Étude tracéologique des incisives de castor des collections iroquoiennes de Saint-Anicet

Ce mémoire présente une analyse tracéologique, c’est-à-dire l’analyse fonctionnelle d’un objet à partir des microtraces d’usure, appliquée à une collection d’incisives de castor issue des sites iroquoiens de la région de Saint-Anicet: McDonald, Droulers et Mailhot-Curran. L’objectif est de mieux comprendre la fonction de ces objets fréquents sur les sites archéologiques iroquoiens, étant donné que la fonction précise est soit inconnue, soit présumée de façon spéculative. Pour répondre à cette question de recherche, l’analyse se déploie en trois volets : expérimental, analytique et comparatif. Le premier permettra d’éclairer la relation entre différentes matières travaillées et les traces laissées sur les outils en incisives de castor, ainsi que les mouvements effectués et la durée d’utilisation. Le deuxième volet aborde la tracéologie des incisives de castor de nos trois sites à l’étude, à partir des résultats des expérimentations. Le troisième volet de l’étude est dédié à la comparaison inter-sites. Ce projet permet de déterminer à quelles activités les outils sur dents de castor des collections ont servi, puis de comprendre les choix qui les sous-tendent. Cela permet donc de mieux comprendre l’humain derrière l’objet. Les résultats des analyses ont permis de démontrer l’utilisation des incisives de castor iroquoiennes comme outils servant à travailler le bois, mais plus spécifiquement comme outils servant à travailler des bois verts, tendres et mi-durs. De plus, il a été confirmé que les incisives de castor à double fonction, ciseau-racloir, sont le résultat d’outils recyclés ou réutilisés qui servaient à des usages divers.This dissertation presents a traceological analysis, that is to say the functional analysis of an object based on microtraces of wear, applied to a collection of beaver incisors from Iroquoian sites in the Saint-Anicet region. : McDonald, Droulers and Mailhot-Curran. The goal is to better understand the function of these common objects at Iroquoian archaeological sites, given that the precise function is either unknown or speculated speculatively. To answer this research question, the analysis is deployed in three parts: experimental, analytical and comparative. The first will shed light on the relationship between different materials worked and the traces left on beaver incisor tools, as well as the movements made and the duration of use. The second part addresses the traceology of beaver incisors from our three sites under study, based on the results of the experiments. The third part of the study is dedicated to the inter-site comparison. This project makes it possible to determine what activities the beaver tooth tools in the collections were used for, then to understand the choices behind them. This therefore allows us to better understand the human behind the object. The results of the analyzes demonstrated the use of Iroquoian beaver incisors as tools for working wood, but more specifically as tools for working green, soft and semi-hard wood. Furthermore, it was confirmed that the double-function beaver incisors, chisel-scraper, are the result of recycled or reused tools that were used for various purposes

Corrigendum: Metagenomic and whole-genome analysis reveals new lineages of gokushoviruses and biogeographic separation in the sea.

[This corrects the article on p. 404 in vol. 4, PMID: 24399999.]

The role of antibiosis in the antagonism of different bacteria towards Helminthosporium solani, the causal agent of potato silver scurf

Bacterial antagonists of Helminthosporium solani were submitted to different tests in order to determine the role of antibiosis in their antagonistic interaction. Among the bacterial strains tested, seven (Alcaligenes piechaudii, Aquaspirillum autotrophicum, Cellulomonas fimi, Pseudomonas chlororaphis, Pseudomonas putida (strains 94-19 and E-30) and Streptomyces griseus) were shown to produce agar diffusible metabolites inhibiting H. solani mycelial growth and/or conidial germination. Differential activity was revealed when diffusible metabolites were extracted from either pure cultures of these antagonists or dual culture in the presence of H. solani. The results presented indicate that the methodology employed could be a decisive factor in whether or not antibiosis can be identified as a mode of action of biocontrol agents.Des antagonistes bactériens envers Helminthosporium solani ont été soumis à différents essais en vue de déterminer le rôle de l'antibiose dans l'antagonisme observé. Parmi les souches bactériennes évaluées, sept (Alcaligenes piechaudii, Aquaspirillum autotrophicum, Cellulomonas fimi, Pseudomonas chlororaphis, Pseudomonas putida (souches 94-19 et E-30) et Streptomyces griseus) ont produit dans le milieu gélosé des métabolites inhibant la croissance mycélienne et/ou la germination des conidies de H. solani. Les métabolites produits en culture pure et en culture mixte ont présenté une activité différente sur la croissance mycélienne de H. solani. Les résultats présentés indiquent que la méthodologie employée peut être un facteur déterminant dans l'identification de l'antibiose comme mode d'action d'un agent antagoniste

Influence of Igneous Basement on Deep Sediment Microbial Diversity on the Eastern Juan de Fuca Ridge Flank

Microbial communities living in deeply buried sediment may be adapted to long-term energy limitation as they are removed from new detrital energy inputs for thousands to millions of years. However, sediment layers near the underlying oceanic crust may receive inputs from below that influence microbial community structure and/or activity. As part of the Census of Deep Life, we used 16S rRNA gene tag pyrosequencing on DNA extracted from a spectrum of deep sediment-basement interface samples from the subsurface of the Juan de Fuca Ridge flank (collected on IODP Expedition 327) to examine this possible basement influence on deep sediment communities. This area experiences rapid sedimentation, with an underlying basaltic crust that hosts a dynamic flux of hydrothermal fluids that diffuse into the sediment. Chloroflexi sequences dominated tag libraries in all sediment samples, with variation in the abundance of other bacterial groups (e.g., Actinobacteria, Aerophobetes, Atribacteria, Planctomycetes, and Nitrospirae). These variations occur in relation to the type of sediment (clays versus carbonate-rich) and the depth of sample origin, and show no clear connection to the distance from the discharge outcrop or to basement fluid microbial communities. Actinobacteria-related sequences dominated the basalt libraries, but these should be viewed cautiously due to possibilities for imprinting from contamination. Our results indicate that proximity to basement or areas of seawater recharge is not a primary driver of microbial community composition in basal sediment, even though fluids diffusing from basement into sediment may stimulate microbial activity

Single cell genomics-based analysis of gene content and expression of prophages in a diffuse-flow deep-sea hydrothermal system

© The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Labonte, J. M., Pachiadaki, M., Fergusson, E., McNichol, J., Grosche, A., Gulmann, L. K., Vetriani, C., Sievert, S. M., & Stepanauskas, R. Single cell genomics-based analysis of gene content and expression of prophages in a diffuse-flow deep-sea hydrothermal system. Frontiers in Microbiology, 10, (2019): 1262, doi:10.3389/fmicb.2019.01262.Phage–host interactions likely play a major role in the composition and functioning of many microbiomes, yet remain poorly understood. Here, we employed single cell genomics to investigate phage–host interactions in a diffuse-flow, low-temperature hydrothermal vent that may be reflective of a broadly distributed biosphere in the subseafloor. We identified putative prophages in 13 of 126 sequenced single amplified genomes (SAGs), with no evidence for lytic infections, which is in stark contrast to findings in the surface ocean. Most were distantly related to known prophages, while their hosts included bacterial phyla Campylobacterota, Bacteroidetes, Chlorobi, Proteobacteria, Lentisphaerae, Spirochaetes, and Thermotogae. Our results suggest the predominance of lysogeny over lytic interaction in diffuse-flow, deep-sea hydrothermal vents, despite the high activity of the dominant Campylobacteria that would favor lytic infections. We show that some of the identified lysogens have co-evolved with their host over geological time scales and that their genes are transcribed in the environment. Functional annotations of lysogeny-related genes suggest involvement in horizontal gene transfer enabling host’s protection against toxic metals and antibacterial compounds.This work was supported by the U.S. National Science Foundation’s Dimensions of Biodiversity Program [OCE-1136488 (to RS), OCE-1136727 (to SMS) and OCE-1136451 (to CV)], as well as DEB-1441717 and OCE-1335810 (to RS), and the DOE JGI CSP project 1477

The Unconventional Xer Recombination Machinery of Streptococci/Lactococci

Homologous recombination between circular sister chromosomes during DNA replication in bacteria can generate chromosome dimers that must be resolved into monomers prior to cell division. In Escherichia coli, dimer resolution is achieved by site-specific recombination, Xer recombination, involving two paralogous tyrosine recombinases, XerC and XerD, and a 28-bp recombination site (dif) located at the junction of the two replication arms. Xer recombination is tightly controlled by the septal protein FtsK. XerCD recombinases and FtsK are found on most sequenced eubacterial genomes, suggesting that the Xer recombination system as described in E. coli is highly conserved among prokaryotes. We show here that Streptococci and Lactococci carry an alternative Xer recombination machinery, organized in a single recombination module. This corresponds to an atypical 31-bp recombination site (difSL) associated with a dedicated tyrosine recombinase (XerS). In contrast to the E. coli Xer system, only a single recombinase is required to recombine difSL, suggesting a different mechanism in the recombination process. Despite this important difference, XerS can only perform efficient recombination when difSL sites are located on chromosome dimers. Moreover, the XerS/difSL recombination requires the streptococcal protein FtsKSL, probably without the need for direct protein-protein interaction, which we demonstrated to be located at the division septum of Lactococcus lactis. Acquisition of the XerS recombination module can be considered as a landmark of the separation of Streptococci/Lactococci from other firmicutes and support the view that Xer recombination is a conserved cellular function in bacteria, but that can be achieved by functional analogs

Semi-groupe de Lie associé à un cône symétrique

Volcanic arcs are the surface expression of magmatic systems that result from the subduction of mostly oceanic lithosphere at convergent plate boundaries. Arcs with a submarine component include intraoceanic arcs and island arcs that span almost 22,000 km on Earth\u27s surface, the vast majority of which are located in the Pacific region. Hydrothermal systems hosted by submarine arc volcanoes commonly contain a large component of magmatic fluid. This magmatic-hydrothermal signature, coupled with the shallow water depths of arc volcanoes and their high volatile contents, strongly influences the chemistry of the fluids and resulting mineralization and likely has important consequences for the biota associated with these systems. The high metal contents and very acidic fluids in these hydrothermal systems are thought to be important analogs to numerous porphyry copper and epithermal gold deposits mined today on land

Peripartum depression and anxiety as an integrative cross domain target for psychiatric preventative measures

Exposure to high levels of early life stress has been identified as a potent risk factor for neurodevelopmental delays in infants, behavioral problems and autism in children, but also for several psychiatric illnesses in adulthood, such as depression, anxiety, autism, and posttraumatic stress disorder. Despite having robust adverse effects on both mother and infant, the pathophysiology of peripartum depression and anxiety are poorly understood. The objective of this review is to highlight the advantages of using an integrated approach addressing several behavioral domains in both animal and clinical studies of peripartum depression and anxiety. It is postulated that a greater focus on integrated cross domain studies will lead to advances in treatments and preventative measures for several disorders associated with peripartum depression and anxiety. Exposure to high levels of early life stress has been identified as a potent risk factor for neurodevelopmental delays in infants, behavioral problems and autism in children, but also for several psychiatric illnesses in adulthood, such as depression, anxiety, autism, and posttraumatic stress disorder. Despite having robust adverse effects on both mother and infant, the pathophysiology of peripartum depression and anxiety are poorly understood. The objective of this review is to highlight the advantages of using an integrated approach addressing several behavioral domains in both animal and clinical studies of peripartum depression and anxiety. It is postulated that a greater focus on integrated cross domain studies will lead to advances in treatments and preventative measures for several disorders associated with peripartum depression and anxiety

Diversity and evolution of single-stranded DNA viruses in marine environments

Viruses are the most abundant and genetically diverse life forms in the biosphere. By infecting specific subsets of microbial communities, they influence community composition, thereby affecting nutrient and energy cycling. Single-stranded (ss) DNA viruses are major pathogens of plants and animals that have been well studied for years due to their economic and human-health effects. Recent advances in metagenomics show that marine ssDNA viruses are widespread in marine and freshwater environments, but their diversity and evolutionary relationships remain relatively unexplored. This dissertation focuses on characterizing the diversity and evolutionary relationships among marine ssDNA viruses. First, metagenomic data were gathered and analyzed to assess the genetic diversity of ssDNA viruses, leading to the identification 129 genetically distinct groups of ssDNA viruses that had no recognizable similarity to each other or to other sequenced viruses. Each group was represented by at least one complete genome, with most falling into 11 well-defined groups. Comparison and phylogenetic analysis of sequences from marine and terrestrial viruses indicate that ssDNA viruses share a common origin and that terrestrial viruses likely co-evolved with their hosts when they transitioned from the ocean to the land. The second part focused on one particular subfamily of viruses, the Gokushovirinae (family Microviridae) to understand their relationship with the environment. Five complete genomes were assembled and primers were designed to amplify a fragment of the major capsid protein to look at the distribution of gokushoviruses in various marine environments. Phylogenetic analysis revealed that most sequences were distantly related to those from cultured representatives, falling into many new distinct evolutionary groups. Finally, a protocol for fluorescence in situ hybridization was developed to observe cells infected by gokushoviruses. The results presented in this dissertation greatly expand the known sequence space for ssDNA, nearly doubling the number of complete available genomes, and revealing much greater genetic richness than previously though. The vast diversity of ssDNA viruses in the sea and their similarity with viruses infecting eukaryotes is consistent with their role as significant pathogens of marine phytoplankton and microzooplankton.Science, Faculty ofMicrobiology and Immunology, Department ofGraduat