Inference of genomic landscapes using ordered Hidden Markov Models with emission densities (oHMMed).

BACKGROUND: Genomes are inherently inhomogeneous, with features such as base composition, recombination, gene density, and gene expression varying along chromosomes. Evolutionary, biological, and biomedical analyses aim to quantify this variation, account for it during inference procedures, and ultimately determine the causal processes behind it. Since sequential observations along chromosomes are not independent, it is unsurprising that autocorrelation patterns have been observed e.g., in human base composition. In this article, we develop a class of Hidden Markov Models (HMMs) called oHMMed (ordered HMM with emission densities, the corresponding R package of the same name is available on CRAN): They identify the number of comparably homogeneous regions within autocorrelated observed sequences. These are modelled as discrete hidden states; the observed data points are realisations of continuous probability distributions with state-specific means that enable ordering of these distributions. The observed sequence is labelled according to the hidden states, permitting only neighbouring states that are also neighbours within the ordering of their associated distributions. The parameters that characterise these state-specific distributions are inferred. RESULTS: We apply our oHMMed algorithms to the proportion of G and C bases (modelled as a mixture of normal distributions) and the number of genes (modelled as a mixture of poisson-gamma distributions) in windows along the human, mouse, and fruit fly genomes. This results in a partitioning of the genomes into regions by statistically distinguishable averages of these features, and in a characterisation of their continuous patterns of variation. In regard to the genomic G and C proportion, this latter result distinguishes oHMMed from segmentation algorithms based in isochore or compositional domain theory. We further use oHMMed to conduct a detailed analysis of variation of chromatin accessibility (ATAC-seq) and epigenetic markers H3K27ac and H3K27me3 (modelled as a mixture of poisson-gamma distributions) along the human chromosome 1 and their correlations. CONCLUSIONS: Our algorithms provide a biologically assumption free approach to characterising genomic landscapes shaped by continuous, autocorrelated patterns of variation. Despite this, the resulting genome segmentation enables extraction of compositionally distinct regions for further downstream analyses.

The expected sample allele frequencies from populations of changing size via orthogonal polynomials.

In this article, discrete and stochastic changes in (effective) population size are incorporated into the spectral representation of a biallelic diffusion process for drift and small mutation rates. A forward algorithm inspired by Hidden-Markov-Model (HMM) literature is used to compute exact sample allele frequency spectra for three demographic scenarios: single changes in (effective) population size, boom-bust dynamics, and stochastic fluctuations in (effective) population size. An approach for fully agnostic demographic inference from these sample allele spectra is explored, and sufficient statistics for stepwise changes in population size are found. Further, convergence behaviours of the polymorphic sample spectra for population size changes on different time scales are examined and discussed within the context of inference of the effective population size. Joint visual assessment of the sample spectra and the temporal coefficients of the spectral decomposition of the forward diffusion process is found to be important in determining departure from equilibrium. Stochastic changes in (effective) population size are shown to shape sample spectra particularly strongly.

The influence of GC-biased gene conversion on non-adaptive sequence evolution in short introns of Drosophila melanogaster.

Population genetic inference of selection on the nucleotide sequence level often proceeds by comparison to a reference sequence evolving only under mutation and population demography. Among the few candidates for such a reference sequence is the 5' part of short introns (5SI) in Drosophila. In addition to mutation and population demography, however, there is evidence for a weak force favouring GC bases, likely due to GC-biased gene conversion (gBGC), and for the effect of linked selection. Here, we use polymorphism and divergence data of Drosophila melanogaster to detect and describe the forces affecting the evolution of the 5SI. We separately analyse mutation classes, compare them between chromosomes, and relate them to recombination rate frequencies. GC-conservative mutations seem to be mainly influenced by mutation and drift, with linked selection mostly causing differences between the central and the peripheral (i.e., telomeric and centromeric) regions of the chromosome arms. Comparing GC-conservative mutation patterns between autosomes and the X chromosome showed differences in mutation rates, rather than linked selection, in the central chromosomal regions after accounting for differences in effective population sizes. On the other hand, GC-changing mutations show asymmetric site frequency spectra, indicating the presence of gBGC, varying among mutation classes and in intensity along chromosomes, but approximately equal in strength in autosomes and the X chromosome.

Transcriptomic profiling of different developmental stages reveals parasitic strategies of Wohlfahrtia magnifica, a myiasis-causing flesh fly.

BACKGROUND: Wohlfahrtia magnifica is an obligatory parasite that causes myiasis in several warm-blooded vertebrates. Adult females deposit the first-stage larvae directly onto wounds or natural body orifices (e.g., genitalia) of the host, from where they quickly colonize the host tissue and feed on it for development. The infestation of W. magnifica can lead to health issues, welfare concerns, and substantial economic losses. To date, little is known about the molecular mechanisms of the W. magnifica-causing myiasis. RESULTS: In this study, we collected parasitic-stage larvae of W. magnifica from wounds of naturally infested Bactrian camels, as well as pupae and adult flies reared in vitro from the wound-collected larvae, for investigating the gene expression profiles of the different developmental stages of W. magnifica, with a particular focus on examining gene families closely related to the parasitism of the wound-collected larvae. As key proteins related to the parasite-host interaction, 2049 excretory/secretory (ES) proteins were identified in W. magnifica through the integration of multiple bioinformatics approaches. Functional analysis indicates that these ES proteins are primarily involved in cuticle development, peptidase activity, immune response, and metabolic processes. The global investigation of gene expression at different developmental stages using pairwise comparisons and weighted correlation network analysis (WGCNA) showed that the upregulated genes during second-stage larvae were related to cuticle development, peptidase activity, and RNA transcription and translation; during third-stage larvae to peptidase inhibitor activity and nutrient reservoir activity; during pupae to cell and tissue morphogenesis and cell and tissue development; and during adult flies to signal perception, many of them involved in light perception, and adult behavior, e.g., feeding, mating, and locomotion. Specifically, the expression level analysis of the likely parasitism-related genes in parasitic wound-collected larvae revealed a significant upregulation of 88 peptidase genes (including 47 serine peptidase genes), 110 cuticle protein genes, and 21 heat shock protein (hsp) genes. Interestingly, the expression of 2 antimicrobial peptide (AMP) genes, including 1 defensin and 1 diptericin, was also upregulated in the parasitic larvae. CONCLUSIONS: We identified ES proteins in W. magnifica and investigated their functional distribution. In addition, gene expression profiles at different developmental stages of W. magnifica were examined. Specifically, we focused on gene families closely related to parasitism of wound-collected larvae. These findings shed light on the molecular mechanisms underlying the life cycle of the myiasis-causing fly, especially during the parasitic larval stages, and provide guidance for the development of control measures against W. magnifica.

Purifying selection against spurious splicing signals contributes to the base composition evolution of the polypyrimidine tract.

Among eukaryotes, the major spliceosomal pathway is highly conserved. While long introns may contain additional regulatory sequences, the ones in short introns seem to be nearly exclusively related to splicing. Although these regulatory sequences involved in splicing are well-characterized, little is known about their evolution. At the 3' end of introns, the splice signal nearly universally contains the dimer AG, which consists of purines, and the polypyrimidine tract upstream of this 3' splice signal is characterized by over-representation of pyrimidines. If the over-representation of pyrimidines in the polypyrimidine tract is also due to avoidance of a premature splicing signal, we hypothesize that AG should be the most under-represented dimer. Through the use of DNA-strand asymmetry patterns, we confirm this prediction in fruit flies of the genus Drosophila and by comparing the asymmetry patterns to a presumably neutrally evolving region, we quantify the selection strength acting on each motif. Moreover, our inference and simulation method revealed that the best explanation for the base composition evolution of the polypyrimidine tract is the joint action of purifying selection against a spurious 3' splice signal and the selection for pyrimidines. Patterns of asymmetry in other eukaryotes indicate that avoidance of premature splicing similarly affects the nucleotide composition in their polypyrimidine tracts.

Genome and Transcriptome Analyses Facilitate Genetic Control of Wohlfahrtia magnifica, a Myiasis-Causing Flesh Fly.

Myiasis caused by Wohlfahrtia magnifica is a widespread parasitic infestation in mammals. The infested host suffers from damage as the developing larvae feed on its tissues. For the control of myiasis infestation, genetic methods have been shown to be effective and promising as an alternative to insecticides. Combining genome, isoform sequencing (Iso-Seq), and RNA sequencing (RNA-seq) data, we isolated and characterized two sex-determination genes, W. magnifica transformer (Wmtra) and W. magnifica transformer2 (Wmtra2), whose orthologs in a number of insect pests have been utilized to develop genetic control approaches. Wmtra transcripts are sex-specifically spliced; only the female transcript encodes a full-length functional protein, while the male transcript encodes a truncated and non-functional polypeptide due to the presence of the male-specific exon containing multiple in-frame stop codons. The existence of five predicted TRA/TRA2 binding sites in the male-specific exon and the surrounding intron of Wmtra, as well as the presence of an RNA-recognition motif in WmTRA2 may suggest the auto-regulation of Wmtra by its own protein interacting with WmTRA2. This results in the skipping of the male-specific exon and translation of the full-length functional protein only in females. Our comparative study in dipteran species showed that both the WmTRA and WmTRA2 proteins exhibit a high degree of similarity to their orthologs in the myiasis-causing blow flies. Additionally, transcriptome profiling performed between adult females and adult males reported 657 upregulated and 365 downregulated genes. Functional analysis showed that among upregulated genes those related to meiosis and mitosis Gene Ontology (GO) terms were enriched, while, among downregulated genes, those related to muscle cell development and aerobic metabolic processes were enriched. Among the female-biased gene set, we detected five candidate genes, vasa (vas), nanos (nanos), bicoid (bcd), Bicaudal C (BicC), and innexin5 (inx5). The promoters of these genes may be able to upregulate Cas9 expression in the germline in Cas9-based homing gene drive systems as established in some flies and mosquitoes. The isolation and characterization of these genes is an important step toward the development of genetic control programs against W. magnifica infestation.

Drivers of genomic landscapes of differentiation across a Populus divergence gradient.

Speciation, the continuous process by which new species form, is often investigated by looking at the variation of nucleotide diversity and differentiation across the genome (hereafter genomic landscapes). A key challenge lies in how to determine the main evolutionary forces at play shaping these patterns. One promising strategy, albeit little used to date, is to comparatively investigate these genomic landscapes as progression through time by using a series of species pairs along a divergence gradient. Here, we resequenced 201 whole-genomes from eight closely related Populus species, with pairs of species at different stages along the divergence gradient to learn more about speciation processes. Using population structure and ancestry analyses, we document extensive introgression between some species pairs, especially those with parapatric distributions. We further investigate genomic landscapes, focusing on within-species (i.e. nucleotide diversity and recombination rate) and among-species (i.e. relative and absolute divergence) summary statistics of diversity and divergence. We observe relatively conserved patterns of genomic divergence across species pairs. Independent of the stage across the divergence gradient, we find support for signatures of linked selection (i.e. the interaction between natural selection and genetic linkage) in shaping these genomic landscapes, along with gene flow and standing genetic variation. We highlight the importance of investigating genomic patterns on multiple species across a divergence gradient and discuss prospects to better understand the evolutionary forces shaping the genomic landscapes of diversity and differentiation.

Prevalence of the SigB-Deficient Phenotype among Clinical Staphylococcus aureus Isolates Linked to Bovine Mastitis.

Phenotypic adaptation has been associated with persistent, therapy-resistant Staphylococcus aureus infections. Recently, we described within-host evolution towards a Sigma factor B (SigB)-deficient phenotype in a non-human host, a naturally infected dairy cow with chronic, persistent mastitis. However, to our knowledge, the prevalence of SigB deficiency among clinical S. aureus isolates remains unknown. In this study, we screened a collection of bovine mastitis isolates for phenotypic traits typical for SigB deficiency: decreased carotenoid pigmentation, increased proteolysis, secretion of α-hemolysin and exoproteins. Overall, 8 out of 77 (10.4%) isolates of our bovine mastitis collection exhibited the SigB-deficient phenotype. These isolates were assigned to various clonal complexes (CC8, CC9, CC97, CC151, CC3666). We further demonstrated a strong positive correlation between asp23-expression (a marker of SigB activity) and carotenoid pigmentation (r = 0.6359, p = 0.0008), underlining the role of pigmentation as a valuable predictor of the functional status of SigB. Sequencing of the sigB operon (mazEF-rsbUVW-sigB) indicated the phosphatase domain of the RsbU protein as a primary target of mutations leading to SigB deficiency. Indeed, by exchanging single nucleotides in rsbU, we could either induce SigB deficiency or restore the SigB phenotype, demonstrating the pivotal role of RsbU for SigB functionality. The data presented highlight the clinical relevance of SigB deficiency, and future studies are needed to exploit its role in staphylococcal infections.

Disposable Airway Pressure Manometers for Endotracheal Tube Cuff Inflation.

This study aimed to assess the performance, accuracy, precision and repeatability of two single-use airway pressure manometers as a cost-effective alternative for inflation of endotracheal tubes with high-volume, low-pressure cuffs. The manometers were tested in a bench top model against a U-tube manometer. Eighteen units of each device were tested. Three consecutive measurements were performed at pressures of 20, 25 and 30 cmH2O each. The mean ± SD of the recorded pressures and maximum deviation from the target pressures were calculated for each device and each target pressure. For device A, the mean ± SD pressures were 19.6 ± 0.7, 23.6 ± 0.8 and 28.3 ± 0.8 cmH2O; for device B, the mean ± SD pressures were 19.3 ± 0.6, 24.3 ± 0.9 and 29.2 ± 0.67 cmH2O for target pressures of 20, 25 and 30 cmH2O, respectively. The bias for device A was -0.4, -1.4, and -1.7 cmH2O and for device B, -0.7, -0.7, and -0.8 cmH2O for target pressures of 20, 25, and 30 cmH2O, respectively. Both devices showed results comparable to those reported for commercial cuff manometers. They represent inexpensive tools that provide clinically sufficient accuracy, precision and repeatability for ETT cuff inflation between pressures of 20 and 30 cmH2O.

Sedative effects and changes in cardiac rhythm with intravenous premedication of medetomidine, butorphanol and ketamine in dogs.

OBJECTIVE: To determine the sedative effects and characteristics of cardiac rhythm with intravenous (IV) premedication of medetomidine, butorphanol and ketamine in dogs. STUDY DESIGN: Prospective, blinded, randomized clinical trial. ANIMALS: A total of 116 client-owned healthy dogs undergoing elective surgery. METHODS: Dogs were randomly allocated one of four groups: group M, medetomidine 5 µg kg-1; group B, butorphanol 0.2 mg kg-1; group MB, medetomidine 5 µg kg-1 and butorphanol 0.2 mg kg-1; or group MBK, medetomidine 5 µg kg-1, butorphanol 0.2 mg kg-1 and ketamine 1 mg kg-1 IV. Sedation was assessed using a numerical descriptive scale. Heart rate (HR) and rhythm were monitored; propofol dose (mg kg-1 IV) to allow orotracheal intubation was documented. Data were analysed using anova, accounting for multiple testing with the Tukey honest significant difference test. RESULTS: Sedation scores varied significantly between all groups at all time points, except between groups MB and MBK at four time points. HR decreased in all groups: most in groups M and MB, least in group B. HR was initially higher in group MBK than in groups M and MB. Arrhythmias occurred in all groups: group B showed second-degree atrioventricular blocks occasionally, all other groups showed additionally ventricular escape complexes and bundle branch blocks. Dose of propofol required for orotracheal intubation was significantly higher in group B (5.0 ± 2.0 mg kg-1) than in group M (2.6 ± 0.6 mg kg-1). Although no difference could be demonstrated between groups MB (1.4 ± 0.6 mg kg-1) and MBK (0.9 ± 0.8 mg kg-1), both groups required significantly less propofol than group M. CONCLUSION AND CLINICAL RELEVANCE: Medetomidine-based premedication protocols led to various bradyarrhythmias. Addition of subanaesthetic doses of ketamine to medetomidine-based protocols resulted in higher HRs, fewer bradyarrhythmias and fewer animals that required propofol for intubation without causing side effects in healthy dogs.

Oncogenic TYK2 P760L kinase is effectively targeted by combinatorial TYK2, mTOR and CDK4/6 kinase blockade.

Tyrosine kinase 2 (TYK2) is a member of the Janus kinase/signal transducer and activator of transcription pathway, which is central in cytokine signaling. Previously, germline TYK2 mutations have been described in two patients developing de novo T-cell acute lymphoblastic leukemias (T-ALL) or precursor B-ALL. The mutations (P760L and G761V) are located within the regulatory pseudokinase domain and lead to constitutive activation of TYK2. We demonstrate the transformation capacity of TYK2 P760L in hematopoietic cell systems including primary bone marrow cells. In vivo engraftment of TYK2 P760L-expressing cell lines led to development of leukemia. A kinase inhibitor screen uncovered that oncogenic TYK2 acts synergistically with the PI3K/AKT/mTOR and CDK4/6 pathways. Accordingly, the TYK2-specific inhibitor deucravacitinib (BMS986165) reduces cell viability of TYK2 P760L-transformed cell models and ex vivo cultured TYK2 P760L-mutated patient- derived xenograft cells most efficiently when combined with mTOR or CDK4/6 inhibitors. Our study thereby pioneers novel treatment options for patients suffering from TYK2-driven acute leukemia.

Development, refinement, and validation of an equine musculoskeletal pain scale.

Musculoskeletal disease is a common cause of chronic pain that is often overlooked and inadequately treated, impacting the quality of life of humans and horses alike. Lameness due to musculoskeletal pain is prevalent in horses, but the perception of pain by owners is low compared with veterinary diagnosis. Therefore, this study aims to establish and validate a pain scale for chronic equine orthopaedic pain that is user-friendly for horse owners and veterinarians to facilitate the identification and monitoring of pain in horses. The newly developed musculoskeletal pain scale (MPS) was applied to 154 horses (mean age 20 ± 6.4 years SD) housed at an equine sanctuary, of which 128 (83%) suffered from chronic orthopaedic disease. To complete the MPS, the horses were observed and videotaped from a distance while at rest in their box or enclosure. In addition, they received a complete clinical and orthopaedic exam. The need for veterinary intervention to address pain (assessed and executed by the sanctuary independent from this study) was used as a longitudinal health outcome to determine the MPS's predictive validity. To determine the interrater agreement, the MPS was scored for a randomly selected subset of 30 horses by six additional blinded raters, three equine veterinary practitioners, and three experienced equestrians. An iterative process was used to refine the tool based on improvements in the MPS's correlation with lameness evaluated at the walk and trot, predictive validity for longitudinal health outcomes, and interrater agreement. The intraclass correlation improved from 0.77 of the original MPS to 0.88 of the refined version (95% confidence interval: 0.8-0.94). The refined MPS correlated significantly with lameness at the walk (r = 0.44, p = 0.001) and trot (r = 0.5, p < 0.0001). The refined MPS significantly differed between horses that needed veterinary intervention (mean MPS = 8.6) and those that did not (mean MPS = 5.0, p = 0.0007). In summary, the MPS showed good interrater repeatability between expert and lay scorers, significant correlation with lameness at the walk and trot, and good predictive validity for longitudinal health outcomes, confirming its ability to identify horses with orthopaedic health problems.

Genomic insights into evolution and control of Wohlfahrtia magnifica, a widely distributed myiasis-causing fly of warm-blooded vertebrates.

Wohlfahrtia magnifica is a pest fly species, invading livestock in many European, African and Asian countries, and causing heavy agroeconomic losses. In the life cycle of this obligatory parasite, adult flies infect the host by depositing the first-stage larvae into body cavities or open wounds. The feeding larvae cause severe (skin) tissue damage and potentially fatal infections if untreated. Despite serious health detriments and agroeconomic concerns, genomic resources for understanding the biology of W. magnifica have so far been lacking. Here, we present a complete genome assembly from a single adult female W. magnifica using a Low-DNA Input workflow for PacBio HiFi library preparation. The de novo assembled genome is 753.99 Mb in length, with a scaffold N50 of 5.00 Mb, consisting of 16,718 predicted protein-encoding genes. Comparative genomic analysis revealed that W. magnifica has the closest phylogenetic relationship to Sarcophaga bullata followed by Lucilia cuprina. Evolutionary analysis of gene families showed expansions of 173 gene families in W. magnifica that were enriched for gene ontology (GO) categories related to immunity, insecticide-resistance mechanisms, heat stress response and cuticle development. In addition, 45 positively selected genes displaying various functions were identified. This new genomic resource contributes to the evolutionary and comparative analysis of dipterous flies and an in-depth understanding of many aspects of W. magnifica biology. Furthermore, it will facilitate the development of novel tools for controlling W. magnifica infection in livestock.

Detection of synovial sepsis in horses using enzymes as biomarkers.

BACKGROUND: Synovial sepsis is a commonly occurring, potentially career-ending or even life-threatening orthopaedic emergency. Diagnosis of synovial sepsis is currently primarily based on synovial fluid analysis, which often leaves diagnostic ambiguity due to overlap of clinicopathological parameters between septic and aseptic inflammatory synovitis. OBJECTIVES: To evaluate the reliability of lysozyme (LYS), myeloperoxidase (MPO) and elastase (ELT) as biomarkers for synovial sepsis in horses using a photometric assay to measure increased enzyme activity. STUDY DESIGN: Prospective, single-blinded, analytical, clinical study. METHODS: Equine synovial samples were assigned to one of three groups: (1) healthy controls (n = 10), (2) aseptic (n = 27) and (3) septic synovitis (n = 30). The enzyme activity assays (LYS, MPO and ELT) were compared with standard synovial fluid parameters and broad-range bacterial 16S rDNA PCR. RESULTS: LYS and MPO activities were significantly different between septic synovial samples, and both aseptic and control samples (P < .001, LYS: confidence interval [CI]: 2.25-3.41, resp., 2.21-3.8, MPO: CI 0.752-1.6, resp., 0.639-1.81). LYS achieved a 100% sensitivity and 100% specificity in differentiating between septic and aseptic (cut-off value 751.4) or control (cut-off: 484.6) samples (P < .001). MPO reached 93.33% sensitivity, 100% specificity for distinguishing septic from control (cut-off value: 0.1254) synovial samples and 93.33% sensitivity, 81.48% specificity for discriminating between septic and aseptic (cut-off value: 0.1305) synovial samples (P < .001). ELT activity could not be measured in any synovial sample. Both the LYS and the MPO measurements showed a highly significant correlation with PCR (LYS r = .79, MPO r = .69), synovial leukocyte count (LYS r = .752, MPO r = .571), % neutrophils (LYS r = .751, MPO r = 0.663) and each other (r = .744, all P < .001). MAIN LIMITATIONS: Variation in horses' signalment, affected synovial structures and synovial fluid freezing times may have affected the discriminative power of this study. CONCLUSIONS: Increased MPO and LYS activities allow reliable, rapid diagnosis of synovial sepsis with high sensitivity and specificity.

Equine Activity Time Budgets: The Effect of Housing and Management Conditions on Geriatric Horses and Horses with Chronic Orthopaedic Disease.

Housing and management conditions strongly influence the health, welfare and behaviour of horses. Consequently, objective and quantifiable comparisons between domestic environments and their influence on different equine demographics are needed to establish evidence-based criteria to assess and optimize horse welfare. Therefore, the present study aimed to measure and compare the time budgets (=percentage of time spent on specific activities) of horses with chronic orthopaedic disease and geriatric (≥20 years) horses living in different husbandry systems using an automated tracking device. Horses spent 42% (range 38.3-44.8%) of their day eating, 39% (range 36.87-44.9%) resting, and 19% (range 17-20.4%) in movement, demonstrating that geriatric horses and horses suffering from chronic orthopaedic disease can exhibit behaviour time budgets equivalent to healthy controls. Time budget analysis revealed significant differences between farms, turn-out conditions and time of day, and could identify potential areas for improvement. Horses living in open-air group housing on a paddock had a more uniform temporal distribution of feeding and movement activities with less pronounced peaks compared to horses living in more restricted husbandry systems.

Species variations in tenocytes' response to inflammation require careful selection of animal models for tendon research.

For research on tendon injury, many different animal models are utilized; however, the extent to which these species simulate the clinical condition and disease pathophysiology has not yet been critically evaluated. Considering the importance of inflammation in tendon disease, this study compared the cellular and molecular features of inflammation in tenocytes of humans and four common model species (mouse, rat, sheep, and horse). While mouse and rat tenocytes most closely equalled human tenocytes' low proliferation capacity and the negligible effect of inflammation on proliferation, the wound closure speed of humans was best approximated by rats and horses. The overall gene expression of human tenocytes was most similar to mice under healthy, to horses under transient and to sheep under constant inflammatory conditions. Humans were best matched by mice and horses in their tendon marker and collagen expression, by horses in extracellular matrix remodelling genes, and by rats in inflammatory mediators. As no single animal model perfectly replicates the clinical condition and sufficiently emulates human tenocytes, fit-for-purpose selection of the model species for each specific research question and combination of data from multiple species will be essential to optimize translational predictive validity.

A nearly-neutral biallelic Moran model with biased mutation and linear and quadratic selection.

In this article, a biallelic reversible mutation model with linear and quadratic selection is analysed. The approach reconnects to one proposed by Kimura (1979), who starts from a diffusion model and derives its equilibrium distribution up to a constant. We use a boundary-mutation Moran model, which approximates a general mutation model for small effective mutation rates, and derive its equilibrium distribution for polymorphic and monomorphic variants in small to moderately sized populations. Using this model, we show that biased mutation rates and linear selection alone can cause patterns of polymorphism within and substitution rates between populations that are usually ascribed to balancing or overdominant selection. We illustrate this using a data set of short introns and fourfold degenerate sites from Drosophila simulans and Drosophila melanogaster.

STAT1 Isoforms Differentially Regulate NK Cell Maturation and Anti-tumor Activity.

Natural killer (NK) cells are important components of the innate immune defense against infections and cancers. Signal transducer and activator of transcription 1 (STAT1) is a transcription factor that is essential for NK cell maturation and NK cell-dependent tumor surveillance. Two alternatively spliced isoforms of STAT1 exist: a full-length STAT1α and a C-terminally truncated STAT1ß isoform. Aberrant splicing is frequently observed in cancer cells and several anti-cancer drugs interfere with the cellular splicing machinery. To investigate whether NK cell-mediated tumor surveillance is affected by a switch in STAT1 splicing, we made use of knock-in mice expressing either only the STAT1α (Stat1α/α) or the STAT1ß (Stat1ß/ß ) isoform. NK cells from Stat1α/α mice matured normally and controlled transplanted tumor cells as efficiently as NK cells from wild-type mice. In contrast, NK cells from Stat1ß/ß mice showed impaired maturation and effector functions, albeit less severe than NK cells from mice that completely lack STAT1 (Stat1-/- ). Mechanistically, we show that NK cell maturation requires the presence of STAT1α in the niche rather than in NK cells themselves and that NK cell maturation depends on IFNγ signaling under homeostatic conditions. The impaired NK cell maturation in Stat1ß/ß mice was paralleled by decreased IL-15 receptor alpha (IL-15Rα) surface levels on dendritic cells, macrophages and monocytes. Treatment of Stat1ß/ß mice with exogenous IL-15/IL-15Rα complexes rescued NK cell maturation but not their effector functions. Collectively, our findings provide evidence that STAT1 isoforms are not functionally redundant in regulating NK cell activity and that the absence of STAT1α severely impairs, but does not abolish, NK cell-dependent tumor surveillance.

Maximum likelihood estimators for scaled mutation rates in an equilibrium mutation-drift model.

The stationary sampling distribution of a neutral decoupled Moran or Wright-Fisher diffusion with neutral mutations is known to first order for a general rate matrix with small but otherwise unconstrained mutation rates. Using this distribution as a starting point we derive results for maximum likelihood estimates of scaled mutation rates from site frequency data under three model assumptions: a twelve-parameter general rate matrix, a nine-parameter reversible rate matrix, and a six-parameter strand-symmetric rate matrix. The site frequency spectrum is assumed to be sampled from a fixed size population in equilibrium, and to consist of allele frequency data at a large number of unlinked sites evolving with a common mutation rate matrix without selective bias. We correct an error in a previous treatment of the same problem (Burden and Tang, 2017) affecting the estimators for the general and strand-symmetric rate matrices. The method is applied to a biological dataset consisting of a site frequency spectrum extracted from short autosomal introns in a sample of Drosophila melanogaster individuals.

In-vitro testing of bacteriostatic and bactericidal efficacy of commercial disinfectants against Salmonella Infantis reveals substantial differences between products and bacterial strains.

Salmonella (S.) Infantis is currently the most common serovar in broilers and boiler meat in the European Union. In the field, eradication of S. Infantis in affected poultry flocks is considered extremely difficult. Despite stringent cleaning and disinfection measures between the placement of flocks, recurrent infections are often reported. So far, the efficacy of disinfectants on S. Infantis has rarely been studied. Therefore, in the present in-vitro study the bacteriostatic and bactericidal efficacy of ten commercial disinfectants were tested against seven S. Infantis field isolates. Combinations of aldehyde and quarternary ammonium were the active compounds of five, peroxygen of three, cresol and alkylamines of one disinfectant, respectively. Investigations were performed according to standard protocols and regulations. Different concentrations of disinfectants were used to test the bacteriostatic efficacy. Different temperatures and low and high protein exposures were applied as variables to investigate the bactericidal efficacy. Following neutralization of the disinfectants an additional incubation step was introduced to investigate the revitalisation potential of S. Infantis. The bacteriostatic efficacy could be assessed for seven disinfectants. For three disinfectants a bacteriostatic effect was observed when the recommended concentration was used, whereas with four disinfectants only increased concentrations led to this effect. The bactericidal efficacy was not influenced by temperature, whereas high protein exposure decreased the efficacy of nine disinfectants. Furthermore, reactivation of S. Infantis was revealed after application of disinfectants for the majority of products. Interestingly, the strain of S. Infantis influenced the efficacy of the disinfectants. Overall, products based on aldehydes and quarternary ammonium compounds proved most efficient, followed by peroxgen, cresol and alkylamines.