Polyclonal antibodies against the first two enzymes of the Arabidopsis thaliana flavonoid biosynthetic pathway were developed using conventional and phage antibody technology. cDNAs from Arabidopsis coding regions of chalcone synthase (CHS) and chalcone isomerase (CHI) were sub-cloned in frame into a bacterial expression vector as fusions with glutathione Stransferase (GST) using standard directional cloning techniques. Analysis of crude extracts of Escherichia coli containing GST .. CHS or GST .. CHI fusion protein indicated that the cells expressed equivalent amounts per volume of culture. CHS and CHI were purified to near homogeneity, yielding approximately 100 micrograms of GST .. CHS and 1 milligram of GST-CHI per liter of culture. The purified fusion proteins were injected into chickens and polyclonal lgY·s were purified from egg yolk Accumulation of CHS and CHI, as well as products of the pathway, were compared during the first eight days of Arabidopsis development. CHS and CHI are sequentially induced and reach maximal accumulation levels by day 5. Anthocyanidin levels are offset by one reaching maximal levels at day 6. The fusion proteins were also used to screen a phage-display library for Fabl fragments that recognize CHS and CHI epitopes. Preliminary data indicated that enrichment of phage displaying antibodies against CHS and CHI was successful. Phage-derived antibodies against CHS and CHI provide valuable tools for future experiments addressing Western blot analysis, immunolocalization experiments, and disruption of the flavonoid biosynthetic pathway by introduction of the corresponding genes into transgenic Arabidopsis plants. / Master of Science

Viruses have huge impact on controlling diseases and regulating many key ecosystem processes. As metagenomic data can contain many microbiomes including many viruses, by analyzing metagenomic data we can analyze many viruses at the same time. The first step towards analyzing metagenomic data is to identify and quantify viruses present in the data. In order to answer this question, we developed a computational pipeline, FastViromeExplorer. FastViromeExplorer leverages a pseudoalignment based approach, which is faster than the traditional alignment based approach to quickly align millions/billions of reads. Application of FastViromeExplorer on both human gut samples and environmental samples shows that our tool can successfully identify viruses and quantify the abundances of viruses quickly and accurately even for a large data set. As viruses are getting increased attention in recent times, most of the viruses are still unknown or uncategorized. To discover novel viruses from metagenomic data, we developed a computational pipeline named FVE-novel. FVE-novel leverages a hybrid of both reference based and de novo assembly approach to recover novel viruses from metagenomic data. By applying FVE-novel to an ocean metagenome sample, we successfully recovered two novel viruses and two different strains of known phages. Analysis of viral assemblies from metagenomic data reveals that viral assemblies often contain assembly errors like chimeric sequences which means more than one viral genomes are incorrectly assembled together. In order to identify and fix these types of assembly errors, we developed a computational tool called VirChecker. Our tool can identify and fix assembly errors due to chimeric assembly. VirChecker also extends the assembly as much as possible to complete it and then annotates the extended and improved assembly. Application of VirChecker to viral scaffolds collected from an ocean meatgenome sample shows that our tool successfully fixes the assembly errors and extends two novel virus genomes and two strains of known phage genomes. / Doctor of Philosophy / Virus, the most abundant micro-organism on earth has a profound impact on human health and environment. Analyzing metagenomic data for viruses has the beneFIt of analyzing many viruses at a time without the need of cultivating them in the lab environment. Here, in this dissertation, we addressed three research problems of analyzing viruses from metagenomic data. To analyze viruses in metagenomic data, the first question needs to answer is what viruses are there and at what quantity. To answer this question, we developed a computational pipeline, FastViromeExplorer. Our tool can identify viruses from metagenomic data and quantify the abundances of viruses present in the data quickly and accurately even for a large data set. To recover novel virus genomes from metagenomic data, we developed a computational pipeline named FVE-novel. By applying FVE-novel to an ocean metagenome sample, we successfully recovered two novel viruses and two strains of known phages. Examination of viral assemblies from metagenomic data reveals that due to the complex nature of metagenome data, viral assemblies often contain assembly errors and are incomplete. To solve this problem, we developed a computational pipeline, named VirChecker, to polish, extend and annotate viral assemblies. Application of VirChecker to virus genomes recovered from an ocean metagenome sample shows that our tool successfully extended and completed those virus genomes.

<p dir="ltr">Bacteriophages are viruses that infect, replicate in, and kill bacteria. In industries that utilize microbes for production, like <i>E.coli</i> in the production of insulin or <i>A. globiformis</i> in the production of cheese, bacteriophages can pose a huge threat to manufacturing. However, bacteriophages aren’t entirely detrimental: we can use the destructive nature of bacteriophages to kill bacterial infections in the human body. This process is known as phage therapy, and while it isn’t a new concept, it is being seen as an increasingly necessary alternative to traditional antibiotics due to the increasing rise of antimicrobial resistance. Because bacteriophages have an entirely different mechanism of destroying bacteria, they can be used in tandem with traditional antibiotic regimens to help wipe out infections. Also, phages have a highly specific host range, meaning that an injection of a certain type of phage will only infect the bacteria it is targeting, sparing important gut microbes.</p><p dir="ltr">The search for new phages to treat infections has resulted in the discovery of over 25,000 actinobacteriophages, with about 4898 of them being sequenced. This is extremely important and necessary, but 49% of these sequenced phages are all mycobacteriophages. This bias towards mycobacteriophages is likely because they infect the genus mycobacterium, where the deadly <i>M. tuberculosis</i> resides. The discovery of new phages using less studied hosts results in novel phages that exhibit rarely seen morphologies, phenotypes, and genotypes. This leads to a better overall understanding of the phage proteome and can lead to new breakthroughs in phage therapy.</p><p dir="ltr">The purpose of this research is to study the differences between different types of phages and try to determine the impact it may have on phage therapy. This thesis is divided into three chapters. In the first chapter, novel phages from different hosts, including <i>M. smegmatis</i> and <i>A. globiformis</i>, were discovered and annotated, and the differences between them were characterized. The discovery of arthrobacteriophages immediately resulted in rare and previously unseen phage characteristics. In the second chapter, proteomic mass spectrometry data of various diverse mycobacteriophages was analyzed to determine differences. Despite being from multiple clusters and lifecycles, the expression data had more similarities than differences. In the third chapter, an alternative method of extracting DNA from phages is explored to determine the result of discrepancies in gel quality from <i>M. smegmatis</i> and <i>A. globiformis.</i><i> </i>Although a large amount of nucleic material was derived, it was not stable DNA and was unsuitable for use. The reason for poor gel quality is still unknown.</p>

Lorsqu’il est surexprimé ou activé constitutivement par mutation, le récepteur tyrosine kinase KIT est impliqué dans le développement de pathologies prolifératives comme les mastocytoses, les tumeurs stromales gastro-intestinales (GIST) et certaines leucémies. La voie de signalisation KIT représente donc une cible thérapeutique majeure en oncologie. Le développement d’une nouvelle classe de molécules pharmacologiques appelées inhibiteurs de tyrosine kinase (ITK) est en plein essor. Un exemple majeur d’ITK est l’imatinib qui cible, entre autre, KIT et est efficace dans la plupart des GIST. Cependant, le traitement aux ITK est souvent confronté au phénomène de résistance primaire ou acquise par mutation secondaire. C’est pourquoi nous cherchons à développer de nouveaux composés ciblant KIT ou les voies de transductions activées par ses formes oncogéniques, et ce par 3 approches.Nous avons récemment montré que les mutants oncogéniques de KIT ont une localisation intracellulaire alors que KIT sauvage est exprimé à la membrane. L’inhibition de l’activité kinase des mutants restaure une localisation normale. A partir de cette observation, nous avons créé et validé un test de criblage par cytométrie mesurant la relocalisation de KIT muté à la surface cellulaire. Le criblage d’une chimiothèque nous a permis de sélectionner de nouveaux inhibiteurs de la signalisation KIT actifs sur des lignées cellulaires mutées pour KIT.Nous avons utilisé la technique du phage display pour sélectionner des anticorps au format scFv et VHH spécifiques de la partie intracellulaire de KIT mutant. Lors de leur expression dans le cytosol (on parle alors d’intrabodies), leur fixation au niveau de KIT inhibe soit directement l’activité kinase, soit le recrutement de partenaires de signalisation. Nous avons obtenu des intrabodies de différentes spécificités vis-à-vis des formes de KIT dont la caractérisation fonctionnelle est en cours Les intrabodies inhibiteurs seront utilisés pour cribler des chimiothèques par ELISA. Les molécules chimiques recherchées empêcheront la fixation des intrabodies sur la région intracellulaire de KIT. On sélectionnera donc des molécules inhibant potentiellement l’oncogénicité de KIT.Nous avons développé des anticorps au format scFv-Fc par phage display qui reconnaissent le domaine extracellulaire de KIT. Deux des anticorps sélectionnés inhibent donc la signalisation induite par le SCF. Dans des lignées de leucémie exprimant KIT WT, nous avons montré que l’utilisation de ces anticorps entraîne une diminution de la viabilité cellulaire. De plus, ils diminuent également la prolifération de lignées de leucémie à mastocytes sensibles et résistantes à l’imatinib (HMC11 et HMC12, respectivement). Ils représentent donc des outils thérapeutiques potentiels pour le traitement des pathologies impliquant KIT ainsi que pour contourner la résistance aux ITK de certains mutants. / When overexpressed or constitutively active by mutation, the tyrosine kinase receptor KIT is involved in some proliferative diseases such as gastro-intestinal stromal tumors (GIST), mastocytosis and some leukemia. Therefore, KIT signaling represents a major target in oncology. Development of a new therapeutic class called tyrosine kinase inhibitors is in full expansion. A major example of TKI is imatinib which targets KIT and is efficient in the majority of GIST cases. However, TKI treatment is often unpaired by primary or acquired resistance due to secondary mutations. That is why we aim to develop new compounds to target KIT or associated signaling pathways by three strategies.We have recently shown that oncogenic KIT mutants are intracellularely localized whereas WT KIT is expressed at the cell surface. Kinase activity inhibition leads to membrane mutants’ relocalization. Based on this finding, we developed and validated a screening assay measuring mutants’ relocalization by cytometry. Chemicals library screening allows us to select new KIT signaling inhibitors active on KIT mutant cell lines.We used phage display to generate scFv and VHH antibodies which are specific to KIT intracellular domain. When expressed in cytoplasm (they are called intrabodies), their binding on KIT inhibits kinase activity directly or signaling partners’ recruitment. Selected intrabodies are specific to various KIT isoforms and their functional characterization is ongoing. KIT inhibitory intrabodies will be used to screen chemical libraries by ELISA for drugs that block intrabodies binding on KIT intracellular domain. We will then select molecules that potentially inhibit KIT oncogenicity.We developed scFv-Fc antibodies by phage display that recognize KIT extracellular domain. Two selected antibodies inhibit SCF induced signaling. In WT KIT expressing leukemic cell lines, we showed that antibody treatment reduces cell viability. Moreover, they also diminish cell proliferation of 2 imatinib sensitive and resistant mast cell leukemia cell lines (HMC1.1 and HMC1.2, respectively). They represent potential therapeutic tools for treatment of KIT involved diseases and for bypass TKI resistance of some mutants.

No description available.

No description available.

O uso de diferentes tipos de medicação intracanal para o controle do processo infeccioso, principalmente nos casos em que há presença de microrganismos resistentes às manobras de desinfecção, tem sido alvo de muitas pesquisas. A proposta deste estudo foi avaliar, in vitro, o efeito antimicrobiano de bacteriófagos específicos diante de cinco cepas de Enterococcus faecalis e a ação de um lisado híbrido polivalente na eliminação da infecção causada por essas cinco cepas da mesma espécie. Foram utilizados 37 dentes unirradiculares humanos, recentemente extraídos e de proporções aproximadas. As coroas foram removidas e os canais instrumentados até a lima tipo K de número 45. Os espécimes foram, então, esterilizados e utilizados em dois experimentos distintos. O primeiro experimento utilizou 25 raízes divididas em cinco grupos de cinco espécimes. Três espécimes de cada grupo foram inoculados com uma das culturas bacterianas e seus fagos correspondentes na proporção 1:1, por um período de três horas a 37 °C, enquanto os outros dois, receberam a cultura de microrganismos ou somente meio de cultura (controle positivo e negativo, respectivamente). No segundo experimento, 11 espécimes receberam um inóculo formado pelas cinco cepas por um período de 10 dias de incubação a 37 °C, com o propósito de manter condições apropriadas para a penetração das bactérias no interior dos túbulos dentinários, e um outro espécime recebeu apenas meio de cultura (controle negativo). Essa penetração foi confirmada empregando-se microscopia ótica e eletrônica realizada em dois espécimes. Após o período de incubação, o lisado polivalente, preparado com os cinco fagos, foi aplicado por 24 horas a 37 °C em 8 espécimes, e os demais preenchidos com meio de cultura (controle positivo e negativo). Alíquotas do interior de todos os canais foram colhidas antes e depois do contato com os fagos e no segundo experimento, também 24 e 48 horas depois, para semeadura e contagem de unidades formadoras de colônia. Os resultados do primeiro experimento mostraram 100% de redução do crescimento bacteriano nos espécimes que receberam a suspensão de fagos específicos, em comparação a seus respectivos controles positivos, em todos os grupos. No segundo experimento, foi comparado o crescimento obtido após os 10 dias de infecção com aquele posterior a aplicação dos fagos, redução que variou entre 50% e 100%. Diante desses resultados, conclui-se que os bacteriófagos foram eficazes na diminuição dos microrganismos presentes no interior de canais radiculares e nos túbulos dentinários de dentes humanos. / Many studies have investigated different intracanal medications to control infection processes, especially in cases of microbial resistance to disinfection procedures. The purpose of this study was to evaluate the in vitro antimicrobial effect of specific bacteriophages on five isolates of Enterococcus faecalis, as well as the activity of a lysate cocktail in eliminating the infection caused by these bacteria. Thirty-seven recently extracted human teeth of approximately equal size and with single roots were used. The crowns were removed and each canal was prepared using K files,up to # 45, and sterile physiological saline. Specimens were then sterilized and used in two separate studies. The first study utilized 25 individual roots divided into five groups of five specimens each. Three specimens of each group were inoculated with one of the bacterial cultures and the corresponding bacteriophage in a proportion of 1:1, and incubated for three hours at 37°C; the other two specimens were inoculated with only the bacterial culture or only the culture medium (positive and negative controls, respectively). In the second study, 11 specimens were inoculated with all five strains and incubated for ten days at 37°C in order to allow bacteria to penetrate the interior of the dental tubules, and another one, received just the culture medium (negative control). Penetration into the tubules was confirmed by optical and electron microscopy of two specimens. Following incubation, the lysate cocktail prepared using all five bacteriophages was applied to the other 8 specimens for 24 hours at 37°C, and 2 specimens were filled with the culture medium (positive and negative controls). In the first study, samples were taken from the lumen of all canals before and after contact with bacteriophages; in the second, aliquots were also taken 24 and 48 hours after the bacteria were exposed to the phages. All samples were diluted and plated and the number of colony forming units was counted. In the first study, there was a 100% reduction in bacterial growth in specimens that received the specific bacteriophage suspension compared to the positive controls within each group. In the second study, after ten days the number of bacteria was reduced by 50% to 100% following the bacteriophage application. These results suggest that bacteriophages are effective in reducing the number of bacteria inside the root canal and in the dental tubules of human teeth.

<div> <div> <div> <p>Mycobacteriophages are the viruses that infect mycobacteria. Due to the high death rate and antibiotic-resistant strains, phage therapy is considered to be a promising treatment of tuberculosis. Current understanding of phage-bacteria interaction is abstracted as phage lytic and lysogenic life cycles. However, bacterial physiology may impact phage life cycles and bacterial cells with different physiology may have different responses to phage infection. In order to improve the understanding of phage-bacteria interaction and update phage therapy strategy, the impact of mycobacterial physiology on mycobacteriophage life cycles was studied in this research. In this research, a mass spectrometry-based method was first developed to study phage proteins in phage-bacteria mixture. Then five mycobacteriophages isolated at Purdue University were selected to infect exponential and stationary <i>Mycobacterium smegmatis</i> (<i>M. smegmatis</i>) cell cultures. Growth curves of the <i>M. smegmatis</i> cell cultures infected by the five phages were determined. Proteomics and lipidomics of the <i>M. smegmatis</i> cells cultures infected by phages FrenchFry and MrGordo were analyzed by mass spectrometry. The correlations between individual proteins/lipids and the experimental factors (bacterial growth phases, phages and phage infection time) were studied by developing linear regression models using SAS. The mass spectrometry-based method was proved to be able to detect phage proteins other than the structural proteins. It also verified the phage protein annotation that had been accomplished <i>in silico</i>. X! Tandem and a database consisting of six frame translation of the phage genome and the annotated proteins of <i>M. smegmatis</i> were the optimal option for analyzing mass spectra data of phage-bacteria mixture. The growth curves of the <i>M. smegmatis</i> infected by the phages displayed that growth of exponential <i>M. smegmatis</i> cell cultures were depressed by phages (except FrenchFry) and stationary <i>M. smegmatis</i> cell cultures were not actively lysed by any of the phages. The proteomics results showed that MrGrodo infection impacted more proteins than other factors did. Exponential phase up-regulated proteins involved in cell division. Stationary phase up-regulated proteins that may change cell surface properties. FrenchFry up-regulated LuxR protein. Infection time up-regulated the proteins associated with mycobacterial virulence. The lipidomics results indicated that growth phases impacted the most lipids. Phage infection time increased the amount of the lipids related to mycobacterial virulence. In summary, the mass spectrometry-based method developed in this research can be employed to study phage proteins in phage-bacteria mixture and verify phage genome annotation. Mycobacterial physiology alters mycobacteriophage life cycles. Phage-bacteria interaction is the interaction between the two populations instead of between an individual phage particle and an individual bacterial cell. Virulence of <i>M. smegmatis</i> improves as a response to phage infection.</p></div></div></div>

Mon travail de thèse a porté sur le ciblage de la vascularisation tumorale : des molécules ciblant l'endothélium tumoral ont été recherchées dans le but d'amener des molécules thérapeutiques spécifiquement vers l'endothélium tumoral afin de le détruire et d'atteindre la tumeur qui en dépendait. D'après les données de la littérature, deux cibles ont été choisies pour notre étude : la sélectine E et l'endogline. La sélectine E est une glycoprotéine surexprimée à la surface de l'endothélium activé des zones inflammatoires et tumorales. Classiquement, des antagonistes de son ligand naturel, le SleX, sont recherchés. En nous appuyant sur les groupements clés de l'interaction entre la sélectine E et le SleX, plusieurs familles de mimes du SleX ont été élaborées. La capacité de ces mimes à déplacer l'interaction du SleX exprimé à la surface des cellules HL-60 avec la sélectine E a été évaluée dans un test d'adhésion. Cependant, aucun des mimes testés n'a présenté une affinité suffisante pour envisager son utilisation comme tête de ciblage. Une deuxième stratégie a consisté à rechercher des ligands peptidiques de la sélectine E en criblant des HUVECs activées avec une banque de peptides sur phages. Plusieurs phages-peptides testés en ELISA ont montré une meilleure affinité pour la sélectine E et / ou avec la sélectine P par rapport au phage sans insert. Des tests de compétition avec des peptides synthétiques correspondants permettront d'évaluer leur spécificité pour la cible. En ce qui concerne l'endogline, des ligands peptidiques ont été recherchés avec une banque de peptides sur phages. Dans un premier temps, le gène codant l'endogline humaine a été cloné dans un vecteur d'expression eucaryote afin de réaliser la sélection sur la protéine cellulaire. Une sélection sur la protéine recombinante a été réalisée par la suite pour diminuer le bruit de fond lié aux cellules. Parmi les peptides obtenus, certains ont montré des homologies de séquence avec des ligands de l'endogline et le test de ces phages-peptides en ELISA sur la protéine recombinante a donné un fort signal par rapport au phage sans insert. Ces peptides seront caractérisés prochainement. En conclusion, des ligands peptidiques des sélectines E et P et de l'endogline ont peut-être été identifiés. Ce travail a par ailleurs permis de mettre en place les outils nécessaires à l'utilisation de la technologie de sélection avec des banques de peptides sur phages dans les meilleures conditions possibles.

Protein engineering and in vitro selection systems are powerful methods to generate binding proteins. In nature, antibodies are the primary affinity proteins and their usefulness has led to a widespread use both in basic and applied research. By means of combinatorial protein engineering and protein library technology, smaller antibody fragments or alternative non-immunoglobulin protein scaffolds can be engineered for various functions based on molecular recognition. In this thesis, a 46 amino acid small albumin-binding domain derived from streptococcal protein G was evaluated as a scaffold for the generation of affinity proteins. Using protein engineering, the albumin binding has been complemented with a new binding interface localized to the opposite surface of this three-helical bundle domain. By using in vitro selection from a combinatorial library, bispecific protein domains with ability to recognize several different target proteins were generated. In paper I, a bispecific albumin-binding domain was selected by phage display and utilized as a purification tag for highly efficient affinity purification of fusion proteins. The results in paper II show how protein engineering, in vitro display and multi-parameter fluorescence-activated cell sorting can be used to accomplish the challenging task of incorporating two high affinity binding-sites, for albumin and tumor necrosis factor-alpha, into this new bispecific protein scaffold. Moreover, the native ability of this domain to bind serum albumin provides a useful characteristic that can be used to extend the plasma half-lives of proteins fused to it or potentially of the domain itself. When combined with a second targeting ability, a new molecular format with potential use in therapeutic applications is provided. The engineered binding proteins generated against the epidermal growth factor receptors 2 and 3 in papers III and IV are aimed in this direction. Over-expression of these receptors is associated with the development and progression of various cancers, and both are well-validated targets for therapy. Small bispecific binding proteins based on the albumin-binding domain could potentially contribute to this field. The new alternative protein scaffold described in this thesis is one of the smallest structured affinity proteins reported. The bispecific nature, with an inherent ability of the same domain to bind to serum albumin, is unique for this scaffold. These non-immunoglobulin binding proteins may provide several advantages as compared to antibodies in several applications, particularly when a small size and an extended half-life are of key importance. / <p>QC 20121122</p>