<p> </p> <p>Learning about ‘behavior’ has always been at the heart of my research endeavors. While my undergraduate work in evolution and ecology exposed me to the science behind why a behavior exists, in my graduate work, I intended to explore how to use something’s behavior to widen its applicability. In this thesis, <em>I will present three works that utilize some of the fundamental</em></p> <p><em>behaviors (i.e., properties) of elastin-like polypeptides (ELP) to improve existing protein purification methods or explore their applicability in bladder cancer imaging and immunotherapy. </em></p> <p>Bladder cancer has high recurrence rates (60-70 % annually) that necessitate multiple follow-up therapies making it one of the costliest cancers per patient. In this work, we have attempted to address two leading causes of the recurrence. First is a low sensitivity (62-84 %) and variable specificity (43-95 %) of white light cystoscopy used to diagnose and remove tumors. We aimed to address the heart of this problem, i.e., the non-specific mode of detection using white light. Only the trained eyes can discern abnormal from normal-appearing tissues even then, leaving up to 45% of tumors unresected to colonize and spread. <em>We developed and characterized near infrared dye-peptide-ligand conjugates (NIR-ELP-ligand) that undergo receptor-mediated binding and internalization to human bladder cancer cells in vitro and tissues ex vivo.</em> By using a molecular target-based probe in combination with NIR imaging, we can aid in improving the detection limit via selective binding to the tumor and reduction in background autofluorescence.</p> <p>Bacillus-Calmette Guérin (BCG) instillation in the bladder is the gold-standard</p> <p>immunotherapy used after surgical removal of bladder tumors. This was approved as a response to the inefficiency of surgery alone in improving cancer status. It has succeeded by reducing the recurrence rate to 30-50 %. But it comes with the complications of putting a live mycobacterium</p> <p>in the human body and giving a patient a urinary tract infection right after surgical tumor resection. <em>Thus, we aimed to deliver nucleic acid as immunotherapeutic cargo in a selective manner to elicit robust anti-tumor immune responses while minimizing the side effects due to its carrier.</em> Towards</p> <p>this goal, we have developed a highly modular and adaptable ELP-ligand fusion protein-based nucleic acid delivery carrier targeted toward bladder cancer. Before developing targeted peptide-based cancer imaging and nucleic acid delivery modalities, we addressed the Achilles heel of peptide-based approaches. The peptide and protein industry suffers</p> <p>through complex, time-consuming, inconsistent, and low-yielding purification methods. <em>We have developed a scalable, facile, and reproducible protein purification method that delivers ELP and ELP fusion proteins free of host cell proteins and nucleic acids and has low lipopolysaccharide</em></p> <p><em>content in just 3 h starting from a bacterial pellet. </em>Thus, for a coherent narrative, the thesis is structured as follows:</p> <p>1. Introduction</p> <p>2. ELP as a protein purification tag: Development of a rapid purification method for ELPs and ELP fusion proteins.</p> <p>3. ELP as a cancer imaging agent: Development of NIR-ELP-Ligand imaging probe targeting bladder cancer.</p> <p>4. ELP as a drug delivery agent: Utilizing ELP-ligand fusion protein in the formulation of targeted nucleic acid delivery carrier to bladder cancer.</p>

Ce travail a pour objectif de tester des solutions viables et durables pour la phytoremédiation de sols contaminés en éléments traces. Il inclut à la fois des données sur l'évaluation initiale et résiduelle des risques (biomonitoring) et sur des solutions de phytomanagement à long terme utilisant des plantes et microorganismes associés, en particulier la phytoextraction aidée couplant l’épuisement du pool labile de contaminants du sol, la production de matière première végétale et la restauration de services écosystémiques. La phytotoxicité du Cu, le rôle améliorant des amendements organiques et minéraux et la tolérance des plantes ont été examinés utilisant des essais biologiques ainsi qu’une technique de dilution du sol. L'utilité d’une lignée de mutant de tournesol (Helianthus annuus) et d’une lignée parental de tabac (Nicotiana tabacum) pour le biomonitoring de sols contaminés en Cu a été investiguée. Les paramètres biochimiques qui sont en relation avec le statut antioxidant des plantes et leurs réponses moléculaires à l’excès de Cu ont en général montré une plus grande sensibilité que les traits morphologiques. Le tabac est plus tolérant au Cu que le tournesol. Des bactéries endophytes issues de différentes sources, notamment des graines d’une population métallicole d’une graminée (Agrostis capillaris) peuvent stimuler la croissance du tournesol et du tabac aux expositions en Cu modérément en excès. Pour ces plantes annuelles, accumulatrices secondaires du Cu et à phénotype d’exclusion, l'augmentation de la capacité de phytoextraction de Cu par les parties aériennes s’effectue principalement par l’accroissement de la biomasse aérienne, plutôt que par celui de sa concentration en Cu. Par conséquent, une attention a été prêtée aux pratiques agricoles dans les essais en parcelles sur site. Plusieurs options d’amélioration ont été examinées in situ: l'application d’amendements du sol, l'utilisation de lignées de mutants et de variants somaclonaux, la rotation de cultures et des cultivars, la bioaugmentation, la fertilisation, l’irrigation, etc. Deux lignées de mutants et des cultivars commerciaux de tournesol ainsi qu’une lignée parentale de tabac ont montré un fort potentiel pour la phytoextraction du Cu, accompagné d’une production significative de graines et/ou autre biomasse valorisable. Les solutions de restauration écologique basées sur la phytoextraction, utilisant des plantes annuelles accumulatrices secondaires de Cu permettraient (1) la décontamination progressive des sols contaminés en Cu au cours des rotations culturales, (2) un retour financier lié à la valorisation de la biomasse végétale, et (3) la restauration de services écosystémiques. / This work aimed at assessing sustainable phytoremediation options for trace element-contaminated soils. It includes both the assessment of initial and residual risks (biomonitoring) and long-term sustainable decontamination options using plants and associated microbes, especially aided phytoextraction with the secondary purposes of producing plant-based feedstock and restoring ecosystem services. Copper phytotoxicity, the improving role of soil conditioners, and plant tolerance were tested using a bioassay as well as a fading technique. The usefulness of a mutant line of sunflower (Helianthus annuus) and a motherline of tobacco (Nicotiana tabacum) for the biomonitoring of Cu-contaminated soils was investigated. Biochemical parameters in relation to antioxidant status of plants and molecular responses to Cu excess generally showed a greater sensitivity than morphologic ones. Tobacco has a higher Cu tolerance than sunflower. Endophytic bacteria from various sources, notably from the seeds of metallicolous populations of grasses (Agrostis capillaris) can promote the growth of sunflower and tobacco exposed to Cu excess. For annual Cu-secondary accumulator plants with an excluder phenotype, increase in shoot Cu removal occurred primarily through increase in shoot biomass, rather than in shoot Cu concentration. Therefore, attention in field trials was paid to agricultural practices. Various improving options were tested in situ: application of soil amendments, the use of mutant lines and somaclonal variation, cultivars and crop rotation, bioaugmentation, fertilization, irrigation, etc. Two mutant lines and some commercial cultivars of sunflower as well as the motherline of tobacco showed a high potential for Cu phytoextraction as well as for plant-based feedstock. Ecological restoration options for Cu-contaminated soils based on phytoextraction using annual Cu-secondary accumulator plants with a high shoot biomass would (1) result in the progressive decontamination of Cu-contaminated soils during crop rotations, (2) provide a financial return through biomass valorization, and (3) promote ecosystem services.

Ce travail de thèse s'attache à identifier des plantes et/ou molécules à activités cytotoxique, antioxydante, anti-inflammatoire et antivirale ciblant le virus du chikungunya (CHIKV) dans le but de trouver des alternatives thérapeutiques vis-à-vis du stress oxydatif et de l'inflammation, mécanismes impliqués dans les maladies chroniques non transmissibles (diabète, obésité…), et de la maladie du chikungunya, maladie vectorielle réémergente. La première partie de ces travaux présente les résultats obtenus lors d'un criblage d'activités biologiques réalisé sur une sélection de dix-huit plantes endémiques et indigènes de La Réunion. Les activités ciblées ont été les activités cytotoxiques sur une lignée cellulaire humaine (cellules THP-1), les activités antioxydantes évaluées par un test in cellulo d'hémolyse et par quatre tests chimiques (TEAC/DPPH/FRAP/ORAC) ainsi qu'une évaluation de la teneur en composés phénoliques (test FOLIN) et les activités anti-inflammatoires testées sur des macrophages murins (cellules RAW-BlueTM). Les résultats obtenus ont permis de mettre, plus particulièrement, en évidence les activités de différents extraits : cytotoxique pour Carissa spinarum, antioxydantes pour Agarista buxifolia et Dryopteris wallichiana et anti-inflammatoire pour Stillingia lineata et Indigofera ammoxylum. La deuxième partie du travail est consacrée à l'étude phytochimique d'une espèce indigène de La Réunion, Stillingia lineata, choisie en raison des résultats obtenus lors de ce criblage biologique préliminaire et de ceux du programme Phytochik. Un fractionnement bioguidé par un test antiviral, réalisé sur des cellules Vero (cellules rénales de singe vert Cercopithecus aethiops) contaminées par le CHIKV, a conduit à l'isolement de trois macrocycles diterpéniques rares de type tonantzitlolone dont l'un présente une structure non caractérisée jusque-là, et d'un pimarane de structure nouvelle. La 4'-acétoxytonantzitlolone a été identifiée comme molécule candidate contre le CHIKV (CE50 = 7 μM). Des relations structure-activité ont pu être définies ; la présence d'un groupement oxygéné sur la chaîne latérale des tonantzitlolones semble jouer un rôle important sur la réponse antivirale de ces squelettes diterpéniques. / The aims of this PhD work were to identify plants and/or molecules with cytotoxic, antioxidant, anti-inflammatory or antiviral (chikungunya virus , CHIKV) activities in order to find therapeutic alternatives towards oxidative stress and inflammation, mechanisms involved in chronic noncommunicable diseases (diabetes, obesity ...), and chikungunya disease, reemerging vector-borne disease. The first part of this work presents the results obtained from a biological screening carried out on a selection of eighteen endemic and indigenous plants of La Réunion. The targeted activities were cytotoxicity on a human cell line (THP-1), antioxidant activities evaluated using an in cellulo hemolysis assay and four chemical tests (TEAC / DPPH / FRAP / ORAC) together with an evaluation of the content of phenolic compounds (FOLIN test) and anti-inflammatory activity tested in murine macrophages (RAW cells-BlueTM). The results allowed to highlight activities of different extracts in particular : cytotoxic for Carissa spinarum, antioxidant for Dryopteris wallichiana and Agarista buxifolia and anti-inflammatory for Stillingia lineata and Indigofera ammoxylum.The second part of this work is devoted to the phytochemical study of Stillingia lineata, an indigenous species of La Réunion chosen because of the results obtained in this preliminary biological screening and those carried out in Phytochik programme. Bioassay-guided fractionation performed on Vero cells (green monkey kidney cells Cercopithecus aethiops) infected with CHIKV led to the isolation of three rare macrocycle-type diterpenes called tonantzitlolone and a new pimarane. The 4'-acetoxytonantzitlolone was identified as a candidate molecule against CHIKV (EC50 = 7 μM). Structure-activity relationships have been defined, the presence of an oxygenated group on the side chain of tonantzitlolones seems to play an important role in the antiviral response of the diterpene skeleton.

Optics are a powerful probe of chemical structure that can often be linked to theoretical predictions, providing robustness as a measurement tool. Not only do optical interactions like second harmonic generation (SHG), single and two-photon excited fluorescence (TPEF), and infrared absorption provide chemical specificity at the molecular and macromolecular scale, but the ability to image enables mapping heterogeneous behavior across complex systems such as biological tissue. This thesis will discuss nonlinear and linear optics, leveraging theoretical predictions to provide frameworks for interpreting analytical measurement. In turn, the causal mechanistic understanding provided by these frameworks will enable structurally specific quantitative tools with a special emphasis on application in biological imaging. The thesis will begin with an introduction to 2nd order nonlinear optics and the polarization analysis thereof, covering both the Jones framework for polarization analysis and the design of experiment. Novel experimental architectures aimed at reducing 1/f noise in polarization analysis will be discussed, leveraging both rapid modulation in time through electro-optic modulators (Chapter 2), as well as fixed-optic spatial modulation approaches (Chapter 3). In addition, challenges in polarization-dependent imaging within turbid systems will be addressed with the discussion of a theoretical framework to model SHG occurring from unpolarized light (Chapter 4). The application of this framework to thick tissue imaging for analysis of collagen local structure can provide a method for characterizing changes in tissue morphology associated with some common cancers (Chapter 5). In addition to discussion of nonlinear optical phenomena, a novel mechanism for electric dipole allowed fluorescence-detected circular dichroism will be introduced (Chapter 6). Tackling challenges associated with label-free chemically specific imaging, the construction of a novel infrared hyperspectral microscope for chemical classification in complex mixtures will be presented (Chapter 7). The thesis will conclude with a discussion of the inherent disadvantages in taking the traditional paradigm of modeling and measuring chemistry separately and provide the multi-agent consensus equilibrium (MACE) framework as an alternative to the classic meet-in-the-middle approach (Chapter 8). Spanning topics from pure theoretical descriptions of light-matter interaction to full experimental work, this thesis aims to unify these two fronts. <br>