The impact of mutation and gene conversion on the local diversification of antigen genes in African trypanosomes

Patterns of genetic diversity in parasite antigen gene families hold important information about their potential to generate antigenic variation within and between hosts. The evolution of such gene families is typically driven by gene duplication, followed by point mutation and gene conversion. There is great interest in estimating the rates of these processes from molecular sequences for understanding the evolution of the pathogen and its significance for infection processes. In this study, a series of models are constructed to investigate hypotheses about the nucleotide diversity patterns between closely related gene sequences from the antigen gene archive of the African trypanosome, the protozoan parasite causative of human sleeping sickness in Equatorial Africa. We use a hidden Markov model approach to identify two scales of diversification: clustering of sequence mismatches, a putative indicator of gene conversion events with other lower-identity donor genes in the archive, and at a sparser scale, isolated mismatches, likely arising from independent point mutations. In addition to quantifying the respective probabilities of occurrence of these two processes, our approach yields estimates for the gene conversion tract length distribution and the average diversity contributed locally by conversion events. Model fitting is conducted using a Bayesian framework. We find that diversifying gene conversion events with lower-identity partners occur at least five times less frequently than point mutations on variant surface glycoprotein (VSG) pairs, and the average imported conversion tract is between 14 and 25 nucleotides long. However, because of the high diversity introduced by gene conversion, the two processes have almost equal impact on the per-nucleotide rate of sequence diversification between VSG subfamily members. We are able to disentangle the most likely locations of point mutations and conversions on each aligned gene pair

Comparison of antimicrobial resistance phenotypes and genotypes in enterotoxigenic Escherichia coli isolated from Australian and Vietnamese pigs

This study aimed to compare the antibiogram phenotype and carriage of antimicrobial resistance genes (ARGs) of 97 porcine multidrug-resistant (MDR) enterotoxigenic Escherichia coli (ETEC) isolates obtained from Vietnam and 117 porcine MDR-ETEC obtained from Australia, two countries with different antimicrobial regulation systems. An antimicrobial resistance index (ARI) was calculated to quantify their potential significance to public health. Both Vietnamese and Australian isolates had moderate to high levels of resistance to commonly used antibiotics (ampicillin, tetracycline and sulphonamides). None of the Australian isolates were resistant to fluoroquinolones or third-generation cephalosporins and none possessed associated plasmid-mediated ARGs. However, 23.1% of Australian isolates were resistant to gentamicin owing to ARGs associated with apramycin or neomycin resistance [e.g. aac(3)-IV] that impart cross-resistance to gentamicin. Whilst Vietnamese isolates carried aminoglycoside ARGs, 44.4% of commercial pig isolates were resistant to gentamicin in comparison with 0% of village pig isolates. The plasmid-mediated fluoroquinolone ARG qnrB was commonly detected in Vietnamese isolates (52.3% commercial, 44.1% village), but phenotypic resistance was low (3.2% and 11.8%, respectively). The mean ARI for Vietnamese isolates (26.0) was significantly different (P < 0.001) from the mean ARI for Australian isolates (19.8), primarily reflecting fluoroquinolone resistance in the former collection. This comparison suggests the effectiveness of regulations that slow the dissemination of 'critical' resistance by restricting the availability of important classes of antimicrobials

Phylogenetic grouping, antibiotic resistance profile, fluoroquinolone susceptibility and ST131 status of canine extra intestinal Escherichia Coli isolated from submissions to a veterinary diagnostic laboratory 2005-08

Fluoroquinolones (FQs) are a recommended treatment for Escherichia coli infections in companion animals, particularly in cases of resistance to other drug classes. In a retrospective study, 162 canine clinical E. coli isolates, obtained from veterinary diagnostic submissions (January 2005 - June 2008), were analyzed for phylogenetic group and antibiogram phenotype, using nine antimicrobials and enrofloxacin, ciprofloxacin, moxifloxacin and pradofloxacin minimum inhibitory concentrations (MICs), either in the absence or presence of an efflux pump inhibitor. The isolate susceptibility distribution was bimodal; a high proportion (141/162;87%) showed a sensitivity equivalent to wildtype E. coli (enrofloxacin MIC 0.004 - 0.06 μg/mL), while a minority (4/162;2%) showed reduced susceptibility (enrofloxacin MICs of 0.125 - 0.5 μg/mL), and the remainder (17/162;10%) yielding enrofloxacin MICs in the highlevel resistance range of ≥16 μg/mL. All FQ-resistant isolates were also multidrug-resistant. The majority of FQsensitive isolates belonged to phylogenetic group B2 (101/162;62%), and the majority of resistant isolates to group D (8/17;47%). A single resistant B2 isolate and three FQ-sensitive isolates were identified as ST131. Efflux pump activity contributed significantly to MICs for all FQs, except for ciprofloxacin, which may be attributable to its higher polarity compared to the other FQs. These findings confirm a low prevalence of FQ resistance in Australian canine E. coli isolates. Detection of a high moxifloxacin: low ciprofloxacin MIC efflux-associated phenotype (102/162;63%) amongst canine strains may indicate previous exposure to moxifloxacin selective pressure, providing more evidence of exchange of E. coli strains between humans and dogs. The presence of sensitive ST131 strains in the isolate collection does suggest, however, that resistant ST131 strains could potentially emerge under both human and veterinary antimicrobial selection pressure, a risk that could be mitigated by using the most active fluoroquinolone (i.e. pradofloxacin in dogs) against wild-type E. coli at mutant prevention concentrations.Joanne L, Platell, Darren J. Trott, Heinz-Georg Wetzstein, Micheal Leitner and Rowland N. Cobbol

The Impact of Mutation and Gene Conversion on the Local Diversification of Antigen Genes in African Trypanosomes

. Abstract Patterns of genetic diversity in parasite antigen gene families hold important information about their potential to generate antigenic variation within and between hosts. The evolution of such gene families is typically driven by gene duplication, followed by point mutation and gene conversion. There is great interest in estimating the rates of these processes from molecular sequences for understanding the evolution of the pathogen and its significance for infection processes. In this study, a series of models are constructed to investigate hypotheses about the nucleotide diversity patterns between closely related gene sequences from the antigen gene archive of the African trypanosome, the protozoan parasite causative of human sleeping sickness in Equatorial Africa. We use a hidden Markov model approach to identify two scales of diversification: clustering of sequence mismatches, a putative indicator of gene conversion events with other lower-identity donor genes in the archive, and at a sparser scale, isolated mismatches, likely arising from independent point mutations. In addition to quantifying the respective probabilities of occurrence of these two processes, our approach yields estimates for the gene conversion tract length distribution and the average diversity contributed locally by conversion events. Model fitting is conducted using a Bayesian framework. We find that diversifying gene conversion events with lower-identity partners occur at least five times less frequently than point mutations on variant surface glycoprotein (VSG) pairs, and the average imported conversion tract is between 14 and 25 nucleotides long. However, because of the high diversity introduced by gene conversion, the two processes have almost equal impact on the per-nucleotide rate of sequence diversification between VSG subfamily members. We are able to disentangle the most likely locations of point mutations and conversions on each aligned gene pair

Class I major histocompatibility complexes loaded by a periodate trigger

Class I major histocompatibility complexes (MHCs) present peptide ligands on the cell surface for recognition by appropriate cytotoxic T cells. The unstable nature of unliganded MHC necessitates the production of recombinant class I complexes through in vitro refolding reactions in the presence of an added excess of peptides. This strategy is not amenable to high-throughput production of vast collections of class I complexes. To address this issue, we recently designed photocaged MHC ligands that can be cleaved by a UV light trigger in the MHC bound state under conditions that do not affect the integrity of the MHC structure. The results obtained with photocaged MHC ligands demonstrate that conditional MHC ligands can form a generally applicable concept for the creation of defined peptide−MHCs. However, the use of UV exposure to mediate ligand exchange is unsuited for a number of applications, due to the lack of UV penetration through cell culture systems and due to the transfer of heat upon UV irradiation, which can induce evaporation. To overcome these limitations, here, we provide proof-of-concept for the generation of defined peptide−MHCs by chemical trigger-induced ligand exchange. The crystal structure of the MHC with the novel chemosensitive ligand showcases that the ligand occupies the expected binding site, in a conformation where the hydroxyl groups should be reactive to periodate. We proceed to validate this technology by producing peptide−MHCs that can be used for T cell detection. The methodology that we describe here should allow loading of MHCs with defined peptides in cell culture devices, thereby permitting antigen-specific T cell expansion and purification for cell therapy. In addition, this technology will be useful to develop miniaturized assay systems for performing high-throughput screens for natural and unnatural MHC ligands

Новые языковые реальности употребления претерита в немецком гипотаксисе

Целью статьи являются обобщение и теоретическое обоснование нового употребления претерита в относительном значении в конкретных видах придаточных предложений с презенсом в главном предложении. В статье анализируются коннотативные нюансы относительного значения претерита, регулярность замены префекта-пассива и перфекта именного составного сказуемого с глаголом "sein" на претеритальные формы в гипотаксисе, а также особое место претерита в системе немецких временных форм.Метою статті є узагальнення та теоретичне обґрунтування нового вживання претериту у релятивному значенні у конкретних видах сурядно-підрядних речень з презентом у сурядному реченні. У статті подано аналіз конототивні нюанси претериту і регулярність зміни перфекту пасиву та іменного присудка з дієсловом "sein" на претеритальні форми у гіпотаксису, а також особливе місце претериту у системі німецьких часових форм.The article aims at generalization and theoretical Explanation of modern preterit usage in relative meaning in certain types of clauses, with the Present tense in the main clause. The article deals with the analysis of connotative component meanings of the relative preterit and the regularity of substitution of preterit forms in hypotaxes for the passive perfect tense and the perfect form of the nominal compound predicate with the verb 'sein' as well as the specificity of preterit in the system of German tenses

Resolving Salmonella infection reveals dynamic and persisting changes in murine bone marrow progenitor cell phenotype and function

The generation of immune cells from BM precursors is a carefully regulated process. This is essential to limit the potential for oncogenesis and autoimmunity yet protect against infection. How infection modulates this is unclear. Salmonella can colonize systemic sites including the BM and spleen. This resolving infection has multiple IFN-γ-mediated acute and chronic effects on BM progenitors, and during the first week of infection IFN-γ is produced by myeloid, NK, NKT, CD4+ T cells, and some lineage-negative cells. After infection, the phenotype of BM progenitors rapidly but reversibly alters, with a peak ∼30-fold increase in Sca-1hi progenitors and a corresponding loss of Sca-1lo/int subsets. Most strikingly, the capacity of donor Sca-1hi cells to reconstitute an irradiated host is reduced; the longer donor mice are exposed to infection, and Sca-1hic-kitint cells have an increased potential to generate B1a-like cells. Thus, Salmonella can have a prolonged influence on BM progenitor functionality not directly related to bacterial persistence. These results reflect changes observed in leucopoiesis during aging and suggest that BM functionality can be modulated by life-long, periodic exposure to infection. Better understanding of this process could offer novel therapeutic opportunities to modulate BM functionality and promote healthy aging

Machine learning approaches to enhance diagnosis and staging of patients with MASLD using routinely available clinical information

\ua9 2024 McTeer et al.Aims Metabolic dysfunction Associated Steatotic Liver Disease (MASLD) outcomes such as MASH (metabolic dysfunction associated steatohepatitis), fibrosis and cirrhosis are ordinarily determined by resource-intensive and invasive biopsies. We aim to show that routine clinical tests offer sufficient information to predict these endpoints. Methods Using the LITMUS Metacohort derived from the European NAFLD Registry, the largest MASLD dataset in Europe, we create three combinations of features which vary in degree of procurement including a 19-variable feature set that are attained through a routine clinical appointment or blood test. This data was used to train predictive models using supervised machine learning (ML) algorithm XGBoost, alongside missing imputation technique MICE and class balancing algorithm SMOTE. Shapley Additive exPlanations (SHAP) were added to determine relative importance for each clinical variable. Results Analysing nine biopsy-derived MASLD outcomes of cohort size ranging between 5385 and 6673 subjects, we were able to predict individuals at training set AUCs ranging from 0.719-0.994, including classifying individuals who are At-Risk MASH at an AUC = 0.899. Using two further feature combinations of 26-variables and 35-variables, which included composite scores known to be good indicators for MASLD endpoints and advanced specialist tests, we found predictive performance did not sufficiently improve. We are also able to present local and global explanations for each ML model, offering clinicians interpretability without the expense of worsening predictive performance. Conclusions This study developed a series of ML models of accuracy ranging from 71.9—99.4% using only easily extractable and readily available information in predicting MASLD outcomes which are usually determined through highly invasive means