Biofilmes são comunidades bacterianas tridimensionais complexas, que vivem organizadas e aderidas a uma superfície, biótica ou abiótica, embebidas em uma matriz exopolimérica. Cerca de 80% das bactérias vivem organizadas na forma de biofilmes, pois dentro destas estruturas são menos sensíveis aos antibióticos e à resposta imune do hospedeiro. Dentre as principais bactérias formadoras de biofilmes têm-se Staphylococcus spp., Pseudomonas aeruginosa e enterobacteriaceas. Estas bactérias formadoras de biofilmes são importantes colonizadoras da superfície de dispositivos médicos e implantes, aumentando a morbidade e mortalidade dos pacientes que apresentam este tipo de infecção. A investigação de novas estratégias para prevenção e tratamento de infecções por biofilmes é urgentemente necessária. Dentre estas estratégias estão a pesquisa de diferentes mecanismos ou substâncias capazes de provocar a inibição da formação ou a erradicação do biofilme formado. Neste contexto, os venenos animais representam uma fonte ainda inexplorada de uma vasta quantidade de moléculas bioativas, candidatas ao desenvolvimento de novas terapias, inclusive antibiofilme. O principal objetivo deste estudo é avaliar diferentes venenos de serpentes e análogos sintéticos como fonte de moléculas contra biofilmes bacterianos patogênicos. O capítulo 1 revisa estudos que relatam a atividade antimicrobiana (contra bactérias, vírus, protozoários e fungos) de 170 peptídeos isolados de venenos de oito diferentes animais. Peptídeos antimicrobianos vêm ganhando destaque em pesquisas para o tratamento de infecções e peptídeos com atividade antibiofilme são uma nova e promissora abordagem, para o tratamento de infecções relacionadas. O capítulo 2 mostra as atividades antimicrobiana, antibiofilme e de erradicação de biofilmes pré-estabelicidos de 18 análogos de peptídeos de oriundos de venenos de serpentes. Inicialmente foram analisadas e alinhadas 170 sequências peptídeos oriundos de venenos animais. O pepptídeos 16 apresentou considerável atividade antimicrobiana contra cepas bacterianas Gram-positivas, sensíveis e resistentes. Para S. epidermidis os peptídeos 1, 2, 3, 4, 12, 13 e 16 apresentaram menos de 50% de formação de biofilme e os peptídeos 2, 3 e 16 reduziram o biofilme pré-formad. A citotoxicidade e a actividade hemolítica foram testadas e os peptídeos ativos 2 e 16 apresentaram citotoxicidade e hemólise significativas em comparação com os controles. A posição dos aminoácidos pode contribuir para as atividades, sendo que mais testes são necessários para entender a relação das posições de aminoácidos na ação. O capítulo 3 mostra as atividades antiformação e erradicação de biofilmes pré-estabelecidos de dezessete diferentes venenos de serpentes, duas de escorpiões e três de anêmonas marinhas, bem como as secreções de pele de três espécies de sapos. Consideráveis atividades antiformação e de erradicação foram verificadas contra as cepas de S. aureus, S. epidermidis e E. cloaceae por todos os venenos de serpentes testados, em diferentes concentrações. Além disso, um fracionamento inicial foi realizado e as melhores condições foram selecionadas para um novo fracionamento, onde foram testadas 27 frações de veneno de B. diporus. As frações 8, 14 e 23 apresentaram atividades com menos de 50% de formação de biofilme e menos de 80% do biofilme remanescente. Os resultados indicam a capacidade dos venenos, especialmente da serpente de B. diporus, de serem potenciais fontes de moléculas como estratégia para combater os biofilmes patogênicos bacterianos. O presente estudo aborda o potencial de venenos animais, principalmente venenos de serpentes, como fonte de moléculas, que podem apresentar inúmeras atividades farmacológicas inéditas, incluindo àquelas relacionadas com a prevenção da formação e de erradicação de biofilmes bacterianos patogênicos. Atualmente, existem seis medicamentos aprovados pelo Food and Drug Administration (FDA), oriundos de venenos, como o Captopril (Capoten®). Este estudo mostra a capacidade de venenos como fonte de novas moléculas ativas contra biofilmes patogênicos. / Biofilms are complex three-dimensional bacterial communities living organized and attached on a surface, embedded in exopolimeric matrix. About 80% of live bacteria are organized in the form of biofilms because in these structures are less sensitive to antibiotics and host immune response. Staphylococcus spp., Pseudomonas aeruginosa and enterobacteriaceas are the main biofilm forming bacteria. These forming biofilms bacteria are important colonizing surface of medical devices and implants, increasing the morbidity and mortality of patients with this kind of infection. The investigation of new strategies for prevention and treatment of infections caused by biofilms is urgently needed. Among these strategies, there are the research of different mechanisms or substances capable of inhibit the formation or to eradicate the formed biofilm. In this context, animal venoms represent an untapped source of vast amounts of bioactive molecules, candidates for the development of new therapies, including antibiofilm. The main objective of this study is to evaluate different venoms of snakes and synthetic analogs as source of molecules against pathogenic bacterial biofilms. The chapter 1 reviewed numerous studies reporting the antimicrobial activity (against bacteria, viruses, protozoa and fungi) of 170 peptides isolated from venoms of eight different animals. Antimicrobial peptides have been gaining attention in research for the treatment of infections and peptides with antibiofilm activity are a new and promising approach for the treatment of infections related. The chapter 2 shows the antimicrobial, antibiofilm and eradication of established biofilms activities of 18 analogs of peptides derived from snake venoms. Initially, 170 peptide sequences from animal venoms were analyzed and aligned. The peptide 16 showed considerable antimicrobial activity against Gram-positive bacterial strains, sensitive and resistant. For S. epidermidis, the peptides 1, 2, 3, 4, 12, 13 and 16 showed less than 50% of biofilm formation and peptides 2, 3 and 16 reduced preformed biofilm. Cytotoxicity and hemolytic activity were tested and active peptides 2 and 16 showed significant cytotoxicity and hemolysis compared with the controls. The position of the amino acids can contribute to the activities and more tests are needed to understand the relationship of the amino acid positions in the action. The chapter 3 shows the antiformation and eradication of established biofilms activities of seventeen different venoms of snakes, two of scorpions and three of marine anemones, as well as the skin secretions of three species of frogs. Significant activities were observed against strains of S. aureus, S. epidermidis and E. cloaceae for all venom of snakes tested at different concentrations. In addition, an initial fractionation was performed and the best conditions were selected for a new fractionation, where 27 fractions of B. diporus enom were tested. Fractions 8, 14 and 23 presented activities with less than 50% of biofilm formation and less than 80% of the remaining biofilm. The results indicate the ability of venoms, especially the snake B. diporus, to be potential sources of molecules as a strategy to combat bacterial pathogenic biofilms. This study addresses the potential of animal venoms, especially snake venoms, as source of molecules, which can present numerous unpublished pharmacological activities, including those related to the prevention of the formation and eradication of pathogenic bacterial biofilms. Currently, there are six drugs approved by Food and Drug Administration (FDA), derived from venoms, such as Captopril®. This study shows the ability of venoms as source of new bioactive molecules against pathogenic biofilms.

Os microrganismos podem apresentar-se tanto em forma de vida livre como aderidos a uma superfície ou interface ar-líquido, formando comunidades complexas e dinâmicas conhecidas como biofilmes. Nos últimos anos, com o avanço das pesquisas em nível molecular, foi identificado que a maioria das bactérias utilizam guanosina monofosfato (3´-5´)-cíclica dimérica (c-di-GMP) como um segundo mensageiro. De forma geral, essa molécula controla a sinalização celular, virulência, comunicação entre células e a expressão de proteínas relacionadas com o fenótipo de biofilmes, em resposta à sua concentração intracelular. Sua síntese e degradação são controladas respectivamente por diguanilto ciclases (DGCs) contendo domínio GGDEF e fosfodiesterases (PDEs) que possuem os domínios EAL ou HD-GYP. Em Pseudomonas aeruginosa (PA14) foi identificada uma nova classe de receptor específico para c-di-GMP, a proteína transmembranar PelD, cuja porção citoplasmática contém os domínios GAF e GGDEF degenerado. Sua modulação através desse dinucleotídeo controla a produção de exopolissacarídeos pelos componentes do conservado operon pel e influencia diretamente na capacidade de formação de biofilmes. Devido à escassez de dados a respeito dos eventos moleculares do mecanismo de sinalização mediado por c-di-GMP, este trabalho teve como objetivo principal a caracterização biofísica/estrutural da proteína PelD, bem como o reconhecimento de interação entre este ligante e a porção citoplasmática da proteína. Diversas construções solúveis de PelD foram clonadas e expressas, sendo que a construção compreendendo os resíduos 176-455 (PelD176-455) foi cristalizada com sucesso e teve sua estrutura determinada por iodo-SAD. O modelo final apresentou os dois domínios com enovelamentos característicos das famílias GAF e GGDEF, sendo a interface inter-domínios composta majoritariamente por resíduos hidrofóbicos. Visando uma compreensão das bases moleculares de reconhecimento e ativação de PelD por c-di-GMP, uma estrutura em complexo com o ligante foi resolvida. Como esperado, o dinucleotídeo foi encontrado no sítio inibitório do domínio GGDEF, onde o motivo R367xxD370 e o resíduo R402 são responsáveis pela maior parte das interações com c-di-GMP. No entanto, nenhuma grande mudança estrutural foi observada entre as formas apo e holo de PelD, ao contrário de outros sistemas efetores tal como LapD e domínios PilZ. Curiosamente, apenas uma molécula de c-di-GMP foi encontrada no sítio, contrastando com a forma dimérica intercalada normalmente ligada aos sítios inibitórios de domínios GGDEF, tais como em PleD e WspR. Estudos de ITC confirmaram a estequiometria 1:1 em solução. Isso mostra a versatilidade dos diversos receptores já identificados até o momento, frente à ligação desse dinucleotídeo. Estudos de bioinformática identificaram uma potencial região de coiled-coil na hélice juxtamembrana de PelD, resíduos 115-160, provavelmente responsável pela homodimerização. Visando uma comprovação experimental dessa hipótese, uma construção contendo toda a porção citoplasmática, PelD111-455, foi expressa e purificada. Estudos comparativos de dicroísmo circular e ultracentrifugação analítica entre as construções PelD176-455 e PelD111-455 realmente demonstraram que os resíduos extras presentes em PelD111-455 formam uma hélice-α e são responsáveis pela dimerização da porção citoplasmática da proteína. De modo geral, os resultados aqui apresentados não só contribuirão para o entendimento dos mecanismos de regulação das vias de sinalização mediadas por c-di-GMP como, em longo prazo, poderão levar ao desenvolvimento de agentes contra infecções bacterianas. / Microorganisms may be presented either in planktonic free-swimming life-style or adhered to surfaces, forming a complex and dynamic community known as biofilm. In recent years, with the progress of research at the molecular level, it was identified that the majority of bacteria use guanosine monophosphate (3\'-5 \')-cyclic dimeric (c-di-GMP) as a second messenger. Generally, this molecule controls the cell signaling, virulence, communication between cells and expression of proteins related to the phenotype of biofilms in response to its intracellular concentration. Its synthesis and degradation are controlled respectively by diguanylate cyclases (DGC) containing the GGDEF domain and phosphodiesterases (PDE) with the domains EAL or HD-GYP. In Pseudomonas aeruginosa (PA14) a novel class of receptor specific for c-di-GMP has been identified, the transmembrane protein PelD, which contains a GAF and degenerate GGDEF domains in the cytoplasmic portion. Its modulation through this dinucleotide controls the production of exopolysaccharides by the components of the conserved operon pel and directly influences the ability of biofilm formation. Due to the paucity of data about the molecular events of the signaling mechanism mediated by c-di-GMP, this study aimed to characterize biophysically and structurally the protein PelD. Various soluble constructions of PelD were cloned and expressed, and the construction comprising the residues 176-455 (PelD176-455) was successfully crystallized and its structure was determined by iodine-SAD. The final model showed the two characteristic domains of families GAF and GGDEF, and the inter-domain interface composed primarily of hydrophobic residues. Seeking an understanding of the molecular basis of recognition and activation of PelD by c-di-GMP, a structure in complex with the ligand was solved. As expected, the dinucleotide was found at the inhibitory site of the GGDEF domain, where the motif R367xxD370 and the residue R402 are responsible for most of the interactions with c-di-GMP. However, no major structural change was observed between the apo and holo forms of PelD, unlike other effector systems such as LapD and domains PilZ. Interestingly, only one molecule of c-di-GMP was present on the site, in contrast to the dimeric intercalated form normally found at I-sites GGDEF domains, such as PleD and in WspR. ITC studies confirmed the 1:1 stoichiometry in solution. This shows the versatility of the various receptors identified so far, compared to the binding of dinucleotide. Bioinformatics studies have identified a potential coiled-coil region in the juxtamembrane helix of PelD, residues 115-160, probably responsible for homodimerization. Aiming at an experimental confirmation of this hypothesis, a construct containing the full cytoplasmic portion, PelD111-455 was expressed and purified. Comparative studies of circular dichroism and analytical ultracentrifugation between constructs PelD176-455 and PelD111-455 indeed demonstrated that the extra residues present in PelD111-455 form an α-helix and are responsible for dimerization of the cytoplasmic portion of the protein. Overall, the results presented here not only contribute to the understanding of the mechanisms of regulation of signaling pathways mediated by c-di-GMP as in the long run, may lead to the development of agents against bacterial infections.

Nanocrystalline diamond (NCD) films possess great mechanical properties (low friction coefficient, high hardness etc.), chemical properties (e.g. low corrosivity or chemical inertness) and good biocompatibility. This makes them perspective materials for protective coatings of medical implants and devices. As bacteria biofilms are often very resistant to antibacterial treatment, materials with anti-bacterial or at least anti-adhesive properties are needed. The interaction of NCD films with bacteria has not been properly examined yet. The aim of this thesis was to introduce and optimize the methods for routine bacterial biofilm cultivation and analysis, use them to investigate the ability of NCD films to inhibit the attachment and biofilm formation of Escherichia coli and correlate it with the NCD surface hydrophobicity. The materials used for the study were hydrogenated NCD (hydrophobic), oxidized NCD (hydrophilic) and uncoated glass. For bacterial biofilm growth, cultivation in six-well plates and continuous cultivation in CDC Bioreactor was used. Several methods were tested for quantitative biofilm detachment and analysis. The putative anti-bacterial properties of NCD material were not confirmed in this work. Higher bacterial attachment to NCD films in comparison to the uncoated glass was...

Ce travail décrit certains aspects du réseau d’assainissement en tant que réacteur bio-physico-chimique. Les objectifs principaux sont : d’identifier et de quantifier les sources des eaux circulant dans les collecteurs en se basant sur les signatures isotopiques des eaux et des sulfates dissous; de déterminer la nature minéralogique des phases porteuses des métaux lourds et d’étudier leur cycle géochimique par MET et MEB couplés à la EDXS ; de mettre en évidence la présence d’échange de matière entre les eaux usées et les biofilms par CLSM et MET et d’étudier les conditions hydrodynamiques impliquées dans cet échange dans un réacteur pilote (Couette-Poiseuille). On montre que les données isotopiques permettent d’évaluer la présence des évolutions de concentration des éléments transportés dans le réseau. Le rôle du réseau en tant que réacteur apparaît dans l’évolution de la nature minéralogique des phases phosphatées vers l’aval du réseau et dans la précipitation des métaux lourds dans les compartiments anaérobiques sous forme de phases sulfurées néoformées. Les dépôts des regards de façade et les biofilms sont les lieux de cette néoformation. A l’échelle de la matière organique, l’auto-épuration est révélée par les échanges entre les biofilms et les matières en suspension (MES) suite à la présence des fibres de cellulose dans la structure des biofilms et de morceaux de biofilms au sein de la MES. La majeure partie de ces évolutions se situe en amont du réseau où les contrastes physicochimiques sont les plus importants. Finalement, les expériences modèles au sein du réacteur ont montré l’implication de l’hydrodynamisme dans le détachement des biofilms / This work describes the sewer system as an integrated part of the wastewater treatment system. The main objectives of this study were: identification and quantification of water sources collected in sewer system, referring to isotopic signatures of water and dissolved sulfates; identification of the mineralogical nature of trace element carriers and determination of their geochemical evolution within the sewer by TEM and SEM coupled with EDSX ; Evidencing exchanges between sewage and biofilms, using CLSM and TEM, and investigating hydrodynamic conditions controlling this exchange in an experimental set-up (Couette-Poiseuille reactor). The results indicate that isotopic data may be used to study the tightness of sewer lines and to evaluate the evolution of element concentrations along sewer. Implication of the sewer system as a true biophysicochemical reactor is evidenced in our study by the evolution of the mineralogical nature of phosphate phases downstream of the sewer and by heavy metal precipitations in anaerobic conditions as neoformed sulfide phases. Sump pit deposits and biofilms represent the earlier stage of this neoformation. Organic matter biodegradation was revealed by TEM examination of SM whereas the exchange between biofilms and SM was shown by CLSM. Cellulose fibers from SM were found embedded in exopolymer biofilm matrices and detached fragments from biofilms were identified in sewage. The majority of these evolutions are located upstream of sewer system in which the contrast in physicochemical properties are the most significant. Finally, biofilm model investigations and image processing showed that hydrodynamic conditions are largely implicated in biofilm detachment

A persistência bacteriana correlacionada à formação de biofilmes bacterianos é, há algum tempo, fonte de grande preocupação médica em virtude de sua ampla associação com a dificuldade de tratamento de infecções crônicas. Por outro lado, as perspectivas de utilização de biofilmes bacterianos em novas aplicações biotecnológicas e até mesmo para fins terapêuticos são promissoras. Há, portanto, grande interesse em compreender os mecanismos que levam as células bacterianas a deixar o estado planctônico, de vida livre, e associarem-se nesses conglomerados celulares altamente complexos. Ao longo das últimas décadas, o segundo mensageiro c-di-GMP – em conjunto com as moléculas que catalisam sua síntese (diguanilato ciclases) e sua degradação (fosfodiesterases) e seus receptores – estabeleceu-se como um elemento central de regulação de uma série de respostas celulares que determinam a formação ou a dispersão de biofilmes. Curiosamente, as proteínas que participam do metabolismo deste segundo mensageiro estão, frequentemente, codificadas múltiplas vezes em um mesmo genoma bacteriano. Em vista dessa observação, estudos mais recentes apontam que, para reger paralelamente uma variedade tão ampla de fenótipos, este sistema opera em modo de alta especificidade de sinalização e que, portanto, o sinal metabolizado por determinados conjuntos de diguanilato ciclases e fosfodiesterases tem alvos celulares específicos. Evidências robustas, porém isoladas até o momento, apontaram que um dos meios pelo qual ocorre a segregação entre sinal produzido e alvo específico é a interação direta entre as proteínas componentes das vias de sinalização. Mais, demonstrou-se que, em algumas vias, a transmissão de sinal ocorre exclusivamente via interação proteica, dispensando a intermediação do sinalizador em si. Para avaliar a validade e relevância global deste mecanismo, propôs-se, neste estudo, a investigação da rede total de interações entre as proteínas tipicamente associadas às vias de sinalização por c-di-GMP em Pseudomonas aeruginosa, utilizando ensaios de duplo-hibrido bacteriano. Para tanto, foram construídas duas bibliotecas de DNA direcionadas e foram feitos testes de interação de forma estratégica para possibilitar o esgotamento e averiguação de todas as possíveis interações entre as proteínas alvo identificadas. O resultado obtido, um mapa inicial, porém abrangente, da rede de interações proteicas em P. aeruginosa, indica uma grande probabilidade de que os mecanismos previamente descritos sejam realmente recorrentes e relevantes para o intermédio da sinalização nesse organismo. Algumas das interações mais robustas encontradas são bastante interessantes e serão, em estudos futuros, mais extensivamente estudadas. / Persister bacteria are correlated to biofilm formation and have been a source of great medical concern due to its close association with the impairment of traditional treatment in combating chronic infections. On the other hand, using bacterial biofilms to create original biotechnological applications or even as a means of therapeutic treatment in medical settings constitutes a promising prospect. There is, therefore, a great interest in understanding the mechanisms that allow bacteria to leave the free-living planktonic lifestyle and associate in these highly complex cellular aggregates. Over the last decades, the second messenger c-di-GMP – and also the molecules involved in its synthesis (diguanylate ciclases) and degradation (phosphodiesterases) along with its receptors – has been established as a key element implicated in regulation of a series of cellular responses that determine biofilm formation or dispersion. Curiously, the proteins that play a part in the metabolism of this second messenger are frequently coded multiple times in single bacterial genomes. Taking this into account, recent studies indicate that, in order to control such a wide range of phenotypes, this system operates via high specificity of signaling – which means that the signal metabolized by a certain set of diguanylate ciclases and phosphodiesterases has specific cellular targets. Robust but yet isolated evidence indicate that a means by which a signal is segregated with its correlated phenotypic response is through direct protein-protein interaction involving the components of these signaling pathways. Even more, there has been strikingly evidence that, in some of these pathways, signal transduction occurs exclusively through protein-protein interaction, entirely dismissing any mediation by the signal molecule. In order to validate and evaluate the global relevance of this type of mechanism, this study proposed the investigation of the entire network of interactions between proteins typically associated with c-di-GMP signaling pathways of Pseudomonas aeruginosa by employing bacterial two-hybrid system assays. To make that possible, two DNA libraries were constructed and interaction essays were performed in a strategic way so that all possibilities of interaction between target proteins were explored. The results obtained from these experiments allowed the construction of a broad map of interactions that, although still primitive, indicates that, chances are, the mechanisms previously described are both recurrent and relevant to signaling regulation in this organism. Some of the interaction partners found are particularly interesting and will be further investigated in future studies.

L’émergence et la multiplication des infections impliquant des bactéries résistantes et multi-résistantes aux traitements par voie antibiotique sont actuellement un défi majeur dans le domaine de la santé. En effet, la résistance des microorganismes aux molécules antibiotiques est devenue un phénomène de plus en plus préoccupant notamment en milieu hospitalier d’où la nécessité de faire appel à de nouvelles thérapies et à de nouveaux agents antimicrobiens plus efficaces. De nombreux agents antibiotiques classiques ont été développés ces dernières années, mais beaucoup d’entre eux présentent encore des risques d'effets secondaires plus ou moins toxiques sur les cellules eucaryotes, et en dépit de leur efficacité importante contre des microorganismes multi-résistants. Ainsi, les peptides antimicrobiens sont considéré comme de bons candidats dans la lutte contre multi-résistantes microorganismes, principalement en raison de leur faible toxicité sur les cellules eucaryotes et de leurs différents modes d'action par rapport aux antibiotiques classiques. En effet, ces derniers sont généralement non spécifiques et sont moins susceptibles de mener aux phénomènes de résistance observés pour les antibiotiques classiques. L'objectif des travaux menés dans ce mémoire était d'étudier les modes d'action des deux agents antimicrobiens différents; i) la colistine, un polypeptide cyclique déjà utilisé pour traiter les infections causées par des bactéries multi-résistantes et ii) la catestatine bovine (CAT), un peptide linéaire récemment découvert faisant partie de la famille des HDP (Host Defense Peptides), c’est-à-dire produite par le système endocrinien et immunitaire des mammifères. Cette étude a été réalisée principalement à l’aide de différentes méthodes de caractérisation physico-chimique telles que la microscopie à force atomique (AFM) et la spectroscopie infrarouge à transformée de Fourier en réflexion totale atténuée (ATR-FTIR). L'activité de la colistine sur des membranes phospholipidiques pures et mixtes (à base de DPPC, DOPC et DPPE) a été suivie en temps réel et in-situ par ces deux techniques. Les modifications de l'empreinte biochimique des membranes, en particulier au niveau de la bande Amide II et du rapport d'intensité intégré Amide II/C=O nous a permis de renforcer l'hypothèse selon laquelle l'activité du peptide était plus intense sur les membranes mixtes que sur les membranes purs. Des modifications similaires dans l'empreinte biochimique de ces membranes ont été observées quand elles avaient été exposées à la catestatine. En outre, la spectroscopie infrarouge a également mis en évidence des changements conformationnels dans la structure de la catestatine, notamment par le passage d’une structure en pelote dite « random coil » à une structure en hélice alpha, et ce uniquement au contact avec la membrane. De tels changements conformationnels pourraient être impliqués dans l'activité antimicrobienne et le mode d'action de ce peptide. En outre, nous nous sommes également intéressé à l’action des deux peptides sur des membranes phospholipidiques plus complexes puisque constituées principalement d’extraits naturels de lipopolysaccharides bactériens (lipide A, LPS-s et le LPS-re). Nos résultats ont mis en évidence que les deux agents antimicrobiens étaient à l’origine d’une réorganisation de la structure des membranes et dans certains cas, le peptide était à l’origine de la formation des pores de différentes tailles. L'influence de l'élasticité de la membrane a également été étudiée à l’aide de la spectroscopie de force (AFM). Cette étude a mis en évidence un impact considérable des peptides sur les propriétés mécaniques des membranes et en particulier sur leur élasticité. Afin de se rapprocher des conditions réelles d'un traitement antimicrobien, nous avons exposé des biofilms bactériens de E. coli différentes de doses de deux peptides antimicrobiens. [...] / The emergence and multiplication of infections involving resistant and multi-resistant antibiotic-resistant bacteria is currently a major challenge in the field of health. Indeed, the resistance of microorganisms to antibiotic molecules has become an increasingly worrying phenomenon, particularly in hospitals, hence the need for new therapies and new antimicrobial agents that are more effective. Many conventional antibiotic agents have been developed in recent years, but many of them still present risks of more or less toxic side effects on eukaryotic cells, and despite their high effectiveness against multi-resistant microorganisms. Thus, antimicrobial peptides are considered good candidates in the fight against multi-resistant microorganisms, mainly because of their low toxicity to eukaryotic cells and their different modes of action compared to conventional antibiotics. Indeed, the latter are generally non-specific and are less likely to lead to the observed resistance phenomena for conventional antibiotics.The aim of the work carried out in this thesis was to study the modes of action of the two different antimicrobial agents; (I) colistin, a cyclic polypeptide already used to treat infections caused by multi-resistant bacteria; and (ii) bovine catestatin (CAT), a recently discovered linear peptide belonging to the Host Defense Peptides Ie produced by the endocrine and immune system of mammals. This study was carried out mainly using different physico-chemical characterization methods such as Atomic Force Microscopy (AFM) and Fourier Transform Infrared Spectroscopy (ATR-FTIR). The activity of colistin on pure and mixed phospholipid membranes (based on DPPC, DOPC and DPPE) was monitored in real time and in situ by these two techniques. The changes in the biochemical fingerprint of the membranes, in particular in the Amide II band and in the Amide II / C = O integrated intensity ratio allowed us to reinforce the hypothesis that the activity of the peptide was more intense On mixed membranes than on pure membranes. Similar changes in the biochemical footprint of these membranes were observed when they were exposed to catestatin. In addition, infrared spectroscopy has also demonstrated conformational changes in the structure of catestatin, in particular by the passage from a so-called random coil structure to an alpha-helix structure, and only in contact with the structure membrane. Such conformational changes could be implicated in the antimicrobial activity and mode of action of this peptide. In addition, we have also been interested in the action of the two peptides on more complex phospholipid membranes since they consist mainly of natural extracts of bacterial lipopolysaccharides (lipid A, LPS-s and LPS-re). Our results showed that the two antimicrobial agents were responsible for a reorganization of the structure of the membranes and in some cases the peptide was at the origin of the formation of the pores of different sizes. The influence of the elasticity of the membrane has also been studied using force spectroscopy (AFM). This study revealed a considerable impact of the peptides on the mechanical properties of the membranes and in particular on their elasticity. In order to approximate the actual conditions of antimicrobial treatment, we exhibited different bacterial E. coli biofilms from doses of two antimicrobial peptides. This latter study was carried out in real time and in situ using infrared spectroscopy and atomic force microscopy. Infrared spectroscopy allowed us to follow the modifications of the biochemical fingerprint of the biofilm on the course of the treatment. Also provided information on possible changes in bacterial metabolism. In parallel with these measurements, the AFM allowed us to observe the changes in the morphology and mechanical properties of the bacterial biofilm as a function of the antimicrobial treatment applied. [...]

A persistência bacteriana correlacionada à formação de biofilmes bacterianos é, há algum tempo, fonte de grande preocupação médica em virtude de sua ampla associação com a dificuldade de tratamento de infecções crônicas. Por outro lado, as perspectivas de utilização de biofilmes bacterianos em novas aplicações biotecnológicas e até mesmo para fins terapêuticos são promissoras. Há, portanto, grande interesse em compreender os mecanismos que levam as células bacterianas a deixar o estado planctônico, de vida livre, e associarem-se nesses conglomerados celulares altamente complexos. Ao longo das últimas décadas, o segundo mensageiro c-di-GMP – em conjunto com as moléculas que catalisam sua síntese (diguanilato ciclases) e sua degradação (fosfodiesterases) e seus receptores – estabeleceu-se como um elemento central de regulação de uma série de respostas celulares que determinam a formação ou a dispersão de biofilmes. Curiosamente, as proteínas que participam do metabolismo deste segundo mensageiro estão, frequentemente, codificadas múltiplas vezes em um mesmo genoma bacteriano. Em vista dessa observação, estudos mais recentes apontam que, para reger paralelamente uma variedade tão ampla de fenótipos, este sistema opera em modo de alta especificidade de sinalização e que, portanto, o sinal metabolizado por determinados conjuntos de diguanilato ciclases e fosfodiesterases tem alvos celulares específicos. Evidências robustas, porém isoladas até o momento, apontaram que um dos meios pelo qual ocorre a segregação entre sinal produzido e alvo específico é a interação direta entre as proteínas componentes das vias de sinalização. Mais, demonstrou-se que, em algumas vias, a transmissão de sinal ocorre exclusivamente via interação proteica, dispensando a intermediação do sinalizador em si. Para avaliar a validade e relevância global deste mecanismo, propôs-se, neste estudo, a investigação da rede total de interações entre as proteínas tipicamente associadas às vias de sinalização por c-di-GMP em Pseudomonas aeruginosa, utilizando ensaios de duplo-hibrido bacteriano. Para tanto, foram construídas duas bibliotecas de DNA direcionadas e foram feitos testes de interação de forma estratégica para possibilitar o esgotamento e averiguação de todas as possíveis interações entre as proteínas alvo identificadas. O resultado obtido, um mapa inicial, porém abrangente, da rede de interações proteicas em P. aeruginosa, indica uma grande probabilidade de que os mecanismos previamente descritos sejam realmente recorrentes e relevantes para o intermédio da sinalização nesse organismo. Algumas das interações mais robustas encontradas são bastante interessantes e serão, em estudos futuros, mais extensivamente estudadas. / Persister bacteria are correlated to biofilm formation and have been a source of great medical concern due to its close association with the impairment of traditional treatment in combating chronic infections. On the other hand, using bacterial biofilms to create original biotechnological applications or even as a means of therapeutic treatment in medical settings constitutes a promising prospect. There is, therefore, a great interest in understanding the mechanisms that allow bacteria to leave the free-living planktonic lifestyle and associate in these highly complex cellular aggregates. Over the last decades, the second messenger c-di-GMP – and also the molecules involved in its synthesis (diguanylate ciclases) and degradation (phosphodiesterases) along with its receptors – has been established as a key element implicated in regulation of a series of cellular responses that determine biofilm formation or dispersion. Curiously, the proteins that play a part in the metabolism of this second messenger are frequently coded multiple times in single bacterial genomes. Taking this into account, recent studies indicate that, in order to control such a wide range of phenotypes, this system operates via high specificity of signaling – which means that the signal metabolized by a certain set of diguanylate ciclases and phosphodiesterases has specific cellular targets. Robust but yet isolated evidence indicate that a means by which a signal is segregated with its correlated phenotypic response is through direct protein-protein interaction involving the components of these signaling pathways. Even more, there has been strikingly evidence that, in some of these pathways, signal transduction occurs exclusively through protein-protein interaction, entirely dismissing any mediation by the signal molecule. In order to validate and evaluate the global relevance of this type of mechanism, this study proposed the investigation of the entire network of interactions between proteins typically associated with c-di-GMP signaling pathways of Pseudomonas aeruginosa by employing bacterial two-hybrid system assays. To make that possible, two DNA libraries were constructed and interaction essays were performed in a strategic way so that all possibilities of interaction between target proteins were explored. The results obtained from these experiments allowed the construction of a broad map of interactions that, although still primitive, indicates that, chances are, the mechanisms previously described are both recurrent and relevant to signaling regulation in this organism. Some of the interaction partners found are particularly interesting and will be further investigated in future studies.

Non-invasive and continuous spatiotemporal pathogen monitoring at biological interfaces (e.g., human tissue) holds promise for transformative applications in personalized healthcare (e.g., wound infection monitoring) and environmental surveillance (e.g., airborne virus surveillance). Despite notable progress, current receptor-based biosensors encounter inherent limitations, including inadequate long-term performance, restricted spatial resolutions and length scales, and challenges in obtaining multianalyte information. Surface-enhanced Raman spectroscopy (SERS) has emerged as a robust analytical method, merging the molecular specificity of Raman spectroscopy's vibrational fingerprinting with the enhanced detection sensitivity from strong light-matter interaction in plasmonic nanostructures. As a receptor-free and noninvasive detection tool capable of capturing multianalyte chemical information, SERS holds the potential to actualize bio-interfaced spatiotemporal pathogen monitoring. Nonetheless, several challenges must be addressed before practical adoption, including the development of plasmonic bio-interfaces, sensitive capture of multianalyte information from pathogens, regeneration of nanogap hotspots for long-term sensing, and extraction of meaningful information from spatiotemporal SERS datasets. This dissertation tackles these fundamental challenges. Plasmonic bio-interfaces were created using innovative nanoimprint lithography-based scalable nanofabrication methods for reliable bio-interfaced spatiotemporal measurements. These plasmonic bio-interfaces feature sensitive, dense, and uniformly distributed plasmonic transducers (e.g., plasmonic nano dome arrays, optically-coupled plasmonic nanodome and nanohole arrays, self-assembled nanoparticle micro patches) on ultra-flexible and porous platforms (e.g., biomimetic polymeric meshes, textiles). Using these plasmonic bio-interfaces, advancements were made in SERS signal transduction, machine-learning-enabled data analysis, and sensor regeneration. Large-area multianalyte spatiotemporal monitoring of bacterial biofilm components and pH was demonstrated in in-vitro biofilm models, crucial for wound biofilm diagnostics. Additionally, novel approaches for sensitive virus detection were introduced, including monitoring spectral changes during viral infection in living biofilms and direct detection of decomposed viral components. Spatiotemporal SERS datasets were analyzed using unsupervised machine-learning methods to extract biologically relevant spatiotemporal information and supervised machine-learning tools to classify and predict biological outcomes. Finally, a sensor regeneration method based on plasmon-induced nanocavitation was developed to enable long-term continuous detection in protein-rich backgrounds. Through continuous implementation of spatiotemporal SERS signal transduction, machine-learning-enabled data analysis, and sensor regeneration in a closed loop, our solution has the potential to enable spatiotemporal pathogen monitoring at the bio-interface. / Doctor of Philosophy / Continuous monitoring of pathogens within our bodies and surrounding environments is indispensable for various applications in personalized healthcare (e.g., monitoring wound infections) and environmental surveillance (e.g., airborne virus tracking). To accomplish this, we require sensors capable of seamlessly interfacing with biological systems, such as human tissue, and consistently providing pathogen-related information (e.g., spatial location and pathogen type) over prolonged periods. Our research relies on Surface-enhanced Raman spectroscopy (SERS) to address this challenge. SERS enables noninvasive sensing by providing unique fingerprints of molecules near the sensor's surface. SERS holds the potential to enable bio-interfaced spatiotemporal pathogen monitoring, but several challenges must be tackled before practical adoption. In this dissertation, we address various fundamental challenges in SERS, including constructing SERS devices that can seamlessly interface with biological systems while maintaining performance, sensitively capturing pathogen-related information, extracting meaningful insights from SERS datasets, and continuously regenerating the sensor surface to ensure long-term performance. We developed SERS devices capable of seamlessly interfacing with biological systems using innovative scalable nanofabrication methods. These devices contain sensitive, dense, and uniformly distributed SERS sensors on flexible and porous platforms, such as polymeric scaffolds and textiles. Leveraging these SERS devices, we made advancements in pathogen sensing, data analysis, and sensor regeneration. We demonstrated large-area spatiotemporal monitoring of biofilm components and pH in lab-grown biofilm models, critical for wound biofilm diagnostics. Additionally, we introduced novel approaches for sensitive virus detection, including monitoring changes in SERS signals during viral infection in living biofilms and directly detecting decomposed viral components. The SERS datasets were analyzed using machine learning models to extract biologically relevant spatial and temporal information, such as the spatial location of pathogen components and the temporal stage of pathogen growth, and to predict biological outcomes. Finally, we developed a sensor regeneration method to enable long-term continuous detection in complex backgrounds, such as blood. By continuously performing spatiotemporal pathogen sensing, data analysis, and sensor regeneration in a closed loop, our solution has the potential to realize bio-interfaced spatiotemporal pathogen monitoring.

La plupart des bactéries vivent en communautés organisées, appelées biofilms, augmentant leur résistance aux traitements antibiotiques. Ainsi, la formation de biofilms sur les organes et matériels médicaux est considérée comme la cause de la majorité des infections bactériennes. Il est alors important de trouver des traitements pour empêcher ou perturber la formation de ces biofilms. Il a été proposé que les porines de P. Stuartii, Omp-Pst1 et Omp-Pst2, peuvent s’auto-assembler via un steric-zipper, étape responsable du développement initial du biofilm. Ainsi, notre objectif est de synthétiser des inhibiteurs d’interactions entre porines pour limiter ce contact intercellulaire. Nous avons développé des molécules peptidomimétiques basées sur la séquence LGNYR, active dans les deux porines. Pour cela, des réactions de chimie click sur phase solide ont été mises en oeuvre afin de synthétiser des analogues de cette séquence, comme la CuAAC pour introduire un motif triazole, dans une position variable au sein du peptide. Nous avons ainsi développé une méthode rapide et efficace afin de réaliser cette réaction par l’utilisation d’un catalyseur cuivre(I)-N-hétérocyclique carbène stable à l’air. Similairement, de nouvelles conditions ont aussi été mises au point en phase solide afin d’obtenir régiosélectivement des peptides comportant un motif isoxazole 3,4- ou 3,5-disubstitué, par la réaction entre un alcyne et un oxyde de nitrile. Ces cycloadditions 1,3-dipolaires nous ont ainsi permis d’obtenir une première librairie de peptidotriazoles et de peptidoisoxazoles. Il sera enfin possible d’étudier les biofilms grâce à la synthèse de sondes fluorescentes basées sur les inhibiteurs montrant de fortes affinités avec la cible, couplées à un fluorophore dérivé de coumarine. / In the environment, most of bacteria live as organized communities, known as biofilms, enhancing their resistance to antibiotic treatments. Thus the formation of biofilms on organ and indwelling medical devices is considered to cause the majority of bacterial infections in the human body. Thus, to enhance antibiotics efficacy, there is a high need to find treatments to prevent or disrupt biofilm formation. It has been proposed that P. stuartii porins, Omp-Pst1 and Omp-Pst2, can self-associate through a steric zipper, being responsible for the initial development of biofilms. Thus, our objective is to synthesize porin’s self-matching interactions (PSMI) inhibitors to counterfeit this intercellular contact. We developed peptidomimetic molecules based on the LGNYR sequence, that have shown to be active in both porins. Then we used click chemistry to synthesize on solid phase analogues of this sequence, as the solid phase Cu(I)-catalyzed azide-alkyne cycloaddition (CuAAC) to introduce a triazole moiety into the peptide chain at different positions. We thus developed a fast and efficient method to perform this reaction using a stable copper(I)-N-heterocyclic carbene catalyst. Similarly, new conditions were developed on solid phase to synthesize regioselectively peptides containing a 3,4- or 3,5-disubstituted isoxazole moiety, through the reaction between an alkyne and a nitrile oxide. These 1,3-dipolar cycloadditions allowed us to developed a first library of peptidotriazoles and peptidoisoxazoles. We also obtained fluorescent probes based on the inhibitors showing higher affinity for the target as tools to study biofilm formation.

Chapter–I Introduction Shock waves appear in nature whenever the different elements in a fluid approach one another with a velocity larger than the local speed of sound. Shock waves are essentially non-linear waves that propagate at supersonic speeds. Such disturbances occur in steady transonic or supersonic flows, during explosions, earthquakes, tsunamis, lightening strokes and contact surfaces in laboratory devices. Any sudden release of energy (within few μs) will invariably result in the formation of shock wave since it is one of the efficient mechanisms of energy dissipation observed in nature. The dissipation of mechanical, nuclear, chemical, and electrical energy in a limited space will result in the formation of a shock wave. However, it is possible to generate micro-shock waves in laboratory using different methods including controlled explosions. One of the unique features of shock wave propagation in any medium (solid, liquid or gases) is their ability to instantaneously enhance pressure and temperature of the medium. Shock waves have been successfully used for disintegrating kidney stones, non-invasive angiogenic therapy and osteoporosis treatment. In this study, we have generated a novel method to produce micro-shock waves using micro-explosions. Different biological applications were developed by further exploring the physical properties of shock waves. Chapter – II Bacterial transformation using micro-shock waves In bacteria, uptake of DNA occurs naturally by transformation, transduction and conjugation. The most widely used methods for artificial bacterial transformation are procedures based on CaCl2 treatment and electroporation. In this chapter, controlled micro-shock waves were harnessed to develop a unique bacterial transformation method. The conditions have been optimized for the maximum transformation efficiency in E. coli. The highest transformation efficiency achieved (1 × 10-5 transformants per cell) was at least 10 times greater than the previously reported ultrasound mediated transformation (1 × 10-6 transformants per cell). This method has also been successfully employed for the efficient and reproducible transformation of Pseudomonas aeruginosa and Salmonella Typhimurium. This novel method of transformation has been shown to be as efficient as electroporation with the added advantage of better recovery of cells, economical (40 times cheaper than commercial electroporator) and growth-phase independent transformation. Chapter – III Needle-less vaccine delivery using micro-shock waves Utilizing the instantaneous mechanical impulse generated behind the micro-shock wave during controlled explosion, a novel non-intrusive needleless vaccine delivery system has been developed. It is well established, that antigens in the epidermis are efficiently presented by resident Langerhans cells, eliciting the requisite immune response, making them a good target for vaccine delivery. Unfortunately, needle free devices for epidermal delivery have inherent problems from the perspective of patient safety and comfort. The penetration depth of less than 100 µm in the skin can elicit higher immune response without any pain. Here the efficient utilization of the device for micro-shock wave mediated vaccination was demonstrated. Salmonella enterica serovar Typhimurium vaccine strain pmrG-HM-D (DV-STM-07) was delivered using our device in the murine salmonellosis model and the effectiveness of the delivery system for vaccination was compared with other routes of vaccination. The device mediated vaccination elicits better protection as well as IgG response even in lower vaccine dose (ten-fold lesser), compare to other routes of vaccination. Chapter – IV In vitro and in vivo biofilm disruption using shock waves Many of the bacteria secrete highly hydrated framework of extracellular polymer matrix on encountering suitable substrates and get embedded within the matrix to form biofilm. Bacterial colonization in biofilm form is observed in most of the medical devices as well as during infections. Since these bacteria are protected by the polymeric matrix, antibiotic concentration of more than 1000 times of the MIC is required to treat these infections. Active research is being undertaken to develop antibacterial coated medical implants to prevent the formation of biofilm. Here, a novel strategy to treat biofilm colonization in medical devices and infectious conditions by employing shock waves was developed. Micro-shock waves assisted disintegration of Salmonella, Pseudomonas and Staphylococcus biofilm in urinary catheters was demonstrated. The biofilm treated with micro-shock waves became susceptible to antibiotics, whereas the untreated was resistant. Apart from medical devices, the study was extended to Pseudomonas lung infection model in mice. Mice exposed to shock waves responded well to ciprofloxacin while ciprofloxacin alone could not rescue the mice from infection. All the mice survived when antibiotic treatment was provided along with shock wave exposure. These results clearly demonstrate that shock waves can be used along with antibiotic treatment to tackle chronic conditions resulting from biofilm formation in medical devices as well as biological infections. Chapter – V Shock wave responsive drug delivery system for therapeutic application Different systems have been used for more efficient drug delivery as well as targeted delivery. Responsive drug delivery systems have also been developed where different stimuli (pH, temperature, ultrasound etc.) are used to trigger the drug release. In this study, a novel drug delivery system which responds to shock waves was developed. Spermidine and dextran sulfate was used to develop the microcapsules using layer by layer method. Ciprofloxacin was loaded in the capsules and we have used shock waves to release the drug. Only 10% of the drug was released in 24 h at pH 7.4, whereas 20% of the drug was released immediately after the particles were exposed to shock waves. Almost 90% of the drug release was observed when the particles were exposed to shock waves 5 times. Since shock waves can be used to induce angiogenesis and wound healing, Staphylococcus aureus skin infection model was used to show the effectiveness of the delivery system. The results show that shock wave can be used to trigger the drug release and can be used to treat the wound effectively. A brief summary of the studies that does not directly deal with the biological applications of shock waves are included in the Appendix. Different drug delivery systems were developed to check their effect in Salmonella infection as well as cancer. It was shown for the first time that silver nanoparticles interact with serum proteins and hence the antimicrobial properties are affected. In a nutshell, the potential of shock waves was harnessed to develop novel experimental tools/technologies that transcend the traditional boundaries of basic science and engineering.