Search Results (2,363)

Urban soundscape management is a central challenge to the livability and sustainability of cities and requires approaches that complement level indicators with frameworks capable of integrating context, use and experience. In this framework, the present work applies a multilayer methodology to the Old Town of Bilbao, understood as a useful case study to explore the applicability of soundscape reading in historic centers with intense coexistence of commercial, hospitality and catering uses, pedestrian, logistical and cultural uses. The methodology is organized into two phases. The first focuses on the recording and documentation of control points and routes through sound fieldwork, perceptual descriptions and homogeneous systematization of information. From this corpus, a qualified sound map and a first visual characterization of the sound identity are elaborated. The second phase presented in this article, consists of the interpretative synthesis of the corpus through five analytical dimensions and the preparation of fragments and sound sequences conceived for future application through reactivated listening. The results are presented at three levels: (1) a traceable documentary corpus of records, files and synthetic representations; (2) a comparative reading by dimensions that identifies spatial contrasts between interior, exterior and perimeter, as well as relationships between urban form, uses, persistence, masking and salience; and (3) a set of operational audio materials prepared for subsequent comparison with inhabitants and users. In a transversal way, type–token reading distinguishes between the diversity of sounds and dominance by repetition. The article does not yet carry out participatory validation of these materials; its contribution consists of proposing and applying a traceable analytical protocol as a basis for future phases of social contrast and applied discussion. Full article

Bovine leukemia virus (BLV) is an oncogenic retrovirus and the etiological agent of enzootic bovine leukosis (EBL), which is spread worldwide. This study presents data on the genetic diversity of BLV in the Novosibirsk region of Russia. ELISA-positive samples were selected from six districts of the Novosibirsk region (Dovolnoye, Barabinsk, Tatarsk, Toguchin, Bolotnoye, and Kochenyovo districts). To assess the diversity of circulating BLV genotypes, samples were collected from settlements and districts that were geographically distant from each other and had no shared pasture lands. In total, 1410 bp fragments encoding the env gene region were obtained from 417 BLV-positive samples. Phylogenetic analysis classified 325 BLV strains (77.9%) as genotype 4 (G4) and 92 strains (22.1%) as genotype 7 (G7). A pairwise identity matrix was constructed for 268 amino acid residues. Pairwise identity of BLV amino acid sequences in the gp51 region ranged from 96.6% to 100% for G4 and from 97.4% to 100% for G7. Multiple alignment of the amino acid sequences identified 74 mutations found in the Russian BLV variants. Through the addition of 417 novel env BLV sequences to GenBank, this study significantly expands the foundational data and knowledge of BLV molecular epidemiology in Russia. Full article

This study presents a structured narrative review integrating methodological and decision-oriented perspectives. Milk proteins, particularly β-casein, have attracted increasing scientific and commercial attention due to their genetic variability and role in dairy production and product differentiation. Among β-casein variants, the A1 and A2 alleles of the CSN2 gene are of particular relevance, as their single-nucleotide difference has influenced breeding strategies and the expansion of A2-oriented dairy markets. Although multiple validated molecular genotyping approaches are available for CSN2 A1/A2 discrimination, guidance on their context-appropriate deployment in agricultural systems remains largely technique-centric. The present framework integrates analytical performance, sample complexity, and operational constraints to support the selection of fit-for-purpose methods across breeding, diagnostic, and dairy authentication contexts. Classical and advanced approaches, including polymerase chain reaction–restriction fragment length polymorphism (PCR-RFLP), allele-specific polymerase chain reaction (AS-PCR) and amplification refractory mutation system PCR (ARMS-PCR), high-resolution melting (HRM) analysis, sequencing-based methods, single nucleotide polymorphism (SNP) arrays, and digital polymerase chain reaction (dPCR), are comparatively evaluated not only in terms of sensitivity and throughput but also with respect to scalability, reproducibility, and decision risk. This framework provides a practical decision-support tool for aligning genotyping strategies with application-specific risk profiles, thereby improving reliability, transparency, and regulatory compliance in modern dairy systems. Full article

Background/Objectives: Castanopsis tibetana Hance (C. tibetana) is a valuable timber species in southern China. Its chloroplast and nuclear genomes have been characterized, but its mitochondrial genome (mitogenome) remains unknown. This study assembles and characterizes the first complete mitogenome of C. tibetana, elucidating its structural and evolutionary features. Methods: A hybrid approach combining Oxford Nanopore long reads and Illumina short reads was used. The mitogenome was assembled via iterative seed-based mapping and annotated via GeSeq and tRNAscan-SE. Repeats were identified via MISA, TRF, and REPuter. The RNA editing sites were predicted with the PREP suite. Phylogenetic analysis was performed on 14 conserved protein-coding genes from 13 species via maximum likelihood and Bayesian inference. Results: The mitogenome is a 554,078 bp circular molecule (GC 45.27%) encoding 51 genes (32 PCGs, 16 tRNAs, 3 rRNAs). It contains 202 simple sequence repeats (37.1% tetrameric). We predicted 53 C-to-U RNA editing sites, most frequently in nad7 and nad5. Codon usage showed bias, with 28 codons having RSCU > 1. Twenty fragments (6001 bp, 1.08% of the mitogenome) were transferred from the chloroplast. Phylogenomic analysis placed C. tibetana within Fagaceae, close to other Castanopsis species. Conclusions: This study provides the first comprehensive characterization of the C. tibetana mitogenome, revealing its structural architecture, repetitive landscape, RNA editing profile, and phylogenetic placement. These findings offer valuable genomic resources for understanding mitogenome evolution in Fagaceae and support future research on the conservation genetics and molecular breeding of this important tree species. Full article

‘Qing Zhou Mi’ (QZM) is a typical representative landrace of the late-ripening, high-resistance, and small-fruited peaches found in northern China. However, its genetic information has not been systematically analyzed. In this study, we sequenced and de novo assembled the QZM genome. The chromosome-level genome was 252.39 Mb in size, with a contig N50 of 24.35 Mb. Comparative genomic analysis found a total of 9.24 Mb unique fragments and 418 genes in the QZM genome, most of which were associated with resistance. Compared with the genomes of some early maturing peach accessions, the differentiation ability of the ACC oxidase and ethylene receptor gene families related to ethylene synthesis and transport in QZM was significantly weakened. In the genome-wide association study, we identified PpNAC1 as a major gene regulating the late-ripening trait of QZM. In addition, we discovered a novel locus associated with fruit weight and focused on a candidate gene in its regulation, PpLOB33. The findings of this study can serve as a foundation for further research on the genetic basis underlying the core traits of QZM, providing precise targets for molecular breeding. Full article

Ammopiptanthus nanus (Fabaceae) is a Class II nationally protected endangered evergreen shrub in China and is endemic to the arid regions of Central Asia. To assess how contrasting ex situ management histories are associated with sequence-variant retention at an ecologically relevant gene, we analyzed a 594 bp coding fragment of the antifreeze protein gene (AnAFP) in one wild population and two ex situ collections maintained under active versus passive management contexts. Only two variable sites were detected across 75 individuals, both represented by single-base indels near the 5′ end of the coding region. The wild population contained both rare variants, the actively managed ex situ collection retained one of them at low frequency, and the passively maintained collection was monomorphic across the analyzed fragment. Rarefaction analysis indicated that the absence of variation in the passive collection is unlikely to be explained by sample-size disparity alone at this targeted locus. Because only one locus was analyzed, these results are interpreted as locus-specific patterns rather than evidence of genome-wide diversity change. Nevertheless, the observed pattern is consistent with reduced retention of rare sequence variants in the passive ex situ collection and with the possibility that a narrow founder base, together with the absence of subsequent genetic supplementation, contributed to this outcome. These results support the view that ex situ conservation of A. nanus may benefit from maximizing founder representation, maintaining sufficiently large managed collections, and combining neutral marker approaches with targeted monitoring of ecologically relevant loci. Targeted loci such as AnAFP should, however, be regarded as complementary indicators rather than stand-alone proxies for broader genetic diversity or adaptive potential. Full article

Background: Respiratory syncytial virus (RSV) causes severe lung infections in infants and the elderly. The conserved central domain (CCD) of the RSV G protein is a key antigenic fragment for inducing protective antibodies. In this study, we used the hepatitis B surface antigen (HBsAg) as a platform to present this RSV G CCD fragment. Methods: We first sequenced and compared several HBsAg genotypes from clinical samples and selected one as an expression candidate for further development. The RSV G CCD was then inserted into the selected candidate to generate a recombinant expression construct. Subviral particles (SVPs) were produced using both CHO cells and yeast expression systems. Particle assembly was examined using electron microscopy. Finally, the safety and immunogenicity of the recombinant vaccine were evaluated in mice. Results: We successfully identified HBsAg38 as a potential recombinant vaccine expression candidate due to its abundant expression and secretion. The RSV G CCD fragment was inserted into the candidate and efficiently expressed in both CHO cells and yeast. The expressed protein was effectively secreted and formed uniform, spherical particles. The resulting vaccine candidate was safe for mice, causing no detectable weight loss or organ damage. Immunization with the recombinant SVPs elicited antibody responses against both HBsAg and the RSV G CCD. Upon intranasal RSV challenge, vaccinated mice exhibited markedly reduced RSV F protein and mRNA levels in lung tissues compared to PBS controls, with the yeast-derived SVP group showing the most pronounced reduction. Histopathological analysis further revealed that immunized mice had significantly less alveolar destruction and inflammatory cell infiltration than the control group, confirming that the vaccine conferred effective protection against RSV-induced lung pathology. Conclusions: We successfully developed a novel antigen-displaying HBsAg platform for generating vaccines targeting multiple pathogens. The RSV G CCD-expressing HBsAg induced a strong antibody response and provided effective protection against RSV infection. This platform offers a promising new approach for the development of next-generation vaccines. Full article

In this study, systematic experiments are conducted on a vertical rigid cylinder with two degrees of freedom in the subcritical Reynolds-number regime. The selected flow conditions cover the excitation stage, the lock-in stage, and the post-lock-in stage of vortex-induced vibration. Structural displacements, hydrodynamic forces, and wake vorticity fields are measured simultaneously using laser displacement sensors, force transducers, and particle image velocimetry. The results show that the cross-flow motion remains dominant throughout the investigated range, while the in-line motion is activated through phase coupling within the lock-in region. A stage-dependent redistribution of hydrodynamic loading is identified. The loading first concentrates in the cross-flow direction during synchronization, then partially shifts toward the in-line direction under coupled motion, and finally becomes spatially dispersed as desynchronization develops. This directional redistribution moderates the peak cross-flow amplitude, broadens the lock-in region, and alters the sequence of force-coefficient peaks. The synchronized wake measurements reveal that the flow evolves from incoherent structures to organized vortex streets and then to fragmented and irregular patterns, directly reflecting the formation and collapse of directional load concentration. These findings establish a consistent linkage between hydrodynamic loading, structural response, and wake evolution, and provide experimental evidence for the coupled dynamics of two-degree-of-freedom vortex-induced vibration, offering physical insight for the design and assessment of realistic marine cylindrical structures. Full article

This study systematically evaluated the taxonomic relationship between Streptococcus taoyuanensis ST2^T and Streptococcus caecimuris CLAAV18^T. Comparative genomic analysis revealed a high 16S rRNA gene sequence similarity of 99.6%, with the two strains clustering closely in the 16S rRNA-based phylogenetic tree. The genetic relatedness was further validated by Multi-Locus Sequence Typing (MLST) analysis: assessments of seven conserved housekeeping genes (atpD, gapA, gyrB, GdhA, recA, dnaK, and sdhA) demonstrated complete concordance in target fragment lengths (ranging from 33 bp to 121 bp). No size polymorphisms, insertions, or deletions were detected, indicating a highly conserved core genome. At the whole-genome level, the Average Amino Acid Identity (AAI), Average Nucleotide Identity (ANI), and digital DNA-DNA hybridization (dDDH) values between the two strains were 96.8%, 95.7%, and 84.6%, respectively. These values significantly exceed the established thresholds for species delineation (AAI: 95.5%; ANI: 95%; dDDH: 70%), providing robust genomic evidence that both strains belong to the same species. Furthermore, phenotypic testing confirmed nearly identical physiological characteristics, with only minor biochemical variations. Based on the integration of phylogenetic, genomic, and phenotypic evidence, we formally propose Streptococcus taoyuanensis as a later heterotypic synonym of Streptococcus caecimuris. Full article

Cascade dams fragment river habitats, but how seasonal hydrology modulates the biogeography and assembly of fish gut microbiota remains unclear. We surveyed gut bacterial communities of the omnivorous fish Saurogobio punctatus across 10 reaches separated by cascade dams in the Qijiang River during the wet (summer) and dry (winter) seasons using 16S rRNA gene amplicon sequencing. Sampling was synchronized among reaches to minimize temporal variability. Winter exhibited stronger differentiation among reaches and a steeper distance–decay pattern, and reach-scale environmental heterogeneity (especially dissolved inorganic nitrogen) was more stable under weak hydrodynamics. Null model analyses showed that stochastic processes dominated in summer, with dispersal-related processes and drift being prominent under high connectivity, whereas deterministic assembly increased in winter and was mainly associated with homogeneous selection. Compositionality-aware differential abundance analysis (ANCOM-BC2) identified 409 genera with a significant seasonal differential abundance after adjusting for reach (FDR q < 0.05). Random forest classification, used as a complementary prediction-oriented feature-ranking analysis, indicated higher reach discriminability in winter, with Nitrospirota ranking among the top features. PLS-PM indicated that α-diversity had the strongest direct association with β-diversity in the specified model, whereas spatial and environmental effects were linked to β-diversity mainly through indirect, α-diversity-mediated pathways. Biologically, α-diversity may reflect an integrative summary of the within-gut taxon pool shaped by host filtering and environmentally derived inputs (e.g., diet- and habitat-associated sources), which can influence the magnitude of between-reach compositional turnover. Together, these results show that seasonal hydrological regimes tune spatial turnover and assembly of fish gut microbiota in cascade-regulated rivers. Full article

The alpine meadows on the Qinghai-Tibetan Plateau function as critical reservoirs for regional water resources, yet face severe degradation driven by climate warming and overgrazing. Although establishing Poa pratensis artificial grasslands is a common restoration strategy, their effectiveness in recovering hydrological functions along restoration chronosequence remains poorly quantified. This study evaluated the changes in water conservation capacity and its drivers across a degradation–restoration sequence in the Qilian Mountains comprising alpine meadow (AM), degraded meadow (DM), and 2-, 3-, and 13-year artificial grasslands (AG2, AG3, AG13). Vegetation characteristics, soil structural properties, and water-holding indices were measured to assess restoration outcomes. The results showed that compared to AM, water-holding capacity at 0–30 cm in DM declined by 75.3–85.8%, primarily due to fragmentation of the mattic epipedon and deterioration of soil aggregates. While artificial restoration improved vegetation traits and some soil properties, hydrological recovery exhibited a distinct lag. Specifically, soil water-holding capacity in artificial grasslands showed no statistically significant improvement compared to DM. Even in AG13, soil water storage remained significantly lower than that in AM. Mantel tests and regression analyses identified root mass density and mean weight diameter as the primary drivers governing water conservation capacity. These findings reveal that artificial grasslands cannot serve as functional hydrological reservoirs in a timely manner, highlighting the importance of conserving intact alpine ecosystems. Full article

The guinea fowl (Numida meleagris), a thermo-tolerant and disease-resilient poultry species, holds great potential for sustainable poultry production in climate-vulnerable regions. The genomic aspects of this species remain largely understudied. The present study aims to delineate the patterns of domestication and understand the evolutionary dynamics of guinea fowl populations (wild and domestic) across three continents, utilizing whole-genome sequencing data from 122 genomes. The population structure analyses (ADMIXTURE, PCA, phylogeny, F_ST, LD, and MAF) revealed that Indian guinea fowl (CARI) shared close ancestry with Iranian (IRAD) and Chinese (CHID) domesticated populations while remaining distinct from wild lineages. The runs of homozygosity (ROH) identified 49,088 segments, with short fragments (ROHs) preponderant in Indian and domestic populations, reflecting historical inbreeding and effects of domestication cum selection. Copy number variation (CNV) analysis revealed 105,178 CNVs concatenated into 40,067 CNV regions (CNVRs) across 11 populations, establishing the first CNV atlas for guinea fowl at the global level. Gene annotation of overlapping ROH and CNVRs revealed 1080 common candidates across Asian guinea fowl populations, i.e., the Indian guinea fowl (CARI), IRAD, and CHID, including FOS, EPAS1, CD74, and CSF1R. These genes have earlier been associated with immune regulation, stress response, and thermal adaptation. Selection signature scans, integrating intra-population (iHS) and inter-population (XP-EHH) approaches, uncovered genes under positive selection linked to immune response (like BCL11B, IL18, and GPC3), thermo-tolerance (like TRPV4 and BAG3), lipid metabolism (like AACS and ELOVL4), and pigmentation (BCO2). These signatures highlight the molecular basis of resilience in guinea fowl and their potential to withstand climate-induced stresses. This study presents the first global CNV atlas for guinea fowl and provides the first comprehensive genomic characterization of the Indian domestic population, integrating ROH, CNV, and selection signature analyses. It offers a comprehensive assessment of guinea fowl genomes (wild and domesticated) across three continents, offering insights into domestication, evolutionary dynamics, and the genetic basis of their adaptation and resilience. Full article

Background/Objectives: Influenza, RSV, and SARS-CoV-2 co-circulate and evolve under immune and therapeutic pressures, complicating decision-making for both vaccine formulation and antiviral use. Fragmented, pathogen-specific sequencing approaches limit cross-virus comparability. Methods: We applied a standardized, multiplexed, amplicon-based next-generation sequencing (NGS) workflow to 34 diagnostic specimens (Ct < 35) positive for influenza A/B, RSV-A/B, or SARS-CoV-2. Sequencing libraries were generated and run on an Illumina MiSeq platform (2 × 250 bp). Although the wet-lab workflow is standardized across pathogens, consensus generation and annotation utilized two different analysis environments: Geneious Prime for influenza and MicrobioChek for RSV and SARS-CoV-2. Quality metrics included genome breadth and depth of coverage. Results: Near-complete genomes (mean coverage ≥98%) were recovered for all samples. Influenza A(H1N1)pdm09 sequences clustered in clade 6B.1A; A(H3N2) clustered in subclade 3C.2a1b.2a.2; and influenza B belonged to the Victoria lineage V1A.3a.2. RSV sequences were assigned to Nextclade clades A.D.5.1, A.D.1.10, A.D.2.1, and A.D.3 (RSV-A) and to B.D.4.1.3 and B.D.E.1 (RSV-B), consistent with the ON1 (RSV-A) and BA (RSV-B) genotypes prevalent in recent seasons. Clinically relevant mutations included changes in the influenza HA site and neuraminidase substitutions, RSV F-protein polymorphisms, and spike protein substitutions associated with recent Omicron sublineages (L455F/S, F456L) in SARS-CoV-2. Conclusions: A unified amplicon–NGS approach yields harmonized genomic data across respiratory viruses, enabling timely detection of antigenic drift and resistance markers while supporting integrated, cross-pathogen surveillance. Full article

Onchocerca flexuosa is a vector-borne filarial nematode infecting red deer (Cervus elaphus) throughout Europe. Despite numerous reports from Central, Northern, and Southern Europe, its occurrence in South-Eastern Europe has remained largely undocumented. This study provides the first molecularly confirmed report and the first systematic epidemiological assessment of O. flexuosa in red deer in Croatia. During the 2024–2025 hunting season, 110 legally harvested red deer from central Croatia were examined for subcutaneous nodules. Nodules were evaluated morphologically, and adult nematodes were identified and confirmed by sequencing of a fragment of the mitochondrial cytochrome c oxidase subunit I (COI) gene. Subcutaneous nodules were detected in 53.6% (59/110) of examined animals. O. flexuosa was confirmed in 52 deer, corresponding to an overall prevalence of 47.3%. Co-infection with Hypoderma diana occurred in 21.2% of infected animals. Sequence similarity ranged from 96.37% to 99.85% compared to published European O. flexuosa isolates. Phylogenetic analysis placed Croatian sequences within the established European lineage, without evidence of regional genetic divergence. The observed prevalence falls within the intermediate range reported across Europe and indicates stable local transmission. These findings close an important geographical knowledge gap and demonstrate that nodular onchocercosis is established in red deer populations in South-Eastern Europe. Full article

During eukaryotes evolution, mitochondrial DNA (mtDNA) fragments integrate into nuclear genomes, forming nuclear mitochondrial DNA sequences (Numts). Tortricidae (Lepidoptera), a species-rich and economically critical family, lacks systematic characterization of Numts, which hinders reliable molecular research. Here, we systematically characterized Numts in 27 Tortricidae species spanning two subfamilies via genome download, mitochondrial genome annotation, and Numt identification and characterization. With each species’ mtDNA as query, Numt identification was performed with an E-value threshold of 10⁻⁴ and a sequence similarity cut-off of >60%, with a minimum length of 50 bp to exclude spurious hits. Results showed that all species contained Numts, with copy numbers varying drastically (9–208). Numt numbers positively correlated with nuclear genome length, but not mitochondrial genome length. Numts insertion flanking regions had significantly higher AT content than nuclear genome, indicating the insertion preference for AT-rich regions. Numts were predominantly derived from the mitochondrial cox1 gene, highlighting the risk of co-amplification when cox1 is used as a DNA barcode for species identification or phylogenetic studies. This study represents a systematic charaterizition of copy number, length distribution, insertion sequence preferences, and mitochondrial gene origins of Numts in Tortricidae, offering valuable references for refining molecular systematics, comparative genomics, and pest management in Tortricidae and related lepidopteran groups. Full article