Identification of Genes Differentially Expressed in Response to Cold in Pisum sativum Using RNA Sequencing Analyses

International audienceLow temperature stress affects growth and development in pea (Pisum sativum L.) and decreases yield. In this study, RNA sequencing time series analyses performed on lines, Champagne frost-tolerant and Térèse frost-sensitive, during a low temperature treatment versus a control condition, led us to identify 4981 differentially expressed genes. Thanks to our experimental design and statistical analyses, we were able to classify these genes into three sets. The first one was composed of 2487 genes that could be related to the constitutive differences between the two lines and were not regulated during cold treatment. The second gathered 1403 genes that could be related to the chilling response. The third set contained 1091 genes, including genes that could be related to freezing tolerance. The identification of differentially expressed genes related to cold, oxidative stress, and dehydration responses, including some transcription factors and kinases, confirmed the soundness of our analyses. In addition, we identified about one hundred genes, whose expression has not yet been linked to cold stress. Overall, our findings showed that both lines have different characteristics for their cold response (chilling response and/or freezing tolerance), as more than 90% of differentially expressed genes were specific to each of them

A High-Quality Grapevine Downy Mildew Genome Assembly Reveals Rapidly Evolving and Lineage-Specific Putative Host Adaptation Genes

Downy mildews are obligate biotrophic oomycete pathogens that cause devastating plant diseases on economically important crops. Plasmopara viticola is the causal agent of grapevine downy mildew, a major disease in vineyards worldwide. We sequenced the genome of Pl. viticola with PacBio long reads and obtained a new 92.94 Mb assembly with high contiguity (359 scaffolds for a N50 of 706.5 kb) due to a better resolution of repeat regions. This assembly presented a high level of gene completeness, recovering 1,592 genes encoding secreted proteins involved in plant–pathogen interactions. Plasmopara viticola had a two-speed genome architecture, with secreted protein-encoding genes preferentially located in gene-sparse, repeat-rich regions and evolving rapidly, as indicated by pairwise dN/dS values. We also used short reads to assemble the genome of Plasmopara muralis, a closely related species infecting grape ivy (Parthenocissus tricuspidata). The lineage-specific proteins identified by comparative genomics analysis included a large proportion of RxLR cytoplasmic effectors and, more generally, genes with high dN/dS values. We identified 270 candidate genes under positive selection, including several genes encoding transporters and components of the RNA machinery potentially involved in host specialization. Finally, the Pl. viticola genome assembly generated here will allow the development of robust population genomics approaches for investigating the mechanisms involved in adaptation to biotic and abiotic selective pressures in this species

Биофизика зрительной сенсорной системы человека

Зрительная сенсорная система – это система, которая воспринимает излучение видимого спектра, после чего формируется изображение предметов окружающей среды в виде определенных ощущений (сенсорных чувств)

The future of biotic indices in the ecogenomic era: Integrating (e)DNA metabarcoding in biological assessment of aquatic ecosystems

The bioassessment of aquatic ecosystems is currently based on various biotic indices that use the occurrence and/or abundance of selected taxonomic groups to define ecological status. These conventional indices have some limitations, often related to difficulties in morphological identification of bioindicator taxa. Recent development of DNA barcoding and metabarcoding could potentially alleviate some of these limitations, by using DNA sequences instead of morphology to identify organisms and to characterize a given ecosystem. In this paper, we review the structure of conventional biotic indices, and we present the results of pilot metabarcoding studies using environmental DNA to infer biotic indices. We discuss the main advantages and pitfalls of metabarcoding approaches to assess parameters such as richness, abundance, taxonomic composition and species ecological values, to be used for calculation of biotic indices. We present some future developments to fully exploit the potential of metabarcoding data and improve the accuracy and precision of their analysis. We also propose some recommendations for the future integration of DNA metabarcoding to routine biomonitoring programs.info:eu-repo/semantics/publishedVersio

COVID-19 symptoms at hospital admission vary with age and sex: results from the ISARIC prospective multinational observational study

Background: The ISARIC prospective multinational observational study is the largest cohort of hospitalized patients with COVID-19. We present relationships of age, sex, and nationality to presenting symptoms. Methods: International, prospective observational study of 60 109 hospitalized symptomatic patients with laboratory-confirmed COVID-19 recruited from 43 countries between 30 January and 3 August 2020. Logistic regression was performed to evaluate relationships of age and sex to published COVID-19 case definitions and the most commonly reported symptoms. Results: ‘Typical’ symptoms of fever (69%), cough (68%) and shortness of breath (66%) were the most commonly reported. 92% of patients experienced at least one of these. Prevalence of typical symptoms was greatest in 30- to 60-year-olds (respectively 80, 79, 69%; at least one 95%). They were reported less frequently in children (≤ 18 years: 69, 48, 23; 85%), older adults (≥ 70 years: 61, 62, 65; 90%), and women (66, 66, 64; 90%; vs. men 71, 70, 67; 93%, each P < 0.001). The most common atypical presentations under 60 years of age were nausea and vomiting and abdominal pain, and over 60 years was confusion. Regression models showed significant differences in symptoms with sex, age and country. Interpretation: This international collaboration has allowed us to report reliable symptom data from the largest cohort of patients admitted to hospital with COVID-19. Adults over 60 and children admitted to hospital with COVID-19 are less likely to present with typical symptoms. Nausea and vomiting are common atypical presentations under 30 years. Confusion is a frequent atypical presentation of COVID-19 in adults over 60 years. Women are less likely to experience typical symptoms than men

Evolution of non conventional tracers dependent on age and sex : the paleopathology contribution

De nombreuses méthodes ont été développées pour estimer l’âge au décès de l’adulte mature. De plus, l’observation de certaines lésions dégénératives amène parfois l’anthropologue à classer un sujet chez les individus âgés, plus spécifiquement lorsqu’elles atteignent la colonne vertébrale. Or si l’ostéoarthrose rachidienne a fait l’objet de nombreux articles en paléopathologie, l’exploitation de l’ensemble des articulations vertébrales au sein d’une méthodologie est quasi inexistante. Ainsi, afin de déterminer le rôle d’une étude paléopathologique dans le vieillissement osseux, nous avons mis au point une méthode originale d’enregistrement des données.Cette méthode, basée sur un découpage topographique du rachis et un système de cotation des lésions arthrosiques, permet d’étudier l’atteinte dégénérative grâce à l’obtention d’un score de sévérité pondéré à l’état de conservation de la vertèbre. Le matériel d’étude est constitué de 750 individus répartis équitablement sur 3 périodes historiques (médiévale, moderne et contemporaine) permettant ainsi d’effectuer une comparaison diachronique des résultats. Les 250 individus constituant l’échantillon contemporain proviennent de collections documentées (Schoten, Belgique ; Bologne, Italie ; Sassari, Sardaigne). L’âge des sujets ostéoarchéologiques a été estimé grâce aux méthodes utilisant la surface auriculaire de l’os coxal (Lovejoy, 1985 et Schmitt, 2005). La même estimation a été faite sur les collections âge/sexe connus afin de déterminer le pourcentage d’erreur commis sur nos échantillons médiéval et moderne. Pour chaque articulation rachidienne nous avons testé statistiquement la relation entre l’âge au décès et les scores de sévérité, ainsi que les dissemblances d’atteinte en fonction du sexe et de la latéralité. Des études qualitatives ont également été entreprises, permettant ainsi d’observer l’expansion des modifications dégénératives en fonction des différentes classes d’âge.Au terme de ce travail de recherche, nous avons constaté l’existence d’une relation entre l’âge et la sévérité des atteintes dégénératives vertébrales. Cependant ce lien est modéré par divers facteurs variant en fonction des articulations et des segments vertébraux. Parmi ces facteurs, nous avons relevé le sexe et la latéralité. Des informations concernant le mode de développement des lésions dégénératives rachidiennes ont également été acquises. Ainsi, nous avons observé que l’OA se développait dans un premier temps de manière progressive le long du rachis, puis, avec l’âge et selon le type d’articulation, les lésions se concentrent sur les mêmes vertèbres (celles étant le plus soumises aux forces biomécaniques). C’est également sur ces mêmes vertèbres que se manifestent les lésions les plus sévères. Ainsi, il semble indispensable, lors d’une étude paléoépidémiologique, d’avoir un nombre minimum de vertèbres et parmi celles-ci les vertèbres les plus sollicitées en pré requis. De plus, nous préconisons lors d’un examen paléopathologique, de considérer plus que la sévérité même de la lésion, le nombre de zone atteintes comme estimateur de l’âge au décès.Various methods have been developed to estimate age at death of adults and anthropologists sometimes use degenerative vertebral lesions. In paleopathology contrary to vertebral degenerative disease (VDD) that has been extensively studied, the whole vertebral joints have almost never been investigated by standardized methodology that allows approximating the epidemiological performance of various vertebral joints in relation to articular degeneration. In order to better define the paleoepidemiological aspects of bone ageing we have developed a research program based on the recording of degenerative lesions in the vertebral joints.This approach is based on a topographic division of spine and a grading system of degenerative lesions, permits the study VDD using “a severity score” according to the state of vertebral preservation. We studied 750 spines provided equally from three samples (medieval, modern and contemporary) to compare periods. The 250 contemporary spines are from documented collections of Schoten (Belgium), Bologna (Italy) and Sassari (Sardinia). Age estimation was made for each archaeological sample using methods based on the observation of the sacro-iliac joint surface (Lovejoy, 1985 and Schmitt, 2005). The same estimation of age has been made with known sex and age collections in order to calculate error estimates. For each joint of the spine, statistical tests have been made to study relationship between the age at death and “the severity score” and to compare variability between sex and spine laterality. Quantitative studies have also been made to observe degenerative change resulting from advancing age.At the end of this work, we observed the relation between age and the severity of VDD. That link can vary according to joint type, spinal segment and various factors such as sex or laterality. Information concerning the evolution of degenerative lesions has been acquired. VDD appears initially to progressively affect the entire spine and then with aging, degenerative lesions focus on the same vertebrae (those that are the most used biomechanically). Those vertebrae always show the most severe lesions. Thus it is essential for paleoepidemiologic studies to include a minimal number of vertebrae and among them those that are the most used. We also suggest considering the number of affected zones to estimate age at death instead of the lesion severity

Existe-t-il un recrutement particulier à l’intérieur des tranchées d’inhumation du cimetière des Petites Crottes (Marseille)?

International audienc

Evolution des marqueurs non conventionnels âge et sexe dépendants (apport de la paléopathologie)

De nombreuses méthodes ont été développées pour estimer l âge au décès de l adulte mature. De plus, l observation de certaines lésions dégénératives amène parfois l anthropologue à classer un sujet chez les individus âgés, plus spécifiquement lorsqu elles atteignent la colonne vertébrale. Or si l ostéoarthrose rachidienne a fait l objet de nombreux articles en paléopathologie, l exploitation de l ensemble des articulations vertébrales au sein d une méthodologie est quasi inexistante. Ainsi, afin de déterminer le rôle d une étude paléopathologique dans le vieillissement osseux, nous avons mis au point une méthode originale d enregistrement des données.Cette méthode, basée sur un découpage topographique du rachis et un système de cotation des lésions arthrosiques, permet d étudier l atteinte dégénérative grâce à l obtention d un score de sévérité pondéré à l état de conservation de la vertèbre. Le matériel d étude est constitué de 750 individus répartis équitablement sur 3 périodes historiques (médiévale, moderne et contemporaine) permettant ainsi d effectuer une comparaison diachronique des résultats. Les 250 individus constituant l échantillon contemporain proviennent de collections documentées (Schoten, Belgique ; Bologne, Italie ; Sassari, Sardaigne). L âge des sujets ostéoarchéologiques a été estimé grâce aux méthodes utilisant la surface auriculaire de l os coxal (Lovejoy, 1985 et Schmitt, 2005). La même estimation a été faite sur les collections âge/sexe connus afin de déterminer le pourcentage d erreur commis sur nos échantillons médiéval et moderne. Pour chaque articulation rachidienne nous avons testé statistiquement la relation entre l âge au décès et les scores de sévérité, ainsi que les dissemblances d atteinte en fonction du sexe et de la latéralité. Des études qualitatives ont également été entreprises, permettant ainsi d observer l expansion des modifications dégénératives en fonction des différentes classes d âge.Au terme de ce travail de recherche, nous avons constaté l existence d une relation entre l âge et la sévérité des atteintes dégénératives vertébrales. Cependant ce lien est modéré par divers facteurs variant en fonction des articulations et des segments vertébraux. Parmi ces facteurs, nous avons relevé le sexe et la latéralité. Des informations concernant le mode de développement des lésions dégénératives rachidiennes ont également été acquises. Ainsi, nous avons observé que l OA se développait dans un premier temps de manière progressive le long du rachis, puis, avec l âge et selon le type d articulation, les lésions se concentrent sur les mêmes vertèbres (celles étant le plus soumises aux forces biomécaniques). C est également sur ces mêmes vertèbres que se manifestent les lésions les plus sévères. Ainsi, il semble indispensable, lors d une étude paléoépidémiologique, d avoir un nombre minimum de vertèbres et parmi celles-ci les vertèbres les plus sollicitées en pré requis. De plus, nous préconisons lors d un examen paléopathologique, de considérer plus que la sévérité même de la lésion, le nombre de zone atteintes comme estimateur de l âge au décès.Various methods have been developed to estimate age at death of adults and anthropologists sometimes use degenerative vertebral lesions. In paleopathology contrary to vertebral degenerative disease (VDD) that has been extensively studied, the whole vertebral joints have almost never been investigated by standardized methodology that allows approximating the epidemiological performance of various vertebral joints in relation to articular degeneration. In order to better define the paleoepidemiological aspects of bone ageing we have developed a research program based on the recording of degenerative lesions in the vertebral joints.This approach is based on a topographic division of spine and a grading system of degenerative lesions, permits the study VDD using a severity score according to the state of vertebral preservation. We studied 750 spines provided equally from three samples (medieval, modern and contemporary) to compare periods. The 250 contemporary spines are from documented collections of Schoten (Belgium), Bologna (Italy) and Sassari (Sardinia). Age estimation was made for each archaeological sample using methods based on the observation of the sacro-iliac joint surface (Lovejoy, 1985 and Schmitt, 2005). The same estimation of age has been made with known sex and age collections in order to calculate error estimates. For each joint of the spine, statistical tests have been made to study relationship between the age at death and the severity score and to compare variability between sex and spine laterality. Quantitative studies have also been made to observe degenerative change resulting from advancing age.At the end of this work, we observed the relation between age and the severity of VDD. That link can vary according to joint type, spinal segment and various factors such as sex or laterality. Information concerning the evolution of degenerative lesions has been acquired. VDD appears initially to progressively affect the entire spine and then with aging, degenerative lesions focus on the same vertebrae (those that are the most used biomechanically). Those vertebrae always show the most severe lesions. Thus it is essential for paleoepidemiologic studies to include a minimal number of vertebrae and among them those that are the most used. We also suggest considering the number of affected zones to estimate age at death instead of the lesion severity.AIX-MARSEILLE2-Bib.electronique (130559901) / SudocSudocFranceF