In the ecologically fragile area, water production and carbon sequestration services increased by an average of 0.26 × 10⁴ t and 0.58 × 10⁵ t, respectively. During the optimization process, the reasonable allocation of grassland and unused land played a key role in balancing service conflicts. This study provides a scientific basis for coordinating trade-offs in watershed ecosystem services and achieving land use optimization management through the framework of service clusters, functional zones, and multi-objective optimization. Full article

Cadmium (Cd) contamination severely threatens crop productivity and food safety, particularly in maize (Zea mays L.), which exhibits relatively high capacities for metal uptake and translocation. Metal tolerance proteins (MTPs) play essential roles in metal homeostasis and detoxification; however, the functions of maize MTP under Cd stress remain poorly understood. In this study, a comprehensive expression analysis of the maize MTP gene family revealed that two Zn-CDF members, ZmMTP1-1 and ZmMTP1-2, displayed the strongest and most consistent transcriptional induction in response to Cd stress, especially in roots. Phylogenetic and structural analyses confirmed that both genes are closely related to MTP1 homologs from other plant species, while exhibiting distinct gene structures and regulatory features. Functional characterization in transgenic Arabidopsis thaliana demonstrated that overexpression of ZmMTP1-1 or ZmMTP1-2 significantly enhanced tolerance to Cd and Zn stress, as reflected by improved seed germination, root growth, survival, and biomass accumulation. Enhanced metal tolerance was associated with elevated antioxidant enzyme activities, reduced oxidative damage, and coordinated upregulation of endogenous metal transporter genes. Moreover, heterologous expression of ZmMTP1-1 in yeast further supported its conserved role in Cd tolerance. Collectively, these findings indicate that ZmMTP1-1 and ZmMTP1-2 contribute to Cd detoxification through coordinated metal transport and stress-response pathways, providing potential genetic resources for improving heavy metal tolerance in maize. Full article

Sirtuins are conserved proteins regulating oxidative stress and lifespan. While they enhance cellular adaptability, the long-term biological consequences of combining bioactive compounds with nanomaterials remain poorly understood. This study examined the effects of combined resveratrol and nanodiamonds (RV+NDs) in two Acheta domesticus strains: wild-type (H) and longevity-selected (D). The impact was assessed across developmental stages, focusing on survival, total sirtuin activity, specific isoforms (SIRT1, SIRT6), oxidative stress, antioxidant enzymes, and DNA damage markers. RV+NDs exposure did not result in consistent lifespan extension or sustained oxidative stress. Molecular responses were strongly dictated by genetic background and age, as reflected by significant survival differences between strains H and D (p < 0.001) Notably, a persistent increase in total sirtuin activity (~60% ↑ across developmental stages) occurred exclusively in the longevity-selected strain, though no stable activation of SIRT1 or SIRT6 was detected. While classical redox parameters showed only transient changes, DNA damage response markers emerged as the most sensitive indicators of RV+NDs exposure. Overall, the findings demonstrate that RV+NDs treatment induces context-dependent, adaptive molecular responses. This highlights the critical role of genetic background and age in shaping ageing-related pathways, suggesting that nanodelivery systems do not produce universal effects across different genotypes. Full article

Passiflora species are recognized for their intense evolutionary dynamics within the chloroplast genome (cp), serving as a primary model for studying structural variations in natural populations. This study investigates the phylogenetic relationships of 47 Passiflora accessions from Boyacá, Colombia, utilizing a multilocus approach with chloroplast genes (trnL), non-coding regions (psbA-trnH), and nuclear markers (ITS). Multiple sequence alignments identified fragment sizes of ~264 bp (trnL), ~333 bp (psbA-trnH), and ~706 bp (ITS), each displaying distinct nucleotide compositions. Evolutionary patterns and substitution rates were evaluated using the Maximum Likelihood approach in IQ-TREE, with best-fit models selected via the Bayesian Information Criterion (BIC). The analysis revealed that transitional substitution rates consistently exceeded transversions across all markers, with the trnL region exhibiting a notably high G-to-A substitution rate of 22.15. These genomic data resolved robust evolutionary proximity between P. edulis f. edulis and P. edulis f. flavicarpa, while highlighting significant genetic divergence from P. ligularis and P. maliformis. The results demonstrate that while these specific markers effectively clarify lineage relationships, an integrated multi-marker system is essential to provide a precise understanding of the complex evolutionary divergence patterns in Andean Passiflora, offering a foundational genetic background for regional biodiversity conservation. Full article

Background: Inherited kidney diseases represent a genetically and clinically heterogeneous group of disorders affecting both pediatric and adult populations. Advances in next-generation sequencing (NGS) have improved diagnostic precision; however, genotype–phenotype correlations and diagnostic yield vary substantially across disease entities. Methods:We retrospectively evaluated 165 patients referred for genetic testing due to suspected inherited kidney disease. Patients were classified into three clinical groups: polycystic kidney disease, Alport syndrome, and other syndromic patients with inherited kidney diseases. Genetic analysis was performed using NGS with Human Phenotype Ontology–based gene filtering and included evaluation of both single-nucleotide variants and copy number variations. Results: Overall diagnostic yield differed markedly between groups. A molecular diagnosis was achieved in 71.4% of Alport patients, 41.0% of PKD patients, and 70.2% of patients in the Other syndromic group. In the Alport group, variants were identified exclusively in COL4A3, COL4A4, and COL4A5, with pathogenicity and gene involvement correlating with disease severity and the presence of extrarenal manifestations. The PKD group showed predominant involvement of PKD1, followed by PKHD1 and PKD2, while a substantial proportion of patients remained genetically negative, reflecting technical and biological complexity. The Other group exhibited pronounced genetic heterogeneity, with variants distributed across multiple genes involved in tubular, glomerular, metabolic, and ciliopathy-related pathways. Computational assessments demonstrated that several variants of uncertain significance (VUS) were located in functionally critical domains and were predicted to disrupt protein stability, intermolecular interactions, or conserved structural motifs, thereby supporting the biological plausibility of their potential pathogenic impact. Conclusions: Phenotype-driven NGS enables effective molecular diagnosis across diverse inherited kidney diseases while revealing disease-specific differences in diagnostic yield and genotype–phenotype correlations. Systematic inclusion of variants of uncertain significance and careful integration of genetic and clinical data are essential for accurate interpretation and long-term patient management. Collectively, this study enhances understanding of inherited kidney diseases and underscores the value of integrating comprehensive genomic and computational approaches into routine nephrogenetic practice. Full article

Background/Objectives: Pygmy rabbits (Brachylagus idahoensis) are closely associated with sagebrush steppe habitat across the western United States, and loss and fragmentation of this habitat has contributed to the near extirpation of the Columbia Basin population in Washington state (CB). The CB pygmy rabbit was listed under the Endangered Species Act in 2003, and recovery efforts have included captive breeding, reintroduction, and genetic rescue with the translocation of rabbits from populations across the species range. Methods: We used restriction site-associated DNA sequencing (RADseq) on samples from across the species range, including CB pygmy rabbits captured prior to genetic rescue and admixture. We determined population genetic structure across the pygmy rabbit range, tested for genomic signatures of adaptive divergence among populations, assessed the genetic distinctiveness of the ancestral CB population, and identified loci useful for monitoring ancestry in the current admixed CB population. Results: Our dataset included 9794 single-nucleotide polymorphisms (SNPs) across 123 individuals. We identified four distinct genetic groups, including the central portion of the species range and three peripheral populations: CB, northern Utah/Wyoming, and southern Utah. The ancestral CB population showed the highest degree of genetic distinctiveness using multiple clustering, ordination, and genetic differentiation analyses. We identified evidence for putatively adaptive variation among populations, but no significant gene ontology associated with local adaptation. Conclusions: Our results highlight the long-term isolation of the ancestral CB population as well as historical isolation of other peripheral populations. Our results also provide SNP loci for monitoring the consequences of genetic rescue efforts in the current admixed CB population. Full article

This study employs Western Anhui as a case study, establishing a three-dimensional quantitative analytical framework comprising ‘genetic map analysis—architectural feature coding—distribution pattern analysis’ to systematically describe and measure the cross-regional dissemination characteristics of Huizhou architectural culture within Western Anhui. Through field surveys and quantitative analysis of 20 traditional buildings (10 dwellings and 10 ancestral halls), this study employs order and law to determine feature weights and uses Spearman’s correlation coefficient to analyse feature associations, revealing the selective distribution pattern of Huizhou characteristics within Western Anhui architecture. Findings indicate: (1) the frequency of Huizhou features in ancestral halls (71%) significantly exceeds that in dwellings (36%), demonstrating typological differentiation; (2) plan-related features (plan form, courtyard configuration, compositional arrangement) appear most frequently in dwellings (60%), while stone carvings achieve comprehensive coverage in ancestral halls (100%); and (3) wood carvings and stone carvings co-occurred highly (ρ = 0.90), reflecting systematic application of decorative features; doors and plan forms showed a weak negative correlation (ρ = −0.17), potentially suggesting distinct adoption pathways, though not entirely mutually exclusive. The quantitative descriptive framework and feature database constructed in this study provide a replicable methodological reference for research into cross-regional architectural cultural transmission, while also offering scientific grounds for the conservation and restoration of traditional architecture in Western Anhui. Full article

Influenza A virus remains a major cause of respiratory disease worldwide and poses a persistent challenge to vaccine development due to its rapid genetic evolution and antigenic variability. T-cell-based immunity has therefore gained increasing importance, as it can provide broader and more durable protection by targeting conserved viral regions. Accurate identification of T-cell epitopes (TCEs) is a fundamental requirement for epitope-based vaccine design and immunological research. Although numerous computational methods have been proposed, many existing approaches rely on handcrafted physicochemical features, which offer limited ability to capture contextual sequence dependencies. In this study, a transformer-based viroinformatics framework is proposed for the binary prediction of TCEs from Influenza A virus peptide sequences. The framework employs a pretrained Evolutionary Scale Modeling-2 (ESM-2) protein language model (PLM) to generate rich, contextualized embeddings directly from raw amino acid sequences, eliminating the need for manual feature engineering. These embeddings are processed using a lightweight attention-based transformer classifier to learn epitope-specific sequence patterns. The model achieves strong and stable predictive performance, attaining an accuracy of approximately 97% and an AUC close to 0.99 under stratified cross-validation. Ablation analysis further confirms that protein language model representations and self-attention contribute substantially to performance gains over classical machine learning baselines. To enhance practical reliability, Monte Carlo dropout is incorporated during inference to provide uncertainty-aware predictions, enabling differentiation between high-confidence and ambiguous peptide candidates. In addition, attention-based interpretability is used to identify residue-level contributions to model decisions, offering biologically meaningful insights into epitope recognition. Overall, this study demonstrates that PLMs combined with Transformer architectures provide an effective, interpretable, and a promising computational framework for Influenza A TCE discovery and vaccine research. Full article

Non-specific Lipid Transfer Proteins (nsLTPs) constitute a ubiquitous family of plant proteins that play a critical role in mediating plant adaptation and tolerance to abiotic stress. While their functions have been extensively characterized in model plants such as Arabidopsis thaliana and rice (Oryza sativa L.), they remain largely unexplored in Cucurbitaceae crops. We identified 31 CmnsLTP genes in the melon (Cucumis melo L.) genome, these genes were unevenly distributed across 11 chromosomes and classified into 8 subfamilies. Members of the same subfamily have similar gene structures and conserved domains, with all family members having motif 1 and motif 3. The promoter region contains cis elements that respond to light, hormones (ABA and MeJA response elements), and abiotic stress, suggesting that this gene is involved in melon growth, development, and stress response. Previous studies have identified copper resistant candidate MELO3C031073.2 through forward genetics, which belongs to the nsLTP family and was named CmnsLTPY.9 in this study. The RT qPCR results showed that the CmnsLTPY.9 exhibited specific expression in different tissues, The expression levels of CmnsLTPY.9 in leaves ranged from 0.3 to 3.2. Under copper stress, the ‘M625’ (copper-sensitive) showed a 3.2-fold increase, indicating marked upregulation. Additionally, CmnsLTPY.9 was localized to the endoplasmic reticulum, and the position remains unchanged after copper stress. This study provides the first systematic analysis of the CmnsLTP gene family in melon; these findings provide fundamental insights into their specific functions in plant development and stress response, as well as valuable genetic resources for future research on copper-tolerant molecular breeding. Full article

Familial Mediterranean fever (FMF) is a monogenic autoinflammatory disease in which renal involvement is a major determinant of prognosis and is classically dominated by amyloid A (AA) amyloidosis. Non-amyloid renal manifestations are uncommon and poorly characterized. We report a case of clinically overt FMF associated with anti-phospholipase A2 receptor (PLA2R) antibody-positive membranous nephropathy (MN). A 46-year-old man with recurrent febrile episodes fulfilling Tel Hashomer criteria for FMF developed progressive proteinuria with detectable anti-PLA2R antibodies. Genetic testing identified a heterozygous missense MEFV variant in exon 10 (p.Lys695Arg), a mutation with variable penetrance and conflicting pathogenic classification. Kidney biopsy demonstrated PLA2R-positive MN, excluding amyloidosis. After initial conservative management, the patient progressed to nephrotic syndrome complicated by renal vein thrombosis, requiring immunosuppressive therapy according to the Ponticelli regimen in addition to colchicine and anticoagulation, resulting in clinical and immunological remission. In parallel, we performed a systematic review of the literature, identifying only isolated reports of biopsy-proven MN in FMF patients. This case highlights the diagnostic importance of kidney biopsy in FMF patients with proteinuria and illustrates that immune-mediated glomerular disease may occur even in association with non-founder or variably penetrant MEFV mutations, requiring disease-specific management beyond standard autoinflammatory control. Full article

Background/Objectives: The NHX gene family plays a critical role in regulating ion homeostasis and enhancing plant tolerance to abiotic stresses. This study aimed to comprehensively analyze the structural, phylogenetic, and functional characteristics of the NHX gene family in the genome of Spinacia oleracea L. Methods: Through bioinformatic approaches, a total of 44 NHX genes were identified, and their chromosomal distribution, exon-intron organization, and conserved motifs were thoroughly characterized. Protein-protein interaction network analysis revealed that SoNHX14, SoNHX20, and SoNHX33 act as central regulators, playing key roles in cellular stress response mechanisms. Furthermore, the majority of SoNHX proteins were predicted to localize primarily to the plasma membrane, endoplasmic reticulum, and vacuole. Promoter analyses indicated a widespread presence of cis-acting elements responsive to stresses such as low temperature, drought, and wounding, as well as elements responsive to plant hormones, suggesting a complex and multilayered regulatory mechanism. Results: miRNA target predictions demonstrated that NHX genes are extensively regulated at the post-transcriptional level, predominantly by stress-associated miRNA families. Conclusions: These findings support a central role for the NHX gene family in abiotic stress adaptation in S. oleracea and provide a valuable foundation for future genetic interventions aimed at improving stress tolerance. Full article

As an elite indigenous poultry breed under national protection in China, the Xupu goose is renowned for its large body size, superior fatty liver production, premium meat quality, and high tolerance to roughage. To elucidate its genomic architecture, genetic diversity, and evolutionary selection signatures, we conducted whole-genome resequencing on 15 purposively selected, unrelated male Xupu geese. An average of 6.79 Gb of high-quality sequence data was generated per individual, yielding approximately 4.27 million single-nucleotide polymorphisms (SNPs) with a transition/transversion (Ti/Tv) ratio of 2.49. Population genomic analyses revealed that while the population retains a moderate genetic reservoir (H_E = 0.298), it exhibits a distinct heterozygote deficit (H_O = 0.217) and a moderate genomic inbreeding coefficient F_ROH = 0.204). This structural pattern underscores the genetic impact of historical ex situ closed-flock conservation and the consequent formation of cryptic family lineages. Furthermore, genome-wide integrated haplotype score (iHS) scans detected distinct regions under recent positive selection. Functional annotation of these regions highlighted candidate genes tightly associated with the breed’s hallmark traits, specifically lipid metabolism and hepatic fat deposition (ACSS2, ACSS3, PECR), alongside muscle development (CMYA5, MTPN, LEPR). Conclusively, this study delineates a comprehensive genomic landscape of the Xupu goose, providing a robust foundational resource for future germplasm conservation, molecular marker development, and precision breeding programs. Full article

Platonia insignis Mart. (Clusiaceae) is a native fruit tree of great ecological and socioeconomic importance in the Brazilian Amazon and Cerrado. However, habitat loss is threatening its genetic variability. We investigated whether habitat fragmentation across the Amazon, Cerrado, and transition zones shapes the genetic diversity and population structure of five natural populations of P. insignis, using ISSR markers. Leaf samples from 13–15 individuals per population were collected, and DNA was extracted using the CTAB protocol. Twelve ISSR primers amplified 149 loci, used to estimate genetic parameters. AMOVA showed that 73.58% of genetic variation occurred within populations and 26.41% among populations (F_ST = 0.261). Amazonian populations exhibited the highest genetic diversity, while transition zone populations had the lowest values. The Cerrado population was genetically distinct and maintained moderate intrapopulation diversity. Bayesian clustering, PCoA, and UPGMA revealed three genetic groups corresponding to the sampled regions. Transitional populations showed high genetic admixture, indicating their role as potential corridors for gene flow. Our results highlight the need to preserve genetically diverse Amazonian populations, safeguard the Cerrado population as an evolutionarily significant unit, and maintain transitional populations to promote landscape connectivity. The study provides a genetic baseline to support conservation and management of P. insignis germplasm resources. Full article

Valorisation of rabbit biodiversity plays a significant role in enhancing production by preserving genetic diversity, which is crucial for maintaining adaptability and resilience in rabbit populations, thereby supporting sustainable development and conservation efforts. With this in mind, the present research aimed at comparing live performance, carcass traits, meat quality and muscle fibre characteristics of different rabbit genotypes. Forty-five weaned rabbits (15 commercial hybrids—C; 15 Burgundy Fawn crosses—BF; 15 Vienna Blue crosses—VB) were farmed until slaughter (n = 15 replicated cages/rabbit genotype). The slaughter age was scheduled when all genotypes reached the same live weight (approx. 2800 g). After slaughtering and carcass dissection, the hind legs and longissimus lumborum muscles were excised and subjected to different evaluations. Hind legs were exploited for physicochemical analyses, while longissimus lumborum muscles were used for physical evaluations and for fibre typing, morphometric traits and enzymatic activity. As a direct response to the experimental design, results highlighted that the three genotypes exhibited different slaughter ages. Commercial hybrids displayed the fastest growth cycle, but they showed an efficiency comparable to that of VB crosses (p > 0.05). Genotypes displayed some differences in carcass characteristics, namely perirenal fat (p < 0.01) and hind leg weight (p < 0.05). The physical characteristics of meat were overall similar in the three genotypes, except for biceps femoris L*, which showed the highest value in the BF group. Meat chemical composition differed depending on the genotype, with BF rabbits having the highest ether extract (p < 0.05) content. The three genotypes displayed an overall similar fatty acid profile with some minor differences: VB rabbits had the highest C18:2 n-6 proportion (p < 0.01) and thus n-6/n-3 (p < 0.05). Cholesterol content was the highest in C rabbits (p < 0.05). Overall, the present research highlighted that BF and VB genotypes provided interesting potentialities which would be further valorised in rural farming conditions, given their higher resilience and adaptability than commercial hybrids. Full article

RNA tailing, the non-templated addition of nucleotides to RNA 3′ ends, is a conserved post-transcriptional modification that plays a critical role in regulating RNA metabolism. In plants, this process is primarily mediated by nucleotidyltransferase proteins (NTPs). In this review, we analyze current knowledge of plant NTPs by integrating evidence from genetic, biochemical, and phylogenetic analyses of the gene-family across model plants and crops. We summarize the composition and evolutionary diversification of the plant NTP gene family, with emphasis on lineage-specific expansion and conservation patterns. Using Arabidopsis thaliana as a reference framework, we then describe the molecular roles of NTPs in the tailing of distinct RNA classes, emphasizing how tail type and length confer context-dependent regulatory outcomes including stabilization versus degradation and processing/maturation versus clearance. We further examine the determinants of substrate choice, focusing on RNA type, terminal structure, and subcellular localization. Finally, we discuss the biological functions of NTP-mediated RNA tailing in plants, linking RNA tailing to development, stress responses, antiviral immunity, and agronomic traits in crops. We conclude by outlining key mechanistic and physiological challenges that define future directions for understanding and harnessing NTP-mediated RNA regulation. Collectively, this review provides an integrated framework for understanding how RNA tailing by NTPs shapes plant RNA metabolism and biological fitness. Full article