Simulations numériques de la dynamique des protéines : translation de ligands, flexibilité et dynamique des boucles

La flexibilité est une caractéristique intrinsèque des protéines qui doivent, dès le mo- ment de leur synthèse, passer d’un état de chaîne linéaire à un état de structure tridimen- sionnelle repliée et enzymatiquement active. Certaines protéines restent flexibles une fois repliées et subissent des changements de conformation de grande amplitude lors de leur cycle enzymatique. D’autres contiennent des segments si flexibles que leur structure ne peut être résolue par des méthodes expérimentales. Dans cette thèse, nous présentons notre application de méthodes in silico d’analyse de la flexibilité des protéines : • À l’aide des méthodes de dynamique moléculaire dirigée et d’échantillonnage pa- rapluie, nous avons caractérisé les trajectoires de liaison de l’inhibiteur Z-pro- prolinal à la protéine Prolyl oligopeptidase et identifié la trajectoire la plus pro- bable. Nos simulations ont aussi identifié un mode probable de recrutement des ligands utilisant une boucle flexible de 19 acides aminés à l’interface des deux domaines de la protéine. • En utilisant les méthodes de dynamique moléculaire traditionnelle et dirigée, nous avons examiné la stabilité de la protéine SAV1866 dans sa forme fermée insérée dans une membrane lipidique et étudié un des modes d’ouverture possibles par la séparation de ses domaines liant le nucléotide. • Nous avons adapté auproblème de la prédiction de la structure des longues boucles flexibles la méthode d’activation et de relaxation ART-nouveau précédemment uti- lisée dans l’étude du repliement et de l’agrégation de protéines. Appliqué au replie- ment de boucles de 8 à 20 acides aminés, la méthode démontre une dépendance quadratique du temps d’exécution sur la longueur des boucles, rendant possible l’étude de boucles encore plus longues.Flexibility is an intrinsic characteristic of proteins who from the moment of synthesis into a linear chain of amino acids, have to adopt an enzymatically active tridimensionnel structure. Some proteins stay flexible once folded and display large amplitude confor- mational changes during their enzymatic cycles. Others contain parts that are so flexible that their structure can’t be resolved using experimental methods. In this thesis, we present our application of in silico methods to the study of protein flexibility. • Using steered molecular dynamics and umbrella sampling, we characterized the binding trajectories of the Z-pro-prolinal inhibiter to the Prolyl oligopeptidase pro- tein and we identified the most probable trajectory. Our simulations also found a possible ligand recrutement mechanism that involves a 19 amino acids flexible loop at the interface of the two domains of the protein. • Using traditional and steered molecular dynamics, we examined the stability of the SAV1866 protein in its closed conformation in a lipid membrane and we studied one of its proposed opening modes by separating its nucleotide binding domains. • We also adapted the activation-relaxation technique ART-nouveau which was pre- viously used to study protein folding and aggregation to the problem of structure prediction of large flexible loops. When tested on loops of 8 to 20 amino acids, the method demonstrate a quadratic execution time dependance on the loop length, which makes it possible to use the method on even larger loops

Méthodes de simulations moléculaires accélérées : application et développement

Mémoire numérisé par la Direction des bibliothèques de l'Université de Montréal

In-depth sequencing of the siRNAs associated with peach latent mosaic viroid infection

<p>Abstract</p> <p>Background</p> <p>It has been observed that following viroid infection, there is an accumulation of viroid-derived siRNAs in infected plants. Some experimental results suggest that these small RNAs may be produced by the plant defense system to protect it from infection, indicating that viroids can elicit the RNA-silencing pathways. The objective of this study is to identify in the peach latent mosaic viroid (PLMVd), a model RNA genome, the regions that are most susceptible to RNA interference machinery.</p> <p>Results</p> <p>The RNA isolated from an infected tree have been used to sequence in parallel viroid species and small non-coding RNA species. Specifically, PLMVd RNAs were amplified, cloned and sequenced according to a conventional approach, while small non-coding RNAs were determined by high-throughput sequencing. The first led to the typing of 18 novel PLMVd variants. The second provided a library of small RNAs including 880 000 sequences corresponding to PLMVd-derived siRNAs, which makes up 11.2% of the sequences of the infected library. These siRNAs contain mainly 21-22 nucleotide RNAs and are equivalently distributed between the plus and the minus polarities of the viroid. They cover the complete viroid genome, although the amount varies depending on the regions. These regions do not necessarily correlate with the double-stranded requirement to be a substrate for Dicer-like enzymes. We noted that some sequences encompass the hammerhead self-cleavage site, indicating that the circular conformers could be processed by the RNA-silencing machinery. Finally, a bias in the relative abundance of the nature of the 5' nucleotides was observed (A, U >> G, C).</p> <p>Conclusions</p> <p>The approach used provided us a quantitative representation of the PLMVd-derived siRNAs retrieved from infected peach trees. These siRNAs account for a relatively large proportion of the small non-coding RNAs. Surprisingly, the siRNAs from some regions of the PLMVd genome appear over-represented, although these regions are not necessarily forming sufficiently long double-stranded structures to satisfy Dicer-like criteria for substrate specificity. Importantly, this large library of siRNAs gave several hints as to the components of the involved silencing machinery.</p

Potential impact of a nonavalent HPV vaccine on the occurrence of HPV-related diseases in France

International audienceBackground : Human Papillomavirus (HPV) infection is known to be associated with a number of conditions including cervical, vaginal, vulvar, penile, anal neoplasias and cancers, oropharynx cancers and genitals warts (GW). Two prophylactic vaccines are currently available: a bivalent vaccine designed to prevent HPV type 16 and 18 infection and a quadrivalent vaccine targeting HPV 6, 11, 16, and 18. In France, HPV vaccination is recommended in 11-14 year-old girls with a catch-up for girls aged 15-19. The objective of this study was to assess the potential impact of an HPV 6/11/16/18/31/33/45/52/58 nonavalent vaccine on anogenital and oropharyngeal HPV-related diseases in France.Methods : HPV genotype distributions from 6 multicentric retrospective studies (EDiTH I to VI) were analyzed including 516 cases of invasive cervical cancers (ICC), 493 high-grade cervical neoplasias (CIN2/3), 397 low-grade squamous intraepithelial lesions (LSIL), 423 GW, 366 anal cancer and 314 oropharyngeal carcinomas. Low and high estimates of HPV vaccine impact were calculated as follows: low estimate: prevalence of HPV 6/11/16/18/31/33/45/52/58 genotypes alone or in association but excluding presence of another HPV type; high estimate: prevalence of HPV 6/11/16/18/31/33/45/52/58 genotypes alone or in association, possibly in presence of another HPV type.Results : Estimates of potential impact varied from 85% (low estimate) to 92% (high estimate) for ICC, 77% to 90% for CIN2/3, 26% to 56% for LSIL, 69% to 90% for GW, 81% to 93% for anal cancer, and 41% to 44% for oropharyngeal carcinomas. Compared to the quadrivalent vaccine, the proportion of additional cases potentially prevented by the nonavalent vaccine was 9.9%-15.3% for ICC, 24.7%-33.3% for CIN2/3, 12.3%-22.7% for LSIL, 2.1%-5.4% for GW, 8.5%-10.4% for anal cancer, and 0.0%-1.6% for oropharyngeal carcinoma.Conclusions : The nonavalent HPV vaccine showed significant increased potential impact compared to the HPV 6/11/16/18 quadrivalent vaccine for ICC, CIN2/3 and LSIL. Considering a 100% vaccine efficacy and high vaccine coverage, about 90% of ICC, CIN2/3, GW or anal cancer cases could be prevented by a nonavalent HPV vaccine in France

Impact of ultraviolet radiation on marine crustacean zooplankton and ichthyoplankton: a synthesis of results from the estuary and Gulf of St. Lawrence, Canada

The objectives of the research program reported upon here were (1) to measure ambient levels of UV radiation and determine whichvariables most strongly affected its attenuation in the waters of the estuary and Gulf of St. Lawrence, Canada; and (2) to investigate the potential direct impacts of W radiation on species of crustacean zooplankton and fish whose early life stages are planktonic. In this geographic region, productivity-determining biophysical interactions occur in the upper 0 to 30 m of the water column. Measurements of the diffuse attenuation coefficients for ultraviolet-B radiation (W-B, 280 to 320 nm) at various locations in this region indicated maximum 10% depths (the depth to which 10% of the surface energy penetrates at a given wavelength) of 3 to 4 m at a wavelength of 310 nm. Organisms residing in this layer-including the eggs and larvae of Calanus finmarchicus and Atlantic cod Gadus morhua-are exposed to biologically damaging levels of W radiation. As a result of these physical and biological characteristics, this system offered a relevant opportunity to assess the impacts of UV on subarctic marine ecosystems. Eggs of C. finmarchicus were incubated under the sun, with and without the W-B and/or UV-A (320 to 400 nm) wavebands. W-exposed eggs exhibited low percent hatchmg compared to those protected from W : W radiation had a strong negative impact on C. finmarchicus eggs. Further, percent hatching in W-B-exposed eggs was not significantly lower than that in eggs exposed to UV-A only: under natural sunlight, UV-A radiation appeared to be more detrimental to C. finmarchicus embryos than was UV-B. In analogous experiments with Atlantic cod eggs, exposure to UV-B produced a significant negative effect. However, UV-A had no negative effect on cod eggs. Additional experiments using a solar simulator (SS) revealed high wavelength-dependent mortality in both C. finmarchicus and cod embryos exposed to UV. The strongest effects occurred under exposures to wavelengths below 312 nm. At the shorter wavelengths (<305 nm) UV-B-induced mortality was strongly dose-dependent, but (for both C. finmarchicus and cod) not significantly influenced by dose-rate. Thus, at least within the limits of the exposures under which the biological weighting functions (BWFs) were generated, reciprocity held. The BWFs derived for UV-B-induced mortality in C. finmarchicus and cod eggs were similar in shape to the action spectrum for UV-B effects on naked DNA. Further, the wavelengthdependence of DNA damage was similar to that for the mortality effect. These observations suggest that W-induced mortality in C. finmarchicus and cod eggs is a direct result of DNA damage. There was no evidence of a detrimental effect of UV-A radiation in these SS-derived results. A mathematical model that includes the BWFs, vertical mixing of eggs, meteorological and hydrographic conditions, and ozone depletion, indicates that W-induced mortality in the C. finmarchicus egg population could be as high as 32.5 %, while the impact on the cod egg population was no more than 1.2%. Variability in cloud cover, water transparency (and the variables that affect it), and vertical distribution and displacement of planktonic organisms within the mixed layer can all have a greater effect on the flux of UV-B radiation to which they are exposed than will ozone layer depletion at these latitudes. Our observations indicate that C, finmarchicus and cod eggs present in the first meter of the water column (likely only a small percentage of the total egg populations) are susceptible to W radiation. However, although exposure to UV can negatively impact crustacean zooplankton and ichthyoplankton populations, these direct effects are likely minimal within the context of all the other environmental factors that produce the very high levels of mortality typically observed in their planktonic early life stages. The impact of indnect effects-which may well be of much greater import-has yet to be evaluated

Revue d'histoire du Bas-Saint-Laurent, vol. 12 (3-4)

Mot de l'éditeur -- Au micro de CJBR -- La grande histoire de CJBR -- Jules-A. Brillant et le poste CJBR -- Avec CJBR, un bon en avant pour le Bas St-Laurent -- CJBR, l'école -- L'annonceur: un éducateur populaire -- Sandy Burgess : le journaliste que j'ai connu -- "Ce pays qui est le mien" -- Un demi-siècle d'information: que de nouvelles! -- Journaliste de père en fils à CJBR -- Le théâtre à CJBR -- 50 ans de musique à CJBR, le château fort de la mélodie française -- Poésie, théâtre, jazz et originalité avec Michel Garneau -- Les "Chroniques du dimanche", l'âge d'or de la critique culturelle à CJBR -- "Si CJBR m'était conté..." -- L'évolution technologique, un élément-clef de l'histoire des 50 ans de radiodiffusion -- La publicité à CJBR, quarante ans de croissance -- Des pionnières à CJBR -- 1958-1972, des années enrichissantes -- De Trois-Pistoles à Rimouski -- Le sport et son enracinement dans le milieu régional -- "Debout c'est l'heure", c'est Jean Brisson qui sonne le réveil -- "Par une belle journée de tempête" -- Et on repart vers la centain

L’EROP : 10 ans pour le rétablissement des oiseaux de proie au Québec

L’Équipe de rétablissement des oiseaux de proie du Québec (EROP) a été fondée en 2004, à la suite de la fusion des équipes de rétablissement du faucon pèlerin (Falco peregrinus), du pygargue à tête blanche (Haliaeetus leucocephalus) et de l’aigle royal (Aquila chrysaetos). À ces espèces d’intérêt pour l’EROP s’est ajouté récemment le hibou des marais (Asio flammeus). À l’aide des plans de rétablissement de chacune des espèces, l’EROP veille à la mise en oeuvre de mesures de conservation (p. ex. acquisition de connaissances, sensibilisation, protection) visant à redresser la situation des populations d’oiseaux de proie en situation précaire au Québec. Cet article présente le mandat, le mode de fonctionnement et les principales réalisations de l’EROP au cours de la dernière décennie. The Québec raptor recovery team (EROP) was established in 2004 following the merger of the peregrine falcon (Falcoperegrinus), bald eagle (Haliaeetus leucocephalus) and golden eagle (Aquilachrysaetos) recovery teams. Recently, the short-eared owl (Asioflammeus) has also been added to the list of species covered by EROP. The team aims to foster conservation measures (e.g., data collection, public awareness and protection) to improve the population status of endangered birds of prey, and achieves this through the publication of species recovery plans. This article outlines the mission, and the working and main achievements of EROP over the past decade

Longitudinal blood biomarker trajectories in preclinical Alzheimer's disease

INTRODUCTION: Plasma biomarkers are altered years prior to Alzheimer's disease (AD) clinical onset. METHODS: We measured longitudinal changes in plasma amyloid-beta (Aβ)42/40 ratio, pTau181, pTau231, neurofilament light chain (NfL), and glial fibrillary acidic protein (GFAP) in a cohort of older adults at risk of AD (n = 373 total, n = 229 with Aβ and tau positron emission tomography [PET] scans) considering genetic and demographic factors as possible modifiers of these markers' progression. RESULTS: Aβ42/40 ratio concentrations decreased, while NfL and GFAP values increased over the 4-year follow-up. Apolipoprotein E (APOE) ε4 carriers showed faster increase in plasma pTau181 than non-carriers. Older individuals showed a faster increase in plasma NfL, and females showed a faster increase in plasma GFAP values. In the PET subsample, individuals both Aβ-PET and tau-PET positive showed faster plasma pTau181 and GFAP increase compared to PET-negative individuals. DISCUSSION: Plasma markers can track biological change over time, with plasma pTau181 and GFAP markers showing longitudinal change in individuals with preclinical AD. HIGHLIGHTS: Longitudinal increase of plasma pTau181 and glial fibrillary acidic protein (GFAP) can be measured in the preclinical phase of AD. Apolipoprotein E ε4 carriers experience faster increase in plasma pTau181 over time than non-carriers. Female sex showed accelerated increase in plasma GFAP over time compared to males. Aβ42/40 and pTau231 values are already abnormal at baseline in individuals with both amyloid and tau PET burden

Severe Asthma Standard-of-Care Background Medication Reduction With Benralizumab: ANDHI in Practice Substudy

Background: The phase IIIb, randomized, parallel-group, placebo-controlled ANDHI double-blind (DB) study extended understanding of the efficacy of benralizumab for patients with severe eosinophilic asthma. Patients from ANDHI DB could join the 56-week ANDHI in Practice (IP) single-arm, open-label extension substudy. Objective: Assess potential for standard-of-care background medication reductions while maintaining asthma control with benralizumab. Methods: Following ANDHI DB completion, eligible adults were enrolled in ANDHI IP. After an 8-week run-in with benralizumab, there were 5 visits to potentially reduce background asthma medications for patients achieving and maintaining protocol-defined asthma control with benralizumab. Main outcome measures for non-oral corticosteroid (OCS)-dependent patients were the proportions with at least 1 background medication reduction (ie, lower inhaled corticosteroid dose, background medication discontinuation) and the number of adapted Global Initiative for Asthma (GINA) step reductions at end of treatment (EOT). Main outcomes for OCS-dependent patients were reductions in daily OCS dosage and proportion achieving OCS dosage of 5 mg or lower at EOT. Results: For non-OCS-dependent patients, 53.3% (n = 208 of 390) achieved at least 1 background medication reduction, increasing to 72.6% (n = 130 of 179) for patients who maintained protocol-defined asthma control at EOT. A total of 41.9% (n = 163 of 389) achieved at least 1 adapted GINA step reduction, increasing to 61.8% (n = 110 of 178) for patients with protocol-defined EOT asthma control. At ANDHI IP baseline, OCS dosages were 5 mg or lower for 40.4% (n = 40 of 99) of OCS-dependent patients. Of OCS-dependent patients, 50.5% (n = 50 of 99) eliminated OCS and 74.7% (n = 74 of 99) achieved dosages of 5 mg or lower at EOT. Conclusions: These findings demonstrate benralizumab's ability to improve asthma control, thereby allowing background medication reduction