Potential Inhibitors of Lumpy Skin Disease's Viral Protein (DNA Polymerase): A Combination of Bioinformatics Approaches.

Lumpy skin disease (LSD), caused by a virus within the Poxviridae family and Capripoxvirus genus, induces nodular skin lesions in cattle. This spreads through direct contact and insect vectors, significantly affecting global cattle farming. Despite the availability of vaccines, their efficacy is limited by poor prophylaxis and adverse effects. Our study aimed to identify the potential inhibitors targeting the LSDV-encoded DNA polymerase protein (gene LSDV039) for further investigation through comprehensive analysis and computational methods. Virtual screening revealed rhein and taxifolin as being potent binders among 380 phytocompounds, with respective affinities of -8.97 and -7.20 kcal/mol. Canagliflozin and tepotinib exhibited strong affinities (-9.86 and -8.86 kcal/mol) among 718 FDA-approved antiviral drugs. Simulating the molecular dynamics of canagliflozin, tepotinib, rhein, and taxifolin highlighted taxifolin's superior stability and binding energy. Rhein displayed compactness in RMSD and RMSF, but fluctuated in Rg and SASA, while canagliflozin demonstrated stability compared to tepotinib. This study highlights the promising potential of using repurposed drugs and phytocompounds as potential LSD therapeutics. However, extensive validation through in vitro and in vivo testing and clinical trials is crucial for their practical application.

Parasitic Characteristics of Ticks (Acari: Ixodidae) Collected from Water Deer (Hydropotes inermis argyropus) and Spatiotemporal Distribution Prediction within Host-Influenced Cultivated Areas.

Tick-borne diseases result from human-ixodid tick encounters, making it crucial to understand host-ixodid tick interactions and host-dependent distribution for epidemiology and prevention. This study examines water deer patterns and ixodid tick interactions in designated croplands of South Korea over two years, finding that the highest deer presence occurred in July and the lowest in May, during crop harvesting. Four tick species were identified, with Haemaphysalis longicornis being predominant (92.2%). Tick life stage analysis revealed peak nymphs and adults in July and larvae in October. Nymph abundance correlated positively with nearby water deer. MaxEnt biodiversity prediction results indicated wider water deer distribution in summer, reflecting their tendency to use multiple croplands. Areas with nymphs and adults aligned with predicted deer presence in summer, while larval areas aligned in autumn. Increased agroforestry expanded water deer habitats, enhancing tick dispersion. Prevention involved minimizing human-deer encounters by strategic land use in tick-prone areas. This comprehensive study provides insights into preventing severe fever with thrombocytopenia syndrome in agricultural workers, emphasizing the need for targeted interventions based on host behavior and tick life stages in different seasons.

Potential Tick Defense Associated with Skin and Hair Characteristics in Korean Water Deer (Hydropotes inermis argyropus).

The Korean water deer (WD), a predominant wildlife species in South Korea, is listed as vulnerable by the IUCN Red List. Despite belonging to the same family, Cervidae, WD show significantly fewer adult ixodid tick infestations compared to roe deer (RD). Ticks, which cannot fly, engage in questing behavior in natural environments to latch onto hosts. They detect signals like body temperature and host skin chemicals to navigate through the hair coat to the preferred epidermis. In light of this, we performed an extensive comparative study of the skin tissue and hair characteristics of both deer species, focusing on elements contributing to the reduced tick bite incidence in WD. Remarkably, WD exhibited more prominent blood vessels, sebaceous glands, and sweat glands, which are crucial for skin barrier functions (p < 0.005). Moreover, WD had irregular scale patterns on their hair cuticles and possessed hair that was significantly stiffer and 2.83 times thicker than that of RD (p < 0.001). These characteristics potentially impede ticks from reaching the epidermis hair in WD and RD in the context of tick bite prevention. Further investigations in this area could enhance our understanding of tick-host dynamics and contribute to developing preventive measures against tick-borne diseases in other deer species.

Habitat utilization distribution of sika deer (Cervus nippon).

Habitat-specific and movement-related behavioral studies are essential for the development of sustainable biodiversity management practices. Although the number of studies on sika deer is increasing, habitat utilization distribution (UD)-related studies remain limited. In this study, we investigated the habitat UD behavior of sika deer (Cervus nippon) using a literature survey and an experimental study on Suncheon Bonghwasan Mountain, South Korea. We reviewed home range-related literature on sika deer published between 1982 and 2019 in order to assess their estimation methods, study region, and research background. We observed that the number of studies on sika deer has increased. The minimum convex polygon (MCP) has been utilized the most to estimate habitat UD, followed by the kernel density (KD), the Brownian bridge model, and a combination of these methods. The average home ranges (95 % utilization distribution) of sika deer from the literature survey were 236.99 ha and 1183.96 ha using the minimum convex polygon and kernel density approaches, respectively. The five female deer in our experimental study on Suncheon Bonghwasan Mountain had a mean home range of 66.831 ± 15.241 ha using the MCP approach and 78.324 ± 20.82 ha using the KD approach. The UD behavior of sika deer explored in this research is expected to benefit future scholars and policymakers when formulating deer management and wildlife conservation strategies.

Genome-Wide Searching Single Nucleotide-Polymorphisms (SNPs) and SNPs-Targeting a Multiplex Primer for Identification of Common Salmonella Serotypes.

A rapid and high-quality single-nucleotide polymorphisms (SNPs)-based method was developed to improve detection and reduce salmonellosis burden. In this study, whole-genome sequence (WGS) was used to investigate SNPs, the most common genetic marker for identifying bacteria. SNP-sites encompassing 15 sets of primers (666-863 bp) were selected and used to amplify the target Salmonella serovar strains, and the amplified products were sequenced. The prevalent Salmonella enterica subspecies enterica serovars, including Typhimurium; Enteritidis, Agona, enterica, Typhi, and Abony, were amplified and sequenced. The amplified sequences of six Salmonella serovars with 15 sets of SNP-sites encompassing primers were aligned, explored SNPs, and SNPs-carrying primers (23 sets) were designed to develop a multiplex PCR marker (m-PCR). Each primer exists in at least two SNPs bases at the 3' end of each primer, such as one was wild, and another was a mismatched base by transition or transversion mutation. Thus, twenty-three sets of SNP primers (242-670 bp), including 13 genes (SBG, dedA, yacG, mrcB, mesJ, metN, rihA/B, modA, hutG, yehX, ybiY, moeB, and sopA), were developed for PCR confirmation of target Salmonella serovar strains. Finally, the SNPs in four genes, including fliA gene (S. Enteritidis), modA (S. Agona and S. enterica), sopA (S. Abony), and mrcB (S. Typhimurium and S. Typhi), were used for detection markers of six target Salmonella serotypes. We developed an m-PCR primer set in which Salmonella serovars were detected in a single reaction. Nevertheless, m-PCR was validated with 21 Salmonella isolates (at least one isolate was taken from one positive animal fecal, and n = 6 reference Salmonella strains) and non-Salmonella bacteria isolates. The SNP-based m-PCR method would identify prevalent Salmonella serotypes, minimize the infection, and control outbreaks.

Molecular Identification of Bacillus Isolated from Korean Water Deer (Hydropotes inermis argyropus) and Striped Field Mouse (Apodemus agrarius) Feces by Using an SNP-Based 16S Ribosomal Marker.

Ambiguous, heterogeneous, endospore-forming Bacillus species, notably Bacillus cereus, often produce fatal toxins that threaten human health. We identified Bacillus from wild animal fecal samples (n = 80), including the Korean water deer (n = 25) and striped field mouse (n = 55). Using traditional culture-based methods, 25 animal fecal samples (31.25%; 25/80) were found to be positive for Bacillus species, whereas using molecular techniques, 19 samples (23.75%; 19/80) were found to be positive for the same. In addition, we designed a Bacillus species-specific 16S ribosomal RNA (rRNA) gene marker and utilized it to identify 19 samples by means of PCR amplification and sequencing, using at least one colony from the 19 Bacillus positive samples. The recovered sequences were matched to sequences of three Bacillus species (B. cereus, B. amyloliquefaciens, and B. megaterium) from the GenBank database. Moreover, the phylogenetic tree generated in this study established specific clades for the Bacillus group. In addition, to differentiate between B. cereus, B. anthracis, and B. thuringiensis, we designed a single nucleotide polymorphism (SNP)-based primer by identifying SNPs in the alignment of 16S rRNA gene sequences of B. cereus group strains. The SNPs were used to design primer sets for discrimination between highly similar species from the B. cereus group. The study could be used in surveillance of agricultural fresh-produce-associated Bacillus outbreaks, for accurate identification of each Bacillus species, and in the development of control measures.

Development of Single Nucleotide Polymorphism (SNP)-Based Triplex PCR Marker for Serotype-specific Escherichia coli Detection.

Single-nucleotide polymorphisms (SNPs) are one of the most common forms of genetic variation and as such are powerful tools for the identification of bacterial strains, their genetic diversity, phylogenetic analysis, and outbreak surveillance. In this study, we used 15 sets of SNP-containing primers to amplify and sequence the target Escherichia coli. Based on the combination of the 15-sequence primer sets, each SNP site encompassing forward and reverse primer sequences (620-919 bp) were aligned and an SNP-based marker was designed. Each SNP marker exists in at least two SNP sites at the 3' end of each primer; one natural and the other artificially created by transition or transversion mutation. Thus, 12 sets of SNP primers (225-488 bp) were developed for validation by amplifying the target E. coli. Finally, a temperature gradient triplex PCR kit was designed to detect target E. coli strains. The selected primers were amplified in three genes (ileS, thrB, and polB), with fragment sizes of 401, 337, and 232 bp for E. coli O157:H7, E. coli, and E. coli O145:H28, respectively. This allele-specific SNP-based triplex primer assay provides serotype-specific detection of E. coli strains in one reaction tube. The developed marker would be used to diagnose, investigate, and control food-borne E. coli outbreaks.

The complete mitochondrial genome of Eurasian Sparrowhawk Accipiter nisus (Accipitriformes: Accipitridae).

The mitogenome of the Accipiter nisus is a circular module of 18,352 bp, which consists of 39 genes, containing 2 rRNA genes (12S rRNA and 16S rRNA), 13 protein-coding genes, 22 tRNA genes, and two non-coding regions (control region and pseudo control region). The mitogenome of A. nisus is composed of 31.3% A, 25.5% T, 30.4% C, 12.8% G, and 76.3% AT. The phylogenetic analysis revealed that A. nisus individuals was well grouped in Accipitridae and more closely related to genus Circus than other Accpiter species.

Morphological keys for identifying long-tailed gorals (Naemorhedus caudatus) and population composition in the Osaek Region of South Korea.

The objectives of this study were to select morphological keys for the identification of individual endangered long-tailed gorals through analysis of photographic data and to use these morphological keys to determine the number and population composition of gorals living in the Osaek Region of Seoraksan National Park. Amongst 8149 photos taken using 73 cameras in the Osaek Region, 2057 photos of faces and horns were analysed. The presence and absence of horns, shape of the horns, proportion of the ring to the length of the horn and facial colour pattern were selected as morphological keys to identify individual gorals. To verify the accuracy of the morphological keys for identifying gorals, a blind test was performed on gorals residing in the sanctuary of the Yanggu Goral Restoration Center. The test revealed that the population and age of gorals were discerned correctly by the morphological keys, but there was a 12.5% error in discriminating between sexes in gorals aged over 10 years. Fifty-six gorals were identified from 2057 pictures, based on the morphological keys and methods developed in this study. The population of 56 individuals consisted of 43 individuals aged over 2 years (subadult or adult) and 13 offspring aged less than 2 years, with a ratio of 3.3:1. Of the total 56 individuals, 45% were adults aged 10 years or older, 18% were adults aged 3-10 years, 7% were subadults aged 2-3 years, 23% were offspring aged less than 2 years and 7% were individuals aged 2 years or older, whose age and sex could not be confirmed. The sex ratio of males to females was 1.17:1, with a corrected sex ratio of 1:1 considering the 12.5% error rate for gorals aged over 10 years, amongst the 39 gorals aged over 2 years.

Phylogenetic reconstruction of the wolf spiders (Araneae: Lycosidae) using sequences from the 12S rRNA, 28S rRNA, and NADH1 genes: implications for classification, biogeography, and the evolution of web building behavior.

Current knowledge of the evolutionary relationships amongst the wolf spiders (Araneae: Lycosidae) is based on assessment of morphological similarity or phylogenetic analysis of a small number of taxa. In order to enhance the current understanding of lycosid relationships, phylogenies of 70 lycosid species were reconstructed by parsimony and Bayesian methods using three molecular markers; the mitochondrial genes 12S rRNA, NADH1, and the nuclear gene 28S rRNA. The resultant trees from the mitochondrial markers were used to assess the current taxonomic status of the Lycosidae and to assess the evolutionary history of sheet-web construction in the group. The results suggest that a number of genera are not monophyletic, including Lycosa, Arctosa, Alopecosa, and Artoria. At the subfamilial level, the status of Pardosinae needs to be re-assessed, and the position of a number of genera within their respective subfamilies is in doubt (e.g., Hippasa and Arctosa in Lycosinae and Xerolycosa, Aulonia and Hygrolycosa in Venoniinae). In addition, a major clade of strictly Australasian taxa may require the creation of a new subfamily. The analysis of sheet-web building in Lycosidae revealed that the interpretation of this trait as an ancestral state relies on two factors: (1) an asymmetrical model favoring the loss of sheet-webs and (2) that the suspended silken tube of Pirata is directly descended from sheet-web building. Paralogous copies of the nuclear 28S rRNA gene were sequenced, confounding the interpretation of the phylogenetic analysis and suggesting that a cautionary approach should be taken to the further use of this gene for lycosid phylogenetic analysis.