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Abstract Background Inhomogeneous patterns of chromatin-chromatin contacts within 10–100-kb-sized regions of the genome are a generic feature of chromatin spatial organization. These features, termed topologically associating domains (TADs), have led to the loop extrusion factor (LEF) model. Currently, our ability to model TADs relies on the observation that in vertebrates TAD boundaries are correlated with DNA sequences that bind CTCF, which therefore is inferred to block loop extrusion. However, although TADs feature prominently in their Hi-C maps, non-vertebrate eukaryotes either do not express CTCF or show few TAD boundaries that correlate with CTCF sites. In all of these organisms, the counterparts of CTCF remain unknown, frustrating comparisons between Hi-C data and simulations. Results To extend the LEF model across the tree of life, here, we propose the conserved-current loop extrusion (CCLE) model that interprets loop-extruding cohesin as a nearly conserved probability current. From cohesin ChIP-seq data alone, we derive a position-dependent loop extrusion rate, allowing for a modified paradigm for loop extrusion, that goes beyond solely localized barriers to also include loop extrusion rates that vary continuously. We show that CCLE accurately predicts the TAD-scale Hi-C maps of interphase Schizosaccharomyces pombe, as well as those of meiotic and mitotic Saccharomyces cerevisiae, demonstrating its utility in organisms lacking CTCF. Conclusions The success of CCLE in yeasts suggests that loop extrusion by cohesin is indeed the primary mechanism underlying TADs in these systems. CCLE allows us to obtain loop extrusion parameters such as the LEF density and processivity, which compare well to independent estimates.

Agricultural intensification and expansion are regarded as main drivers of biodiversity loss. This conclusion is mainly based on observed declines of local diversity (α-diversity), while effects on community composition homogenization (decrease of β-diversity) at a larger spatial scale are less well understood. Carabid beetles and spiders represent two widespread guilds and are important predators of pest species. Here we surveyed carabid beetles and spiders in 66 winter wheat fields in four northwestern European countries (Germany, the Netherlands, Sweden and UK) and analyzed how their community composition was related to geographic distance (separation distance between any pairwise fields) and three environmental variables: crop yield (proxy for land-use intensity), percentage cropland (proxy for landscape complexity) and soil organic carbon content (proxy for local soil conditions). We further analyzed whether the relationship between carabid beetle and spider community composition and geographic distance was influenced by environmental variables. We found that, 55 % and 75 % of all observed carabid and spider individuals, respectively, belonged to species that occurred in all four countries. However, individuals of species that were unique to a particular country only accounted for 3 % of all collected individuals for both taxa. Furthermore, we found a negative relationship between distance and similarity of spider communities but not for carabid beetle communities. None of the environmental variables were related to similarity of carabid beetle and spider communities, nor moderated the effects of distance. Our study indicates that across a great part of the European continent, arthropod communities (especially carabid beetles) in agricultural landscapes are composed of very similar species that are robust to current variations in environment and land-use.

Abstract The integration of extrinsic signaling with cell-intrinsic transcription factors can direct progenitor cells to differentiate into distinct cell fates. In the developing Drosophila eye, differentiation of photoreceptors R1–R7 requires EGFR signaling mediated by the transcription factor Pointed, and our single-cell RNA-Seq analysis shows that the same photoreceptors require the eye-specific transcription factor Glass. We find that ectopic expression of Glass and activation of EGFR signaling synergistically induce neuronal gene expression in the wing disc in a Pointed-dependent manner. Targeted DamID reveals that Glass and Pointed share many binding sites in the genome of developing photoreceptors. Comparison with transcriptomic data shows that Pointed and Glass induce photoreceptor differentiation through intermediate transcription factors, including the redundant homologs Scratch and Scrape, as well as directly activating neuronal effector genes. Our data reveal synergistic activation of a multi-layered transcriptional network as the mechanism by which EGFR signaling induces neuronal identity in Glass-expressing cells.

Abstract The yield of pearl millet, a resilient cereal crop crucial for African food security, is severely impacted by the root parasitic weed Striga hermonthica, which requires host-released hormones, called strigolactones (SLs), for seed germination. Herein, we identify four SLs present in the Striga-susceptible line SOSAT-C88-P10 (P10) but absent in the resistant 29Aw (Aw). We generate chromosome-scale genome assemblies, including four gapless chromosomes for each line. The Striga-resistant Aw lacks a 0.7 Mb genome segment containing two putative CARLACTONOIC ACID METHYLTRANSFERASE1 (CLAMT1) genes, which may contribute to SL biosynthesis. Functional assays show that P10CLAMT1b produces the SL-biosynthesis intermediate methyl carlactonoate (MeCLA) and that MeCLA is the precursor of P10-specific SLs. Screening a diverse pearl millet panel confirms the pivotal role of the CLAMT1 section for SL diversity and Striga susceptibility. Our results reveal a reason for Striga susceptibility in pearl millet and pave the way for generating resistant lines through marker-assisted breeding or direct genetic modification.

Abstract Background Centromere function is highly conserved across eukaryotes, but the underlying centromeric DNA sequences vary dramatically between species. Centromeres often contain a high proportion of repetitive DNA, such as tandem repeats and/or transposable elements (TEs). Einkorn wheat centromeres lack tandem repeat arrays and are instead composed mostly of the two long terminal repeat (LTR) retrotransposon families RLG_Cereba and RLG_Quinta which specifically insert in centromeres. However, it is poorly understood how these two TE families relate to each other and if and how they contribute to centromere function and evolution. Results Based on conservation of diagnostic motifs (LTRs, integrase and primer binding site and polypurine-tract), we propose that RLG_Cereba and RLG_Quinta are a pair of autonomous and non-autonomous partners, in which the autonomous RLG_Cereba contributes all the proteins required for transposition, while the non-autonomous RLG_Quinta contributes GAG protein. Phylogenetic analysis of predicted GAG proteins showed that the RLG_Cereba lineage was present for at least 100 million years in monocotyledon plants. In contrast, RLG_Quinta evolved from RLG_Cereba between 28 and 35 million years ago in the common ancestor of oat and wheat. Interestingly, the integrase of RLG_Cereba is fused to a so-called CR-domain, which is hypothesized to guide the integrase to the functional centromere. Indeed, ChIP-seq data and TE population analysis show only the youngest subfamilies of RLG_Cereba and RLG_Quinta are found in the active centromeres. Importantly, the LTRs of RLG_Quinta and RLG_Cereba are strongly associated with the presence of the centromere-specific CENH3 histone variant. We hypothesize that the LTRs of RLG_Cereba and RLG_Quinta contribute to wheat centromere integrity by phasing and/or placing CENH3 nucleosomes, thus favoring their persistence in the competitive centromere-niche. Conclusion Our data show that RLG_Cereba cross-mobilizes the non-autonomous RLG_Quinta retrotransposons. New copies of both families are specifically integrated into functional centromeres presumably through direct binding of the integrase CR domain to CENH3 histone variants. The LTRs of newly inserted RLG_Cereba and RLG_Quinta elements, in turn, recruit and/or phase new CENH3 deposition. This mutualistic interplay between the two TE families and the plant host dynamically maintains wheat centromeres.

Abstract Many disease resistance genes have been introgressed into wheat from its wild relatives. However, reduced recombination within the introgressed segments hinders the cloning of the introgressed genes. Here, we have cloned the powdery mildew resistance gene Pm13, which is introgressed into wheat from Aegilops longissima, using a method that combines physical mapping with radiation-induced chromosomal aberrations and transcriptome sequencing analysis of ethyl methanesulfonate (EMS)-induced loss-of-function mutants. Pm13 encodes a kinase fusion protein, designated MLKL-K, with an N-terminal domain of mixed lineage kinase domain-like protein (MLKL_NTD domain) and a C-terminal serine/threonine kinase domain bridged by a brace. The resistance function of Pm13 is validated through transient and stable transgenic complementation assays. Transient over-expression analyses in Nicotiana benthamiana leaves and wheat protoplasts reveal that the fragment Brace-Kinase122-476 of MLKL-K is capable of inducing cell death, which is dependent on a functional kinase domain and the three α-helices in the brace region close to the N-terminus of the kinase domain.

Ion beam figuring (IBF) is a powerful technique for figure correction of X-ray mirrors to a high accuracy. Here, recent technical advancements in the IBF instrument developed at Diamond Light Source are presented and experimental results for figuring of X-ray mirrors are given. The IBF system is equipped with a stable DC gridded ion source (120 mm diameter), a four-axis motion stage to manipulate the optic, a Faraday cup to monitor the ion-beam current, and a camera for alignment. A novel laser speckle angular measurement instrument also provides on-board metrology. To demonstrate the IBF system's capabilities, two silicon X-ray mirrors were processed. For 1D correction, a height error of 0.08 nm r.m.s. and a slope error of 44 nrad r.m.s. were achieved. For 2D correction over a 67 mm × 17 mm clear aperture, a height error of 0.8 nm r.m.s. and a slope error of 230 nrad r.m.s. were obtained. For the 1D case, this optical quality is comparable with the highest-grade, commercially available, X-ray optics.

Abstract Background Heart failure (HF) with preserved or mildly reduced ejection fraction includes a heterogenous group of patients. Reclassification into distinct phenogroups to enable targeted interventions is a priority. This study aimed to identify distinct phenogroups, and compare phenogroup characteristics and outcomes, from electronic health record data. Methods 2,187 patients admitted to five UK hospitals with a diagnosis of HF and a left ventricular ejection fraction ≥ 40% were identified from the NIHR Health Informatics Collaborative database. Partition-based, model-based, and density-based machine learning clustering techniques were applied. Cox Proportional Hazards and Fine-Gray competing risks models were used to compare outcomes (all-cause mortality and hospitalisation for HF) across phenogroups. Results Three phenogroups were identified: (1) Younger, predominantly female patients with high prevalence of cardiometabolic and coronary disease; (2) More frail patients, with higher rates of lung disease and atrial fibrillation; (3) Patients characterised by systemic inflammation and high rates of diabetes and renal dysfunction. Survival profiles were distinct, with an increasing risk of all-cause mortality from phenogroups 1 to 3 (p

Abstract Self-reported shorter/longer sleep duration, insomnia, and evening preference are associated with hyperglycaemia in observational analyses, with similar observations in small studies using accelerometer-derived sleep traits. Mendelian randomization (MR) studies support an effect of self-reported insomnia, but not others, on glycated haemoglobin (HbA1c). To explore potential effects, we used MR methods to assess effects of accelerometer-derived sleep traits (duration, mid-point least active 5-h, mid-point most active 10-h, sleep fragmentation, and efficiency) on HbA1c/glucose in European adults from the UK Biobank (UKB) (n = 73,797) and the MAGIC consortium (n = 146,806). Cross-trait linkage disequilibrium score regression was applied to determine genetic correlations across accelerometer-derived, self-reported sleep traits, and HbA1c/glucose. We found no causal effect of any accelerometer-derived sleep trait on HbA1c or glucose. Similar MR results for self-reported sleep traits in the UKB sub-sample with accelerometer-derived measures suggested our results were not explained by selection bias. Phenotypic and genetic correlation analyses suggested complex relationships between self-reported and accelerometer-derived traits indicating that they may reflect different types of exposure. These findings suggested accelerometer-derived sleep traits do not affect HbA1c. Accelerometer-derived measures of sleep duration and quality might not simply be ‘objective’ measures of self-reported sleep duration and insomnia, but rather captured different sleep characteristics.

Abstract Background Autism Spectrum Disorder (ASD) is a group of neurodevelopmental disorders with higher incidence in males and is characterized by atypical verbal/nonverbal communication, restricted interests that can be accompanied by repetitive behavior, and disturbances in social behavior. This study investigated brain mechanisms that contribute to sociability deficits and sex differences in an ASD animal model. Methods Sociability was measured in C58/J and C57BL/6J mice using the 3-chamber social choice test. Bulk RNA-Seq and snRNA-Seq identified transcriptional changes in C58/J and C57BL/6J amygdala within which DMRseq was used to measure differentially methylated regions in amygdala. Results C58/J mice displayed divergent social strata in the 3-chamber test. Transcriptional and pathway signatures revealed immune-related biological processes differ between C58/J and C57BL/6J amygdala. Hypermethylated and hypomethylated genes were identified in C58/J versus C57BL/6J amygdala. snRNA-Seq data in C58/J amygdala identified differential transcriptional signatures within oligodendrocytes and microglia characterized by increased ASD risk gene expression and predicted impaired myelination that was dependent on sex and sociability. RNA velocity, gene regulatory network, and cell communication analysis showed diminished oligodendrocyte/microglia differentiation. Findings were verified using Bulk RNA-Seq and demonstrated oxytocin’s beneficial effects on myelin gene expression. Limitations Our findings are significant. However, limitations can be noted. The cellular mechanisms linking reduced oligodendrocyte differentiation and reduced myelination to an ASD phenotype in C58/J mice need further investigation. Additional snRNA-Seq and spatial studies would determine if effects in oligodendrocytes/microglia are unique to amygdala or if this occurs in other brain regions. Oxytocin’s effects need further examination to understand its’ potential as an ASD therapeutic. Conclusions Our work demonstrates the C58/J mouse model’s utility in evaluating the influence of sex and sociability on the transcriptome in concomitant brain regions involved in ASD. Our single-nucleus transcriptome analysis elucidates potential pathological roles of oligodendrocytes and microglia in ASD. This investigation provides details regarding regulatory features disrupted in these cell types, including transcriptional gene dysregulation, aberrant cell differentiation, altered gene regulatory networks, and changes to key pathways that promote microglia/oligodendrocyte differentiation. Our studies provide insight into interactions between genetic risk and epigenetic processes associated with divergent affiliative behavior and lack of positive sociability.

Abstract Acoel flatworms have played a relevant role in classical (and current) discussions on the evolutionary origin of bilaterian animals. This is mostly derived from the apparent simplicity of their body architectures. This tenet has been challenged over the last couple of decades, mostly because detailed studies of their morphology and the introduction of multiple genomic technologies have unveiled a complexity of cell types, tissular arrangements and patterning mechanisms that were hidden below this 'superficial' simplicity. One tissue that has received a particular attention has been the nervous system (NS). The combination of ultrastructural and single cell methodologies has revealed unique cellular diversity and developmental trajectories for most of their neurons and associated sensory systems. Moreover, the great diversity in NS architectures shown by different acoels offers us with a unique group of animals where to study key aspects of neurogenesis and diversification od neural systems over evolutionary time. In this review we revisit some recent developments in the characterization of the acoel nervous system structure and the regulatory mechanisms that contribute to their embryological development. We end up by suggesting some promising avenues to better understand how this tissue is organized in its finest cellular details and how to achieve a deeper knowledge of the functional roles that genes and gene networks play in its construction.

The skeleton in question derives from the Late Iron Age monument of Nor Armavir and was unearthed from burial No. 19. The deceased was buried in an unusual position. In this article, we characterize the pathological bony changes indicative of tuberculous spondylitis. The skeleton was subject to a detailed macroscopic investigation. Besides age at death estimation and sex determination, a careful palaeopathological evaluation was performed on the bone remains. In addition, volumetric (3D) computed tomography was carried out on four lumbar vertebrae (L2–5) to complement the macromorphology-based diagnosis.

Abstract A critical step to maximize the usefulness of genome-wide association studies (GWAS) in plant breeding is the identification and validation of candidate genes underlying genetic associations. This is of particular importance in disease resistance breeding where allelic variants of resistance genes often confer resistance to distinct populations, or races, of a pathogen. Here, we perform a genome-wide association analysis of rice blast resistance in 500 genetically diverse rice accessions. To facilitate candidate gene identification, we produce de-novo genome assemblies of ten rice accessions with various rice blast resistance associations. These genome assemblies facilitate the identification and functional validation of novel alleles of the rice blast resistance genes Ptr and Pia. We uncover an allelic series for the unusual Ptr rice blast resistance gene, and additional alleles of the Pia resistance genes RGA4 and RGA5. By linking these associations to three thousand rice genomes we provide a useful tool to inform future rice blast breeding efforts. Our work shows that GWAS in combination with whole-genome sequencing is a powerful tool for gene cloning and to facilitate selection of specific resistance alleles for plant breeding.

Abstract While chronological age is a strong predictor for health-related risk factors, it is an incomplete metric that fails to fully characterize the unique aging process of individuals with different genetic makeup, neurodevelopment, and environmental experiences. Recent advances in epigenomic array technologies have made it possible to generate DNA methylation-based biomarkers of biological aging, which may be useful in predicting a myriad of cognitive abilities and functional brain network organization across older individuals. It is currently unclear which cognitive domains are negatively correlated with epigenetic age above and beyond chronological age, and it is unknown if functional brain organization is an important mechanism for explaining these associations. In this study, individuals with accelerated epigenetic age (i.e. AgeAccelGrim) performed worse on tasks that spanned a wide variety of cognitive faculties including both fluid and crystallized intelligence (N = 103, average age = 68.98 years, 73 females, 30 males). Additionally, fMRI connectome-based predictive models suggested a mediating mechanism of functional connectivity on epigenetic age acceleration-cognition associations primarily in medial temporal lobe and limbic structures. This research highlights the important role of epigenetic aging processes on the development and maintenance of healthy cognitive capacities and function of the aging brain.

Abstract Glioblastoma (GBM) remains an untreatable malignant tumor with poor patient outcomes, characterized by palisading necrosis and microvascular proliferation. While single-cell technology made it possible to characterize different lineage of glioma cells into neural progenitor-like (NPC-like), oligodendrocyte-progenitor-like (OPC-like), astrocyte-like (AC-like) and mesenchymal like (MES-like) states, it does not capture the spatial localization of these tumor cell states. Spatial transcriptomics empowers the study of the spatial organization of different cell types and tumor cell states and allows for the selection of regions of interest to investigate region-specific and cell-type-specific pathways. Here, we obtained paired 10x Chromium single-nuclei RNA-sequencing (snRNA-seq) and 10x Visium spatial transcriptomics data from three GBM patients to interrogate the GBM microenvironment. Integration of the snRNA-seq and spatial transcriptomics data reveals patterns of segregation of tumor cell states. For instance, OPC-like tumor and NPC-like tumor significantly segregate in two of the three samples. Our differentially expressed gene and pathway analyses uncovered significant pathways in functionally relevant niches. Specifically, perinecrotic regions were more immunosuppressive than the endogenous GBM microenvironment, and perivascular regions were more pro-inflammatory. Our gradient analysis suggests that OPC-like tumor cells tend to reside in areas closer to the tumor vasculature compared to tumor necrosis, which may reflect increased oxygen requirements for OPC-like cells. In summary, we characterized the localization of cell types and tumor cell states, the gene expression patterns, and pathways in different niches within the GBM microenvironment. Our results provide further evidence of the segregation of tumor cell states and highlight the immunosuppressive nature of the necrotic and perinecrotic niches in GBM.

Abstract Aims Population‐wide, person‐level, linked electronic health record data are increasingly used to estimate epidemiology, guide resource allocation, and identify events in clinical trials. The accuracy of data from NHS Digital (now part of NHS England) for identifying hospitalization for heart failure (HHF), a key HF standard, is not clear. This study aimed to evaluate the accuracy of NHS Digital data for identifying HHF. Methods and results Patients experiencing at least one HHF, as determined by NHS Digital data, and age‐ and sex‐matched patients not experiencing HHF, were identified from a prospective cohort study and underwent expert adjudication. Three code sets commonly used to identify HHF were applied to the data and compared with expert adjudication (I50: International Classification of Diseases‐10 codes beginning I50; OIS: Clinical Commissioning Groups Outcomes Indicator Set; and NICOR: National Institute for Cardiovascular Outcomes Research, used as the basis for the National Heart Failure Audit in England and Wales). Five hundred four patients underwent expert adjudication, of which 10 (2%) were adjudicated to have experienced HHF. Specificity was high across all three code sets in the first diagnosis position {I50: 96.2% [95% confidence interval (CI) 94.1–97.7%]; NICOR: 93.3% [CI 90.8–95.4%]; OIS: 95.6% [CI 93.3–97.2%]} but decreased substantially as the number of diagnosis positions expanded. Sensitivity [40.0% (CI 12.2–73.8%)] and positive predictive value (PPV) [highest with I50: 17.4% (CI 8.1–33.6%)] were low in the first diagnosis position for all coding sets. PPV was higher for the National Heart Failure Audit criteria, albeit modestly [36.4% (CI 16.6–62.2%)]. Conclusions NHS Digital data were not able to accurately identify HHF and should not be used in isolation for this purpose.

Objective: To correlate the operative characteristics and complications of transforaminal lumbar interbody fusion (TLIF) to patient frailty status for the first time in a multicenter study. Methods: Using the American College of Surgeons National Surgical Quality Improvement (ACS-NSQIP) database, all patients who underwent TLIF in 2015–2020 were filtered for their demographics, operative characteristics, and 30-day complication outcomes. Patients were stratified into 2 cohorts, low and high frailty, based on their modified frailty index 5 score. Univariate analysis was performed between the 2 cohorts for each collected variable, and multivariable analysis was performed to observe adjusted odds ratios (OR). Results: The frail cohort experienced more unplanned readmission (4.3 vs 6.6 %, p

We provide a detailed and first description of the skull, hyoid apparatus, and trachea of the Turks and Caicos rock iguana, Cyclura carinata (Squamata: Iguanidae). Cyclura is a radiation of iguanas restricted to islands of the Caribbean Sea. Species of Cyclura have high rates of endemism, and all species are severely threatened with extinction. Our anatomical description of this threatened iguana is based on high-resolution computed tomography scans of one adult, one putative adult or near adult, and one juvenile specimen, and includes three-dimensional segmented renderings and visualizations. We discuss some observations of intraspecific and ontogenetic variation, and provide a brief comparison with specimens of another species of Cyclura and published descriptions of other iguanas. Our study provides a cranial osteological framework for Cyclura and augments the body of knowledge on iguana anatomy generally. Finally, we posit that our description and future studies may facilitate identification of fossil Cyclura, which could help understand the paleobiogeography of the genus.

Abstract Infectious and parasitic agents (IPAs) and their associated diseases are major environmental stressors that jeopardize bee health, both alone and in interaction with other stressors. Their impact on pollinator communities can be assessed by studying multiple sentinel bee species. Here, we analysed the field exposure of three sentinel managed bee species (Apis mellifera, Bombus terrestris and Osmia bicornis) to 11 IPAs (six RNA viruses, two bacteria, three microsporidia). The sentinel bees were deployed at 128 sites in eight European countries adjacent to either oilseed rape fields or apple orchards during crop bloom. Adult bees of each species were sampled before their placement and after crop bloom. The IPAs were detected and quantified using a harmonised, high-throughput and semi-automatized qPCR workflow. We describe differences among bee species in IPA profiles (richness, diversity, detection frequencies, loads and their change upon field exposure, and exposure risk), with no clear patterns related to the country or focal crop. Our results suggest that the most frequent IPAs in adult bees are more appropriate for assessing the bees’ IPA exposure risk. We also report positive correlations of IPA loads supporting the potential IPA transmission among sentinels, suggesting careful consideration should be taken when introducing managed pollinators in ecologically sensitive environments.

Abstract Introduction The skin of patients with atopic dermatitis (AD) is characterised by elevated pH. As a central homeostatic regulator, an increased pH accelerates desquamation and suppresses lipid processing, resulting in diminished skin barrier function. The aim of this study was to determine whether a novel zinc lactobionate emollient cream can strengthen the skin barrier by lowering skin surface pH. Methods A double-blind, forearm-controlled cohort study was undertaken in patients with AD. Participants applied the test cream to one forearm and a vehicle cream to the other (randomised allocation) twice daily for 56 days. Skin surface pH and barrier function (primary outcomes) were assessed at baseline and after 28 days and 56 days of treatment, amongst other tests. Results A total of 23 adults with AD completed the study. During and after treatment, a sustained difference in skin surface pH was observed between areas treated with the test cream and vehicle (4.50 ± 0.38 versus 5.25 ± 0.54, respectively, p

Abstract Background Fonio (Digitaria exilis), an orphan millet crop, is the oldest indigenous crop in West Africa. Although the yield is low due to pre-domestication characteristics, the quick maturation time, drought tolerance, and the ability to thrive on poor soils make fonio a climate-smart crop. Being holobionts, plants evolve in close interaction with microbial partners, which is crucial for plant phenology and fitness. As seeds are the bottleneck of vertically transmitting plant microbiota, we proposed to unravel the seed microbiome of the under-domesticated and resilient crop fonio. Our study investigated the bacterial seed endophyte diversity across 126 sequenced fonio accessions from distinct locations in West Africa. We conducted a correlation study of the structures and functions of the seed-associated microbiomes with the native geo-climate and soil structure data. We also performed Genome-wide association studies (GWAS) to identify genetic loci associated with seed endophyte diversity. Result We report that fonio millet has diverse heritable seed endophytic taxa. We analyzed the seed microbiomes of 126 fonio accessions and showed that despite the diversity of microbiomes from distinct geographical locations, all fonio genetic groups share a core microbiome. In addition, we observed that native soil composition, geo-climatic factors, and host genotype correlate with the seed microbiomes. GWAS analysis of genetic loci associated with endophyte seed bacterial diversity identified fonio SNPs associated with genes functioning in embryo development and stress/defense response. Conclusion Analysis of the seed endophyte of the climate-smart crop fonio indicated that despite possessing a heritable core microbiome, native conditions may shape the overall fonio seed microbiomes in different populations. These distinct microbiomes could play important roles in the adaptation of fonio to different environmental conditions. Our study identified the seed microbiome as a potential target for enhancing crop resilience to climate stress in a sustainable way. Video Abstract

Vascularized Composite Allotransplantation (VCA) offers a unique option to restore form and function after limb loss or facial trauma that cannot be satisfactorily accomplished through traditional prosthetics or reconstructions. Establishing a successful Upper Extremity Transplantation (UET) program requires strong leadership and a structured surgical team, and extensive interdisciplinary collaboration. We conducted a qualitative study among 12 health care professionals and patients. Informed consent was obtained per protocol, and semi-structured interviews were conducted online and recorded. Participants reported their perceptions of factors that either favored or hindered a successful outcome, including functional status before and after surgery, preparation for transplant, shared decision-making, rehabilitation, and psychosocial support. Thematic analysis revealed that it is essential to establish a team comprising various disciplines well before performing VCA procedures. Defining a common goal and choosing a defined leader is a key factor in procedural success and requires open collaboration beyond what is typical. Primary described categories are interdisciplinary collaboration and skills of the VCA team, building and leading a VCA team, pre-transplant procedures, post-transplant course, and factors to consider when establishing a program. The basic roles of team science play an outsized role in establishing a VCA program. Transplantation medicine involves various overlapping scientific and medical categories requiring health professionals to consciously work together to establish complex vertical and horizontal communication webs between teams to obtain positive outcomes. In addition to medical considerations, patient-specific factors such as transparent communication, therapy plan establishment, plan adherence, and continual follow-up are significant factors to overall success.

Abstract Despite increasing recognition of the importance of the multiple dimensions of biodiversity, including functional or genetic diversity as well as species diversity, most conservation studies on ecosystem service‐providing insects focus on simple diversity measures such as species richness and abundance. In contrast, relatively little is known about the genetic diversity and resilience of pollinators or natural enemies of crop pests to population fragmentation and local extinction. The genetic diversity and demographic dynamics of remnant populations of beneficial insects in agricultural areas can be a useful indicator proving additional insights into their conservation status, but this is rarely evaluated. Although gene flow between agricultural and seminatural areas is key to maintaining genetic diversity, its extent and directionality remain largely unexplored. Here, we apply a pan‐European sampling protocol to quantify genetic diversity and structure and assess gene flow between agricultural and nearby seminatural landscapes in populations of two key ecosystem service‐providing insect species, the lady beetle Coccinella septempunctata, an important predator of aphids and other crop pests, and the bee pollinator Andrena flavipes. We show that A. flavipes populations are genetically structured at the European level, whereas populations of C. septempunctata experience widespread gene flow across the continent and lack any defined genetic structure. In both species, we found that there is high genetic connectivity between populations established in croplands and nearby seminatural areas and, as a consequence, they harbor similar levels of genetic diversity. Interestingly, demographic models for some regions support asymmetric gene flow from seminatural areas to nearby agricultural landscapes. Collectively, our study demonstrates how seminatural areas can serve as genetic reservoirs of both pollinators and natural enemies for nearby agricultural landscapes, acting as sources for recurrent recolonization and, potentially, contributing to enhancing ecosystem service and crop production resilience in the longer term.

Background: Lumbar decompression is a commonly performed procedure for the operative management of several degenerative lumbar spinal pathologies. Although open approaches are considered the traditional method, endoscopic techniques represent a relatively novel, less-invasive option to achieve neural element decompression. Here within, we examine if the use of endoscopic techniques decreases the risk of post operative infections. Methods: We performed a retrospective cohort analysis to directly compare patients who underwent either open or endoscopic lumbar decompression at a single institution. Rates of postoperative outcomes such as surgical site infection, hospital length of stay, estimated blood loss, and others were compared between the two treatment groups. A multivariate logistic regression model was constructed using patient comorbidities and procedural characteristics to identify the risk factors for surgical site infection. Results: 150 patients were identified as undergoing lumbar spine decompression surgeries that met inclusion criteria for the study, of whom 108 (72.0%) underwent open and 61 (28.0%) underwent endoscopic approaches. Unpaired analysis revealed positive associations between operative duration, estimated blood loss, drain placement rates. Multivariate logistic regression did not reveal an association between surgical approach (open versus endoscopic) and the development of surgical site infection. Conclusions: Surgical site infections following endoscopic lumbar spine decompression are relatively uncommon, however, after adjusting for baseline differences between patient populations, surgical approach does not independently predict the development of postoperative infection.

Abstract Wild wheat relatives have been explored in plant breeding to increase the genetic diversity of bread wheat, one of the most important food crops. Aegilops umbellulata is a diploid U genome-containing grass species that serves as a genetic reservoir for wheat improvement. In this study, we report the construction of a chromosome-scale reference assembly of Ae. umbellulata accession TA1851 based on corrected PacBio HiFi reads and chromosome conformation capture. The total assembly size was 4.25 Gb with a contig N50 of 17.7 Mb. In total, 36,268 gene models were predicted. We benchmarked the performance of hifiasm and LJA, two of the most widely used assemblers using standard and corrected HiFi reads, revealing a positive effect of corrected input reads. Comparative genome analysis confirmed substantial chromosome rearrangements in Ae. umbellulata compared to bread wheat. In summary, the Ae. umbellulata assembly provides a resource for comparative genomics in Triticeae and for the discovery of agriculturally important genes.

Abstract Managed bee species provide essential pollination services that contribute to food security worldwide. However, managed bees face a diverse array of threats and anticipating these, and potential opportunities to reduce risks, is essential for the sustainable management of pollination services. We conducted a horizon scanning exercise with 20 experts from across Europe to identify emerging threats and opportunities for managed bees in European agricultural systems. An initial 63 issues were identified, and this was shortlisted to 21 issues through the horizon scanning process. These ranged from local landscape-level management to geopolitical issues on a continental and global scale across seven broad themes—Pesticides & pollutants, Technology, Management practices, Predators & parasites, Environmental stressors, Crop modification, and Political & trade influences. While we conducted this horizon scan within a European context, the opportunities and threats identified will likely be relevant to other regions. A renewed research and policy focus, especially on the highest-ranking issues, is required to maximise the value of these opportunities and mitigate threats to maintain sustainable and healthy managed bee pollinators within agricultural systems.

Background: Metabolic dysfunction-associated steatotic liver disease (MASLD) is the most common liver disease in adolescents with obesity. Nonetheless, the guidelines for screening and managing this disease are contradictory. The purpose of this study is to non-invasively assess the prevalence, patient characteristics, and potential associated factors of MASLD in this demographic. Methods: This study used baseline data from an RCT in adolescents eligible for bariatric surgery. MASLD was determined by measuring the hepatorenal index (HRI) with ultrasonography, blood liver tests, and the fatty liver index (FLI). Results: A total of 56 adolescents enrolled in the analyses; the majority were female n = 44 (79%); the mean age was 15.75 (±1.01) years; the average body mass index (BMI) was 44.08 (±5.16) kg/m2. In 35 (62.5%) of the patients, the HRI was abnormal. This group had a higher waist/hip ratio, elevated liver biochemistry, and significantly lower leptin levels (mean difference = −46.35, 95% CI −76.72, −15.99) compared to the group with a normal HRI. In 32 (55.2%) of the patients, ALT levels were elevated and the FLI was abnormal in all (100%) participants. Linear regression analysis indicated associations between the HRI and typical anthropometric and metabolic measurements; and an inverse association between HRI and leptin B = −0.003 (95% CI −0.005, −0.00), independently of sex- and age-adjusted BMI. Conclusions: MASLD is highly prevalent in adolescents with severe obesity. However, the prevalence strongly depends on which tool is used, namely the HRI (62.5%), alanine transaminase levels (55.2%), and FLI (100%). Our findings suggest that leptin may be a valuable biomarker in supporting the diagnosis of MASLD.

Abstract Many pollinators, including bumble bees, are in decline. Such declines are known to be driven by a number of interacting factors. Decreases in bee populations may also negatively impact the key ecosystem service, pollination, that they provide. Pesticides and parasites are often cited as two of the drivers of bee declines, particularly as they have previously been found to interact with one another to the detriment of bee health. Here we test the effects of an insecticide, sulfoxaflor, and a highly prevalent bumble bee parasite, Crithidia bombi, on the bumble bee Bombus terrestris. After exposing colonies to realistic doses of either sulfoxaflor and/or Crithidia bombi in a fully crossed experiment, colonies were allowed to forage on field beans in outdoor exclusion cages. Foraging performance was monitored, and the impacts on fruit set were recorded. We found no effect of either stressor, or their interaction, on the pollination services they provide to field beans, either at an individual level or a whole colony level. Further, there was no impact of any treatment, in any metric, on colony development. Our results contrast with prior findings that similar insecticides (neonicotinoids) impact pollination services, and that sulfoxaflor impacts colony development, potentially suggesting that sulfoxaflor is a less harmful compound to bee health than neonicotinoids insecticides.

Abstract Human WIPI β-propellers function as PI3P effectors in autophagy, with WIPI4 and WIPI3 being able to link autophagy control by AMPK and TORC1 to the formation of autophagosomes. WIPI1, instead, assists WIPI2 in efficiently recruiting the ATG16L1 complex at the nascent autophagosome, which in turn promotes lipidation of LC3/GABARAP and autophagosome maturation. However, the specific role of WIPI1 and its regulation are unknown. Here, we discovered the ABL-ERK-MYC signalling axis controlling WIPI1. As a result of this signalling, MYC binds to the WIPI1 promoter and represses WIPI1 gene expression. When ABL-ERK-MYC signalling is counteracted, increased WIPI1 gene expression enhances the formation of autophagic membranes capable of migrating through tunnelling nanotubes to neighbouring cells with low autophagic activity. ABL-regulated WIPI1 function is relevant to lifespan control, as ABL deficiency in C. elegans increased gene expression of the WIPI1 orthologue ATG-18 and prolonged lifespan in a manner dependent on ATG-18. We propose that WIPI1 acts as an enhancer of autophagy that is physiologically relevant for regulating the level of autophagic activity over the lifespan.

Abstract Einkorn wheat (Triticum monococcum) is an ancient grain crop and a close relative of the diploid progenitor (T. urartu) of polyploid wheat. It is the only diploid wheat species having both domesticated and wild forms and therefore provides an excellent system to identify domestication genes and genes for traits of interest to utilize in wheat improvement. Here, we leverage genomic advancements for einkorn wheat using an einkorn reference genome assembly combined with skim-sequencing of a large genetic population of 812 recombinant inbred lines (RILs) developed from a cross between a wild and a domesticated T. monococcum accession. We identify 15,919 crossover breakpoints delimited to a median and average interval of 114 Kbp and 219 Kbp, respectively. This high-resolution mapping resource enables us to perform fine-scale mapping of one qualitative (red coleoptile) and one quantitative (spikelet number per spike) trait, resulting in the identification of small physical intervals (400 Kb to 700 Kb) with a limited number of candidate genes. Furthermore, an important domestication locus for brittle rachis is also identified on chromosome 7A. This resource presents an exciting route to perform trait discovery in diploid wheat for agronomically important traits and their further deployment in einkorn as well as tetraploid pasta wheat and hexaploid bread wheat cultivars.

Vascularized composite allotransplantation (VCA) is an emerging field in transplant surgery. Despite overall positive outcomes, VCA confers risk for multiple complications related to the procedure and subsequent immunosuppression. Post-transplant lymphoproliferative disorder (PTLD) is a heterogeneous group of lymphoproliferative disorders occurring after solid organ and hematopoietic stem cell transplant. A patient with PTLD after bilateral upper extremity transplantation is presented as well as a review of all known cases of PTLD after VCA, with a focus on the unique epidemiology, presentation, and treatment in this population.

ABSTRACT: Background: Heart failure (HF) most commonly occurs in patients who have had a myocardial infarction (MI), but factors other than MI size may be deterministic. Fibrosis of myocardium remote from the MI is associated with adverse remodeling. We aimed to 1) investigate the association between remote myocardial fibrosis, measured using cardiovascular magnetic resonance (CMR) extracellular volume fraction (ECV), and HF and death following MI, 2) identify predictors of remote myocardial fibrosis in patients with evidence of MI and determine the relationship with infarct size. Methods: Multicenter prospective cohort study of 1199 consecutive patients undergoing CMR with evidence of MI on late gadolinium enhancement. Median follow-up was 1133 (895–1442) days. Cox proportional hazards modeling was used to identify factors predictive of the primary outcome, a composite of first hospitalization for HF (HHF) or all-cause mortality, post-CMR. Linear regression modeling was used to identify determinants of remote ECV. Results: Remote myocardial fibrosis was a strong predictor of primary outcome (χ2: 15.6, hazard ratio [HR]: 1.07 per 1% increase in ECV, 95% confidence interval [CI]: 1.04–1.11, p

Background Arvicoline rodents are one of the most speciose and rapidly evolving mammalian lineages. Fossil arvicolines are also among the most common vertebrate fossils found in sites of Pliocene and Pleistocene age in Eurasia and North America. However, there is no taxonomically robust, well-supported, time-calibrated phylogeny for the group. Methods Here we present well-supported hypotheses of arvicoline rodent systematics using maximum likelihood and Bayesian inference of DNA sequences of two mitochondrial genes and three nuclear genes representing 146 (82% coverage) species and 100% of currently recognized arvicoline genera. We elucidate well-supported major clades, reviewed the relationships and taxonomy of many species and genera, and critically compared our resulting molecular phylogenetic hypotheses to previously published hypotheses. We also used five fossil calibrations to generate a time-calibrated phylogeny of Arvicolinae that permitted some reconciliation between paleontological and neontological data. Results Our results are largely congruent with previous molecular phylogenies, but we increased the support in many regions of the arvicoline tree that were previously poorly-sampled. Our sampling resulted in a better understanding of relationships within Clethrionomyini, the early-diverging position and close relationship of true lemmings (Lemmus and Myopus) and bog lemmings (Synaptomys), and provided support for recent taxonomic changes within Microtini. Our results indicate an origin of ∼6.4 Ma for crown arvicoline rodents. These results have major implications (e.g., diversification rates, paleobiogeography) for our confidence in the fossil record of arvicolines and their utility as biochronological tools in Eurasia and North America during the Quaternary.

Pleurodonta is an ancient, diverse clade of iguanian lizard distributed primarily in the Western Hemisphere. Although the clade is a frequent subject of systematic research, phylogenetic resolution among the major pleurodontan clades is elusive. That uncertainty has complicated the interpretations of many fossil pleurodontans. I describe a fossil skull of a pleurodontan lizard from the Palaeogene of Wyoming that was previously allocated to the puzzling taxon Aciprion formosum, and provide an updated morphological matrix for iguanian lizards. Phylogenetic analyses using Bayesian inference demonstrate that the fossil skull is the oldest and first definitive stem member of Crotaphytidae (collared and leopard lizards), establishing the presence of that clade in North America during the Palaeogene. I also discuss new or revised hypotheses for the relationships of several early pleurodontans. In particular, I examine potential evidence for crown-Pleurodonta in the Cretaceous of Mongolia (Polrussia), stem Pleurodonta in the Cretaceous of North America (Magnuviator) and a stem anole in the Eocene of North America (Afairiguana). I suggest that the placement of the fossil crotaphytid is stable to the uncertain phylogeny of Pleurodonta, but recognize the dynamic nature of fossil diagnosis and the potential for updated systematic hypotheses for the other fossils analysed here.

Abstract Monoamines like serotonin, dopamine, and adrenaline/noradrenaline (epinephrine/norepinephrine) act as neuromodulators in the nervous system. They play a role in complex behaviours, cognitive functions such as learning and memory formation, as well as fundamental homeostatic processes such as sleep and feeding. However, the evolutionary origin of the genes required for monoaminergic modulation is uncertain. Using a phylogenomic approach, in this study, we show that most of the genes involved in monoamine production, modulation, and reception originated in the bilaterian stem group. This suggests that the monoaminergic system is a bilaterian novelty and that its evolution may have contributed to the Cambrian diversification.

Abstract Background Developmental Dysplasia of the Hip (DDH) is one of the most common pediatric orthopedic disorders, affecting 1–3% of all newborns. The optimal treatment of centered DDH is currently under debate. This randomized controlled trial aims to study the (cost-)effectiveness of active monitoring versus abduction treatment for infants with centered DDH. Methods This is a multicenter, parallel-group, open-label, non-inferiority randomized controlled trial studying the (cost-)effectiveness of active monitoring versus abduction treatment for infants with centered DDH in fourteen hospitals in the Netherlands. In total, 800 infants with centered DDH (Graf IIa-/IIb/IIc), aged 10–16 weeks, will be randomly allocated to the active monitoring or abduction treatment group. Infants will be followed up until the age of 24 months. The primary outcome is the rate of normal hips, defined as an acetabular index lower than 25 degrees on an antero-posterior radiograph, at the age of 12 months. Secondary outcomes are the rate of normal hips at the age of 24 months, complications, time to hip normalization, the relation between baseline patient characteristics and the rate of normal hips, compliance, costs, cost-effectiveness, budget impact, health-related quality of life (HRQoL) of the infant, HRQoL of the parents/caregivers, and parent/caregiver satisfaction with the treatment protocol. Discussion The outcomes of this randomized controlled trial will contribute to improving current care-as-usual for infants with centered DDH. Trial registration Dutch Trial Register, NL9714, registered September 6, 2021. https://clinicaltrialregister.nl/en/trial/29596

Claviceptaceous endophytic fungi in the genus Epichloë mostly form a symbiotic relationship with cool-season grasses. Epichloë spp. are capable of producing bioactive alkaloids such as peramines, lolines, ergot alkaloids, and indole-diterpenes, which protect the host plant from herbivory by animals, insects, and nematodes. The host also benefits from enhanced tolerance to abiotic stresses, such as salt, drought, waterlogging, cold, heavy metals, and low nitrogen stress. The bioactive alkaloids produced can have both direct and indirect effects towards plant parasitic nematodes. Direct interaction with nematodes’ motile stages can cause paralysis (nematostatic effect) or death (nematicidal effect). Indirectly, the metabolites may induce host immunity which inhibits feeding and subsequent nematode development. This review highlights the different mechanisms through which this interaction and the metabolites produced have been explored in the suppression of plant parasitic nematodes and also how the specific interactions between different grass genotypes and endophyte strains result in variable suppression of different nematode species. An understanding of the different grass–endophyte interactions and their successes and failures in suppressing various nematode species is essential to enable the proper selection of grass–endophyte combinations to identify the alkaloids produced, concentrations required, and determine which nematodes are sensitive to which specific alkaloids.

Abstract Ayahuasca is a psychedelic plant brew originating from the Amazon rainforest. It is formed from two basic components, the Banisteriopsis caapi vine and a plant containing the potent psychedelic dimethyltryptamine (DMT), usually Psychotria viridis. Here we review the history of ayahuasca and describe recent work on its pharmacology, phenomenological responses, and clinical applications. There has been a significant increase in interest in ayahuasca since the turn of the millennium. Anecdotal evidence varies significantly, ranging from evangelical accounts to horror stories involving physical and psychological harm. The effects of the brew on personality and mental health outcomes are discussed in this review. Furthermore, phenomenological analyses of the ayahuasca experience are explored. Ayahuasca is a promising psychedelic agent that warrants greater empirical attention regarding its basic neurochemical mechanisms of action and potential therapeutic application.

IntroductionSmall Island Developing States have disproportionately high food insecurity rates, related to complex challenges and vulnerabilities. The COVID-19 pandemic highlighted that within these settings, crises often overlap. We aimed to assess the impact of the concurrent COVID-19 pandemic and volcanic eruption on food production and security in St. Vincent and the Grenadines (SVG).MethodsAn interpretive mixed-methods study was conducted among a convenience sample of consenting adults ≥18 years from 100 households in SVG through a cross-sectional survey and participant interviews (10 households) between September 2021 and March 2022. Food insecurity prevalence over the past year was assessed using the Food Insecurity Experience Scale (FIES; Rasch modeling) and impacts to livelihoods from the pandemic and volcanic eruption was assessed using an adapted Caribbean COVID-19 Food Security and Livelihoods Impact Survey (Caribbean COVID-19 FS&L Survey). Data were analyzed using logistic regression.ResultsDuring the pandemic, 59% of the participants reported decreased income, 63% had no access to markets, 81% had no access to food aid; 34% of the participants had a change in food sources, and 81% reported that food production was negatively impacted by the volcanic eruptions, of which 68% reported decreased food production. The interviews highlighted that access to markets were restricted by fear of leaving home and contracting the COVID-19 virus, and participants who received food aid stated that the number of items were not sufficient for larger families. Almost half of the participants were severely food insecure [48% (95% C.I. 31.2,57.8)]; almost two thirds were moderately to severely food insecure [64% (95% C.I. 50.0, 74.2)]; mean FIES score 5.31 (95% C.I. 5.0,5.6). After adjusting for gender, age, education, and household size, moderate to severe food insecurity was associated with no access to food aid during the pandemic and post-eruptions (odds ratio 3.7; 95% confidence interval 1.5, 9.1; p = 0.004).ConclusionFood insecurity rates were high during the COVID-19 pandemic, exacerbated by volcanic eruptions and insufficient access to food aid. Our results suggest the need for the development of strategies and interventions aimed at increasing the resilience of food systems to mitigate the effects of future disasters.

Objective To determine the magnitude of any excess risk of mortality and hospitalisation due to COVID-19 infection in patients with congenital heart disease (CHD) in the UK healthcare system.Methods Matched case–control study within the Clinical Practice Research Datalink study of anonymised general practice records in the National Health Service in England. Patients with CHD were stratified for disease severity according to the European Society of Cardiology guidelines. Presence of a positive COVID-19 test, hospitalisation with a diagnosis of COVID-19 and COVID-19-related mortality were compared in case and control groups.Results 86 441 patients with CHD and 335 839 controls were studied. Of patients with a positive COVID-19 test, patients with CHD were more likely than controls to be hospitalised (22.4% vs 14.5%; OR=1.77 (95% CI 1.60 to 1.96); p=2.11e−28) and suffer COVID-19-related death (6.1% vs 3.8%; OR=1.60 (95% CI 1.35 to 1.89); p=7.00e−08). The excess risk of COVID-19 hospitalisation and death rose with increasing physiological severity of CHD (presence of pulmonary vascular disease and/or cyanosis), rather than anatomical complexity.Conclusions In this study of the COVID-19 pandemic experience, using population health records in over 86000 patients with CHD in England, patients with CHD with COVID-19 were at around 50–75% higher risk of hospitalisation and mortality compared with matched controls with COVID-19. We provide the first primary care-derived estimates for COVID-19 hospitalisation and case-fatality rates in patients with CHD. Some factors predictive of worse COVID-19 outcome in general populations (such as non-white ethnic group), and other CHD-specific comorbidities (such as pulmonary hypertension), influenced outcomes among patients with CHD.

Abstract Climate plays a major role in determining where species occur, and when they are active throughout the year. In the face of a changing climate, many species are shifting their ranges poleward. Many species are also shifting their emergence phenology. Wild bees in Great Britain are susceptible to changes in climatic conditions but little is known about historic or potential future spatio‐temporal trends of many species. This study utilized a sliding window approach to assess the impacts of climate on bee emergence dates, estimating the best temperature window for predicting emergence dates for 88 species of wild bees. Using a ‘middle‐of‐the‐road’ (RCP 4.5) and ‘worst‐case’ (RCP 8.5) climate scenario for the period 2070–2079, predictions of future emergence dates were made. In general, the best predicting climate window occurred in the 0–3 months preceding emergence. Across the 40 species that showed a shift in emergence dates in response to a climate window, the mean advance was 13.4 days under RCP 4.5 and 24.9 days under RCP 8.5. Species distribution models (SDMs) were used to predict suitable climate envelopes under historic (1980–1989), current (2010–2019) and future (2070–2079 under RCP 4.5 and RCP 8.5 scenarios) climate conditions. These models predict that the climate envelope for 92% of studied species has increased since the 1980s, and for 97% and 93% of species under RCP 4.5 and RCP 8.5 respectively, this is predicted to continue, due to extension of the northern range boundary. While any range changes will be moderated by habitat availability, it highlights that Great Britain will likely experience northward shifts of bee populations in the future. By combining spatial and temporal trends, this work provides an important step towards informing conservation measures suitable for future climates, directing how interventions can be provided in the right place at the right time.

Most living reptile diversity is concentrated in Squamata (lizards, including snakes), which have poorly known origins in space and time. Recently, †Cryptovaranoides microlanius from the Late Triassic of the United Kingdom was described as the oldest crown squamate. If true, this result would push back the origin of all major lizard clades by 30–65 Myr and suggest that divergence times for reptile clades estimated using genomic and morphological data are grossly inaccurate. Here, we use computed tomography scans and expanded phylogenetic datasets to re-evaluate the phylogenetic affinities of †Cryptovaranoides and other putative early squamates. We robustly reject the crown squamate affinities of †Cryptovaranoides, and instead resolve †Cryptovaranoides as a potential member of the bird and crocodylian total clade, Archosauromorpha. Bayesian total evidence dating supports a Jurassic origin of crown squamates, not Triassic as recently suggested. We highlight how features traditionally linked to lepidosaurs are in fact widespread across Triassic reptiles. Our study reaffirms the importance of critically choosing and constructing morphological datasets and appropriate taxon sampling to test the phylogenetic affinities of problematic fossils and calibrate the Tree of Life.

Abstract Background Interruption in Treatment (IIT) is a challenge in HIV care and treatment programs in sub- Saharan Africa. High IIT among HIV adolescents has both individual and potential public health consequences including discontinuation of treatment, increased HIV transmission and risk of death. In this era of test and treat policy it is important to ensure that patients remain connected to HIV clinics to enable achieve UNAIDS 95-95-95 targets timely. This study aimed to assess risk factors for IIT among HIV-positive adolescence in Tanzania. Methods We conducted retrospective longitudinal cohort study using secondary data of adolescent patients enrolled in care and treatment clinics in Tanga from October 2018 to December 2020. We defined Interuption in Treatment as missing clinic visits for 90 consecutive days after the last scheduled appointment date on anti-retroviral therapy (ART). Cox proportional hazard regression models were employed to identify risk factors of the outcome variable. Results Among 2,084 adolescents of age between 15 and 19 years were followed for two years, whereby 546 (26.2%) had interrupted treatment. The median age of the participants was 14.6 years (interquartile range, IQR: 12.6–16.6 years), with age between 15 and 19 years, male sex, with advanced HIV disease and were not on Dolutegravir (DTG) related regimens were associated with interruption in treatment; (Hazard ratio (HR) 1.43, 95% CI: 1.23–1.66, p

Abstract Gangliogliomas are brain tumors composed of neuron-like and macroglia-like components that occur in children and young adults. Gangliogliomas are often characterized by a rare population of immature astrocyte-appearing cells expressing CD34, a marker expressed in the neuroectoderm (neural precursor cells) during embryogenesis. New insights are needed to refine tumor classification and to identify therapeutic approaches. We evaluated five gangliogliomas with single nucleus RNA-seq, cellular indexing of transcriptomes and epitopes by sequencing, and/or spatially-resolved RNA-seq. We uncovered a population of CD34+ neoplastic cells with mixed neuroectodermal, immature astrocyte, and neuronal markers. Gene regulatory network interrogation in these neuroectoderm-like cells revealed control of transcriptional programming by TCF7L2/MEIS1-PAX6 and SOX2, similar to that found during neuroectodermal/neural development. Developmental trajectory analyses place neuroectoderm-like tumor cells as precursor cells that give rise to neuron-like and macroglia-like neoplastic cells. Spatially-resolved transcriptomics revealed a neuroectoderm-like tumor cell niche with relative lack of vascular and immune cells. We used these high resolution results to deconvolute clinically-annotated transcriptomic data, confirming that CD34+ cell-associated gene programs associate with gangliogliomas compared to other glial brain tumors. Together, these deep transcriptomic approaches characterized a ganglioglioma cellular hierarchy—confirming CD34+ neuroectoderm-like tumor precursor cells, controlling transcription programs, cell signaling, and associated immune cell states. These findings may guide tumor classification, diagnosis, prognostication, and therapeutic investigations.

Scientists have long sought a technology to humanely control populations of damaging invasive pests in a species-specific manner. Gene drive technology could see this become a reality. This review charts the twists and turns on the road to developing gene drives in vertebrates. We focus on rodents, as these will likely be the first targets, and trace the journey from the early understanding of selfish genetic elements to engineering gene drives in mice; before discussing future research focuses and the crucial role that public perception and governance will play in the application of this technology. The realisation of robust gene drive strategies in vertebrate pests has the potential to revolutionise biocontrol.

Animals must sense their surroundings and be able to distinguish between relevant and irrelevant cues. An enticing area of research aims to uncover the mechanisms by which animals respond to chemical signals that constitute critical sensory input. In this review, we describe the principles of a model chemosensory system: the Drosophila larva. While distinct in many ways, larval behaviour is reminiscent of the dogmatic goals of life: to reach a stage of reproductive potential. It takes into account a number of distinct and identifiable parameters to ultimately provoke or modulate appropriate behavioural output. In this light, we describe current knowledge of chemosensory anatomy, genetic components, and the processing logic of chemical cues. We outline recent advancements and summarize the hypothesized neural circuits of sensory systems. Furthermore, we note yet-unanswered questions to create a basis for further investigation of molecular and systemic mechanisms of chemosensation in Drosophila and beyond.

Abstract Wild bees are declining, mainly due to the expansion of urban habitats that have led to land-use changes. Effects of urbanization on wild bee communities are still unclear, as shown by contrasting reports on their species and functional diversities in urban habitats. To address this current controversy, we built a large dataset, merging 16 surveys carried out in 3 countries of Western Europe during the past decades, and tested whether urbanization influences local wild bee taxonomic and functional community composition. These surveys encompassed a range of urbanization levels, that were quantified using two complementary metrics: the proportion of impervious surfaces and the human population density. Urban expansion, when measured as a proportion of impervious surfaces, but not as human population density, was significantly and negatively correlated with wild bee community species richness. Taxonomic dissimilarity of the bee community was independent of both urbanization metrics. However, occurrence rates of functional traits revealed significant differences between lightly and highly urbanized communities, for both urbanization metrics. With higher human population density, probabilities of occurrence of above-ground nesters, generalist and small species increased. With higher soil sealing, probabilities of occurrence of above-ground nesters, generalists and social bees increased as well. Overall, these results, based on a large European dataset, suggest that urbanization can have negative impacts on wild bee diversity. They further identify some traits favored in urban environments, showing that several wild bee species can thrive in cities.

Abstract Adults with congenital heart disease (CHD) face increased risk of various comorbid diseases. Previous work on lung dysfunction in this population has mainly focused on restrictive lung disease, in patients with severe CHD phenotypes. We examined the association of mild CHD with chronic obstructive pulmonary disease (COPD) in the UK Biobank (UKB). Electronic health records (EHR) were used to identify 3385 CHD cases and 479,765 healthy controls in UKB, before performing a case–control analysis over a 20-year study period for a total of > 9.5 M person-years of follow-up. Our analysis showed that UKB participants with CHD are at substantially greater risk of developing COPD than healthy controls (8.7% vs 3.1% prevalence, unadjusted OR 2.98, 95% CI 2.63, 3.36, P = 1.40e−53). Slightly increased rates of smoking were observed amongst CHD cases, however the association with COPD was shown to be robust to adjustment for smoking and other factors known to modulate COPD risk within a multivariable-adjusted Cox regression framework (fully adjusted HR 2.21, 95% CI 1.97, 2.48, P = 5.5e−41). Care for adults with CHD should aim to mitigate their increased risk of COPD, possibly via increased smoking cessation support.