Single Genotype Research Articles

Molecular detection and genotyping of Dientamoeba fragilis and Blastocystis sp. in housefly Musca domestica (Diptera: Muscidae): first report for Dientamoeba fragilis.

Dientamoeba fragilis and Blastocystis sp. are single-celled protozoan parasites of humans and animals. Although they are found in the intestines of healthy hosts, the pathogenicity of them is still unclear. To date, there is no report on D. fragilis and only two studies (without subtyping) on the occurrence of Blastocystis sp. in Musca domestica. In this study, fly samples were collected from livestock farms and their surroundings in the Kirsehir province (Central Anatolia Region) of Türkiye from May to August 2023. A total of 150 microscopically identified M. domestica samples were analyzed for the detection of D. fragilis and Blastocystis sp. molecularly. The overall prevalence of Blastocystis sp. and D. fragilis in M. domestica was determined to be 3.3% (5/150) and 8.0% (12/150), respectively. The SSU rRNA gene sequences of the isolates indicated genotype 1 of D. fragilis. Eleven isolates were identical and represented a single isolate (KAU-Dfrag1). BLAST analysis of KAU-Dfrag1 indicated identity with the isolates reported from humans, cattle, sheep, and budgerigars. The other isolate (KAU-Dfrag2) was polymorphic at two nucleotides from KAU-Dfrag1 and three nucleotides from known genotypes from GenBank and represented a variant of genotype 1. The Blastocystis sp. isolates were found to be identical and represent a single genotype (KAU-Blast1). BLAST analysis revealed that the KAU-Blast1 genotype belonged to the potentially zoonotic subtype 5 (ST5) and exhibited the highest genetic identity (ranging from 99.4 to 99.6%) with pigs, cattle, and sheep from different countries. Our study provides the first data on the molecular prevalence, epidemiology, and genotypic characterization of D. fragilis and Blastocystis sp. in M. domestica.

Distribution of Aspergillus species and prevalence of azole resistance in clinical and environmental samples from a Spanish hospital during a three-year study period.

Surveillance studies are crucial for updating trends in Aspergillus species and antifungal susceptibility information. Determine the Aspergillus species distribution and azole resistance prevalence during this 3-year prospective surveillance study in a Spanish hospital. Three hundred thirty-five Aspergillus spp. clinical and environmental isolates were collected during a 3-year study. All isolates were screened for azole resistance using an agar-based screening method and resistance was confirmed by EUCAST antifungal susceptibility testing. The azole resistance mechanism was confirmed by sequencing the cyp51A gene and its promoter. All Aspergillus fumigatus strains were genotyped using TRESPERG analysis. Aspergillus fumigatus was the predominant species recovered with a total of 174 strains (51.94%). The rest of Aspergillus spp. were less frequent: Aspergillus niger (14.93%), Aspergillus terreus (9.55%), Aspergillus flavus (8.36%), Aspergillus nidulans (5.37%) and Aspergillus lentulus (3.28%), among other Aspergillus species (6.57%). TRESPERG analysis showed 99 different genotypes, with 72.73% of the strains being represented as a single genotype. Some genotypes were common among clinical and environmental A. fumigatus azole-susceptible strains, even when isolated months apart. We describe the occurrence of two azole-resistant A. fumigatus strains, one clinical and another environmental, that were genotypically different and did not share genotypes with any of the azole-susceptible strains. Aspergillus fumigatus strains showed a very diverse population although several genotypes were shared among clinical and environmental strains. The isolation of azole-resistant strains from both settings suggest that an efficient analysis of clinical and environmental sources must be done to detect azole resistance in A. fumigatus.

Assessment of Breeding Potential of Taro (Colocasia esculenta L.) Genotypes Using D2 Analysis under Hill Zone of Karnataka

Using Mahalanobis D2 statistics, the genetic diversity of 20 genotypes of taro for 21 characteristics was assessed as part of a breeding work to increase production potential. Five clusters were formed from the genotypes, indicating a significant level of genetic variation in the material being studied. With eight genotypes, Cluster I was the largest, followed by Cluster II with seven, and Cluster III with three. Each of the solitary clusters IV and V has a single genotype. The clusters that exhibit the greatest number of genotypes are indicative of limited genetic diversity. The intra-cluster distance was highest in cluster III and lowest in clusters IV and V. Clusters I and V have the highest inter-cluster distance, followed by II and V. These clusters could potentially be used as prospective genotypes for a hybridization programme. Tuber yield/plot (13%) showed the largest contribution to the overall divergence, followed by Corm yield/plant (12.20%) and Tuber yield/plant (11.43%). The finding that clusters V and III showed high cluster means for plant height, number of leaves per plant, leaf breadth, leaf area, leaf area index, tuber yield per plant, tuber yield per plot, and estimated tuber yield is noteworthy. These clusters can be effectively used in hybridization programmes to obtain desired transgressive segregants.

Synergistic response to climate stressors in coral is associated with genotypic variation in baseline expression.

As environments are rapidly reshaped due to climate change, phenotypic plasticity plays an important role in the ability of organisms to persist and is considered an especially important acclimatization mechanism for long-lived sessile organisms such as reef-building corals. Often, this ability of a single genotype to display multiple phenotypes depending on the environment is modulated by changes in gene expression, which can vary in response to environmental changes via two mechanisms: baseline expression and expression plasticity. We used transcriptome-wide expression profiling of eleven genotypes of common-gardened Acropora cervicornis to explore genotypic variation in the expression response to thermal and acidification stress, both individually and in combination. We show that the combination of these two stressors elicits a synergistic gene expression response, and that both baseline expression and expression plasticity in response to stress show genotypic variation. Additionally, we demonstrate that frontloading of a large module of coexpressed genes is associated with greater retention of algal symbionts under combined stress. These results illustrate that variation in the gene expression response of individuals to climate change stressors can persist even when individuals have shared environmental histories, affecting their performance under future climate change scenarios.

Interference between Escherichia coli genotypes from the E. coli peritonitis syndrome given simultaneously to productive SPF White Leghorn hens by intratracheal inoculation

ABSTRACT The purpose of the present study was to examine if potentiation of mortality occurred after simultaneous administration of several Escherichia coli genotypes, each capable of inducing the E. coli peritonitis syndrome, in comparison with single genotype application. Five groups of productive specified pathogen free White Leghorn hens were housed in isolators. Groups 1–4 consisted of 32 hens each, group 5 of 10 hens. At 32 weeks of age all groups were inoculated intratracheally. Groups 1 and 2 were inoculated with a mix of four E. coli genotypes and groups 3 and 4 with a mix of four other genotypes. Groups 1 and 3 were given 1 median lethal dose (LD50) of each genotype per hen and groups 2 and 4 had a dose of 0.1 LD50 per genotype per hen; group 5 was mock inoculated. The experiment ended one week after inoculations. In Group 5, no mortality occurred and gross lesions were absent at post-mortem examination. Mortality in groups 1 and 3 was 84% and 81%, respectively; in groups 2 and 4 59% and 66%, respectively. Although mortality in groups 1 and 3 exceeded the expected 50%, this could not be due to potentiation as cluster analysis of reisolates showed that in individual hens only one genotype was found, indicating interference between E. coli genotypes. In groups all four or only two genotypes were recovered, showing that not all genotypes will induce colibacillosis in all experimental groups. Therefore, broad protection can be best assessed by challenging with various single genotypes. RESEARCH HIGHLIGHTS All four or only two E. coli genotypes were found in groups of hens given mixes of four genotypes. In contrast, only one genotype was found in individual hens. E. coli genotypes interfere with each other in hens after given as a mix. Interference is likely based on a random process. Broad protection can best be assessed by challenging with single genotypes.

Dominance complementation of parental heading date alleles of Hd1, Ghd7, DTH8, and PRR37 confers transgressive late maturation in hybrid rice.

Rice (Oryza sativa L.) is a short-day plant whose heading date is largely determined by photoperiod sensitivity (PS). Many parental lines used in hybrid rice breeding have weak PS, but their F1 progenies have strong PS and exhibit an undesirable transgressive late-maturing phenotype. However, the genetic basis for this phenomenon is unclear. Therefore, effective methods are needed for selecting parents to create F1 hybrid varieties with the desired PS. In this study, we used bulked segregant analysis with F1 Ningyou 1179 (strong PS) and its F2 population, and through analyzing both parental haplotypes and PS data for 918 hybrid rice varieties, to identify the genetic basis of transgressive late maturation which is dependent on dominance complementation effects of Hd1, Ghd7, DTH8, and PRR37 from both parents rather than from a single parental genotype. We designed a molecular marker-assisted selection system to identify the genotypes of Hd1, Ghd7, DTH8, and PRR37 in parental lines to predict PS in F1 plants prior to crossing. Furthermore, we used CRISPR/Cas9 technique to knock out Hd1 in Ning A (sterile line) and Ning B (maintainer line) and obtained an hd1-NY material with weak PS while retaining the elite agronomic traits of NY. Our findings clarified the genetic basis of transgressive late maturation in hybrid rice and developed effective methods for parental selection and gene editing to facilitate the breeding of hybrid varieties with the desired PS for improving their adaptability.

Abstract 5335: Immune cell population variations in the livers of commonly used mouse strains

Abstract Previous studies have shown that the distribution of major immune cell populations differ across mouse strains in peripheral blood and hematopoietic organs at baseline. Additionally, variations in immune responses exist between mouse strains in Leishmania spp. and Melanoma models, but these studies in the context of liver diseases including Non Alcoholic Fatty Liver Disease (NAFLD) and Hepatocellular Carcinoma (HCC) have not been carried out. With the effort to state if these variations exist within the liver, we performed comprehensive spectral flow cytometry analysis on the liver and spleens of three female mouse strains commonly used in cancer research (BALB/c, C57BL/6, and FVBN). NAFLD was induced by providing mice with a methionine choline deficient diet. To promote HCC, a single genotype (myc/p53+/-) was induced by administering transposon-based vectors to overexpress Myc-Luc and CRISPR/Cas-9 vectors to knock down p53 via hydrodynamic tail-vein injection. To confirm vector integration and monitor tumor growth (luciferase activity), in vivo imaging was performed at different time points. As a result, we confirm throughout this study that differences exist within immune cell populations of the liver and spleen at baseline. Moreover, we depict differences in the shift of immune cell populations across mouse strains in the pathologic states included. In NAFLD, there is an increase of dendritic cells (DCs), macrophages, NK cells, ILC1s, T regulatory cells (Tregs), TH1, and TH2, and a decrease of CD4+ T cells, B cells, γδ-T cells, and NKT cells in the liver across all mouse strains, when compared to controls. However, the population of neutrophils in BALB/c decreases, and the population of CD8+ T cells increases in C57BL/6 mice, which differs from the patterns of change seen in the other mouse strains. Moreover, in spleens, NAFLD promotes an increase of TH1 and NK cells, and a decrease of TH2 and NKT Cells across the mouse strains included in the study, whereas the patterns of change differ between mouse strains among the remaining immune cell types. When evaluating liver immune cell population shifts on our HCC model, BALB/c mice showed a decrease in macrophages and ILC1s, C57BL/6 mice showed a decrease in γδ-T cells, prominent shifts across Neutrophils, TH1, and NKT cells, and null changes in TH2 and CD4+ T cell shifts, and FVBN mice had a less prominent decrease of B cells, which differed from the shifts observed in the mouse strains used for comparison. Immune cell populations in the spleens of our HCC mouse model also presented with differences across the mouse strains studied. In conclusion, we highlight that key differences in immune profiles exist across commonly used mouse strains for cancer research in the presence of liver pathology including HCC, suggesting that mouse strains could be possible confounders in the study of immune oncology of HCC. Citation Format: Francisco J. Rodriguez-Matos, Patrick Huang, Rajiv Trehan, Benjamin Ruf, Chi Ma, Tim F. Greten. Immune cell population variations in the livers of commonly used mouse strains [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5335.

Molecular and biological characterization of pepino mosaic virus isolates occurring in the main tomato-producing areas in Mexico

Pepino mosaic virus (PepMV) has caused major epidemics in tomatoes (Solanum lycopersicum L.) worldwide. Five genotypes have been identified: Peruvian (LP), European (EU), American (US1), Chilean (CH2), and Southern Peruvian (PES). The aim of this study was to determine the current distribution of PepMV in the main tomato-producing areas of Mexico, as well as to identify the predominant genotypes and their biological behavior in alternative hosts and indicator species. A total of 77 samples of tomato plants showing PepMV symptoms-like with leaf mottling, mosaic, and chlorosis symptoms, as well as marbled fruit, were analyzed by multiplex reverse transcription PCR (RT-PCR). Sequencing data confirmed the identification of PepMV genotypes in 15 samples from six states. Six samples with single CH2 genotype infection, two with LP genotype, two with EU genotype, and five LP + CH2 co-infections were detected. Moreover, a high prevalence of ToBRFV was found, either in single infection or in co-infection with PepMV. Five PepMV sources (three CH2, one EU, and one with LP + CH2 co-infection) were used in the biological indexing. All isolates induced systemic infection in Solanum lycopersicum, Datura stramonium, Nicotiana occidentalis, and Solanum melongena. In tomato, CH2 isolates induced mild mosaics and chlorosis, whereas the EU isolate caused chlorotic mosaics typical of PepMV. In D. stramonium and S. melongena, chlorosis, interveinal yellowing, and mosaics were observed. Nicotiana occidentalis showed symptoms with all isolates, particularly with the CH2-MXM01 isolate, which caused necrotic lesions. Overall, PepMV is present in at least six states in Mexico, with the CH2 genotype and mixed LP + CH2 infection prevailing. US1 and PES genotypes were not detected. Interestingly, an EU isolate was characterized as an aggressive variant, causing mosaics and severe chlorosis.

A Critical Review of Conventional and Modern Approaches to Develop Herbicide-Resistance in Rice.

Together with rice, weeds strive for nutrients and space in farmland, resulting in reduced rice yield and quality. Planting herbicide-resistant rice varieties is one of the effective ways to control weeds. In recent years, a series of breakthroughs have been made to generate herbicide-resistant germplasm, especially the emergence of biotechnological tools such as gene editing, which provides an inherent advantage for the knock-out or knock-in of the desired genes. In order to develop herbicide-resistant rice germplasm resources, gene manipulation has been conducted to enhance the herbicide tolerance of rice varieties through the utilization of techniques such as physical and chemical mutagenesis, as well as genome editing. Based on the current research and persisting problems in rice paddy fields, research on the generation of herbicide-resistant rice still needs to explore genetic mechanisms, stacking multiple resistant genes in a single genotype, and transgene-free genome editing using the CRISPR system. Current rapidly developing gene editing technologies can be used to mutate herbicide target genes, enabling targeted genes to maintain their biological functions, and reducing the binding ability of target gene encoded proteins to corresponding herbicides, ultimately resulting in herbicide-resistant crops. In this review article, we have summarized the utilization of conventional and modern approaches to develop herbicide-resistant cultivars in rice as an effective strategy for weed control in paddy fields, and discussed the technology and research directions for creating herbicide-resistant rice in the future.

Rickettsia species identified in adult, host-seeking Dermacentor occidentalis (Acari: Ixodidae) from Baja California, Mexico, and Oregon and Washington, United States.

The Pacific Coast tick (Dermacentor occidentalis Marx, 1892) is a frequently encountered and commonly reported human-biting tick species that has been recorded from most of California and parts of southwestern Oregon, southcentral Washington, and northwestern Mexico. Although previous investigators have surveyed populations of D. occidentalis for the presence of Rickettsia species across several regions of California, populations of this tick have not been surveyed heretofore for rickettsiae from Baja California, Oregon, or Washington. We evaluated 1,367 host-seeking, D. occidentalis adults collected from 2015 to 2022 by flagging vegetation at multiple sites in Baja California, Mexico, and Oregon and Washington, United States, using genus- and species-specific assays for spotted fever group rickettsiae. DNA of Rickettsia 364D, R. bellii, and R. tillamookensis was not detected in specimens from these regions. DNA of R. rhipicephali was detected in D. occidentalis specimens obtained from Ensenada Municipality in Baja California and southwestern Oregon, but not from Washington. All ompA sequences of R. rhipichephali that were amplified from individual ticks in southwestern Oregon were represented by a single genotype. DNA of the Ixodes pacificus rickettsial endosymbiont was amplified from specimens collected in southwestern Oregon and Klickitat County, Washington; to the best of our knowledge, this Rickettsia species has never been identified in D. occidentalis. Collectively, these data are consistent with a relatively recent introduction of Pacific Coast ticks in the northernmost extension of its recognized range.

Cytochrome P450 Family 4F2 and 4F11 Haplotype Mapping and Association with Hepatic Gene Expression and Vitamin K Hydroxylation Activity.

This study evaluated the underlying mechanistic links between genetic variability in vitamin K metabolic pathway genes (CYP4F2 and CYP4F11) and phylloquinone hydroxylation activity using genotype- and haplotype-based approaches. Specifically, we characterized genetic variability in the CYP4F2/CYP4F11 locus and compared common single allele genotypes and common haplotypes as predictors of hepatic gene expression, enzyme abundance, and phylloquinone (VK1) ω-hydroxylation kinetics. We measured CYP4F2 and CYP4F11 mRNA levels, CYP4F2 and CYP4F11 protein abundances, and the VK1 concentration-dependent ω-hydroxylation rate in matched human liver nucleic acid and microsome samples, utilizing a novel in vitro population modeling approach. Results indicate that accounting for the CYP4F2*3 allele alone is sufficient to capture most of the genetic-derived variability in the observed phenotypes. Additionally, our findings highlight the important contribution that CYP4F11 makes toward vitamin K metabolism in the human liver.

Human papillomavirus genotyping in high-grade vaginal intraepithelial neoplasia: Amulticentric Italian study.

This study aimed to analyze the human papillomavirus (HPV) genotype distribution in a large cohort of high-grade vaginal intraepithelial neoplasia (VaIN) (vaginal HSIL, VaIN2/3) patients from two Italian referral centers. We included all patients with histologically confirmed VaIN2/3 from the Department of Surgical Sciences, Sant'Anna Hospital, University of Torino, Torino, Italy, and Ospedale Maggiore della Carità, Novara, Italy, between 2003 and 2022. After the histological evaluation of formalin-fixed paraffin-embedded samples, we performed HPV genotyping with VisionArray HPV Chip 1.0. We detected HPV DNA in 94.4% of VaIN2/3 (168/178), with HPV 16 as the most prevalent genotype, accounting for 51.8% of all infections, 41.2% of VaIN2and 77.6% of VaIN3 cases. Other frequent genotypes were HPV 58 (8.3%, 10.9% of VaIN2and 2.0% of VaIN3), HPV 73 (5.4%, 5.0% of VaIN2and 6.1% of VaIN3), and HPV 31 (5.4%, 6.7% of VaIN2and 2.0% of VaIN3). 73.2% of VaIN2/3 had a single HPV genotype infection and 26.8% a multiple infection (20.8% a double infection, 4.8% a triple infection, and 1.2% a quadruple infection). Single infection was more frequently present in VaIN3 than VaIN2 (81.6% vs. 69.8%). 69.1% of single infections and 73.3% of multiple infections had one or more genotypes covered by nine-valent HPV vaccine. HPV vaccination is expected to have a large impact on reducing the incidence of vaginal intraepithelial neoplasia.

Probabilistic genetic identification of wild boar hybridization to support control of invasive wild pigs (Sus scrofa)

AbstractThe rapid expansion of wild pigs (Sus scrofa) throughout the United States has been fueled by unlawful introductions, with invasive populations causing extensive crop losses, damaging native ecosystems, and serving as a reservoir for disease. Multiple states have passed laws prohibiting the possession or transport of wild pigs. However, genetic and phenotypic similarities between domestic pigs and invasive wild pigs—which overwhelmingly represent domestic pig and wild boar hybrids—pose a challenge for the enforcement of such regulations. We sought to exploit wild boar ancestry as a common attribute among the vast majority of invasive wild pigs as a means of genetically differentiating wild pigs from breeds of domestic pig found within the United States. We organized reference high‐density single nucleotide polymorphism genotypes (1039 samples from 33 domestic breeds and 382 samples from 16 wild boar populations) into five genetically cohesive reference groups: mixed‐commercial breeds, Durocs, heritage breeds, primitive breeds, and wild boar. Building upon well‐established genetic clustering approaches, we structured the test statistic to describe the difference in the likelihood of a given genotype's ancestry vectors (sensu genetic clustering analysis) if derived strictly from the four described domestic pig reference groups versus allowing for admixture from the wild boar group. By fitting statistical distributions to test statistics of reference domestic pigs, we characterized the distribution of the null hypothesis that a given genotype descends strictly from domestic pig reference groups. We tested the approach with simulated genotypes and empirical data from an additional 29 breeds of domestic pig represented by 435 unique genotypes; all associated test statistics for simulated and empirical domestic pig challenge sets fell within the distribution of reference domestic pigs. We then evaluated 6566 invasive wild pigs sampled across the contiguous United States, of which 63% exceeded the maximum threshold for domestic pigs and could be statistically classified as possessing wild boar ancestry. This approach provides a scientific foundation to enforce regulations prohibiting the possession of this destructive invasive species. Further, this computationally efficient and generalizable approach could be readily adapted to quantify gene flow among ecological systems of conservation or management concern.

A Retrospective Longitudinal Study of 460 Patients with ABCA4-Associated Retinal Disease

PurposeTo investigate the distribution of genotypes and natural history of ABCA4-associated retinal disease in a large cohort of patients seen at a single institution. DesignRetrospective, single institution, cohort review. SubjectsPatients seen at the University of Iowa between November 1986 and August 2022 clinically suspected to have disease caused by sequence variations in ABCA4. MethodsDNA samples from participants were subjected to a tiered testing strategy progressing from allele-specific screening to whole genome sequencing. Charts were reviewed and clinical data were tabulated. The pathogenic severity of the most common alleles was estimated by studying groups of patients that shared one allele. Groups of patients with shared genotypes were reviewed for evidence of modifying factor effects. Main Outcome MeasuresAge of first uncorrectable vision loss, best corrected visual acuity, and the area of the I2e isopter of the Goldmann visual field. ResultsA total of 460 patients from 390 families had convincing clinical features of ABCA4-associated retinal disease. Complete genotypes were identified in 399 patients and partial genotypes in 61. The median age of first vision loss was 16 years (range 4-76 years). 265 of the families (68%) had a unique genotype and no more than 10 patients shared any single genotype. Review of the patients with shared genotypes revealed evidence of modifying factors that in several cases resulted in a greater than 15-year difference in age of first vision loss. 241 different alleles were identified among the members of this cohort and 161 of these (67%) were found in only a single individual. ConclusionsABCA4-associated retinal disease ranges from a very severe photoreceptor disease with an onset before age 5 years to a late-onset RPE-based condition resembling pattern dystrophy. Modifying factors frequently impact the ABCA4 disease phenotype to a degree that is similar in magnitude to the detectable ABCA4 alleles themselves. It is likely that the majority of patients in any cohort will have a unique genotype. The latter observations taken together suggest that patients’ clinical findings will in most cases be more useful for predicting their clinical course than their genotype.

Spatial and temporal heterogeneity alter the cost of plasticity in Pristionchus pacificus.

Phenotypic plasticity, the ability of a single genotype to produce distinct phenotypes under different environmental conditions, has become a leading concept in ecology and evolutionary biology, with the most extreme examples being the formation of alternative phenotypes (polyphenisms). However, several aspects associated with phenotypic plasticity remain controversial, such as the existence of associated costs. While already predicted by some of the pioneers of plasticity research, i.e. Schmalhausen and Bradshaw, experimental and theoretical approaches have provided limited support for the costs of plasticity. In experimental studies, one common restriction is the measurement of all relevant parameters over long time periods. Similarly, theoretical studies rarely use modelling approaches that incorporate specific experimentally-derived fitness parameters. Therefore, the existence of the costs of plasticity remains disputed. Here, we provide an integrative approach to understand the cost of adaptive plasticity and its ecological ramifications, by combining laboratory data from the nematode plasticity model system Pristionchus pacificus with a stage-structured population model. Taking advantage of measurements of two isogenic strains grown on two distinct diets, we illustrate how spatial and temporal heterogeneity with regard to the distribution of resources on a metapopulation can alter the outcome of the competition and alleviate the realized cost of plasticity.

Study on genetic diversity in Amaranthus (Amaranthus hypochondriacus L.)

Grain amaranth is a protein rich psuedocereal, assumes an important position in terms of quality breeding activities. Systematic characterization, evaluation and utilization of the potential genotype in the crop are prerequisite to any crop improvement. Genetic diversity study was conducted in one hundred fifty genotypes using Mahalanobis D2 Statistics during Kharif 2017 at College of Agriculture Badnapur. Based on D2 values, 150 genotypes were grouped into XII clusters. In the present investigation, the cluster II was with the highest number of genotypes (62) followed by cluster I (33), clusters VI (25), cluster VI (16), IX (3), X (3) and cluster III, V, VII, VIII, XI , XII had single genotype. The intra cluster distance (D) range from 4.74 to 48.64. The maximuminter cluster distance (D= 48.64) was observed between cluster XII and IX cluster, followed by cluster XI and IX (D= 46.25), cluster XI and cluster IV (D= 45.43), cluster IX and cluster VIII (D= 43.92), cluster IX and cluster II (D= 39.03) indicating that the genotypes falling in these clusters were highly divergent from each other implying large amount of diversity within and between groups, which could be exploited in breeding programmes. As crosses between genotypes belonging to the clusters with maximum inter cluster distance, may give high heterotic response resulting in better recombinants.

Comparative genomic analysis of Microcystis strain diversity using conserved marker genes

Microcystis-dominated cyanobacterial harmful algal blooms (cyanoHABs) have a global impact on freshwater environments, affecting both wildlife and human health. Microcystis diversity and function in field samples and laboratory cultures can be determined by sequencing whole genomes of cultured isolates or natural populations, but these methods remain computationally and financially expensive. Amplicon sequencing of marker genes is a lower cost and higher throughput alternative to characterize strain composition and diversity in mixed samples. However, the selection of appropriate marker gene region(s) and primers requires prior understanding of the relationship between single gene genotype, whole genome content, and phenotype. To identify phylogenetic markers of Microcystis strain diversity, we compared phylogenetic trees built from each of 2,351 individual core genes to an established phylogeny and assessed the ability of these core genes to predict whole genome content and bioactive compound genotypes. We identified single-copy core genes better able to resolve Microcystis phylogenies than previously identified marker genes. We developed primers suitable for current Illumina-based amplicon sequencing with near-complete coverage of available Microcystis genomes and demonstrate that they outperform existing options for assessing Microcystis strain composition. Results showed that genetic markers can be used to infer Microcystis gene content and phenotypes such as potential production of bioactive compounds , although marker performance varies by bioactive compound gene and sequence similarity. Finally, we demonstrate that these markers can be used to characterize the Microcystis strain composition of laboratory or field samples like those collected for surveillance and modeling of Microcystis-dominated cyanobacterial harmful algal blooms.

Deciphering the potential of diverse barley genotypes for improving the malt quality

The quality of barley grains and malt significantly influences the fermentation process and the ultimate quality of beer. However, the diverse range of desired quality requirements complicates the selection of suitable malting barley varieties. Achieving a combination of all desirable traits within a single genotype poses a significant challenge. This study aimed to identify the most promising malting genotypes by evaluating the malting potential of 29 barley genotypes, considering various grain (plumpness, hectolitre weight, grain protein, starch and β-glucan content) and malt quality (diastatic power, filtration rate, hot water extract, kolbach index and green malt β-glucanase activity and β-glucan content) traits. Significant genotypic variations were observed for individual grain and malt traits. Low malt β-glucanase activity led to high β-glucan content and low diastatic power, affecting the profile of fermentable sugars in the wort. Therefore, β-glucanase activity and β-glucan content were identified as potential additional selection criteria for producing high-quality malt. A weighted scoring system based on eight quality traits identified ten barley genotypes that outperformed the check varieties. Among them, three genotypes (BL1523 > PL807 > BL1748) exhibited exceptionally higher scores than the check varieties. Furthermore, wort sugar profiling confirmed the potential of these genotypes as valuable contributors to future barley improvement programs aimed at enhancing malt quality.

High rate of non-vaccine targeted high-risk HPV genotypes circulate among women in Eastern Ethiopia

The World Health Organization [WHO] recommends a genotype-specific human papillomavirus [HPV] vaccination as a primary prevention strategy to control the burden of cervical cancer globally. In Ethiopia, where the non-vaccine-targeted HPV genotypes have not been adequately studied, a vaccination initiative was launched in 2018 targeting HPV-6,-11, -16, and -18 for girls aged 14–18 years. The co-existence of both vaccine-targeted and non-targeted genotypes is a serious concern, as it can accelerate cancer progression. Therefore, this study was conducted to determine the prevalence of non-vaccine-targeted HPV genotypes and assess the level of multiple infections with other genotypes in eastern Ethiopia. A health facility-based cross-sectional study including 110 women with positive HPV DNA results was conducted from April to August 2021. A structured questionnaire to collect demographic and clinical data was used. Cervical swabs were collected using L-shaped FLOQSwabs. Women's cytological profile was determined based on Pap smear test results. An automated nucleic acid extraction system using STARMag 96 ProPrep Universal Extraction Kit was utilized following the manufacturer's protocol. An amplification assay in real-time was employed to amplify and identify the HPV Late 1 [L1] gene, which is utilized for genotyping purposes. Following this, the collected data was entered into Epi data version 3.1 software, and the analysis was performed using STATA version 14. A total of 110 women [age range 30–60 years, mean age = 36.5 years and SD ± 6.9] had positive HPV DNA results and were included in the study. Among these, 108 women had valid co-testing [Pap test and HPV DNA test] results for further analysis, and the results of the remaining 2 women were rejected. Overall, the prevalence of non-vaccine-targeted HPV was 56 (51.8%, 95%CI [0.42, 0.61]), of which 28 women (25.4%, 95%CI [0.18, 0.34]) had a single non-vaccine HPV genotype infection. The remaining 29 women (26.4%, 95% CI: 0.190–0.355) experienced multiple infections. The non-vaccine-targeted genotypes of HPV-35 accounted for 11 cases (10%, 95%CI [0.06, 0.17]), HPV-68 was detected in 9 women (8.2%, 95%CI [0.04, 0.15]), HPV-56 and HPV-66 were both found in 8 cases each (7.3%, 95%CI [0.04, 0.14]) of the total. In addition, out of these 108 women, 93 (86.1%, 95%CI [0.78, 0.91]) had low-grade squamous intraepithelial lesions, 13 (12%, 95%CI [0.07, 0.20]) no intraepithelial lesion or malignancy, and two (1.9%, 95%CI [0.01, 0.07]) high-grade squamous intraepithelial lesions. Furthermore, there was no statistical difference [p = 0.755] between vaccine-targeted and non-vaccine-targeted genotypes as the primary cause of cervical lesions. In conclusion, the findings of the present study highlight the existence of a notable prevalence of multiple infections caused by non-vaccine-targeted HPV genotypes. Therefore, it is recommended that both the Federal and regional health bureaus to evaluate the range of hr HPV genotypes protected by the current HPV vaccine and explore the option of transitioning from the quadrivalent HPV vaccine to a novavalent vaccine that includes seven high-risk HPV genotypes.

Molecular survey of canine tick-borne pathogens in ticks and stray dogs in Dhaka city, Bangladesh

Molecular surveillance of canine tick-borne pathogens (TBPs) in Bangladesh has constantly been undervalued. Therefore, the emergence of new pathogens often remains undetected. This study aimed to screen tick-borne pathogens in stray dogs and ticks in the Dhaka metropolitan area (DMA). Eighty-five dog blood and 53 ticks were collected in six city districts of DMA from September 2022 to January 2023. The ticks were identified by morphology. Screening of TBPs was performed by polymerase chain reaction (PCR), followed by sequencing. The PCR assays were conducted to analyze the 18S rRNA (Babesia gibsoni, B. vogeli, and Hepatozoon canis), 16S rRNA (Anaplasma phagocytophilum, A. platys, and A. bovis), gltA (Ehrlichia canis and Rickettsia spp.), flagellin B (Borrelia spp.) and 16-23S rRNA (Bartonella spp.). Three tick species, Rhipicephalus sanguineus (50/53), R. microplus (1/53), and Haemaphysalis bispinosa (2/53), were identified. Babesia gibsoni (38 out of 85) and A. platys (7 out of 85) were detected in dog blood. In contrast, four pathogens, B. gibsoni (1 out of 53), B. vogeli (1 out of 53), H. canis (22 out of 53), and A. platys (1 out of 53), were detected in the ticks. However, the detection rates of TBPs in dog blood and ticks were not correlated in this study. The phylogenetic analyses suggested that a single genotype for each of the four pathogens is circulating in DMA. This study reports the existence of B. vogeli, H. canis, and A. platys in Bangladesh for the first time.