Large Bottleneck Size in Cauliflower Mosaic Virus Populations during Host Plant Colonization

The effective size of populations (Ne) determines whether selection or genetic drift is the predominant force shaping their genetic structure and evolution. Despite their high mutation rate and rapid evolution, this parameter is poorly documented experimentally in viruses, particularly plant viruses. All available studies, however, have demonstrated the existence of huge within-host demographic fluctuations, drastically reducing Ne upon systemic invasion of different organs and tissues. Notably, extreme bottlenecks have been detected at the stage of systemic leaf colonization in all plant viral species investigated so far, sustaining the general idea that some unknown obstacle(s) imposes a barrier on the development of all plant viruses. This idea has important implications, as it appoints genetic drift as a constant major force in plant virus evolution. By co-inoculating several genetic variants of Cauliflower mosaic virus into a large number of replicate host plants, and by monitoring their relative frequency within the viral population over the course of the host systemic infection, only minute stochastic variations were detected. This allowed the estimation of the CaMV Ne during colonization of successive leaves at several hundreds of viral genomes, a value about 100-fold higher than that reported for any other plant virus investigated so far, and indicated the very limited role played by genetic drift during plant systemic infection by this virus. These results suggest that the barriers that generate bottlenecks in some plant virus species might well not exist, or can be surmounted by other viruses, implying that severe bottlenecks during host colonization do not necessarily apply to all plant-infecting viruses

Molecular analysis of iduronate -2- sulfatase gene in Tunisian patients with mucopolysaccharidosis type II

Mucopolysaccharidosis type II (MPS II, Hunter syndrome) is X-linked recessive lysosomal storage disorder resulting from the defective activity of the enzyme iduronate-2-sulfatase (IDS). Hunter disease can vary from mild to severe, depending on the level of enzyme deficiency. We report the IDS mutation and polymorphisms causing the Hunter syndrome in patients from one family in Tunisi

In Silico Characterisation of Putative Prophages in Lactobacillaceae Used in Probiotics for Vaginal Health

While live biotherapeutics offer a promising approach to optimizing vaginal microbiota, the presence of functional prophages within introduced Lactobacillaceae strains could impact their safety and efficacy. We evaluated the presence of prophages in 895 publicly available Lactobacillaceae genomes using Phaster, Phigaro, Phispy, Prophet and Virsorter. Prophages were identified according to stringent (detected by ≥4 methods) or lenient criteria (detected by ≥2 methods), both with >80% reciprocal sequence overlap. The stringent approach identified 448 prophages within 359 genomes, with 40.1% genomes harbouring at least one prophage, while the lenient approach identified 1671 prophages within 83.7% of the genomes. To confirm our in silico estimates in vitro, we tested for inducible prophages in 57 vaginally-derived and commercial Lactobacillaceae isolates and found inducible prophages in 61.4% of the isolates. We characterised the in silico predicted prophages based on weighted gene repertoire relatedness and found that most belonged to the Siphoviridae or Myoviridae families. ResFam and eggNOG identified four potential antimicrobial resistance genes within the predicted prophages. Our results suggest that while Lactobacillaceae prophages seldomly carry clinically concerning genes and thus unlikely a pose a direct risk to human vaginal microbiomes, their high prevalence warrants the characterisation of Lactobacillaceae prophages in live biotherapeutics

Presence and Persistence of Putative Lytic and Temperate Bacteriophages in Vaginal Metagenomes from South African Adolescents

The interaction between gut bacterial and viral microbiota is thought to be important in human health. While fluctuations in female genital tract (FGT) bacterial microbiota similarly determine sexual health, little is known about the presence, persistence, and function of vaginal bacteriophages. We conducted shotgun metagenome sequencing of cervicovaginal samples from South African adolescents collected longitudinally, who received no antibiotics. We annotated viral reads and circular bacteriophages, identified CRISPR loci and putative prophages, and assessed their diversity, persistence, and associations with bacterial microbiota composition. Siphoviridae was the most prevalent bacteriophage family, followed by Myoviridae, Podoviridae, Herelleviridae, and Inoviridae. Full-length siphoviruses targeting bacterial vaginosis (BV)-associated bacteria were identified, suggesting their presence in vivo. CRISPR loci and prophage-like elements were common, and genomic analysis suggested higher diversity among Gardnerella than Lactobacillus prophages. We found that some prophages were highly persistent within participants, and identical prophages were present in cervicovaginal secretions of multiple participants, suggesting that prophages, and thus bacterial strains, are shared between adolescents. The number of CRISPR loci and prophages were associated with vaginal microbiota stability and absence of BV. Our analysis suggests that (pro)phages are common in the FGT and vaginal bacteria and (pro)phages may interact

Mucopolysaccharidosis type I: molecular characteristics of two novel alpha-L-iduronidase mutations in Tunisian patients

<p>Abstract</p> <p>Background</p> <p>Mucopolysaccharidosis type I (MPS I) is an autosomal storage disease resulting from defective activity of the enzyme α-L-iduronidase (IDUA). This glycosidase is involved in the degradation of heparan sulfate and dermatan sulfate. MPS I has severe and milder phenotypic subtypes.</p> <p>Aim of study: This study was carried out on six newly collected MPS I patients recruited from many regions of Tunisia.</p> <p>Patients and methods: Mutational analysis of the IDUA gene in unrelated MPS I families was performed by sequencing the exons and intron-exon junctions of IDUA gene.</p> <p>Results</p> <p>Two novel IDUA mutations, p.L530fs (1587_1588 insGC) in exon 11 and p.F177S in exon 5 and two previously reported mutations p.P533R and p.Y581X were detected. The patient in family 1 who has the Hurler phenotype was homozygous for the previously described nonsense mutation p.Y581X.</p> <p>The patient in family 2 who also has the Hurler phenotype was homozygous for the novel missense mutation p.F177S. The three patients in families 3, 5 and 6 were homozygous for the p.P533R mutation. The patient in family 4 was homozygous for the novel small insertion 1587_1588 insGC. In addition, eighteen known and one unknown IDUA polymorphisms were identified.</p> <p>Conclusion</p> <p>The identification of these mutations should facilitate prenatal diagnosis and counseling for MPS I in Tunisia.</p> <p>Background</p> <p>Mucopolysaccharidosis type I (MPS I) is an autosomal recessive lysosomal storage disorder caused by the deficient activity of the enzyme of α-L-iduronidase (IDUA, EC 3.2.1.76). This glycosidase is involved in the degradation of heparan sulfate and dermatan sulfate. The clinical phenotype of MPS I ranges from the very severe in Hurler syndrome (MPS IH) to the relatively benign in Scheie syndrome (MPS IS), with an intermediate phenotype designated Hurler/Scheie (MPS IH/S) <abbrgrp><abbr bid="B1">1</abbr></abbrgrp>. Isolation of complementary and genomic DNAs encoding human α -L- iduronidase <abbrgrp><abbr bid="B2">2</abbr><abbr bid="B3">3</abbr></abbrgrp> have enable the identification of mutations underlying the enzyme defect and resulting in MPS I clinical phenotype. More than 100 mutations have been reported in patients with the MPS I subtypes (Human Gene Mutation Database; <url>http://www.hgmd.org</url>). High prevalence of the common mutations p.W402X and p.Q70X has been described; both of them in the severe clinical forms <abbrgrp><abbr bid="B4">4</abbr><abbr bid="B5">5</abbr></abbrgrp>. A high prevalence of common mutation p.P533R has also been described in MPS I patients with various phenotypes <abbrgrp><abbr bid="B5">5</abbr><abbr bid="B6">6</abbr></abbrgrp>. In addition, rare mutations including single base substitution, deletion, insertion and splicing site mutation have been identified <abbrgrp><abbr bid="B7">7</abbr></abbrgrp>, indicating a high degree of allelic heterogeneity in IDUA gene.</p> <p>Here, we described two novel IDUA mutations in MPS I Tunisian patients. These lesions were homoallelic in all the patients of the six families investigated as consanguineous marriages are still frequent in Tunisia <abbrgrp><abbr bid="B8">8</abbr></abbrgrp>.</p

Etude expérimentale de l'évolution du mode de transmission du Cauliflower mosaic virus

Diplôme : otherLe CaMV est le membre type du genre Caulimovirus infectant principalement les Brassicaceae et transmis par vecteurs selon le mode non-circulant. L’interaction entre le virus et le vecteur se fait par l’intermédiaire de la protéine P2 qui est nommée Helper Component (HC). Ce mécanisme moléculaire de transmission (présence d’un HC) permet à un génome X d’assister la transmission d’un génome Y (phénomène nommé HC-trans-complémentation). Nous posons ici l’hypothèse selon laquelle la HC-trans-complémentation constitue une stratégie permettant de mieux gérer la contrainte imposée par les goulots d’étranglement survenant à chaque événement de transmission. Chaque goulot d’étranglement est susceptible de provoquer la chute de la valeur sélective des populations virales (notamment à cause de la fixation des mutations délétères). Nous avons mis en place quatre lignées virales dont les goulots d’étranglement ont été composés d’un, deux, cinq et dix génomes viraux. Après quatre goulots, l’expérience n’a malheureusement pas pu être menée à son terme, à cause de problèmes expérimentaux non-suspectés a priori. La recombinaison pourrait être un moyen de re-créer des génomes sans mutation délétère. Nous avons estimé la fréquence de recombinaison durant un cycle d’infection du CaMV. Les génomes viraux issus de cinq plantes co-inoculées par deux clones quasi-isogéniques ont été analysés. La proportion de génomes recombinants présents semble particulièrement élévée et le taux de recombinaison semble homogène le long de tout le génome. Nous nous sommes attachés à déterminer si l’épissage de 70% des ARN 35S viraux avait pour fonction primaire de réguler l’expression de P2 et nous avons pu le confirmer. De manière indirecte, le HC pourrait donc imposer un coût sélectif par (i) la régulation du complexe réalisant l’épissage des ARN totaux et (ii) la synthèse de 70 % d’ARN viral ne servant pas de matrice lors de la réplication. Par ailleurs, des expériences de compétitions entre un isolat non-self-transmissible (ne produisant pas P2) et un isolat self-transmissible n’ont pas mis en évidence de coût sélectif puisque l’isolat self-transmissible a été largement majoritaire à la suite des co-inoculations, quelque soit la fréquence de départ. Ces deux résultats sont largement discutés

Evolutionary biology and development model of medicines: A necessary ‘pas de deux’ for future successful bacteriophage therapy

International audienceThe increase in frequency of multidrug-resistant bacteria worldwide is largely the result of the massive use of antibiotics in the second half of the 20th century. These relatively recent changes in human societies revealed the great evolutionary capacities of bacteria towards drug resistance. In this article, we hypothesize that the success of future antibacterial strategies lies in taking into account both these evolutionary processes and the way human activities influence them. Faced with the increasing prevalence of multidrug-resistant bacteria and the scarcity of new antibacterial chemical molecules, the use of bacteriophages is considered as a complementary and/or alternative therapy. After presenting the evolutionary capacities of bacteriophages and bacteria, we show how the development model currently envisaged (based on the classification of bacteriophages as medicinal products similar to antibacterial chemical molecules) ignores the evolutionary processes inherent in bacteriophage therapy. This categorization imposes to bacteriophage therapy a specific conception of what a treatment and a therapeutic scheme should be as well as its mode of production and prescription. We argue that a new development model is needed that would allow the use of therapeutic bacteriophages fully adapted (after in vitro ‘bacteriophage training’) to the aetiologic bacteria and/or aimed at rendering bacteria either avirulent or antibiotic-susceptible (‘bacteriophage steering’). To not repeat the mistakes made with antibiotics, we must now think about and learn from the ways in which the materialities of microbes (e.g. evolutionary capacities of both bacteriophages and bacteria) are intertwined with those of societies

Evoluciones e involuciones en biomedicine. Fagoterapia y tratamiento de infecciones bacterianas resistentes a los antibióticos

La thérapie phagique, l’utilisation de virus bactériophages pour traiter les infections bactériennes, est une pratique centenaire méconnue qui connaît un regain d’intérêt depuis le début des années 2000 en grande partie en raison de l’augmentation de la résistance bactérienne aux molécules chimiques antibiotiques. Cet article, issu d’une collaboration de longue date entre une anthropologue et un biologiste, explore les possibilités de développement d’une thérapie prenant véritablement en compte les capacités évolutives et involutives des vivants. En revenant brièvement sur l’histoire du développement et de l’utilisation des antibiotiques, et en nous fondant sur plus de quatre années de terrain, nous montrons, avec les acteurs et actrices de la thérapie phagique, qu’un tel développement implique de repenser conjointement certaines des infrastructures matérielles de nos sociétés et le statut ontologique accordé aux microorganismes.Phage therapy, the use of bacteriophage viruses to treat bacterial infections, is a lesser-known, century-old practice that has seen a resurgence of interest since the early 2000s largely due to the increase in bacterial resistance to chemical antibiotic molecules. This article, the result of a long-standing collaboration between an anthropologist and a biologist, explores the possibilities of developing a therapy that truly takes into account the evolutionary and involutionary capacities of the living. By briefly reviewing the history of the development and use of antibiotics, and based on more than four years of fieldwork, we show, together with the actors of phage therapy, that such a development implies a joint rethinking of some of the material infrastructures of our societies and the ontological status accorded to microorganisms.Des virus pour soigner: le difficile développement d'une innovation biomédicale contre-intuitiveLa fagoterapia, el uso de virus bacteriófagos para tratar infecciones bacterianas, es una práctica centenaria aunque poco conocida. El interés en la fatogerapia ha renacido desde principios de los 2000, en gran parte debido al aumento de las resistencia bacterianas a los antibióticos convencionales. Este artículo, fruto de una larga colaboración entre una antropóloga y un biólogo, explora las posibilidades de desarrollar una terapia que tenga en cuenta las capacidades evolutivas e involutivas de los organismos vivos (p.ej. bacteriófagos y bacterias). Repasando brevemente la historia del desarrollo y el uso de los antibióticos, y basándonos en más de cuatro años de trabajo de campo, mostramos, junto con los actores de la fagoterapia, que tal desarrollo implica un replanteamiento conjunto de determinadas infraestructuras materiales de nuestras sociedades así como del estatus ontológico otorgado a los microorganismos