Personne : Moineau, Sylvain
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Université Laval. Département de biochimie, de microbiologie et de bio-informatique
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- PublicationAccès libreMachine learning assisted design of highly active peptides for drug discovery(Public Library of Science, 2015-04-07) Tremblay, Denise; Biron, Éric; Giguère, Sébastien; Moineau, Sylvain; Laviolette, François; Liang, Xinxia; Marchand, Mario; Corbeil, JacquesThe discovery of peptides possessing high biological activity is very challenging due to the enormous diversity for which only a minority have the desired properties. To lower cost and reduce the time to obtain promising peptides, machine learning approaches can greatly assist in the process and even partly replace expensive laboratory experiments by learning a predictor with existing data or with a smaller amount of data generation. Unfortunately, once the model is learned, selecting peptides having the greatest predicted bioactivity often requires a prohibitive amount of computational time. For this combinatorial problem, heuristics and stochastic optimization methods are not guaranteed to find adequate solutions. We focused on recent advances in kernel methods and machine learning to learn a predictive model with proven success. For this type of model, we propose an efficient algorithm based on graph theory, that is guaranteed to find the peptides for which the model predicts maximal bioactivity. We also present a second algorithm capable of sorting the peptides of maximal bioactivity. Extensive analyses demonstrate how these algorithms can be part of an iterative combinatorial chemistry procedure to speed up the discovery and the validation of peptide leads. Moreover, the proposed approach does not require the use of known ligands for the target protein since it can leverage recent multi-target machine learning predictors where ligands for similar targets can serve as initial training data. Finally, we validated the proposed approach in vitro with the discovery of new cationic antimicrobial peptides.
- PublicationRestreintRole of galK and galM in galactose metabolism by Streptococcus thermophilus(American Society for Microbiology, 2008-02-07) Vadeboncoeur, Christian; Frenette, Michel; Christian, Bart; Moineau, Sylvain; Vaillancourt, Katy; Robitaille, Gilles; Turgeon, Nathalie; Bédard, NathalieStreptococcus thermophilus is unable to metabolize the galactose moiety of lactose. In this paper, we show that a transformant of S. thermophilus SMQ-301 expressing Streptococcus salivarius galK and galM was able to grow on galactose and expelled at least twofold less galactose into the medium during growth on lactose.
- PublicationAccès libreA protocol for extraction of infective viromes suitable for metagenomics sequencing from low volume fecal samples(Molecular Diversity Preservation International, 2019-07-20) Deng, Ling; Moineau, Sylvain; Silins, Ronalds; Castro-Mejía, Josué L.; Kot, Witold; Jessen, Leon; Thorsen, Jonathan; Shah, Shiraz A.; Stokholm, Jakob; Bisgaard, Hans; Nielsen, Dennis SandrisThe human gut microbiome (GM) plays an important role in human health and diseases. However, while substantial progress has been made in understanding the role of bacterial inhabitants of the gut, much less is known regarding the viral component of the GM. Bacteriophages (phages) are viruses attacking specific host bacteria and likely play important roles in shaping the GM. Although metagenomic approaches have led to the discoveries of many new viruses, they remain largely uncultured as their hosts have not been identified, which hampers our understanding of their biological roles. Existing protocols for isolation of viromes generally require relatively high input volumes and are generally more focused on extracting nucleic acids of good quality and purity for down-stream analysis, and less on purifying viruses with infective capacity. In this study, we report the development of an efficient protocol requiring low sample input yielding purified viromes containing phages that are still infective, which also are of sufficient purity for genome sequencing. We validated the method through spiking known phages followed by plaque assays, qPCR, and metagenomic sequencing. The protocol should facilitate the process of culturing novel viruses from the gut as well as large scale studies on gut viromes.
- PublicationAccès libreMethods for Sampling of Airborne Viruses(American Society for Microbiology, 2008-09-01) Verreault, Daniel; Duchaine, Caroline; Moineau, SylvainSummary: To better understand the underlying mechanisms of aerovirology, accurate sampling of airborne viruses is fundamental. The sampling instruments commonly used in aerobiology have also been used to recover viruses suspended in the air. We reviewed over 100 papers to evaluate the methods currently used for viral aerosol sampling. Differentiating infections caused by direct contact from those caused by airborne dissemination can be a very demanding task given the wide variety of sources of viral aerosols. While epidemiological data can help to determine the source of the contamination, direct data obtained from air samples can provide very useful information for risk assessment purposes. Many types of samplers have been used over the years, including liquid impingers, solid impactors, filters, electrostatic precipitators, and many others. The efficiencies of these samplers depend on a variety of environmental and methodological factors that can affect the integrity of the virus structure. The aerodynamic size distribution of the aerosol also has a direct effect on sampler efficiency. Viral aerosols can be studied under controlled laboratory conditions, using biological or nonbiological tracers and surrogate viruses, which are also discussed in this review. Lastly, general recommendations are made regarding future studies on the sampling of airborne viruses
- PublicationRestreintComparison of polycarbonate and polytetrafluoroethylene filters for sampling of airborne bacteriophages(Elsevier, 2010-01-22) Duchaine, Caroline; Moineau, Sylvain; Massé, Daniel; Verreault, Daniel; Rousseau, Geneviève M.; Gendron, LouisAerosolized coliphage phiX174 and lactococcal phage P008 were sampled with two types of filter, polycarbonate (PC) and polytetrafluoroethylene (PTFE). The recovery was determined by plaque assays and quantitative polymerase chain reaction (qPCR). Recovery by qPCR was greater than by culture and PC filters outperformed PTFE filters both by culture and by qPCR relative recovery. The results of the plaque assays showed that the infectivity of the recovered phages was affected by the aerosolization/air sampling. The presence of viruses in air samples should be determined by culture-independent assays.
- PublicationAccès libreDetection of airborne lactococcal bacteriophages in cheese manufacturing plants(American Society for Microbiology, 2011-01-01) Duchaine, Caroline; Veillette, Marc; Moineau, Sylvain; Massé, Daniel; Verreault, Daniel; Lindsley, William G.; Rousseau, Geneviève M.; Gendron, LouisThe dairy industry adds starter bacterial cultures to heat-treated milk to control the fermentation process during the manufacture of many cheeses. These highly concentrated bacterial populations are susceptible to virulent phages that are ubiquitous in cheese factories. In this study, the dissemination of these phages by the airborne route and their presence on working surfaces were investigated in a cheese factory. Several surfaces were swabbed, and five air samplers (polytetrafluoroethylene filter, polycarbonate filter, BioSampler, Coriolis cyclone sampler, and NIOSH two-stage cyclone bioaerosol personal sampler) were tested. Samples were then analyzed for the presence of two Lactococcus lactis phage groups (936 and c2), and quantification was done by quantitative PCR (qPCR). Both lactococcal phage groups were found on most swabbed surfaces, while airborne phages were detected at concentrations of at least 103 genomes/m3 of air. The NIOSH sampler had the highest rate of air samples with detectable levels of lactococcal phages. This study demonstrates that virulent phages can circulate through the air and that they are ubiquitous in cheese manufacturing facilities.
- PublicationRestreintInactivation of dairy bacteriophages by commercial sanitizers and disinfectants(Elsevier, 2013-11-19) Duchaine, Caroline; Moineau, Sylvain; Labrie, Simon; Campagna, Céline; Villion, ManuelaMany commercial sanitizers and disinfectants have been used over the years to control microbial contamination but their efficacy on phages is often unknown. Here, 23 commercial chemical products, including 21 food-grade sanitizers were tested against virulent dairy phages. These food-grade chemicals included oxidizing agents, halogenated agents, alcohols, quaternary ammonium compounds, anionic acids, iodine-based acids, and an amphoteric chemical. Phage P008 was first exposed to each sanitizer for 2 and 15 min at room temperature and at two different concentrations, namely the lowest and highest no-rinse sanitizing concentrations. Organic matter (whey or milk) was also added to the testing solutions. At the end of the exposure period, the test solution was neutralized and the number of infectious phages was determined by plaque assays. The five most efficient sanitizers against phage P008 (< 4 log of inactivation) were then tested against virulent lactococcal phages P008, CB13, AF6, P1532 of the 936 group, P001 (c2), Q54, and 1358 as well as Lactobacillus plantarum phage B1 and Streptococcus thermophilus phage 2972 using the same protocol. The oxidizing agents and the quaternary ammonium compounds were the most efficient against all phages although phages CB13 and P1532 were less sensitive to these chemicals than the other phages. This study may help in the selection of appropriate chemicals for controlling phage contamination in industrial factories and research laboratories.
- PublicationAccès libreThe CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA(Macmillan, 2010-11-03) Garneau, Josiane; Devillers, Rodolphe; Moineau, Sylvain; Romero, Dennis A.; Dupuis, Marie-Ève; Magadán, Alfonso H.; Boyaval, Patrick; Villion, Manuela; Fremaux, Christophe; Horvath, PhilippeBacteria and Archaea have developed several defence strategies against foreign nucleic acids such as viral genomes and plasmids. Among them, clustered regularly interspaced short palindromic repeats (CRISPR) loci together with cas (CRISPR-associated) genes form the CRISPR/Cas immune system, which involves partially palindromic repeats separated by short stretches of DNA called spacers, acquired from extrachromosomal elements. It was recently demonstrated that these variable loci can incorporate spacers from infecting bacteriophages and then provide immunity against subsequent bacteriophage infections in a sequence-specific manner. Here we show that the Streptococcus thermophilus CRISPR1/Cas system can also naturally acquire spacers from a self-replicating plasmid containing an antibiotic-resistance gene, leading to plasmid loss. Acquired spacers that match antibiotic-resistance genes provide a novel means to naturally select bacteria that cannot uptake and disseminate such genes. We also provide in vivo evidence that the CRISPR1/Cas system specifically cleaves plasmid and bacteriophage double-stranded DNA within the proto-spacer, at specific sites. Our data show that the CRISPR/Cas immune system is remarkably adapted to cleave invading DNA rapidly and has the potential for exploitation to generate safer microbial strains.
- PublicationAccès libreComparison of five bacteriophages as models for viral aerosol studies(American Society for Microbiology, 2014-04-29) Duchaine, Caroline; Toulouse, Marie-Josée; Moineau, Sylvain; Martel, Bruno; Turgeon, NathalieBacteriophages are perceived to be good models for the study of airborne viruses because they are safe to use, some of them display structural features similar to those of human and animal viruses, and they are relatively easy to produce in large quantities. Yet, only a few studies have investigated them as models. It has previously been demonstrated that aerosolization, environmental conditions, and sampling conditions affect viral infectivity, but viral infectivity is virus dependent. Thus, several virus models are likely needed to study their general behavior in aerosols. The aim of this study was to compare the effects of aerosolization and sampling on the infectivity of five tail-less bacteriophages and two pathogenic viruses: MS2 (a single-stranded RNA [ssRNA] phage of the Leviviridae family), F6 (a segmented double-stranded RNA [dsRNA] phage of the Cystoviridae family), FX174 (a single-stranded DNA [ssDNA] phage of the Microviridae family), PM2 (a double-stranded DNA [dsDNA] phage of the Corticoviridae family), PR772 (a dsDNA phage of the Tectiviridae family), human influenza A virus H1N1 (an ssRNA virus of the Orthomyxoviridae family), and the poultry virus Newcastle disease virus (NDV; an ssRNA virus of the Paramyxoviridae family). Three nebulizers and two nebulization salt buffers (with or without organic fluid) were tested, as were two aerosol sampling devices, a liquid cyclone (SKC BioSampler) and a dry cyclone (National Institute for Occupational Safety and Health two-stage cyclone bioaerosol sampler). The presence of viruses in collected air samples was detected by culture and quantitative PCR (qPCR). Our results showed that these selected five phages behave differently when aerosolized and sampled. RNA phage MS2 and ssDNA phage FX174 were the most resistant to aerosolization and sampling. The presence of organic fluid in the nebulization buffer protected phages PR772 and F6 throughout the aerosolization and sampling with dry cyclones. In this experimental setup, the behavior of the influenza virus resembled that of phages PR772 and F6, while the behavior of NDV was closer to that of phages MS2 and FX174. These results provide critical information for the selection of appropriate phage models to mimic the behavior of specific human and animal viruses in aerosols.
- PublicationAccès libreResistance of aerosolized bacterial viruses to relative humidity and temperature(American Society for Microbiology, 2015-10-01) Duchaine, Caroline; Marcoux-Voiselle, Mélissa; Moineau, Sylvain; Verreault, Daniel; Turgeon, NathalieThe use of aerosolized bacteriophages as surrogates to hazardous viruses could simplify and accelerate the discovery of links between viral components and their persistence in the airborne state under diverse environmental conditions. In this study, four structurally distinct lytic phages, MS2 (ssRNA), F6 (dsRNA), FX174 (ssDNA) and PR772 (dsDNA), were nebulised into a rotating chamber and exposed to various levels of relative humidity (RH) and temperature as well as to germicidal ultraviolet radiations. The aerosolized viral particles were allowed to remain airborne for up to fourteen hours before being sampled for analysis by plaque assays and quantitative PCR. Phages F6 and MS2 were most resistant at low levels of relative humidity whilst FX174 was more resistant at 80% RH. Phage F6 lost its infectivity immediately after exposure to 30°C and 80% RH. The infectivity of all tested phages rapidly declined as a function of the exposure time to UV-C radiations, phage MS2 being the most resistant. Taken altogether, our data indicate that these aerosolized phages behave differently under various environmental conditions and highlight the necessity of carefully selecting viral simulants in bioaerosols studies.