Dissertations / Theses on the topic 'Cell-PCA'

Worldwide, 3.575 million people die each year from water-related diseases. The water and sanitation crisis claims more lives than any warfare and is predicted to be one of the biggest global challenges of this century. The rapid, accurate detection of viral pathogens from environmental samples is an ongoing and pertinent challenge in biological engineering. Currently employed methods are lacking in either efficiency or specificity. Here we explore a novel method for virus detection and concurrently use this method to learn more about the very early stages of the virus infection process. The method combines Fourier transform infrared (FTIR) spectroscopy, a method of visualizing molecules based on changes in vibration of particles, and mammalian cells as the biosensor. This method is used to detect and investigate viruses from the family picornaviridae, chosen due to their public health burden and their widespread presence in environmental samples, especially water sources. This family includes the Polioviruses, echoviruses and Coxsackieviruses, among others, many of which are human pathogens.The research outlined in this dissertation is aimed at developing and implementing a new cell-based biosensor that combines the advantages of FTIR spectroscopy with the ability of buffalo green monkey kidney (BGMK) cells to sense diverse stimuli, including infective enteroviruses. The goal of developing this biosensor is outlined in the first paper. The second paper focuses on the application of advanced statistical methods to analyze the spectra to discriminate different viral infections in BGMK cells. Finally, we designed a non-reactive metal biochamber to use with attenuated total reflectance-FTIR. This allowed near-continuous acquisition of real-time spectral data for the study of biochemical changes in mammalian cells caused by poliovirus (PV1) infection. This system is capable of tracking changes in cell biochemistry in minute intervals for many hours at a time.This work demonstrates the feasibility of FTIR spectroscopy in combination with the broad sensitivity of mammalian cells for potential use in the detection of infective viruses from environmental samples. We envision this method being extended to high throughput, automated systems to screen for viruses or other toxins in drinking water systems and medical applications.

L’identité et le devenir de chaque cellule dépend du contenu en protéines et, en particulier, des réseaux d'interactions protéine-protéine (IPP, également appelés interactomes). Les protéines ont la propriété générale de s'engager dans des assemblages macromoléculaires très variés, chacun ayant des fonctions bien distinctes. Par conséquent, identifier les IPP et les lier à des complexes particuliers est un enjeu crucial mais difficile en biologie. Cette problématique a été au cœur de mon travail de doctorat. Une première partie de mon travail est dédiée à l'amélioration d'une méthode existante pour capturer de nouvelles IPP dans le contexte de fonctions biologiques définies. Ce travail a été réalisé avec ERK1, un régulateur clé en aval de plusieurs voies de signalisation impliquées dans de nombreux cancers. Les nouveaux outils ont été testés dans le contexte de fonctions de ERK1 sensibles à deux molécules inhibitrices dans les cellules humaines HEK293T. Une interaction a été confirmée aux niveaux fonctionnel et moléculaire, ainsi qu’en utilisant une stratégie d'imagerie originale pour accéder à la dynamique des IPP dans les cellules vivantes. La deuxième partie de mon travail de doctorat est dédiée à l'établissement d'une méthodologie pionnière pour capturer les IPP endogènes établies par un complexe protéique dimérique spécifique dans les cellules humaines vivantes. Cette méthodologie couple la Complémentation de Fluorescence Bimoléculaire (BiFC) et les technologies démarquage par la biotine de proximité. Plus précisément, elle repose sur l’utilisation d’un petit anticorps (appelé aussi « nanobody ») dirigé contre le complexe BiFC et fusionné à la ligase biotine TurboID. Ces outils ont été établis avec les complexes TAZ/14-3-3e et TAZ/TEAD2, qui traduisent respectivement l'activité de la voie de signalisation Hippo dans le cytoplasme et le noyau. Notre approche a permis de capturer les interactomes spécifiques de ces deux complexes protéiques et d'identifier un nouveau régulateur clé du complexe TAZ/14-3-3e pour contrôler ses fonctions de prolifération cellulaire. Dans son ensemble, mon travail de doctorat a introduit deux méthodologies complémentaires pour déchiffrer les réseaux d'IPP au niveau de fonctions biologiques spécifiques ou pour un complexe protéique spécifique en contexte cellulaire vivant. Ces approches offrent une nouvelle dimension pour comprendre les fonctions des protéines et les interactomes sous-jacents dans des contextes cellulaires normaux ou pathologiques
Cell fate and fitness depend on the protein content, and in particular on the interaction networks (also called interactomes) connecting the different proteins. Proteins have the general property to engage in diverse and occasionally overlapping macromolecular assemblies, each serving distinct purposes. Therefore, identifying protein-protein interactions (PPIs) and linking them to complexes is a crucial yet challenging issue in biology. This issue was at the core of my PhD work. The first part of my work was dedicated to the improvement of an existing method for capturing novel PPIs in the context of defined biological functions. This work was established with ERK1, which is a key downstream regulator of several signaling pathways involved in many different cancers. The new tools were tested in the context of two different inhibitory molecules to capture drug-sensitive interactions of ERK1 in human HEK293T cells. One such interaction was confirmed at the functional and molecular levels, by using an original imaging strategy to access the PPI dynamics in live cells. The second part of my PhD work was dedicated to the establishment of a pioneer methodology to capture endogenous PPIs established by a specific dimeric protein complex in human live cells. This methodology couples Bimolecular Fluorescence Complementation (BiFC) and proximity biotin labelling technologies. More specifically, it is based on a GFP-nanobody directed toward the BiFC complex and fused to the TurboID biotin ligase. Tools were established to map TAZ/14-3-3 and TAZ/TEAD complexes interactome, which translate the activity of the Hippo signaling pathway in the cytoplasm and nucleus, respectively. Our approach allowed capturing specific interactomes of the two dimeric protein complexes and identifying a novel key regulator of TAZ/14-3-3 complexes in a cancer cell context. Collectively, my PhD work introduced two complementary methodologies for deciphering PPI networks in the context of specific biological functions or in the context of a specific protein complex in human live cells. These approaches provide a novel dimension for understanding protein functions and the underlying interactomes in normal or pathological cell contexts

Les virus manipulent la machinerie centrale de l’hôte à leur avantage. Afin de créer un environnement favorable pour leur survie et propagation ils bloquent les réponses antivirales de la cellule hôte. Le virus de la rougeole (MV) possède deux protéines non-structurales MV-V et MV-C, dont on a observé qu’elles jouent un rôle dans ce contournement la réponse interféron de l’hôte et la régulation des voies de signalisation de mort cellulaire. Plusieurs mécanismes moléculaires expliquant la régulation de l’immunité et la mort cellulaire par MV-V ont été proposés, alors que ceux de la protéine MV-C restent encore peu étudiés. On pense que certains facteurs cellulaires contrôlés par MV-C lors de la réplication virale font partie des voies de signalisation d’immunité innée et de mort cellulaire. Dans le but d’identifier ces facteurs ciblés par le virus, nous avons purifié les protéines cellulaires qui interagissent directement ou indirectement avec MV-C. Nous avons utilisé des virus recombinants exprimant certaines protéines virales tagguées et une méthode de purification par affinité couplée à l’identification par spectrométrie de masse. Nous avons pu en extraire une liste de protéines interagissant spécifiquement avec MV-C dans différentes lignées cellulaires. Nous avons ensuite sélectionné certaines protéines appartenant aux voies de signalisation d’immunité innée et de mort cellulaire. Pour tester leur interaction directe avec MV-C, des méthodes de complémentation protéique (PCA) et de transfert d'énergie de résonance de bioluminescence (BRET) ont été utilisées. Ainsi, nous avons mis en évidence l’interaction directe de la protéine C avec les protéines iASPP, p65 et p53 qui contrôlent à la fois les voies de mort cellulaire et d’immunité innée
Viruses manipulate central machineries of host cells to their advantage. They prevent host cell antiviral responses in order to create a favorable environment for their survival and propagation. Measles virus (MV) encodes two non-structural proteins MV-V and MV-C, proposed to counteract the host interferon response and to regulate cell death pathways in various functional assays. Several molecular mechanisms underlining MV-V regulation of innate immunity and cell death responses have been proposed, whereas MV-C host protein partners are less studied. We suggest that some cellular factors that are controlled by MV-C protein during viral replication could be components of innate immunity and the cell death pathways. In order to determine which host factors are targeted by MV-C, we captured both direct and indirect host protein partners of MV-C protein. For this we used a strategy based on recombinant viruses expressing tagged viral proteins followed by affinity purification and a bottom-up mass spectrometry analysis. A list of host proteins specifically interacting with MV-C protein in different cell lines was identified. Then we have selected proteins that belong to immunity and cell death biological pathways. Direct protein partners of MV-C were determined by applying protein complementation assay (PCA) and the bioluminescence resonance energy transfer (BRET) approach. As a result, we found that MV-C protein specifically interacts p65/iASPP/p53 protein complex that controls both death and innate immunity pathways

This research assessed landuse changes and trends in vegetation cover in the Sandveld, using remote sensing images. Landsat TM satellite images of 1990, 2004 and 2007 were classified using the maximum likelihood classifier into seven landuse classes, namely water, agriculture, fire patches, natural vegetation, wetlands, disturbed veld, and open sands. Change detection using remote sensing algorithms and landscape metrics was performed on these multi-temporal landuse maps using the Land Change Modeller and Patch Analyst respectively. Markov stochastic modelling techniques were used to predict future scenarios in landuse change based on the classified images and their transitional probabilities. MODIS NDVI multi-temporal datasets with a 16day temporal resolution were used to assess seasonal and annual trends in vegetation cover using time series analysis (PCA and time profiling).Results indicated that natural vegetation decreased from 46% to 31% of the total landscape between 1990 and 2007 and these biodiversity losses were attributed to an increasing agriculture footprint. Predicted future scenario based on transitional probabilities revealed a continual loss in natural habitat and increase in the agricultural footprint. Time series analysis results (principal components and temporal profiles) suggested that the landscape has a high degree of overall dynamic change with pronounced inter and intra-annual changes and there was an overall increase in greenness associated with increase in agricultural activity. The study concluded that without future conservation interventions natural habitats would continue to disappear, a condition that will impact heavily on biodiversity and significant waterdependent ecosystems such as wetlands. This has significant implications for the long-term provision of water from ground water reserves and for the overall sustainability of current agricultural practices.

A wide range of screening strategies have been employed to isolate antibodies and other proteins with specific attributes, including binding affinity, specificity, stability and improved expression. However, there remains no high-throughput system to screen for target-binding proteins in a mammalian, intracellular environment. Such a system would allow binding reagents to be isolated against intracellular clinical targets such as cell signalling proteins associated with tumour formation (p53, ras, cyclin E), proteins associated with neurodegenerative disorders (huntingtin, betaamyloid precursor protein), and various proteins crucial to viral replication (e.g. HIV-1 proteins such as Tat, Rev and Vif-1), which are difficult to screen by phage, ribosome or cell-surface display. This study used the β-lactamase protein complementation assay (PCA) as the display and selection component of a system for screening a protein library in the cytoplasm of HEK 293T cells. The colicin E7 (ColE7) and Immunity protein 7 (Imm7) *Escherichia coli* proteins were used as model interaction partners for developing the system. These proteins drove effective β-lactamase complementation, resulting in a signal-to-noise ratio (9:1 – 13:1) comparable to that of other β-lactamase PCAs described in the literature. The model Imm7-ColE7 interaction was then used to validate protocols for library screening. Single positive cells that harboured the Imm7 and ColE7 binding partners were identified and isolated using flow cytometric cell sorting in combination with the fluorescent β-lactamase substrate, CCF2/AM. A single-cell PCR was then used to amplify the Imm7 coding sequence directly from each sorted cell. With the screening system validated, it was then used to screen a protein library based the Imm7 scaffold against a proof-of-principle target. The wild-type Imm7 sequence, as well as mutants with wild-type residues in the ColE7- binding loop were enriched from the library after a single round of selection, which is consistent with other eukaryotic screening systems such as yeast and mammalian cell-surface display. In summary, this thesis describes a new technology for screening protein libraries in a mammalian, intracellular environment. This system has the potential to complement existing screening technologies by allowing access to intracellular proteins and expanding the range of targets available to the pharmaceutical industry.

A wide range of screening strategies have been employed to isolate antibodies and other proteins with specific attributes, including binding affinity, specificity, stability and improved expression. However, there remains no high-throughput system to screen for target-binding proteins in a mammalian, intracellular environment. Such a system would allow binding reagents to be isolated against intracellular clinical targets such as cell signalling proteins associated with tumour formation (p53, ras, cyclin E), proteins associated with neurodegenerative disorders (huntingtin, betaamyloid precursor protein), and various proteins crucial to viral replication (e.g. HIV-1 proteins such as Tat, Rev and Vif-1), which are difficult to screen by phage, ribosome or cell-surface display. This study used the â-lactamase protein complementation assay (PCA) as the display and selection component of a system for screening a protein library in the cytoplasm of HEK 293T cells. The colicin E7 (ColE7) and Immunity protein 7 (Imm7) Escherichia coli proteins were used as model interaction partners for developing the system. These proteins drove effective â-lactamase complementation, resulting in a signal-to-noise ratio (9:1 – 13:1) comparable to that of other â-lactamase PCAs described in the literature. The model Imm7-ColE7 interaction was then used to validate protocols for library screening. Single positive cells that harboured the Imm7 and ColE7 binding partners were identified and isolated using flow cytometric cell sorting in combination with the fluorescent â-lactamase substrate, CCF2/AM. A single-cell PCR was then used to amplify the Imm7 coding sequence directly from each sorted cell. With the screening system validated, it was then used to screen a protein library based the Imm7 scaffold against a proof-of-principle target. The wildtype Imm7 sequence, as well as mutants with wild-type residues in the ColE7- binding loop were enriched from the library after a single round of selection, which is consistent with other eukaryotic screening systems such as yeast and mammalian cell-surface display. In summary, this thesis describes a new technology for screening protein libraries in a mammalian, intracellular environment. This system has the potential to complement existing screening technologies by allowing access to intracellular proteins and expanding the range of targets available to the pharmaceutical industry.

To be able to make informed descicions regarding the research of new drug molecules (ligands), it is crucial to have access to information regarding the chemical interaction between the drug and its biological target (protein). Computer-based methods have a given role in drug research today and, by using methods such as molecular docking, it is possible to investigate the way in which ligands and proteins interact. Despite the acceleration in computer power experienced in the last decades many problems persist in modelling these complicated interactions. The main objective of this thesis was to investigate and improve molecular modelling methods aimed to estimate protein-ligand binding. In order to do so, we have utilised chemometric tools, e.g. design of experiments (DoE) and principal component analysis (PCA), in the field of molecular modelling. More specifically, molecular docking was investigated as a tool for reproduction of ligand poses in protein 3D structures and for virtual screening. Adjustable parameters in two docking software were varied using DoE and parameter settings were identified which lead to improved results. In an additional study, we explored the nature of ligand-binding cavities in proteins since they are important factors in protein-ligand interactions, especially in the prediction of the function of newly found proteins. We developed a strategy, comprising a new set of descriptors and PCA, to map proteins based on their cavity physicochemical properties. Finally, we applied our developed strategies to design a set of glycopeptides which were used to study autoimmune arthritis. A combination of docking and statistical molecular design, synthesis and biological evaluation led to new binders for two different class II MHC proteins and recognition by a panel of T-cell hybridomas. New and interesting SAR conclusions could be drawn and the results will serve as a basis for selection of peptides to include in in vivo studies.

Il tumore prostatico si sviluppa come una iper-proliferazione dipendente dagli androgeni delle cellule epiteliali ghiandolari e viene inizialmente affrontato con una terapia anti-androgenica. Tuttavia, dopo una regressione iniziale, il tumore si evolve in una forma più aggressiva indipendente dagli androgeni per cui ad oggi non è stata ancora trovata una cura (Grossmann et al., 2001). Nel nostro laboratorio è stata precedentemente descritta l’attivazione della tirosin chinasi Src in un gruppo di tumori prostatici avanzati, correlata alla fosforilazione in tirosina della RNA-binding protein Sam68 (Pronetto et al., 2004) appartenente alla famiglia STAR (Signal transduction and RNA metabolism), coinvolta nello splicing e nel processamento dei pre-mRNA (Lukong and Richard, 2003). Da qui abbiamo analizzato l’espressione e la funzione di Sam68 in cellule tumorali. Abbiamo osservato che, nei pazienti affetti da PCa, Sam68 è up-regolata sia a livello di mRNA che a livello di proteina. La down-regolazione di Sam68 tramite RNAi o interferire con la sua funzione in vivo con una proteina chimerica (GFP-Sam68GSG ) determinano un rallentamento della proliferazione di cellule tumorali prostatiche e le rendono più suscettibili all’apoptosi indotta da agenti chemoterapici. Questi dati mostrano quindi che l’espressione di Sam68 favorisce la proliferazione delle cellule tumorali di prostata e la sopravvivenza ad agenti chemoterapici (Busà et al., 2007). Ci siamo poi concentrati sullo studio del ruolo di Sam68 in questi eventi a livello molecolare. Abbiamo osservato che nelle cellule PC3, una linea di tumore prostatico non responsiva agli androgeni, in seguito a trattamento con l’agente chemoterapico mitoxantrone Sam68 rilocalizza all’interno di granuli nucleari. Abbiamo caratterizzato questi granuli nucleari ed abbiamo visto che in essi Sam68 colocalizza con diverse RNA-binding protein, sia appartenenti alla famiglia SR (SC35 e ASF/SF2) sia coinvolte nella risposta cellulare allo stress(hnRNP A1 e TIA1) (Guil et al., 2006). Sam68 si accumula anche in granuli citoplasmatici in cui co-localizza sia con hnRNP A1 che con TIA1, confermando si tratti dei cosiddetti stress granules (SGs). Questi dati suggeriscono che Sam68 faccia parte di una risposta cellulare allo stress “RNA-mediata”. Inoltre, poiché questa proteina è in grado di legare gli mRNA e di mediare lo splicing alternativo di pre-mRNA, abbiamo cercato di identificare i target modulati dal trattamento con il chemoterapico. In particolare ci siamo concentrati sullo splicing alternativo di un target già noto di Sam68, CD44 (Matter et al., 2002). Siamo andati ad analizzare lo splicing alternativo del pre-mRNA di CD44 in seguito a una dose-risposta con il mitoxantrone ed abbiamo riscontrato delle variazioni di splicing di alcuni esoni variabili, in particolare per v5 e v6, che sono noti essere regolati da Sam68 (Matter et al., 2002; Cheng and Sharp, 2006). Per valutare se le differenze osservate sono dovute alla rilocalizzazione di Sam68 effettueremo trattamenti con il chemoterapico su cellule silenziate per Sam68. Abbiamo individuato le vie biochimiche e di trasduzione del segnale che si accendono in risposta al trattamento con il mitoxantrone, la via del DNA damage di ATM e la via delle MAPkinasi indotta da stress di JNK1/2 e p38. Attraverso l’uso di inibitori specifici, per ATM, p38 e JNK, abbiamo osservato che queste vie non sono necessarie per la rilocalizzazione di Sam68. E ‘ dunque possibile che cambiamenti di conformazione della cromatina stimolino l’accumulo si Sam68 ed altri splicing factors nei granuli nucleari. Infine, alcune evidenze emerse nel corso dei nostri studi suggeriscono un nuovo ruolo di Sam68 nel metabolismo degli rRNA. In un esperimento di co-immunoprecipitazione per Sam68, tra le proteine lin grado di interagire con Sam68 abbiamo identificato Nucleolina, una proteina nucleolare coinvolta nel metabolismo del rRNA (Rickards et al., 2007). Abbiamo confermato quest’interazione e mappato la regione di legame nel dominio carbossi-terminale di Sam68. Inoltre, in un esperimento di co-immunoprecipitazione per Sam68 ed RNA, abbiamo identificato il 18S rRNA tra gli RNA legati da questa proteina. Abbiamo inoltre osservato, attraverso esperimenti di FISH confermati poi da real time PCR, che la down-regolazione di Sam68 determina un aumento significativo dei livelli del pre-rRNA in confronto alle cellule di controllo. Infine esperimenti di ChIP hanno dimostrato che Sam68 è in grado di legare il rDNA a cavallo della regione codificante per il 18S rRNA. Questi risultati suggeriscono un nuovo ruolo di Sam68 nel metabolismo del pre-rRNA. References: Busà R, Paronetto MP, Farini D, Pierantozzi E, Botti F, Angelini DF, Attisani F, Vespasiani G, Sette C., Oncogene 2007 26(30):4372-82. Cheng C, Sharp PA. (2006). Regulation of CD44 alternative splicing by SRm160 and its potential role in tumor cell invasion. Mol Cell Biol. 26(1):362-70. Grossmann ME, Tindall DJ (2001). Androgen receptor signaling in androgen-refractory prostate cancer. J Natl Cancer Inst. 93:1687-97; Guil S, Long JC, Cáceres JF. (2006). hnRNP A1 relocalization to the stress granules reflects a role in the stress response. Mol Cell Biol. 26(15):5744-58. Lukong KE, Richard S (2003). Sam68, the KH domain-containing superSTAR. Bioch. Biophys. Acta 1653: 73-86. Matter N, Herrlich P, Konig H (2002). Signal-dependent regulation of splicing via phosphorylation of Sam68. Nature 420:691-695. Paronetto MP, Farini D, Sammarco I, Maturo G, Vespasiani G, Geremia R et al (2004). Expression of a truncated form of the c-Kit tyrosine kinase receptor and activation of Src kinase in human prostatic cancer. Am. J. Path. 164:1243-1251; Rickards B, Flint SJ, Cole MD, LeRoy G. (2007). Nucleolin is required for RNA polymerase I transcription in vivo. Mol Cell Biol. 27(3):937-48.
Prostate carcinoma (PCa) is one of the main causes of death in the western male population. Although initially controlled by anti-androgenic therapies, PCa often evolves to become androgen-insensitive and highly metastatic. A predominant role in the development of androgen-refractoriness is played by the upregulation of signal transduction pathways that allow prostate cancer cells to autonomously produce their own requirements of growth factors and nutrients (Grossmann et al., 2001). The tyrosine kinase Src is frequently activated in advanced human prostate carcinomas and in our laboratory we have observed that its activation correlates with tyrosine phosphorylation of the RNA-binding protein Sam68 (Paronetto et al., 2004), belonging to the STAR family (Signal transduction and RNA metabolism) and involved in RNA metabolism. In the first part of this PhD Thesis, we have investigated the expression and function of Sam68 in human prostate cancer cells. We observed that Sam68 is up-regulated both at protein and mRNA levels in patients affected by PCa. Moreover, it was observed that down-regulation of Sam68 by RNAi in LNCaP prostate cancer cells delayed cell cycle progression, reduced the proliferation rate and sensitized cells to apoptosis induced by DNA-damaging agents. Microarray analyses revealed that a subset of genes involved in proliferation and apoptosis were altered when Sam68 was knocked down in LNCaP cells. Finally, stable cell lines expressing a truncated GFP-Sam68GSG protein, that interacts with endogenous Sam68 affecting its activity, displayed reduced growth rates and higher sensitivity to cisplatin-induced apoptosis, resembling down-regulation of Sam68 by RNAi. Together, these results indicate that Sam68 expression supports prostate cancer cells proliferation and survival to cytotoxic agents (Busà et al., 2007). Stemming from this evidence, we then aimed to investigate the role played by Sam68 in the response to genotoxic drugs such as mitoxantrone (MTX), a topoisomerase II inhibitor.We observed that MTX caused a subcellular re-localization of Sam68 from nucleoplasm to nuclear granules. Co-staining experiments indicated that Sam68-positive nuclear granules are sites of accumulation of several RNA-binding proteins involved in alternative splicing, such as SR proteins like SC35 and ASF/SF2, and TIA-1 and hnRNP A1, involved in cellular stress responses to various stimuli (Guil et al., 2006). Sam68 also accumulated in cytoplasmic granules that were also co-stained with hnRNP A1 and TIA-1, suggesting that these structures are the well described cytoplasmic stress granules (SGs). These data strongly suggest that Sam68 is part of a RNA-mediated stress response of the cell. Thus, we have begun to investigate whether changes in subcellular localization of Sam68 induced by genotoxic drugs affect alternative splicing of Sam68 target mRNAs, such as CD44 (Matter et al., 2002). Preliminary experiments have shown that MTX treatment in PC3 cells induces changes in alternative splicing of CD44 pre-mRNA. In particular, inclusion of variable exons v5 and v6, known to be regulated by Sam68 (Matter et al., 2002; Cheng and Sharp, 2006), was stimulated. We are current extending these studies to determine whether downregulation of Sam68 by RNAi affects these modifications of CD44 alternative splicing caused by MTX Since Sam68 is known to link signal transduction pathways to RNA metabolism (Lukong and Richard, 2003), we asked whether changes in Sam68 subcellular localization induced by MTX are determined by activation of specific signal transduction pathways. Our data show that although MTX triggers activation of DNA damage pathway, through ATM kinase, and stress-induced MAPKs p38 and JNK1/2 pathways, specific inhibition of these pathways did not affect the subcellular relocalization of Sam68. Thus, it is possible that direct changes in the chromatin structure or function trigger the observed accumulation of Sam68 and splicing factors in nuclear granules. Finally, a set of observations performed during our studies implicate Sam68 in nucleolar functions. In a co-immunoprecipitation experiment aimed at the identification of Sam68-interacting proteins in LNCaP cells we found Nucleolin, a nucleolar protein involved in rRNA metabolism (Rickards et al., 2007). This interaction has been confirmed and mapped to the carboxyterminal region of Sam68 by in vitro studies. Moreover, a RNA-protein co-immunoprecipitation experiment revealed that Sam68 binds 18S rRNA These observations lead us to investigate whether Sam68 plays a role in rRNA metabolism. First, we observed by FISH analysis, and then confermed by real time PCR, that downregulation of Sam68 caused a significant increase in the levels of pre-rRNA compared with control siRNA treated cells. Moreover, ChIP assays aimed at determining the site of the association of Sam68 with rDNA in PC3 cells revealed that Sam68 binds the 18S rRNA coding region. Thus, the results presented herein strongly suggest a novel role of Sam68 in the regulation of pre-rRNA maturation. Our current studies are aimed at investigating this hypothesis further. References: Busà R, Paronetto MP, Farini D, Pierantozzi E, Botti F, Angelini DF, Attisani F, Vespasiani G, Sette C., Oncogene 2007 26(30):4372-82. Cheng C, Sharp PA. (2006). Regulation of CD44 alternative splicing by SRm160 and its potential role in tumor cell invasion. Mol Cell Biol. 26(1):362-70. Grossmann ME, Tindall DJ (2001). Androgen receptor signaling in androgen-refractory prostate cancer. J Natl Cancer Inst. 93:1687-97; Guil S, Long JC, Cáceres JF. (2006). hnRNP A1 relocalization to the stress granules reflects a role in the stress response. Mol Cell Biol. 26(15):5744-58. Lukong KE, Richard S (2003). Sam68, the KH domain-containing superSTAR. Bioch. Biophys. Acta 1653: 73-86. Matter N, Herrlich P, Konig H (2002). Signal-dependent regulation of splicing via phosphorylation of Sam68. Nature 420:691-695. Paronetto MP, Farini D, Sammarco I, Maturo G, Vespasiani G, Geremia R et al (2004). Expression of a truncated form of the c-Kit tyrosine kinase receptor and activation of Src kinase in human prostatic cancer. Am. J. Path. 164:1243-1251; Rickards B, Flint SJ, Cole MD, LeRoy G. (2007). Nucleolin is required for RNA polymerase I transcription in vivo. Mol Cell Biol. 27(3):937-48.

Cette thèse transdisciplinaire réalisée en collaboration avec le laboratoire SPCTS (Sciences des Procédés Céramiques et Traitement de Surface) et l’EA 3842 (Homéostasie cellulaire et pathologies) de l’université de Limoges est un projet de recherche à l’interface entre la biologie et la chimie et a été consacrée à l’étude de l’influence des propriétés physico-chimiques de biocéramiques de phosphate de calcium sur leur comportement biologique in vitro.L’exploration des processus d’interaction entre matériaux et cellules reste une problématique scientifique de premier plan tant d’un point de vue fondamental qu’appliqué pour la mise au point de biomatériaux performants. L’objectif final est d’optimiser l’efficacité thérapeutique des céramiques phosphocalciques comme matériaux de substitution pour la régénération osseuse. La première partie de la thèse est une revue bibliographique générale présentant la problématique actuelle abordée en lien avec les besoins cliniques et les limitations des études actuelles. Les connaissances sur la biologie du tissu osseux sain ainsi que les aspects de régulation du processus de remodelage osseux ont également été abordés dans ce chapitre. Ce chapitre se termine par une synthèse bibliographique sur les biomatériaux et la régénération osseuse. Le chapitre 2 est relatif à la synthèse puis à la caractérisation physico-chimique des matériaux céramiques. Des céramiques de trois compositions chimiques : HA (hydroxyapatite : Ca10(PO4)6(OH)2 , SiHA (hydroxyapatite silicatée : Ca10(PO4)5,6(SiO4)0,42(OH)1,6 et CHA (hydroxyapatite carbonatée : Ca9,5(PO4)5,5(CO3)0,48(OH)1,08(CO3)0,23 , chacune avec deux microstructures différentes : dense ou poreuse, ont été élaborées et rigoureusement caractérisées (porosité, topographie de surface, mouillabilité, potentiel zêta, taille des grains, distribution et taille des pores, surface spécifique). Le chapitre 3 décrit l’approche expérimentale employée pour l’évaluation biologique des interactions matériaux/cellules explorées dans ce travail. Les analyses biologiques ont été réalisées avec deux lignées cellulaires différentes. La lignée cellulaire pré-ostéoblastique MC3T3-E1 et la lignée cellulaire de monocytes/macrophages, précurseurs des ostéoclastes RAW 264.7, (très importantes pour les aspects osseux, mais moins souvent explorées que les lignées ostéoblastiques dans la littérature). Enfin, le chapitre 4 reporte et commente les résultats biologiques obtenus dans ce travail. Tous les biomatériaux évalués dans cette étude sont biocompatibles, néanmoins, le biomatériau poreux CHA s’est avéré le plus prometteur des six variantes de biomatériaux testés
This transdisciplinary thesis, carried out in collaboration with the SPCTS laboratory (sciences of ceramic processes and surface treatment) and EA 3842 (Cellular homoeostasis and pathologies) of the University of Limoges, is a research project at the interface between biology and chemistry and was devoted to the study of the influence of the physico-chemical properties of calcium phosphate bioceramics on their biological behavior in vitro.The exploration of the processes of interaction between materials and cells remains a major scientific issue, both from a fundamental and applied point of view for the development of highperformance biomaterials. The ultimate objective is to optimize the therapeutic efficiency of phosphocalcic ceramics as substitute materials for bone regeneration.The first part of the thesis is a general bibliographic review presenting the current issues tackled with the clinical needs and limitations of current studies. Knowledge of the biology of healthy bone tissue as well as the regulatory aspects of the bone remodeling process was also discussed in this chapter. It includes also a bibliographic overview of biomaterials and bone regeneration.Chapter 2 relates to the synthesis and the physico-chemical characterization of ceramic materials. HA (hydroxyapatite: Ca10 (PO4) 6 (OH) 2, SiHA (silicated hydroxyapatite: Ca10 (PO4) 5.6 (SiO4) 0.42 (OH) 1.6 and CHA (carbonated hydroxyapatite: Ca9.5 (PO4) 5.5 (CO3) 0.48 (OH) 1.08 (CO3) 0.23, ceramics each with two different microstructures : dense or porous, have been elaborated and thoroughly characterized (porosity, surface topography, wettability, zeta potential, grain size, pore size and distribution, specific surface area). Chapter 3 describes the experimental approach used for the biological evaluation of the interactions between materials and cells. Biological analyzes were performed with two different cell lines. The pre-osteoblastic MC3T3-E1 cell line and the RAW 264.7cell line of monocytes / macrophages, precursors of the steoclasts, (very important for the bone aspects, but less often explored than the osteoblastic lines in the literature). Finally, Chapter 4 reports and comments on the biological results obtained in this work. All biomaterials evaluated are biocompatible, nevertheless, the porous CHA biomaterial was the most promising of the six variants of biomaterials tested

碩士
國立成功大學
電腦與通信工程研究所
102
In this thesis, a novel resource allocation algorithm is presented for the downlinks of multi-cell multiuser-multiple-input-multiple-output (MU-MIMO) OFDM systems. The proposed scheme raises the overall received power by proper subcarrier allocation and reduces co-channel interference (CCI) among users by robust precoding and aims to support more users with quality of service (QoS) requirements. The proposed algorithm employs the concept of principle component analysis (PCA) in the precoding design. Based on PCA, the dimension of the vector space of the mutual interference channel metrics among neighboring cells can be reduced to meet the dimension constraint imposed by the precoding design. Consequently, the interference reduction effect can be preserved well. Finally, with more CSI (channel state information) information sharing, the proposed algorithm also provides a way to further compensate the users, who do not get enough resource originally, to be satisfied with the requirement of QoS.

Prostate cancer is the second leading cause of cancer death in men in Europe and the US. In the context of previous preclinical experiments and clinical studies there are certain assumptions predicating successful application of immunotherapy in the treatment of patients with prostate cancer. Promising results have been achieved by a combination of different treatment modalities which provide a synergistic antitumor effect. One of these combinatorial options is the use of antitumor vaccines and adoptive T cell transfer. The topic of this thesis is to provide a fresh insight into the past and current trends following the long-term candidate's department program in the field of anti-tumor immunotherapy. The experimental part of this thesis revolves around our own results published in this field. The introductory chapter delivers a basic overview of cellular mechanisms of anti-tumor immunity and the role of individual immune components in these processes. Following chapters are dedicated to current immunotherapeutic approaches with emphasis on the adoptive T cell transfer and implication of this technology in the treatment of prostate cancer. The results section describes the establishment of our protocol for adoptive T cell transfer as well as the protocol for ex vivo enrichment of human T cell...

Age related macular degeneration (AMD) is a public health concern in an aging society. The retinal pigment epithelium (RPE) layer of the eye is a principal site of pathogenesis for AMD. Morphological characteristics of the cells in the RPE layer can be used to discriminate age and disease status of individuals. In this thesis three genotypes of mice of various ages are used to study the predictive abilities of these characteristics. The disease state is represented by two mutant genotypes and the healthy state by the wild-type. Classification analysis is applied to the RPE morphology from the different spatial regions of the RPE layer. Variable reduction is accomplished by principal component analysis (PCA) and classification analysis by the k-nearest neighbor (k-NN) algorithm. In this way the differential ability of the spatial regions to predict age and disease status by cellular variables is explored.

The study examined the properties of stalk and cob fibres from recombinant inbred corn lines and their parents, grown at two locations, in a polylactic acid (PLA) matrix. The objectives were to: determine fibre compositions; evaluate the effects of fibres on the functional properties of biocomposites and identify quantitative trait loci (QTLs) and gene markers for fibre performance in biocomposites. Significant Genotype*Location effects were observed. Composites had lower strength (impact, tensile, and flexural) but higher tensile/flexural modulus values than pure PLA. The latter were positively affected by cellulose and hemicellulose but negatively affected by free phenolic levels and 93 fibre QTLs and 62 composite markers were detected. This study identified fibre traits and markers for genes that may be important for the use of corn fibres in biocomposites.
Ontario BioCar Initiative Project funded by Ontario Ministry of Research and Innovation, Agriculture and Agri-Food Canada, The Natural Sciences and Engineering Research Council, The Ontario Ministry of Agriculture, Food and Rural Affairs (OMAFRA) and Ontario Public Sector