Search Results (33)

Preimplantation embryo genomic selection (eGS) enables selection prior to implantation and could accelerate genetic gain in cattle. A major hurdle is the limited DNA from embryo biopsies, requiring efficient whole-genome amplification (WGA) for accurate genomic analyses. However, alternative WGA methods and genotyping strategies have not been systematically compared in cattle. This study evaluated different methods for WGA (multiple displacement amplification (MDA) or multiple annealing and looping-based amplification cycles (MALBAC)) and for genotyping (single nucleotide polymorphism array (SNP-array), genotyping by targeted sequencing (GBTS), or whole-genome sequencing (WGS)) using 3-, 6-, and 9-cell bovine samples. MDA consistently outperformed MALBAC across various performance metrics, including amplification length, call rates, genome coverage (93.43–94.40% vs. 53.01–67.08%), and genotyping concordance (0.89–0.98 vs. 0.75–0.92). GBTS achieved the highest call rates, while SNP-array and GBTS showed excellent concordance and low error rates. WGS provided genome-wide data for precise aneuploidy detection. We further validated the workflow in trophectoderm biopsies and arrested embryos, generating reliable data for genomic evaluation, sex determination, and aneuploidy screening. MDA from ≥6 cells combined with GBTS or SNP-array showed a favorable balance of efficiency and accuracy for bovine eGS. This framework may facilitate the application of eGS in cattle breeding by enhancing selection intensity and accelerating genetic improvement. Full article

The growing antimicrobial resistance (AMR) is threatening traditional treatments for oral diseases like dental caries and periodontitis, which constitute a significant global health burden. The study aimed to isolate Bacillus species from marine samples, to assess their biosurfactant-producing capabilities, and to evaluate their antibacterial activity against oral pathogens. Bacillus strains were isolated from marine water and sediment samples, identified by phenotypic and genotypic methods, and screened for their biosurfactant-producing ability by drop collapse, hemolytic activity, bacterial adhesion to hydrocarbons (BATH), oil displacement, and emulsification assays. Ethyl acetate extracts of these Bacillus strains were tested for antibacterial efficacy against four oral pathogens (MTCC strains) by the agar-well diffusion method. Among 81 bacterial isolates, 13 were confirmed as Bacillus species by phenotypic and 16S rRNA gene sequencing. Six Bacillus isolates displayed significant antibacterial activity, and the majority were beta-hemolytic. Bacillus strain TVD12 (50 mg/mL) exhibited superior performance by inhibiting S. mutans (31 mm ± 0), S. anginosus (30.5 mm ± 0.7), S. aureus (20 mm ± 1.4), and E. faecalis (29 mm ± 4.24). Bacillus strain TVW12 (500 μg/mL) performs better in antibiofilm activity by inhibiting E. faecalis 90%, S. aureus 87.4%, and S. mutans 76.8%. Statistical analysis revealed a distinct dual-activity profile, characterized by consistent broad-spectrum antimicrobial efficacy (p = 0.809) alongside specialized, pathogen-specific antibiofilm inhibition (p = 0.004). Marine-derived Bacillus strains, such as TVW12, and TVD12 demonstrated effective antibacterial and antibiofilm properties, offering a feasible approach to combat oral pathogens, contributing to sustainable development goals (SDGs) by addressing the challenges of antimicrobial resistance (SDG 3) through sustainable marine bioprospecting (SDG 14). These findings suggest their possibility in developing novel antibacterial agents against oral pathogens in future therapeutic applications. Full article

The highly pathogenic avian influenza virus HPAI A(H5N1) genotype AF was detected in southern Europe during the 2021/2022 season and spread widely. It emerged in Bulgaria in 2022/2023, mainly affecting mallard ducks. The DA genotype of the virus was detected in a diverse group of birds, including wild birds, zoo birds, and domestic poultry, across a wide area of eastern and southern Europe in 2023. In Bulgaria, following its introduction in 2023, the DA genotype became the predominant virus in laying hens. During 2024–2025, DA spread throughout the country, displacing AF from mallard flocks. The predominant subtype in Europe in 2025 was H5N1 genotype DI.2. This genotype became dominant after December 2024, accounting for over 90% of viruses within the EA-2024-DI genotype lineage, and has been detected in a wide range of bird species. In Bulgaria, DI.2 was identified in only one outbreak in a flock of laying hens in autumn 2024 and in a single case involving a western marsh harrier (Circus aeruginosus) in early 2025. These observations are consistent with a pattern of putative hidden circulation of avian influenza virus in duck farms in Bulgaria, potentially establishing a cycle of continuous circulation of the same viral subtype. In this study, we analysed viruses originating from Bulgaria, with a particular focus on EA-2024-DI genotype DI.2, and examined mutations related to host cell receptor binding, host specificity shifts, ligand binding, antibody recognition sites, viral oligomerization interfaces, and other functional regions. Some of these mutations have been associated with antigenic drift, immune escape, and virulence. Importantly, several are linked to changes in host specificity, a critical step in the potential transition of avian influenza viruses to humans. Consequently, such mutations represent key factors in the spread of highly pathogenic avian influenza and may pose a pandemic risk. Full article

Objectives: Cervical cancer remains a major health concern worldwide. In women aged ≥ 50, diagnostic accuracy may be compromised due to menopausal changes such as atrophy and squamocolumnar junction displacement. Cytology remains the primary screening tool in many regions, including Poland, although its sensitivity and specificity are limited. This study assessed the concordance between cytological diagnoses of high-grade squamous intraepithelial lesions (HSILs); atypical squamous cells, which cannot exclude HSIL (ASC-H); atypical glandular cells (AGCs); and histopathological verification in women aged ≥ 50 years, highlighting the limitations of current diagnostic pathways. Methods: A retrospective analysis was conducted on women aged ≥ 50 years referred between 2018–2024 with abnormal cytology. All patients underwent colposcopic assessment followed by histopathological verification supported by p16 immunostaining. Cytological and histopathological results were compared. Associations between clinical variables and diagnostic concordance were tested using the chi-square test (α = 0.05). Results: Among 79 patients, histopathology confirmed high-grade squamous intraepithelial lesions with cervical intraepithelial neoplasia grade 2 or higher (HSIL/CIN2+) in 38%. Low-grade squamous intraepithelial lesions with cervical intraepithelial neoplasia grade 1 (LSIL/CIN1) were found in 11%, and vaginal intraepithelial neoplasia grade 1 (VAIN1) in 4%, while 47% demonstrated inflammatory changes or no abnormalities. HSIL cytology showed the highest concordance, whereas AGC was more frequently associated with benign findings. No statistically significant association was detected between cytology accuracy and clinical characteristics (p > 0.05), highlighting the need for further studies in larger cohorts. Conclusions: In women aged ≥ 50, abnormal cytology frequently overestimated the severity of cervical pathology. Reliance on cytology alone may lead to overtreatment or misclassification, particularly in the presence of atrophic or inflammatory changes. Complementary use of human papillomavirus (HPV) genotyping and molecular markers alongside histopathological verification is recommended to enhance diagnostic precision in this population. Full article

Embryo genomic selection (EGS) is a contemporary breeding strategy that combines genomic selection (GS) methodology with embryo biotechnology. By conducting genotyping and genomic prediction at the pre-implantation stage, embryos with superior breeding value can be identified for transfer, markedly increasing breeding efficiency while reducing the uncertainty and temporal expenditure associated with conventional GS. This study establishes a reliable embryo biopsy-based GS pipeline for sheep, incorporating optimized whole-genome amplification and microcell genotyping techniques. We developed a high-efficiency in vitro sheep embryo production platform compatible with embryo biopsy. Systematic comparison of Multiple Displacement Amplification (MDA) and Multiple Annealing and Looping Based Amplification Cycles (MALBAC) whole-genome amplification systems yielded high-quality genotypes from biopsy samples of embryos containing as few as 10 cells. Imputation using 10× whole-genome sequencing data significantly increased both genotype call rates and accuracy. High concordance was observed between embryo and lamb genotypes, and genomic estimated breeding values (GEBVs) for key growth traits exhibited strong correlations (R²: 0.91–0.98). This system enables accurate preimplantation genomic evaluation and provides an efficient strategy to accelerate genetic improvement in sheep breeding programs. Full article

Pear (Pyrus communis L.) is a widely cultivated fruit tree species, valued for its significant economic impact and cultural relevance. The rise in commercial cultivars, characterized by genetic uniformity and high yield, is increasingly displacing traditional landraces. However, traditional varieties are highly adapted to local environmental conditions, having resulted from centuries of selection. In this study, 51 pear (Pyrus communis L.) accessions conserved in the Greek national germplasm collection were genotyped using eight SSR markers recommended by the European Cooperative Programme for Plant Genetic Resources (ECPGR). A total of 44 alleles were detected, including several private alleles, indicative of localized adaptation or potential genetic isolation. Analyses of population structure and genetic diversity, using Principal Coordinate Analysis (PCoA), UPGMA clustering, and Bayesian inference via STRUCTURE, uncovered distinct genetic groupings within the collection. The results revealed moderate genetic variability among the 51 accessions and identified some accessions with significant genetic divergence. These findings underscore the importance of conserving Greek pear germplasm, as it represents an ideal source of desirable traits, such as stress tolerance and fruit quality, which can be utilized in breeding programs. Full article

Genetic mutation detection for colorectal cancer (CRC) is crucial for precision diagnosis and treatment, yet current methods often suffer from challenges such as low sensitivity, time consumption, and high costs. In our preliminary bioinformatic analysis of 751 CRC cases from The Cancer Genome Atlas and 131 Chinese patient samples, APC, TP53, and KRAS were identified as the most frequently mutated genes. Among them, KRAS missense mutations emerged as key diagnostic biomarkers. In this study, we applied a fluorescence-based long block displacement amplification (LBDA) sensing method for the rapid, high-throughput, and cost-effective detection of KRAS genetic mutations. In the LBDA system, SYBR Green dye binds to the amplified double-stranded DNA, generating a fluorescence signal that directly reflects the abundance of mutant types (MTs). This real-time signal output enables the enrichment and sensitive detection of MTs, establishing LBDA as an efficient biosensing platform for KRAS genotyping. Using this technique, a detection limit of 0.08% variant allele frequency was achieved with 20 ng of synthetic DNA input. To evaluate clinical performance, the LBDA method was applied to 118 tissue samples from 59 CRC patients, including tumor and matched peritumoral tissues. For 59 CRC tumor samples, LBDA successfully identified KRAS mutations in 37.29% of cases, closely matching results (42.37%) obtained by next-generation sequencing and achieving 88% sensitivity and 100% specificity. In conclusion, this study presents a rapid and cost-effective mutation detection method based on optical biosensing, offering strong potential for advancing personalized CRC diagnosis and treatment. Full article

Dengue fever remains a significant public health concern in tropical regions, including Central India, where outbreaks are frequent and associated with high morbidity and mortality. This study investigated the dynamics of dengue virus transmission and evolution in Central India from 2019 to 2023, focusing on the emergence of new strains and their impact on outbreak patterns. For this, 40 mosquito pools and 300 patient samples were recruited for the study. Phylogenetic and Bayesian evolutionary analyses performed on CPrM region and whole genome sequences generated by Sanger and Illumina sequencing, respectively, revealed the emergence and predominance of a novel DENV-2 genotype IV lineage III strain in the 2019 and 2023 outbreaks, which displaced the previously circulating DENV-1 genotype responsible for the 2016–2017 outbreak. Despite pre-existing DENV-1 neutralizing antibodies in the community (67 healthy volunteers), the novel DENV-2 strain exhibited higher viral loads and a greater reproduction number (R0), contributing to rapid disease spread. Molecular clock and Shannon entropy analyses suggest that DENV evolution occurred within the mosquito vector, driven by natural selection. Our findings highlight the importance of continuous DENV surveillance, including genetic characterization in both vectors and hosts, to understand viral evolution and predict future outbreaks. Rapid urbanization and inadequate sanitation in densely populated regions like India create ideal breeding grounds for mosquitoes, facilitating the introduction and establishment of novel DENV strains. Interrupting the vector–DENV–host cycle through targeted interventions is crucial for effective dengue control. Full article

African swine fever virus (ASFV) is the etiological agent of African swine fever, a highly contagious hemorrhagic disease affecting both wild boars and domestic pigs with lethality rates up to 100%. Until now, the most effective measure to prevent an outbreak of ASFV was early detection. In this situation, whole genome sequencing (WGS) allows the gathering of detailed information about the identity and epidemiology of the virus. However, due to the large genome size and complex genome ends, WGS is challenging. Current WGS workflows require either elaborate enrichment methods or are based on tiled PCR approaches, which are susceptible to genetic differences between ASFV strains. To overcome this, we developed a novel approach for WGS of ASFV, using the Phi29 DNA polymerase-based multiple displacement amplification in combination with only seven primers. Furthermore, we applied an alkaline-based DNA denaturation step to significantly increase the number of viral reads, which resolves the near-full genome of ASFV. This novel isothermal WGS approach can be used in authorized laboratories for the genomic epidemiological analysis of ASFV outbreaks caused by different genotypes. Full article

Within the whitefly Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) complex, two cryptic species, namely Middle East-Asia Minor 1 (MEAM1) and Mediterranean (MED), are important invasive pests affecting global agriculture and horticulture. They were introduced into China sequentially in the mid-1990s and around 2003, respectively. Subsequently, the latter invader MED has outcompeted the earlier invader MEAM1, becoming the dominant population in the field. Although extensive studies have explored the underlying mechanisms driving this shift, the contribution of population genetics remains notably underexplored. In this study, we analyzed the genetic diversity and structure of 22 MED and 8 MEAM1 populations from various regions of China using mitochondrial DNA sequencing and microsatellite genotyping. Our results indicate low and moderate levels of genetic differentiation among geographically separate populations of MED and MEAM1, respectively. Median-joining network analysis of mtCOI gene haplotypes revealed no clear geographic structuring for either, with common haplotypes observed across provinces, although MED had more haplotypes. Comparative analyses revealed that MED presented greater genetic diversity than MEAM1 on the basis of two markers. Furthermore, analysis of molecular variance supported these findings, suggesting that while some genetic variation exists between populations, a significant amount is also present within populations. These findings reveal the population genetics of the two invasive cryptic species of the B. tabaci complex in China and suggest that the disparities in genetic diversity drive the displacement of their populations in the field. This work also provides valuable information on the genetic factors influencing the population dynamics and dominance of these invasive whitefly species. Full article

Infectious pancreatic necrosis virus (IPNV) causes economic losses with a highly variable mortality rate worldwide, especially in rainbow trout. The virus has a double-stranded bi-partite RNA genome designated segment A and B. New complete genome sequences of nine rainbow trout isolates from Turkey were determined and subjected to phylogenetic analysis, identifying all as genotype 5 (serotype Sp). A time-dependent change in the extended pathogenicity motif of VP2 from P217T221A247 (PTA) to PTE P217T221E247 over a period of 10 years was identified. A wider analysis of 99 IPNV sequences from Turkey and Iran revealed the emergence of the motif PTE from 2007 to 2017, inducing significant morbidity in fry by 2013. In fact, displacement of the PTA motif, by the PTE motif in IPNV isolates appeared to be connected to a production peak of rainbow trout in 2013. An additional CAI analysis provided more evidence, indicating that rainbow trout culture in Turkey has an influence on the evolution of IPNV. Full article

Cherry eye is the common name for prolapse of the nictitans gland, a tear-producing gland situated under the third eyelid of dogs. Cherry eye is characterized by a red fleshy protuberance in the corner of the eye, resembling a cherry. This protrusion is a displacement of the normal gland of the third eyelid, thought to be caused by a defect in the connective tissue that secures the gland in place. Options for treatment may include anti-inflammatory medications in mild cases, but surgical replacement of the gland is usually indicated. Cherry eye is most often seen in dogs under the age of two years, with certain breeds having a higher incidence, suggesting a potential genetic association. Integration of panel genetic testing into routine clinical practice allows for the generation of large numbers of genotyped individuals paired with clinical records and enables the investigation of common disorders using a genome-wide association study (GWAS) approach at scale. In this investigation, several thousand cases and controls for cherry eye in both purebred dogs and mixed breeds are used for a large-scale GWAS, revealing a single peak of genome-wide significance on canine chromosome 18, directly at the location of the previously identified FGF4 insertion known to cause chondrodysplasia in several breeds. Full article

At the end of 2021, the SARS-CoV-2 Omicron variant of concern (VOC) displaced the previously dominant Delta VOC and enhanced diagnostic and therapeutic challenges worldwide. Respiratory specimens submitted to the Riga East University Hospital Laboratory Service by the central and regional hospitals of Latvia from January to March 2022 that were positive for SARS-CoV-2 RNA were tested by commercial multiplexed RT-qPCR targeting three of the Omicron VOC signature mutations: ΔH69/V70, E484A, and N501Y. Of the specimens tested and analyzed in parallel by whole-genome sequencing (WGS), 964 passed the internal quality criteria (genome coverage ≥90%, read depth ≥400×) and the Nextstrain’s quality threshold for “good”. We validated the detection accuracy of RT-qPCR for each target individually by using WGS as a control. The results were concordant with both approaches for 938 specimens, with the correct classification rate exceeding 96% for each target (CI 95%); however, the presumptive WHO label was misassigned for 21 specimens. The RT-qPCR genotyping provided an acceptable means to pre-monitor the prevalence of the two presumptive Omicron VOC sublineages, BA.1 and BA.2. Full article

The present work aimed to evaluate the wood of fourteen genetic materials (nine species, between native and exotic, and five clones of Eucalyptus) cultivated under two post-planting irrigation regimes in the Brazilian semiarid region. For each genotype, six trees (11 years old) were selected and subjected to two initial irrigation regimes (up to 12 months and up to 36 months) after planting. Discs of different stem heights were taken: 0% (base), breast height (DBH), 20%, 40%, 60%, 80%, and 100%. Samples were extracted along the radial axis of each disk at three regions (the pith-adjacent region, intermediate region, and bark-adjacent region). Samples were subsequently saturated in water to determine their density via the water displacement method. The irrigation systems caused changes in the pattern of radial and longitudinal variation in the clones regarding the proportion of woody material in the stem. Among the native species, Angico stood out with a high density and little juvenile wood, and Pau d’arco, with a low density and a high rate of juvenile wood. Among the exotic species, Nim presented a high density and a low rate of juvenile wood, and Chichá presented a high rate of juvenile wood and a low density. In the Eucalyptus hybrids, VE38 stood out with a high density. Overall, there was an influence from irrigation management, observed with greater intensity in exotic species for Mahogany and Acacia and for the VE41 and AEC1528 clones of Eucalyptus. The values of basic densities in the trees varied from 0.35 to 0.85 g·cm⁻³. There was good adaptation of native and exotic species and clones to the planting area in the Semiarid region. Full article

Outbreaks of Anticarsia gemmatalis (Hübner, 1818) (Lepidoptera: Erebidae), a major pest of soybean, can be controlled below economic thresholds with methods that do not involve the application of synthetic insecticides. Formulations based on natural isolates of the Anticarsia gemmatalis multiple nucleopolyhedrovirus (AgMNPV) (Baculoviridae: Alphabaculovirus) played a significant role in integrated pest management programs in the early 2000s, but a new generation of chemical insecticides and transgenic soybean have displaced AgMNPV-based products over the past decade. However, the marked genotypic variability present among and within alphabaculovirus isolates suggests that highly insecticidal genotypic variants can be isolated and used to reduce virus production costs or overcome isolate-dependent host resistance. This study aimed to select novel variants of AgMNPV with suitable insecticidal traits that could complement the existing AgMNPV active ingredients. Three distinct AgMNPV isolates were compared using their restriction endonuclease profile and in terms of their occlusion body (OB) pathogenicity. One isolate was selected (AgABB51) from which eighteen genotypic variants were plaque purified and characterized in terms of their insecticidal properties. The five most pathogenic variants varied in OB pathogenicity, although none of them was faster-killing or had higher OB production characteristics than the wild-type isolate. We conclude that the AgABB51 wild-type isolates appear to be genotypically structured for fast speed of kill and high OB production, both of which would favor horizontal transmission. Interactions among the component variants are likely to influence this insecticidal phenotype. Full article