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1
Ouennane, Siham. "Interactions phage-hôte chez Streptococcus pneumoniae". Doctoral thesis, Université Laval, 2017. http://hdl.handle.net/20.500.11794/27790.
Testo completoAbstract (sommario):
Streptococcus pneumoniae est une bactérie à la fois commensale et pathogène opportuniste chez l’humain. Elle est responsable de nombreuses infections telles que la pneumonie, la méningite, l’otite moyenne et la sinusite. En maladie infectieuse, S. pneumoniae occupe une place importante en tant que l’une des principales causes de morbidité et de mortalité dans le monde. Elle est dotée de plusieurs capacités fascinantes, comme la compétence naturelle pour l’aider à résister aux antibiotiques et la grande diversité des sérotypes capsulaires pour contourner la vaccination. Puisque la résistance aux antibiotiques ne cesse de menacer l’efficacité des thérapies standards, la thérapie par phage est maintenant reconsidérée comme une des alternatives thérapeutiques. La réévaluation des phages fait renaitre l’espoir thérapeutique, mais sans élucider leur mécanisme d’interaction et décortiquer leur mystère cet espoir restera modeste. Ce projet de doctorat consiste à mieux comprendre les phages infectant S. pneumoniae et les interactions phage-hôte. Dans un premier temps, le potentiel des pneumophages à infecter Streptococcus mitis, une espèce phylogénétiquement proche de S. pneumoniae, a été mis en évidence. Deux pneumophages se sont avérés les premiers phages virulents capables d’infecter S. mitis, bactérie pathogène responsable d’endocardite. Les deux phages pouvaient non seulement se répliquer dans S. mitis mais également produisent des plages de lyses plus visibles. Ensuite, la comparaison du génome des phages a confirmé que le changement de l’hôte n’induit aucune variation aux génomes des phages testés. Cependant, plusieurs mutations ont été observées dans la séquence génomique du podophage sauvage et il a fait ensuite l’objet d’une nouvelle annotation. Dans un deuxième temps, l’étude des interactions phage-hôte chez S. pneumoniae a été approfondie. Pour ce faire, l’implication de plusieurs facteurs de l’hôte dans la réplication des pneumophages a été étudiée. Plusieurs gènes pneumococciques se sont avérés nécessaires ou impliqués pour assurer l'efficacité de la réplication des phages seuls ou en cocktail. D’un autre côté, en étudiant ces facteurs de l’hôte, des gènes/ protéines potentiellement essentiels à la viabilité de S. pneumoniae ont été identifiés. Cette étude a aussi permis d’identifier de nouvelles cibles thérapeutiques et donne un nouvel aperçu du réseau complexe des interactions phage-hôte.Streptococcus pneumoniae is a commensal and opportunistic pathogen bacterium, exclusively found in humans. It is the main agent of many infections such as pneumonia, meningitis, otitis media and sinusitis. S. pneumoniae infections are a major cause of morbidity and mortality worldwide. S. pneumoniae has several fascinating abilities, such as natural competence to facilitate the acquisition of antibiotic resistance genes and diversity of capsular serotypes to circumvent the vaccination. The rise of antibiotic resistant bacteria continues to threaten the effectiveness of standard therapies and as such phage therapy is now reconsidered as a therapeutic alternative. The reevaluation of phages as therapeutic agents must go through a better understanding of phage-bacterium interactions. This PhD thesis aims to better understand S. pneumoniae virulent phages and phage-host interactions. First, the ability of pneumophages to infect Streptococcus mitis, a species phylogenetically related to S. pneumoniae, was demonstrated. The pneumophages are the first two virulent phages able to infect this pathogenic bacterium, the common cause of bacterial endocarditis. Both pneumophages could not only replicate in S. mitis but also produced more visible plaques on this host. The comparison of the genomes of each phage grown on both hosts produced identical nucleotide sequences, confirming that S. mitis as a host does not induce any nucleotide variation. However, the genomic sequence of wild-type podophage was different than the previously reported sequence and it was the subject of a new annotation. In addition, S. pneumoniae phage-host interactions were investigated. The involvement of several host factors in replication of both pneumophages was observed. Indeed, several pneumococcal genes were found to be necessary or involved to ensure efficient phage replication. Moreover, the study of these host factors has led to the identification of new genes that appear to be essential for viability and normal growth of S. pneumoniae. This project led to identify new potential therapeutic targets and provided new insight into the complex network of phage-host interactions.
2
Eccleston, Jacqueline Dawn. "Community richness and host-phage interactions in soil". Thesis, University of Liverpool, 1991. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.316817.
Testo completo
3
Marcinkiewicz, Ashley. "Bacterial and phage interactions influencing Vibrio parahaemolyticus ecology". Thesis, University of New Hampshire, 2016. http://pqdtopen.proquest.com/#viewpdf?dispub=10127507.
Testo completoAbstract (sommario):
Vibrio parahaemolyticus, a human pathogenic bacterium, is a naturally occurring member of the microbiome of the Eastern oyster. As the nature of this symbiosis in unknown, the oyster presents the opportunity to investigate how microbial communities interact with a host as part of the ecology of an emergent pathogen of importance. To define how members of the oyster bacterial microbiome correlate with V. parahaemolyticus, I performed marker-based metagenetic sequencing analyses to identify and quantify the bacterial community in individual oysters after culturally-quantifying V. parahaemolyticus abundance. I concluded that despite shared environmental exposures, individual oysters from the same collection site varied both in microbiome community and V. parahaemolyticus abundance, and there may be an interaction with V. parahaemolyticus and Bacillus species. In addition, to elucidate the ecological origins of pathogenic New England ST36 populations, I performed whole genome sequencing and phylogenetic analyses. I concluded ST36 strains formed distinct subpopulations that correlated both with geographic region and unique phage content that can be used as a biomarker for more refined strain traceback. Furthermore, these subpopulations indicated there may have been multiple invasions of this non-native pathogen into the Atlantic coast.
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Yang, Joy Ph D. (Joy Yu)Massachusetts Institute of Technology. "Statistically inferring the mechanisms of phage-host interactions". Thesis, Massachusetts Institute of Technology, 2019. https://hdl.handle.net/1721.1/123250.
Testo completoAbstract (sommario):
Thesis: Ph. D., Massachusetts Institute of Technology, Computational and Systems Biology Program, 2019Cataloged from PDF version of thesis.
Includes bibliographical references (pages 113-121).
Bacteriophage and their hosts are locked in an age-old arms race. Successful bacteria are subject to predation, forcing the population to diversify, and phage are also quick to adapt tactics for infecting these potential hosts. Sampling of closely related bacterial strains that differ in phage infection profiles can further elucidate the mechanisms of infection. The Polz Lab maintains the Nahant Collection - 243 Vibrio strains challenged by 241 unique phage, all with sequenced genomes. This is the largest phylogenetically resolved host-range cross test available to date. Genetically mapping out the depths of this dataset requires carefully designed analysis techniques as well as further experimental exploration. First, we narrow in on a specific phage in the Nahant Collection, 2.275.0, to characterize the pressures that may select for phage that shuttle their own translational machinery.
While translation is generally considered a hallmark of cellular life, some phage carry abundant tRNA. 2.275.0 carries 18 tRNA spanning 13 amino acids. We find that while encoding translation-related components requires shuttling a larger phage genome, it also reduces dependence on host translational machinery, allowing the phage to be more aggressive in degrading and recycling the host genome and other resources required for replication. Next we develop a systematic approach for uncovering genomic features that underlie phage-host interactions. We find that correcting for phylogenetic relationships allows us to pick out relevant signals that would otherwise be drowned out by spurious correlations resulting from statistically oversampled blooms of microbes. Using these results, we wrote an interative javascript visualization to facilitate the process of developing testable hypotheses concerning the mechanisms of phage infection and host response.
From the visualization, we are able to identify, in the hosts, mobile genetic elements containing restriction modification systems that may defend against infection, as well as membrane protein modifications that may serve as phage attachment sites.
by Joy Yang.
Ph. D.
Ph.D. Massachusetts Institute of Technology, Computational and Systems Biology Program
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Samson, Julie. "Interactions phage-hôte et caractérisation de la résistance aux phages chez Lactococcus lactis". Thesis, Université Laval, 2013. http://www.theses.ulaval.ca/2013/30167/30167.pdf.
Testo completoAbstract (sommario):
Bactéries et phages sont en perpétuelle compétition dans l’environnement et évoluent conjointement. Plusieurs mécanismes ont été développés de part et d’autre pour maintenir un état d’équilibre. D’un côté, les phages sont des entités qui se répliquent efficacement et rapidement en parasitant leur bactérie hôte. D’un autre côté, les bactéries ont acquis des mécanismes de résistance aux bactériophages tels que les systèmes d’avortement de l’infection (Abi) pour limiter l’infection et la propagation des phages dans les populations bactériennes. Plus spécifiquement, le système antiphage AbiQ a été isolé de la bactérie Lactococcus lactis. Cette dernière est utilisée pour la production de divers produits laitiers fermentés. Malgré cet environnement contrôlé, des phages peuvent perturber les fermentations s’ils sont présents dans le lait et les usines. Il n’est donc pas surprenant que cette bactérie possède des systèmes contre ces envahisseurs. Le système antiphage AbiQ serait similaire à un mécanisme de type toxine-antitoxine (TA), mais son fonctionnement demeure jusqu’à maintenant inconnu. Au cours de ce projet de doctorat, trois objectifs ont été poursuivis afin de comprendre la relation entre la bactérie Lactococcus lactis et ses phages. Dans un premier temps, le génome du phage 949, un membre d’un groupe rare de lactophages portant son nom, a été séquencé et caractérisé. Une comparaison de tous les génomes de phages infectant L. lactis a été réalisée afin de confirmer la classification actuelle. Dans un deuxième temps, le mode d’action toxine-antitoxine du système AbiQ de L. lactis a été approfondi. Pour ce faire, des expériences ont été réalisées afin de démontrer que ce système est un mécanisme de type TA composé d’une antitoxine d’ARN et d’une toxine protéique avec une activitée ribonucléase. Dans un troisième temps, l’effet d’AbiQ sur la réplication des phages a été évalué. En isolant des phages mutants ayant la capacité de contourner le mécanisme, des cibles phagiques potentielles du système AbiQ ont été identifiées. Comprendre la relation phage-hôte est la clé pour le développement de bactéries résistantes aux phages dans un contexte de production industrielle ou pour limiter l’apparition de résistance aux phages lors du traitement des infections bactériennes par la thérapie phagique.Bacteria and phages are continuously challenging each other and evolve in most ecosystems. Many strategies have been adapted by both of them to reach an equilibrium state. On one side, phages can infect efficiently and rapidly their bacterial host. On the other side, bacteria have acquired antiphage mechanisms to resist phage infection and limit their propagation such as abortive infection mechanisms (Abi). Specifically, the AbiQ antiphage system was isolated from Lactococcus lactis. This bacterium is used to produce an array of fermented dairy products. Even if this environment is tightly controlled, phages are ubiquitous in milk and in factories, and they can affect fermentations. The AbiQ antiphage system ressembles to a toxin-antitoxin (TA) system, but its mode of action is still unknown. In this study, three objectives were persued in order to better understand the relationship between Lactococcus lactis and its phages. First, the phage 949 genome, a member of a rare lactophage group that bears its name, was sequenced and characterized. A genome comparison of all lactococcal phages sequenced to date was done to confirm the current phage classification. In the second objective, we have confirmed that AbiQ is indeed a toxin-antitoxin system. Experiments were performed to demonstrate that this TA mechanism is composed of a RNA antitoxin and a protein toxin with ribonuclease activity. In the third objective, the effect of AbiQ on the phage replication was evaluated. By isolating phage mutants able to escape the mechanism, different phage targets were identified. Understanding the phage-host relationships is the key to develop efficient tools to reduce phage infection in industrial settings or to limit the development of phage resistance in other applications such as in phage therapy.
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Ramkissoon, Yashin Danjay. "Interaction cloning by phage display : protein interactions of the human testis determining factor, SRY". Thesis, University of Cambridge, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.627297.
Testo completo
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Bankier, Claire. "Coevolutionary interactions between bacteria and phage in natural environments". Thesis, Imperial College London, 2016. http://hdl.handle.net/10044/1/44556.
Testo completoAbstract (sommario):
Bacteria and their viruses (bacteriophage, phage) are the most abundant and diverse taxonomic groups, but ecological and evolutionary research on bacteria-phage interactions has largely focused on studies of simplified communities using a few model organisms. The goal of the thesis is to understand how bacteria and phage interact within natural environments, and how these interactions impact the patterns of phage infectivity and bacterial resistance. Here I investigate the effects of natural environments on the coevolutionary patterns of bacteria (Pseudomonas fluorescens) and phage (SBW25Φ2). In chapter 3 I investigate the effects of nineteen different communities on the coevolutionary interactions of SBW25 and phage, and the degree to which the infectivity of phage to its host, SBW25, changes depending on their local microbial community. Chapter 4 aimed to understand the effects of varying diversities of communities on coevolutionary interactions. In Chapter 5, I looked at how coevolutionary interactions were affected by different communities in different abiotic conditions (pH, temperature and nutrient concentration) and the effect communities had on the ability of SBW25 to adapt to the abiotic conditions. Understanding how biological and physical factors affect coevolutionary interactions in natural environments allows predictions of how phage and bacteria coevolve in natural and unnatural settings.
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Räisänen, L. (Liisa). "Phage-host interactions in Lactobacillus delbrueckii: host recognition and transcription of early phage genes". Doctoral thesis, University of Oulu, 2007. http://urn.fi/urn:isbn:9789514284250.
Testo completoAbstract (sommario):
Abstract
The scope of this study includes aspects of phage evolution and antagonistic/mutualistic coevolution between a phage and its host. As a basic study it may provide tools for developing phage resistant starters and offer regulatory elements and factors for biotechnological applications.
The LL-H anti-receptor was characterized by isolation of spontaneous LL-H host range mutants and subsequent sequencing of candidate genes. All LL-H host range mutants carried a single point mutation at the 3' end of a minor tail protein encoding gene g71. The genomic location of g71 is congruent with the other verified anti-receptor genes found in the λ supergroup. The C-terminus of Gp71 determines the adsorption specificity of phage LL-H similarly for the number of phages infecting Gram-positive and Gram-negative bacteria. A Gp71 homolog of phage JCL1032 showed 62% identity to LL-H Gp71 within the last 300 amino acids at the C-terminus.
Lactobacillus delbrueckii phage receptors were investigated by the purification of different cell surface structures. Certain Lb. delbrueckii phages from homology groups a and c including LL-H, LL-H host range mutants and JCL1032, were specifically inactivated by the LTAs. In structural analyses LTAs showed differences in the degree of α-glucosyl and ᴅ-alanyl substitution. α-glucose is necessary for LL-H adsorption. A high level of ᴅ-alanine esters in LTA backbones inhibited Lb. delbrueckii phage inactivation in general. Lysogenization of strain ATCC 15808 with the temperate phage JCL1032 revealed a rarely described coexistence of phage adsorption resistance and phage immunity, which could not be explained by lysogenic conversion. In this case the role of spontaneously induced JCL1032 may be significant.
The LL-H early gene region was localized between the dysfunctional lysogeny module and the terminase encoding genes. The function of five ORFs could be connected to phage DNA replication and/or homologous recombination. Transcription of LL-H genes could be divided into two, possibly three, phases in which large gene clusters were sequentially transcribed. The intensity of the late transcripts exceeded the intensity of the early transcripts by several times. Two candidate genes for transcription regulators were found. One of the two candidates is the first ORF in the LL-H early gene region.
9
Gonzalez, Floricel. "Investigation of flagellotropic phage interactions with their motile host bacteria". Diss., Virginia Tech, 2021. http://hdl.handle.net/10919/103940.
Testo completoAbstract (sommario):
Bacteriophages cohabit with their bacterial hosts and shape microbial communities. To initiate infection, phages use bacterial components as receptors to recognize and attach to hosts. Flagellotropic phages utilize bacterial flagella as receptors. Studies focused on uncovering mechanistic details of flagellotropic phage infection are lacking. As the number of phage-based applications grows, it is important to understand these details to predict the potential outcomes of phage therapy. To this end, we studied two flagellotropic phages: Agrobacterium phage 7-7-1 and bacteriophage χ. Phage 7-7-1 infects Agrobacterium spp., while bacteriophage χ infects Salmonella and Escherichia coli.
Chapter 1 consists of a literature review. Chapter 2 addresses factors underlying phage-bacteria coexistence. We document the emergence of a sector-shaped lysis pattern following co-inoculation of phage χ and one of its Salmonella hosts on swim plates. We propose that this pattern serves as a reporter for balanced phage-bacteria coexistence. Using a combined experimental and mathematical modelling approach, we discovered that variations to intrinsic factors (i.e., bacterial motility, phage adsorption) skews the pattern towards either bacterial or phage predominance. Thus, this computational model may be used to predict phage therapy application outcomes.
Chapter 3 details the identification of cell surface receptors essential for phage 7-7-1 infection using a transposon mutagenesis approach. We identified three Agrobacterium sp. H13-3 genes involved in phage 7-7-1 infection. Using mass spectrometry and other analyses, we determined that the LPS profiles of strains lacking these genes varied compared to the wild type. Thus, LPS is a secondary cell surface receptor for phage 7-7-1. Chapter 4 focuses on the discovery of phage encoded receptor binding proteins (RBPs) in Agrobacterium phage 7-7-1. Using an RBP screen, we discovered three candidate RBPs. We learned that our top candidate, Gp4, inhibits the growth of Agrobacterium sp. H13-3 cells in a motility and glycan dependent manner. Because of its bacteriostatic activities, this protein is a promising candidate for therapeutic use. Overall, the described works contribute to a deepened understanding of flagellotropic phage infection and the factors influencing their coexistence with motile bacteria. These works will contribute towards the development of phage therapies using whole phage or their components.Doctor of Philosophy
Bacteriophages, or phages for short, are the natural killers of bacteria. Like antibiotics, they can also be used as medicines to treat bacterial infections. Their attack on bacteria begins by recognizing specific parts of the bacterial cell and attaching to them. These parts are called receptors. To use phages as medicines it is important to understand how they recognize and kill bacteria. This information is helpful when deciding which phage should be given to treat a bacterial infection and to predict the outcomes of these treatments. In this work, we focused on two phages to answer different questions. Both phages use long helical thread-like structures, called flagella, as receptors. Flagella help the bacteria to move through the environment and reach new areas with more nutrients. One of these flagella-dependent phages, called phage 7-7-1, infects plant pathogens that cause tumor-like growth in plants. We found that this phage uses two very different host cell components during infection and identified one of the phage proteins that interacts with these receptors. This protein prevents the growth of the plant pathogen, which makes it a promising candidate for therapeutic use. We also investigated how another bacterial virus, bacteriophage χ, is spread throughout the environment and co-exists with its motile bacterial host. We built a computational model that can predict how altering different variables affects phage-bacteria coexistence. With additional research, this model will be a useful tool for predicting the outcomes following phage treatment.
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Fan, Yan Baranger Anne M. Katzenellenbogen John A. Zhao Huimin Silverman Scott K. "Exploring protein-RNA interactions with site-directed mutagenesis and phage display". Urbana, IL.: University of Illinois, 2009. http://hdl.handle.net/2142/14755.
Testo completo
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McLean, Hector Alexander. "Application of phage display to the study of toxin-receptor interactions". Thesis, University of Glasgow, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.301779.
Testo completo
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Lerat, Guilhem. "Interactions d'agents antitumoraux avec la neocarzinostatine : ingénierie combinatoire par exposition sur phage". Paris 11, 2001. http://www.theses.fr/2001PA112283.
Testo completoAbstract (sommario):
L'apo-néocarzinostatin est une protéine transportant un chromophore. Cette protéine est aussi capable de fixer la doxorubicine, une molécule utilisée en thérapie anti-cancéreuse. La néocarzinostatin est une proteine stable, susceptible d'être modifié afin de lui conférer la capacité de cibler la doxorubicine par reconnaissance de récepteurs cellulaires spécifiques. L'affinité de la neocarzinostatin pour la doxorubicine est de 10mM, ce qui est trop faible pour envisager l'utilisation de ce complexe. Le but de ce travail est d'augmenter l'affinité de la protéine pour le composé chimique par mutagenèse aléatoire. La mutagenèse affectera uniquement les résidus du site de fixation n'étant pas en interaction avec la doxorubicine. Le criblage de la banque combinatoire est réalisé en utilisant la technique d'exposition sur phage. La banque combinatoire construite se caractérise par une taille permettant l'exploration exhaustive du répertoire. Il n'y a aucun biais notable. Le criblage de la banque est réalisé de manière à sélectionner les mutants présentant une meilleur affinité pour la doxorubicine. Le criblage se révèle délicat en raison de l'instabilité du gène de la néocarzinostatine, ce dernier étant délété par recombinaison au cours des tours de sélection. Le criblage de la banque a permis d'isoler plusieurs clones capable de fixer la doxorubicine. Parmi ces différents clones, un seul possède une phase ouverte de lecture correcte permettant d'exprimer de la neocarzinostatine. Ce mutant de la neocarzinostatine se caractérise par la présence de glutation au niveau du site de fixation. L'affinité de ce mutant pour la doxorubicine est plus mauvaise que celle de la neocarzinostatine sauvage. L'élimination du glutation n'améliore pas l'affinitéThe apo-néocarzinostatin is a protein which carries a chromophore. This protein is also able to fix doxorubicin, a molecule used in anti-cancerous therapy. The néocarzinostatin is a stable protein, which can be modified in order to give it the ability to target the doxorubicin with the specific cellulars receivers recognition. The neocarzinostatin affinity for the doxorubicine is about 10 mM, which is too weak to use this kind of complex. The goal of this work is to increase the protein affinity of the chemical composition thanks to the aleatory mutagen. The mutagen will only affect the residues of the fixation site since they do not interact with the doxorubicin. The combinative bank sifting is carried out with the use of the exhibition technic on phage. The combinative bank is characterized by a dimension, which facilitates the repertory large exploration. There is not any other remedy. The bank sifting is carried out in order to select the mutants who seem to have more affinity with the doxorubicine. The sifting seems very difficult due to the neocarzinostatin gen instability, this one deleted by recombination during the selections. The bank sifting permits to isolate several clons able to fix the doxorubicin. Among these different clons, only one have a correct opened stage of reading, which can produce neocarzinostatin. This neocarzinostatin mutant is characterized by the presence of glutation found in the fixation site. This mutant affinity towards the doxorubicin is more bad than the one of the brute neocarzinostatin. The glutation elimination does not improve affinity
13
Kuno, Sotaro. "Genetic analysis of host-phage interactions involving the toxic cyanobacterium Microcystis aeruginosa". Kyoto University, 2013. http://hdl.handle.net/2433/175039.
Testo completoAbstract (sommario):
Kyoto University (京都大学)0048
新制・課程博士
博士(農学)
甲第17610号
農博第1972号
新制||農||1008(附属図書館)
学位論文||H25||N4731(農学部図書室)
30376
京都大学大学院農学研究科応用生物科学専攻
(主査)教授 左子 芳彦, 教授 平田 孝, 教授 澤山 茂樹
学位規則第4条第1項該当
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Klenow, Laura. "Characterization of the Interactions between Staphylococcal Phage 80 Alpha Scaffold and Capsid Proteins". VCU Scholars Compass, 2015. http://scholarscompass.vcu.edu/etd/3917.
Testo completoAbstract (sommario):
Staphylococcal phage 80α can serve as a helper bacteriophage for a family of mobile genetic elements called Staphylococcus aureus pathogenicity islands (SaPIs). The prototype island, SaPI1, is able to hijack the 80α capsid assembly process and redirect capsid formation to yield smaller, phage-like transducing particles carrying SaPI DNA. Capsid size redirection is accomplished through two SaPI1-encoded gene products, CpmA and an alternate scaffold protein, CpmB. The normal 80α scaffold and the SaPI1 CpmB scaffold share a small block of conserved residues at their C-termini, several of which had been shown to be essential for CpmB function. This led to the hypothesis that the C-termini of both the phage and SaPI scaffolds interact in similar ways with the major capsid protein. The goal of this study was to test this hypothesis and to identify the amino acid residues at the capsid-scaffold interface, using a genetic approach.
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Feichtmayer, Judith [Verfasser], Christian [Akademischer Betreuer] Griebler, Wolfgang [Gutachter] Liebl e Christian [Gutachter] Griebler. "Bacteria-phage interactions: Insights into quorum sensing-induced anti-phage defense, phage therapy and the pulmonary human virome composition / Judith Feichtmayer ; Gutachter: Wolfgang Liebl, Christian Griebler ; Betreuer: Christian Griebler". München : Universitätsbibliothek der TU München, 2019. http://d-nb.info/1193650429/34.
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Marsh, Peter. "Interactions between actinophage and streptomycetes in soil and the fate of phage-borne genes". Thesis, University of Warwick, 1993. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.387392.
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Rimbault, Charlotte. "Modulation des interactions impliquant les domaines PDZ par une approche d’évolution dirigée". Thesis, Bordeaux, 2016. http://www.theses.fr/2016BORD0438/document.
Testo completoAbstract (sommario):
Les interactions protéine-protéine (IPPs), complexes et dynamiques, sont le cœur des réseaux protéiques cellulaires. Au niveau des synapses excitatrices, la densité post-synaptique (PSD) est un exemple typique de réseau protéique dont la structure et la composition à l’échelle nanoscopique détermine la fonction cellulaire. Ainsi, la régulation dynamique de la composition de la PSD et des mouvements des récepteurs au glutamate dans ou hors de la PSD constitue la base des théories moléculaires actuelles sur l’apprentissage et la mémoire. Dans ce contexte, durant ma thèse, j’ai étudié une classe d’IPPs faisant intervenir les domaines PDZ. En effet, durant ces dernières années, de nombreuses études ont démontré l’implication de ces interactions impliquant les domaines PDZ de la famille de PSD95 dans le ciblage synaptique et l’ancrage des récepteurs au glutamate. Cependant, en partie dû au manque d’outils adaptés, les mécanismes moléculaires sous-jacents qui contrôlent de façon dynamique leur rétention à la synapse restent mal compris. Dans le but d’étudier ces interactions impliquant des domaines PDZ, j’ai développé plusieurs stratégies de sélection par phage display basées sur l’utilisation du dixième domaine de type III de la fibronectine humaine (10Fn3) dans le but de cibler les motifs d’interaction aux domaines PDZ des récepteurs (Stargazin pour les rAMPA et GluN2A pour les rNMDA) ou les domaines PDZ eux-mêmes. En utilisant une approche multidisciplinaire, mes objectifs principaux ont été de concevoir de petits anticorps synthétiques qui nous permettront de rompre ou de stabiliser spécifiquement ces complexes protéiques, ainsi que d’observer les interactions endogènesComplex and dynamic protein-protein interactions are the core of protein-based networks in cells. At excitatory synapses, the postsynaptic density (PSD) is a typical example of protein-based network whose nanoscale structure and composition determines the cellular function. For instance, the dynamic regulation of PSD composition and glutamate receptors movements into or out of the PSD are the base of current molecular theories of learning and memory. In this context, during my PhD, I focused on a class of protein-protein interactions mediated by PDZ domains. Indeed, over the last decade, numerous studies have shown the critical implication of PDZ domain-mediated interactions from the PSD95 scaffolding protein family in the synaptic targeting and anchoring of glutamate receptors. However, in part due to the lack of adapted tools, the molecular mechanisms that dynamically govern their respective synaptic retention remain poorly understood. In order to investigate these PDZ domain-mediated interactions, I developed several selection strategies by phage-display based on the fibronectin type III (FN3) scaffold in order to either target the PDZ domain-binding motifs of the receptors complexes (e.g., stargazin for AMPARs and GluN2A for NMDARs) or the PDZ domains themselves. Using a multidisciplinary approach, my main objectives were to engineer small synthetic antibodies that will allow us to acutely and specifically disrupt or stabilize these protein complexes, as well as monitor endogenous interactions
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Flores, Garcia César O. "Phage--Bacteria Infection networks: from nestedness to modularity and back again". Diss., Georgia Institute of Technology, 2014. http://hdl.handle.net/1853/53007.
Testo completoAbstract (sommario):
Bacteriophages (viruses that infect bacteria) are the most abundant biological life-forms on Earth. However, very little is known regarding the structure of phage-bacteria infections. In a recent study we showed that phage-bacteria infection assay datasets are statistically nested in small scale communities while modularity is not statistically present. We predicted that at large macroevolutionary scales, phage-bacteria infection assay datasets should be typified by a modular structure, even if there is nested structure at smaller scales. We evaluate and confirm this hypothesis using the largest study of the kind to date.
The study in question represents a phage-bacteria infection assay dataset in the Atlantic Ocean region between the European continental shelf and the Sargasso Sea. We present here a digitized version of this study that consist of a bipartite network with 286 bacteria and 215 phages including 1332 positive interactions, together with an exhaustive structural analysis of this network. We evaluated the modularity and nestedness of the network and its communities using a variety of algorithms including BRIM (Bipartite, Recursively Induced Modules), NTC (Nestedness Temperature Calculator) and NODF (Nestedness Metric based on Overlap and Decreasing Filling). We also developed extensions of these standard methods to identify multi-scale structure in large phage-bacteria interaction datasets. In addition, we performed an analysis of the degree of geographical diversity and specialization among all the hosts and phages.
We find that the largest-scale ocean dataset study, as anticipated by Flores et al. 2013, is highly modular and not significantly nested (computed in comparison to null models). More importantly is the fact that some of the communities extracted from Moebus and Nattkemper dataset were found to be nested. We examine the role of geography in driving these modular patterns and find evidence that phage-bacteria interactions can exhibit strong similarity despite large distances between sites. We discuss how models can help determine how coevolutionary dynamics between strains, within a site and across sites, drives the emergence of nested, modular and other complex phage-bacteria interaction networks.
Finally, we releases a computational library (BiMAT)to help to help the ecology research community to perform bipartite network analysis of the same nature I did during my PhD.
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Olonade, Israel Temiloluwa. "Development of a novel high throughput method for identifying phage-host pairs in an extreme environment". University of the Western Cape, 2017. http://hdl.handle.net/11394/5664.
Testo completoAbstract (sommario):
Philosophiae Doctor - PhDThere are approximately 10³¹ bacteriophages in the biosphere, outnumbering bacteria 10:1, hence, the dynamic and specific nature of phage-host interactions exerts significant influence on microbial communities. Bacteriophages also represent the reservoir of the highest known genetic diversity making them a potential source of novel biotechnological products. However, the isolation of novel bacteriophages is limited by the observation that less than 1% of bacterial hosts have been cultured. This study aimed to bypass this problem by developing novel culture independent approaches to improve our ability to isolate novel phage-host pairs. Samples were collected from an abandoned copper prospecting site near the Gobabeb Desert Research and Training Station and a Salt lake located in the Swakopmund region of the Namibian desert. Two approaches were explored in this study namely viral tagging and reverse metaviromics. For viral tagging, fluorescently labelling the environmental phage fraction before challenging the environmental bacterial fraction with tagged phages proved difficult. This was most likely due to the complex interaction of the labelling agent with phages and requires further studies. For the reverse metaviromics approach, total DNA from the environmental phage fractions was extracted, sequenced and analyzed for novel phages. Analysis of the phage diversity showed that the copper site was dominated by tailed viruses as has been shown for other extreme arid environments. However, the saline site was atypical of marine environments, with tailed viruses being the most abundant, suggesting that the diversity present is not only driven by salinity. Using the metaviromic sequence data to guide the selection of potential bacterial hosts, two strategies were employed. In the first, putative hosts were predicted based on similarity of phage sequences to those identified in databases. Media targeting these specific genera were employed, 8 bacterial species were isolated and based on 16S rRNA similarity to the closest known species were identified as Halomonas caseinilytica, Halomonas eurihalina, Halomonas sinaiensis, Idiomarina loihiensis, Marinobacter xestospongiae, Virgibacillus salarius and two Salinivibrio species. The 16S rRNA analysis also suggested that H. sinaiensis, V. salarius and both Salinivibrio species are novel. All 8 isolates were challenged with the environmental phage fraction. A novel phage, SMHB1, was isolated on one of the Salinivibrio spp. and is only the second characterized phage ever described for this genus. SMHB1 is a 32 kb myovirus, with a head diameter of 56 nm, and a tail length of 106 nm. The second approach involved the design of fluorescently labelled probes targeting phages identified from the metaviromic sequence data. In a control E. coli system to detect cloned phage DNA fragments, 87% of the interrogated cells showed significant hybridization of the phage specific probe to the target. The optimized method was applied to a simulated environmental bacterial fraction and a detection limit of 1:100 was observed for the bacteria containing the phage DNA fragment of interest. This study demonstrates the possibility of improving the specificity of isolating phage-host pairs in a culture-independent manner by incorporating sequence data in the experimental design; and contributes to our knowledge of the phage diversity of an understudied extreme environment.
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Tremblay-Bouliane, Karl. "Caractérisation des interactions phage-minerai et développement de bio-réactifs potentiels pour les procédés de flottation". Master's thesis, Université Laval, 2015. http://hdl.handle.net/20.500.11794/25979.
Testo completoAbstract (sommario):
La flottation est un procédé de séparation important dans l’industrie minière. Un in-térêt particulier est porté aux réactifs employés dans ce procédé en raison de leur impact sur les performances économiques des mines. Avec pour objectif de développer des réactifs efficaces d’origine biologique et moins nocifs pour l’environnement, une librairie d’expression phagique a été criblée afin d’identifier des ligands pour différents minerais d’intérêt industriel, notamment l'or, la chalcopyrite, la sphalérite, la pyrite et la silice. Après plusieurs rondes de sélection et d'enrichissement, des séquences peptidiques ont été isolées pour chacun de ces minerais. Toutefois, la détermination des isothermes d'adsorption pour chacune de ces interactions a révélé une faible spécificité. L’effet de l’adsorption de bacté-riophages, arborant certaines séquences, à la surface de ces minerais a été étudié afin d’évaluer leur potentiel en tant que bio-réactifs de flottation. Ceci a permis de confirmer une diminution de l’hydrophobicité, c’est-à-dire un effet déprimant. Les bactériophages seraient donc des candidats potentiels pour certains types d'application en flottation, ce-pendant leur coût de production devrait être significativement réduit afin d'en faire une alternative viable.Flotation is an important separation process in mining industry. Because of their im-pact on mines economic performances, special attention is directed to flotation reagents. In order to develop efficient bio-based reagents with a lower environmental footprint, a phage display library was screened as a mean to identify peptides able to bind to ores of economi-cal interest, including gold, chalcopyrite, pyrite, sphalerite and silica. After many biopan-ning rounds, peptide sequences were successfully isolated for each of these ores. However, adsorption isotherm determination for these interactions revealed a low specificity of the obtained sequences. The possibility to use bacteriophages as flotation bio-reagents was as-sessed by studying effect produced by adsorption of phages displaying selected peptide sequences on surface properties of some of the ores. A decrease in hydrophobicity was con-firmed, suggesting a depressing effect on ores. Thus, bacteriophages might be potential candidates for some types of flotation applications but their production cost will have to be brought down significantly in order to be considered a viable alternative.
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Howard-Varona, Cristina. "Phage Fate: Infection Dynamics and Outcomes in a Marine Virus - Host System". Diss., The University of Arizona, 2015. http://hdl.handle.net/10150/556856.
Testo completoAbstract (sommario):
Viruses infecting bacteria (phages) are the most abundant and ubiquitous entities on Earth and likely critical to any ecosystem, as they influence nutrient cycling, mortality and evolution. Ultimately, their impact depends on whether phage—host interactions lead to intracellular phage coexistence (temperate phage) or cell death (lytic phage). Temperate phages in the lysogenic cycle replicate their genome (either integrated into the host chromosome or extrachromosomally), until induced to become lytic, when they create and release progeny via cell lysis. While knowledge on lytic versus lysogenic outcomes is vast, it largely derives from few model systems that underrepresent natural diversity. Further, less is known about the efficiency of phage—host interactions and the regulation of optimal versus sub-optimal lytic infections, which are predicted as relevant under environmental (nutrients, temperature) and host (availability, density) conditions that are common in the ocean. In this dissertation I characterize the phage—host interactions in a new marine model system, phage ϕ38:1 and its Cellulophaga baltica bacterial host, member of the ubiquitous Bacteroidetes phylum. First, I show ϕ38:1’s ability to infect numerous, genetically similar strains of the C. baltica species, two of which display contrasting infection outcomes–lytic versus sub-optimally lytic or lysogenic on the original versus alternative hosts, respectively. Second, I collaboratively apply new gene marker-based approaches (phageFISH and geneELISA) to study ϕ38:1’s infection at the single-cell level and show that it is sub-optimal on the alternative host, rather than lysogenic. Third, I collaboratively develop whole-genome transcriptome datasets for ϕ38:1 infecting both, the optimal and sub-optimal hosts, to characterize the cellular response to infection and hypothesize potential transcriptional and post-transcriptional regulation of the sub-optimal infection. Together, these findings advance our knowledge of naturally-occurring phage—host interactions with a focus on nearly-unstudied sub-optimal infections.
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Hosseinidoust, Zeinab. "An investigation of bacteriophage-bacteria interactions: development of phage resistance and associated variations in virulence and biofilm formation". Thesis, McGill University, 2013. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=114443.
Testo completoAbstract (sommario):
The rise of antibiotic resistance has rekindled interest in the development of alternative antimicrobial agents. Bacteriophages, bacteria's obligate parasites, have drawn a lot of interest from the scientific community and from the industry due to their many advantages. However, there are various challenges hindering the use of bacteriophages as antimicrobial agents. In this dissertation, a number of these challenges have been addressed. After a brief introduction on the advantages and drawbacks of using phage in chapter one, the inherent limitation of using immobilized phage for antimicrobial surfaces is presented in chapter two. In the subsequent three chapters, one of the main issues of challenging bacterial communities with phage was addressed, namely emergence of phage-resistant bacteria variants. The effect of phage on biofilm formation was investigated and it was observed that in some cases they can lead to increase in biofilm formation. Furthermore the colonies of phage-resistant bacteria emerged in contact with phage were studied. It was reported that their phenotype, their virulence traits as well as their in vitro virulence towards mammalian cells had been significantly affected. This investigation highlights the importance of awareness of the effect of phage on bacterial communities for effective utilization of their potential.L'augmentation de la résistance aux antibiotiques a ravivé l'intérêt dans le développement d'agents antimicrobiens alternatifs. Les bactériophages, parasites bactériens obligatoires, ont suscité beaucoup d'intérêt de la part de la communauté scientifique et de l'industrie à cause de leurs nombreux avantages. Cependant, plusieurs défis restent à relever pour résoudre les problèmes qui empêchent l'utilisation des bactériophages comme agents antimicrobiens. Un certain nombre de ces défis sont adressés dans cette dissertation. Après une brève introduction sur les avantages et désavantages de l'utilisation des bactériophages dans le premier chapitre, nous présentons dans le second chapitre les limitations intrinsèques de l'utilisation de bactériophages immobilisés pour créer des surfaces antimicrobiennes. Dans les trois chapitres suivants, nous traitons de l'une des principales questions concernant l'infection de cultures bactériennes par les bactériophages, à savoir l'émergence de variants bactériens résistants. L'effet des bactériophages sur la formation de biofilms a été étudié et nous avons observé que dans certains cas, les bactériophages peuvent augmenter la formation de biofilms. En outre, nous avons étudié les colonies bactériennes résistantes qui émergent après l'infection par des bactériophages. Nous avons trouvé que leur phénotypes, leurs caractères de virulence ainsi que leurs virulences in vitro envers les cellules mammifères avaient été affectés de manière significative. Cette investigation souligne l'importance des effets des bactériophages sur les cultures bactériennes pour une utilisation efficace de leur potentiel antimicrobien.
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Kurup, Sindhulakshmi. "Design of Oligosaccharide Libraries to Characterize Heparan Sulfate – Protein Interactions". Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis, 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-7095.
Testo completo
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Gamage, Shantini. "Shiga toxin-encoding phage from escherichia coli O157:H7- interactions with non-pathogenic E. coli and implications for toxin production". Cincinnati, Ohio : University of Cincinnati, 2004. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=ucin1078410327.
Testo completo
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Foutel--Rodier, Théo. "Genome-wide effects of T4 phage Ndd protein expression on the Escherichia coli nucleoid". Electronic Thesis or Diss., Sorbonne université, 2021. http://www.theses.fr/2021SORUS553.
Testo completoAbstract (sommario):
La principale partie de ma thèse s’intéresse aux principes d'organisation du génome de la bactérie Escherichia coli. Le génome des bactéries est contenu dans le nucléoïde, un espace fortement organisé par de nombreux facteurs tels que la transcription, le sur-enroulement de l'ADN ou la présence de protéines spécifiques. Toutefois, les mécanismes précis qui régissent l'organisation du nucléoïde restent vaguent. La protéine Ndd du phage T4 provoque une désorganisation radicale du nucléoïde quand elle est exprimée chez E. coli. J'ai utilisé cette protéine Ndd pour tenter de révéler des structures encore inconnues liées à l'organisation du nucléoïde. En utilisant un nouveau système d'expression de Ndd chez E. coli il a été possible de montrer que cette protéine impacte l'ensemble du génome d'E. coli, aussi bien structurellement que transcriptionnellement. Des études en Hi-C ont permis de révéler que la structuration locale du nucléoïde n'est pas affectée par la présence de Ndd. Toutefois, l'expression de Ndd provoque une altération du profil de réplication d'E. coli avec une possible surreplication de la région proximale de l'origine de réplication. Nous avons aussi observé que l'expression de Ndd depuis le chromosome menait à des conséquences très différentes de son expression depuis un plasmide. La recherche de partenaires de Ndd qui pourraient expliquer ces effets par un screen dCas9 n'a donné que peu de candidats qui sont en cours de validation. Nous montrons ici que Ndd semble agir sur un ou des aspects précis mais encore indéterminés de l'organisation du nucléoïde et potentiellement indépendamment de la participation de gènes d'E. coliThe main project of my PhD concerned the principles of organization of the genome of the bacterium Escherichia coli. Bacterial genomes are held in the nucleoid, a space highly organized by many factors such as transcription, DNA supercoiling or the presence of specific proteins. However, some of the precise mechanisms that govern its organization remain unclear. The Ndd protein from phage T4 causes a radical disorganization of the nucleoid when expressed in E. coli. I used this Ndd protein to try to reveal previously unknown structures related to nucleoid organization. Using a novel expression system for Ndd in E. coli, it was possible to show that this protein impacts the entire genome of E. coli, both structurally and transcriptionally. Hi-C studies revealed that the Ndd-disrupted nucleoid remains locally structured in a manner similar to a normal nucleoid. However, Ndd expression causes an alteration in the replication profile of E. coli with possible over-replication at the origin of replication. We also observed that expression of Ndd from the chromosome leads to very different consequences than its expression from a plasmid. The search for a partner of Ndd that could explain these effects by a dCas9 screen yielded few candidates that are currently undergoing validation. Here we show that Ndd appears to act on one or more specific aspects of nucleoid organization and potentially independently of the involvement of genes from E. coli
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Nusbaum, Julien. "Caractérisation structurale et fonctionnelle de la peptide déformylase du phage Vp16T". Thesis, Université Paris-Saclay (ComUE), 2016. http://www.theses.fr/2016SACLS510/document.
Testo completoAbstract (sommario):
Les protéines en cours de synthèse subissent des modifications très précoces de leur extrémité N-terminale, dès lors que celle-ci émerge du tunnel de sortie du ribosome. La première modification est l’excision de la méthionine initiatrice, assurée par une méthionine aminopeptidase (MetAP), précédée de sa déformylation par une enzyme peptide déformylase (PDF) chez les bactéries et dans les mitochondries et chloroplastes. Ce processus est ubiquitaire et essentiel, et a été décrit dans tout le règne du vivant. Chez les bactéries, les PDFs de type 1B se fixeraient au ribosome à proximité de l’extrémité du tunnel de sortie du peptide naissant, via son hélice α C-terminale. Or des analyses métagénomiques récentes ont révélé la présence insoupçonnée de gènes codant des PDFs putatives chez des virus marins. De manière inattendue, toutes les PDF virales présentent des séquences C-terminales très courtes et dépourvues de l’hélice α3. L’identification de ces PDFs atypiques soulève alors de nouvelles questions quant à leur possible interaction au ribosome et à leur fonction biologique. L’objectif de ma thèse a donc été de réaliser la caractérisation complète et intégrée de la peptide déformylase du bactériophage Vp16T, dont la séquence est l’une des plus courtes connues à ce jour. J’ai montré que le phage Vp16T code une protéine active, in vivo et in vitro, et qu’elle peut se lier au ribosome malgré l’absence d’hélice α C-terminale. La caractérisation structure-fonction de Vp16PDF a révélé des caractéristiques uniques qui pourraient alors expliquer sa fonction au cours de la réplication du phage. Ainsi j’ai montré que l’expression de Vp16PDF chez E. coli modifie la structure de l’enveloppe, induit l’accumulation d’agrégats et finalement inhibe la croissance bactérienne. De plus, l’étude de souches bactériennes mutantes a montré que Vp16PDF interfère spécifiquement avec le repliement et l’adressage de protéines membranaires. Cette dernière fonction pourrait permettre de déstabiliser la membrane de l’hôte et ainsi favoriser la libération des particules viralesBeing synthesized proteins undergo very early changes in their N-terminal end, since it emerges from the outlet channel of the ribosome. The first modification is the excision of the initiator methionine, provided by a methionine aminopeptidase (MetAP), preceded by its deformylating enzyme peptide deformylase (PDF) in bacteria and in mitochondria and chloroplasts. This process is ubiquitous and essential, and has been described in the kingdom of life. In bacteria, Type 1B PDFs would bind to the ribosome near the end of the outlet tunnel of the nascent peptide via its C-terminal helix α. But recent metagenomic analyzes revealed the unexpected presence of genes encoding putative PDFs in marine viruses. Unexpectedly, all viral PDF have very short C-terminal sequences and lacking the α3 helix. The identification of these atypical PDFs then raises new questions about their possible interaction with ribosome and their biological function. The aim of my thesis was therefore to achieve the complete and integrated characterization of peptide deformylase bacteriophage Vp16T, the sequence is one of the shortest known to date. I showed that the phage Vp16T code an active protein in vivo and in vitro, and can bind to the ribosome despite the absence of the C-terminal helix α. The structure-function characterization Vp16PDF revealed unique features that could then explain its function in the replication of the phage. Thus I have shown that expression in E. coli Vp16PDF modifies the envelope structure, induces accumulation of aggregates and ultimately inhibits bacterial growth. In addition, the study of mutant bacterial strains showed that Vp16PDF specifically interfere with the folding and addressing of membrane proteins. This latter function could help destabilize the membrane of the host and thereby promote release of viral particles
27
Vieu, Erwann. "Dissection du mécanisme de terminaison-antiterminaison au niveau du terminateur tR1 du phage lambda : application à l'étude des complexes ARN-protéine in vivo". Orléans, 2004. http://www.theses.fr/2004ORLE2075.
Testo completoAbstract (sommario):
Chez Escherichia coli la terminaison de la transcription peut intervenir selon deux mécanismes distincts : tout d'abord la terminaison intrinsèque qui correspond à une séquence ADN, codant pour une structure en tige boucle riche en GC suivie d'une répétition d'uridine sur l'ARN, induisant le relargage de l'ARN polymérase. Le second mécanisme est gouverné par un facteur de terminaison nommé Rho qui gouverne environ 50% des évènements de terminaison chez E. Coli. Au cours de ma thèse, je me suis interessé à ce deuxième mécanisme, et plus particulièrement à sa régulation in vivo (antiterminaison). Rho, sous la forme d'un anneau héxamèrique, se fixe à l'ARN naissant au niveau d'un site d'entrée (également appelé RUT), puis utilise son activité ATPase pour longer l'ARN et disssocier le complexe ternaire d'élongation stoppé au niveau d'un site de pause. Les terminateurs Rho-dépendants sont assez mal définis et peu d'entre eux ont été analysés en détail. Le terminateur tR1 du phage lambda (l) est le terminateur Rho-dépendant le plus étudié à la fois in vitro et in vivo. La terminaison Rho-dépendante au niveau de ce terminateur est gouvernée principalement par les séquences localisées en 5', codant deux régions du transcript nommées RUTA et RUTB. Ces deux régions sont séparées par le motif ARN BOXB qui n'est pas indispensable à l'action de Rho mais sert, dans le mécanisme d'antiterminaison, de site de fixation pour la protéine N du phage l. Grâce à un système minimal d'étude in vivo, nous avons montré que le motif BOXB possède une fonction double dans les mécanismes de terminaison/antiterminaison au niveau de ltR1 régulant l'expression temporale du génome du phage l. Sous la forme d'une tige boucle hautement structurée, BOXB agit comme un lien permettant de placer RUTA et RUTB l'un à coté de l'autre pour une interaction optimale avec Rho et une terminaison efficace. A l'inverse, la fixation de la protéine N sur BOXB induit l'antiterminaison au niveau de ltR1 en empèchant l'accès de Rho à l'ARN. Ce double rôle à été démontré in vivo en substituant au couple N/BOXB la "coat protein" du phage MS2 et son motif cible en tige boucle. En complément de ce travail, j'ai utilisé cette faculté d'un complexe ribonucléoprotéique de bloquer la terminaison Rho-dépendante, pour développer une nouvelle approche d'étude, in vivo, des complexes ARN-protéine.
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GAMAGE, SHANTINI D. "Shiga toxin-encoding phage from Escherichia coli O157:H7 - interactions with non-pathogenic E. coli and implications for toxin production". University of Cincinnati / OhioLINK, 2004. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1078410327.
Testo completo
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Bou, habib Michèle. "Développement et analyse d'un modèle dynamique d'attaque de phages lors de l'acidification du lait pour la fabrication du fromage". Electronic Thesis or Diss., université Paris-Saclay, 2024. http://www.theses.fr/2024UPASB061.
Testo completoAbstract (sommario):
Avec l'augmentation de la demande pour les produits fromagers, l'optimisation des procédés de production est devenue essentielle. L'une des premières étapes de la fabrication du fromage est l'acidification du lait, qui influence fortement les propriétés organoleptiques, la texture et la sécurité du produit final. Elle consiste à convertir le lactose, sucre du lait, en acide lactique par des bactéries lactiques. Cependant, ces bactéries sont sensibles aux attaques de virus appelés bactériophages. Ces attaques peuvent entraîner la lyse bactérienne, retardant ou arrêtant l'acidification, ce qui engendre des pertes économiques dues au rejet du lait et à la nécessité de nettoyer les installations. Cela souligne l'importance d'une meilleure compréhension des interactions phages-bactéries en fromagerie.Une approche novatrice pour étudier ces interactions est la modélisation mécaniste dynamique. Cette étude vise donc à contribuer à une meilleure compréhension des interactions phages-bactéries dans les processus de fermentation du lait en établissant un modèle dynamique.Pour ce faire, nous avons utilisé une méthode de mesure à haut débit du pH pour générer des données sur l'acidification dans différentes conditions initiales de bactéries et de phages. Cette approche nous a permis de distinguer trois résultats distincts en fonction de ces conditions : pour certaines conditions, l'acidification a été une réussite ; pour d'autres, elle a échoué ; et pour le reste, le résultat n'a été ni un échec complet ni une réussite complète.Le modèle mécaniste développé comprend cinq équations différentielles ordinaires (EDO) et prend en compte divers phénomènes, tels que l'inhibition par le produit, le temps de latence, l'adsorption des phages et la lyse cellulaire. Le modèle a donné des résultats satisfaisants, prédisant avec précision les données expérimentales et identifiant correctement le résultat de l'acidification. Nous avons également comparé différentes structures de modèle et effectué une analyse de sensibilité pour révéler les phénomènes dominants, ce qui a aussi aidé à concevoir de nouvelles expériences informatives.Une analyse théorique du modèle a révélé trois phases temporelles de l'attaque : d'abord, la phase de contamination, un court laps de temps où les phages s'adsorbent aux bactéries ; puis la phase de propagation, dominée par la propagation des phages et l'infection des bactéries sensibles ; et enfin, la phase de décharge, caractérisée par la lyse bactérienne et la libération de nouveaux phages. Le temps de transition entre les deux dernières phases, noté t*, a été relié aux conditions initiales. Nous avons également identifié une composante dynamique rapide qui peut être séparée des dynamiques lentes. En utilisant l'approximation de l'état quasi-stationnaire, nous avons établi une relation analytique entre les conditions initiales des bactéries et des phages et le pH final. Cela montre que l'acidification ne dépend pas uniquement du rapport des conditions initiales. Cette approximation a permis de réduire le modèle, économisant 83 % du temps de simulation.Enfin, nous avons développé un outil pour prédire le nombre d'acidifications réussies possibles avant qu'un nettoyage ne soit nécessaire. Les résultats sont basés sur des données faciles à obtenir, comme la quantité de bactéries utilisée et les résultats d'une acidification précédente. Cela représente une première étape vers la conception d'un outil d'aide à la décision pour les fromagers.Cette étude améliore notre compréhension des dynamiques d'attaque des phages lors de l'acidification du lait et permet des prédictions précises grâce à un système d'EDO et un modèle réduitAs the demand for diverse cheeses increases, there is a growing interest in optimizing production processes. One of the earliest steps in cheese-making is milk acidification, which highly influences the final product's organoleptic properties, texture, and safety. Milk acidification involves the conversion of lactose, the sugar in milk, into lactic acid by lactic acid bacteria. However, these bacteria are susceptible to attack by viruses known as bacteriophages. This attack can lead to bacterial lysis, resulting in delayed or halted acidification, which incurs significant economic losses as milk is discarded and production facilities require extensive cleaning. This highlights the need for a deeper understanding of phage-bacteria interactions in cheese-making. Research efforts in the dairy industry have primarily focused on characterizing the phages involved and finding new strategies to mitigate phage attacks.One novel approach to studying these interactions is through dynamic mechanistic modeling. Previous models have been developed but have never been applied to the dairy industry. This study aims to fill this gap by contributing to the broader understanding of phage-bacteria interactions in milk fermentation through the establishment of a dynamic model.To achieve this, we first employed a high-throughput pH measurement method to generate acidification data under different initial conditions of bacteria and phages. This methodology proved useful in distinguishing various dynamic behaviors depending on these conditions. It allowed us to delineate three distinct outcomes depending on these conditions: for some conditions the acidification was a success; for some others, it was a failure; and for the rest, the result was neither a complete failure nor a complete success.The mechanistic model we developed consists of five ordinary differential equations (ODEs) and accounts for various phenomena, including product inhibition, lag time, phage adsorption, and cell lysis. The model yielded satisfactory results, accurately predicting experimental data and correctly identifying the acidification outcome. We further investigated the model's structure by comparing various candidate structures and performing a sensitivity analysis to reveal the dominant phenomena throughout the process. The sensitivity analysis also contributed to the design of new informative experimental setups.A theoretical analysis of the model provided insights into the intrinsic dynamics of the system, revealing three time frames of the attack. First, the contamination phase, a short initial time where phages adsorb to the bacteria. Next, the spread phase, where the dominant dynamics involve the spread of phages and the infection of susceptible bacteria. Finally, the discharge phase, where the dominant dynamics are the lysis of bacteria and the release of new phages. The switch time between the last two phases was defined as t∗ and its dependency on the initial conditions was characterized.We also identified a faster dynamic component of the system that can be separated from slower ones. Utilizing the quasi-steady state approximation, we established an analytical relationship between the initial conditions of bacteria and phages and the resulting pH. This relationship indicates that the final outcome of acidification does not solely depend on the ratio of initial conditions but is more complex. The approximation resulted in a reduced model that saved 83% of the simulation time.Finally, we developed a tool to predict the number of potential successful acidifications that can be run before cleaning is required. The results are based on easily obtainable inputs. This represents a first step toward designing a decision aid tool to help cheese makers in their production.This study enhances our understanding of the dynamics of phage attack in milk acidification and facilitates accurate predictions of these dynamics through an ODE system and a reduced model
30
VIEU, Erwann. "DISSECTION DU MÉCANISME DE TERMINAISON/ANTITERMINAISON AU NIVEAU DU TERMINATEUR TRI DU PHAGE LAMBDA : APPLICATION A L'ÉTUDE DES COMPLEXES ARN-PROTÉINE IN VIVO". Phd thesis, Université d'Orléans, 2004. http://tel.archives-ouvertes.fr/tel-00009769.
Testo completoAbstract (sommario):
Chez Escherichia coli la terminaison de la transcription peut intervenir selon deux mécanismes distincts : tout d'abord la terminaison intrinsèque qui correspond à une séquence ADN, codant pour une structure en tige boucle riche en GC suivie d'une répétition d'uridine sur l'ARN, induisant le relargage de l'ARN polymérase. Le second mécanisme est gouverné par un facteur de terminaison nommé Rho qui gouverne environ 50 % des événements de terminaison chez E. coli. Au cours de ma thèse, je me suis intéressé à ce deuxième mécanisme, et plus particulièrement à sa régulation in vivo (antiterminaison). Rho, sous la forme d'un anneau héxamèrique, se fixe à l'ARN naissant au niveau d'un site d'entrée (également appelé RUT), puis utilise son activité ATPase pour longer l'ARN et dissocier le complexe ternaire d'élongation stoppé au niveau d'un site de pause. Les terminateurs Rho-dépendants sont assez mal définis et peu d'entre eux on été analysés en détail. Le terminateur du tR1 du phage lambda (λ) est le terminateur Rho-dépendant le plus étudié à la fois in vitro et in vivo. La terminaison Rho-dépendante au niveau de ce terminateur est gouvernée principalement par les séquences localisées en 5', codant deux régions du transcript nommées RUTA et RUTB. Ces deux régions sont séparées par le motif ARN BOXB qui n'est pas indispensable à l'action de Rho mais sert, dans le mécanisme d'antiterminaison, de site de fixation pour la protéine N du paghe λ. Grâce à un système minimal d'étude in vivo, nous avons montré que le motif BOXB possède une fonction double dans les mécanismes de terminaiso/antiterminaison au niveau de λtR1 régulant l'expression temporale du génome du phage λ. Sous la forme d'une tige boucle hautement structurée, BOXB agit comme un lien permettant de placer RUTA et RUTB l'un à côté de l'autre pour une interaction optimale avec Rho et une terminaison efficace. A l'inverse, la fixation de la protéine N sur BOXB induit l'antiterminaison au niveau de λtR1 en empêchant l'accès de Rho à l'ARN. Ce double rôle a été démontré in vivo en substituant au couple N/BOXB la « coat protein » du phage MS2 et son motif cible en tige boucle. En complément de ce travail, j'ai utilisé cette faculté d'un complexe ribonucléoprotéïque de bloquer la terminaison Rho-dépendante, pour développer une nouvelle approche d'étude in vivo, des complexe ARN-protéine.
31
Drevelle, Antoine. "Évolution dirigée de la néocarzinostatine : ingénierie d’une ossature protéique alternative aux anticorps". Paris 11, 2007. http://www.theses.fr/2007PA112185.
Testo completoAbstract (sommario):
Les anticorps monoclonaux sont des outils moléculaires remarquables utilisés dans des applications thérapeutiques, diagnostiques et biotechnologiques. Néanmoins, certains inconvénients, liés à leur structure moléculaire, entraînent des coûts élevés de développement et de production. Malgré d’importants efforts de recherche ces limitations n’ont pu être dépassées. C’est pourquoi plusieurs laboratoires développent des ossatures alternatives aux anticorps monoclonaux. Il s’agit d’effectuer par évolution dirigée un remodelage fonctionnel sur une ossature protéique différente des anticorps et présentant des propriétés plus favorables. Les travaux décrits dans ce manuscrit concernent différents aspects du remodelage fonctionnel de la néocarzinostatine (NCS). Le chapitre I porte sur la résolution de structures de complexe NCS-ligand. Ces mutants de NCS sont capables de reconnaître de façon spécifique la testostérone, un ligand non naturel. Le chapitre II présente les résultats obtenus pour un projet d’optimisation de l’ossature NCS visant à supprimer ses ponts disulfure pour disposer d’une ossature fonctionnelle dans le compartiment cytoplasmique. Ce travail a permis d’isoler des mutants sans pont disulfure, exprimés sous forme soluble et repliée dans le cytoplasme bactérien. Ces mutants devraient permettre de développer des applications intracellulaires de type interférences à protéine. Le chapitre III concerne le remodelage des boucles exposées de la NCS dans l’objectif de créer des interactions protéine-protéine entre la NCS et des cibles d’intérêt. Ce chapitre décrit les outils développés pour construire une bibliothèque de mutants optimisée pour le repliement[Monoclonal antibodies are powerful tools in biomedical sciences. Nevertheless, they present some limitations, due to their molecular structures, responsible for high cost of development and production. Despite intense research, these limitations haven’t been overcome. That’s why several laboratories try to develop alternative proteic scaffold to monoclonal antibodies. They use directed evolution to perform functional remodelling of alternative scaffold with better properties. This work deals with functional remodelling of néocarzinostatine (NCS). The 1st chapter presents the structure of complexes between evolved NCS mutant and a new ligand. These mutants binds tightly an unnatural ligand : testosterone. The 2nd chapter present the results obtained for scaffold optimisation to cytoplasmic expression. The aim is to remove disulfide bonds of NCS-scaffold to allow cytoplasmic expression. This work has led to new mutants expressed in soluble and folded form in bacterial cytoplasm. Those mutants should allow the development of intracellular targeting applications. The 3rd chapter deals with functional remodelling of scaffold exposed loops to create new binding site for protein recognition. The strategy and developed tools to obtain high quality mutant library are described in this chapter. ]
32
Mansos, Lourenço Marta. "Deciphering in vivo efficacy of virulent phages in the mammalian gut". Electronic Thesis or Diss., Sorbonne université, 2019. https://accesdistant.sorbonne-universite.fr/login?url=https://theses-intra.sorbonne-universite.fr/2019SORUS260.pdf.
Testo completoAbstract (sommario):
L'intestin des mammifères est peuplé de nombreux et divers microbes comprenant des bactéries et leurs prédateurs viraux, des bactériophages (phages). Les interactions entre les phages et les bactéries intestinales sont encore mal comprises. Des expériences indépendantes ont montré que les phages virulents n’avaient aucun effet majeur sur l’abondance des bactéries intestinales ciblées, en dépit de leur amplification durable. Cela suggère que des facteurs encore inconnus de l'environnement intestinal modulent ces interactions. À l’aide d’une analyse transcriptomique comparative de la bactérie Escherichia coli cultivée in vitro et in vivo (dans l’intestin de mammifères), nous avons constaté que, dans l’intestin, les bactéries réduisent l’expression de gènes liés aux récepteurs du phage. Ceci permet d’expliquer l’absence de sélection des bactéries mutées devenues résistantes aux phages lors d'expériences in vivo. D’autre part, nous avons montré que l'acquisition d'un îlot de pathogénicité, souvent associé aux souches intestinales humaines d'E. coli, affecte la susceptibilité aux phages en régulant négativement un mécanisme de défense contre l'ADN étranger. Enfin, nous avons examiné la répartition des phages et des bactéries dans les parties mucosales et luminales de l’intestin et avons observé une distribution spatiale hétérogène de ces deux populations antagonistes, corroborant l'hypothèse d'une dynamique « source-sink ». Globalement, nos données démontrent que de multiples facteurs incluant la distribution spatiale, la physiologie bactérienne et les défenses contre l’ADN étranger modulent les interactions entre bactéries et phages dans l’intestin des mammifèresThe mammalian gut is a heterogeneous environment inhabited by a large and diverse microbial community, including bacteria and their viral predators, bacteriophages (phages). Dynamic interactions between virulent phages and bacteria in the gut are still poorly understood, which is also an obstacle for the design of successful therapeutic interventions based on phages. Independent experiments have shown that virulent phages were found to have no major effects on their targeted bacteria in the gut, in spite of sustainable phage amplification. This suggests that there are unknown factors in the gut environment that modulate these interactions. Using comparative transcriptomics analysis of E. coli grown in vitro and in vivo (within the mammalian gut) we found that in the gut, bacteria downregulate the expression of genes related to phage receptors, which provides an explanation for the lack of selection of phage-resistant bacteria during in vivo experiments. We also found that the acquisition of a pathogenicity island commonly found in human E. coli isolates affects phage susceptibility possibility by downregulating a defense mechanism against invading DNA. Finally, we examined the repartition of phages and bacteria through mucosal and luminal gut sections and observed a heterogeneous spatial distribution of these two antagonist populations, supporting the hypothesis of source-sink dynamics. Altogether our data demonstrates that multiple factors encompassing, spatial distribution, bacterial physiology and defenses against foreign DNA modulate the interactions between bacteria and phages within the gut
33
Shaha, Jonathan. "Phase interactions in transient stratified flow". Thesis, Imperial College London, 2000. http://hdl.handle.net/10044/1/8653.
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Stevens, Kimberly Ann. "Two-Phase Interactions on Superhydrophobic Surfaces". BYU ScholarsArchive, 2018. https://scholarsarchive.byu.edu/etd/7711.
Testo completoAbstract (sommario):
Superhydrophobic surfaces have gained attention as a potential mechanism for increasing condensation heat transfer rates. Various aspects related to condensation heat transfer are explored. Adiabatic, air-water mixtures are used to explore the influence of hydrophobicity on two-phase flows and the hydrodynamics which might be present in flow condensation environments. Pressure drop measurements in a rectangular channel with one superhydrophobic wall (cross-section approximately 0.37 X 10 mm) are obtained, revealing a reduction in the pressure drop for two-phase flow compared to a control scenario. The observed reduction is approximately 10% greater than the reduction that is observed for single-phase flow (relative to a classical channel). Carbon nanotubes have been used to create superhydrophobic coatings due to their ability to offer a relatively uniform nanostructure. However, as-grown carbon nanotubes often require the addition of a thin-film hydrophobic coating to render them superhydrophobic, and fine control of the overall nanostructure is difficult. This work demonstrates the utility of using carbon infiltration to layer amorphous carbon on multi-walled nanotubes to achieve superhydrophobic behavior with tunable geometry. The native surface can be rendered superhydrophobic with a vacuum pyrolysis treatment, with contact angles as high as 160 degrees and contact angle hysteresis less than 2-3 degrees. Drop-size distribution is an important aspect of heat transfer modeling that is difficult to measure for small drop sizes. The present work uses a numerical simulation of condensation to explore the influence of nucleation site distribution approach, nucleation site density, contact angle, maximum drop size, heat transfer modeling to individual drops, and minimum jumping size on the distribution function and overall heat transfer rate. The simulation incorporates the possibility of coalescence-induced jumping over a range of sizes. Results of the simulation are compared with previous theoretical models and the impact of the assumptions used in those models is explored. Results from the simulation suggest that when the contact angle is large, as on superhydrophobic surfaces, the heat transfer may not be as sensitive to the maximum drop-size as previously supposed. Furthermore, previous drop-size distribution models may under-predict the heat transfer rate at high contact angles. Condensate drop behavior (jumping, non-jumping, and flooding) and size distribution are shown to be dependent on the degree of subcooling and nanostructure size. Drop-size distributions for surfaces experiencing coalescence-induced jumping are obtained experimentally. Understanding the drop-size distribution in the departure region is important since drops in this size are expected to contribute significantly to the overall heat transfer rate.
35
Olsson, Stefan. "Phase Transitions and Phase Formation of Hydrogen in Quasi-2D Lattices". Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis : Univ.-bibl. [distributör], 2003. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-3571.
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Codina, Sala Joan. "Activity Mediated Interactions in Soft Matter. Structure, Interactions, and Phase Transitions". Doctoral thesis, Universitat de Barcelona, 2018. http://hdl.handle.net/10803/663988.
Testo completoAbstract (sommario):
In this thesis we asses the phenomena of arising interactions in soft matter in coexistence with soft active matter. As a non-equilibrium bath we introduce ensembles of self-propelled particles, granular shaken beds, and photo active catalytic particles. We start the thesis with a detailed study of the widely used Active Brownian Particle (ABP) model. This model exhibits a non-equilibrium phase transition which has been intensively studied in recent years, we have finally reported that this transition satisfies all features of equilibrium first order phase transitions. Then, we introduce aligning interactions in ABP and characterize the emergent collective phenomena. In parallel, we explore the emergent forces, from mechanical contact forces, in probe particles in suspensions of aligning active particles and horizontally shaken granular beds. We characterize the forces and identify the emergence of long range interactions in both systems, in aligning active particles long range attractive interactions appear as alignment is increased, and in granular shaken media when the pair of particles align in the shaking direction. Finally, we conclude this thesis with the study of emergent interactions in spherically symmetric systems of catalytic active particles. Symmetry does not permit such particles to propell but the symmetry is broken with the addition of neighboring particles. We model the pair interaction in terms of the relative velocity between particles, and proceed to explore the emergent structures in mixtures of catalytic magnetic particles, and passive particles. We have unveiled the formation of clusters of passive particles. The addition of magnetic interactions between active particles leads to the formation of ramified gel-like structures for dense configurations of active particles. In this case, experimentalists have checked the formation of structures with the same morphologies in experiments in the laboratory.En aquesta tesi abordem el fenomen de les interaccions emergents en matèria tova en coexistència amb matèria tova activa. Com a sistemes de matèria tova activa introduïm col·lectius de partícules autopropulsades, col·loides amb capacitat de catalitzar productes químics i medis granulars agitats. Primer de tot estudiem en detall un model molt estès per a partícules actives, el model de les partícules actives brownianes (ABP). D'aquest model estudiem amb detall una transició de fase de no equilibri i comprovem que la transició satisfà amb les característiques d'una transició en equilibri de primer ordre. Seguidament incorporem interaccions d'alineació en el model de partícules actives i procedim a estudiar les propietats col·lectives de les suspensions de partícules actives amb alineació. Per tal d'abordar l'objectiu de la tesi introduïm partícules de prova en suspensions de partícules actives, i en medis granulars amb forçament periòdic horitzontal, amb diferents paràmetres d'activitat per tal d'estudiar les forces, des d'un punt de vista mecànic, que emergeixen entre les parelles. Hem caracteritzat les forces i hem identificat l'aparició d'interaccions de llarg abast per sistemes de partícules amb alineació i en sistemes granulars en la direcció del forçament. Finalment, tanquem la tesi amb l'estudi i modelització d'interaccions emergents per a partícules catalítiques amb simetria esfèrica. La simetria no permet a les partícules d'autopropulsar-se però la presència de partícules al seu entorn sí que dóna lloc a interaccions, en forma de velocitats induïdes. Amb un model raonable de la interacció a distància hem calibrat la magnitud de la interacció amb sistemes experimentals i procedit a caracteritzar les estructures emergents per a mescles de partícules actives i passives que van des de la formació d'agregats en forma de clústers. L'addició d'interaccions magnètiques entre partícules actives permet la formació d'estructures ramificades de tipus gel. En aquest cas l'equip experimental ha pogut comparar l'aparició d'estructures amb les mateixes característiques al laboratori.
37
Manchester, L. N. "Modelling the interaction of streptomycetes and their phage". Thesis, University of Liverpool, 1986. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.372675.
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38
Smith, Mark Anthony. "Grating interactions in photorefractive polymers". Thesis, University of Reading, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.314312.
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Beck, Markus. "Boron in Palladium: interaction, phase formation and phase transformation". [S.l. : s.n.], 2001. http://www.bsz-bw.de/cgi-bin/xvms.cgi?SWB9556602.
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40
Mason, Daniel R. "Modelling diffusional phase transformations with elastic interactions". Thesis, University of Oxford, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.400203.
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41
James, Stephen Wayne. "Phase conjugate interactions in photorefractive BaTiOâ†3". Thesis, University of Southampton, 1991. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.385148.
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42
Brown, Alexander. "The effects of phase in laser-molecule interactions". Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1997. http://www.collectionscanada.ca/obj/s4/f2/dsk2/tape16/PQDD_0015/NQ28478.pdf.
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Yu, Xiaohong. "Polymer interactions and the phase transition of gels". Thesis, Massachusetts Institute of Technology, 1993. http://hdl.handle.net/1721.1/12451.
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44
Kanao, Eisuke. "Studies on π-interactions in liquid phase separations". Kyoto University, 2020. http://hdl.handle.net/2433/254521.
Testo completo
45
Amin, Shara Jalal. "Studies of competing interactions in hydrogen bonded systems". Thesis, University of Edinburgh, 1988. http://hdl.handle.net/1842/11976.
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46
Ghadimi, nassiri Mikaël. "Mise en forme topologique large-bande de la lumière". Thesis, Bordeaux, 2019. http://www.theses.fr/2019BORD0187/document.
Testo completoAbstract (sommario):
Aujourd'hui les outils permettant de moduler la phase d'une onde lumineuse sont nombreux etpour certains disponibles commercialement, seulement ces éléments ne fonctionnentgénéralement que pour une seule longueur d'onde de travail simultanément. Nous développonsplusieurs approches expérimentales pour la mise en forme de la phase de faisceaux à largebande spectrales. Après un état de l'art sur les principales techniques, nous focalisons notreétude sur la mise en forme de vortex optiques large-bande par l'intermédiaire d'élémentspermettant de moduler la phase géométrique, dont nous abordons quatre approches. Lapremière est basée sur la réflexion de Fresnel anisotrope sur les dioptres mettant en jeu aumoins un matériau biréfringent uniaxe, un choix optimal de leurs indices de réfraction et de leursdispersions permet de réfléchir un faisceau dont la phase dépend de l'orientation de l'axe optiquedes milieux. Dans la seconde, également réflective, nous exploitons le phénomène de réflexionde Bragg circulaire qui se produit au sein des cristaux liquides cholestériques, dont la particularitéest de réfléchir efficacement toute une bande spectrale avec acquisition d'une phase de naturegéométrique. Nous appliquons cette propriété en particulier pour la conception d'élémentsinhomogènes pour la mise en forme, à une bonne approximation, de modes de Laguerre-Gauss.Les deux dernières approches sont basées sur la mise en forme de vortex optiques par desmilieux biréfringents inhomogènes en transmission, en particulier les défauts se formantspontanément dans les films de cristaux liquides nématiques à anisotropie diélectrique négative.L'une consiste à mettre deux éléments en série permettant de traiter successivement différentescomposantes spectrales. L'autre consiste à paralléliser ce procédé en séparant le faisceau initialen différents canaux spectraux, adressés sur des défauts topologiques localisés en réseau etindividuellement contrôlables électriquement. Cette dernière solution peut être vue comme unmodulateur spatial de lumière dont les pixels sont inhomogènes et nous a amené à proposer desapplications potentielles en imagerie optique super-résolue et pour la mise en forme spatiotemporelled'impulsions ultracourtesToday, several beam shaping tools are available, some of them commercially, but most of themare designed for only one working wavelength. This thesis aims to develop several experimentalapproaches for broadband topological beam shaping of light. After the presentation of the state ofthe art, our work focuses on vortex shaping of polychromatic beam exploiting the spin-orbitinteraction of light. Concretely, we report the development of four techniques to modulate the socalledgeometric phase of polychromatic light fields. First, we describe anisotropic reflection frominterfaces that involves at least one uniaxial crystal. We identify a refractive index matchingcriterion enabling highly pure broadband phase control. Then we discuss the use of circularBragg reflection phenomenon inherent to the optics of cholesteric liquid crystals. This propertyallows the selective reflection of circularly polarized light over a bandgap while the reflected fieldacquires a geometric phase. These properties are exploited to design, fabricate and characterizestructured mirrors reflecting Laguerre-Gauss optical modes to a good approximation. The last twosolutions consist of vortex beam shaping using inhomogeneous anisotropic planar opticalelements, namely, topological defects that spontaneously appear in homeotropic nematic liquidcrystal films characterized by negative dielectric anisotropy. The first option is based on using twodefects in series while the other is based of parallel processing using an array of independentlycontrolled topological defects, each of them being dedicated to process distinct spectralchannels. The latter approach can be viewed as a spatial light modulator whose pixels areinhomogeneous and potential applications are proposed in the field of super-resolution opticalimaging and spatio-temporal beam shaping of ultrashort pulses
47
Gomes, Zoby Maria Regina. "Liquid Droplets and Gas Interactions in Two-phase Flow". Thesis, Imperial College London, 2010. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.526366.
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Omnes, Laurent. "Towards the biaxial nematic phase via specific intermolecular interactions". Thesis, University of Exeter, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.368368.
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He, Shuang. "Interactions and phase stability in Ni-rich binary alloys". Licentiate thesis, KTH, Materialvetenskap, 2016. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-189865.
Testo completoAbstract (sommario):
Ni-based superalloys are the important materials for gas turbines in advancedaeroplane engines . The addition of refractory elements to these superalloys,such as rhenium and tungsten, can significantly improve the hightemperatureperformance by so-called solid-solution hardening. Although thestrengthening effect of refractory elements in Ni-based superalloys have beenknown for a long time, the effective interactions among alloying componentsas well as the atomic ordering in the alloy systems are still under investigationand even under debate. In this work, we study these interactions and thisordering for two binary alloys, Ni-rich Ni-Re and Ni-rich Ni-W, by means ofab initio simulations and statistical mechanics simulations based on the IsingHamiltonian. For the Ni-rich Ni-Re alloys, we show that the effective cluster interactionsvary substantially depending on the temperature, concentration of the componentsand the magnetic state of the matrix. The strain-induced interactionshave large contribution to the nearest-neighbor pair-interactions and some multisitecluster-interactions in the ferromagnetic and nonmagnetic states. Theordering tendency of binary Ni-Re alloy systems can be predicted in terms ofordering energy and enthalpy of formation. We show that the D1a orderedstructure should be stable at the concentration of 20 at.% Re in the Ni-rich Ni–Re alloy system. The Monte Carlo simulations of Ni-Re random alloysshow the existence with the D1a-Ni4Re ordered structure at low temperatures. We also calculated lattice parameters for different compositions of Ni-rich Ni-W alloys, and we find that lattice parameters of random Ni-W alloys increaselinearly with the concentration of W. This is in good agreement withthe Vegard’s law predictions and experimental data. We investigated phasestability of Ni-rich Ni-W alloys in terms of the enthalpies of formation andordering energies. We find the chemical pair interactions are sensitive to themagnetic state and concentration. The calculated strain-induced interactionsare quite large for the first coordination shell, which is due to a large sizemismatch of Ni and W. Taking local lattice relaxation into account, the Ni-Wsystems were modeled by Monte Carlo method. The D1a-Ni4W ordered structurecan be observed up to 22 at.% W. In higher concentrations of W, in ourMC calculations, the DO22-Ni3W and Pt2Mo-Ni2W ordered structures can beobserved in Ni-25 at.% W alloy and Ni-33 at.% W alloy, respectively.QC 20160721
50
Rhodes, Nicholas Peter. "Platelet interactions and contact phase activation on polymeric catheters". Thesis, University of Liverpool, 1992. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.317216.
Testo completoAbstract (sommario):
There are many conflicting views about the blood-response to polymeric materials. In order to be satisfied that a material performs appropriately when used as a device in contact with blood it must be evaluated under relevant conditions. Central venous catheters suffer from problems related to thrombosis and embolism since they are implanted for very long periods of time within the vascular system. The aim of this study was to evaluate the most appropriate method for assessing catheter thrombogenicity, establish data for a number of relevant parameters and correlate these findings with various physico-chemica1 characteristics of the materials. Accordingly, a dynamic model was developed which allowed the assessment of platelet adhesion by measurement of "Cr-labelled platelets and platelet a-granule and lysosomal secretion by flow cytometry, after labelling with anti- GMPl40 and anti-GPS3 antibodies, in whole blood after the perfusion of the blood along the tubing at physiologically relevant shear rates (up to 1000 s") at 37OC. In addition, contact phase activation was assessed by measuring the time taken for an aliquot of plateletfree plasma to clot after contact with catheter material (partial thromboplastin time or P'IT) and the ability of the materials to cause factor XII activation by measuring the quantity of FXIIa-Cl-Inh complexes formed by enzyme-linked immunosorbent assay after the contact of platelet-free plasma with catheter tubing. An attempt was made at finding the identity of the proteins adsorbed onto silicone using a number of electrophoretic techniques. The ability of the materials to cause haemolysis and the cytotoxicity of an extract derived from the materials after SO days incubation in PBS including the identification of these potential leachables by supercritical fluid extraction was also investigated. In addition, these data were discussed in relation to parameters of surface roughness, as viewed by SEM and the ratio of hard and soft segments appearing at the material surface by XPS. It was found that significant differences could be detected in (i) platelet adhesion, where Pellethane was shown to have poor performance; (ii) a-granule release, where all the polyurethanes displayed better performance than any of the other materials and (iii) lysosomal granule release where most materials fared similarly, except for glass which was much worse. Silicone was shown to be best in the PIT assay, Pellethane worst. Surprisingly, no correlation was found with these results and those from FXIIa assay, where Desmopan and Davathane were highly active. New and important data on the initial activation kinetics and the ability of materials to activate factor XII are shown. Silicone produced the greatest haemolysis, PVC the greatest extract toxicity. No correlation was found between the physico-cbemical data and any of the biocompatibility data.