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Abstract Human alveolar echinococcosis is increasingly documented in Alberta, Canada. Its causative agent, Echinococcus multilocularis (Em), can be transmitted to humans by infected dogs. We assessed the prevalence and associated risk factors for Em infections in domestic dogs in Calgary, Alberta, Canada. In this cross-sectional study that coupled collection and assessment of dog feces with a survey on potential risk factors, 13 of 696 (Bayesian true prevalence, 2.4%; 95% CrI: 1.3–4.0%) individual dogs’ feces collected during August and September 2012 were qPCR positive for Em. Sequencing two of these cases indicated that both were from the same Em European strain responsible for human infections in Alberta. Likelihood of intestinal Em was 5.6-times higher in hounds than other breeds, 4.6-times higher in dogs leashed at dog parks than those allowed off-leash, 3.1-times higher in dogs often kept in the backyard during spring and summer months than those rarely in the yard, and 3.3-times higher in dogs living in neighbourhoods bordering Bowmont park than those in other areas of Calgary. This situation warrants surveillance of dog infections as a preventative measure to reduce infections in North America.

Livestock have been and continue to be an important part of the agricultural landscape in North America. Research on how to mitigate livestock predation by North American carnivores developed quickly during the 20th century. We collected information on 75 field-based experiments published since 1970 that evaluated strategies to mitigate livestock predation by wolves and coyotes. Collected research came from journal articles and grey literature, and we identified 22 mitigation strategies. We developed a ‘robustness index’ to compare each experiment based on its empirical design, temporal/spatial coverage, and sample size. We found the robustness index values increased over time, particularly for lethal mitigation strategies. Overall robustness of research on lethal mitigation strategies was similar to the robustness of research on non-lethal mitigation strategies. Some strategies were not well evaluated as 12 of the 22 mitigation strategies were evaluated only once or twice; some common lethal mitigation strategies (e.g., shooting) were not formally evaluated until the 1990s. We identified some robust assessments of mitigation strategies that reported positive effects (e.g., predator sterilization, protection llamas). In some cases, these were the only evaluation or the only robust evaluation of a strategy. In the few cases where there were multiple robust assessments for a single strategy, the outcomes were inconsistent. No strategies evaluated more than once had consistently high robustness index values and positive outcomes. Importantly, older practices based on less robust research should be re-evaluated or discarded.

Abstract Purpose Various surgical treatments have been described for the treatment of reverse Hill–Sachs lesions (rHSls) sized between 20% and 50% in the case of posterior shoulder dislocation. The aim of this systematic review is to report the clinical and radiological outcomes of subscapularis or lesser tuberosity transfer (McLaughlin and modified procedures) compared to bone or osteochondral autograft or allograft. Methods A systematic review was performed on five medical databases up to December 2022. The inclusion criteria were clinical studies of all levels of evidence describing clinical or radiological outcomes of either procedure. The assessment of the quality of evidence was performed with the Modified Coleman Score. Results A total of 14 studies (five prospective and nine retrospective) were included. A total of 153 patients (155 shoulders, 78.4% male) with a mean age of 37.2 (22–79) years were reviewed at an average follow‐up of 53.1 (7.1–294) months. No relevant difference was found for the clinical scores, range of motion, complications and redislocation rate between the two treatments. Radiological osteoarthritis (OA) was reported in 11% (10/87) in the McLaughlin group and in 21% (16/73) in the humeral reconstruction group. Conclusions McLaughlin and anatomic humeral reconstruction lead to similar satisfactory clinical results and a low redislocation rate in the treatment of rHSls. Anatomic humeral reconstruction seems associated with an increased risk of OA progression. Level of Evidence Level IV.

Mitochondrial ATP synthase (Complex V) catalyzes the last step of oxidative phosphorylation and provides most of the energy (ATP) required by human cells. The mitochondrial genes MT-ATP6 and MT-ATP8 encode two subunits of the multi-subunit Complex V. Since the discovery of the first MT-ATP6 variant in the year 1990 as the cause of Neuropathy, Ataxia, and Retinitis Pigmentosa (NARP) syndrome, a large and continuously increasing number of inborn variants in the MT-ATP6 and MT-ATP8 genes have been identified as pathogenic. Variants in these genes correlate with various clinical phenotypes, which include several neurodegenerative and multisystemic disorders. In the present review, we report the pathogenic variants in mitochondrial ATP synthase genes and highlight the molecular mechanisms underlying ATP synthase deficiency that promote biochemical dysfunctions. We discuss the possible structural changes induced by the most common variants found in patients by considering the recent cryo-electron microscopy structure of human ATP synthase. Finally, we provide the state-of-the-art of all therapeutic proposals reported in the literature, including drug interventions targeting mitochondrial dysfunctions, allotopic gene expression- and nuclease-based strategies, and discuss their potential translation into clinical trials.

Abstract Background Development of large single nucleotide polymorphism (SNP) arrays can make genomic data promptly available for conservation problematic. Medium and high-density panels can be designed with sufficient coverage to offer a genome-wide perspective and the generated genotypes can be used to assess different genetic metrics related to population structure, relatedness, or inbreeding. SNP genotyping could also permit sexing samples with unknown associated metadata as it is often the case when using non-invasive sampling methods favored for endangered species. Genome sequencing of wild species provides the necessary information to design such SNP arrays. We report here the development of a SNP-array for endangered Rangifer tarandus using a multi-platform sequencing approach from animals found in diverse populations representing the entire circumpolar distribution of the species. Results From a very large comprehensive catalog of SNPs detected over the entire sample set (N = 894), a total of 63,336 SNPs were selected. SNP selection accounted for SNPs evenly distributed across the entire genome (~ every 50Kb) with known minor alleles across populations world-wide. In addition, a subset of SNPs was selected to represent rare and local alleles found in Eastern Canada which could be used for ecotype and population assignments - information urgently needed for conservation planning. In addition, heterozygosity from SNPs located in the X-chromosome and genotyping call-rate of SNPs located into the SRY gene of the Y-chromosome yielded an accurate and robust sexing assessment. All SNPs were validated using a high-throughput SNP-genotyping chip. Conclusion This design is now integrated into the first genome-wide commercially available genotyping platform for Rangifer tarandus. This platform would pave the way to future genomic investigation of populations for this endangered species, including estimation of genetic diversity parameters, population assignments, as well as animal sexing from genetic SNP data for non-invasive samples.

Abstract Protected areas are important in species conservation, but high rates of human-caused mortality outside their borders and increasing popularity for recreation can negatively affect wildlife populations. We quantified wolverine (Gulo gulo) population trends from 2011 to 2020 in > 14,000 km2 protected and non-protected habitat in southwestern Canada. We conducted wolverine and multi-species surveys using non-invasive DNA and remote camera-based methods. We developed Bayesian integrated models combining spatial capture-recapture data of marked and unmarked individuals with occupancy data. Wolverine density and occupancy declined by 39%, with an annual population growth rate of 0.925. Density within protected areas was 3 times higher than outside and declined between 2011 (3.6 wolverines/1000 km2) and 2020 (2.1 wolverines/1000 km2). Wolverine density and detection probability increased with snow cover and decreased near development. Detection probability also decreased with human recreational activity. The annual harvest rate of ≥ 13% was above the maximum sustainable rate. We conclude that humans negatively affected the population through direct mortality, sub-lethal effects and habitat impacts. Our study exemplifies the need to monitor population trends for species at risk—within and between protected areas—as steep declines can occur unnoticed if key conservation concerns are not identified and addressed.

Abstract Genetic diversity is theorized to decrease in populations closer to a species' range edge, where habitat may be suboptimal. Generalist species capable of long‐range dispersal may maintain sufficient gene flow to counteract this, though the presence of significant barriers to dispersal (e.g., large water bodies, human‐dominated landscapes) may still lead to, and exacerbate, the edge effect. We used microsatellite data for 2421 gray wolves (Canis lupus) from 24 subpopulations (groups) to model how allelic richness and expected heterozygosity varied with mainland–island position and two measures of range edge (latitude and distance from range center) across >7.3 million km2 of northern North America. We expected low genetic diversity both at high latitudes, due to harsh environmental conditions, and on islands, but no change in diversity with distance to the range center due to the species' exceptional dispersal ability and favorable conditions in far eastern and western habitats. We found that allelic richness and expected heterozygosity of island groups were measurably less than that of mainland groups, and that these differences increased with the island's distance to the species' range center in the study area. Our results demonstrate how multiple axes of geographic isolation (distance from range center and island habitation) can act synergistically to erode the genetic diversity of wide‐ranging terrestrial vertebrate populations despite the counteracting influence of long‐range dispersal ability. These findings emphasize how geographic isolation is a potential threat to the genetic diversity and viability of terrestrial vertebrate populations even among species capable of long‐range dispersal.

Abstract Species at the periphery of their range are typically limited in density by poor habitat quality. As a result, the central–marginal hypothesis (CMH) predicts a decline in genetic diversity of populations toward the periphery of a species' range. Grizzly bears (Ursus arctos) once ranged throughout most of North America but have been extirpated from nearly half of their former range, mainly in the south. They are considered a species at risk even in Canada's remote North, where they occupy the northernmost edge of the species' continental distribution in a low‐productivity tundra environment. With climate change, one of their main prey species in the tundra (caribou), which has always shown yearly fluctuations, is declining, but simultaneously, grizzlies appear to be expanding their range northward in the same tundra environment. Yet, a lack of population density estimates across the North is hindering effective conservation action. The CMH has implications for the viability of peripheral populations, and the links between population fluctuations, potential bottlenecks, and genetic diversity need to be determined to contribute to species' conservation. Using noninvasive genetic sampling from 2012 to 2014 and autosomal DNA genotyping (via microsatellites), we estimated bear density using a spatial capture–recapture framework and analyzed genetic diversity using observed heterozygosity (Ho), allelic richness (AR), and expected heterozygosity (He). We compared our findings to other studies that used comparable methodologies on grizzly bears and a related species (black bears; Ursus americanus). We found densities of grizzly bears that were low for the species but characteristic for the region (5.9 ± 0.4 bears/1000 km2), but with high Ho (0.81 ± 0.05), AR (7 ± 0.78), and He (0.71 ± 0.03), despite a signal of recent bottlenecks. In both species, peripherality was not correlated with Ho but was negatively correlated with density. We suggest that the apparent growth of this expanding population of grizzlies offsets the negative impacts of recent bottlenecks on Ho. Indigenous knowledge provides historical context (on the order of centuries, e.g., arctic large mammal fluctuations, grizzly bear bottlenecks) for the current bear population dynamics (on the order of decades, e.g., climate change, northern grizzly bear expansion).

Erwinia amylovora is a Gram-negative bacterium, responsible for the fire blight disease in Rosaceae plants. Its virulence is correlated with the production of an exopolysaccharide (EPS) called amylovoran, which protects the bacterium from the surrounding environment and helps its diffusion inside the host. Amylovoran biosynthesis relies on the expression of twelve genes clustered in the ams operon. One of these genes, amsI, encodes for a Low Molecular Weight Protein Tyrosine Phosphatase (LMW-PTP) called EaAmsI, which plays a key role in the regulation of the EPS production pathway. For this reason, EaAmsI was chosen in this work as a target for the development of new antibacterial agents against E. amylovora. To achieve this aim, a set of programs (DOCK6, OpenEye FRED) was selected to perform a virtual screening using a database of ca. 700 molecules. The six best-scoring compounds identified were tested in in vitro assays. A complete inhibition kinetic characterization carried out on the most promising molecule (n-Heptyl β-D-glucopyranoside, N7G) showed an inhibition constant of 7.8 ± 0.6 µM. This study represents an initial step towards the development of new EaAmsI inhibitors able to act as antibacterial agents against E. amylovora infections.

Abstract Compact Ni−Rh alloys are electrodeposited potentiostatically on rotating disk and sheet electrodes; film compositions are adjusted by varying bath composition and deposition potential Edep. SEM images of these alloys show a compact, globular morphology for Rh contents up to 30 at%, and a smoother aspect for films with a medium‐to‐high content of Rh. XRD spectra show the formation of a single crystalline phase, with diffraction peaks in intermediate positions between those of the constituent elements. Data analysis indicates that crystal lattice parameters vary with composition according to Vegard's law. Linear voltammetries of nitrate reduction in alkali highlight a maximum of activity, in terms of reduction current, for alloys in the range of 10–30 at.% Rh. Prolonged electrolysis at appropriate potential performed with Ni85Rh15 alloy shows, in comparison with pure Ni and pure Rh: much increased activity and faster abatement of nitrate; lower production of the undesired nitrite species; higher selectivity towards production of ammonia.

The seamless integration of human disease-related mutation data into protein structures is an essential component of any attempt to correctly assess the impact of the mutation. The key step preliminary to any structural modelling is the identification of the isoforms onto which mutations should be mapped due to there being several functionally different protein isoforms from the same gene. To handle large sets of data coming from omics techniques, this challenging task needs to be automatized. Here we present the MoNvIso (Modelling eNvironment for Isoforms) code, which identifies the most useful isoform for computational modelling, balancing the coverage of mutations of interest and the availability of templates to build a structural model of both the wild-type isoform and the related variants.

Abstract Background Several migratory ungulates, including caribou, are dramatically declining. Caribou of the Barren-ground ecotype, which forms its own subspecies, are known to be mainly migratory. By contrast, within the Woodland subspecies, animals of the Boreal ecotype are known to be mainly sedentary, while those within the Northern and Central Mountain ecotypes to be partially migratory, with only some individuals migrating. Promotion of conservation actions (e.g., habitat protection) that are specific to both residents and migrants, as well as to the areas they frequent seasonally (which may be separate for migrants), requires distinguishing migration from other movement behaviours, which might be a challenge. Methods We aimed at assessing seasonal movement behaviours, including migratory, resident, dispersing, and nomadic, for caribou belonging to the Barren-ground and Woodland subspecies and ecotypes. We examined seasonal displacement, both planar and altitudinal, and seasonal ranges overlap for 366 individuals that were GPS-collared in Northern and Western Canada. Lastly, we assessed the ability of caribou individuals to switch between migratory and non-migratory movement behaviours between years. Results We detected migratory behaviour within each of the studied subspecies and ecotypes. However, seasonal ranges overlap (an index of sedentary behaviour) varied, with proportions of clear migrants (0 overlap) of 40.94% for Barren-ground caribou and 23.34% for Woodland caribou, and of 32.95%, 54.87%, and 8.86% for its Northern Mountain, Central Mountain, and Boreal ecotype, respectively. Plastic switches of individuals were also detected between migratory, resident, dispersing, and nomadic seasonal movements performed across years. Conclusions Our unexpected findings of marked seasonal movement plasticity in caribou indicate that this phenomenon should be better studied to understand the resilience of this endangered species to habitat and climatic changes. Our results that a substantial proportion of individuals engaged in seasonal migration in all studied ecotypes indicate that caribou conservation plans should account for critical habitat in both summer and winter ranges. Accordingly, conservation strategies are being devised for the Woodland subspecies and its ecotypes, which were found to be at least partially migratory in this study. Our findings that migration is detectable with both planar and altitudinal analyses of seasonal displacement provide a tool to better define seasonal ranges, also in mountainous and hilly environments, and protect habitat there.

Inhibition of respiratory complex I (CI) is becoming a promising anti-cancer strategy, encouraging the design and the use of inhibitors, whose mechanism of action, efficacy and specificity remain elusive. As CI is a central player of cellular bioenergetics, a finely tuned dosing of targeting drugs is required to avoid side effects. We compared the specificity and mode of action of CI inhibitors metformin, BAY 87-2243 and EVP 4593 using cancer cell models devoid of CI. Here we show that both BAY 87-2243 and EVP 4593 were selective, while the antiproliferative effects of metformin were considerably independent from CI inhibition. Molecular docking predictions indicated that the high efficiency of BAY 87-2243 and EVP 4593 may derive from the tight network of bonds in the quinone binding pocket, although in different sites. Most of the amino acids involved in such interactions are conserved across species and only rarely found mutated in human. Our data make a case for caution when referring to metformin as a CI-targeting compound, and highlight the need for dosage optimization and careful evaluation of molecular interactions between inhibitors and the holoenzyme.

Integrin receptors mediate cell–cell interactions via the recognition of cell-adhesion glycoproteins, as well as via the interactions of cells with proteins of the extracellular matrix, and upon activation they transduce signals bi-directionally across the cell membrane. In the case of injury, infection, or inflammation, integrins of β2 and α4 families participate in the recruitment of leukocytes, a multi-step process initiated by the capturing of rolling leukocytes and terminated by their extravasation. In particular, α4β1 integrin is deeply involved in leukocyte firm adhesion preceding extravasation. Besides its well-known role in inflammatory diseases, α4β1 integrin is also involved in cancer, being expressed in various tumors and showing an important role in cancer formation and spreading. Hence, targeting this integrin represents an opportunity for the treatment of inflammatory disorders, some autoimmune diseases, and cancer. In this context, taking inspiration from the recognition motives of α4β1 integrin with its natural ligands FN and VCAM-1, we designed minimalist α/β hybrid peptide ligands, with our approach being associated with a retro strategy. These modifications are expected to improve the compounds’ stability and bioavailability. As it turned out, some of the ligands were found to be antagonists, being able to inhibit the adhesion of integrin-expressing cells to plates coated with the natural ligands without inducing any conformational switch and any activation of intracellular signaling pathways. An original model structure of the receptor was generated using protein–protein docking to evaluate the bioactive conformations of the antagonists via molecular docking. Since the experimental structure of α4β1 integrin is still unknown, the simulations might also shed light on the interactions between the receptor and its native protein ligands.

Abstract Disease lesion mimic (DLM) or necrotic mutants display necrotic lesions in the absence of pathogen infections. They can show improved resistance to some pathogens and their molecular dissection can contribute to revealing components of plant defense pathways. Although forward‐genetics strategies to find genes causal to mutant phenotypes are available in crops, these strategies require the production of experimental cross populations, mutagenesis, or gene editing and are time‐ and resource‐consuming or may have to deal with regulated plant materials. In this study, we described a collection of 34 DLM mutants in barley (Hordeum vulgare L.) and applied a novel method called complementation by sequencing (CBS), which enables the identification of the gene responsible for a mutant phenotype given the availability of two or more chemically mutagenized individuals showing the same phenotype. Complementation by sequencing relies on the feasibility to obtain all induced mutations present in chemical mutants and on the low probability that different individuals share the same mutated genes. By CBS, we identified a cytochrome P450 CYP71P1 gene as responsible for orange blotch DLM mutants, including the historical barley nec3 locus. By comparative phylogenetic analysis we showed that CYP71P1 gene family emerged early in angiosperm evolution but has been recurrently lost in some lineages including Arabidopsis thaliana (L.) Heynh. Complementation by sequencing is a straightforward cost‐effective approach to clone genes controlling phenotypes in a chemically mutagenized collection. The TILLMore (TM) collection will be instrumental for understanding the molecular basis of DLM phenotypes and to contribute knowledge about mechanisms of host–pathogen interaction.

Wide-ranging animals, including migratory species, are significantly threatened by the effects of habitat fragmentation and habitat loss. In the case of terrestrial mammals, this results in nearly a quarter of species being at risk of extinction. Caribou are one such example of a wide-ranging, migratory, terrestrial, and endangered mammal. In populations of caribou, the proportion of individuals considered as "migrants" can vary dramatically. There is therefore a possibility that, under the condition that migratory behavior is genetically determined, those individuals or populations that are migratory will be further impacted by humans, and this impact could result in the permanent loss of the migratory trait in some populations. However, genetic determination of migration has not previously been studied in an endangered terrestrial mammal. We examined migratory behavior of 139 GPS-collared endangered caribou in western North America and carried out genomic scans for the same individuals. Here we determine a genetic subdivision of caribou into a Northern and a Southern genetic cluster. We also detect >50 SNPs associated with migratory behavior, which are in genes with hypothesized roles in determining migration in other organisms. Furthermore, we determine that propensity to migrate depends upon the proportion of ancestry in individual caribou, and thus on the evolutionary history of its migratory and sedentary subspecies. If, as we report, migratory behavior is influenced by genes, caribou could be further impacted by the loss of the migratory trait in some isolated populations already at low numbers. Our results indicating an ancestral genetic component also suggest that the migratory trait and their associated genetic mutations could not be easily re-established when lost in a population.

For over twenty years, alternative forms of organising and networking – fuelled by the Internet but sometimes pre-dating it – have been discussed as possible responses to the dynamics of concentration, centralisation and capture exemplified in the current pervasively digital world by Internet giants such as Google and Facebook. This article takes stock of the lessons learned by the authors in over a decade of research on decentralised/P2P network architectures and on information commons, to suggest some ‘ways forward’ for these alternatives for the Internet.

Varestrongylus eleguneniensis (Nematoda; Protostrongylidae) is a recently described species of lungworm that infects caribou (Rangifer tarandus), muskoxen (Ovibos moschatus) and moose (Alces americanus) across northern North America. Herein we explore the geographic distribution of V. eleguneniensis through geographically extensive sampling and discuss the biogeography of this multi-host parasite. We analyzed fecal samples of three caribou subspecies (n = 1485), two muskox subspecies (n = 159), and two moose subspecies (n = 264) from across northern North America. Protostrongylid dorsal-spined larvae (DSL) were found in 23.8%, 73.6%, and 4.2% of these ungulates, respectively. A portion of recovered DSL were identified by genetic analyses of the ITS-2 region of the nuclear rDNA or the cytochrome oxidase c subunit I (COI) region of the mtDNA. We found V. eleguneniensis widely distributed among caribou and muskox populations across most of their geographic prange in North America but it was rare in moose. Parelaphostrongylus andersoni was present in caribou and moose and we provide new geographic records for this species. This study provides a substantial expansion of the knowledge defining the current distribution and biogeography of protostrongylid nematodes in northern ungulates. Insights about the host and geographic range of V. eleguneniensis can serve as a geographically extensive baseline for monitoring current distribution and in anticipating future biogeographic scenarios under a regime of accelerating climate and anthropogenic perturbation. Keywords: Arctic parasitology, Climate change, Geographic distribution, Metastrongyloidea, Nearctic, Rangifer

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the pandemic that broke out in 2020 and continues to be the cause of massive global upheaval. Coronaviruses are positive-strand RNA viruses with a genome of ~30 kb. The genome is replicated and transcribed by RNA-dependent RNA polymerase together with accessory factors. One of the latter is the protein helicase (NSP13), which is essential for viral replication. The recently solved helicase structure revealed a tertiary structure composed of five domains. Here, we investigated NSP13 from a structural point of view, comparing its RNA-free form with the RNA-engaged form by using atomistic molecular dynamics (MD) simulations at the microsecond timescale. Structural analyses revealed conformational changes that provide insights into the contribution of the different domains, identifying the residues responsible for domain–domain interactions in both observed forms. The RNA-free system appears to be more flexible than the RNA-engaged form. This result underlies the stabilizing role of the nucleic acid and the functional core role of these domains.

Molecular docking is a key method for structure-based drug design used to predict the conformations assumed by small drug-like ligands when bound to their target. However, the evaluation of molecular docking studies can be hampered by the lack of a free and easy to use platform for the complete analysis of results obtained by the principal docking programs. To this aim, we developed PacDOCK, a freely available and user-friendly web server that comprises a collection of tools for positional distance-based and interaction-based analysis of docking results, which can be provided in several file formats. PacDOCK allows a complete analysis of molecular docking results through root mean square deviation (RMSD) calculation, molecular visualization, and cluster analysis of docked poses. The RMSD calculation compares docked structures with a reference structure, also when atoms are randomly labelled, and their conformational and positional differences can be visualised. In addition, it is possible to visualise a ligand into the target binding pocket and investigate the key receptor–ligand interactions. Moreover, PacDOCK enables the clustering of docking results by identifying a restrained number of clusters from many docked poses. We believe that PacDOCK will contribute to facilitating the analysis of docking results to improve the efficiency of computer-aided drug design.

Echinococcus multilocularis (Em) is a zoonotic parasite considered a global emergent pathogen. Recent findings indicate that the parasite is expanding its range in North America and that European-type haplotypes are circulating in western Canada. However, genetic analyses are usually conducted only on a few parasites out of thousands of individuals within each definitive host, likely underestimating the prevalence of less common haplotypes. Moreover, mixed infections with several mtDNA haplotypes in the same host have been reported, but their relative abundance within the host was never estimated. We aimed to 1) estimate the frequency of co-infections of different Em haplotypes in coyotes (Canis latrans) and red foxes (Vulpes vulpes) from western Canada and their relative abundance within the definitive hosts, 2) detect less prevalent haplotypes by sampling a larger proportion of the parasite subpopulation per host, and 3) investigate differences in the distribution of Em haplotypes in these main definitive hosts; foxes and coyotes. We extracted DNA from ~10% of the worm subpopulation per host (20 foxes and 47 coyotes) and used deep amplicon sequencing (NGS technology) on four loci, targeting the most polymorphic regions from the mitochondrial genes cox1 (814 bp), nad1 (344 bp), and cob (387 bp). We detected the presence of mixed infections with multiple Em haplotypes and with different Echinococcus species including Em and E. granulosus s.l. genotypes G8/G10, low intraspecific diversity of Em, and a higher abundance of the European-type haplotypes in both hosts. Our results suggest a population expansion of the European over the North American strain in Alberta and a limited distribution of some European-type haplotypes. Our findings indicate that deep amplicon sequencing represents a valuable tool to characterize Em in multiple hosts, to assess the current distribution and possible origins of the European strain in North America. The potential use of next-generation sequencing technologies is particularly important to understand the patterns of geographic expansion of this parasite.

While infrastructures are governed by institutions and rules, they also govern us, as social actors, by their very design. This special issue is dedicated to the study of the governance embedded in infrastructures, as opposed to the governance of the effects they might produce. From machine learning to artificial intelligence, from gig economy platforms to the infrastructures used by governments for advertising or social security, the articles in this special issue highlight the digital governance we are subject to, while exploring alternatives we might consider. [ABSTRACT FROM AUTHOR]

Abstract Aim The influence of humans on large carnivores, including wolves, is a worldwide conservation concern. In addition, human‐caused changes in carnivore density and distribution might have impacts on prey and, indirectly, on vegetation. We therefore tested wolf responses to infrastructure related to natural resource development (i.e., human footprint). Location Our study provides one of the most extensive assessments of how predators like wolves select habitat in response to various degrees of footprint across boreal ecosystems encompassing over a million square kilometers of Canada. Methods We deployed GPS‐collars on 172 wolves, monitored movements and used a generalized functional response (GFR) model of resource selection. A functional response in habitat selection occurs when selection varies as a function of the availability of that habitat. GFRs can clarify how human‐induced habitat changes are influencing wildlife across large, diverse landscapes. Results Wolves displayed a functional response to footprint. Wolves were more likely to select forest harvest cutblocks in regions with higher cutblock density (i.e., a positive functional response to high‐quality habitats for ungulate prey) and to select for higher road density in regions where road density was high (i.e., a positive functional response to human‐created travel routes). Wolves were more likely to use cutblocks in habitats with low road densities, and more likely to use roads in habitats with low cutblock densities, except in winter when wolves were more likely to use roads regardless of cutblock density. Main conclusions These interactions suggest that wolves trade‐off among human‐impacted habitats, and adaptively switch from using roads to facilitate movement (while also risking encounters with humans), to using cutblocks that may have higher ungulate densities. We recommend that conservation managers consider the contextual and interacting effects of footprints when assessing impacts on carnivores. These effects likely have indirect impacts on ecosystems too, including on prey species.

This article analyses an ensemble of interdisciplinary research efforts, grounded mainly in science and technology studies (STS), which – based upon Geoffrey Bowker and Susan Leigh Star’s seminal work – seeks to study informational and digital infrastructures according to their “materiality”, arguing that there is a need to overcome an understanding of infrastructures as purely physical. The article shows the usefulness of this perspective for the researcher seeking to use the “infrastructure” notion as a heuristic tool in order to understand the governance of digital information and networks, the Internet first and foremost.

The finding that the most common mitochondrial DNA mutation m.11778G>A/MT-ND4 (p.R340H) associated with Leber’s hereditary optic neuropathy (LHON) induces rotenone resistance has produced a long-standing debate, because it contrasts structural evidence showing that the ND4 subunit is far away from the quinone-reaction site in complex I, where rotenone acts. However, recent cryo-electron microscopy data revealed that rotenone also binds to the ND4 subunit. We investigated the possible structural modifications induced by the LHON mutation and found that its amino acid replacement would disrupt a possible hydrogen bond between native R340 and Q139 in ND4, thereby destabilizing rotenone binding. Our analysis thus explains rotenone resistance in LHON patients as a biochemical signature of its pathogenic effect on complex I.

Since the Cancer Genome Atlas (TCGA) project identified four distinct groups based on molecular alterations, mutation analyses have been integrated into the characterization of endometrial carcinomas (ECs). ARID1A seems to be the subunit more involved in the loss of function of the SWI/SNF complex in ECs. The aim of this study is to define the relevance of ARID1A alterations in a cohort of EC, studying the possible associations between DNA mutation (genomic level), RNA expression (transcriptomic level), and protein expression (proteomic level). A total of 50 endometrial carcinomas were characterized for ARID1A mutations (using targeted DNA next-generation sequencing—NGS), ARID1A gene expression (using RNAseq and qRT-PCR), and ARID1A protein expression (using immunohistochemistry—IHC). Moreover, we have investigated if ARID1A mutations may alter the protein structure, using the Protein Data Bank sequence. We found a good correlation between ARID1A mutations and protein immunostaining, even if we did not find statistically significant differences in the ARID1A expression levels. In conclusion, our data demonstrated that the molecular characterization of ARID1A should be associated with IHC analysis, mainly in those cases harboring “novel” ARID1A mutations or in those alterations with “uncertain” pathogenic significance.

Summary: Protein arginine methyltransferase 1 (PRMT1) is overexpressed in various human cancers and linked to poor response to chemotherapy. Various PRMT1 inhibitors are currently under development; yet, we do not fully understand the mechanisms underpinning PRMT1 involvement in tumorigenesis and chemoresistance. Using mass spectrometry-based proteomics, we identified PRMT1 as regulator of arginine methylation in ovarian cancer cells treated with cisplatin. We showed that DNA-dependent protein kinase (DNA-PK) binds to and phosphorylates PRMT1 in response to cisplatin, inducing its chromatin recruitment and redirecting its enzymatic activity toward Arg3 of histone H4 (H4R3). On chromatin, the DNA-PK/PRMT1 axis induces senescence-associated secretory phenotype through H4R3me2a deposition at pro-inflammatory gene promoters. Finally, PRMT1 inhibition reduces the clonogenic growth of cancer cells exposed to low doses of cisplatin, sensitizing them to apoptosis. While unravelling the role of PRMT1 in response to genotoxic agents, our findings indicate the possibility of targeting PRMT1 to overcome chemoresistance in cancer. : Protein arginine methyltransferase 1 (PRMT1) overexpression is linked to cancer chemoresistance, but the mechanism is still unclear. Musiani et al. show that, upon cisplatin, PRMT1 is recruited by DNA-dependent protein kinase (DNA-PK) to chromatin, where it sustains the transcription of genes involved in the senescence-associated secretory phenotype (SASP), thus protecting cells from drug-induced apoptosis. Keywords: arginine methylation, MS-based proteomics, replication stress response, PRMT1, SASP, transcription, cisplatin, epigenetic drugs, DNA-PK

Abstract Accurate detection and classification of predation events is important to determine predation and consumption rates by predators. However, obtaining this information for large predators is constrained by the speed at which carcasses disappear and the cost of field data collection. To accurately detect predation events, researchers have used GPS collar technology combined with targeted site visits. However, kill sites are often investigated well after the predation event due to limited data retrieval options on GPS collars (VHF or UHF downloading) and to ensure crew safety when working with large predators. This can lead to missing information from small‐prey (including young ungulates) kill sites due to scavenging and general site deterioration (e.g., vegetation growth). We used a space–time permutation scan statistic (STPSS) clustering method (SaTScan) to detect predation events of grizzly bears (Ursus arctos) fitted with satellite transmitting GPS collars. We used generalized linear mixed models to verify predation events and the size of carcasses using spatiotemporal characteristics as predictors. STPSS uses a probability model to compare expected cluster size (space and time) with the observed size. We applied this method retrospectively to data from 2006 to 2007 to compare our method to random GPS site selection. In 2013–2014, we applied our detection method to visit sites one week after their occupation. Both datasets were collected in the same study area. Our approach detected 23 of 27 predation sites verified by visiting 464 random grizzly bear locations in 2006–2007, 187 of which were within space–time clusters and 277 outside. Predation site detection increased by 2.75 times (54 predation events of 335 visited clusters) using 2013–2014 data. Our GLMMs showed that cluster size and duration predicted predation events and carcass size with high sensitivity (0.72 and 0.94, respectively). Coupling GPS satellite technology with clusters using a program based on space–time probability models allows for prompt visits to predation sites. This enables accurate identification of the carcass size and increases fieldwork efficiency in predation studies.

Furan is a volatile compound that is formed in foods during thermal processing. It is classified as a possible human carcinogen by international authorities based on sufficient evidence of carcinogenicity from studies in experimental animals. Although a vast number of studies both in vitro and in vivo have been performed to investigate furan genotoxicity, the results are inconsistent, and its carcinogenic mode of action remains to be clarified. Here, we address the mutagenic and clastogenic activity of furan and its prime reactive metabolite cis-2 butene-1,4-dial (BDA) in mammalian cells in culture and in mouse animal models in a search for DNA lesions responsible of these effects. To this aim, Fanconi anemia-derived human cell lines defective in the repair of DNA inter-strand crosslinks (ICLs) and Ogg1−/− mice defective in the removal of 8-hydroxyguanine from DNA, were used. We show that both furan and BDA present a weak (if any) mutagenic activity but are clear inducers of clastogenic damage. ICLs are strongly indicated as key lesions for chromosomal damage whereas oxidized base lesions are unlikely to play a critical role.

HP1043 is an essential orphan response regulator of Helicobacter pylori orchestrating multiple crucial cellular processes. Classified as a member of the OmpR/PhoB family of two-component systems, HP1043 exhibits a highly degenerate receiver domain and evolved to function independently of phosphorylation. Here, we investigated the HP1043 binding mode to a target sequence in the hp1227 promoter (Php1227). Scanning mutagenesis of HP1043 DNA-binding domain and consensus sequence led to the identification of residues relevant for the interaction of the protein with a target DNA. These determinants were used as restraints to guide a data-driven protein-DNA docking. Results suggested that, differently from most other response regulators of the same family, HP1043 binds in a head-to-head conformation to the Php1227 target promoter. HP1043 interacts with DNA largely through charged residues and contacts with both major and minor grooves of the DNA are required for a stable binding. Computational alanine scanning on molecular dynamics trajectory was performed to corroborate our findings. Additionally, in vitro transcription assays confirmed that HP1043 positively stimulates the activity of RNA polymerase.

In response to the growing censorship of their national Internet, Russian users, content producers and service providers have developed several resistance tactics. This paper analyzes these tactics with particular attention paid to their materiality. It first addresses the different levels of Internet “governance by infrastructure” in Russia, then focuses on the different tactics of individual and collective resistance and concludes by discussing how forms of control enacted at different levels of infrastructure are reconfiguring the geopolitics of the Russian Internet.

The 3CL-Protease appears to be a very promising medicinal target to develop anti-SARS-CoV-2 agents. The availability of resolved structures allows structure-based computational approaches to be carried out even though the lack of known inhibitors prevents a proper validation of the performed simulations. The innovative idea of the study is to exploit known inhibitors of SARS-CoV 3CL-Pro as a training set to perform and validate multiple virtual screening campaigns. Docking simulations using four different programs (Fred, Glide, LiGen, and PLANTS) were performed investigating the role of both multiple binding modes (by binding space) and multiple isomers/states (by developing the corresponding isomeric space). The computed docking scores were used to develop consensus models, which allow an in-depth comparison of the resulting performances. On average, the reached performances revealed the different sensitivity to isomeric differences and multiple binding modes between the four docking engines. In detail, Glide and LiGen are the tools that best benefit from isomeric and binding space, respectively, while Fred is the most insensitive program. The obtained results emphasize the fruitful role of combining various docking tools to optimize the predictive performances. Taken together, the performed simulations allowed the rational development of highly performing virtual screening workflows, which could be further optimized by considering different 3CL-Pro structures and, more importantly, by including true SARS-CoV-2 3CL-Pro inhibitors (as learning set) when available.

The development of highly conductive structured catalysts with enhanced mass- and heat-transfer features is required for the intensification of the strongly exothermic catalytic hydrogenation of CO2 in which large temperature gradients should be avoided to prevent catalyst deactivation and to control selectivity. Therefore, in this work we set out to investigate the preparation of novel structured catalysts obtained from a commercial open cell Ni foam with high pore density (75 ppi) onto which a CeO2 layer was deposited via electroprecipitation, and, eventually, Ru was added by impregnation. Composite Ru/Ce/Ni foam catalysts, as well as simpler binary Ru/Ni and Ce/Ni catalysts were characterized by SEM-EDX, XRD, cyclic voltammetry, N2 physisorption, H2-temperature programmed reduction (TPR), and their CO2 methanation activity was assessed at atmospheric pressure in a fixed bed flow reactor via temperature programmed tests in the range from 200 to 450 °C. Thin porous CeO2 layers, uniformly deposited on the struts of the Ni foams, produced active catalytic sites for the hydrogenation of CO2 at the interface between the metal and the oxide. The methanation activity was further boosted by the dispersion of Ru within the pores of the CeO2 layer, whereas the direct deposition of Ru on Ni, by either impregnation or pulsed electrodeposition methods, was much less effective.

Urease is a nickel-containing enzyme that is essential for the survival of several and often deadly pathogenic bacterial strains, including Helicobacter pylori. Notwithstanding several attempts, the development of direct urease inhibitors without side effects for the human host remains, to date, elusive. The recently solved X-ray structure of the HpUreDFG accessory complex involved in the activation of urease opens new perspectives for structure-based drug discovery. In particular, the quaternary assembly and the presence of internal tunnels for nickel translocation offer an intriguing possibility to target the HpUreDFG complex in the search of indirect urease inhibitors. In this work, we adopted a theoretical framework to investigate such a hypothesis. Specifically, we searched for putative binding sites located at the protein–protein interfaces on the HpUreDFG complex, and we challenged their druggability through structure-based virtual screening. We show that, by virtue of the presence of tunnels, some protein–protein interfaces on the HpUreDFG complex are intrinsically well suited for hosting small molecules, and, as such, they possess good potential for future drug design endeavors.

Across the boreal forest of Canada, habitat disturbance is the ultimate cause of caribou (Rangifer tarandus caribou) declines. Habitat restoration is a focus of caribou recovery efforts, with a goal to finding ways to reduce predator use of disturbances, and caribou-predator encounters. One of the most pervasive disturbances within caribou ranges in Alberta, Canada are seismic lines cleared for energy exploration. Seismic lines facilitate predator movement, and although vegetation on some seismic lines is regenerating, it remains unknown whether vegetation regrowth is sufficient to alter predator response. We used Light Detection and Ranging (LiDAR) data, and GPS locations, to understand how vegetation and other attributes of seismic lines influence movements of two predators, wolves (Canis lupus) and grizzly bears (Ursus arctos). During winter, wolves moved towards seismic lines regardless of vegetation height, while during spring wolves moved towards seismic lines with higher vegetation. During summer, wolves moved towards seismic lines with lower vegetation and also moved faster near seismic lines with vegetation

This article discusses some of the results of a five-year-long (and ongoing) investigation of alternative approaches to the design of internet services, based on decentralized network architectures. In particular, the paper focuses on the implications of this research for the study and the practice of internet governance, inasmuch as architectural changes affect the repartition of responsibilities between service providers, content producers, users and network operators; contribute to the shaping of user rights, of the ways to produce and enforce law; reconfigure the boundary between public and private uses of the internet as a global facility. I argue that delving into the tensions between the dwarfs and the giants of the Net – between different technical and organizational architectures, and their political consequences – helps us to disengage from what is often a predominantly institutional view of internet governance, and give due emphasis to its less visible, infrastructure-embedded arrangements, its materiality and its practice.