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The use of medicinal plants for managing diabetes and related conditions has been an integral part of traditional healthcare systems throughout the world including Nagaland, India. Authentic identification of these medicinal plants is crucial for their safe and effective use. A study was aimed for authentic identification of some anti-diabetic potential ethnomedicinal plants from Nagaland, India using DNA sequence based molecular characterization by amplifying and sequencing of ITS, rbcL and matK barcode regions. DNA barcode loci from the nuclear and chloroplast genomes from 15 different ethnomedicinal anti-diabetic plants of Nagaland, India, were studied for molecular characterisation. Based on the ITS, rbcL and matK region sequences, three main discrimination methods, i.e., BLAST, Phylogenetic tree and genetic distance, were adopted to identify the species. Utilising DNA markers for identification is both highly advantageous and efficient due to its reliability and rapidity. Successful amplification across species and high blast hits (100 % identity) highlighted their potential for molecular characterisation. Phylogenetic trees constructed using various models showed distinct clades and subclades, with matK revealing hypervariability and rbcL demonstrating consistent matches. Genetic distances revealed varying levels of similarity, with certain species establishing close relationships based on pairwise comparisons. GC% variations were detected, potentially indicating nucleotide composition differences and functional constraints among species genomes. The findings of this study highlight that the ITS, rbcL , and matK regions serve as effective markers for verifying the authenticity of anti-diabetic medicinal plants indigenous to Nagaland, India. [Display omitted] • DNA markers based species identification of 15 antidiabetic plants from Nagaland. • ITS, matK and rbcL based identification complemented with phonological identification. • Consistency in rbcL and matK regions showing reliability as DNA barcode markers. • Sequence length variations attributed to genomic differences among plants. [ABSTRACT FROM AUTHOR]

In the present study, we report for the first time the presence of Vitrina pellucida and Arion silvaticus as invasive species in Isla Grande of Tierra del Fuego, Argentina. Additionally, our research confirmed the presence in the same region of Deroceras reticulatum a previously reported invasive species from continental Patagonia. Taxonomic identification was achieved through morphological and molecular analyses (ribosomal 5.8S-ITS2-28S region and 16S rRNAgene). The finding of V. pellucida constitutes the first record of Vitrinidae for South America. This species is already naturalized in southern Tierra del Fuego and invaded natural areas of the National Park but still with small populations. In the case of Arion silvaticus , we observed a comparable situation, as this species has not only been collected from urban areas but also from within the forests of the protected area. These exotic species of land snails are exclusively cold-adapted Pulmonates. Their feeding types and diets range from herbivores on fresh plant material to omnivorous, occasionally on dead animals. The native micro snail species, coexisting in the same habitats, due to their minimal dispersal capacity and probable dependence on particular microhabitats, are particularly vulnerable not only to anthropogenic disturbances but also to the impacts and activities of these exotic species. Given the tourist impact in the region, the introduction of V. pellucida and Arion silvaticus in Tierra del Fuego has most likely occurred through accidental transport in soil by tourists arriving on the island. Another possible pathway of introduction is plant transportation. [ABSTRACT FROM AUTHOR]

The precise classification of DNA sequences is pivotal in genomics, holding significant implications for personalized medicine. The stakes are particularly high when classifying key genetic markers such as BRAC, related to breast cancer susceptibility; BRAF, associated with various malignancies; and KRAS, a recognized oncogene. Conventional machine learning techniques often necessitate intricate feature engineering and may not capture the full spectrum of sequence dependencies. To ameliorate these limitations, this study employs an adapted U-Net architecture, originally designed for biomedical image segmentation, to classify DNA sequences.The attention mechanism was also tested LONG WITH u-Net architecture to precisely classify DNA sequences into BRAC, BRAF, and KRAS categories. Our comprehensive methodology includes rigorous data preprocessing, model training, and a multi-faceted evaluation approach. The adapted U-Net model exhibited exceptional performance, achieving an overall accuracy of 0.96. The model also achieved high precision and recall rates across the classes, with precision ranging from 0.93 to 1.00 and recall between 0.95 and 0.97 for the key markers BRAC, BRAF, and KRAS. The F1-score for these critical markers ranged from 0.95 to 0.98. These empirical results substantiate the architecture's capability to capture local and global features in DNA sequences, affirming its applicability for critical, sequence-based bioinformatics challenges. [ABSTRACT FROM AUTHOR]

Plasmodium falciparum is an apicomplexan parasite responsible for lethal cases of malaria. According to WHO recommendations, P falciparum cases are treated with artemisinin-based combination therapy including dihydroartemisinin–piperaquine. However, the emergence of resistant parasites against dihydroartemisinin–piperaquine was reported in southeast Asia in 2008 and, a few years later, suspected in South America. To characterise resistance emergence, a treatment efficacy study was performed on the reported patients infected with P falciparum and treated with dihydroartemisinin–piperaquine in French Guiana (n=6, 2016–18). Contemporary isolates collected in French Guiana were genotyped for P falciparum chloroquine resistance transporter (pfCRT ; n=845) and pfpm2 and pfpm3 copy number (n=231), phenotyped using the in vitro piperaquine survival assay (n=86), and analysed through genomic studies (n=50). Additional samples from five Amazonian countries and one outside the region were genotyped (n=1440). In field isolates, 40 (47%) of 86 (95% CI 35·9–57·1) were resistant to piperaquine in vitro; these phenotypes were more associated with pfCRT C350R (ie, Cys350Arg) and pfpm2 and pfpm3 amplifications (Dunn test, p<0·001). Those markers were also associated with dihydroartemisinin–piperaquine treatment failure (n=3 [50%] of 6). A high prevalence of piperaquine resistance markers was observed in Suriname in 19 (83%) of 35 isolates and in Guyana in 579 (73%) of 791 isolates. The pfCRT C350R mutation emerged before pfpm2 and pfpm3 amplification in a temporal sequence different from southeast Asia, and in the absence of artemisinin partial resistance, suggesting a geographically distinctive epistatic relationship between these genetic markers. The high prevalence of piperaquine resistance markers in parasite populations of the Guianas, and the risk of associated therapeutic failures calls for caution on dihydroartemisinin–piperaquine use in the region. Furthermore, greater attention should be given to potential differences in genotype to phenotype mapping across genetically distinct parasite populations from different continents. Pan American Health Organization and WHO, French Ministry for Research, European Commission, Santé publique France, Agence Nationale de la Recherche, Fundação de Amparo à Pesquisa do Estado do Amazonas, Ministry of Health of Brazil, Oswaldo Cruz Foundation, and National Institutes of Health. For the French and Portuguese translations of the abstract see Supplementary Materials section. [ABSTRACT FROM AUTHOR]

Molecular markers for genotyping malaria parasites have enabled detailed and informative studies of infection epidemiology and transmission dynamics. Genotyping delivers critical data for public health to optimize and enhance malaria control and elimination strategies. Whole-genome sequencing (WGS), although comprehensive, is not suitable for epidemiological use cases as it is time-consuming, requires specialist skills, and is not cost effective. Genetic marker approaches are affordable, attainable, and targeted; however, they have specific features that make them suitable for some use cases but not others. Over recent years, progress in molecular markers for genotyping malaria parasites has enabled informative studies of epidemiology and transmission dynamics. Results have highlighted the value of these tools for surveillance to support malaria control and elimination strategies. There are many different types and panels of markers available for malaria parasite genotyping, and for end users, the nuances of these markers with respect to 'use case', resolution, and accuracy, are not well defined. This review clarifies issues surrounding different molecular markers and their application to malaria control and elimination. We describe available marker panels, use cases, implications for different transmission settings, limitations, access, cost, and data accuracy. The information provided can be used as a guide for molecular epidemiology and surveillance of malaria. [ABSTRACT FROM AUTHOR]

Prostate cancer (PC) represents one of the most common cancer types worldwide and many patients suffering from this kind of cancer are treated with radiotherapy (RTH). Ionizing irradiation is closely associated with reactive oxygen species (ROS) production and oxidative stress. Over the years the role of vitamin C (VC) in cancer prevention has been highlighted as it may be mediated by its ability to neutralize pro-carcinogenic ROS. However, the debate concerning the presence of VC in blood and its beneficial effect on the survival of cancer patients is inconsistent and controversial. To our best knowledge until recently there have been no studies concerning such a role of intracellular VC (iVC). In the present study, blood and intracellular concentrations of vitamin C were analyzed along with the level of 8-oxo-7,8-dihydro-2′-deoxyguanosine (8-oxodG), as an established marker of the stress condition, in leukocytes of PC patients during the course of radiotherapy. The level of intracellular vitamin C significantly decreased in PC patients in comparison with the healthy group, while there were no differences in blood VC. It was observed that a sub-group of the PC patients reacted to RTH decreasing VC in leukocytes (group A), while the other sub-group acted the other way round, significantly increasing its level (group B). Under stressful conditions (RTH) leukocytes react in two different ways. Both ways are in good agreement with two well recognized functions, proposed for iVC; it may serve as a save factor, to protect the cellular DNA, increasing its concentration inside the cell (group B), and as a reservoir decreasing the VC level inside leukocytes and releasing VC into the plasma to rescue its physiological level (group A). It was also demonstrated that there was a relationship between the level of 8-oxodG in leukocytes' DNA and the markers of RTH toxicity. [Display omitted] • -iVC may serve as a save factor, to protect the cellular DNA. • iVC may serve as a reservoir decreasing its level inside leukocytes and simultaneously releasing this content into the plasma. • 8-oxodG in leukocytes' DNA may be a good marker of the deleterious side effect of RTH. [ABSTRACT FROM AUTHOR]

Different groups of fungi have been reported to interact with ants. Recent studies have shown that fungi of the order Chaetothyriales are important components of ant–fungus networks, including members of the family Trichomeriaceae , which is particularly rich in fungi isolated from carton ants nests. One of the still understudied ant-related environments are ants' infrabuccal pockets and pellets, which often contain fungal matter. The aim of this work was to determine the systematic and phylogenetic position of two slow growing strains of Trichomeriaceae isolated from infrabuccal pellets of Formica polyctena ants. Molecular analyses based on maximum likelihood and bayesian inference, using sequences of two ribosomal DNA markers: ITS and LSU have shown that the isolated strains form a monophyletic clade within the family Trichomeriaceae , sister to a clade formed by representatives of the genus Trichomerium. Morphological analyses additionally justified distinctiveness of the isolated strains, which have different morphology of conidia and conidiophores than Trichomerium representatives. Therefore, our results show that the isolated strains represent a new species within a not yet described fungal genus. Due to the strains' isolation source and their close relatedness to a fungal strain isolated from a carton nest of Lasius fuliginosus , we propose a name Formicomyces microglobosus Siedlecki & Piątek for this fungus. While our discovery strengthens a hypothesis of the multiple, independent evolution of ant-associated fungi in the family Trichomeriaceae , the ecology of F. microglobosus still remains to be characterized. [Display omitted] • Ants' infrabuccal pellets can be a source of yet undiscovered fungi. • Formicomyces gen. nov. described from infrabuccal pellets of Formica polyctena. • Formicomyces microglobosus - first species described for this genus. • Our discovery strengthens the hypothesis of multiple evolution of ant-association in Trichomeriaceae. [ABSTRACT FROM AUTHOR]

• Genetic diversity was assessed among 14 saffron accessions using 7 SSRg markers and chloroplast DNA SNP markers. • Chloroplast DNA SNP markers detected a high level of genetic diversity among saffron accessions. • Mantel and Kendall's tests show a positive correlation between genetic distance, geographical distance, and altitudes. • SSRg markers show that the investigated saffron accessions are from a single clone. • According to chloroplast markers, Moroccan saffron originated in south-eastern Europe (Greece). The molecular characterization of C. sativus accessions is of great interest for clonal selection and preservation of valuable resources with the best productive traits and specific patterns related to local products. To analyze the genetic diversity of Moroccan saffron, fourteen new saffron accessions were evaluated, twelve of which were from Morocco and two from Kozani in Greece, and the Quercy region of France. These accessions differ by their geographical distribution and altitudes. Seven specific C. sativus Simple-sequence repeats (SSRs) primers were considered. Their combinations generated 13 monomorphic alleles across all studied accessions with an average of 1.85 allele/locus. Additionally, fourteen unique ABRII/Cs30 SSR locus sequences were obtained and registered in the NCBI database (MZ868510-MZ868523). Single nucleotide polymorphism (SNP) was also assessed considering the ABRII/Cs30 locus. By excluding gaps and missing data from the sequence alignment, 161 sites were produced. The DnaSP analysis of all accessions revealed 40 polymorphic sites, including thirty-two among the Moroccan accessions. Nucleotide diversity (PiT) was 0.03896, while the average nucleotide difference was 6.27273. The haplotype diversity (HD) of Moroccan and all accessions was 0.848 and 0.875, respectively, demonstrating a strong capacity of the ABRII/Cs30 locus to distinguish saffron accessions. The Tazenakht (TK) population was the most polymorphic, while the Low land (TB) population was monomorphic. Sequence-based genetic relationships imply that Moroccan saffron likely originated from Greece. Our results show that the SNPs approach is a powerful tool to evaluate genetic diversity among C. sativus accessions. The present molecular analysis indicates that Moroccan saffron is not a single clone. This outcome constitutes a sound basis for developing a core collection representative of the biodiversity of Moroccan saffron to conserve and enhance this critical commodity. [ABSTRACT FROM AUTHOR]

Mosaicism refers to the presence of genetically distinct cell populations in an individual derived from a single zygote, which occurs during the process of development, aging, and genetic diseases. To date, a variety of genetically engineered mosaic analysis models have been established and widely used in studying gene function at exceptional cellular and spatiotemporal resolution, leading to many ground-breaking discoveries. Mosaic analysis with a repressible cellular marker and mosaic analysis with double markers are genetic mosaic analysis models based on trans-recombination. These models can generate sibling cells of distinct genotypes in the same animal and simultaneously label them with different colors. As a result, they offer a powerful approach for lineage tracing and studying the behavior of individual mutant cells in a wildtype environment, which is particularly useful for determining whether gene function is cell autonomous or nonautonomous. Here, we present a comprehensive review on the establishment and applications of mosaic analysis with a repressible cellular marker and mosaic analysis with double marker systems. Leveraging the capabilities of these mosaic models for phenotypic analysis will facilitate new discoveries on the cellular and molecular mechanisms of development and disease. [ABSTRACT FROM AUTHOR]

• Cassava is one of the major root and tuber crops cultivated globally. • Genetic diversity studies help to select superior and diverse parents for breeding programmes. • SSR markers determine the genetic similarity among genotypes eliminating environmental effects. Thirty cassava accessions, including released and pre-release varieties in India were selected for morphological, statistical and molecular analysis to evaluate their genetic divergence. Based on ANOVA (Analysis of Variance), significant differences were observed in thirty genotypes for the fifteen characters used in the study. Most of the characters such as plant height, stem weight plant−1, number of leaves plant−1 and mean weight of tuber exhibited high GCV and PCV along with a positive correlation to tuber yield plant−1. Path analysis showed that stem weight plant−1, number of tubers plant−1, number of leaves plant−1, leaf dry matter content and number of nodes plant−1 directly affected tuber yield plant−1. The genotypes were then grouped into nine clusters following Mahalanobis' D2 statistics with clusters IV and VIII recording the maximum inter-cluster distance, which gave an idea about the diversity prevailing among them. PCA analysis showed that stem girth, number of nodes and tuber yield plant−1 accounted for greater variability among the genotypes. Molecular analysis using SSR markers showed polymorphism for eighteen markers and molecular dendrogram clustering grouped the genotypes into three principal clusters with different subclusters. Overall, the study highlights the genomic diversity of cassava accessions and provides valuable insights into their characteristics and yield potential. [ABSTRACT FROM AUTHOR]

Urothelial carcinoma with squamous differentiation (UCS) is a common variant of bladder cancer for which treatment outcomes with novel agents are largely unknown. In this retrospective analysis comparing 40 patients with UCS and 120 patients with pure UC, we found inferior outcomes for UCS patients treated with immune checkpoint inhibitors or Enfortumab vedotin. This highlights an important unmet clinical need that should be addressed with further studies. Introduction: Urothelial carcinoma with squamous differentiation (UCS) is associated with increased resistance to chemotherapy, but outcomes associated with newer therapies approved in this space over the last 5 to 10 years are less well defined. We investigated clinical outcomes and molecular profiling of patients with UCS treated with an immune checkpoint inhibitor (ICI) and/or Enfortumab vedotin (EV). Patients and Methods: We undertook a retrospective analysis of UC patients treated with ICI and/or EV. Objective response rate (ORR), progression free survival (PFS) and overall survival (OS) were compared between pure UC (pUC) and UCS using X 2 and log-rank tests, respectively. Prevalence of the most commonly detected somatic alterations were also compared between the 2 histologic subgroups. Results: A total of 160 patients (40 UCS, 120 pUC) were identified for this analysis. Among 151 patients treated with ICI (38 UCS, 113 pUC), UCS patients had a shorter mPFS (1.9 vs. 4.8 months, P < 0.01) and mOS (9.2 vs. 20.7 months, P < 0.01) compared to pUC. Among 37 patients treated with EV (12 UCS, 25 pUC), UCS patients had a lower ORR (17% vs. 70%, P < 0.01) and shorter mPFS (3.4 vs. 15.8 months, P < 0.01). UCS samples were enriched for CDKN2A, CDKN2B, PIK3CA, while pUC samples were enriched for ERBB2 alterations. Conclusion: In this single-center retrospective analysis, patients with UCS had a distinct somatic genomic profile relative to patients with pUC. Patients with UCS also had inferior outcomes to ICIs and EV compared to patients with pUC. [ABSTRACT FROM AUTHOR]

In this review, we have summarized the existing knowledge of ulcerative colitis (UC) markers based on current literature, specifically, the roles of potential new biomarkers, such as circulating, fecal, genetic, and epigenetic alterations, in UC onset, disease activity, and in therapy response. UC is a complex multifactorial inflammatory disease. There are many invasive and non-invasive diagnostic methods in UC, including several laboratory markers which are employed in diagnosis and disease assessment; however, colonoscopy remains the most widely used method. Common laboratory abnormalities currently used in the clinical practice include inflammation-induced alterations, serum autoantibodies, and antibodies against bacterial antigens. Other new serum and fecal biomarkers are supportive in diagnosis and monitoring disease activity and therapy response; and potential salivary markers are currently being evaluated as well. Several UC-related genetic and epigenetic alterations are implied in its pathogenesis and therapeutic response. Moreover, the use of artificial intelligence in the integration of laboratory biomarkers and big data could potentially be useful in clinical translation and precision medicine in UC management. [ABSTRACT FROM AUTHOR]

Subterranean fauna is an important contributor to the global fauna, but it is still understudied and a large part of its taxonomy is not yet resolved. One species complex with unresolved taxonomy is the groundwater amphipod Niphargus ruffoi , endemic to the Alpine chain. Here, we used new samples from across the Alpine arc to review the taxonomic status of the entire clade, including the species N. ruffoi and Niphargus arolaensis. We sequenced four genetic markers from the collected specimens, assessed the phylogenetic position of N. ruffoi within the genus, and studied the structure of this species complex using four molecular species delimitation methods. We tested for recombination using the alignments of the concatenated nuclear rDNA genes. The phylogenetic analyses revealed high support for the monophyly of the studied species complex, defining two lineages (i.e., N. arolaensis and N. ruffoi) within the clade. Molecular species delimitation methods suggested that N. arolaensis is a single species, while N. ruffoi should be considered as a species complex of three (using ITS) to eight (using COI) putative species. Moreover, we found a discrepancy between the different nuclear ribosomal DNA markers, indicating a possible recombination with fragments of 28S DNA of N. ruffoi s. lat. present in the genome of N. arolaensis. For the above-mentioned reasons, the internal phylogenetic structure of N. ruffoi s. lat. could not be fully resolved. Moreover, no clear morphological evidence supported the molecular species delimitation. Consequently, no taxonomic changes were proposed. We postulate that this complex scenario was influenced by Pleistocene climate oscillations with subsequent fragmentation events and secondary contacts, making this an interesting study system to investigate the evolution and biogeography of Alpine clades. [ABSTRACT FROM AUTHOR]

Copy number variations (CNV) contribute significantly to genetic variations. Numerous studies have shown that CNV affects phenotypic traits in livestock. The SMAD family member 2 (SMAD2) is a leading candidate gene in reproduction and has a crucial effect on litter size. Additionally, SMAD2 is also required for male reproduction and influences male germ cell development. However, there are no reports on investigating the effect of CNVs in the SMAD2 gene on reproductive traits in goat. Therefore, the goal of this study was to explore associations between CNV of the SMAD2 gene and litter size and semen quality in Shaanbei white cashmere (SBWC) goats. In this study, two CNVs within the SMAD2 were identified in 352 SBWC goats (50 males and 302 females). The association analysis revealed that only CNV2 was significantly associated with female goat first-born litter size (P = 3.59 × 10−4), male semen concentration (P < 0.01), ejaculation volume, live sperm count, and sperm deformity rate (P < 0.05). In terms of phenotypic performance, the individuals with loss genotypes outperformed those with other genotypes. CNV1 and CNV2 genotype combinations containing their dominant genotypes were also associated with goat litter size (P = 1.7 × 10−5), but no differences in semen quality were found. In summary, CNV2 of the SMAD2 gene is useful for molecular marker-assisted selection breeding, as it is associated with essential goat reproductive traits. • Two CNV loci within the SMAD2 gene were identified in SBWC goats. • CNV2 was significantly associated with litter size in female goats (P < 0.01). • In male goats, CNV2 had a significant effect on semen quality traits (P < 0.05). • Therefore, CNV2 in the SMAD2 gene could be an effective DNA marker for breeding. [ABSTRACT FROM AUTHOR]

The integration of CRISPR-Cas systems and surface-enhanced Raman spectroscopy (SERS) has emerged as a powerful approach for developing highly sensitive biosensors. This review explores recent studies that demonstrate the potential of CRISPR-Cas12a and Cas13a systems combined with SERS technology in detecting nucleic acids with exceptional sensitivity and specificity. This review examines studies that showcase the application of CRISPR-Cas and SERS technology in various fields, including healthcare, food safety, environmental monitoring, and biodefense. The reviewed studies highlight the capability of CRISPR-Cas systems to target specific DNA or RNA sequences, while SERS serves as a highly sensitive detection method. The combination of these technologies enables the development of biosensors for the detection of pathogens, genetic markers, drug resistance genes, chemical compounds, and adulterants in food. The reviewed studies demonstrate the significant findings and potential of integrating CRISPR-Cas and SERS technologies for biosensing applications. The studies showcase the ability of CRISPR-Cas12a and Cas13a systems to detect nucleic acids with high sensitivity and specificity, even at trace levels. The use of SERS as a detection method offers advantages such as enhanced sensitivity, selectivity, and reliability. The combination of CRISPR-Cas and SERS technology has the potential to revolutionize diagnostic testing in various sectors. Although challenges remain, including improving detection limits and reducing interference from complex matrices, the promise of these biosensors in early disease diagnosis, pathogen detection, and environmental monitoring is evident. Further research and development are warranted to harness the full potential of CRISPR-Cas and SERS technology for future biosensing applications. • Integration of CRISPR-Cas systems with surface-enhanced Raman spectroscopy (SERS) enables highly sensitive biosensing. • Biosensors utilizing CRISPR-Cas and SERS technology have applications in healthcare, food safety, and biodefense. • CRISPR-Cas systems target specific DNA or RNA sequences, while SERS serves as a highly sensitive detection method. • SERS provides advantages such as enhanced sensitivity, selectivity, and reliability in biosensing. • Integration of CRISPR-Cas and SERS technology has the potential to revolutionize diagnostic testing in various sectors. [ABSTRACT FROM AUTHOR]

African catfish (Clarias gariepinus) is a promising food fish species with significant potential and growing mass of production in freshwater aquaculture. Male African catfish possess improved production characteristics over females, therefore the use of monosex populations could be advantageous for aquaculture production. However, our knowledge about the sex determination mechanism of this species is still limited and controversial. A previously isolated male-specific DNA marker (CgaY1) was validated using offspring groups from targeted crosses (n = 630) and it was found to predict the sex of 608 individuals correctly (96.43% accuracy). Using the proportion of recombinants, we estimated the average genetic distance between the potential sex determination locus and the sex-specific marker to be 3.57 cM. As an earlier study suggested that both XX/XY and ZZ/ZW systems coexist in this species, we tested the applicability of their putative 'moderately sex-linked loci' and found that no sex-specific amplification could be detected for any of them. In addition, temperature-induced masculinization suggested by others was also tested, but no such effect was detected in our stocks when the published parameters were used for heat treatment. Altogether, our results support an exclusive XX/XY sex determination system in our African catfish stock and indicate a good potential for the future use of this male-specific DNA marker in research and commercial production. • Validation of a male-specific marker confirms XX/XY-type sex determination in Hungarian strains of African catfish. • Strong linkage was detected between the male-specific CgaY1 marker and the sex determination region. • Temperature-induced masculinization at 36 °C between 5-8, 7–10 or 9–12 dph failed. • Validation of others' 'moderately sex-associated' DNA markers is failed, suggesting no ZZ/ZW system in these strains. [ABSTRACT FROM AUTHOR]

• This is the first report that analyses the genetic diversity of Aerides multiflora and Rhyncostylis retusa from a variety of locations in Uttarakhand. • The study indicating a genetic connection between the orchids that were collected from host trees and altitudes that were similar to one another. • Data can help in developing sustainable natural resource management, as well as conservation and hybridization strategies for A. multiflora and R. retusa. Aim of the study was to analyze genetic variability among natural populations of two endemic orchids (Aerides multiflora and Rhynchostylis retusa) of Uttarakhand, India using inter-simple sequence repeat (ISSR) makers. Both the species, known for their ornamental and medicinal potential, were collected from different locations in Uttarakhand region, and isolated DNA samples were amplified using fourteen ISSR primers. In the case of A. multiflora , eight of the fourteen primers tested showed amplification products with an average polymorphism of 35.39% and in the case of R. retusa , the average polymorphism was 63.32%. Cluster analysis for both species showed that samples collected from sites of similar latitudes and elevations were clustered together. Another key observation in the case of R. retusa was that the sub-clusters were formed on the basis of host tree association. This is the first report on the diversity analysis of A. multiflora and R. retusa in Uttarakhand. This study suggests that the orchids collected from locations with similar altitudes and host trees are genetically related to each other. This genetic profiling can be used as the basis to develop conservation protocols for these orchids to prevent them from entering the threatened category, as the epiphytic orchids are more susceptible to natural and anthropogenic pressures. Besides, the genetic variation analysis can be used to select the parent plants for developing commercial hybrids in both species. [ABSTRACT FROM AUTHOR]

In recent years, sports analytics has gained significant attention, particularly in the area of using machine learning techniques to analyze athlete performance and injury risks. This paper focuses on the use of machine learning for predicting injuries in football players and proposes a concept for an intelligent system that can provide early warnings of potential injuries. To achieve this, the proposed intelligent system will gather input from various sources such as athlete performance data, muscle strength assessments, and DNA markers. Using this information, the system will employ machine learning algorithms to identify patterns and predict the probability of injury occurrence. The intelligent system will offer coaches and medical staff actionable insights to help them take preventative measures and decrease the likelihood of injuries. [ABSTRACT FROM AUTHOR]

• The research will help tackling the longstanding problems of citrus germplasm evaluation, classification and Identification in Nepal. • Result is based on codominant markers i.e. SSR. • Powerful statistical software NTSYS is used for data analysis. Nepal has very low Citrus fruit production compared to other countries, which is due to lack of elite varieties and cultivars having desirable traits. Therefore, breeding of elite cultivars is crucial to address ever increasing market demand of citrus fruits in Nepal. Genetic diversity characterization of Citrus germplasm at molecular level is important and crucial step for their utilization in breeding and conservation. In the present investigation, we aimed to utilize 12 SSR markers to characterize genetic diversity of forty-five Citrus accessions of Citrus collected from National Citrus Research Program (NCRP), Dhankuta and Kathmandu valley. A total of 60 putative alleles were amplified at 12 SSR loci with an average of five alleles per locus. PIC value ranged from 0.497 with primer TAA 27 to 0.802 with primer TAA 41 with an average value of 0.662. Probability of identity (PI) ranged from 0.075 to 0.383 with an average value of 0.143. Observed Heterozygosity (Ho) ranged from 0.460 to 0.794 and Expected Heterozygosity (He) ranged from 0.460 to 0.794. Shannon's Information Index (I) ranged from 0.677 to 1.678. Principal co-ordinate analysis (PCO) revealed the first principal co-ordinate axis accounting 20.35% and second axis accounting 11.43% of the total variation. UPGMA clustering using Jaccard's similarity coefficient grouped 45 accessions into four clusters. The information generated from this investigation will be useful for National Agriculture Genetic Resources Center (Gene bank) of Nepal and other relevant Citrus researchers and breeders for their conservation, Molecular Breeding-based Research & Development and their sustainable future utilization. [ABSTRACT FROM AUTHOR]

HLA alloimmunization is one of the most troublesome consequence of regular transfusion which is itself a mainstay measure to provide longevity to the thalassemia patients. Febrile non-hemolytic transfusion reaction (FNHTR) is one of the most common complication which might be related to the HLA alloimmunization. Here, we studied the HLA antigenic system and alloimmunization rate in the Iranian β-thalassemia patients who suffered from FNHTR compare to the β-thalassemia patients without FNHTR. Total of 60 β-thalassemia patients with FNHTR (case group) and 20 β-thalassemia patients without FNHTR (control group) randomly have been selected and enrolled in the study. All were tested for HLA-A and -B loci by PCR-SSP method and also for the presence of anti-lymphocyte antibodies by LIFT method. Comparisons between two groups were performed by Pearsonʼs χ2 test. Totally, a significant predominance was noted for two HLA alleles, HLA-A*24 (P = 0.029) and B*55 (P = 0.034) which have higher prevalence in control group. Although no significant association was found between the presence of anti-leukocyte antibodies and the development of FNHTR, the HLA-A*32 (P = 0.047) allele was considered as possible genetic markers in the susceptibility to the development of anti-leukocyte antibodies. Here some evidences about the possible role of HLA polymorphism in susceptibility to FNHTR are provided. Those results indicated that HLA-A*24 and HLA-B*55 might play protective role on inducing FNHTR in β-thalassemia patients. Further studies which investigate the allele level of HLA-I alongside with specific reactivity of HLA-I antibodies might reveal more deep data about these phenomena. [ABSTRACT FROM AUTHOR]

This study tackles several challenges of evaluating histology-independent treatments using entrectinib as an example. Histology-independent treatments are provided based on genetic marker(s) of tumors, regardless of the tumor type. We evaluated the lifetime cost-effectiveness of testing all patients for NTRK fusions and treating the positive cases with entrectinib compared with no testing and standard of care (SoC) for all patients. The health economic model consisted of a decision tree reflecting the NTRK testing phase followed by a microsimulation model reflecting treatment with either entrectinib or SoC. Efficacy of entrectinib was based on data from basket trials, whereas historical data from NTRK-negative patients were corrected for the prognostic value of NTRK fusions to model SoC. "Testing" (testing for NTRK fusions, with subsequent entrectinib treatment in NTRK-positive patients and SoC in NTRK-negative patients) had higher per-patient quality-adjusted life-years (QALYs) and costs than "No testing" (SoC for all patients), with a difference of 0.0043 and €732, respectively. This corresponded to an incremental cost-effectiveness ratio (ICER) of €169 957/QALY and, using a cost-effectiveness threshold of €80 000/QALY, an incremental net monetary benefit of −€388. When excluding the costs of genetic testing for NTRK fusions, the ICER was reduced to €36 290/QALY and the incremental net monetary benefit increased to €188. When treatment requires the identification of a genetic marker, the associated costs and effects need to be accounted for. Because of the low prevalence of NTRK fusions, the number needed-to-test to identify patients eligible for entrectinib is large. Excluding the testing phase reduces the ICER substantially. • The first 2 histology-independent cancer drugs have recently received regulatory approval based on data from single-arm basket trials. Such data pose challenges for the assessment of relative effectiveness and cost-effectiveness, especially when the targeted genetic marker is rare. • We estimated the cost-effectiveness of testing cancer patients for NTRK gene fusions and subsequently providing the histology-independent treatment entrectinib if they test positive and standard of care (SoC) if they test negative compared with no testing and SoC for all patients. Given that only single-arm trial data are available for entrectinib, we estimated a synthetic control arm that accounted for the prognostic value of NTRK fusions. We show that, in The Netherlands, entrectinib is not cost-effective compared with SoC. Nevertheless, entrectinib might be cost-effective if next-generation sequencing of RNA panel testing costs decreased substantially or broad genetic testing were to become standard practice. • Excluding the costs and health effects of required (genetic) testing may have a large effect on cost-effectiveness outcomes for the evaluated treatment, especially for rare diseases. The prognostic value of the genetic marker targeted by the treatment may also largely impact results. Economic evaluations that do not account for the consequences of testing or the prognostic value of the genetic marker may therefore render inaccurate results. [ABSTRACT FROM AUTHOR]

Takayasu arteritis (TA) is a rare large vasculitis with unknown etiology, which affects the aorta and its primary branches, as well as the pulmonary and coronary arteries. Cellular and humoral immunity, chronic inflammation, and genetic factors are involved into TA pathogenesis. Several biomarkers, such as MMPs, TIMPs, cytokines, cell adhesion molecules, autoantibodies, complements, PTX3, sRAGE, NT-proBNP, 8-isoPGF 2α, NO 2 −, acute-phase and immunology-related proteins, thrombogenicity markers, ghrelin leptin and adipokines, endothelial damage and repair factors, genetic markers etc., related to the pathogenesis could be observed in patients with TA. These biomarkers have revealed great values in early diagnosis, evaluating disease activity, guiding clinical treatment options, and thus demonstrated significant clinical application values in TA. The combination of biomarkers assay and imaging examination may detect TA more accurately. The aim of this review is to systemically observe the clinical significance of these biomarkers in TA. • Autoimmune, inflammation, and genetic factors are associated with TA pathogenesis. Biomarkers related to the pathogenesis could be observed in TA. • There is a need for better biomarkers in TA, including diagnosis, assessment of current disease activity, and prognosis. • Progress has been made in identifying TA biomarkers in early diagnosis, evaluating disease activity, guiding clinical treatment options, and thus demonstrated significant clinical application values of TA. Combination of biomarkers assay and imaging examination may detect TA more accurately. [ABSTRACT FROM AUTHOR]

Senescent cells are highly associated with aging and pathological conditions and could be targeted to slow the aging process. One commonly used marker to examine senescent cells in vivo is p16, which has led to important discoveries. Recent studies have also described new senescence markers beyond p16 and have highlighted the importance of investigating senescence heterogeneity in cell types and tissues. With the development of high-throughput technologies, such as single-cell RNA-seq and single-nucleus RNA-seq, we can examine senescent cells at the single-cell level and potentially uncover new markers. This review emphasizes that there is an urgent need to investigate senescence heterogeneity and discuss how this could be accomplished by using advanced technologies and sequencing datasets. Currently, senescent cells do not have a known gold standard genetic marker. Single cell RNA-seq and single-nucleus RNA-seq have emerged as powerful methods for investigating senescence heterogeneity. It is unknown what cell populations are being targeted by senolytics in vivo. Gaining a greater understanding of senescent cell heterogeneity can have large clinical implications and improve patient treatment. [ABSTRACT FROM AUTHOR]

• Even known endometriosis diagnostic procedures, such as laparoscopy, may fail to detect the disease in its early stages. • To enhance the capacity for early diagnosis, it is necessary to identify new biomarkers that may be applied for non-invasive assessment. • Immunological, genetic and heterogenous markers are capable of determining the presence, progression, and stage of endometrial lesions. Endometriosis, a benign gynecologic and chronic inflammatory disease, is defined by the presence of endometrial tissue outside the uterus characterized mainly by pelvic pain and infertility. Because endometriosis affects approximately 10% of females, it represents a significant socioeconomic burden worldwide having tremendous impact on daily quality of life. Accurate and prompt diagnosis is crucial for the management of this debilitating disorder. Unfortunately, diagnosis is typically delayed to lack of specific symptoms and readily accessible biomarkers. Although histopathologic examination remains the current gold standard, this approach is highly invasive and not applicable for early screening. Recent work has focused on the identification of reliable biomarkers including immunologic, ie, immune cells, antibodies and cytokines, as well as genetic and biochemical markers, ie, microRNAs, lncRNAs, circulating and mitochondrial nucleic acids, along with some hormones, glycoproteins and signaling molecules. Confirmatory research studies are, however, needed to more fully establish these markers in the diagnosis, progression and staging of these endometrial lesions. [ABSTRACT FROM AUTHOR]

For genomic prediction of crossbred animals, models that account for the breed origin of alleles (BOA) in marker genotypes can allow the effects of marker alleles to differ depending on their ancestral breed. Previous studies have shown that genomic estimated breeding values for crossbred cows can be calculated using the marker effects that are estimated in the contributing pure breeds and combined based on estimated BOA in the genotypes of the crossbred cows. In the presented study, we further exploit the BOA information for improving the prediction of genomic breeding values of crossbred dairy cows. We investigated 2 types of BOA-derived breed proportions: global breed proportions, defined as the proportion of marker alleles assigned to each breed across the whole genome; and local breed proportions (LBP), defined as the proportions of alleles on chromosome segments which were assigned to each breed. Further, we investigated 2 BOA-derived measures of heterozygosity for the prediction of total genetic value. First, global breed heterozygosity, defined as the proportion of marker loci that have alleles originating in 2 different breeds over the whole genome. Second, local breed heterozygosity (LBH), defined as proportions of marker loci on chromosome segments that had alleles originating in 2 different breeds. We estimated variance related to LBP and LBH on the remaining variation after accounting for prediction with solutions from the genomic evaluations of the pure breeds and validated alternative models for production traits in 5,214 Danish crossbred dairy cows. The estimated LBP variances were 0.9, 1.2, and 1.0% of phenotypic variance for milk, fat, and protein yield, respectively. We observed no clear LBH effect. Cross-validation showed that models with LBP effects had a numerically small but statistically significantly higher predictive ability than models only including global breed proportions. We observed similar improvement in accuracy by the model having an across crossbred residual additive genetic effect, accounting for the additive genetic variation that was not accounted for by the solutions from purebred. For genomic predictions of crossbred animals, estimated BOA can give useful information on breed proportions, both globally in the genome and locally in genome regions, and on breed heterozygosity. [ABSTRACT FROM AUTHOR]

[Display omitted] • We have presented the chronological evolution of DNA techniques used in cancer. diagnostics. • DNA techniques ranging from FISH to NGS are summarized with their applications in. cancer research. • We have summarized the role of PCR and its forms in exploring the mutational and. epigenetic landscape of cancer biology. Cancer remains the second leading cause of death worldwide and newly diagnosed cases have increased at an alarming rate. One in every four people has a lifetime risk of being afflicted with cancer. Early diagnosis, which is essential in reducing morbidity and mortality, requires the development of highly sensitive and specific techniques to identify and monitor molecular changes for cancer-specific genetic and epigenetic markers. Among these, fluorescent in situ hybridization (FISH), Polymerase Chain Reaction (PCR), DNA microarray and NanoString technologies are notable. Recent advances in the development of efficient and cost-effective next-generation sequencing (NGS) has enabled whole genome, exome and transcriptome analysis. This review focuses on the features and applications of important molecular techniques to detect various genetic mutations thus enabling improved diagnosis, treatment and outcome. [ABSTRACT FROM AUTHOR]

Ideally, a panel of Y short tandem repeats (Y-STRs) should include markers with gene diversity (GD) ≥ 0.70 to guarantee a highly accurate and precise individual identification in all forensic situations where Y loci analysis is necessary to support the findings obtained with autosomal STRs. Since not all markers in a multiplex set reach the optimal GD value, to achieve a greater discrimination capacity (DC), the number of Y-STRs has been gradually expanded also with the addition of rapidly mutating Y-STRs (RM Y-STRs). The present study has tried to assess, based on the genetic diversity of each Y-STR and the cumulative haplotype diversity provided by the single Y-STR panels tested, whether to increase in the number of Y-STRs is effective. For this purpose, three commercially available forensic kits - the PowerPlex® Y23 System, the Yfiler™ Plus PCR Amplification Kit, and the ForenSeq™ DNA Signature Prep Kit - that allow for the simultaneous analysis of 22–25 Y chromosome markers (including Y-STRs and RM Y-STRs) have been used for typing 115 unrelated male individuals from North-East Italy employing two capillary electrophoresis (Applied Biosystems® 3130 Genetic Analyzer and SeqStudio Genetic Analyzer for HID) and one massively parallel sequencing (MiSeq FGx™ Forensic Genomics System) systems. Forensic parameters, such as gene diversity, cumulative haplotype diversity (cHD), and discrimination capacity, were determined for the three Y-STRs kits and the virtual pool of 30 Y-STRs obtained by the overall combination of the Y-loci of the three kits. From the findings, it emerges that twelve markers in the virtual panel of 30 Y-STRs, are characterized by a value of GD ≥ 0.70, and of these, eleven included in the Yfiler™ Plus kit seem to be sufficient to ensure the achievement of haplotype resolution. In light of this, it does not appear necessary to expand the number of Y-STRs in the currently available kits. [ABSTRACT FROM AUTHOR]

Grading and classification of IDH-mutant astrocytomas has shifted from solely histology towards histology combined with molecular diagnostics. In this systematic review, we give an overview of all currently known clinically relevant molecular markers within IDH-mutant astrocytomas grade 2 to 4. A literature search was performed in five electronic databases for English original papers on patient outcome with respect to a molecular marker as determined by DNA/RNA sequencing, micro-arrays, or DNA methylation profiling in IDH-mutant astrocytomas grade 2 to 4. Papers were included if molecular diagnostics were performed on tumour tissue of at least 15 IDH-mutant astrocytoma patients, and if the investigated molecular markers were not limited to the diagnostic markers MGMT , ATRX , TERT , and/or TP53. The literature search identified 4508 unique articles, published between August 2012 and December 2021, of which ultimately 44 articles were included. Numerous molecular markers from these papers were significantly correlated to patient outcome. The associations between patient outcome and non-canonical IDH mutations, PI3K mutations, high expression of MSH2 , high expression of RAD18 , homozygous deletion of CDKN2A/B , amplification of PDGFRA , copy number neutral loss of chromosomal arm 17p, loss of chromosomal arm 19q, the G-CIMP-low DNA methylation cluster, high total CNV, and high tumour mutation burden were confirmed in multiple studies. Multiple genetic and epigenetic markers are associated with survival in IDH-mutant astrocytoma patients. Commonly affected are the RB signalling pathway, the RTK-PI3K-mTOR signalling pathway, genomic stability markers, and (epigenetic) gene regulation. • Multiple molecular markers associated with survival in IDH-mutant astrocytoma patients. • RB and RTK-PI3K-mTOR signalling pathways are commonly affected. • Genomic stability and (epigenetic) gene regulation markers are often affected as well. • Few molecular markers have been validated in independent patient cohorts. • International collaborations should enforce more and uniform data collection. [ABSTRACT FROM AUTHOR]

Over the last decade there has been a rapid expansion of clinically actionable driver mutations in non-small cell lung cancer (NSCLC), with an unprecedented number of corresponding targeted therapies approved and funded for use in the clinic. Here we summarise the approach taken in Wales to embed a NSCLC biomarker testing pathway within the National Optimal Pathway for Lung Cancer. The Welsh Thoracic Oncology Group established a working group tasked with progressing the standardisation of genomic testing. In July 2021, the 10 lung cancer multidisciplinary teams (MDTs) were invited to take part in a national survey of current biomarker testing practices and a retrospective audit of the next generation sequencing (NGS) pathway in Wales was conducted. Seventy per cent of MDTs completed the survey, which confirmed variability in the approach to testing with respect to timing of requests, patient selection and testing technologies used. Only 43% reported having pathology-initiated reflex testing, but 87% had adopted DNA and RNA NGS testing as their standard-of-care genomic testing strategy. Data from 53 patients with stage III–IV NSCLC with genomic testing requested between October 2020 and May 2021 were analysed in the NGS pathway audit. Forty (75.5%) patients had both DNA and RNA NGS requested, with a median turnaround time from biopsy to results of 26 days (range 19–37 days) and 25 days (range 16–38 days), respectively. The geographical location of MDT did not influence turnaround times and MDTs with reflex testing had shorter biopsy-to-result times. DNA NGS testing was successful in 51 (96.2%) patients; in those who had RNA NGS, testing was successful in 30 (75%) patients. Significant progress has been made within Wales to implement a national biomarker testing pathway, with reflex testing becoming standard of care. However, challenges remain in optimising the quantity and quality of tissue available for testing, together with a need to reduce turnaround times. This will need to be addressed to ensure all eligible patients are tested at the right time in the diagnostic pathway to facilitate optimal treatment strategies and ultimately improve outcomes. [ABSTRACT FROM AUTHOR]

The fungus Schizophyllum commune is a cosmopolitan basidiomycete, which is popular as an edible, medical mushroom. It causes wood rot and often used as a model object in research. In this study, we analyzed thirty-two genomes of S. commune strains from the NCBI database and designed forty-seven unique SSR DNA markers. The detailed analysis revealed the enrichment of the S. commune genome for CG, GC, CTC, GAG, and TCG motifs. Principal components analysis confirmed the effectiveness of novel SSR DNA markers that preserve the initial heterogeneity of populations. The construction of a network between strains showed single one at a maximum similarity of 38%, and increasing the similarity to 55% breaks the linkage between large groups while separating two new groups containing strains of the population Ru and test cultures S. commune. The amplicons' presence was identified as a sufficient sign of relation of the culture to a specific population. Testing the novel SSR markers allowed to establish a clear delimitation of all groups by geographic location and to differentiate the H4-8 (GCA_000143185.1) strain from the USA population. This research is the basis for the further analysis of S. commune populations and improvement of approaches to determine its genetic diversity. • Unique SSRs markers of S. commune will help in populations' questions of the species. • The fungus genome is enriched by CG, GC, CTC, GAG, and TCG motifs. • Unique 47 SSR DNA loci were determined. • The novel SSRs markers allowed to confirm delimitation of fungus groups by geographic origin. [ABSTRACT FROM AUTHOR]

• A new allele of mouse Sgms1, Sgms1tm1b , leads to slowly-progressive hearing loss. • Endocochlear potential was reduced to two-thirds of normal values. • Marginal cells of the stria vascularis were disorganised and lost Kcnq1 expression. • The S gms1tm1a allele had only 20% of mRNA detected, but enough for normal hearing. • SGMS1 markers were associated with auditory thresholds in a human population. Sgms1 encodes sphingomyelin synthase 1, an enzyme in the sphingosine-1-phosphate signalling pathway, and was previously reported to underlie hearing impairment in the mouse. A new mouse allele, Sgms1tm1a , unexpectedly showed normal Auditory Brainstem Response thresholds. We found that the Sgms1tm1a mutation led to incomplete knockdown of transcript to 20 % of normal values, which was enough to support normal hearing. The Sgms1tm1b allele was generated by knocking out exon 7, leading to a complete lack of detectable transcript in the inner ear. Sgms1tm1b homozygotes showed largely normal auditory brainstem response thresholds at first, followed by progressive loss of sensitivity until they showed severe impairment at 6 months old. The endocochlear potential was consistently reduced in Sgms1tm1b mutants at 3, 4 and 8 weeks old, to around 80 mV compared with around 120 mV in control littermates. The stria vascularis showed a characteristic irregularity of marginal cell surfaces and patchy loss of Kcnq1 expression at their apical membrane, and expression analysis of the lateral wall suggested that marginal cells were the most likely initial site of dysfunction in the mutants. Finally, significant association of auditory thresholds with DNA markers within and close to the human SGMS1 gene were found in the 1958 Birth Cohort, suggesting that SGMS1 variants may play a role in the range of hearing abilities in the human population. [ABSTRACT FROM AUTHOR]

We investigated the dynamics of feces-associated microorganisms in areas with wrack accumulation in the southeastern part of the Baltic Sea. Our study covered single-day (2021) and multi-day (2022) observations during the recreational season. We collected water, sand, and wrack samples and assessed the abundance of fecal indicator bacteria (FIB), as well metagenomic analysis was conducted to monitor changes in microbial composition. Based on metagenomic data we identified taxa associated with feces, sewage, and ruminant sources. Human-related fecal pollution based on genetic markers correlated with the presence of Lachnospiraceae, Prevotellaceae and Rickenellacea abundance. Higher abundance and diversity of feces-associated and ruminant-associated taxa and the presence of enteric pathogens were observed when wrack accumulated near the river outflow in 2021, suggesting a potential link with fecal pollution from the river. As a preventive measure, it is recommended to remove the wrack to reduce the risk of exposure to potential enteric pathogens if it is accumulated next to the river outflow. [Display omitted] • Fecal pollution levels and sources were studied in wrack-affected environment. • Fecal pollution levels were estimated by cultivation. • Host-specific genetic markers and metagenomics were used to determine the source. • Humans, birds, ruminants and sewage were identified as sources of fecal pollution. • Feces-associated taxa and enteric pathogens were more abundant near river outflow. [ABSTRACT FROM AUTHOR]

With a global towering prevalence of index acute myocardial infarction (nonrecurrent MI, NR-MI), a high incidence of recurrent MI (R-MI) has emerged in recent decades. Despite the extensive occurrence, the promising predictors of R-MI have been elusive within the cohort of survivors. This study investigates and validates the involvement of distinct gene expressions in R-MI and NR-MI. Bioinformatics tools were used to identify DEGs from the GEO dataset, functional annotation, pathway enrichment analysis, and the PPI network analysis to find hub genes. The validation of proposed genes was conceded by qRT-PCR and Western Blot analysis in experimentally induced NR-MI and R-MI models on a temporal basis. The temporal findings based on RT-PCR consequences reveal a significant and constant upregulation of the UBE2N in the NR-MI model out of the proposed three DEGs (UBE2N, UBB, and TMEM189), while no expression was reported in the R-MI model. Additionally, the proteomics study proposed five DEGs (IL2RB, NKG7, GZMH, CXCR6, and GZMK) for the R-MI model since IL2RB was spotted for significant and persistent downregulation with different time points. Further, Western Blot analysis validated these target genes' expressions temporally. I/R-induced NR-MI and R-MI models were confirmed by the biochemical parameters (CKMB, LDH, cTnI, serum nitrite/nitrate concentration, and inflammatory cytokines) and histological assessments of myocardial tissue. These results underscore the importance of understanding genetic mechanisms underlying MI and highlight the potential of UBE2N and IL2RB as biomarkers for non-recurrent and recurrent MI, respectively. [Display omitted] • Integrate bioinformatic tools to explore biomarkers in non-recurring/recurring MI. • Confirms findings via qRT-PCR and Western Blot analysis, ensuring reliability. • Examines temporal gene expression patterns in experimentally induced MI models. • Supplements gene analysis with proteomics data confirms the involved biomarkers. • Genetic marker validation in endorsed MI models highlights translational potential. [ABSTRACT FROM AUTHOR]

• TaqMan based genotyping assay was used to study 23 SNPs in 13 genes related to thrombosis. • A total of 7 SNPs showed significant association with VTE. • These SNPs belonged to genes such as SERPINC1, PLAT, VWF, SELP and SELE. • Panel of seven SNPs could be useful in determining individual susceptibility towards VTE. [ABSTRACT FROM AUTHOR]

This study by Shridhar et al. 2016 reviews the genetic susceptibility to oral potentially malignant disorders (OPMD) through the analysis of single nucleotide polymorphisms (SNPs). By examining data from 47 studies conducted between 2000 and 2016, the research highlights genetic markers involved in carcinogen metabolism, DNA repair, cell cycle control, and immune-inflammatory responses. Despite the insights provided, the over-reliance on small sample sizes limits the statistical power and generalizability of the findings. Future research should focus on larger, more diverse populations and advanced genotyping technologies to enhance detection of significant genetic variants. Integrating multi-omics data and conducting longitudinal studies will further elucidate the molecular mechanisms underlying OPMD and its progression to oral cancer. Collaborative efforts are essential to validate these findings and develop biomarkers for early detection and prevention. [ABSTRACT FROM AUTHOR]

This work reports the development and application of a disposable amperometric sensor built on magnetic microcarriers coupled to an Express PCR strategy to amplify a specific DNA fragment of the chloroplast trnH-psbA. The procedure involves the selective capture of a 68-mer synthetic target DNA (or unmodified PCR products) through sandwich hybridization with RNA capture probe-modified streptavidin MBs and RNA signaling probes, labeled using antibodies specific to the heteroduplexes and secondary antibodies tagged with horseradish peroxidase. Amperometric measurements were performed on screen-printed electrodes using the H 2 O 2 /hydroquinone system. Achieving a LOD of 3 pM for the synthetic target, it was possible to detect 2.5 pg of peanut DNA and around 10 mg kg−1 of peanut in binary mixtures (defatted peanut flours prepared in spelt wheat). However, the detectability decreased between 10 and 1000 times in processed samples depending on the treatment. The Express PCR-bioplatform was applied to the detection of peanut traces in foodstuff. [Display omitted] • First disposable electrochemical nucleic acid sensor for peanut determination. • Sandwich methodology targeting a fragment of the peanut chloroplast DNA sequence. • Magnetic beads-assisted and amperometric transduction at screen-printed electrodes. • The bioplatform/Express PCR coupling allows detecting 10 mg kg−1 of peanut in food. • Successful interrogation of peanut traces in commercial food samples. [ABSTRACT FROM AUTHOR]

eDNA metabarcoding has been increasingly employed in the monitoring of marine invertebrate non-indigenous species (NIS), in particular using filtered seawater. However, comprehensive detection of all NIS may require a diversity of sampling substrates. To assess the effectiveness of 5 sample types (hard and artificial substrates, water, zooplankton) on the recovery of invertebrates' diversity, two marinas were monitored over three time points, using COI and 18S rRNA genes as DNA metabarcoding markers. We detected a total of 628 species and 23 NIS, with only up to 9% species and 17% of NIS detected by all sample types. Hard and artificial substrates were similar to each other but displayed the most significant difference in invertebrate recovery when compared to water eDNA and zooplankton. Five NIS are potential first records for Portugal. No NIS were detected in all sample types and seasons, highlighting the need for varied sampling approaches, and consideration of temporal variation for comprehensive marine NIS surveillance. [Display omitted] • DNA metabarcoding of marine invertebrates is affected by sampling strategy. • Hard/artificial substrates, water eDNA and zooplankton were sampled in two marinas. • 628 species and 23 NIS detected, of which 5 are potential first Portuguese records. • Only ca. 9% species and 17% NIS were detected in common between sample types. • Using only one sample type, 27–67% species and 20–83% NIS would have gone unnoticed. [ABSTRACT FROM AUTHOR]

The high economic value of olive oil has prompted the European Union to support efforts to protect and valorise the olive oil industry through the introduction of designations of origin (PDO/PGI). This review provides an overview of the European regulation on certified PDO and PGI extra virgin olive oils highlighting the importance and the impact of these labels. It examines the main fraudulent practices affecting extra virgin olive oil and the methods of analysis used to detect frauds, with a particular focus on DNA-based methods for varietal and sometimes, geographical identification. Moreover, an in-depth study was carried out on the varieties authorized in PDO and PGI extra virgin olive oils in Europe, addressing the issue of synonyms and the availability of SSR marker profiles. Finally, the data collected were used for the detection of private alleles. All the data and the information collected represent a useful and reliable tool for the varietal traceability and authentication of European PDO and PGI extra virgin olive oils. • European Geographical Indication protects products with unique characteristics. • The high economic value of olive oil leads to a wide range of frauds. • DNA-based methods allow the authenticity assessment of certified olive oils. • The availability of microsatellite markers is useful for the certified olive oil traceability. • Private alleles detection is an instrument for the agrifood traceability. [ABSTRACT FROM AUTHOR]

Toxoplasma gondii ( T. gondii ) is an intracellular protozoan that can cause toxoplasmosis in all warm-blooded hosts. This study focused on the prevalence and genetic characterize of T. gondii in ducks from Fujian province, China. Genomic DNA was extracted from duck tissue samples (heart, liver, lung, and muscle). To assess the genetic diversity of the T. gondii isolates, it was determined by using multilocus polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) technology. A total of 586 ducks from 5 cities in Fujian province were tested, and 35 (6.0%) of which were found to be positive for the T. gondii B1 gene. Further genotyping of these positive samples at 10 genetic markers (SAG1, SAG2, SAG3, BTUB, GRA6, c22-8, c29-2, L358, PK1, and Apico) using PCR-RFLP revealed that one tissue samples (heart samples from Fuzhou ducks) were identified as Type I (ToxoDB#10). This study is the first report on the prevalence and genetic characterization of T. gondii in ducks in Fujian province, and Type I (ToxoDB#10) is found in ducks in China for the first time. The findings document the genetic characterization of T. gondii in free-range ducks from Fujian Province, thereby enriching the understanding of T. gondii genetic diversity in China. Moreover, these results provide essential data support for further prospective studies and underscores the "One Health" concept, emphasizing the integral link among human, animal, and environmental health. [ABSTRACT FROM AUTHOR]

DNA mixtures are a common sample type in forensic genetics, and we typically assume that contributors to the mixture are unrelated when calculating the likelihood ratio (LR). However, scenarios involving mixtures with related contributors, such as in family murder or incest cases, can also be encountered. Compared to the mixtures with unrelated contributors, the kinship within the mixture would bring additional challenges for the inference of the number of contributors (NOC) and the construction of probabilistic genotyping models. To evaluate the influence of potential kinship on the individual identification of the person of interest (POI), we conducted simulations of two-person (2 P) and three-person (3 P) DNA mixtures containing unrelated or related contributors (parent-child, full-sibling, and uncle-nephew) at different mixing ratios (for 2 P: 1:1, 4:1, 9:1, and 19:1; for 3 P: 1:1:1, 2:1:1, 5:4:1, and 10:5:1), and performed massively parallel sequencing (MPS) using MGIEasy Signature Identification Library Prep Kit on MGI platform. In addition, in silico simulations of mixtures with unrelated and related contributors were also performed. In this study, we evaluated 1): the MPS performance; 2) the influence of multiple genetic markers on determining the presence of related contributors and inferring the NOC within the mixture; 3) the probability distribution of MAC (maximum allele count) and TAC (total allele count) based on in silico mixture profiles; 4) trends in LR values with and without considering kinship in mixtures with related and unrelated contributors; 5) trends in LR values with length- and sequence-based STR genotypes. Results indicated that multiple numbers and types of genetic markers positively influenced kinship and NOC inference in a mixture. The LR values of POI were strongly dependent on the mixing ratio. Non- and correct-kinship hypotheses essentially did not affect the individual identification of the major POI; the correct kinship hypothesis yielded more conservative LR values; the incorrect kinship hypothesis did not necessarily lead to the failure of POI individual identification. However, it is noteworthy that these considerations could lead to uncertain outcomes in the identification of minor contributors. Compared to length-based STR genotyping, using sequence-based STR genotype increases the individual identification power of the POI, concurrently improving the accuracy of mixing ratio inference using EuroForMix. In conclusion, the MGIEasy Signature Identification Library Prep kit demonstrated robust individual identification power, which is a viable MPS panel for forensic DNA mixture interpretations, whether involving unrelated or related contributors. • Evaluated the effect of using multiple genetic markers on the analysis of mixtures containing kinship. • The LR values of the person of interest (POI) were strongly dependent on the mixing ratios. • Incorrect kinship hypotheses do not necessarily lead to the failure of POI individual identification. • Based on sequence-based STR genotypes, higher true donor LR and more accurate mixing-ratio values were obtained. [ABSTRACT FROM AUTHOR]

Vibrio parahaemolyticus is the leading bacterial cause of gastroenteritis associated with seafood consumption worldwide. Not all members of the species are thought to be pathogenic, thus identification of virulent organisms is essential to protect public health and the seafood industry. Correlations of human disease and known genetic markers (e.g. thermostable direct hemolysin (TDH), TDH-related hemolysin (TRH)) appear complex. Some isolates recovered from patients lack these factors, while their presence has become increasingly noted in isolates recovered from the environment. Here, we used whole-genome sequencing in combination with mammalian and insect models of infection to assess the pathogenic potential of V. parahaemolyticus isolated from European Atlantic shellfish production areas. We found environmental V. parahaemolyticus isolates harboured multiple virulence-associated genes, including TDH and/or TRH. However, carriage of these factors did not necessarily reflect virulence in the mammalian intestine, as an isolate containing TDH and the genes coding for a type 3 secretion system (T3SS) 2α virulence determinant, appeared avirulent. Moreover, environmental V. parahaemolyticus lacking TDH or TRH could be assigned to groups causing low and high levels of mortality in insect larvae, with experiments using defined bacterial mutants showing that a functional T3SS1 contributed to larval death. When taken together, our findings highlight the genetic diversity of V. parahaemolyticus isolates found in the environment, their potential to cause disease and the need for a more systematic evaluation of virulence in diverse V. parahaemolyticus to allow better genetic markers. • Vibrio parahaemolyticus accumulates in shellfish posing a food safety risk. • Uncertainty over use of hemolysins, TDH/TRH, as species markers of virulence. • Use of genetic mutants and infection models revealed new insights. • Testing of environmental V. parahaemolyticus revealed most isolates could cause disease. [ABSTRACT FROM AUTHOR]

Seafood fraud involves mislabeling and false claims. To avoid this deceptive practice, authentication techniques, including DNA-based methods, have been developed. These techniques detect fraud, ensure accurate labeling, and maintain product integrity, aiding in species identification, verifying origins, and promoting industry transparency. This review aims to provide a detailed list of approaches for the authenticity of mackerel species due to the prevalence of mislabeling and substitution. Utilizing techniques like DNA, we can identify Scomber species by analyzing specific genetic markers. This work advances the evaluation of existing molecular markers through in silico simulations, while also purposing novel primers designed for a more accurate authentication of processed mackerel products. With advances in techniques, we are seeing significant advances in food authentication methods. DNA barcoding has seen substantial evolution, thanks to improvements in databases and NGS sequencing technologies. The advent of DNA metabarcoding is also revolutionizing species identification in highly processed seafoods. Using more comprehensive primers in Metabarcoding can enhance the assessment of scombrid products. In recent times, SNP-based approaches with microfluidic enrichment, DNA-based biosensors and microbiome sequencing techniques have emerged as key tools for assessing the authenticity and identifying the origins of seafood products. • Global mackerel seafood labelling discrepancies affect consumer transparency • Molecular techniques refine Scomber species identification • NGS advancements enhance seafood mackerel authentication for fraud detection • DNA barcoding is crucial for fraud detection and ensures mackerel authenticity • In silico evaluation: DNA metabarcoding for Scomber species [ABSTRACT FROM AUTHOR]

Lungworm infection, or verminous pneumonia, is a parasitic disease that causes serious problems in small and large ruminants. Despite the fact that nematodes of the genus Dictyocaulus in cattle and sheep are the main cause of this disease, there are few studies on the natural infections of South American camelids. For this reason, this study aims to report the natural infection by Dictyocaulus filaria in vicunas (Vicugna vicugna) for the first time. During a shearing season (chaku) in Cuzco, Peru, two accidentally killed adult vicunas were submitted to the IVITA-Marangani research center in Cuzco for their respective necropsies. The tracheas of both vicunas had numerous nematodes, as seen during the necropsy. The nematodes were collected in 70% ethanol and were morphologically identified as D. filaria. Likewise, the DNA of six nematodes was extracted, and the ITS2 region and the 28S rRNA gene were amplified and sequenced. The nucleotide sequences of both genetic markers were up to 100% identical with previously reported D. filaria DNA sequences found in the goat yearlings from Turkey, sheep from Iran, Turkey, and India, and the argali from Uzbekistan, which confirmed the morphological diagnosis. This finding represents the first molecular confirmation of a natural D. filaria infection in a South American camelid. It will be necessary to carry out future studies to know the current situation of verminous pneumonia in domestic and wild South American camelids and to know the negative effects of the disease on them. [ABSTRACT FROM AUTHOR]

Omenn syndrome(OS) is an autosomal recessive early-onset form of severe combined immunodeficiency (SCID) characterized by increased susceptibility to opportunistic infections, hypereosinophilia, protracted diarrhea, rashes, and the enlargement of the lymph nodes and the spleen. Now hematopoietic transplantation is the only curative treatment available and this need to human leukocyte antigen (HLA) typing for the patient. Certain HLA antigens are more likely to lead to certain autoimmune diseases.Here, we reported the one Chinese individual has three HLA loci with Omenn syndrome. The individual has three alleles in HLA loci is rare. The clinical and immunological data of this case was concordance with OS, which is an autosomal recessive form of severe combined immunodeficiency. The patient has deleted T at nucleotide position 2302 in RAG1, which shift the reading frame of the coding sequence and generates a premature termination codon and may lead to the absence of circulating B cells and non-functional oligoclonal T cells. Interestingly, three HLA alleles were identified in the HLA-A,-B,-C,-DRB1,-DQB1,-DPB1 in the patient, one allele come from his father, the other two alleles were original from his mother. The karyotype of patient was identified as 46XY and both parents have normal karyotype, which did not support the blood chimerism by cytogenetic analysis. The polymorphic DNA markers data shows that the alleles of STR loci were come from the patient and did not find any three alleles in STR loci, which also could not demonstrate the blood chimerism exists in the patient. An individual with three alleles in HLA loci was identified, the molecular basis of three alleles of HLA loci in the patient need to further study. [ABSTRACT FROM AUTHOR]

We assessed the potential role of serial circulating tumor DNA (ctDNA) as a biomarker to monitor treatment response to primary systemic therapy (PST) in breast cancer and evaluated the predictive value of ctDNA to further identify patients with residual disease. We prospectively enrolled 208 plasma samples collected at three time points (before PST, after 2 cycles of treatment, before surgery) of 72 patients with stage Ⅱ-III breast cancer. Somatic mutations in plasma samples were identified using a customized 128-gene capture panel with next-generation sequencing. The correlation between early change in ctDNA levels and treatment response or long-term clinical outcomes was assessed. 37 of 72 (51.4%) patients harbored detectable ctDNA alterations at baseline. Patients with complete response showed a larger decrease in ctDNA levels during PST. The median relative change of variant allele fraction (VAF) was −97.4%, −46.7%, and +21.1% for patients who subsequently had a complete response (n = 11), partial response (n = 11), and no response (n = 15) (p = 0.0012), respectively. In addition, the relative change of VAF between the pretreatment and first on-treatment blood draw exhibited the optimal predictive value to tumor response after PST (area under the curve, AUC = 0.7448, p = 0.02). More importantly, early change of ctDNA levels during treatment have significant prognostic value for patients with BC, there was a significant correlation between early decrease of VAF and longer recurrence-free survival compared to those with an VAF increase (HR = 12.54; 95% CI, 2.084 to 75.42, p = 0.0063). Early changes of ctDNA are strongly correlated with therapeutic efficacy to PST and clinical outcomes in BC patients. The integration of preoperative ctDNA evaluation could help improving the perioperative management for BC patients receiving PST. • The detection of ctDNA before primary systemic treatment (PST) is associated with more aggressive tumor. • The early decrease of ctDNA during the course of PST is a good pathological complete response marker. • The presence of baseline ctDNA and early decrease of ctDNA can be a robust relapse predictor for locally advanced BC. • The potential of preoperative ctDNA detection for PST response prediction in BC. [ABSTRACT FROM AUTHOR]

Sex-specific DNA markers are powerful tools for genetic sex identification and sex control breeding of fish. Spotted halibut (Verasper variegatus) is a kind of marine flatfish with important nutritional and economic value, which exhibits significant sex-related growth dimorphism that the female individuals grow faster than the male individuals. However, there is no rapid, effective and universal sex-specific DNA marker used for genetic sex identification and sex control breeding in spotted halibut up to date. In the present study, whole genome resequencing was performed on 17 male and 17 female spotted halibut individuals to identify sex-specific markers. A total of 325.36 Gb and 328.99 Gb data were obtained from females and males, respectively. After reads mapping, sequencing depth and coverage analysis, 359 potential female-specific DNA sequences were identified. Then, after two rounds of verification, two female-specific 66 bp and 68 bp insertions were identified as female-specific markers which can accurately identify the genetic sex of spotted halibut through PCR amplification and 2% agarose gel electrophoresis. Subsequently, these two female-specific DNA markers and the PCR method were further validated using 117 spotted halibut individuals from another breeding population to confirm their genetic sex, which was in accordance with their phenotypic sex determined by histological section of the gonads. This may be the first two rapid, accurate and effective female-specific DNA markers used for genetic sex identification in spotted halibut. The identification of these two female-specific DNA markers will not only provide important genetic evidence to elucidate the sex determination mechanism of spotted halibut, but also help to advance the process of sex control breeding in spotted halibut. • 359 potential female-specific DNA sequences were identified through resequencing. • Two female-specific DNA markers were detected in spotted halibut. • A PCR-based method was developed to identify the genetic sex of spotted halibut. • This work will contribute to the sex control breeding of spotted halibut. [ABSTRACT FROM AUTHOR]

The development of resistance to cisplatin (CDDP) in bladder cancer presents a notable obstacle, with indications pointing to the substantial role of circular RNAs (circRNAs) in this resistance. Nevertheless, the precise mechanisms through which circRNAs govern resistance are not yet fully understood. Our findings demonstrate that circUGGT2 is significantly upregulated in bladder cancer, facilitating cancer cell migration and invasion. Additionally, our analysis of eighty patient outcomes revealed a negative correlation between circUGGT2 expression levels and prognosis. Using circRNA pull-down assays, mass spectrometry analyses, and RNA Immunoprecipitation (RIP), it was shown that circUGGT2 interacts with the KU heterodimer, consisting of KU70 and KU80. Both KU70 and KU80 are critical components of the non-homologous end joining (NHEJ) pathway, which plays a role in CDDP resistance. Flow cytometry was utilized in this study to illustrate the impact of circUGGT2 on the sensitivity of bladder cancer cell lines to CDDP through its interaction with KU70 and KU80. Additionally, a reduction in the levels of DNA repair factors associated with the NHEJ pathway, such as KU70, KU80, DNA-PKcs, and XRCC4, was observed in chromatin of bladder cancer cells following circUGGT2 knockdown post-CDDP treatment, while the levels of DNA repair factors in total cellular proteins remained constant. Thus, the promotion of CDDP resistance by circUGGT2 is attributed to its facilitation of repair factor recruitment to DNA breaks via interaction with the KU heterodimer. Furthermore, our study demonstrated that knockdown of circUGGT2 resulted in reduced levels of γH2AX, a marker of DNA damage response, in CDDP-treated bladder cancer cells, implicating circUGGT2 in the NHEJ pathway for DNA repair. • CircUGGT2, highly expressed in bladder cancer, significantly promotes its invasion and affects patient prognosis. • CircUGGT2 binds to KU70 and KU80, facilitating the dimerization and thereby enhancing the NHEJ pathway. • CircUGGT2 enhances DNA double-strand repair, thereby enhancing cisplatin resistance in bladder cancer. [ABSTRACT FROM AUTHOR]

Reliable detection of bacteria belonging to the Borrelia burgdorferi sensu lato species complex in vertebrate reservoirs, tick vectors, and patients is key to answer questions regarding Lyme borreliosis epidemiology. Nevertheless, the description of characteristics of qPCRs for the detection of B. burgdorferi s. l. are often limited. This study covers the development and validation of two duplex taqman qPCR assays used to target four markers on the chromosome of genospecies of B. burgdorferi s. l. Analytical specificity was determined with a panel of spirochete strains. qPCR characteristics were specified using water or tick DNA spiked with controlled quantities of the targeted DNA sequences of B. afzelii , B. burgdorferi sensu stricto or B. bavariensis. The effectiveness of detection results was finally evaluated using DNA extracted from ticks and biopsies from mammals whose infectious status had been determined by other detection assays. The developed qPCR assays allow exclusive detection of B. burgdorferi s. l. with the exception of the M16 marker which also detect relapsing fever Borreliae. The limit of detection is between 10 and 40 copies per qPCR reaction depending on the sample type, the B. burgdorferi genospecies and the targeted marker. Detection tests performed on various kind of samples illustrated the accuracy and robustness of our qPCR assays. Within the defined limits, this multi-target qPCR method allows a versatile detection of B. burgdorferi s. l., regardless of the genospecies and the sample material analyzed, with a sensitivity that would be compatible with most applications and a reproducibility of 100% under measurement conditions of limits of detection, thereby limiting result ambiguities. • Four qPCR assays used in duplex were developed to detect Borrelia burgdorferi sensu lato. • The limits of detection and quantification were defined according to state of the art standards. • The specifications allow the detection of B. burgdorferi sensu lato from different sampling sources. [ABSTRACT FROM AUTHOR]

• Genetic linkage affects pedigree likelihood ratio used for kinship testing. • The simulation module of GeneVisa is used for investing linkage effects. • The software GeneVisa use Lander-Green to deal with linkage. • Linkage effects on the distributions of likelihood ratios are shown. • Linkage effects on likelihood ratios of routine cases are investigated. The pedigree likelihood ratio (LR) can be used for determining kinship in the forensic kinship testing. LR can be obtained by analyzing the DNA data of Short tandem repeat (STR) and single nucleotide polymorphism (SNP) loci. With the advancement of biotechnology, increasing number of genetic markers have been identified, thereby expanding the pedigree range of kinship testing. Moreover, some of the loci are physically closer to each other and genetic linkage between loci is inevitable. LRs can be calculated by accounting for linkage or ignoring linkage (LR linkage and LR ignore , respectively). GeneVisa is a software for kinship testing (www.genevisa.net) and adopts the Lander–Green algorithm to deal with genetic linkage. Herein, we used the simulation program of the software GeneVisa to investigate the effects of genetic linkage on 1st-degree, 2nd-degree, and 3rd-degree kinship testing. We used this software to simulate LR linkage and LR ignore values based on 43 STRs and 134 SNPs in commercial kits by using the allele frequency rate and genetic distance data of the European population. The effects of linkage on LR distribution and LRs of routine cases were investigated by comparing the LR linkage values with the LR ignore values. Our results revealed that the linkage effect on LR distributions is small, but the effect on LRs of routine cases may be large. Moreover, the results indicated that the discriminatory power of genetic markers for kinship testing can be improved by accounting for linkage. [ABSTRACT FROM AUTHOR]

Previous reports of macrocyclic lactone (ML) resistance in Dirofilaria immitis, the parasitic nematode which causes heartworm disease, have mainly been from the southern Mississippi Delta region. Southeast Missouri (SEMO), forming the northern boundary of this region, has not previously been well studied. The area is an ideal propagation region for heartworm infection and possibly for the spread of ML resistance. To assess whether D. immitis isolates infecting domestic canines in SEMO exhibit evidence of resistance to MLs, domestic canines, presented to veterinary facilities testing positive for heartworms through antigen and microfilariae (MF) examination, were utilized in the study. Using a descriptive epidemiological cross-sectional study, from March 2021 through February 2022, blood sample collection from 96 canines living in SEMO testing positive for heartworms were analyzed. MiSeq technology was utilized to sequence specific genetic markers associated with susceptibility/resistance for MLs in D. immitis isolates. Genomic data revealed most D. immitis isolates had genotypic profiles consistent with resistance to MLs. Of the 96 samples tested, 91 (94.8%) had a resistant genotype, 4 (4.2%) had a mixed genotype, and 1 sample (1%) genotyped as susceptible. While detailed and reliable medical histories were not available for most canines, detailed medical history from 2 canines indicated evidence of phenotypic resistance that was consistent with their genotypes. However, in vivo preventive tests are needed to confirm a high frequency of phenotypic ML resistance in D. immitis from this region. Increasing resistance patterns to MLs indicate the approach to heartworm prevention/treatment protocol should be reconsidered. New measures may be required to stop heartworm disease. [Display omitted] • From 11 southeast Missouri counties, Dirofilaria immitis infected dogs were identified. • Blood was drawn from 96 infected dogs and microfilariae (MF) were isolated for DNA. • DNA analyzed by MiSeq at macrocyclic lactone (ML) resistance-associated SNPs. • Ninety-five percent of the 96 samples showed resistance genotypes. • In a few dogs there was corroborating evidence of phenotypic ML-resistance. [ABSTRACT FROM AUTHOR]