Search Results (91)

The ‘Tenuifoliae irises’ are a distinctive group of beardless, rhizomatous perennial irises, which are characterised by their somewhat vertical rhizomes, typically clothed at the apex with long maroon-brown, sharp fibrous remains of leaf sheaths; perianth tube long, filiform to scapiform; stigma bilobed; capsules often trigonous to six-ribbed, apically beaked; and seeds angulose to subcubic or pyriform, lacking fleshy appendages, and with testa hard, irregularly wrinkled. The representatives of the aggregate are mostly native to the dry steppes and grasslands from lowland to high mountain habitats of Central and Eastern Asia, extending westwards to the Black Sea and Caspian regions. Morphological classification of the ‘Tenuifoliae irises’ recognises about ten to eleven species, which are arranged into two genera, Sclerosiphon and Cryptobasis. Diverse molecular research recovered members of the ‘Tenuifoliae irises’ in contrasting placements within the ‘Iris-flower clade’. Sometimes, Sclerosiphon was sister to Eremiris, but Cryptobasis aligned with the ‘Spuria irises’ (Chamaeiris) and the ‘Spanish irises’ (Xiphion and related genera); in other cases, both Sclerosiphon and Cryptobasis formed a clade sister to Chamaeiris, or Cryptobasis alone was identified as the basal member of the Iris s.l. clade, positioned immediately after Siphonostylis. To examine these taxonomic discrepancies within a rigorous molecular systematic framework and using 12 reliably authenticated specimens, we generated 24 sequences of the matK gene (12) and the trnL (UAA)–trnF (GAA) loci (12) from members of the ‘Tenuifoliae irises’. These sequences were subsequently incorporated into a comprehensive dataset of the ‘Iris-flower clade’, enabling a broader analytical assessment. The obtained three-taxon statement hierarchy of patterns and maximum likelihood phylogenetic trees both recover the ‘Tenuifoliae irises’ as monophyletic and sister to Chamaeiris, and in turn to the ‘Xiphion s.l. clade’. We also found Sclerosiphon and Cryptobasis as sister genera. The morphological and karyological data supporting those relationships are discussed, which allow getting back to Rodionenko’s sources and recovering Sclerosiphon in his original sense, alongside Cryptobasis. Furthermore, the molecular results allow us to expand Sclerosiphon to include the Eastern Chinese members of the aggregate. In consequence, five new combinations (one series and four species) are established in the genus, one lectotype is designated, and data on nomenclature, distribution and ecology of the accepted species are reported. Full article

Background/Objectives: Sex and age influence inflammatory responses, but researchers have not fully characterized their combined association with complicated acute appendicitis (CAA). This study assessed the independent and interactive associations of sex, age, and inflammatory cell counts with CAA. Methods: We conducted a retrospective observational study of 708 patients with histopathologically confirmed uncomplicated appendicitis (UAA) or CAA. We analyzed demographic and clinical data, including preoperative complete blood counts, stratified by sex. We used multivariable logistic regression models with interaction terms to evaluate associations and possible effect modification by sex and age. We explored the direction and magnitude of these interactions by estimating marginal predicted probabilities. Results: The incidence of CAA was significantly higher in men than in women. In men with CAA, complete blood count analysis showed elevated neutrophil and monocyte counts and reduced lymphocyte counts. Male sex (odds ratio (OR) 2.197, 95% confidence interval (CI) 1.610–2.999), continuous age (1.017, 1.002–1.033), lymphocyte count (0.656, 0.526–0.820), monocyte count (1.551, 1.036–2.321), and platelet count (1.004, 1.001–1.006) were independently associated with CAA. Interaction analysis revealed significant interactions between neutrophils and both sex and age (p < 0.05), while lymphocyte counts showed significant interaction with age but not with sex. Conclusions: This study provides new insight into complex sex- and age-related immune cell patterns in CAA and may inform future diagnostic and management strategies by highlighting immune profile variability. Full article

This study evaluates the agri-environmental performance of the EU-27 Member States using the PROMETHEE multiple-criteria decision analysis method, based on three Eurostat indicators linked to the sustainability pillars: Harmonized Risk Indicator 1 (HRI1, social pillar), pesticide sales intensity (kg/ha UAA, environmental pillar), and environmental protection investments (% GDP, economic pillar). The analysis uses the most recent available Eurostat data (primarily from 2023) and examines three weighting scenarios: (i) equal weights, (ii) higher emphasis on the economic pillar, and (iii) higher emphasis on the environmental and social pillars. Across all scenarios, Slovenia ranked first (net flow, φ = 0.4173 to 0.4734), followed by Czechia (φ = 0.2796 to 0.3260) and France (φ = 0.1886 to 0.2240), while Malta (φ = −0.3356 to −0.3691), Cyprus (φ = −0.2916 to −0.3027), and Estonia (φ = −0.2641 to −0.2903) consistently occupied the lowest positions. The stability of rankings across alternative weighting schemes indicates robust performance patterns, with minimal shifts for most Member States. Overall, the results highlight persistent cross-country differences in agri-environmental performance despite common EU regulatory frameworks, underlining the relevance of national implementation capacity and investment strategies. The proposed PROMETHEE-based ranking provides a transparent and policy-aligned benchmarking tool that can support monitoring and prioritization of interventions related to pesticide risk reduction and environmental investment across EU Member States. Full article

Background/Objectives: Acute appendicitis (AA) is among the most common surgical emergencies. Differentiating between complicated (CAA) and uncomplicated (UAA) forms is essential for selecting the appropriate management—operative or non-operative—and for optimizing patient prioritization and outcomes. This study aimed to evaluate the diagnostic performance of emerging inflammatory indices in distinguishing these forms of AA. Methods: A total of 514 adult patients with surgically confirmed AA were retrospectively analyzed. Six immune-inflammatory indices—neutrophil-to-lymphocyte ratio (NLR), platelet-to-lymphocyte ratio (PLR), monocyte-to-lymphocyte ratio (MLR), systemic immune-inflammation index (SII), systemic inflammation response index (SIRI), and pan-immune-inflammation value (PIV)—were calculated and compared with intraoperative and histopathological findings. Postoperative outcomes, including length of hospital stay (LOS) and hospitalization costs, were also evaluated. Results: All six indices were significantly higher in intraoperatively identified complicated cases (p < 0.0001). In histopathological analysis, five indices (NLR, MLR, SII, SIRI, and PIV) remained significantly elevated in patients with wall necrosis or perforation (p = 0.000–0.019), while PLR did not reach statistical significance. The indices showed fair diagnostic accuracy (AUC = 0.664–0.719, p < 0.0001). NLR and MLR were independent risk factors for CAA (p = 0.006 and p = 0.016), and MLR was also independently associated with complicated histopathological findings (p = 0.036). PIV independently predicted both increased LOS and higher hospitalization costs (p = 0.001 for each). Conclusions: These easily calculable inflammatory markers can serve as useful adjuncts for preoperative stratification of AA, supporting timely decision-making and contributing to more cost-effective emergency surgical care. Full article

Background: Kenaf (Hibiscus cannabinus L.) is an important fiber crop belonging to the genus Hibiscus in the Malvaceae family. Research on its chloroplast genome holds significant importance for deciphering the evolutionary relationships of the Hibiscus species, developing genetic markers, and promoting kenaf (H. cannabinus) genetic breeding. Methods: Based on high-throughput sequencing technology, this study completed the sequencing and assembly of the kenaf (H. cannabinus) chloroplast genome. Results: (1) The kenaf (H. cannabinus) chloroplast genome exhibits a typical circular quadripartite structure with a total length of 163,019 bp, including a large single-copy region (LSC) of 90,467 bp, a small single-copy region (SSC) of 19,486 bp, and a pair of inverted repeat regions (IRa/IRb) of 26,533 bp each. The total GC content is 36.62%, among which, the IR region has the highest GC content (42.61%) and the SSC region the lowest (30.87%). (2) A total of 131 genes were annotated, including 85 mRNAs, 37 tRNAs, 8 rRNAs, and 1 pseudogene. Their functions cover photosynthesis (e.g., pet and atp family genes), self-replication (e.g., rpl, rps, and rpo family genes), and genes with unknown functions (e.g., ycf1 and ycf2). A codon usage bias analysis revealed that the relative synonymous codon usage (RSCU) value of the stop codon UAA is the highest (1.6329), and codons ending with A/U are preferentially used (e.g., GCU for alanine with RSCU = 1.778). (3) A repeat sequence analysis identified various interspersed repeat sequences (predominantly 30~31 bp in length, with a relatively high proportion in the 30~40 bp range, including forward and palindromic types) and simple sequence repeats (cpSSRs). Among them, single-base repeat SSRs account for the highest proportion (e.g., (A)8 and (T)9), and specific SSR primers were designed. (4) A comparative evolutionary analysis indicated that the Ka/Ks ratios (nonsynonymous substitution rate/synonymous substitution rate) of core chloroplast genes (e.g., rps2 and rpoC2) in kenaf (H. cannabinus) are all less than 1 (0.145~0.415), suggesting that they are under purifying selection. The collinearity similarity of chloroplast genomes between kenaf (H. cannabinus) and its closely related species reaches over 99.97%, and the IR region boundaries are relatively conserved. The phylogenetic tree shows that kenaf (H. cannabinus) clusters with closely related Hibiscus species with a 100% bootstrap value, indicating a close genetic relationship. Conclusions: This study provides basic data for the functional analysis of the kenaf (H. cannabinus) chloroplast genome, the phylogeny of Hibiscus, and the utilization of genetic resources. Full article

The Mongolian wild ass (Equus hemionus hemionus) is a flagship species of the desert-steppe ecosystem in Asia, and understanding its strategies for coping with cold environments is vital for both revealing its survival mechanisms and informing conservation efforts. In this study, we employed metagenomic sequencing to characterize the composition and functional potential of the gut microbiota, and applied DNA metabarcoding of the chloroplast trnL (UAA) g–h fragment to analyze dietary composition, aiming to reveal seasonal variations and the interplay between dietary plant composition and gut microbial communities. In the cold season, Bacteroidota and Euryarchaeota were significantly enriched, suggesting enhanced fiber degradation and energy extraction from low-quality forage. Moreover, genera such as Bacteroides and Alistipes were also significantly enriched and associated with short-chain fatty acid (SCFA) metabolism, bile acid tolerance, and immune modulation. In the cold season, higher Simpson index values and tighter principal coordinates analysis (PCoA) clustering indicated a more diverse and stable microbiota under harsh environmental conditions, which may represent an important microecological strategy for the host to cope with extreme environments. Functional predictions based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) further indicated upregulation of metabolic and signaling pathways, including ABC transporters, two-component systems, and quorum sensing, suggesting multi-level microbial responses to low temperatures and nutritional stress. trnL-based plant composition analysis indicated seasonal shifts, with Tamaricaceae detected more in the warm season and Poaceae, Chenopodiaceae, and Amaryllidaceae detected more in the cold season. Correlation analyses revealed that dominant microbial phyla were associated with the degradation of fiber, polysaccharides, and plant secondary metabolites, which may help maintain host energy and metabolic homeostasis. Despite the limited sample size and cross-sectional design, our findings highlight that gut microbial composition and structure may be important for host adaptation to cold environments and may also serve as a useful reference for future studies on the adaptive mechanisms and conservation strategies of endangered herbivores, including the Mongolian wild ass. Full article

Background/Objectives: Understanding variabilities in the Major Histocompatibility Complex class I (MHC I) gene is essential for evaluating immunogenetic diversity in clariid catfish. MHC I plays a critical role in immune defense by presenting endogenous antigens to cytotoxic T cells. Therefore, we aimed to investigate the genetic diversity, selection patterns, and phylogenetic relationships of MHC I alleles in three important clariid catfish species (Clarias gariepinus, Clarias macrocephalus, and Clarias batrachus) across wild and hatchery populations in Thailand. Methods: Targeted next-generation sequencing of a 174 bp fragment partial exon 6 of MHC I-UAA gene was performed, along with phylogenetic analyses, neutrality tests and dN/dS analyses. Results: Overall, 91 novel alleles were identified in 674 individuals, all of which were novel (100% novelty), with none matching existing reference sequences, thereby revealing extensive variation in population-specific variants. Phylogenetic analyses revealed allele sharing among species, which was consistent with balanced selection. Neutrality tests and dN/dS analyses provided evidence of both purifying and diversifying selection, with episodic positive selection detected at multiple codon sites associated with the antigen-binding α1 domain. Distinct selection patterns among populations, influenced by local environmental conditions and human pressures, along with high allele richness, are reflected in the diversity of immunogenetic variations. Conclusions: These findings provide critical insights into immune adaptation and highlight the potential of MHC I as a functional marker for genetic monitoring. Although a causal relationship between MHC I polymorphism and disease resistance is debated, studies suggest associations with pathogen survival, indicating future implications for aquaculture breeding and conservation, particularly in marker-assisted selection for broodstock management in Thailand. Full article

Bioregions are examples of true sustainable development. The desire for sustainability within local communities leads to agreements and the formation of bioregions in which sustainable development is based on practical action. This paper analyzes the concept of bioregions, emphasizing holistic approaches applied to, and relationships with, economic, environmental and social factors in pathways and the pace of specialization for the development of territories, thereby complementing the agricultural dimension and paying special attention to the application of organic farming techniques. The formation of bioregions is based on the desires of local communities, but at the same time, we believe that there are objective factors that influence the development of bioregions. Thirteen factors that could affect the creation of bioregions were selected using factors referred to in research papers, as well as by adding original ones. These factors can be divided into the sustainable agriculture and tourism groups, in which high values indicate a high potential for the formation of bioregions, as well as the intensive agriculture factor group, where high values indicate the benefits of large-scale economies that hinder the formation of bioregions. Cluster analysis identified six potential bioregions in Latvia, each with distinct socio-economic, environmental, and agricultural characteristics: the metropolitan region (dominant indicator-PIT per capita, value 890 EUR), the tourism cluster (dominant indicator—tourists served as a % of the total population, value 28%), the extensive agriculture cluster (dominant indicator—organically certified UAA, value 14,645 ha), the nature and education cluster (dominant indicator—protected areas, value 7587 ha), the intensive agriculture cluster (dominant indicator—profit from productive land, value 278 EUR ha⁻¹), as well as a non-specialized cluster (no strongly dominant indicators). This paper describes each cluster and discusses its potential for bioregion development. Full article

The Naozhou stock of large yellow croakers (Larimichthys crocea) exhibits unique phenotypic traits and high genetic diversity, making it a valuable resource for selective breeding and genetic conservation in aquaculture. Despite its importance, simple sequence repeat (SSR) markers have not been developed for this stock, which limits efforts in genetic evaluation, breeding optimization, and sustainable utilization of this commercially important species. In this study, 195,263 SSRs were identified from the genome of the Naozhou stock of large yellow croaker, covering a total length of 16,578,990 bp with a density of 288 bp/Mb. Dinucleotide repeats were the most common, with the AC motif being the most prevalent. The frequency of SSR markers ranged from 245.63 to 346.60 per Mb. A total of 30 primer pairs were synthesized, of which 28 pairs (93.3%) successfully amplified clear and reproducible bands in PCR assays. Among these, 28 SSR markers exhibited distinct and reproducible bands following gel electrophoresis. For eight SSR loci, the number of alleles (Na) ranged from 4 to 22 (mean = 11.375), while the effective number of alleles (Ne) ranged from 1.5401 to 10.4727 (mean = 5.6475). The assembled mitochondrial genome (mtDNA) was 16,467 bp in length and comprised 37 genes, including 13 protein-coding genes (PCGs), 22 tRNA genes, and 2 rRNA genes. The total sequence length of the PCGs was 11,431 bp, accounting for 69.4% of the mtDNA. A large portion of the PCGs (5) used incomplete stop codons (e.g., nad2, nad3, cox2), while others used TAA stop codons (e.g., nad6, nad5, TrnT). The mtDNA encoded a total of 3808 codons, with UAA showing the highest relative synonymous codon usage value. The SSR markers and mtDNA data generated in this study provide valuable tools for future genetic breeding and genomic research on the Naozhou stock of large yellow croakers. Full article

Mechanosensitive ion channels such as OSCA1.2 enable cells to sense and respond to mechanical forces by translating membrane tension into ionic flux. While lipid rearrangement in the inter-subunit cleft has been proposed as a key activation mechanism, the contributions of other domains to OSCA gating remain unresolved. Here, we combined the genetic encoding of the photoactivatable crosslinker p-benzoyl-L-phenylalanine (BzF) with functional Ca²⁺ imaging and molecular dynamics simulations to dissect the roles of specific residues in OSCA1.2 gating. Targeted UV-induced crosslinking at positions F22, H236, and R343 locked the channel in a non-conducting state, indicating their functional relevance. Structural analysis revealed that these residues are strategically positioned: F22 interacts with lipids near the activation gate, H236 lines the lipid-filled cavity, and R343 forms cross-subunit contacts. Together, these results support a model in which mechanical gating involves a distributed network of residues across multiple channel regions, allosterically converging on the activation gate. This study expands our understanding of mechanotransduction by revealing how distant structural elements contribute to force sensing in OSCA channels. Full article

Background: Rosa L. is an economically significant genus with species that are notable for their rich content of phenolic compounds. Despite its importance, the taxonomy of Rosa remains complex and unresolved. Methods: We sequenced, assembled, and performed comparative analyses of the complete plastomes of four Rosa species: R. acicularis, R. iliensis, R. laxa, and R. spinosissima. In addition to the plastome, we sequenced the nuclear ribosomal internal transcribed spacer (ITS). Results: Plastomes ranged in size from 157,148 bp (R. iliensis) to 157,346 bp (R. laxa). In each plastome, 136 genes were annotated, comprising 90 protein-coding, 38 tRNA, and eight rRNA genes. A total of 905 SSRs were identified, ranging from 224 (R. acicularis) to 229 in R. spinosissima. Nine highly variable regions were detected, including two coding genes (rps16 and ycf1) and seven intergenic spacers (ycf3-trnS(GGA), trnT(UGU)-trnL(UAA), rpl14-rpl16, trnR(UCU)-atpA, trnD(GUC), trnG(UCC)-trnfM(CAU), and psbE-petL). Maximum Likelihood (ML) phylogenetic analyses based on the complete plastome and ycf1 gene datasets consistently resolved the Rosa species into three major clades, with strong bootstrap support. In contrast, the ML tree based on ITS resolved species into four clades but showed lower bootstrap values, indicating reduced resolution compared to plastid datasets. Conclusions: Our findings underscore the value of plastome data in resolving phylogenetic relationships within the genus Rosa. Full article

The use of unmanned aerial application systems (UAASs) for precision pesticide applications has increased alongside the demand for sustainable agricultural practices. However, limited studies have standardized the necessary flight parameters ensuring the optimal use of UAASs in specialty crops (e.g., fruits and vegetables). Thus, the objective of this study was to evaluate the effects of flight speed, droplet size, and application volume on the spray deposition of UAASs, creating guidelines to facilitate their use in specialty crops. Field experiments were conducted in a three-factorial experimental design of three flight speeds (i.e., 4, 7, and 10 m/s), three droplet sizes (i.e., 150, 250, and 350 µm), and two application volumes (i.e., 18.75 and 28.10 L/ha). Spraying droplet parameters (i.e., coverage, droplet density, and droplet spectra, and application uniformity), measured through the effective swath width, were recorded to assess spray deposition efficiency. Flight speed, droplet size, and application volume significantly influenced spray deposition. Treatments with slower flight speeds (4 m/s) and higher application volumes (28.10 L/ha) increased spray coverage, while droplet density was maximized at 4 m/s with the finest droplet size (150 µm), which are desirable characteristics for pesticide applications in specialty crops. Ultimately, the effective swath width and spray uniformity were maximized at a flight speed of 7.93 m/s with a droplet size of 350 µm. These results help optimize UAAS-based pesticide application, increasing efficiency and reducing environmental impact; however, understanding pesticide translocation dynamics (i.e., systemic or contact) on plants is key for growers to determine flight parameters. Full article

The ongoing climate crisis and growing water scarcity are exerting increasing pressure on agriculture in Southern and Western Europe, leading to reduced crop yields, greater risk of land abandonment, and deterioration of soil quality. Despite the extensive literature on irrigation and water use in agriculture, the specific relationship between irrigation availability and changes in the type of farming (ToF) remains insufficiently investigated. This study aims to address this gap by analyzing data from the 2010 and 2020 Italian General Agricultural Censuses conducted by ISTAT, in combination with microdata from the Italian Farm Accountancy Data Network (FADN), focusing on irrigated farms in Southern Italy. Descriptive analysis reveals that over 60% of irrigated farms specialize in permanent crops and predominantly adopt efficient irrigation systems such as drip irrigation. Between 2010 and 2020, approximately 23.8% of farms changed their ToF; however, these transitions were not generally associated with improvements in productivity or profitability. Results from logistic regression models suggest that structural variables—including Utilized Agricultural Area (UAA), economic size, and demographic characteristics such as the farmer’s gender—play a more significant role in determining changes in the ToF than the presence of irrigation itself. Moreover, the adoption of organic practices and larger farm sizes are positively associated with ToF changes. These findings suggest that while there has been some shift toward less water-demanding and potentially more sustainable crops, the impact of irrigation on such transitions remains limited. The results underscore the need for more targeted agricultural policies and improved data collection to support effective climate adaptation strategies in the sector. Full article

Biosecurity is vital to Australia’s efforts to prevent and respond to pests and diseases. Here, we report on testing suspected illegal goods (SIGs) as part of an active Australian biosecurity response in Sydney. The Australian Government, Department of Agriculture, Fisheries and Forestry detected and secured consignments containing tuber products of unknown biosecurity risk and origin. Swab samples were collected from vacuum-sealed yam products, organic packing material (background negative controls), and field negative controls to assess possible cross-contamination from the storage facility. DNA from all samples was analysed using high-throughput metabarcoding targeting the Internal Transcribed Spacer 2 (ITS2) and the chloroplast trnL (UAA) P6 Loop gene regions by two independent teams in Australia. A plant community profile comprising Australian native species and other non-native established species would support the notion of produce being harvested and/or packaged domestically, while their absence would suggest foreign production. Of the 5,764,942 total reads produced, the bioinformatic analysis generated 5,181,530 amplicon sequencing variants employed for species identification. Twenty plant taxa were identified via ITS2 and 15 via trnL, corresponding to worldwide distributed plants, non-native species established in Australia, or species not recorded in Australia. No Australian endemic species were detected. The absence of common Australian native plants, combined with the presence of species not known to occur in Australia, provided strong evidence that the suspect tuber products were illegally imported. Full article

Salvia officinalis (common or medicinal sage) is a highly valued member of the genus Salvia. Due to its wide range of applications in various fields, including medicine, pharmacy, cosmetics, and food, S. officinalis is a common target for economic fraud. It is imperative to implement rigorous quality control measures to ensure that fraudulent practices are prevented. Such measures should include fast and simple diagnostic tools that can also be used in the field. The objective of the present study was to ascertain the true plant composition of several Salvia-based products. This was accomplished by using PCR-RFLP and LAMP assays. In both procedures, the chloroplast trnL (UAA)-trnF (GAA) intergenic spacer served as the target analyte. The findings demonstrated the reliability and validity of the two DNA-based methods for the unequivocal identification of S. officinalis as the principal component in various sage products, as well as for the detection of irregularities (mainly the presence of adulterating species) in the production and marketing of some of these products. Nonetheless, the LAMP assay offers a more straightforward, rapid, efficient, and cost-effective approach that facilitates the authentication process for sage. The adoption of this method by quality control laboratories could then ensure safety and protect consumers from potential health risks associated with adulterated sage products. Full article