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As a candidate 'super-Chandrasekhar' or 09dc-like Type Ia supernova (SN Ia), SN 2012dn shares many characteristics with other members of this remarkable class of objects but lacks their extraordinary luminosity. Here, we present and discuss the most comprehensive optical data set of this SN to date, comprised of a densely sampled series of early-time spectra obtained within the Nearby Supernova Factory project, plus photometry and spectroscopy obtained at the Very Large Telescope about 1 yr after the explosion. The light curves, colour curves, spectral time series, and ejecta velocities of SN 2012dn are compared with those of other 09dc-like and normal SNe Ia, the overall variety within the class of 09dc-like SNe Ia is discussed, and new criteria for 09dc-likeness are proposed. Particular attention is directed to additional insight that the late-phase data provide. The nebular spectra show forbidden lines of oxygen and calcium, elements that are usually not seen in late-time spectra of SNe Ia, while the ionization state of the emitting iron plasma is low, pointing to low ejecta temperatures and high densities. The optical light curves are characterized by an enhanced fading starting ∼60 d after maximum and very low luminosities in the nebular phase, which is most readily explained by unusually early formation of clumpy dust in the ejecta. Taken together, these effects suggest a strongly perturbed ejecta density profile, which might lend support to the idea that 09dc-like characteristics arise from a brief episode of interaction with a hydrogen-deficient envelope during the first hours or days after the explosion.

We investigate strongly gravitationally lensed type II supernovae (LSNe II) for time-delay cosmography, incorporating microlensing effects; this expands on previous microlensing studies of type Ia supernovae (SNe Ia). We use the radiative-transfer code TARDIS to recreate five spectra of the prototypical SN 1999em at different times within the plateau phase of the light curve. The microlensing-induced deformations of the spectra and light curves are calculated by placing the SN into magnification maps generated with the code GERLUMPH. We study the impact of microlensing on the color curves and find that there is no strong influence on them during the investigated time interval of the plateau phase. The color curves are only weakly affected by microlensing due to the almost achromatic behavior of the intensity profiles. However, the lack of nonlinear structure in the color curves during the plateau phase of type II-plateau supernovae makes time-delay measurements more challenging compared to SN Ia color curves, given the possible presence of differential dust extinction. Therefore, we further investigate SN phase inference through spectral absorption lines under the influence of microlensing and Gaussian noise. As the spectral features shift to longer wavelengths with progressing time after explosion, the measured wavelength of a specific absorption line provides information on the epoch of the SN. The comparison between retrieved epochs of two observed lensing images then gives the time delay of the images. We find that the phase retrieval method that uses spectral features yields accurate delays with uncertainties of ≲2 days, making it a promising approach. [ABSTRACT FROM AUTHOR]

We present substantial extensions to the Monte Carlo radiative transfer code TARDIS to perform spectral synthesis for type II supernovae. By incorporating a non-LTE ionization and excitation treatment for hydrogen, a full account of free–free and bound-free processes, a self-consistent determination of the thermal state and by improving the handling of relativistic effects, the improved code version includes the necessary physics to perform spectral synthesis for type II supernovae to high precision as required for the reliable inference of supernova properties. We demonstrate the capabilities of the extended version of TARDIS by calculating synthetic spectra for the prototypical type II supernova SN1999em and by deriving a new and independent set of dilution factors for the expanding photosphere method. We have investigated in detail the dependence of the dilution factors on photospheric properties and, for the first time, on changes in metallicity. We also compare our results with the previously published sets of dilution factors and discuss the potential sources of the discrepancies between studies. [ABSTRACT FROM AUTHOR]

A Bayesian method to map quantitative trait loci (QTL) using the descent-graph sampler of marker inheritance patterns for arbitrarily complex mating designs and incomplete marker information is developed. The efficiency of the algorithm by computer simulations is evaluated and compared with other methods for QTL mapping in outbred populations.

More than 6000 samples of 18 different Hungarian sheep breeds were genotyped for 10 unlinked microsatellite loci. After data cleaning, 5434 sheep remained in the analysis. Some locus-breed combinations show deviation from Hardy-Weinberg equilibrium, possibly due to null alleles or the Wahlund effect. All breeds show high genetic variability; the lowest expected heterozygosity is that of the British Milksheep (He = 0.588). The Transylvanian Zackel has the highest expected heterozygosity (He = 0.790). It is also the least differentiated breed (Fst = 0.020). Pairwise genetic distances among breeds range from 0.021 between Hungarian Merino and both Mutton Merino and Transylvanian Zackel to greater than 0.105 between British Milksheep and all other breeds. The three Zackel populations - white, black, and Transylvanian Zackel - show small genetic distances among each other, with pairwise Fst values from 0.030 to 0.058. The Transylvanian Zackel tended to have close relationships to some other breeds too, probably due to its low differentiation. Given the individual genotypic information, a Bayesian analysis assigned individuals to breeds generally correctly. [ABSTRACT FROM AUTHOR]

Achillea (Asteraceae-Anthemideae) offers classical models for speciation by hybridization and polyploidy. Here, we test the suspected allotetraploid origin of two species, Achillea alpina and Achillea wilsoniana between phylogenetically distinct lineages in East Asia. A total of 421 AFLP bands from 169 individuals and 19 populations of five 2x- and two 4x-species were obtained. The data set was analysed with a newly developed model that accounts for polyploidy and assumes lack of recombination between the parental chromosome sets (i.e. disomic inheritance). A. alpina and A. wilsoniana then appear to be allotetraploids between Achillea acuminata-2x (sect. Ptarmica) and Achillea asiatica-2x (sect. Achillea). The two 4x-species share 44% and 48% of their AFLP bands with A. acuminata-2x, and 39% and 38% with A. asiatica-2x, respectively. Eight plastid haplotypes (A–H) were detected by polymerase chain reaction–restriction fragment length polymorphism (PCR–RFLP) analyses. A. alpina-4x and A. wilsoniana-4x share haplotype F only with A. asiatica-2x. This is consistent with the hybrid origin(s) involving the latter as the maternal ancestor. This result corroborates our previous DNA sequence data, where A. alpina-4x and A. wilsoniana-4x are also placed close to A. asiatica-2x. Morphology, ecology, and amplified fragment length polymorphism (AFLP) profiles of the two 2x-species are distinct, whereas the two 4x-species, grouped as A. alpina aggregate , form a nearly continuous link between them. Considering all evidence, this 4x-aggregate is regarded as the product of a hybridization between genetically distant 2x-ancestors limited to China and adjacent areas: one A. acuminata-like, and the other A. asiatica-like. The allopolyploid A. alpina agg. exhibits considerable morphological variation and ecological flexibility, and has expanded throughout eastern Asia and to northern North America, far beyond the ranges of their presumed 2x-ancestors. [ABSTRACT FROM AUTHOR]

This paper reviews scientific literature dealing with farmers' experimentation and innovation. For this a search was conducted in databases, books and journals. Based on this information it can be stated that during the evolution of agricultural systems, farmers' experimentation and innovation have been an integrated part of the development of the worlds' agricultural systems. The capacity of farmers to respond and adapt to external and internal changes is the basis for agricultural evolution. The farmer is part of the system in which he/she is conducting experiments and has direct interest in improving the current situation. The motivation to start farmers' experiments arises from the perceived necessity or wish to find solutions for certain problems or just from the farmer's curiosity to try something. Farmers experiment and innovate with their own methods, which usually differ from scientific ones. The level of complexity ranges between very easy and very complex. The experiments are mainly conducted on the basis of locally available physical and biological resources. They can be classified into technical, economical, social and institutional ones. [ABSTRACT FROM AUTHOR]

This paper reviews scientific literature dealing with farmers' experimentation and innovation. For this a search was conducted in databases, books and journals. Based on this information it can be stated that during the evolution of agricultural systems, farmers' experimentation and innovation have been an integrated part of the development of the worlds' agricultural systems. The capacity of farmers to respond and adapt to external and internal changes is the basis for agricultural evolution. The farmer is part of the system in which he/she is conducting experiments and has direct interest in improving the current situation. The motivation to start farmers' experiments arises from the perceived necessity or wish to find solutions for certain problems or just from the farmer's curiosity to try something. Farmers experiment and innovate with their own methods, which usually differ from scientific ones. The level of complexity ranges between very easy and very complex. The experiments are mainly conducted on the basis of locally available physical and biological resources. They can be classified into technical, economical, social and institutional ones. [ABSTRACT FROM AUTHOR]

The establishment of immunotherapy applying immune checkpoint inhibitors (ICI) has provided an important new option for the treatment of solid malignant diseases. However, different tumor entities show dramatically different responses to this therapy. BCC responds worse to anti-PD-1 ICIs as compared to cSCC. Differential immune checkpoint expression could explain this discrepancy and, therefore, the aim of this study was to analyze activating and inhibitory immune checkpoints in cSCC and BCC tissues. Tissue microarrays of the invasive front as well as the tumor core of BCC and cSCC samples were used to evaluate PD-1, PD-L1, CD28, and CD86 expression and their topographic distribution profiles by chromogenic immunohistochemistry. QuPath was used to determine the labeling index. The expression of PD-1, PD-L1, and CD28 was significantly higher in both the tumor core and the invasive front of cSCC samples as compared to BCC ( p < 0.001). In addition, the ratios of PD-L1/CD86 ( p < 0.001) and CD28/CD86 ( p < 0.001) were significantly higher in cSCC. The invasive front of both tumor entities showed higher expression levels of all immune markers compared to the tumor core in both tumor entities. The significantly higher expression of PD-1, PD-L1, and CD28 in cSCC, along with the predominance of the inhibitory ligand PD-L1 as compared to the activating CD86 in cSCC, provide a potential explanation for the better objective response rates to anti-PD-1 immunotherapy as compared to BCC. Furthermore, the predominant site of interaction between the immune system and the tumor was within the invasive front in both tumor types.

The approval and effectiveness of immune checkpoint inhibitors in head-and-neck squamous cell carcinoma (HNSCC) highlights the role of the immune system in this tumor entity. HNSCCs not only interacts with the immune system in the tumor tissue, but also induce systemic effects that may be additionally influenced by further factors such as the microbiome. Nonetheless, reliable immunological biomarkers that predict treatment response and outcome in HNSCC patients are lacking. The currently available biomarkers are mainly limited to analyses from tumor biopsies, while biomarkers from liquid biopsies, such as peripheral blood are not well-established. Thus, the here presented trial aims to identify interactions of intra-tumoral and systemic immune responses and to define prognostic immune signatures. Consequently, not only samples from the tumor tissue, but also from peripheral blood and the microbiome will be studied/are being evaluated and correlated with the clinical outcome. In this prospective, multi-center trial, 1000 HNSCC patients and 100 patients in the control cohort with non-tumor head-and-neck surgery will be enrolled. The local immune status from of the tumor and the microbiome will be sampled before treatment. In addition, the systemic immune status from peripheral blood will be analyzed before and after surgery and after the adjuvant and definitive radio-chemotherapy (RCT). Clinical baseline characteristics and outcome will additionally be collected. Data mining and modelling approaches will finally be applied to identify interactions of local and systemic immune parameters and to define prognostic immune signatures based on the evaluated immune markers. Approval from the institutional review board of the Friedrich-Alexander-Universität Erlangen-Nürnberg was granted in December 2021 (application number 21-440-B). By now, 150 patients have been enrolled in the intervention cohort. The results will be disseminated to the scientific audience and the general public via presentations at conferences and publication in peer-reviewed journals., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Donaubauer, Frey, Weber, Allner, Vogl, Almajali, Kuczera, Tamse, Balk, Müller, Eckstein, Zülch, Mogge, Weissmann, Fietkau, Kesting, Iro, Gaipl, Hecht and Gostian.)

During dental scaling in dogs under general anaesthesia, contamination of the peripheral intravenous catheter (PIVC) is unavoidable due to splatter and the generated aerosol. Bacterial contamination was compared between two commonly used PIVC placement sites. Thirty-nine client-owned dogs with a minimum length from their nose to their tail base of 50 cm were randomly assigned to receive a PIVC in either their cephalic or saphenous vein. Irrespective of the PIVC placement site, brain heart infusion agar dishes were placed in the cephalic and saphenous vein areas. Their lids were closed 0, 5, and 10 min into the procedure. Contamination was measured by counting the colony-forming units after incubation on different substrates. The data were analysed with descriptive statistics, ANOVA, and ANCOVA ( p < 0.05). The cephalic vein area showed a significantly higher bacterial load than the saphenous vein area ( p ≈ 0.0) regardless of the length of the dog. Furthermore, the dorsal PIVC injection ports were sampled before and after scaling, and the colonies isolated were counted and subjected to MALDI-TOF-MS for identification. The bacteria mainly belonged to the genera Staphylococcus, Neisseria, and Bacillus. Our results suggest that for dental scaling in dogs, the PIVC should be placed in the pelvic limb whenever possible to reduce the potential risk of contamination.

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., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)

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., (© 2024. The Author(s).)

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., (© The Author(s) 2024. Published by Oxford University Press on behalf of the European Society of Evolutionary Biology.)

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., (© 2024. The Author(s).)

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., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (© 2024 Auer, Kelemen, Vogl, von Ritgen, Haddad, Torres Borda, Gabmaier, Breteler and Jenner.)

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., (© 2023 The Authors. Journal of Evolutionary Biology published by John Wiley & Sons Ltd on behalf of European Society for Evolutionary Biology.)

In mammals, spatial orientation is synaptically-encoded by sensory hair cells of the vestibular labyrinth. Vestibular hair cells (VHCs) harbor synaptic ribbons at their presynaptic active zones (AZs), which play a critical role in molecular scaffolding and facilitate synaptic release and vesicular replenishment. With advancing age, the prevalence of vestibular deficits increases; yet, the underlying mechanisms are not well understood and the possible accompanying morphological changes in the VHC synapses have not yet been systematically examined. We investigated the effects of maturation and aging on the ultrastructure of the ribbon-type AZs in murine utricles using various electron microscopic techniques and combined them with confocal and super-resolution light microscopy as well as metabolic imaging up to 1 year of age. In older animals, we detected predominantly in type I VHCs the formation of floating ribbon clusters, mostly consisting of newly synthesized ribbon material. Our findings suggest that VHC ribbon-type AZs undergo dramatic structural alterations upon aging., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Michanski, Henneck, Mukhopadhyay, Steyer, Gonzalez, Grewe, Ilgen, Gültas, Fornasiero, Jakobs, Möbius, Vogl, Pangršič, Rizzoli and Wichmann.)

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., (© 2023 John Wiley & Sons Ltd.)

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.

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.