JournalTOCs

Peer Community Journal
Number of Followers: 5

This is an Open Access Journal

Open Access journal
ISSN (Online) 2804-3871
Published by Peer Community in (PCI)

[1 journal]

Hartasánchez, Diego A.; Kiss, Annamaria et al. - Expression of cell-wall
related genes is highly variable and correlates with sepal morphology
- Abstract: Control of organ morphology is a fundamental feature of living organisms. There is, however, observable variation in organ size and shape within a given genotype. Taking the sepal of Arabidopsis as a model, we investigated whether we can use variability of gene expression alongside variability of organ morphology to identify gene regulatory networks potentially involved in organ size and shape determination. We produced a dataset composed of morphological parameters and genome-wide transcriptome obtained from 27 individual sepals from wild-type plants with nearly identical genetic backgrounds, environment, and developmental stage. Sepals exhibited appreciable variability in both morphology and transcriptome, with response to stimulus genes and cell-wall related genes displaying high variability in expression. We additionally identified five modules of co-expressed genes which correlated significantly with morphology, revealing biologically relevant gene regulatory networks. Interestingly, cell-wall related genes were overrepresented in two of the top three modules. Overall, our work highlights the benefit of using coupled variation in gene expression and phenotype in wild-type plants to shed light on the mechanisms underlying organ size and shape determination. Although causality between gene expression and sepal morphology has not been established, our approach opens the way to informed analysis for mutant characterization and functional studies.
  PubDate: Thu, 28 Sep 2023 14:53:02 +000
Mycobacterium+tuberculosis+complex+and+the+awkward+population+genetics+of+extreme+clonality&rft.title=Peer+Community+Journal&rft.issn=2804-3871&rft.date=2023&rft.volume=">Stritt, Christoph; Gagneux, Sebastien - How do monomorphic bacteria
evolve' The Mycobacterium tuberculosis complex and the awkward population
genetics of extreme clonality
- Abstract: Exchange of genetic material through sexual reproduction or horizontal gene transfer is ubiquitous in nature. Among the few outliers that rarely recombine and mainly evolve by de novo mutation are a group of deadly bacterial pathogens, including the causative agents of leprosy, plague, typhoid, and tuberculosis. The interplay of evolutionary processes is poorly understood in these organisms. Population genetic methods allowing to infer mutation, recombination, genetic drift, and natural selection make strong assumptions that are difficult to reconcile with clonal reproduction and fully linked genomes consisting mainly of coding regions. In this review, we highlight the challenges of extreme clonality by discussing population genetic inference with the Mycobacterium tuberculosis complex, a group of closely related obligate bacterial pathogens of mammals. We show how uncertainties underlying quantitative models and verbal arguments affect previous conclusions about the way these organisms evolve. A question mark remains behind various quantities of applied and theoretical interest, including mutation rates, the interpretation of nonsynonymous polymorphisms, or the role of genetic bottlenecks. Looking ahead, we discuss how new tools for evolutionary simulations, going beyond the traditional Wright-Fisher framework, promise a more rigorous treatment of basic evolutionary processes in clonal bacteria.
  PubDate: Wed, 27 Sep 2023 15:02:09 +000
Babesia+sp.+YLG+in+Yellow-legged+gull+(
Larus+michahellis)+nests&rft.title=Peer+Community+Journal&rft.issn=2804-3871&rft.date=2023&rft.volume=">Bonsergent, Claire; Vittecoq, Marion et al. - A soft tick vector of
Babesia sp. YLG in Yellow-legged gull (Larus michahellis) nests
- Abstract: Abstract Babesia sp. YLG has recently been described in Yellow-legged gull (Larus michahellis) chicks and belongs to the Peircei clade in the new classification of Piroplasms. Here, we studied Babesia sp. YLG vectorial transmission by ticks in the simplified environment of a single seabird breeding colony where the Yellow-legged gull is the sole vertebrate host, Ornithodoros maritimus (syn. Alectorobius maritimus) the sole tick species, and Babesia sp. YLG is the only blood parasite species detected in chicks of the colony. We collected ticks over four years, maintained certain individuals through moulting or oviposition, and dissected fresh ticks to isolate different organs and test for the presence of the parasite using molecular assays. We report the first strong evidence of a Piroplasmidae transmitted by a soft tick. Indeed, Babesia sp. YLG DNA was detected in the salivary glands of nymphs, females and males, a necessary organ to infect for transmission to a new vertebrate host. Parasite DNA was also found in tick ovaries, which could indicate possible transovarial transmission. Our detection of Babesia sp. YLG DNA in several male testes and in endospermatophores, and notably in a parasite-free female (uninfected ovaries and salivary glands), raise the interesting possibility of sexual transmission from infected males to uninfected females. Future work in this system will now need to focus on the degree to which the parasite can be maintained locally by ticks and the epidemiological consequences of infection for both O. maritimus and its avian host.
  PubDate: Mon, 25 Sep 2023 14:41:43 +000
Delignette-Muller, Marie Laure; Siberchicot, Aurélie et al. - DRomics, a
workflow to exploit dose-response omics data in ecotoxicology
- Abstract: Omics technologies has opened new possibilities to assess environmental risks and to understand the mode(s) of action of pollutants. Coupled to dose-response experimental designs, they allow a non-targeted assessment of organism responses at the molecular level along an exposure gradient. However, describing the dose-response relationships on such high-throughput data is no easy task. In a first part, we review the software available for this purpose, and their main features. We set out arguments on some statistical and modeling choices we have made while developing the R package DRomics and its positioning compared to others tools. The DRomics main analysis workflow is made available through a web interface, namely a shiny app named DRomics-shiny. Next, we present the new functionalities recently implemented. DRomics has been augmented especially to be able to handle varied omics data considering the nature of the measured signal (e.g. counts of reads in RNAseq) and the way data were collected (e.g. batch effect, situation with no experimental replicates). Another important upgrade is the development of tools to ease the biological interpretation of results. Various functions are proposed to visualize, summarize and compare the responses, for different biological groups (defined from biological annotation), optionally at different experimental levels (e.g. measurements at several omics level or in different experimental conditions). A new shiny app named DRomicsInterpreter-shiny is dedicated to the biological interpretation of results. The institutional web page https://lbbe.univ-lyon1.fr/fr/dromics gathers links to all resources related to DRomics, including the two shiny applications.
  PubDate: Mon, 25 Sep 2023 14:37:07 +000
Gebhardt-Henrich, Sabine G.; Kashev, Alexander et al. - Validation of a
Radio frequency identification system for tracking location of laying hens
in a quasi-commercial aviary system
- Abstract: Cage-free housing is increasingly chosen in Europe, North America, and Australia as an animal-welfare friendly farm system for laying hens. However, hens are kept in large numbers in those systems which makes checking for health and welfare difficult and individuals cannot be identified. Tracking systems like radio frequency identification allow researchers to monitor these individuals almost continuously. Individual tracking data has revealed substantial individual variation in movement patterns, however, in recent studies, only a subset of animals per flock was tracked. We applied an RFID tracking system to monitor all 1125 laying hens of a flock, which were divided into 5 pens of 225 birds each in a barn with an aviary system. In each pen, 26 antennas were placed on the edges of three tiers and in the litter. For validation purposes, 3 hens in 2 connected pens were fitted with colored backpacks. They were recorded on video and their location throughout the pen was taken from the video and compared with registrations from the RFID system. For 93% of compared transitions, the RFID data matched the observational data regarding the tier or litter whereas the value fell to 39% for specific antennae. When the antennae on the litter were excluded for the validation, the match on tier-level was at least 98% but on antenna-level it remained lower than 50%. The sensitivity of the detection of tiers/litter but not antennae differed among the three hens. We conclude that the RFID tracking system was suitable for studying the movement pattern of individual hens among tiers in an aviary system in a reliable way but tracking birds on the litter needs to be improved.
  PubDate: Mon, 25 Sep 2023 12:48:02 +000
Pseudomonas+syringae+and+Soft+Rot+
Pectobacteriaceae+species+complexes+throughout+the+Durance+River+catchment+from+its+French+Alps+sources+to+its+delta&rft.title=Peer+Community+Journal&rft.issn=2804-3871&rft.date=2023&rft.volume=">Morris, C.E.; Lacroix, C. et al. - Comparative abundance and diversity of
populations of the Pseudomonas syringae and Soft Rot Pectobacteriaceae
species complexes throughout the Durance River catchment from its French
Alps sources to its delta
- Abstract: Rivers, creeks, streams are integrators of biological, chemical and physical processes occurring in a catchment linking land cover from the headwaters to the outlet. The dynamics of human and animal pathogens in catchments have been widely studied in a large variety of contexts allowing the optimization of disease risk reduction. In parallel, there is an emerging awareness that crop pathogens might also be disseminated via surface waters especially when they are used for irrigation. However, there are no studies on the extent to which potential plant pathogens are present – nor about their dynamics - along the full course of a catchment. Here we have compared the seasonal dynamics of populations of the Pseudomonas syringae (Psy) and the Soft Rot Pectobacteriaceae (SRP) species complexes along a 270 km stretch of the Durance River from the upstream alpine reaches to the downstream agricultural production areas at the confluence with the Rhone River at Avignon. Among 168 samples collected at 21 sites in fall, winter, spring and summer of 2016 and 2017, Psy strains were detected at all sampling sites and in 156 of the samples at population densities up to 105 bacteria L-1. In contrast, SRP strains were detected in 98 of the samples, mostly from the southern part of the river, at population densities that did not exceed 3 ´ 104 bacteria L-1. Among the biological and chemical parameters that were characterized at each sampling site, temperature was the only factor that explained a significant amount of the variability in population size for both species complexes. Psy densities decreased with increasing temperature whereas SRP densities increased with increasing temperature. River-borne populations of SRP were composed mainly of Pectobacterium versatile and P. aquaticum that have little known epidemiological importance. Only a few strains of Pectobacterium and Dickeya species reputed for their epidemiological impact were observed. In contrast, Psy populations at all sites were dominated by a genetic lineage of phylogroup 2 known from other studies for its broad host range and its geographic and habitat ubiquity. Our observations suggest that surveillance of river water for SRP could be leveraged to signal diagnostic and management reactions to avoid disease outbreaks. In contrast, the constant presence of Psy throughout the catchment in absence of regular and widespread disease outbreaks due to this group of bacteria suggests that surveillance should focus on future changes in land use, river water conditions and agronomic practices that could destabilize the mechanisms currently holding Psy outbreaks in check.
  PubDate: Thu, 21 Sep 2023 12:59:14 +000
k-mers&rft.title=Peer+Community+Journal&rft.issn=2804-3871&rft.date=2023&rft.volume=">Wittler, Roland - General encoding of canonical class="italique">k-mers
- Abstract: To index or compare sequences efficiently, often k-mers, i.e., substrings of fixed length k, are used. For efficient indexing or storage, k-mers are often encoded as integers, e.g., applying some bijective mapping between all possible σk k-mers and the interval [0, σk −1], where σ is the alphabet size. In many applications, e.g., when the reading direction of a DNA-sequence is ambiguous, canonical k-mers are considered, i.e., the lexicographically smaller of a given k-mer and its reverse (or reverse complement) is chosen as a representative. In naive encodings, canonical k-mers are not evenly distributed within the interval [0, σk −1]. We present a minimal encoding of canonical k-mers on alphabets of arbitrary size, i.e., a mapping to the interval [0, σk/2−1]. The approach is introduced for canonicalization under reversal and extended to canonicalization under reverse complementation. We further present a space and time efficient bit-based implementation for the DNA alphabet.
  PubDate: Wed, 20 Sep 2023 12:55:30 +000
Levallois, Pierre; Leblanc-Maridor, Mily et al. - Combining several
indicators to assess the effectiveness of tailor-made health plans in pig
farms
- Abstract: A tailor-made health plan is a set of recommendations for a farmer to achieve and maintain a high health and welfare status. Tailored to each farm, it is intended to be an effective way of triggering change. This study aimed to assess the effectiveness of tailor-made health plans in pig farms, designed in various situations after a systematic biosecurity and herd health audit. An intervention study was carried out in 20 farrow-to-finish pig farms. An initial standardized audit and discussion between the farm veterinarian and the farmer resulted in a specific plan. Compliance with recommendations was monitored during 8 months. Changes in health, performances and antimicrobial use were monitored. We defined two categories of plans: i) 14 plans targeting a given health disorder present in a farm; ii) 17 plans to improve prevention, not targeting a specific health disorder (a farm could have both types of plans). A small number of priority recommendations were made per farm. In 18 farms, farmers implemented 1 to 4 recommendations (none in 2 farms). Of the 17 non-disorder-specific plans, 11 were considered effective (>50% recommendations implemented), 3 intermediate (at least one but less than half of the recommendations implemented) and 3 ineffective (no implementation). Of the 14 disorder-specific plans, 9 were followed with full or good compliance (>50% recommendations implemented), 2 with intermediate compliance (1 recommendation implemented out of 2) and 3 with no compliance (no recommendation implemented). When at least one recommendation was implemented, change in clinical, performance and antimicrobial use indicators was assessed if a biological association with the disorder was deemed plausible and if their initial value showed room for improvement. Improvement was evidenced 4/9, 1/6 and 1/6 times for these indicators, respectively. Independently, veterinarians concluded that 8/14 plans were effective. Overall, tailor-made health plans were effective in triggering changes in farm management. Three key points were identified for future assessments of the effectiveness of tailor-made health plans. Compliance should be the first indicator of assessment. Outcome indicators and their monitoring periods should be adapted to each farm and to the targeted health disorder. Indicators should be combined to have a holistic description of the evolution of a health disorder. Further research is needed to identify how to select indicators to combine and how to combine them, according to health disorders.
  PubDate: Wed, 20 Sep 2023 12:54:57 +000
Logan, Corina; McCune, Kelsey et al. - Implementing a rapid geographic
range expansion - the role of behavior changes
- Abstract: It is generally thought that behavioral flexibility, the ability to change behavior when circumstances change, plays an important role in the ability of species to rapidly expand their geographic range. Great-tailed grackles (Quiscalus mexicanus) are a social, polygamous species that is rapidly expanding its geographic range by settling in new areas and habitats. They are behaviorally flexible and highly associated with human-modified environments, eating a variety of human foods in addition to foraging on insects and on the ground for other natural food items. They offer an opportunity to assess the role of behavior change over the course of their expansion. We compared behavior in wild-caught grackles from two populations across their range (an older population in the middle of the northern expansion front: Tempe, Arizona, and a more recent population on the northern edge of the expansion front: Woodland, California) to investigate whether certain behaviors (flexibility, innovativeness, exploration, and persistence) have higher averages and variances in the newer or older population. We found that grackles in the edge population had a higher flexibility variance (measured by reversal learning) and a higher persistence average (they participated in a larger proportion of trials), and that there were no population differences in average levels of flexibility, innovativeness (number of loci solved on a multiaccess box), or exploration (latency to approach a novel environment). Our results elucidated that individuals differentially expressing a particular behavior in an edge population could facilitate the rapid geographic range expansion of great-tailed grackles, and we found no support for the importance of several traits that were hypothesized to be involved in such an expansion. Our findings highlight the value of population studies and of breaking down cognitive concepts into direct measures of individual abilities to better understand how species might adapt to novel circumstances.
  PubDate: Wed, 20 Sep 2023 07:22:00 +000
Brachypodium+distachyon+is+shaped+by+distinct+past+and+present+ecological+niches&rft.title=Peer+Community+Journal&rft.issn=2804-3871&rft.date=2023&rft.volume=">Minadakis, Nikolaos; Williams, Hefin et al. - The demographic history of
the wild crop relative Brachypodium distachyon is shaped by distinct past
and present ecological niches
- Abstract: Closely related to economically important crops, the grass Brachypodium distachyon has been originally established as a pivotal species for grass genomics but more recently flourished as a model for developmental biology. Grasses encompass more than 10,000 species and cover more than 40% of the world land area from tropical to temperate regions. Given that grasses also supply about a fifth of the world's dietary protein as cereal grains, unlocking the sources of phenotypic variation in B. distachyon is hence of prime interest in fundamental and applied research in agronomy, ecology and evolution. We present here the B. distachyon diversity panel, which encompasses 332 fully sequenced accessions covering the whole species distribution from Spain to Iraq. By combining population genetics, niche modeling and landscape genomics, we suggest that B. distachyon recolonized Europe and the Middle East following the last glacial maximum. Consequently, the species faced new environmental conditions which led to clear associations between bioclimatic variables and genetic factors as well as footprints of positive selection in the genome. Altogether, this genomic resource offers a powerful alternative to Arabidopsis thaliana to investigate the genetic bases of adaptation and phenotypic plasticity in plants and more specifically in monocots.
  PubDate: Wed, 20 Sep 2023 07:20:30 +000
Karhulahti, Veli-Matti; Siutila, Miia et al. - Life Thinning and Gaming
Disorder: A Longitudinal Qualitative Registered Report
- Abstract: The academic debates regarding the psychiatric relevance of gaming disorder continue largely because the lived experiences of treatment-seekers remain mostly unstudied. This registered report addresses the above research gap with a longitudinal design that pursues a comparative descriptive understanding of how intensive gaming experiences evolve in both clinical and non-clinical life situations. Accompanied by a rich health survey, interpretative phenomenological analysis was adapted to understand in-depth interview data from treatment-seeking (n=5) and esports-playing (n=4) participants, the latter of which did not experience any gaming-related health problems. The interviews were carried out as a 1-year follow-up. The study finds intensive relationships with gaming to be experienced through multidimensional cyclicality. For treatment-seekers, this manifests as a shift in problem processing that involves a search for new gaming and life meanings; meanwhile, for esports-playing participants, the meanings of gaming evolve and can rapidly adapt to unexpected life events. We propose life thinningand resilience integration processes as working models that can help better describe and theoretically explain how some individuals end up seeking gaming-related treatment, whereas for others gaming continues to be part of their identity and resilience. The findings call for more qualitative registered reports with treatment-seekers and other intensively gaming people from different cultures to better understand the spectrum of intensive gaming phenomenologically—and specifically, what it means for people to seek treatment for their gaming.
  PubDate: Tue, 12 Sep 2023 13:30:39 +000
Raatz, Michael - Provision of essential resources as a persistence
strategy in food webs
- Abstract: Pairwise interactions in food webs, including those between predator and prey are often modulated by a third species. Such higher-order interactions are important structural components of natural food webs that can increase the stability of communities against perturbations and ensure continued ecosystem functioning. Particularly the flux of rare organic and inorganic compounds that are essential to species in the community can create higher-order interactions. Even though many such compounds exist, their effect on structuring communities is little understood. In this study, I perform invasion analyses on a general food web model that depicts apparent and exploitative competition. Introducing the provision of essential resources by a prey species to either its competitor or its predator as a higher-order interaction, I find that this mechanism can ensure the focal prey’s persistence. Larger dietary essentiality, i.e. a stronger dependence of the predator or the competitor on the essential resource can increase the invasion growth rate of the focal prey to positive values, thus promoting its persistence when it would go extinct for low essentiality. This research shows that essential resources and the higher-order interactions created by them should be considered in community ecology.
  PubDate: Tue, 12 Sep 2023 08:55:38 +000
Ixodes+ricinus+in+France:+a+systematic+map+and+narrative+review&rft.title=Peer+Community+Journal&rft.issn=2804-3871&rft.date=2023&rft.volume=">Perez, Grégoire; Bournez, Laure et al. - The distribution, phenology,
host range and pathogen prevalence of Ixodes ricinus in France: a
systematic map and narrative review
- Abstract: The tick Ixodes ricinus is the most important vector species of infectious diseases in European France. Understanding its distribution, phenology, and host species use, along with the distribution and prevalence of associated pathogens at a national scale is essential for developing prevention strategies. The aim of this paper is to provide a systematic map and narrative review of the existing knowledge on the eco-epidemiology of I. ricinus in France. Using literature published up to 2020, the present paper provides a distribution map for the species and a summary of environmental factors explaining observed geographical differences in phenology and temporal differences in abundance. The diversity of vertebrate host species used by this tick, along with their degree of infestation when available, are presented and discussed with respect to their potential contribution to the population dynamics of I. ricinus and the circulation of tick-borne zoonotic pathogens. Prevalence data of detected pathogens are summarised in different maps. Results from 187 identified references show that the species is present in most departments, but scarce under Mediterranean climates and in coastal habitats. Its phenology is generally bimodal with climate-associated variations. Abundance seems positively influenced by forest cover and host abundance. Rodents and ruminants are the most studied species groups, but the diversity of sampling protocols (e.g., location, season, exhaustivity of inspection) precluded direct comparisons between groups. Data on pathogens are patchy, with most studies conducted near research laboratories. Among pathogens, Borrelia burgdorferi sensu lato is the most examined and seems most prevalent in north-eastern and central France. The review highlights the gaps in our knowledge of tick-host-pathogen interactions, their ecologies and their distributions, and demonstrates the need to address these gaps in order to optimize tick and tick-borne diseases prevention and control.
  PubDate: Fri, 08 Sep 2023 12:12:50 +000
Bischoff, Robert J. - Geometric morphometric analysis of projectile points
from the Southwest United States
- Abstract: Traditional analyses of projectile points often use visual identification, the presence or absence of discrete characteristics, or linear measurements and angles to classify points into distinct types. Geometric morphometrics provides additional tools for analyzing, visualizing, and comparing projectile point morphology utilizing the whole or parts of the form in either two or three dimensions. This study is an analysis of the effectiveness of geometric morphometric methods for identifying technological similarity in 2D projectile point outlines for previously classified late prehistoric projectile points found in the U.S. Southwest and unclassified projectile points from Tonto Basin, Arizona. Various methods from geometric morphometrics were compared to determine which method best reproduced the original classification scheme. Elliptical Fourier analysis was compared with various configurations of semilandmark and landmark analyses using generalized Procrustes analysis. These methods were applied to the complete projectile point form, and the landmark analysis was also applied to half of the lower quadrant of the projectile point—essentially one corner of the projectile point. The landmark analysis applied to the corner of the projectile point provided the best results. This method was then applied to the Tonto Basin points. Hierarchical clustering was used on the Tonto Basin projectile point morphometric data to explore the variation in shapes between sites. To demonstrate that geometric morphometric methods can be used without relying on typologies, a network analysis of the morphometric distances was also conducted. This network graph produced distinct clusters of technological similarity in projectile point outlines, while also showing the continuous variation between points. These results demonstrate the effectiveness of geometric morphometrics for the 2D analysis of late prehistoric arrow points in the U.S. Southwest.
  PubDate: Mon, 04 Sep 2023 09:31:35 +000
k-mer+based+curation+of+raw+sequence+data:+application+in+
Drosophila+suzukii&rft.title=Peer+Community+Journal&rft.issn=2804-3871&rft.date=2023&rft.volume=">Gautier, Mathieu - Efficient k-mer based curation of raw sequence data:
application in Drosophila suzukii
- Abstract: Several studies have highlighted the presence of contaminated entries in public sequence repositories, calling for special attention to the associated metadata. Here, we propose and evaluate a fast and efficient k–mer-based approach to assess the degree of mislabeling or contamination. We applied it to high-throughput whole-genome raw sequence data for 236 Ind-Seq and 22 Pool-Seq samples of the invasive species Drosophila suzukii. We first used Clark software to build a dictionary of species-discriminating k–mers from the curated assemblies of 29 target drosophilid species (including D. melanogaster, D. simulans, D. subpulchrella, or D. biarmipes) and 12 common drosophila pathogens and commensals (including Wolbachia). Counting the number of k–mers composing each query sample sequence that matched a discriminating k–mer from the dictionary provided a simple criterion for assignment to target species and evaluation of the entire sample. Analyses of a wide range of samples, representative of both target and other drosophilid species, demonstrated very good performance of the proposed approach, both in terms of run time and accuracy of sequence assignment. Of the 236 D. suzukii individuals, five were reassigned to D. simulans and eleven to D. subpulchrella. Another four showed moderate to substantial microbial contamination. Similarly, among the 22 Pool-Seq samples analyzed, two from the native range were found to be contaminated with 1 and 7 D. subpulchrella individuals, respectively (out of 50), and one from Europe was found to be contaminated with 5 to 6 D. immigrans individuals (out of 100). Overall, the present analysis allowed the definition of a large curated dataset consisting of > 60 population samples representative of the worldwide genetic diversity, which may be valuable for further population genetics studies on D. suzukii. More generally, while we advocate careful sample identification and verification prior to sequencing, the proposed framework is simple and computationally efficient enough to be included as a routine post-hoc quality check prior to any data analysis and prior to data submission to public repositories.
  PubDate: Fri, 01 Sep 2023 14:17:20 +000
Van Rooij, Arnoul; Badel, Eric et al. - Modelling the growth stress in
tree branches: eccentric growth vs. reaction wood
- Abstract: This work aims to model the mechanical processes used by tree branches to control their posture despite their increasing weight loading. The two known options for a branch to maintain its orientation are the asymmetry of maturation stress, including reaction wood formation, and eccentric radial growth. Both options can be observed in nature and influence the stress distribution developed in the branch each year. This so-called "growth stress" reflects the mechanical state of the branch. In this work, a growth stress model was developed at the cross-section level in order to quantify and study the biomechanical impact of each process. For illustration, this model was applied to branches of two 50-year-old trees, one softwood Pinus pinaster, and one hardwood Prunus avium (wild cherry tree), both simulated with the AmapSim discrete element software. For the wild cherry tree, the computed outputs highlighted that the eccentricity of radial growth seems to be as efficient as the formation of reaction wood to maintain postural control despite the increasing gravity. For the pine tree, eccentric radial growth appears to be less efficient than the formation of reaction wood. But although it does not necessarily act as a relevant lever for postural control, it greatly modifies the profile pattern of mechanical stress and could provide mechanical safety of the branch. This work opens experimental perspectives to understand the biomechanical processes involved in the formation of branches and their mechanical safety.
  PubDate: Thu, 31 Aug 2023 09:26:02 +000
Newman, Katerina; Forestier, Cyril et al. - Comparing habit-behaviour
relationships for organised versus leisure time physical activity
- Abstract: Evidence shows that people with strong physical activity habits tend to engage in more physical activity than those with weaker habits, but little is known about how habit influences specific types of physical activity. This study aimed to test whether mean level of habit strength and magnitude of the habit strength – behaviour association differed as a function of physical activity modality. Participants (N = 120; M age = 25 years, 75% female) who reported engaging in organised sport separately reported their habit strength for organised sport and leisure time physical activity as well as the time they spent engaging in these physical activity behaviours. Means comparisons and multilevel modelling revealed that people had significantly stronger habit for organised sport than for leisure time physical activity. Crucially, no significant difference was found in the magnitude of the sport-habit and leisure-habit link. Post-hoc analyses revealed that habit was stronger for team sport compared to individual sport, but that there was no significant difference in sport-habit association between team and individual sports. Research should therefore focus on identifying the characteristics of team sports-based activity that are particularly conducive to habit formation as a precursor to developing interventions to promote performance of leisure time activity in a way that would attain such characteristics.
  PubDate: Thu, 31 Aug 2023 09:25:05 +000
Corynebacterium+diphtheriae+genomic+framework+sheds+light+on+current+diphtheria+reemergence&rft.title=Peer+Community+Journal&rft.issn=2804-3871&rft.date=2023&rft.volume=">Hennart, Mélanie; Crestani, Chiara et al. - A global Corynebacterium
diphtheriae genomic framework sheds light on current diphtheria
reemergence
- Abstract: Background: Diphtheria, caused by Corynebacterium diphtheriae, reemerges in Europe since 2022. Genomic sequencing can inform on transmission routes and genotypes of concern, but currently, no standard approach exists to detect clinically important genomic features and to interpret emergence in the global C. diphtheriae population framework. Methods: We developed the bioinformatics pipeline diphtOscan (available at https://gitlab.pasteur.fr/BEBP/diphtoscan) to extract from genomes of Corynebacteria of the diphtheriae species complex, medically relevant features including tox gene presence and disruption. We analyzed 101 human C. diphtheriae isolates collected in 2022 in metropolitan and overseas France (France-2022). To define the population background of this emergence, we sequenced 379 additional isolates (mainly from France, 2018-2021) and collated 870 publicly-available genomes. Results: The France-2022 isolates comprised 45 tox-positive (44 toxigenic) isolates, mostly imported, belonging to 10 sublineages (<500 distinct core genes). The global dataset comprised 245 sublineages and 33.9% tox-positive genomes, with diphtOscan predicting non-toxigenicity in 16.0% of these. 12% of the global isolates, and 43.6% of France-2022 ones, were multidrug resistant. Convergence of toxigenicity with penicillin and erythromycin resistance was observed in 2 isolates from France-2022. Phylogenetic lineages Gravis and Mitis contrasted strikingly in their pathogenicity-associated genes. Conclusions: This work provides a bioinformatics tool and global population framework to analyze C. diphtheriae genomes, revealing important heterogeneities in virulence and resistance features. Emerging genotypes combining toxigenicity and first-line antimicrobial resistance represent novel threats. Genomic epidemiology studies of C. diphtheriae should be intensified globally to improve understanding of reemergence and spatial spread.
  PubDate: Thu, 31 Aug 2023 09:24:20 +000
Emerling, Christopher A; Gibb, Gillian C et al. - Genomic data suggest
parallel dental vestigialization within the xenarthran radiation
- Abstract: The recent influx of genomic data has provided greater insights into the molecular basis for regressive evolution, or vestigialization, through gene loss and pseudogenization. As such, the analysis of gene degradation patterns has the potential to provide insights into the evolutionary history of regressed anatomical traits. We specifically applied these principles to the xenarthran radiation (anteaters, sloths, armadillos), which is characterized by taxa with a gradation in regressed dental phenotypes. Whether the pattern among extant xenarthrans is due to an ancient and gradual decay of dental morphology or occurred repeatedly in parallel is unknown. We tested these competing hypotheses by examining 11 core dental genes in most living species of Xenarthra, characterizing shared inactivating mutations and patterns of relaxed selection during their radiation. Here we report evidence of independent and distinct events of dental gene loss in the major xenarthran subclades. First, we found strong evidence of complete enamel loss in the common ancestor of sloths and anteaters, suggested by the inactivation of five enamel-associated genes (AMELX, AMTN, MMP20, ENAM, ACP4). Next, whereas dental regression appears to have halted in sloths, presumably a critical event that ultimately permitted adaptation to an herbivorous lifestyle, anteaters continued losing genes on the path towards complete tooth loss. Echoes of this event are recorded in the genomes of all living anteaters, being marked by a 2-bp deletion in a gene critical for dentinogenesis (DSPP) and a putative shared 1-bp insertion in a gene linked to tooth retention (ODAPH). By contrast, in the two major armadillo clades, genes pertaining to the dento-gingival junction and amelogenesis appear to have been independently inactivated prior to losing all or some enamel. These genomic data provide evidence for multiple pathways and rates of anatomical regression, and underscore the utility of using pseudogenes to reconstruct evolutionary history when fossils are sparse.
  PubDate: Tue, 29 Aug 2023 15:00:19 +000
Rancilhac, Loïs; Miralles, Aurélien et al. - Phylogeographic breaks and
how to find them: An empirical attempt at separating vicariance from
isolation by distance in a lizard with restricted dispersal
- Abstract: Aim: Discontinuity in the distribution of genetic diversity (often based on mtDNA) is usually interpreted as evidence for phylogeographic breaks, underlying vicariant units. However, a misleading signal of phylogeographic break can arise in the absence of barrier to gene flow, under mechanisms of isolation by distance (IBD). How and under which conditions phylogeographic breaks can be reliably differentiated from populations evolving under IBD remain unclear. Here, we use multi-locus sequence data from a widely distributed lizard species to address these questions in an empirical setting. Location: Morocco. Taxon: Spiny-footed lizard (Acanthodactylus erythrurus), Squamata: Lacertidae. Methods: Using 325 samples from 40 localities, we identified genetic discontinuities within A. erythrurus based on a mitochondrial fragment and nine nuclear markers independently. Using the nuclear markers, we then applied linear regression models to investigate whether genetic divergence could be explained by geographical distances alone, or barriers to gene flow (real phylogeographic breaks). Results: A. erythrurus is characterized by an important mitochondrial diversity, with 11 strongly supported phylogeographic lineages with a crown age of 6 Mya. Nuclear markers, however, yielded weak phylogenetic support for these lineages. Using clustering methods based on genotypes at nine nuclear loci, we identified phylogeographic clusters that were partly discordant with the mtDNA lineages. Tests of IBD delimited at least four groups of populations separated by barriers to gene flow, but unambiguous separation of vicariance from IBD remained challenging in several cases. Main conclusions: The genetic diversity of A. erythrurus originates from a mix of IBD and vicariance, which were difficult to distinguish, and resulted in similar levels of mitochondrial differentiation. These results highlight that phylogeographic breaks inferred from mitochondrial data should be further investigated using multi-locus data and explicit testing to rule out alternative processes generating discontinuities in mitochondrial diversity, including IBD. We identified four groups of populations within A. erythrurus, separated by barriers to gene flow, but even using nine independent nuclear makers the power of our approach was limited, and further investigation using genome-wide data will be required to resolve the phylogeographic history of this species.
  PubDate: Tue, 29 Aug 2023 14:59:38 +000