It is estimated that approximately 2 million fires which occur in United States each year result in 1.2 million burn victims. Fibroblasts are responsible for responding to this tissue damage by breaking down the damaged extracellular matrix (ECM) and secreting a new ECM which aids in wound repair and supports the migration of immune cells. Pseudomonas aeruginosa is an opportunistic pathogen commonly associated with health-care infections (HCAIs) due to its ability to take advantage of immunocompromised hosts. However, little research has investigated how wound invading P. aeruginosa interacts with wound repairing fibroblasts. To address this lack of understanding, this thesis focuses on quantifying changes in fibroblast morphology, migratory behavior, and force exertion to investigate this host cell's response to representative cytotoxic (PAO1) and invasive (PA14) strains of P. aeruginosa. These assays study host cell-pathogen interactions on highly aligned nanofibers of varied spacing and diameter, which mimic the fibroblast deposited ECM and dictate fibroblast morphology. We discovered that the cytotoxic strain of P. aeruginosa induced significantly shorter fibroblast death times. Furthermore, two modes of death, sharp and gradual, were identified and found to be dependent on both fiber configuration and strain of P. aeruginosa. In addition, fibroblasts exposed to PAO1 migrating on the parallel formation were found to be significantly slower and less persistent than those exposed to PA14, however, fibroblasts exposed to both strains of bacteria were shown to exert similar forces. Lastly, exposure to PA14 led to the greatest change in actin, evident by increased actin punctae and less prominent actin stress fiber formation. / Master of Science / It is estimated that approximately 2 million fires which occur in United States each year result in 1.2 million burn victims. Fibroblasts respond to burn wounds by breaking down the damaged tissue fibers, termed extracellular matrix (ECM), and secreting a new ECM. Unfortunately, severe thermal injuries place hospitalized burn victims at high risk of infection. Pseudomonas aeruginosa is an opportunistic pathogen commonly associated with health-care infections (HCAIs) due to its ability to take advantage of immunocompromised hosts. However, little research has investigated how wound invading P. aeruginosa interacts with wound healing fibroblasts. To address this knowledge gap, this thesis focuses on quantifying changes in fibroblast shape, migratory behavior, and force exertion to investigate this host cell's response to two strains of P. aeruginosa, which employ different mechanisms of invasion. These interactions are studied on a platform of suspended nanofibers with controlled spacing and diameter, to dictate fibroblast shape and mimic the fibroblast deposited ECM. We discovered that the two strain of P. aeruginosa induced significantly different fibroblast death times. During death, it was observed that fibroblasts either balled up quickly, termed sharp death, or remained spread out, termed gradual death, dependent upon fibroblast shape and strain of P. aeruginosa introduced. In addition, significant differences in migration speed and persistence were found between fibroblasts exposed to the two strains of bacteria, however, both groups were shown to exert similar forces. Lastly, the fibrous proteins which make up the cytoskeleton of the cell, actin stress fibers, were found to vary among the control and bacteria treated cells.

Yes / Virus-encoded miRNAs are emerging as key regulators of persistent infection and host-cell immune evasion. Merkel cell polyomavirus (MCPyV), the predominant aetiological agent of Merkel cell carcinoma (MCC), encodes a single miRNA, MCV-miR-M1, which targets the oncogenic MCPyV large T antigen (LT). MCV-miR-M1 has previously been shown to play an important role in establishment of long-term infection, however, the underlying mechanism is not fully understood. A key unanswered question is whether, in addition to auto-regulating LT, MCV-miR-M1 also targets cellular transcripts to orchestrate an environment conducive for persistent infection. To address this, we adopted an RNA-Seq-based approach to identify cellular targets of MCV-miR-M1. Intriguingly, bioinformatics analysis of transcripts that are differentially expressed in cells expressing MCV-miR-M1 revealed several genes implicated in immune evasion. Subsequent target validation led to the identification of the innate immunity protein, SP100, as a direct target of MCV-miR-M1. Moreover, MCV-miR-M1-mediated modulation of SP100 was associated with a significant decrease in CXCL8 secretion, resulting in the attenuation of neutrophil chemotaxis towards Merkel cells harbouring synthetic MCPyV. Based on these observations we propose that MCV-miR-M1 targets key immune response regulators to help facilitate persistent infection, which is a pre-requisite for cellular transformation in MCC. / Funded in part by a University of Bradford studentship to PA and a Royal Society research award to JRB.

This work is the result of evaluating a novel strategy for the purification of recombinant His-tagged proteins. Proteins purified in this study were the E. coli translational proteins IF-3, RF-1, and RFF. The study aimed to analyse the potential of using Bio-Works WorkBeads™40 TREN, a multimodal anion ion exchange chromatography resin, as a pretreatment step upstream an immobilized metal ion chromatography (IMAC) resin to enhance performance efficiency of His-tagged protein purification. The method demonstrated here shows potential for anyone seeking to increase the purity of His-tagged protein purification or to introduce an effective purification procedure by replacing a polishing step downstream IMAC with WorkBeads 40 TREN upstream IMAC. The latter contributing to guard the IMAC column from heavy bioburden. This study showed that running WorkBeads 40 TREN prior IMAC captures impurities and removes 97-98 % more dsDNA compared to direct IMAC. WorkBeads 40 TREN is therefore highly advantageous to include early in a purification process to remove protein binding DNA fragments. Moreover, WorkBeads 40 TREN increases purity in the final product by capturing more host cell proteins than when running direct IMAC. This concept is general and WorkBeads 40 TREN could be used upstream a variety of resins such as Protein A and RPC.

Background The foamy virus (FV) replication cycle displays several unique features, which set them apart from orthoretroviruses. First, like other B/D type orthoretroviruses, FV capsids preassemble at the centrosome, but more similar to hepadnaviruses, FV budding is strictly dependent on cognate viral glycoprotein coexpression. Second, the unusually broad host range of FV is thought to be due to use of a very common entry receptor present on host cell plasma membranes, because all cell lines tested in vitro so far are permissive. Results In order to take advantage of modern fluorescent microscopy techniques to study FV replication, we have created FV Gag proteins bearing a variety of protein tags and evaluated these for their ability to support various steps of FV replication. Addition of even small N-terminal HA-tags to FV Gag severely impaired FV particle release. For example, release was completely abrogated by an N-terminal autofluorescent protein (AFP) fusion, despite apparently normal intracellular capsid assembly. In contrast, C-terminal Gag-tags had only minor effects on particle assembly, egress and particle morphogenesis. The infectivity of C-terminal capsid-tagged FV vector particles was reduced up to 100-fold in comparison to wild type; however, infectivity was rescued by coexpression of wild type Gag and assembly of mixed particles. Specific dose-dependent binding of fluorescent FV particles to target cells was demonstrated in an Env-dependent manner, but not binding to target cell-extracted- or synthetic- lipids. Screening of target cells of various origins resulted in the identification of two cell lines, a human erythroid precursor- and a zebrafish- cell line, resistant to FV Env-mediated FV- and HIV-vector transduction. Conclusions We have established functional, autofluorescent foamy viral particles as a valuable new tool to study FV - host cell interactions using modern fluorescent imaging techniques. Furthermore, we succeeded for the first time in identifying two cell lines resistant to Prototype Foamy Virus Env-mediated gene transfer. Interestingly, both cell lines still displayed FV Env-dependent attachment of fluorescent retroviral particles, implying a post-binding block potentially due to lack of putative FV entry cofactors. These cell lines might ultimately lead to the identification of the currently unknown ubiquitous cellular entry receptor(s) of FVs.

Human norovirus (HuNoV) is the leading cause of gastroenteritis worldwide. Despite the significant disease and economic burden, currently there are no licensed vaccines or antivirals. The understanding of norovirus biology has been hampered by the inability to cultivate HuNoV in cell culture. To establish a tissue culture system, infectious HuNoVs were purified from clinical stool samples. HuNoV replication was tested in different cell types. The B-cell and intestinal organoids culture systems were validated. In addition, using organoids culture a DNA-based reverse genetic system was shown to recover infectious HuNoV. Due to the challenges associated with cultivating HuNoV, murine norovirus (MNV) was used as a surrogate system to understand the role of eIF4E phosphorylation in norovirus pathogenesis, and VP1-RdRp interaction in regulating viral genome replication. MNV infection results in the phosphorylation of the translation initiation factor eIF4E, re-programming host-cell translation during infection. Inhibiting eIF4E phosphorylation reduces MNV replication in cell culture suggesting a role in viral replication. A mouse model with eIF4E S209A, a phosphor-ablative mutation, was established to understand the role of eIF4E phosphorylation in MNV pathogenesis. In vitro and in vivo characterisations demonstrated that eIF4E phosphorylation may have multiple roles in norovirus-host interactions, but overall has little impact on MNV pathogenesis. The shell domain (SD) of norovirus major capsid protein VP1 interacts with viral RNA-dependent RNA polymerase (RdRp) in a genogroup-specific manner to enhance de novo initiation of RdRp, and to promote negative-strand RNA synthesis. To understand how VP1 regulates norovirus genome replication, chimeric MNVs with genogroup-specific residues mutagenised were characterised in vitro and in vivo. A single amino acid mutation was shown to destabilise viral capsid. SDs with reduced VP1-RdRp interaction showed less capacity to stimulate RdRp, resulting in delayed virus replication. In vivo, the replication of an MNV-3 with homologous mutations was abolished, highlighting the crucial role of this interaction.

No description available.

Le sélénium est reconnu comme un micronutriment important pour l'homme et les animaux. Plusieurs études ont montré qu'une supplementation en sélénium dans le régime alimentaire pourrait être bénéfique contre les cancers du foie, du colon, du pancréas et de la prostate. Le mécanisme anti-carcinogène du sélénium se produit au niveau systémique, cellulaire et nucléaire. Ces processus peuvent également impliquer le système immunitaire et ne doivent pas être interprétés par un seul mécanisme. Jusqu'à présent son mécanisme d'action est encore inconnu. L'objectif de cette étude était d'étudier l'effet des composés du sélénium, à faibles concentrations, sur la capacité de réparation de l'ADN dans les cellules du cancer de la prostate LNCaP (p53 compétentes). Ce travail est divisé en trois parties. La première partie du travail a été consacrée à étudier l'effet des deux composés du sélénium (SS et SM) sur les propriétés cytotoxiques et génotoxiques de différents stress oxydatifs et non oxydatifs. Les résultats ont montré qu'un prétraitement avec une faible dose en Se stimulait la synthèse des sélénoprotéines, et protègait contre la toxicité et les dommages oxydatifs à l'ADN induites par les UVA ou H2O2, mais pas par MMS ou UVC. La deuxième partie a été consacrée à l'influence de la supplementation en sélénium sur la capacité de réparation de l'ADN. Notre travail a clairement montré l'augmentation de l'efficacité d'excision de certaines glycosylases que n'est pas nécessairement corrélée à une augmentation de l'expression génique et /ou protéiques. Enfin, la troisième partie de notre travail a été dédiée à l'optimisation de la technique Host Cell Reactivation (HCR) qui nous a permis d'étudier la capacité de réparation de l'ADN in cellulo, afin de cibler les partenaires impliqués dans la voie de signalisation affectées par la supplémentation en sélénium. En conclusion, nous pourront penser que le mécanisme d'action du sélénium est représenté par un délicat équilibre entre l'activation et la répression de l'activité de certaines protéines qui induit des changements conformationnels plus ou moins directement impliqués dans la réparation de l'ADN et la progression de la croissance cellulaire.

No description available.

Les récents progrès instrumentaux en spectrométrie de masse, notamment en terme de- rapidité de balayage et de résolution, ont permis l'émergence de l'approche « data independent acquisition» (DIA). Cette approche promet de combiner les points forts des approches « shotgun » et ciblées,mais aujourd'hui l'analyse des données DIA reste compliquée. L'objectif de cette thèse a été de développer des méthodes innovantes de spectrométrie de masse, et en particulier d'améliorer l'analyse des données DIA. De plus, nous avons développé une approche originale Top 3-ID-DIA, permettant à la fois un profilage complet des protéines de la cellule hôte (HCP) ainsi qu'une quantification absolue d'HCP clés dans les échantillons d'anticorps monoclonaux (mAb), au sein d'une même analyse.Cette méthode est prête à être implémentée en industrie, et pourrait fournir un support en temps réel aux développements du procédé de production de mAb, ainsi que pour évaluer la pureté des biomédicaments. / Recent instrumental developments in mass spectrometry, notably in terms of scan speed and resolution, allowed the emergence of “data independent acquisition” (DIA) approach. This approach promises to combine the strengths of both shotgun and targeted proteomics, but today DIA data analysis remains challenging. The objective of my PhD was to develop innovative mass spectrometry approaches, and in particular to improve DIA data analysis. Moreover, we developed an original Top 3-ID-DIA approach, allowing both a global profiling of host cell proteins (HCP) and an absolute quantification of key HCP in monoclonal antibodies samples, within a single analysis. This method is ready to be transferred to industry, and could provide a real time support for mAb manufacturing process development, as well as for product purity assessment.

La leishmaniose viscérale (LV) est la forme la plus sévère de la leishmaniose humaine. Elle est transmise par la piqûre d'un phlébme. La leishmaniose viscérale est mortelle en l'absence de traitement. Les options thérapeutiques courantes contre la leishmaniose viscérale sont limitées. En région méditerranéenne, la LV est due à Leishmania infantum, zoonose dont le chien est le principal réservoir. A côté de quelques cas d'infection systémique, un nombre important d'humains porteurs asymptomatiques a été mis en evidence. En première partie, nous avons étudié l'intérêt du MultiLocus Microsatellite Genotyping (MLMT) pour l'identification des souches de Leishmania du sud de la France. Par MLMT nous avons étudié la variabilité génétique de différentes souches et recherché une association avec les différentes formes cliniques, la résistance aux médicaments et les phénomènes de rechutes. Nous avons observé une hétérogénéité génétique entre les différentes souches de L. infantum MON-1. Si l'association de certains génotypes avec les différentes expressions cliniques de la leishmaniose n'a pu être démontrée, nous avons par contre observé une répartition préférentielle géographique de certains génotypes. En deuxième partie, nous avons mis au point un protocole expérimental destiné au criblage de nouveaux agents anti-Leishmania infantum ayant pour cible la machinerie cellulaire mise en route par la cellule hôte pour l'élimination du parasite intracellulaire. Nos résultats ont montré que les altérations du système de trafic intracellulaire de la cellule-hôte induites par certains composés étaient corrélées à la mort du parasite et à son élimination. / Visceral leishmaniasis (VL) is the most severe form of Human Leishmaniases, which occurs when protozoan parasites Leishmania donovani or L. infantum, given by phlebotomine sandfly bites. The disease is fatal when untreated. Current treatment options against VL are very limited with few drug molecules, often expensive, not always safe and able to induce resistance phenomenon.In this report, we have characterized on one hand, different genetic variants of Leishmania infantum strains isolated in different geographical areas from southern France and on the other hand have identified new potential anti-Leishmania infantum compounds and characterized their molecular mechanism of action.In the first part, we studied the interest of Multilocus Microsatellite Genotyping (MLMT) for the identification of Leishmania strains from southern France. By genotyping technique MLMT, we studied the genetic variability of different strains and sought an association with different clinical forms of leishmaniasis, resistance to drugs and relapse. We observed genetic heterogeneity among different strains of L. infantum-MON-1. we observed a preferential geographic distribution of certain genotypes.In the second part, we have developed an experimental protocol for the screening of new anti-Leishmania infantum compounds that target the host cell machinery responsible for the intracellular parasite killing, we studied the different steps of endocytic pathways potentially targeted by these compounds. Our results showed that with some compounds, modifications of the intracellular trafficking of the host cell were correlated with parasite death and its elimination.