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Abstract Next-generation T-cell-directed vaccines for COVID-19 focus on establishing lasting T-cell immunity against current and emerging SARS-CoV-2 variants. Precise identification of conserved T-cell epitopes is critical for designing effective vaccines. Here we introduce a comprehensive computational framework incorporating a machine learning algorithm—MHCvalidator—to enhance mass spectrometry-based immunopeptidomics sensitivity. MHCvalidator identifies unique T-cell epitopes presented by the B7 supertype, including an epitope from a + 1-frameshift in a truncated Spike antigen, supported by ribosome profiling. Analysis of 100,512 COVID-19 patient proteomes shows Spike antigen truncation in 0.85% of cases, revealing frameshifted viral antigens at the population level. Our EpiTrack pipeline tracks global mutations of MHCvalidator-identified CD8 + T-cell epitopes from the BNT162b4 vaccine. While most vaccine epitopes remain globally conserved, an immunodominant A*01-associated epitope mutates in Delta and Omicron variants. This work highlights SARS-CoV-2 antigenic features and emphasizes the importance of continuous adaptation in T-cell vaccine development.

We identified a novel human circovirus in an immunocompromised 66-year-old woman with sudden onset of self-limiting hepatitis. We detected human circovirus 1 (HCirV-1) transcripts in hepatocytes and the HCirV-1 genome long-term in the patient’s blood, stool, and urine. HCirV-1 is an emerging human pathogen that persists in susceptible patients.

Invasive plant pathogenic fungi have a global impact, with devastating economic and environmental effects on crops and forests. Biosurveillance, a critical component of threat mitigation, requires risk prediction based on fungal lifestyles and traits. Recent studies have revealed distinct genomic patterns associated with specific groups of plant pathogenic fungi. We sought to establish whether these phytopathogenic genomic patterns hold across diverse taxonomic and ecological groups from the Ascomycota and Basidiomycota, and furthermore, if those patterns can be used in a predictive capacity for biosurveillance. Using a supervised machine learning approach that integrates phylogenetic and genomic data, we analyzed 387 fungal genomes to test a proof-of-concept for the use of genomic signatures in predicting fungal phytopathogenic lifestyles and traits during biosurveillance activities. Our machine learning feature sets were derived from genome annotation data of carbohydrate-active enzymes (CAZymes), peptidases, secondary metabolite clusters (SMCs), transporters, and transcription factors. We found that machine learning could successfully predict fungal lifestyles and traits across taxonomic groups, with the best predictive performance coming from feature sets comprising CAZyme, peptidase, and SMC data. While phylogeny was an important component in most predictions, the inclusion of genomic data improved prediction performance for every lifestyle and trait tested. Plant pathogenicity was one of the best-predicted traits, showing the promise of predictive genomics for biosurveillance applications. Furthermore, our machine learning approach revealed expansions in the number of genes from specific CAZyme and peptidase families in the genomes of plant pathogens compared to non-phytopathogenic genomes (saprotrophs, endo- and ectomycorrhizal fungi). Such genomic feature profiles give insight into the evolution of fungal phytopathogenicity and could be useful to predict the risks of unknown fungi in future biosurveillance activities.

Abstract Prematurity is associated with lower exercise capacity, which relies on the integrity of the cardiovascular, pulmonary, and skeletal muscle systems. Our animal model mimicking prematurity-associated conditions showed altered muscle composition and atrophy in adulthood. This study aimed to compare muscle composition and strength in adults born preterm versus full-term controls. This observational cohort study recruited 55 adults born preterm, ≤ 29 weeks’ of gestation and 53 full-term controls who underwent musculoskeletal ultrasound imaging to assess morphology of the rectus femoris at rest and during a maximal voluntary contraction. Maximal voluntary contraction of the hands and legs were measured by manual dynamometry. In adults born preterm, there was lower muscle strength (handgrip: − 4.8 kg, 95% CI − 9.1, − 0.6; knee extensor: − 44.6 N/m, 95% CI − 63.4, − 25.8) and smaller muscle area (− 130 mm2, 95% CI − 207, − 53), which was more pronounced with a history of bronchopulmonary dysplasia. Muscle stiffness was increased in the preterm versus term group (0.4 m/s, 95% CI 0.04, 0.7). Prematurity is associated with alterations in skeletal muscle composition, area, and function in adulthood. These findings highlight the necessity to implement preventive and/or curative approaches to improve muscle development and function following preterm birth to enhance overall health in this population.

Abstract Background Marginal zone lymphomas of mucosa-associated lymphatic tissues (MZL of MALT) are a group of indolent B-cell neoplasms, which are thought to arise from chronic antigenic stimulation of B-cells either due to underlying chronic infection or autoimmune disease. Little is known about potential causative pathogens in pulmonary MZL (PMZL), although some data suggests a potential role of Achromobacter (A.) xylosoxidans. Methods An index case of chronic pulmonary colonisation with Tropheryma (T.) whipplei and subsequent development of PMZL was identified by T. whipplei specific PCR and metagenomic next genome sequencing (mNGS). This case prompted a retrospectively conducted analysis of T. whipplei-specific PCRs in lung tissue from PMZL patients (n = 22), other pulmonary lymphomas, and normal controls. Positive results were confirmed by mNGS. A systematic search for T. whipplei and A. xylosoxidans in our in-house mNGS dataset comprising autopsy lungs, lung biopsies and lung resection specimens (n = 181) was subsequently performed. Results A 69-year-old patient presented with weight loss and persistent pulmonary consolidation. Subsequent mNGS analysis detected T. whipplei in the resected lung specimen. An antibiotic regimen eventually eliminated the bacterium. However, the consolidation persisted, and the diagnosis of PMZL was made in a second lung resection specimen. A second case of T. whipplei-associated PMZL was subsequently detected in the retrospectively analysed PMZL cohort. Both cases showed comparatively few mutations and no mutations in genes encoding for NF-κB pathway components, suggesting that T. whipplei infection may substitute for mutations in these PMZL. None of the samples in our in-house dataset tested positive for T. whipplei. In contrast, A. xylosoxidans was frequently found in both autopsy lungs and lung biopsy / resection specimens that were not affected by PMZL (> 50%). Conclusions Our data suggests that T. whipplei colonisation of lungs may trigger PMZL as a potential driver. Systematic analyses with larger cohorts should be conducted to further support this hypothesis. The frequent detection of A. xylosoxidans in lung tissue suggests that it is a common component of the pulmonary microbiome and therefore less likely to trigger lymphomas.

This study aims to validate a predictive model of school counselors' burnout from occupational activities through "occupational identity suffering" (OIS). OIS is defined as the psyche battle between the individual's need for professional accomplishment and the inability to recognize one's profession in daily work duties. Tested among 269 guidance counselors working in school settings (Quebec, Canada), the model proposes that OIS is positively predicted by administrative work and negatively predicted by guidance and counseling activities. In turn, OIS should positively predict burnout. Results from structural equation modeling mostly support the model. Implications for prevention of school counselors' burnout are discussed.

ABSTRACT Biological invasions pose significant threats to ecological and economic stability, with invasive pests like the Asian longhorned beetle (Anoplophora glabripennis Motschulsky, ALB) causing substantial damage to forest ecosystems. Effective pest management relies on comprehensive knowledge of the insect's biology and invasion history. This study uses genomics to address these knowledge gaps and inform existing biosurveillance frameworks. We used 2768 genome‐wide single nucleotide polymorphisms to compare invasive A. glabripennis populations in North America, using genomic variation to trace their sources of invasion and spread patterns, thereby refining our understanding of this species' invasion history. We found that most North American A. glabripennis infestations were distinct, resulting from multiple independent introductions from the native range. Following their introduction, all invasive populations experienced a genetic bottleneck which was followed by a population expansion, with a few also showing secondary spread to satellite infestations. Our study provides a foundation for a genome‐based biosurveillance tool that can be used to clarify the origin of intercepted individuals, allowing regulatory agencies to strengthen biosecurity measures against this invasive beetle.

Fulvia fulva and Dothistroma septosporum are closely related apoplastic pathogens with similar lifestyles but different hosts: F. fulva is a pathogen of tomato, whilst D. septosporum is a pathogen of pine trees. In 2012, the first genome sequences of these pathogens were published, with F. fulva and D. septosporum having highly fragmented and near-complete assemblies, respectively. Since then, significant advances have been made in unravelling their genome architectures. For instance, the genome of F. fulva has now been assembled into 14 chromosomes, 13 of which have synteny with the 14 chromosomes of D. septosporum, suggesting these pathogens are even more closely related than originally thought. Considerable advances have also been made in the identification and functional characterization of virulence factors (e.g., effector proteins and secondary metabolites) from these pathogens, thereby providing new insights into how they promote host colonization or activate plant defence responses. For example, it has now been established that effector proteins from both F. fulva and D. septosporum interact with cell-surface immune receptors and co-receptors to activate the plant immune system. Progress has also been made in understanding how F. fulva and D. septosporum have evolved with their host plants, whilst intensive research into pandemics of Dothistroma needle blight in the Northern Hemisphere has shed light on the origins, migration, and genetic diversity of the global D. septosporum population. In this review, we specifically summarize advances made in our understanding of the F. fulva-tomato and D. septosporum-pine pathosystems over the last 10 years.

Abstract Live-Attenuated Vaccines (LAVs) stimulate robust mucosal and cellular responses and have the potential to protect against Respiratory Syncytial Virus (RSV) and Human Metapneumovirus (HMPV), the main etiologic agents of viral bronchiolitis and pneumonia in children. We inserted the RSV-F gene into an HMPV-based LAV (Metavac®) we previously validated for the protection of mice against HMPV challenge, and rescued a replicative recombinant virus (Metavac®-RSV), exposing both RSV- and HMPV-F proteins at the virion surface and expressing them in reconstructed human airway epithelium models. When administered to BALB/c mice by the intranasal route, bivalent Metavac®-RSV demonstrated its capacity to replicate with reduced lung inflammatory score and to protect against both RSV and lethal HMPV challenges in vaccinated mice while inducing strong IgG and broad RSV and HMPV neutralizing antibody responses. Altogether, our results showed the versatility of the Metavac® platform and suggested that Metavac®-RSV is a promising mucosal bivalent LAV candidate to prevent pneumovirus-induced diseases.

Abstract Three dimensional sensing is essential in order that machines may operate in and interact with complex dynamic environments. Solid-state beam scanning devices are seen as being key to achieving required system specifications in terms of sensing range, resolution, refresh rate and cost. Integrated optical phased arrays fabricated on silicon wafers are a potential solution, but demonstrated devices with system-level performance currently rely on expensive widely tunable source lasers. Here, we combine silicon nitride photonics and micro-electromechanical system technologies, demonstrating the integration of an active photonic beam-steering circuit into a piezoelectric actuated micro cantilever. An optical phased array, operating at a wavelength of 905 nm, provides output beam scanning over a range of 17° in one dimension, while the inclination of the entire circuit and consequently the angle of the output beam in a second dimension can be independently modified over a range of up to 40° using the piezoelectric actuator.

Abstract Background Flight can drastically enhance dispersal capacity and is a key trait defining the potential of exotic insect species to spread and invade new habitats. The phytophagous European spongy moths (ESM, Lymantria dispar dispar) and Asian spongy moths (ASM; a multi–species group represented here by L. d. asiatica and L. d. japonica), are globally invasive species that vary in adult female flight capability—female ASM are typically flight capable, whereas female ESM are typically flightless. Genetic markers of flight capability would supply a powerful tool for flight profiling of these species at any intercepted life stage. To assess the functional complexity of spongy moth flight and to identify potential markers of flight capability, we used multiple genetic approaches aimed at capturing complementary signals of putative flight–relevant genetic divergence between ESM and ASM: reduced representation genome–wide association studies, whole genome sequence comparisons, and developmental transcriptomics. We then judged the candidacy of flight–associated genes through functional analyses aimed at addressing the proximate demands of flight and salient features of the ecological context of spongy moth flight evolution. Results Candidate gene sets were typically non–overlapping across different genetic approaches, with only nine gene annotations shared between any pair of approaches. We detected an array of flight–relevant functional themes across gene sets that collectively suggest divergence in flight capability between European and Asian spongy moth lineages has coincided with evolutionary differentiation in multiple aspects of flight development, execution, and surrounding life history. Overall, our results indicate that spongy moth flight evolution has shaped or been influenced by a large and functionally broad network of traits. Conclusions Our study identified a suite of flight–associated genes in spongy moths suited to exploration of the genetic architecture and evolution of flight, or validation for flight profiling purposes. This work illustrates how complementary genetic approaches combined with phenotypically targeted functional analyses can help to characterize genetically complex traits.

Abstract Background Nine male and eight female calves born to a Normande artificial insemination bull named “Ly” were referred to the French National Observatory of Bovine Abnormalities for multiple fractures, shortened gestation, and stillbirth or perinatal mortality. Results Using Illumina BovineSNP50 array genotypes from affected calves and 84 half-sib controls, the associated locus was mapped to a 6.5-Mb interval on chromosome 19, assuming autosomal inheritance with germline mosaicism. Subsequent comparison of the whole-genome sequences of one case and 5116 control genomes, followed by genotyping in the affected pedigree, identified a de novo missense substitution within the NC1 domain of the COL1A1 gene (Chr19 g.36,473,965G > A; p.D1412N) as unique candidate variant. Interestingly, the affected residue was completely conserved among 243 vertebrate orthologs, and the same substitution in humans has been reported to cause type II osteogenesis imperfecta (OI), a connective tissue disorder that is characterized primarily by bone deformity and fragility. Moreover, three COL1A1 mutations have been described to cause the same syndrome in cattle. Necropsy, computed tomography, radiology, and histology confirmed the diagnosis of type II OI, further supporting the causality of this variant. In addition, a detailed analysis of gestation length and perinatal mortality in 1387 offspring of Ly and more than 160,000 progeny of 63 control bulls allowed us to statistically confirm in a large pedigree the association between type II OI and preterm delivery, which is probably due to premature rupture of fetal membranes and has been reported in several isolated cases of type II OI in humans and cattle. Finally, analysis of perinatal mortality rates and segregation distortion supported a low level of germ cell mosaicism in Ly, with an estimate of 4.5% to 7.7% of mutant sperm and thus 63 to 107 affected calves born. These numbers contrast with the 17 cases reported and raise concerns about the underreporting of congenital defects to heredo-surveillance platforms, even for textbook genetic syndromes. Conclusions In conclusion, we describe a large animal model for a recurrent substitution in COL1A1 that is responsible for type II OI in humans. More generally, this study highlights the utility of such datasets and large half-sib families available in livestock species to characterize sporadic genetic defects.

ABSTRACT The pale cyst nematode, Globodera pallida, is a pest that poses a significant threat to potato crops worldwide. The most effective chemical nematicides are toxic to nontarget organisms and are now banned. Alternative control methods are therefore required. Crop rotation and biological control methods have limitations for effectively managing nematodes. The use of genetically resistant cultivars is a promising alternative, but nematode populations evolve, and virulent mutants can break resistance after just a few years. Masculinizing resistances, preventing avirulent nematodes from producing females, might be more durable than blocking resistances, preventing infection. Our demo‐genetic model, tracking both nematode population densities and virulence allele frequencies, shows that virulence against masculinizing resistance may not be fixed in the pest population under realistic agricultural conditions. Avirulence may persist despite the uniform use of resistance. This is because avirulent male nematodes may transmit avirulent alleles to their progeny by mating with virulent females. Additionally, because avirulent nematodes do not produce females themselves, they weaken the reproductive rate of the nematode population, leading to a reduction in its density by at least 20%. This avirulence load can even lead to the collapse of the nematode population in theory. Overall, our model showed that combining masculinizing resistance, rotation, and biocontrol may achieve durable suppression of G. pallida in a reasonable time frame. Our work is supported by an online interactive interface allowing users (i.e., growers, plant health authorities, researchers) to test their own control combinations.

Objectives To assess the seroprevalence of infection-acquired SARS-CoV-2 and the mental health of school/daycare staff in the months after reopening of schools in Montreal, Quebec (Canada) in the Fall of 2020 and whether these varied by school and participant characteristics.Design A cross-sectional design based on a convenience sample of schools/daycares and staff was used as the originally planned longitudinal design was no longer feasible due to obstacles in recruitment, for example, teacher’s strike.Setting Forty-nine schools/daycares in four Montreal neighbourhoods from March to October 2021.Participants Three-hundred and sixty-two participants completed both questionnaires and serology tests.Primary and secondary outcome measures SARS-CoV-2 seroprevalence and prevalence of anxiety, depression, resilience and burnout/emotional exhaustion.Results The seroprevalence estimate made representative to the Quebec population of educators was 8.6% (95% CI 5.2 to 13.0). The adjusted seroprevalence in high school was 20% that of elementary school (aRR=0.20, 95% CI 0.07 to 0.58). Thirty per cent of seropositive staff were exposed to a household member with confirmed COVID-19. Prevalence of high emotional exhaustion/burnout was 35%, 44% and 53% in daycare, elementary school and high school staff, respectively. However, moderate/severe anxiety and depression and low resilience did not exceed 18%. After adjusting for confounders, being very afraid of catching COVID-19 at school was associated with moderate–severe anxiety, moderate–severe depression and high emotional exhaustion (aRR=4.4, 95% CI 2.2 to 8.9; aRR=2.8, 95% CI 1.5 to 5.4; aRR=2.2, 95% CI 1.6 to 3.0, respectively).Conclusion The seroprevalence, anxiety and depression among school/daycare staff were comparable to the reported levels in the adult population of Quebec. The prevalence of emotional exhaustion/burnout was high across all school levels and exceeding the average across all occupations in the USA and in teachers in Germany.

Background: Nausea and vomiting is a common and distressing presenting complaint in Emergency Departments (EDs). There is no definite evidence to support the superiority of any anti-emetic therapy over another, or over placebo. Identification of an effective anti-emetic therapy in the ED setting with minimal side effects would be of great benefit. Isopropyl alcohol inhalation has been reported to be an effective treatment for post-operative nausea and vomiting, with no reported adverse events. The objective of this study is to determine if nasally inhaled isopropyl alcohol swabs are effective in alleviating nausea and/or vomiting in patients presenting to the ED with a chief complaint of nausea and/or vomiting. Methods: We will conduct a randomized, controlled, multicenter trial with three subject arms: 1) nasally inhaled isopropyl alcohol swabs every 10 minutes for a total of one hour, 2) nasally inhaled isopropyl alcohol swabs every 20 minutes for a total of one hour, or 3) no intervention. 135 participants ≥18 years old and presenting to the ED with a chief complaint of nausea and/or vomiting with a level of 3 or greater on a verbal numeric rating scale (NRS) will be recruited for a duration of two hours. The primary outcome measure is the mean reduction in nausea scores comparing the pre-intervention score to the lowest post-intervention nausea score. The secondary outcome measures will be participant satisfaction scores using a verbal NRS, receipt of any rescue anti-emetic medications, ED length of stay, and participant disposition (admission or discharge home). Discussion: This study will determine the efficacy of inhaled isopropyl alcohol swabs by determining the optimal dosing frequency achieving adequate anti-emetic action. This has the potential to guide future triage protocols to incorporate this therapy to provide earlier symptomatic relief to patients, and also has the potential to prevent morbidity suffered by patients in the emergency department and improving patient satisfaction and efficiently use in-patient resources. We strongly suspect that once this study is performed, it will be useful for ED physicians in treating nausea and vomiting in the ED.

In this article, we consider the role of ocean literacy in coastal communities as an approach that fosters relevant, community-based learning. We also propose solutions to challenges facing human-ocean relationships by cultivating common understanding and collective action. We present four examples of community-based ocean literacy in Mi'kma'ki/Atlantic Canada demonstrate how intersectional approaches to ocean literacy that are context-specific and responsive to community priorities can foster healthier human-ocean relationships: (1) Oceans Week Halifax's organization of community events to strengthen human-ocean relationships; (2) the Apoqnmatulti'k (Mi'kmaw: we help each other) project's partnerships between Mi'kmaq and local knowledge holders and academia; (3) Fishing For Success's (Newfoundland and Labrador) inclusive approaches to connecting marginalized communities to the ocean; and (4) the Co-Existing With North Atlantic Right Whale Project's protection of whales without jeopardizing coastal community livelihoods. Without denying there are barriers to bridging community learning with formal education, we focus on opportunities for collaborations and the importance of ocean optimism in guiding these urgently needed efforts to benefit future community-based, ocean-focused, and solutions-orientated initiatives.

In recent years, the use of inspection drones has become increasingly popular for high-voltage electric cable inspections due to their efficiency, cost-effectiveness, and ability to access hard-to-reach areas. However, safely landing drones on power lines, especially under windy conditions, remains a significant challenge. This study introduces a semi-autonomous control scheme for landing on an electrical line with the NADILE drone (an experimental drone based on original LineDrone key features for inspection of power lines) and assesses the operating envelope under various wind conditions. A Monte Carlo method is employed to analyze the success probability of landing given initial drone states. The system’s performance is assessed by testing two landing strategies, adjusting controller parameters, and considering four different levels of wind intensity. The results show that a two-stage landing strategy offers higher probabilities of landing success and gives insight regarding the best controller parameters and the maximum wind level for which the system is robust. Finally, an experimental demonstration of the system landing autonomously on a power line is presented.

The United Nations’ Declaration on the Rights of Indigenous Peoples (UNDRIP) recognized Indigenous rights to self-determination. How these rights can be realized in territories governed by settler-states remains unclear. For fisheries, the need to understand processes that support Indigenous self-determination has gained urgency due to government commitments and investor interest in developing ocean and coastal resources, or Blue Economies, amid rapid climatic changes. Here, we explored Indigenous groups’ fishery development experiences following two approaches to reconciling Indigenous fishing rights. In New Zealand, we examined Māori groups’ experiences following the 1992 Treaty of Waitangi (Fisheries Claims) Settlement Act. The Settlement granted Māori iwi (tribes) rights to self-govern non-commercial harvests, restrict fishing pressure in state-approved customary fishing areas, and participate in state-run systems for commercial fisheries management. In Canada, we investigated Indigenous fishery development initiatives following the Supreme Court of Canada’s 1999 ruling R. v. Marshall. Marshall reaffirmed Treaty-protected rights to harvest and trade fish, held by Mi’kmaq, Wolastoqey, and Peskotomuhkati Peoples, to support a “moderate livelihood.” We document how, in both cases, Indigenous groups’ self-determination remains constrained by actions from state regulatory and enforcement agencies that govern market access, other resource users’ activities, and processes for collecting and sharing information about fish populations. Indigenous groups’ experiences highlight that: 1) reallocations of harvest rights, on their own, are an insufficient means to redistribute access to benefits from fisheries; 2) the constraints Indigenous families have experienced in their attempts to develop small-scale fishing operations correspond to settler-state policies and cannot be addressed solely through changes to Indigenous leaders’ management decisions; and 3) polycentricity in governance regimes can pose problems for Indigenous self-determination, when citizens with political authority resist efforts to support Indigenous fisheries. To address these challenges, we call for legal reforms that require settler-state governments to support Indigenous self-determination, to overcome the political risks politicians face when advocating for a non-majority group’s interests.

In oxidative phosphorylation, respiratory complex I serves as an entry point in the electron transport chain for electrons generated in catabolic processes in the form of NADH. An ancestral version of the complex, lacking the NADH-oxidising module, is encoded in a significant number of bacterial genomes. Amongst them is Desulfitobacterium hafniense, a strict anaerobe capable of conserving energy via organohalide respiration. This study investigates the role of the complex I-like enzyme in D. hafniense energy metabolism using rotenone as a specific complex I inhibitor under different growth conditions. The investigation revealed that the complex I-like enzyme was essential for growth with lactate and pyruvate but not in conditions involving H2 as an electron donor. In addition, a previously published proteomic dataset of strain DCB-2 was analysed to reveal the predominance of the complex under different growth conditions and to identify potential redox partners. This approach revealed seven candidates with expression patterns similar to Nuo homologues, suggesting the use of diverse electron sources. Based on these results, we propose a model where the complex I-like enzyme serves as an electron entry point into the respiratory chain for substrates delivering electrons within the cytoplasm, such as lactate or pyruvate, with ferredoxins shuttling electrons to the complex.

Une recherche-intervention-formation axée sur la médiation interculturelle en contexte scolaire mobilise, depuis 2019, un partenariat entre la Haute école pédagogique des cantons de Berne, du Jura et de Neuchâtel (HEP-BEJUNE, Suisse), l’INSPE-UFC et le Centre académique pour la scolarisation des élèves allophones arrivants et des enfants issus de familles itinérantes et de voyageurs (CASNAV) de l’académie de Besançon (France). Dans cet article, les acteurs impliqués mettront en dialogue le contexte d’émergence, les enjeux et les conditions de mise en place d’une formation à la médiation scolaire d’une part, le point de vue de participantes ainsi que le rôle de la recherche d’autre part. Enfin, le projet interfrontalier sera interrogé à l’aune des notions de distance, d’écart et de frontière.

Monitoring the air for airborne plant pathogens is an increasingly common method for the management of economically important plant diseases. In Alberta, Canada, several commodity clusters, including dry bean, canola, potato, and wheat, currently support air monitoring research programs for airborne pathogens of interest. In this study, we assessed the feasibility of monitoring for these, and more, plant fungal pathogens simultaneously using two different sampler types (cyclone versus rotation impaction) and by metabarcoding the ITS1 region using the Illumina sequencing platform. We collected air samples from four geographically distant sites across Alberta and monitored four crop types in southern Alberta. Overall, we found weak, but statistically significant, effects of geographic location and crop type on the aeromycobiota community composition. A few common taxa, such as Ramularia, Alternaria, and Epicoccum, constituted the vast majority of reads across all samples. Nevertheless, in each sample, we identified many plant pathogens of interest and organisms that previous research has found antagonistic to those pathogens, highlighting the utility of these approaches in understanding the pathobiome. In assessing the real-world implications of read counts, we discovered that they were only weakly correlated with spore counts quantified by qPCR. The two types of samplers collected different community profiles, reinforcing the importance of carefully considering which sampler type to use in monitoring programs. Taken together, our results show promise for the future of monitoring the air pathobiome, although much more work is required to understand the relationship of airborne communities to their in-field impact on disease development. [Figure: see text] Copyright © 2023 His Majesty the King in Right of Canada, as represented by the Minister of Agriculture and Agri-Food Canada. This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Abstract Invasive plant pathogenic fungi have a global impact, with devastating economic and environmental effects on crops and forests. Biosurveillance, a critical component of threat mitigation, requires risk prediction based on fungal lifestyles and traits. Recent studies have revealed distinct genomic patterns associated with specific groups of plant pathogenic fungi. We sought to establish whether these phytopathogenic genomic patterns hold across diverse taxonomic and ecological groups from the Ascomycota and Basidiomycota, and furthermore, if those patterns can be used in a predictive capacity for biosurveillance. Using a supervised machine learning approach that integrates phylogenetic and genomic data, we analyzed 387 fungal genomes to test a proof-of-concept for the use of genomic signatures in predicting fungal phytopathogenic lifestyles and traits during biosurveillance activities. Our machine learning feature sets were derived from genome annotation data of carbohydrate-active enzymes (CAZymes), peptidases, secondary metabolite clusters (SMCs), transporters, and transcription factors. We found that machine learning could successfully predict fungal lifestyles and traits across taxonomic groups, with the best predictive performance coming from feature sets comprising CAZyme, peptidase, and SMC data. While phylogeny was an important component in most predictions, the inclusion of genomic data improved prediction performance for every lifestyle and trait tested. Plant pathogenicity was one of the best-predicted traits, showing the promise of predictive genomics for biosurveillance applications. Furthermore, our machine learning approach revealed expansions in the number of genes from specific CAZyme and peptidase families in the genomes of plant pathogens compared to non-phytopathogenic genomes (saprotrophs, endo- and ectomycorrhizal fungi). Such genomic feature profiles give insight into the evolution of fungal phytopathogenicity and could be useful to predict the risks of unknown fungi in future biosurveillance activities.

Although secondary metabolites are typically associated with competitive or pathogenic interactions, the high bioactivity of endophytic fungi in the Xylariales, coupled with their abundance and broad host ranges spanning all lineages of land plants and lichens, suggests that enhanced secondary metabolism might facilitate symbioses with phylogenetically diverse hosts. Here, we examined secondary metabolite gene clusters (SMGCs) across 96 Xylariales genomes in two clades (Xylariaceae s.l. and Hypoxylaceae), including 88 newly sequenced genomes of endophytes and closely related saprotrophs and pathogens. We paired genomic data with extensive metadata on endophyte hosts and substrates, enabling us to examine genomic factors related to the breadth of symbiotic interactions and ecological roles. All genomes contain hyperabundant SMGCs; however, Xylariaceae have increased numbers of gene duplications, horizontal gene transfers (HGTs) and SMGCs. Enhanced metabolic diversity of endophytes is associated with a greater diversity of hosts and increased capacity for lignocellulose decomposition. Our results suggest that, as host and substrate generalists, Xylariaceae endophytes experience greater selection to diversify SMGCs compared with more ecologically specialised Hypoxylaceae species. Overall, our results provide new evidence that SMGCs may facilitate symbiosis with phylogenetically diverse hosts, highlighting the importance of microbial symbioses to drive fungal metabolic diversity.

Abstract The seismic hazard posed by submarine faults and the capacity of submarine earthquakes to trigger mass wasting are poorly understood because we lack detailed characterizations of coseismic ruptures at the seafloor. Here, we present comprehensive mapping of a seafloor rupture caused by the 2004 M w 6.3 Les Saintes earthquake on the Roseau normal fault in the Lesser Antilles. We report the visual characteristics, displacement profile, and note pronounced asymmetry of the rupture that bears similarities with well-studied subaerial normal fault ruptures. We also identify footwall-derived mass wasted debris that locally cover the coseismic rupture, and show that ground accelerations of 0.1–0.2 g can trigger submarine mass wasting events in well consolidated bedrock along unstable, over-steepened, scarps. Our study demonstrates the potential of underwater vehicles for detailed mapping of seafloor ruptures and hints at a key role for earthquakes in shaping submarine bedrock landscapes by triggering mass wasting events.

Since its emergence in the 1990s, the invasive pathogen Phytophthora ramorum has spread in Europe and the west coast of North America, causing sudden oak death in the United States and sudden larch death in the United Kingdom, resulting in the mortality or destruction of millions of trees. Due to its invasive nature, its damage potential, its wide host range, and its ability to disseminate via the plant trade, P. ramorum has been placed on quarantine lists worldwide. Rapid and reliable detection of the pathogen and identification of its lineages are crucial to limit spread and inform mitigation and eradication efforts. SODplex, a suite of new multiplex real-time PCR tools, was developed to streamline the detection and identification of P. ramorum. It offers four multiplexed assays covering different use cases. SODplex-base combines primers and probes for the sensitive and accurate detection of Phytophthora spp. and P. ramorum. SODplex-ITS and SODplex-mito offer a single-step identification of P. ramorum and the EU1, NA1, and NA2 lineages present in the United States and Canada. SODplex-lin targets each of the four P. ramorum lineages present in Europe and North America in a single reaction. The assays have high levels of accuracy and are robust to the use of different instruments, different operators, and different temperatures. The redundancy within the assays reduces the likelihood of false negatives and false positives. The SODplex assays presented here improve the toolbox available for the detection of P. ramorum and its lineages. [Figure: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

ABSTRACT: Objectives: To use serological testing to assess the pre-Omicron seroprevalence, seroconversion, and seroreversion of infection-induced SARS-CoV-2 antibodies in children and adolescents in Montréal, Canada. Design: This analysis is from a prospective cohort study of children aged 2-17 years (at baseline) that included blood spots for antibody detection. The serostatus of participants was determined by enzyme-linked immunosorbent assays using the receptor-binding domain from the spike protein and the nucleocapsid protein as antigens. We estimated seroprevalence, seroconversion rates, and the likelihood of seroreversion at 6 months and 1 year. Results: The baseline (October 2020 to April 2021) seroprevalence was 5.8% (95% confidence interval [CI] 4.8-7.1), which increased to 10.5% (May to September 2021) and 11.0% (November 2021 to March 2022) for the respective follow-ups (95% CI 8.6-12.7; 95% CI 8.8-13.5). The crude rate of seroconversion over the study period was 12.8 per 100 person-years (95% CI 11.0-14.7). The adjusted hazard rates of seroconversion by child characteristics showed higher rates in children who were female, whose parent identified as a racial or ethnic minority, and in households with incomes in the lowest tercile of our study population. The likelihood of remaining seropositive at 6 months was 68% (95% CI 60-77%) and dropped to 42% (95% CI 32-56%) at 1 year. Conclusion: Serological studies continue to provide valuable contributions for infection prevalence estimates and help us better understand the dynamics of antibody levels after infection.

Within-host spread of pathogens is an important process for the study of plant-pathogen interactions. However, the development of plant-pathogen lesions remains practically difficult to characterize beyond the common traits such as lesion area. Here, we address this question by combining image-based phenotyping with mathematical modelling. We consider the spread of Peyronellaea pinodes on pea stipules that were monitored daily with visible imaging. We assume that pathogen propagation on host-tissues can be described by the Fisher-KPP model where lesion spread depends on both a logistic growth and an homogeneous diffusion. Model parameters are estimated using a variational data assimilation approach on sets of registered images. This modelling framework is used to compare the spread of an aggressive isolate on two pea cultivars with contrasted levels of partial resistance. We show that the expected slower spread on the most resistant cultivar is actually due to a significantly lower diffusion coefficient. This study shows that combining imaging with spatial mechanistic models can offer a mean to disentangle some processes involved in host-pathogen interactions and further development may allow a better identification of quantitative traits thereafter used in genetics and ecological studies.

Mechanosensors are emerging players responding to hemodynamic and physical inputs. Their significance in the central nervous system remains relatively uncharted. Using human-derived brain specimens or cells and a pre-clinical model of mesio-temporal lobe epilepsy (MTLE), we examined how the mRNA levels of the mechanosensitive channel PIEZO1 adjust to disease-associated pro-inflammatory trajectories.In brain tissue micro-punches obtained from 18 drug-resistant MTLE patients, PIEZO1 expression positively correlated with pro-inflammatory biomarkers TNFα, IL-1β, and NF-kB in the epileptogenic hippocampus compared to the adjacent amygdala and temporal cortex tissues. In an experimental MTLE model, hippocampal Piezo1 and cytokine expression levels were increased post-status epilepticus (SE) and during epileptogenesis. Piezo1 expression positively correlated with Tnfα, Il1β, and Nf-kb in the hippocampal foci. Next, by combining RNAscope with immunohistochemistry, we identified Piezo1 in glio-vascular cells. Post-SE and during epileptogenesis, ameboid IBA1 microglia, hypertrophic GFAP astrocytes, and damaged NG2DsRed pericytes exhibited time-dependent patterns of increased Piezo1 expression. Digital droplet PCR analysis confirmed the Piezo1 trajectory in isolated hippocampal microvessels in the ipsi and contralateral hippocampi. The combined examinations performed in this model showed Piezo1 expression returning towards basal levels after the epileptogenesis-associated peak inflammation. From these associations, we next asked whether pro-inflammatory players directly regulate PIEZO1 expression. We used human-derived brain cells and confirmed that endothelium, astrocytes, and pericytes expressed PIEZO1. Exposure to human recombinant TNFα or IL1β upregulated NF-kB in all cells. Furthermore, TNFα induced PIEZO1 expression in a dose and time-dependent manner, primarily in astrocytes.This exploratory study describes a spatiotemporal dialogue between PIEZO1 brain cell-mechanobiology and neuro-inflammatory cell remodeling. The precise functional mechanisms regulating this interplay in disease conditions warrant further investigation.