Identical Genotypes Research Articles

Phylogeographical evidence for historical long-distance dispersal in the flightless stick insect Ramulus mikado.

Exploring how organisms overcome geographical barriers to dispersal is a fundamental question in biology. Passive long-distance dispersal events, although infrequent and unpredictable, have a considerable impact on species range expansions. Despite limited active dispersal capabilities, many stick insect species have vast geographical ranges, indicating that passive long-distance dispersal is vital for their distribution. A potential mode of passive dispersal in stick insects is via the egg stage within avian digestive tracts, as suggested by experimental evidence. However, detecting such events under natural conditions is challenging due to their rarity. Therefore, to indirectly assess the potential of historical avian-mediated dispersal, we examined the population genetic structure of the flightless stick insect Ramulus mikado across Japan, based on a multifaceted molecular approach [cytochrome oxidase subunit I (COI) haplotypes, nuclear simple sequence repeat markers and genome-wide single nucleotide polymorphisms]. Subsequently, we identified unique phylogeographic patterns, including the discovery of identical COI genotypes spanning considerable distances, which substantiates the notion of passive long-distance genotypic dispersal. Overall, all the molecular data revealed the low and mostly non-significant genetic differentiation among populations, with identical or very similar genotypes across distant populations. We propose that long-distance dispersal facilitated by birds is the plausible explanation for the unique phylogeographic pattern observed in this flightless stick insect.

Untangling the hedge: Genetic diversity in clonally and sexually transmitted genomes of European wild roses, Rosa L.

While European wild roses are abundant and widely distributed, their morphological taxonomy is complicated and ambiguous. In particular, the polyploid Rosa section Caninae (dogroses) is characterised by its unusual meiosis, causing simultaneous clonal and sexual transmission of sub-genomes. This hemisexual reproduction, which often co-occurs with vegetative reproduction, defies the standard definition of species boundaries. We analysed seven highly polymorphic microsatellite loci, scored for over 2 600 Rosa samples of differing ploidy, collected across Europe within three independent research projects. Based on their morphology, these samples had been identified as belonging to 21 dogrose and five other native rose species. We quantified the degree of clonality within species and at individual sampling sites. We then compared the genetic structure within our data to current rose morpho-systematics and searched for hemisexually co-inherited sets of alleles at individual loci. We found considerably fewer copies of identical multi-locus genotypes in dogroses than in roses with regular meiosis, with some variation recorded among species. While clonality showed no detectable geographic pattern, some genotypes appeared to be more widespread. Microsatellite data confirmed the current classification of subsections, but they did not support most of the generally accepted dogrose microspecies. Under canina meiosis, we found co-inherited sets of alleles as expected, but could not distinguish between sexually and clonally inherited sub-genomes, with only some of the detected allele combinations being lineage-specific.

Population genomic analysis of an emerging pathogen Lonsdalea quercina affecting various species of oaks in western North America

Understanding processes leading to disease emergence is important for effective disease management and prevention of future epidemics. Utilizing whole genome sequencing, we studied the phylogenetic relationship and diversity of two populations of the bacterial oak pathogen Lonsdalea quercina from western North America (Colorado and California) and compared these populations to other Lonsdalea species found worldwide. Phylogenetic analysis separated Colorado and California populations into two Lonsdalea clades, with genetic divergence near species boundaries, suggesting long isolation and populations that differ in genetic structure and distribution and possibly their polyphyletic origin. Genotypes collected from different host species and habitats were randomly distributed within the California cluster. Most Colorado isolates from introduced planted trees, however, were distinct from three isolates collected from a natural stand of Colorado native Quercus gambelii, indicating cryptic population structure. The California identical core genotypes distribution varied, while Colorado identical core genotypes were always collected from neighboring trees. Despite its recent emergence, the Colorado population had higher nucleotide diversity, possibly due to its long presence in Colorado or due to migrants moving with nursery stock. Overall, results suggest independent pathogen emergence in two states likely driven by changes in host-microbe interactions due to ecosystems changes. Further studies are warranted to understand evolutionary relationships among L. quercina from different areas, including the red oak native habitat in northeastern USA.

Study of Phenotype Analysis of Maize Plant: Hyperspectral Image Perspective

Abstract: Maize, alongside rice and wheat, constitutes a trio of crops responsible for over 50% of the global calorie consumption. To address the rising food demand, enhancing the productivity and stress resilience of these crops becomes imperative. However, the progress of plant breeding initiatives is hindered by the cost and time constraints associated with acquiring plant phenotype data. To overcome these limitations and advance the field, there is a need for datasets that connect new forms of highthroughput phenotype data, gathered from plants, to the performance of identical genotypes in diverse agronomic settings and habitats. These datasets will pave the way for the development of innovative statistical and Machine Learning techniques, empowering researchers to expedite crop improvement efforts effectively.

Multivariate Analysis in Wheat (Triticum aestivum L.) for Yield and Attributing Traits under Soil Salinity and Alkalinity in Haryana

Salt-affected soils could be used by improving and developing salt-tolerant genotypes depending upon the amount of genetic variation and salt stress response of adapted and donor sources of wheat. Salt stress affects 20% of global cultivable land and is increasing continuously owing to the change in climate and anthropogenic activities. Globally, saline soils cover 3.1% i.e. 397 mha of the total land area and around 6.74 mha area of India is affected due to salinity. Salinity stress negatively affects the growth and development of wheat leading to low grain yield and quality. A station varietal trial was conducted to identify salt-tolerant genotypes, wherein 24 genotypes including 4 checks, namely, KRL 19, WH 157, KRL 210 and KRL 283 were evaluated in 6 replications in 4.0 m x 1.20 m in RBD under natural saline patch (pH 8.5, ECe 4.2 dsm-1) at Research area of Wheat and Barley Section, Department of Genetics and Plant Breeding and Department of Soil Science (pH 8.5, ECe 4.5 dsm-1), CCS HAU, Hisar during Rabi 2021-22. Observations were recorded for germination (%), days to heading, days to maturity, plant height (cm), tillers per meter row, 1000-grain weight (g), grain yield per plot (g/plot) and hectoliter weight (kg/hl). High positive correlation has been observed for 1000-GW (g) with GY/P (g/plot), PH (cm) with hectoliter weight (kg/hl). Non-significant correlation was observed between days to heading and germination with plant height and hectoliter weight. Clustering of genotypes based on Ward’s Euclidean method was done so that identical genotypes may grouped together; 24 genotypes were grouped into three distinct clusters. Hectolitre weight (kg/hl) expressed as point of dissection of studied traits as GY/P (g/plot), 1000-GW (g), DM and PH (cm) falls at one side and germination (%), DH and T/meter row lies at another side. Entries, namely, WH 1313 (59.6 q/ha), WH 1306 (54.9 q/ha) and WH 1309 (52.9 q/ha) performed better and found significantly superior to the best check WH 157 (43.5+8.2 q/ha) at Department of Genetics and Plant Breeding. P 13582 (61.6 q/ha), P 13650 (62.1 q/ha) performed better and found significantly superior to best check KRL 283 (46.4+13.7 q/ha) at Department of Soil Sciences. Identification of wheat genotypes based on simultaneous selection among contributing traits will improve grain yield. Stable and promising genotypes may be included in breeding program aimed to develop salt tolerant varieties at state and national level to ensure nutritional food security.

Genotyped functional screening of soluble Fab clones enables in-depth analysis of mutation effects

Monoclonal antibodies (mAbs) and their fragments are widely used in therapeutics, diagnostics and basic research. Although display methods such as phage display offer high-throughput, affinities of individual antibodies need to be accurately measured in soluble format. We have developed a screening platform capable of providing genotyped functional data from a total of 9216 soluble, individual antigen binding fragment (Fab) clones by employing next-generation sequencing (NGS) with hierarchical indexing. Full-length, paired variable domain sequences (VL–VH) are linked to functional screening data, enabling in-depth analysis of mutation effects. The platform was applied to four phage display-selected scFv/Fab screening projects and one site-saturation VH affinity maturation project. Genotyped functional screening simultaneously enabled the identification of affinity improving mutations in the VH domain of Fab 49A3 recognizing Dengue virus non-structural protein 1 (NS1) serotype 2 and informed on VH residue positions which cannot be changed from wild-type without decreasing the affinity. Genotype-based identification revealed to us the extent of intraclonal signal variance inherent to single point screening data, a phenomenon often overlooked in the field. Moreover, genotyped screening eliminated the redundant selection of identical genotypes for further study and provided a new analysis tool to evaluate the success of phage display selections and remaining clonal diversity in the screened repertoires.

Genomic features of Klebsiella isolates from artisanal ready-to-eat food production facilities

Increasing reports on K. pneumoniae strains with antimicrobial resistance and virulence traits from food and farm animals are raising concerns about the potential role of Klebsiella spp. as a foodborne pathogen. This study aimed to report and characterize Klebsiella spp. isolates from two artisanal ready-to-eat food (soft cheese and salami) producing facilities, and to track similar genotypes in different ecological niches. Over 1170 samples were collected during the whole production chain of different food batches. The overall Klebsiella prevalence was 6%. Strains were classified into the three Klebsiella species complexes: K. pneumoniae (KpSC, n = 17), K. oxytoca (KoSC, n = 38) and K. planticola (KplaSC, n = 18). Despite high genetic diversity we found in terms of known and new sequence types (STs), core genome phylogeny revealed clonal strains persisting in the same processing setting for over 14 months, isolated from the environment, raw materials and end-products. Strains showed a natural antimicrobial resistance phenotype-genotype. K. pneumoniae strains showed the highest virulence potential, with sequence types ST4242 and ST107 strains carrying yersiniabactin ybt16 and aerobactin iuc3. The latter was detected in all K. pneumoniae from salami and was located on a large conjugative plasmid highly similar (97% identity) to iuc3+ plasmids from human and pig strains circulating in nearby regions of Italy. While identical genotypes may persist along the whole food production process, different genotypes from distinct sources in the same facility shared an iuc3-plasmid. Surveillance in the food chain will be crucial to obtain a more comprehensive picture of the circulation of Klebsiella strains with pathogenic potential.

A pipeline for sample tagging of whole genome bisulfite sequencing data using genotypes of whole genome sequencing

BackgroundIn large-scale high-throughput sequencing projects and biobank construction, sample tagging is essential to prevent sample mix-ups. Despite the availability of fingerprint panels for DNA data, little research has been conducted on sample tagging of whole genome bisulfite sequencing (WGBS) data. This study aims to construct a pipeline and identify applicable fingerprint panels to address this problem.ResultsUsing autosome-wide A/T polymorphic single nucleotide variants (SNVs) obtained from whole genome sequencing (WGS) and WGBS of individuals from the Third China National Stroke Registry, we designed a fingerprint panel and constructed an optimized pipeline for tagging WGBS data. This pipeline used Bis-SNP to call genotypes from the WGBS data, and optimized genotype comparison by eliminating wildtype homozygous and missing genotypes, and retaining variants with identical genomic coordinates and reference/alternative alleles. WGS-based and WGBS-based genotypes called from identical or different samples were extensively compared using hap.py. In the first batch of 94 samples, the genotype consistency rates were between 71.01%-84.23% and 51.43%-60.50% for the matched and mismatched WGS and WGBS data using the autosome-wide A/T polymorphic SNV panel. This capability to tag WGBS data was validated among the second batch of 240 samples, with genotype consistency rates ranging from 70.61%-84.65% to 49.58%-61.42% for the matched and mismatched data, respectively. We also determined that the number of genetic variants required to correctly tag WGBS data was on the order of thousands through testing six fingerprint panels with different orders for the number of variants. Additionally, we affirmed this result with two self-designed panels of 1351 and 1278 SNVs, respectively. Furthermore, this study confirmed that using the number of genetic variants with identical coordinates and ref/alt alleles, or identical genotypes could not correctly tag WGBS data.ConclusionThis study proposed an optimized pipeline, applicable fingerprint panels, and a lower boundary for the number of fingerprint genetic variants needed for correct sample tagging of WGBS data, which are valuable for tagging WGBS data and integrating multi-omics data for biobanks.

#5731 INTRAFAMILIAL HETEROGENEITY AND IMPACT OF FAMILY SCREENING IN PRIMARY HYPEROXALURIA TYPE 1

Abstract Background and Aims Primary hyperoxaluria is a rare genetic disease, caused by an autosomal recessive mutation of the AGXT gene. Clinical variability in outcome is reported within families with primary hyperoxaluria type 1 (PH1) with identical genotypes, leading to the question which differences in the disease course between affected family members can be attributed to environmental factors and which to early diagnosis or therapy. The limited research on this subject results into prognostic challenges and leads to difficult decision-making concerning the timing of transplantation and therapy. Therefore, the objective of this study was to determine whether and to what extent intra-familial heterogeneity is present, based on a clear definition of intra-familial heterogeneity in PH1 and to analyse the impact of therapeutic intervention and early diagnosis via family screening on the prognosis of siblings. Method A retrospective registry study was performed using data from the OxalEurope registry. All families with PH1 were identified and analyzed. A six-point PH1 scoring system was developed to calculate the heterogeneity score within a family, based on the clinical outcome of siblings (Table 1). A score ≥2 was considered as significant intra-familial heterogeneity. Assessment of the impact of family screening was conducted by stratification of the patients based on family screening and symptoms. The Fisher-Freeman-Halton exact test, Mann-Whitney U test, Kruskal Wallis test and Kaplan Meier analysis were used for statistical testing. Results A total of 88 families were included in this study, including a total of 193 patients with PH1. The median (IQR) follow-up time was 7.8 (1.9-17) years. Family screening was conducted in most families (77%), although not all. Intra-familial heterogeneity was found in 38 (43%) families. A (partly) B6-responsive mutation did not lead to a significant difference in intra-familial heterogeneity score. In more than half of the families (54%), affected siblings had a better outcome than the index case and in 67% of families one or more cases of kidney failure occurred. Asymptomatic siblings had a significant better clinical outcome compared to symptomatic siblings and index cases based on clinical outcome score (p<0.001). Kaplan-Meier analyses (Figure 1) revealed that index cases reached kidney failure at an earlier age and earlier in follow-up compared to siblings (Log-rank, p<0.0001). Conclusion Intra-familial heterogeneity is found in nearly half of families with PH1. These findings confirm that intra-familial heterogeneity is present in PH1, in line with previous reports. Asymptomatic siblings found by family screening had a significant better outcome based on clinical outcome score and kidney survival, substantiating the benefit of family screening. Although the exact cause of heterogeneity in PH1 could not be identified, family screening is essential and strongly recommended since it may improve kidney survival in siblings.

P266 Genomic and phenotypic comparisons of Pseudomonas aeruginosa ST27 strains isolated from respiratory tract and domestic environment of a cystic fibrosis patient

Pseudomonas aeruginosa is the major environmental opportunistic pathogen in cystic fibrosis (CF), able to chronically colonize patient’s airways. However, P. aeruginosa acquisition sources are poorly known. A patient attending the Montpellier CF center was sporadically colonized in 2010 by a strain of P. aeruginosa of sequence type (ST) 27 and strains of identical genotype were isolated from all water points in his home during environmental investigations in 2015 and 2020. Our objectives were: i) to compare characteristics of clinical and environmental strains to identify properties that could favor transmission to patient, ii) to study the environmental strains’ evolution between 2015 and 2020 to search for features involved in environmental persistence.

Phenotypic plasticity: The role of a phosphatase family Rap in the genetic regulation of Bacilli.

In the last two decades, an increasing number of bacterial species have been recognized that are able to generate a phenotypically diverse population that shares an identical genotype. This ability is dependent on a complex genetic regulatory network that includes cellular and environmental signals, as well as stochastic elements. Among Bacilli, a broadly distributed family of Rap (Response-regulator aspartyl phosphate) phosphatases is known to modulate the function of the main phenotypic heterogeneity regulators by controlling their phosphorylation. Even more, their related extracellular Phr (Phosphatase regulator) peptides function as signals, creating a cell-cell communication network that regulates the phenotypic development of the entire population. In this review, we examine the role that the Rap phosphatases and their Phr peptides play in the regulation of Bacillus subtilis phenotypic differentiation, and in other members of the Bacillus genus. We also highlight the contribution of these regulatory elements to the fitness of bacterial cells and mobile genetic elements, for example, prophages and conjugative vectors.

Does ethnicity impact CYP2D6 genotype-phenotype relationships?

Polymorphism of the CYP2D6 gene leads to substantial interindividual variability in CYP2D6 enzyme activity. Despite improvements in prediction of CYP2D6 activity based on genotype information, large interindividual variability within CYP2D6 genotypes remains and ethnicity could be a contributing factor. The aim of this study was to investigate interethnic differences in CYP2D6 activity using clinical datasets of three CYP2D6 substrates: (i) brexpiprazole (N=476), (ii) tedatioxetine (N=500), and (iii) vortioxetine (N=1073). The CYP2D6 activity of all individuals in the dataset was estimated through population pharmacokinetic analyses as previously reported. Individuals were assigned a CYP2D6 phenotype and CYP2D6 genotype group based on their CYP2D6 genotype and interethnic differences were investigated within each group. Among individuals categorized as CYP2D6 normal metabolizers, African Americans had a lower CYP2D6 activity compared to Asians (p < 0.01) and in the tedatioxetine and vortioxetine analyses also compared to Whites (p < 0.01). Among CYP2D6 intermediate metabolizers, interethnic differences were also observed, but the findings were not consistent across the substrates. Asian carriers of CYP2D6 decreased function alleles tended to exhibit higher CYP2D6 activity compared to Whites and African Americans. The observed interethnic differences within the CYP2D6 phenotype and genotype groups appeared to be driven by differences in CYP2D6 allele frequencies across ethnicities rather than interethnic differences in enzyme activity for individuals carrying identical CYP2D6 genotypes.

Antimicrobial resistance and genotyping of Mycobacterium leprae in Venezuela

Leprosy is a neglected tropical disease that leads to physical disability and social discrimination. The active surveillance of new cases and vigilance for drug resistance can decrease the incidence, and improve the clinical outcomes of people affected by it. We analyzed, with molecular biology techniques, a set of skin biopsy samples from 25 Venezuelan patients. The patients had been diagnosed with leprosy in 2014 and early 2015, and 15 were relapse cases. The samples were tested for molecular drug resistance to dapsone, rifampicin, and fluoroquinolones. In addition, we performed molecular epidemiology analysis through multiple-locus variable-number tandem repeat analysis (MLVA) and single nucleotide polymorphism (SNP) typing. We did not find evidence of drug resistance and 76% of the samples (n = 16) had isolates belonging to SNP type 3. Genotype profiles allowed us to rule out the possibility of re-infection in a patient with persistent symptoms after treatment, as well as that of household transmission in two more patients. Although our sampling is relatively small, very similar or even identical Mycobacterium leprae genotypes were observed in Miranda State. The presence of this cluster is highly suggestive of high rates of local transmission and, in turn, the need to better control this disease. Finally, the copy number distribution of minisatellite 18–8 in a considerable number of SNP type 3 strains strongly suggests the presence of a sublineage of this disease that is particular to Venezuela.

Does full HPV genotyping perform similarly well in clinician-collected cervical samples and self-collected vaginal samples when using the CLART HPV4S assay?

BackgroundStudies comparing self-collected vaginal samples with clinician-collected cervical samples with respect to high-risk human papillomavirus (HPV) detection and genotype agreement based on clinically validated full HPV genotype assays (e.g. the CLART HPV4S) are limited. This study compared the two types of samples using the CLART assay with respect to HPV detection and genotype agreement in a referral population.MethodsA total of 212 women aged 30–59 years and diagnosed with atypical squamous cells of undetermined significance (ASC-US) within the Danish cervical cancer screening programme had a cervical sample taken at their general practitioner. Afterwards, the women took a vaginal sample with the Evalyn Brush device at home. The paired samples were HPV-tested with the full genotyping CLART HPV4S assay. Histological results, i.e. cervical intraepithelial neoplasia of grade 2 or worse (CIN2+) were available for 14 women with HPV-positive clinician-collected samples.ResultsThe study found the same HPV prevalence in self-collected vaginal samples compared to clinician-collected cervical samples (19.3%, 95% CI 14.3–25.3% vs 18.4%, 95% CI 13.4–24.3%). The CLART HPV4S assay detected approximately the same number of CIN2+ cases in the self-collected vaginal samples compared to the clinician-collected cervical samples (13 vs 11 cases). Exactly the same genotypes were detected in 75% (21/28) of the HPV-positive paired samples, while at least one identical genotype was found in the remaining 25% (7/28) of the paired samples.ConclusionsThe CLART HPV4S assay performed similarly well in self-collected vaginal samples as in clinician-collected cervical samples with respect to both HPV detection and genotype agreement when using the Evalyn Brush and the CLART HPV4S assay in a referral population. Although further evaluation is needed, the findings suggest that full HPV genotyping based on the CLART assay can be useful when establishing HPV genotype-specific referral strategies for women tested HPV-positive by self-sampling.

The impact of adaptor selection on genotyping in 2b-RAD studies

Population genomic studies have increased in the last decade, showing great potential to understand the evolutionary patterns in a great variety of organisms, mostly relying on RAD sequencing techniques to obtain reduced representations of the genomes. Among them, 2b-RAD can provide further secondary reduction to adjust experimental costs by using base-selective adaptors, although its impact on genotyping is unknown. Here we provide empirical comparisons on genotyping and genetic differentiation when using fully degenerate or base-selective adaptors and assess the impact of missing data. We built libraries with the two types of adaptors for the same individuals and generated independent and combined datasets with different missingness filters (presence in 100%, 75% and 50% of the libraries). Our approach, by exploring locus-by-locus, found 92% of identical genotypes between the two libraries of the same individual when using loci shared among 100% of the libraries, which decreased to 35% when working with loci present in at least 50% of them. We show that missing data is a major source of individual genetic differentiation. The loci discordant by genotyping were in low frequency (7.67%) in all filtered files. Only 0.96% of them were directly attributable to base-selective adaptors reducing heterozygosity. An underestimation of heterozygosity in 6.44% of genotypes was found in libraries generated with fully degenerated adaptors, of which ca. 70% had &amp;lt;10 reads per locus indicating that sufficient read depth should be ensured for a correct genotyping. Base-selective adaptors reduce the number of loci, increase their coverage, and provide a reliable genotyping with no heterozygosity underestimation at a lower sequencing cost. We demonstrate that missing data is a major concern for a correct identification of genetic differentiation, and should not be neglected in genomic studies. Thus, we conclude that 2b-RAD libraries using base-selective adaptors are a robust tool to use in population genomics regardless the target species genome size, promoting their use in future studies.

Unravelling the Effect of Blood Type on FVIII:C Levels and Response to DDAVP in 20 Males with a Single Genotype (Twillingate Variant) Causing Mild Hemophilia Α

Introduction: Hemophilia A (HA) occurs secondary to >1000 variants in the F8 gene resulting in decreased/absent production of factor (F) VIII. FVIII:C (coagulant) levels in persons with mild/moderate HA are most impacted by their genotype. ABO blood type (BT) may also impact endogenous FVIII:C levels, but this impact is difficult to assess in a genetically heterogenous group of HA subjects. Canada has a population of mild-moderate HA secondary to a unique large single genotype: c.6104T>C, p.Val2035Ala. This variant arose from a founder effect that occurred about 200 years ago in Twillingate, Newfoundland. We hypothesized that subjects with the Twillingate genotype (despite having the same genotype and thus producing similar amounts of FVIII) would show different endogenous FVIII:C levels related to their BT, as BT impacts FVIII (and VWF) clearance. Our study objectives were to understand the impact of BT on endogenous FVIII:C levels whilst controlling for genotype, and to explore the impact of BT on DDAVP responsiveness. Methods: This was a retrospective, single-center cohort study. Males with a confirmed Twillingate genotype treated at our center between 1980-01-01 to 2022-03-01 were eligible. For each subject, ABO BT, VWF antigen (Ag) and activity, and FVIII:C levels were determined by chart review. We recorded the lowest FVIII:C baseline level; for subjects who had >1 FVIII:C level (done in a non-bleeding state) we also determined their mean baseline FVIII:C level. For DDAVP challenges, the age at the challenge, dose, and route of administration were recorded, as well as pre and 1-hr post FVIII:C levels. Based on 1-hr post-DDAVP FVIII:C levels (IU/mL), subjects were classified on their DDAVP response as responders (≥0.50), partial responders (0.30 to 0.49), or non-responders (<0.30). Median, IQR, mean, and SD were calculated for baseline FVIII:C and VWF:Ag levels, stratified by age (<12; ≥12 y) and by BT (O; non-O). T-tests and Mann-Whitney U (MWU) tests were used to compare normally and non-normally distributed data, respectively. The Fisher-Freeman-Halton Exact Test was used to compare responses to DDAVP between O and non-O subjects. Statistical significance was considered as p≤0.05. All analyses were performed using IBM SPSS Statistics Version 28. Results: 20 males were included: 9 were O BT and 11 were non-O BT (10 were A, 1 was B). There were statistically significant differences between the 2 ABO groups in their median lowest FVIII:C levels: 0.05 IU/mL (O BT) vs. 0.08 IU/mL (non-O BT); p=0.05 (MWU) and in mean FVIII:C levels: medians: 0.08 IU/mL (O BT) vs. 0.12 IU/mL (non-O BT); p=0.02 (t-test). Too few subjects had FVIII:C levels reported at ≥12 y of age to perform statistical analyses. Fifteen subjects (8 O BT: 7 non-O BT) underwent a DDAVP challenge; 13 performed at our center and 2 elsewhere. Median 1-hr post-DDAVP FVIII:C levels were 0.32 IU/mL (O BT) and 0.43 IU/mL (non-O BT); p=0.04 (t-test). The absolute FVIII:C increase with DDAVP was not statistically different between the 2 groups: median increase of 0.22 IU/mL (O BT) vs. 0.28 IU/mL (non-O BT); p=0.10 (t-test) nor was the FVIII:C fold increase: median increase 3.3-fold (O BT) vs. 3.3-fold (non-O BT); p=0.51 (t-test). Among O BT subjects, none were responders, 5 were partial responders and 3 were non-responders. In the non-O BT subjects, 2 were responders and 5 were partial responders. The variation in response between the 2 groups failed to achieve statistical significance (p=0.14). Given uncertainties in DDAVP challenges (e.g. dose, route of administration) done elsewhere, we also analyzed the DDAVP challenge results just for the 13 subjects from our center. The median 1-hr post-DDAVP FVIII:C levels were 0.30 IU/mL in 7 O BT subjects and 0.45 IU/mL in 6 non-O BT subjects; p=0.02 (t-test). Conclusions: This study shows that in HA subjects with an identical genotype, BT significantly impacts FVIII:C levels. Although only 1 unique genotype was studied, we believe that other hemophilic variants leading to mild HA will behave similarly. This may explain why in subjects with mild HA, there is an overrepresentation of O BT. Persons with non-O BT and HA variants that only slightly reduce FVIII production may have FVIII:C levels that are not as reduced and thus may never present with bleeding and be diagnosed with HA. In contrast, if such persons have O BT, they are likely to show much lower FVIII:C levels and thus more likely to bleed and be diagnosed with HA. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Extended epiphenotypes: Integrating epigenotypes into host behavioural manipulation by parasites

Abstract Biologists have long known that environmental context can create diverse phenotypes from identical genotypes. Thus, cells of the same foetus can grow into various organs depending on the molecular environment. Also, animals of the same genetic heritage can show different behaviours in different environments. Conrad Hal Waddington conceptualized epigenotypes in the 1930s, whereby modifications of genetic material could generate alternative modules of development arising out of nonvariant genetic information. His concept paved the way for a neo‐Darwinian synthesis by creating bidirectionality between the environment and genes. In a completely independent intellectual universe, Richard Dawkins introduced the idea of extended phenotype in the early 1980s. The hypothesis posits that the appropriate phenotype of genetic information is not limited to the organism but can ‘extend’ beyond the environment. Parasite manipulation of host behaviour presents a dramatic example of such extended phenotypes. In this perspective, we propose a synthesis between the earlier concept of epigenotypes and the later idea of extended phenotypes, namely a novel concept of extended epiphenotypes.Read the free Plain Language Summary for this article on the Journal blog.

THE USE OF MOLECULAR GENETIC METHODS BASED ON MLVA ANALYSIS TO CONFIRM THE UNIQUENESS OF COLLECTION STRAINS OF BRUCELLA

Collections of pathogenic bacterial cultures are necessary for the storage of commercially valuable and typical strains for the purpose of patenting, production and testing of diagnostic and preventive drugs, as well as epidemiological strains isolated during the diagnosis of infectious diseases for detailed study and monitoring of changes in sanitary and epidemiological well-being. Collections are replenished with new unique strains, so it is very important that the characteristics of these strains should be carried out using highly discriminatory molecular genetic methods. This article presents the results of the evaluation of the genetic diversity of 36 collection strains of Brucella abortus and 57 strains of Brucella melitensis by the Multilocus variable number tandem repeat (VNTR) analysis (MLVA-16). Generic identification and absence of contamination by other bacterial species was confirmed by sequencing of the 16S rRNA gene. MLVA analysis allowed to establish contamination of 4 strains with different genotypes of brucella and to reveal that the deposited 36 strains isolated in 14 outbreaks of brucellosis are identical genotypes of the pathogen. Our studies have confirmed the presence of identical brucella strains in the collection. The use of MLVA-16 in testing isolated bacterial cultures from a single outbreak will allow differentiating unique strains for their subsequent deposition. Verification of deposited strains with MLVA characteristics with a detailed analysis of metadata about deposited strains will optimize the collection, in terms of preserving only unique strains, which will reduce economic costs and risks to ensure biological safety.

Nutrient-Mediated Perception and Signalling in Human Metabolism: A Perspective of Nutrigenomics.

The interaction between selective nutrients and linked genes involving a specific organ reveals the genetic make-up of an individual in response to a particular nutrient. The interaction of genes with food opens opportunities for the addition of bioactive compounds for specific populations comprising identical genotypes. The slight difference in the genetic blueprints of humans is advantageous in determining the effect of nutrients and their metabolism in the body. The basic knowledge of emerging nutrigenomics and nutrigenetics can be applied to optimize health, prevention, and treatment of diseases. In addition, nutrient-mediated pathways detecting the cellular concentration of nutrients such as sugars, amino acids, lipids, and metabolites are integrated and coordinated at the organismal level via hormone signals. This review deals with the interaction of nutrients with various aspects of nutrigenetics and nutrigenomics along with pathways involved in nutrient sensing and regulation, which can provide a detailed understanding of this new leading edge in nutrition research and its potential application to dietetic practice.

Genomic selection in United States dairy cattle.

The genomic selection program for dairy cattle in the United States has doubled the rate of genetic gain. Since 2010, the average annual increase in net merit has been $85 compared to $40 during the previous 5 years. The number of genotypes has been rapidly increasing both domestically and internationally and reached over 6.5 million in 2022 with 1,134,593 submitted in 2021. Evaluations are calculated for over 50 traits. Feed efficiency (residual feed intake), heifer and cow livability, age at first calving, six health traits, and gestation length have been added in recent years to represent the economic value of selection candidates more accurately; work is underway to develop evaluations for hoof health. Evaluations of animals with newly submitted genotypes are calculated weekly. In April 2019, evaluations were extended to crossbreds; to support that effort, evaluations are initially calculated on an all-breed base and then blended by an estimated breed composition. For animals that are less than 90% of one breed, the evaluation is calculated by weighting contributions of each of the five major dairy breeds evaluated (Ayrshire, Brown Swiss, Guernsey, Holstein, and Jersey) by the breed proportion. Nearly 200,000 animals received blended evaluations in July 2022. Pedigree is augmented by using haplotype matching to discover maternal grandsires and great-grandsires. Haplotype analysis is also used to discover undesirable recessive conditions. In many cases, the causative variant has been identified, and results from a gene test or inclusion on a genotyping chip improves the accuracy of those determinations for the current 27 conditions reported. Recently discovered recessive conditions include neuropathy with splayed forelimbs in Jerseys, early embryonic death in Holsteins, and curly calves in Ayrshires. Techniques have been developed to support rapid searches for parent-progeny relationships and identical genotypes among all likely genotypes, which substantially reduces processing time. Work continues on using sequence data to discover additional informative single nucleotide polymorphisms and to incorporate those previously discovered. Adoption of genotyping by sequencing is expected to improve flexibility of marker selection. The success of the Council on Dairy Cattle Breeding in conducting the genetic evaluation program is the result of close cooperation with industry and research groups, including the United States Department of Agriculture, breed associations, genotyping laboratories, and artificial-insemination organizations.