Search Results (12,019)

Accurate sex identification in reptiles with genotypic sex determination is essential for breeding management, veterinary care and evolutionary research, yet commonly used methods are often invasive, stressful or unreliable. This study aimed to evaluate a dosage-based quantitative PCR approach for molecular sex determination in caenophidian snakes, using naturally shed epidermal skin as a non-invasive DNA source. Genomic DNA extracted from shed skin was analysed by qPCR targeting conserved Z-linked genes (ADARB2, ARMC4 and TANC2), together with autosomal and reference genes, to assess sex-specific differences in gene copy number. Sixteen caenophidian snake species were examined, including taxa for which molecular sexing data are currently scarce or unavailable. The autosomal control gene showed dosage ratios close to parity between sexes, supporting DNA quality and reference gene reliability; meanwhile, Z-linked markers generally exhibited reduced dosage in females relative to males, consistent with a ZZ/ZW sex determination system. These results demonstrate that dosage-based qPCR applied to shed epidermal skin provides a promising and non-invasive framework for molecular sex determination in caenophidian snakes, without compromising animal welfare. Full article

Aquatic macrophytes constitute essential bioindicators of the ecological status of Mediterranean wetlands. We evaluated 136 Andalusian wetlands across four biogeographical regions (Sierra Morena, Betic Ranges, Guadalquivir Valley, and Coastal Zone) by contrasting two methodological approaches. We compared a standard biological valuation index, based on hydrophyte valuation and total species richness, with a biogeographical assessment focused strictly on the originality, singularity, and integrity of hydrophyte assemblages. Results revealed a critical nonlinear decoupling between both metrics. Traditional valuation prioritized the Coastal and Guadalquivir zones, inflating the value of communities saturated by widespread taxa and masking their lower structural integrity. Conversely, the biogeographical analysis identified Sierra Morena as the reservoir of highest structural stability despite its natural species poverty. Furthermore, residual analysis exposed highly original hidden jewels systematically undervalued by standard protocols. Since richness-dependent metrics risk neglecting unique hydrophyte components, we propose a dual conservation strategy integrating irreplaceability and structural integrity. Ultimately, this framework provides actionable insights for the sustainable management of Mediterranean aquatic biodiversity, aligning conservation practices with global ecological sustainability goals. We caution that management decisions based solely on richness thresholds may inadvertently prioritize common habitats over functionally unique but species-poor refugia. Full article

Intensive ornamental planting is increasingly prevalent in urban green spaces, yet its effects on soil microbial community assembly and interaction networks remain poorly understood. Here, we examined shifts in soil properties, microbial diversity, community composition, and interaction networks across successive planting cycles. Bacterial alpha-diversity remained relatively stable, whereas fungal communities showed pronounced sensitivity to early planting stages. Beta-diversity analyses revealed that bacterial community composition was jointly influenced by planting stage and site type, while fungal communities were primarily structured by site characteristics. Co-occurrence network analysis revealed contrasting reassembly trajectories between microbial groups. Bacterial networks exhibited increasing complexity and modularity, indicating enhanced interaction intensity and competitive structuring under intensive management. In contrast, fungal networks displayed reduced connectivity but maintained or recovered modular organization, suggesting structural buffering. Notably, keystone taxa remained taxonomically conserved, indicating that network reorganization was driven by interaction rewiring rather than species turnover. We propose a dual-speed reassembly framework in which bacteria function as fast-responding components with dynamic interaction networks, whereas fungi act as slow-buffering, structurally persistent elements. This decoupling of short-term functional responsiveness and long-term stability provides new insights into how intensive management reshapes soil microbiomes in botanical garden ecosystems. Full article

Understanding the genetic changes that allow avian influenza A viruses (IAVs) to switch their natural hosts and establish productive infection in humans is important for pandemic risk assessment. Adaptations in the IAV polymerase are required to overcome species-specific restrictions imposed by host ANP32 proteins. Notably, avian virus polymerase is generally only poorly supported by human ANP32 proteins due to species-specific differences. Consequently, efficient polymerase adaptation to the binding interface of human ANP32 requires distinct amino acid changes, such as PB2 E627K. A separate adaptation, PB2 M631L, has recently been reported in mammalian-adapted IAV; however, its functional role across divergent viral lineages and its relationship to host ANP32-dependent adaptation remain incompletely defined. Here, we examine PB2 M631L in the polymerases of a 1918 pandemic strain, a recombinant contemporary H1N1pdm09, and a recent clade 2.3.4.4b H5N1 virus. Using polymerase activity and protein-interaction assays, we show that PB2 M631L enhances polymerase activity and ANP32 binding in human—but not avian—contexts, and that this effect is conserved across multiple viral backgrounds. In H1N1pdm09, PB2 M631L also increased virus replication in mammalian cells. These findings indicate that PB2 M631L contributes to enhanced polymerase compatibility with human ANP32 proteins and are consistent with a role in adaptation across multiple influenza virus lineages. Our results highlight how analysis of historical pandemic strains can inform risk assessment for future emerging viruses. Full article

Globally, Central Asian wild fruit forests are critical repositories of wild fruit germplasm resources and provide essential ecosystem services. However, their habitats are facing escalating degradation risks driven by climate warming, shifting precipitation regimes, and intensifying anthropogenic disturbances. Accurately quantifying climate-driven spatiotemporal variations in habitat suitability for keystone wild fruit tree species is therefore an essential prerequisite for formulating targeted conservation and management strategies in arid and semi-arid landscapes. In this study, we applied the maximum entropy (MaxEnt) model to simulate the current (2000–2020 baseline) and future (2030s, 2050s, 2070s) potential suitable habitats of two dominant wild fruit tree species, Malus sieversii (Ledeb.) M.Roem. and Prunus cerasifera Ehrh., in the Ili Valley, a core distribution area of Central Asian wild fruit forests in northwestern China. We integrated rigorously screened species occurrence records with key environmental predictors and characterized future climate conditions using three Shared Socioeconomic Pathways (SSPs; SSP126, SSP245, and SSP585) spanning low to high radiative forcing levels. The model exhibited excellent predictive performance (AUC > 0.85), confirming the robustness and reliability of our habitat suitability simulations. Elevation and annual precipitation were identified as the dominant environmental variables governing habitat suitability for both species, highlighting the critical role of terrain–hydroclimate interactions in maintaining viable dryland refugia for wild fruit forests. Under the baseline climate scenario, the total area of suitable habitats reached 24.014 × 10³ km² for Malus sieversii and 18.990 × 10³ km² for Prunus cerasifera. Future climate projections revealed a consistent and significant contraction trend in suitable habitats for both species, with the magnitude of habitat loss escalating with increasing radiative forcing and longer projection time horizons. Specifically, under the high-emission SSP585 scenario by the 2070s, the suitable habitat area is projected to decline by 7.579 × 10³ km² for Malus sieversii and 9.883 × 10³ km² for Prunus cerasifera relative to the baseline. Our findings delineate climate-vulnerable hotspots of wild fruit forests and provide a robust spatial scientific basis for prioritizing in situ conservation, targeted habitat restoration, and anthropogenic disturbance regulation to support the long-term persistence of these irreplaceable wild fruit germplasm resources under accelerating global climate change. Full article

The evaluation of biodiversity is an essential tool for conservation, management of natural resources, and assessment of ecosystem functioning. Choosing an appropriate and understandable diversity metric is critical to ultimately make better decisions and apply more sustainable resource management. However, biodiversity metrics are numerous, and care must be taken when using them. So, should one consider all these metrics to obtain the right information? If not, how should one choose? This paper aims to demonstrate the importance of understanding and selecting the appropriate diversity metrics to reach accurate conclusions. We simulated theoretical plant communities for which calculations of different biodiversity metrics were carried out to understand why and how to use them. We explored Richness, Evenness and Disparity components of biodiversity using both scales of diversity partitioning (i.e., alpha and beta diversity). In doing so, a decision tree is proposed to select diversity metrics according to user objectives. We also suggest an add-in term if alpha metrics are calculated with subsamples to better reflect biodiversity. Finally, we recommend that when dealing with ecosystem functioning or conservation concerns, species-dependent metrics should be used, as they reflect Disparity. However, there is a critical need to increase knowledge and data availability on species traits or phylogeny to be able to better analyze Disparity. Full article

Background: The cochlea is a specialized sensory organ essential for hearing. To elucidate its cellular and molecular architecture and prioritize candidate genes associated with hearing loss (HL), we constructed a cross-species single-cell transcriptomic atlas of human fetal and postnatal mouse cochleae. Methods: We integrated single-cell and single-nucleus RNA sequencing datasets from human fetal cochleae and postnatal mouse cochleae to build a comprehensive cross-species single-cell transcriptomic atlas. Cell-type annotation, transcriptional regulator analysis, intercellular communication, and disease phenotypes were performed to dissect the cochlear cellular landscape, regulatory programs, and potential HL gene candidates. Results: A total of 19 major cochlear cell types were identified in both species, with conserved cellular composition and transcriptional programs. Comparative analysis revealed strong transcriptional conservation between matched human and mouse cell types, particularly in supporting, schwann cells and hair cells. Cell–cell communication analysis revealed conserved signaling pathways, including the BDNF-NTRK2 axis, potentially involved in cochlear development and auditory function. Regulatory network inference uncovered conserved and previously undercharacterized transcription factors, such as SKOR1, RFX2, and PAX2, predicted to be associated with hair cell identity and function. We further defined a conserved gene module of 3138 hair cell-enriched genes, from which 24 candidate HL-associated genes (e.g., ATP8B1, BDNF, and SOD1) were prioritized through integration with human disease databases and mouse auditory phenotype annotations. Conclusions: This study provides a high-resolution cross-species cochlear atlas, revealing conserved molecular programs and candidate HL-associated genes, offering valuable insights into auditory biology and potential avenues for further investigation. Full article

The evolutionary history and contemporary biogeography jointly shape the genetic architecture of marine species. This study investigates the phylogeny and population genetics of two closely related syngnathid fishes, Trachyrhamphus serratus and Trachyrhamphus longirostris. We report the first record of T. longirostris along the mainland coast of China, with samples collected from Yantai, Kenting, Zhanjiang, and Beihai. Population genetic analyses reveal genetic differentiation within T. longirostris, which exhibits low levels of genetic diversity across all sampled populations compared to T. serratus. The star-like haplotype network and significantly negative neutrality test values collectively indicate a recent population expansion event in T. longirostris. This study offers important insights into the evolutionary dynamics and biogeographic patterning of syngnathid fishes, with clear implications for their conservation and management. Full article

Armillaria species hold significant ecological and economic importance and they play a vital role in the growth of traditional Chinese medicine Gastrodia elata (G. elata). In this study, we assembled and compared the mitochondrial genomes (mitogenomes) of six Armillaria mellea (Vahl) P. Kumm. (A. mellea) strains isolated from the main G. elata-producing region of Hanzhong, China. The internal transcribed spacer (ITS) sequencing confirmed that all six strains form a monophyletic clade. Their mitogenomes (120,775 to 120,839 bp) exhibit a highly conserved architecture, each containing 16 protein-coding genes (PCGs), 23 open reading frames (ORFs), 27 tRNAs, and two rRNAs. Codon usage and amino acid frequency were strikingly similar among the six strains, with a strong AT bias. In contrast, comparisons with other Armillaria species revealed marked differences in gene order, repeat structures, and selection pressures. Phylogenetic analyses based on PCGs further resolved the close relationship among the six strains while highlighting distinct molecular variation across species. On the whole, these findings demonstrate that A. mellea strains co-evolving with G. elata maintain a highly uniform mitochondrial genome architecture, suggesting strong purifying selection or recent divergence within this symbiotic population. The pronounced differences from other Armillaria species at the levels of gene arrangement and selection pressure imply that mitochondrial gene rearrangement may have accompanied species diversification in the genus. By providing the first complete mitogenomes of A. mellea from a major G. elata cultivation area, this study not only expands the genomic resources for Armillaria but also establishes a foundation for understanding how mitochondrial variation might influence fungal growth, adaptation, and symbiotic efficiency with G. elata. Full article

Solid oxide fuel cell (SOFC) systems in shipboard power plants exhibit strong thermal–electrochemical coupling and are highly sensitive to both balance-of-plant and stack-related faults under changing operating conditions. In this study, a mechanism–data fusion dynamic model of a standalone SOFC system is developed in MATLAB/Simulink by integrating electrochemical equations with mass, species, and energy conservation and key balance-of-plant components. The model is validated against experimental data, with errors of 0.4–2.8%. Based on the validated model, fuel leakage and electrode delamination are introduced to investigate compound and sequential cross-condition faults. The present results show that fuel leakage causes the most severe degradation in current, power, and temperature, whereas electrode delamination mainly reduces current and power by decreasing the effective reaction area. Compound and sequential faults exhibit non-superimposable dynamic evolution, indicating significant fault interaction effects. A partially monotone decision tree combined with point-biserial correlation is then applied for fault diagnosis. The overall diagnostic accuracy for compound faults reaches 88.5%, while the proposed segmented cross-condition strategy improves the peak accuracy for sequential faults to 87.5%. These results provide an effective framework for SOFC fault modeling and diagnosis under variable operating conditions. Full article

Low temperature critically influences cellular metabolism by impairing processes such as membrane fluidity, enzyme activity, and protein folding. However, the comprehensive genetic landscape and regulatory mechanisms governing cold acclimation remain poorly understood. Here, we performed high-throughput, pooled genetic screening in the model alga Chlamydomonas reinhardtii (C. reinhardtii) to identify genes essential for cold acclimation. Our screening revealed numerous candidate genes implicated not only in early cold response pathways but also in core cellular processes, including DNA dynamics, protein homeostasis, metabolic regulation, and substrate transport. Notably, we identified a member of the RUS (ROOT UVB SENSITIVE) family, encoding a conserved DUF647 domain protein, designated CrRUS1. CRISPR-generated rus1 mutant alleles in C. reinhardtii display a phenotype consistent with our screening: the mutants did not exhibit any visible growth defects, but show severe growth defects at low temperature. Interestingly, the cold-induced phenotypic changes in rus1 can be reversed by dark conditions, suggesting that CrRUS1 likely promotes cold acclimation in C. reinhardtii through a light-dependent pathway. Our work provides novel genetic resources and mechanistic insights into cold acclimation in C. reinhardtii, with potential translational relevance for enhancing cold tolerance in crop species. Full article

Background/Objectives: The IUCN endangered spotted pond turtle (Geoclemys hamiltonii) demonstrates markedly reduced resistance to Aeromonas hydrophila-induced infections compared to the red-eared slider (Trachemys scripta). This study investigates the immunological basis for this disparity by analyzing infection outcomes and splenic transcriptomes of both species post-pathogen challenge. Methods: In a preliminary experiment, 32 turtles (16 G. hamiltonii and 16 T. scripta) were exposed to A. hydrophila. Results: G. hamiltonii developed skin ulcer syndrome at a significantly higher incidence (81.25%) than T. scripta (12.5%) (p < 0.05). Comparative transcriptomic analysis identified 19 differentially expressed immune-related genes, with qPCR validation across five tissues (heart, liver, spleen, intestine, blood) revealing pronounced interspecies differences in IL18, STAT1, IFIH1, and CD28 expression. Notably, IL18 and its downstream effector STAT1 were robustly upregulated in T. scripta but were considerably lower in G. hamiltonii, correlating with delayed IFN-γ pathway activation and impaired epidermal barrier repair. Concurrently, CD28 upregulation in T. scripta facilitated rapid T-cell-mediated pathogen clearance, whereas its delayed induction in G. hamiltonii hindered adaptive immunity. These findings implicate dysregulated innate (IL18/STAT1) and adaptive (CD28) immune pathways as key determinants of G. hamiltonii’s susceptibility to bacterial infection. Conclusions: Despite the critical conservation status of G. hamiltonii, the immunological basis underlying its heightened susceptibility to bacterial infections remains largely unexplored; this study addresses this gap by comparing the splenic transcriptomes of G. hamiltonii and T. scripta following A. hydrophila challenge, identifying the dysregulated IL18-STAT1 Immune Axis and CD28-mediated adaptive immunity as key determinants, thereby providing actionable immune targets for conservation breeding and susceptibility screening in this endangered species. Full article

During a study of cyanobacterial colonization on coal ash dumps at the Apatity Thermal Power Plant (Murmansk Region, NW Russia), two strains of Nostoc-like morphotypes were collected, cultivated, and examined using a polyphasic approach. Both strains KPABG–133801 and KPABG–133804 exhibited high similarity in the 16S rRNA gene (99.93%) and identical 16S–23S ITS regions. Phylogenetically, they provided robustly supported affinity to the genus Pseudoaliinostoc, which currently comprises eight species predominantly distributed in Southeast Asia. The similarity of the 16S rRNA gene (95.74–97.25%), the divergence in the 16S–23S ITS rRNA region (18.56–26.28%), and the unique hypothetical secondary structures of conserved helices (D1–D1′, Box–B, V3) strongly suggest that these Arctic strains represent a new species, Pseudoaliinostoc murmanicum, which is described and illustrated in this study. The species forms bright blue-green colonies that gradually turn olive-green with age and is characterized by elongated cells in young trichomes, vegetative cell width of less than 3.2 µm, and the presence of akinetes wider than 3.5 µm. Full article

Reconciling hydropower development with aquatic biodiversity conservation is a central challenge for sustainable river management worldwide. Cascade dam configurations, in which multiple impoundments are arranged in series along a single channel, impose longitudinal environmental gradients that restructure biological communities across trophic levels. Whether the resulting multi-trophic responses are independently driven by shared abiotic gradients (environmental filtering) or mechanistically coupled through direct food-web interactions (trophic cascading) remains unresolved. We surveyed phytoplankton, zooplankton, and benthic macroinvertebrates simultaneously at seven stations along a 430 km gradient downstream of Danjiangkou Dam in the Hanjiang River, the largest tributary of the Yangtze River and the source of China’s South-to-North Water Diversion Middle Route, over eight seasonal campaigns (2015–2017). Variance partitioning, piecewise structural equation modeling, Mantel tests, and co-occurrence network analysis were applied to partition environmental and trophic pathways. Environmental filtering dominated community restructuring at all three trophic levels, while the biotic proxy for direct trophic interactions explained less than 0.4% of community variation, consistent with weak detectable trophic coupling at seasonal resolution. Distance from Danjiangkou Dam shaped downstream transparency and turbidity gradients that mediated trophic-level-specific responses along distinct environmental axes (pH and water temperature for phytoplankton, conductivity for zooplankton, and transparency for benthic macroinvertebrates). Benthic macroinvertebrates were systematically decoupled from the pelagic analytical framework, absent from the cross-trophic co-occurrence network and structured more by spatial configuration than by water-column variables. Hub species in the network were associated with downstream mineralized conditions, confirming that network architecture reflects shared environmental preferences rather than biotic interactions. These findings support a management shift from single-dam mitigation toward cascade-scale coordination of environmental flow regimes, sediment connectivity, and substrate restoration as integrated strategies for sustaining multi-trophic biodiversity in regulated rivers. Full article

NAC (NAM, ATAF1/2 and CUC2) transcription factors constitute one of the largest plant-specific transcription factor families and play pivotal roles in plant growth, development, and responses to environmental stresses. Systematic characterization of NAC genes is essential for understanding regulatory networks underlying key agronomic and adaptive traits. As a conservation-priority woody species with distinctive biological and horticultural value, Sinojackia xylocarpa Hu lacks comprehensive knowledge of its NAC repertoire, and elucidating its NAC family will facilitate functional studies related to development and environmental adaptation. Based on whole-genome data of S. xylocarpa, we conducted a systematic survey and characterization of the NAC transcription factor family. In total, 115 SxyNAC genes encoding the conserved NAC domain were identified, and their loci were unevenly distributed across 12 chromosomes. Analyses of gene-duplication modes and collinearity indicated that whole-genome/segmental duplication events were the major driving force for the expansion of this family. Phylogenetic relationships, gene structures, and conserved motifs classified the SxyNAC members into 15 subfamilies, revealing a highly conserved N-terminal NAC domain and a markedly diversified C-terminal regulatory region with pronounced member- and lineage-specific differences. Promoter cis-element prediction showed extensive enrichment of light-responsive, phytohormone-responsive, and stress-related elements, suggesting that SxyNAC genes may participate in coordinated regulation of multiple environmental cues and endogenous hormone pathways. Transcriptome data from six fruit developmental stages, together with qRT-PCR validation of ten representative genes, demonstrated diverse temporal and tissue-specific expression patterns during fruit development and close associations with fruit growth regulation. Overall, our findings establish a framework for exploring the evolutionary trajectories and functional diversification of NAC genes in S. xylocarpa, and they offer a valuable resource for NAC-family research and conservation-focused functional genomics in other rare or threatened plant species. Full article