Alzheimer's disease (AD) is a neurodegenerative disorder that manifests in the form of deficiencies in cognitive processes such as memory and learning. The pathological features of AD include hyperphosphorylated tau proteins that form neurofibrillary tangles as well as senile plaques composed primarily of the peptide β-amyloid (Aβ). When present in high concentrations in the brain, Aβ inhibits certain subtypes of neuronal nicotinic acetylcholine receptors (nAChRs) in the hippocampus. The effects of Aβ in the hippocampus have proven to be neurotoxic, resulting in reduced functionality of nAChRs and the subsequent death of neurons in the cholinergic pathway. The early stages of AD are characterized by reduction of nAChR density and by degeneration of the cholinergic neurons that provide input to the hippocampus. Because the hippocampus plays a critical role in memory formation and other cognitive processes, dysfunction in this brain region results in significant cognitive deficiencies. Understanding the interaction between Aβ and the structurally and functionally diverse nAChR subtypes and possible downstream effects in signaling cascades that might result from that interaction are important steps in comprehending AD pathogenesis. Comprehension of this interaction and factors that might influence it could lead to the development of pharmaceutical agents useful in the treatment of AD.

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Esta tese descreve o desenvolvimento e aplicação de sensores particulados (Parte A) e nanomecânicos (Parte B). Nanopartículas de poliestireno (PS) decoradas com Poli (etileno glicol), PEG, foram sintetizadas e caracterizadas antes e após adsorção do corante vermelho do Congo (VC). Colesterol oxidase (Chox), a principal enzima na oxidação do colesterol, foi imobilizada sobre PS/PEG e PS/PEG/VC para gerar sensores de colesterol. A bioconjugação entre VC e Chox permitiu respostas lineares para dosagem de colesterol HDL presente em amostras de sangue artificial. A lipase, uma hidrolase com larga aplicação científica e industrial, também foi imobilizada sobre PS/PEG e PS/PEG/VC. Os parâmetros cinéticos da hidrólise de p-nitrofenil butirato determinados para lipase livre e lipase imobilizada mostraram que sobre PS/PEG/VC a velocidade máxima de reação (Vmax) e número de renovação (kcat) aumentaram em comparação com os valores determinados para enzima livre. Lipase imobilizada sobre PS/PEG/VC pôde ser reutilizado por até sete vezes, perdendo um máximo de 10% ou 30% da atividade enzimática original a 40 °C ou 25 °C, respectivamente. Estes efeitos foram atribuídos à bioconjugação entre lipase e VC. Os comportamentos catalíticos da lipase e da Chox na ausência e na presença de grafeno (G) ou grafeno oxidado (GO) foram sistematicamente investigados. Na presença de G, ambas enzimas apresentaram valores de Vmax e de kcat superiores aos das enzimas livres. Já na presença de GO, Chox não apresenteou atividade e lipase apresentou Vmax e de kcat superiores aos da enzima livre. Estes resultados foram atribuídos à bioconjugação com as partículas de G e GO e grupos hidrofílicos presentes no plano basal de GO. Sensores nanomecânicos foram desenvolvidos a partir de microcantileveres (MC). Respostas nanomecânicas frente à variação de umidade relativa do meio foram detectadas utilizando filmes finos de Poli (hidroxietil metacrilato), PHEMA, com três diferentes massas molares médias depositados sobre MC de silício puros, um substrato hidrofílico, e sobre MC revestidos com PS, um substrato hidrofóbico. Os resultados demonstraram que as respostas nanomecânicas dependem não só do tamanho de cadeia de PHEMA, mas também da camada de água interfacial entre PHEMA e MC. Transdução nanomecânica foi usada para detectar e dosar a presença do biomarcador antígeno carcinoembrionário (CEA) presente em amostras de soro. CEA é um biomarcador de interesse clínico-diagnóstico para acompanhamento e prognóstico de câncer de cólon. O biomarcador é primeiro reconhecido pelo anticorpo (MAb 3C1) ancorado a uma nanopartícula de ouro, e posteriormente reconhecido pelo anticorpo (MAb 3C6) ancorado em um MC de silício, o qual serve como um ressonador mecânico de massa de nanopartículas de ouro capturadas. O biosensor desenvolvido é capaz de dosar CEA sérico em concentrações traços, correspondente a 1,0 10-16 g ml-1. / This thesis reports the development and application of particulate (Part A) and nanomechanics sensors (Part B). Poly (ethylene glycol), PEG, decorated polystyrene (PS) nanoparticles were synthesized and characterized before and after adsorption of the dye Congo red (CR). Cholesterol oxidase (Chox), the key enzyme in the oxidation of cholesterol, was immobilized onto PS/PEG and PS/PEG/CR particles for generating cholesterol sensors. The bioconjugation between CR and Chox allowed linear responses for HDL cholesterol content in artificial blood samples. Lipase, a hydrolase with large scientific and industrial applications, was also immobilized onto PS/PEG and PS/PEG/VC nanoparticles. The kinetic parameters of the hydrolysis of p-nitrophenyl butyrate were determined for free lipase and immobilized onto PS/PEG/CR particles. The results showed that maximum reaction velocity (Vmax) and catalytic efficiency (kcat) increased compared to the values determined for the free enzyme. Lipase immobilized onto PS/PEG/CR particles could be recycled seven times, losing maximum 10% or 30% of the original enzymatic activity at 40 °C or 25 °C, respectively. These effects were attributed to bioconjugation between lipase and CR. Catalytic behavior of lipase and Chox in the absence and in the presence of graphene (G) or graphene oxide (GO) was systematically investigated. In the presence of G, both enzymes showed Vmax and kcat values higher than free enzymes. On the other hand, ChOx was inactive and the interactions between GO and lipase showed Vmax and kcat values higher than those of the free enzyme. These results were attributed to bioconjugation of G and GO particles and hydrophilic groups present in the basal plane of GO. Nanomechanical sensors were developed from microcantilevers (MC). Nanomechanical answers against the relative humidity variation of the medium were detected using thin films of poly (hydroxyethyl methacrylate), PHEMA, with three different average molecular masses deposid onto bare silicon microcantilevers, a hydrophilic substrate, and onto polystyrene (PS) coated microcantilevers, which is a hydrophobic substrate. The results found in the present study demonstrate that the micromechanical responses observed are related not only to the polymer molecular weight, but also to the polymer-interface phenomena and environment-polymer interface. Nanomechanics transductions were used to dose and detect the presence of carcinoembryonic antigen in serum samples. CEA is a biomarker of clinical diagnostic interest for monitoring and prognose of colon cancer. Biomarker is first recognized by a surface-anchored antibody to a gold nanoparticle (MAB 3C1) and later recognized by a surface-anchored antibody to a silicon MC (MAB 3C6), that acts as a mechanical resonator for \'weighing\' the mass of the captured nanoparticles. The biosensor developed is able to dose serum CEA in trace concentrations, corresponding to 1.0 10-16 g ml-1.

Esta tese descreve o desenvolvimento e aplicação de sensores particulados (Parte A) e nanomecânicos (Parte B). Nanopartículas de poliestireno (PS) decoradas com Poli (etileno glicol), PEG, foram sintetizadas e caracterizadas antes e após adsorção do corante vermelho do Congo (VC). Colesterol oxidase (Chox), a principal enzima na oxidação do colesterol, foi imobilizada sobre PS/PEG e PS/PEG/VC para gerar sensores de colesterol. A bioconjugação entre VC e Chox permitiu respostas lineares para dosagem de colesterol HDL presente em amostras de sangue artificial. A lipase, uma hidrolase com larga aplicação científica e industrial, também foi imobilizada sobre PS/PEG e PS/PEG/VC. Os parâmetros cinéticos da hidrólise de p-nitrofenil butirato determinados para lipase livre e lipase imobilizada mostraram que sobre PS/PEG/VC a velocidade máxima de reação (Vmax) e número de renovação (kcat) aumentaram em comparação com os valores determinados para enzima livre. Lipase imobilizada sobre PS/PEG/VC pôde ser reutilizado por até sete vezes, perdendo um máximo de 10% ou 30% da atividade enzimática original a 40 °C ou 25 °C, respectivamente. Estes efeitos foram atribuídos à bioconjugação entre lipase e VC. Os comportamentos catalíticos da lipase e da Chox na ausência e na presença de grafeno (G) ou grafeno oxidado (GO) foram sistematicamente investigados. Na presença de G, ambas enzimas apresentaram valores de Vmax e de kcat superiores aos das enzimas livres. Já na presença de GO, Chox não apresenteou atividade e lipase apresentou Vmax e de kcat superiores aos da enzima livre. Estes resultados foram atribuídos à bioconjugação com as partículas de G e GO e grupos hidrofílicos presentes no plano basal de GO. Sensores nanomecânicos foram desenvolvidos a partir de microcantileveres (MC). Respostas nanomecânicas frente à variação de umidade relativa do meio foram detectadas utilizando filmes finos de Poli (hidroxietil metacrilato), PHEMA, com três diferentes massas molares médias depositados sobre MC de silício puros, um substrato hidrofílico, e sobre MC revestidos com PS, um substrato hidrofóbico. Os resultados demonstraram que as respostas nanomecânicas dependem não só do tamanho de cadeia de PHEMA, mas também da camada de água interfacial entre PHEMA e MC. Transdução nanomecânica foi usada para detectar e dosar a presença do biomarcador antígeno carcinoembrionário (CEA) presente em amostras de soro. CEA é um biomarcador de interesse clínico-diagnóstico para acompanhamento e prognóstico de câncer de cólon. O biomarcador é primeiro reconhecido pelo anticorpo (MAb 3C1) ancorado a uma nanopartícula de ouro, e posteriormente reconhecido pelo anticorpo (MAb 3C6) ancorado em um MC de silício, o qual serve como um ressonador mecânico de massa de nanopartículas de ouro capturadas. O biosensor desenvolvido é capaz de dosar CEA sérico em concentrações traços, correspondente a 1,0 10-16 g ml-1. / This thesis reports the development and application of particulate (Part A) and nanomechanics sensors (Part B). Poly (ethylene glycol), PEG, decorated polystyrene (PS) nanoparticles were synthesized and characterized before and after adsorption of the dye Congo red (CR). Cholesterol oxidase (Chox), the key enzyme in the oxidation of cholesterol, was immobilized onto PS/PEG and PS/PEG/CR particles for generating cholesterol sensors. The bioconjugation between CR and Chox allowed linear responses for HDL cholesterol content in artificial blood samples. Lipase, a hydrolase with large scientific and industrial applications, was also immobilized onto PS/PEG and PS/PEG/VC nanoparticles. The kinetic parameters of the hydrolysis of p-nitrophenyl butyrate were determined for free lipase and immobilized onto PS/PEG/CR particles. The results showed that maximum reaction velocity (Vmax) and catalytic efficiency (kcat) increased compared to the values determined for the free enzyme. Lipase immobilized onto PS/PEG/CR particles could be recycled seven times, losing maximum 10% or 30% of the original enzymatic activity at 40 °C or 25 °C, respectively. These effects were attributed to bioconjugation between lipase and CR. Catalytic behavior of lipase and Chox in the absence and in the presence of graphene (G) or graphene oxide (GO) was systematically investigated. In the presence of G, both enzymes showed Vmax and kcat values higher than free enzymes. On the other hand, ChOx was inactive and the interactions between GO and lipase showed Vmax and kcat values higher than those of the free enzyme. These results were attributed to bioconjugation of G and GO particles and hydrophilic groups present in the basal plane of GO. Nanomechanical sensors were developed from microcantilevers (MC). Nanomechanical answers against the relative humidity variation of the medium were detected using thin films of poly (hydroxyethyl methacrylate), PHEMA, with three different average molecular masses deposid onto bare silicon microcantilevers, a hydrophilic substrate, and onto polystyrene (PS) coated microcantilevers, which is a hydrophobic substrate. The results found in the present study demonstrate that the micromechanical responses observed are related not only to the polymer molecular weight, but also to the polymer-interface phenomena and environment-polymer interface. Nanomechanics transductions were used to dose and detect the presence of carcinoembryonic antigen in serum samples. CEA is a biomarker of clinical diagnostic interest for monitoring and prognose of colon cancer. Biomarker is first recognized by a surface-anchored antibody to a gold nanoparticle (MAB 3C1) and later recognized by a surface-anchored antibody to a silicon MC (MAB 3C6), that acts as a mechanical resonator for \'weighing\' the mass of the captured nanoparticles. The biosensor developed is able to dose serum CEA in trace concentrations, corresponding to 1.0 10-16 g ml-1.

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Atenciosamente, Biblioteca Campus Rio Claro Repositório Institucional UNESP on 2018-04-05T13:45:30Z (GMT) / Submitted by Felipe Lange Shimizu null (felipe_lash@hotmail.com) on 2018-04-05T13:57:48Z No. of bitstreams: 1 Dissertação Final Biblioteca.pdf: 2476461 bytes, checksum: 98bb493283b6d060e268893b026507a0 (MD5) / Approved for entry into archive by Adriana Aparecida Puerta null (dripuerta@rc.unesp.br) on 2018-04-05T17:46:11Z (GMT) No. of bitstreams: 1 shimizu_fl_me_rcla.pdf: 2148045 bytes, checksum: 5ae73bad5319cc903eba26a7980c267c (MD5) / Made available in DSpace on 2018-04-05T17:46:11Z (GMT). No. of bitstreams: 1 shimizu_fl_me_rcla.pdf: 2148045 bytes, checksum: 5ae73bad5319cc903eba26a7980c267c (MD5) Previous issue date: 2018-02-26 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / A biomassa lignocelulósica, como a proveniente da cana-de-açúcar, é uma fonte abundante de resíduo que pode ser usado como matéria-prima na produção de energia. Para melhor aproveitar essa biomassa, moagem e pré-tratamentos podem ser usados para alterar a estrutura do material lignocelulósico, remover lignina e hemicelulose, expondo a celulose e assim aumentando sua acessibilidade. A acessibilidade à celulose tem sido indicada como uma das propriedades mais importantes para uma boa digestibilidade enzimática. Entretanto, as biomassas geradas da cana-de-açúcar possuem características físico-químicas diferentes, respondendo de modo diferente aos pré-tratamentos. Neste contexto, este estudo teve como objetivo verificar os efeitos da remoção de lignina e hemicelulose das biomassas da cana-de-açúcar (fração externa, entrenó, nó e folha) na acessibilidade à celulose. A cana-de-açúcar foi fracionada em fração externa, nó, entrenó e folha. Cada fração passou pelos pré-tratamentos ácido (5, 10, 20 %, m/m massa de ácido por massa de material, a 121°C/30 min), alcalino (5, 10, 20 e 30 % NaOH m/m) e oxidativo (0,5, 1, 2 e 3 horas com clorito de sódio 30 %). As amostras foram caracterizadas quanto ao seu conteúdo de celulose, hemicelulose e lignina. A determinação de acessibilidade foi realizada com corantes Direct, Orange (superfície específica externa), Direct Blue (superfície específica interna) e Vermelho Congo (superfície total). A hidrólise enzimática (15 FPU/g de material, Cellic Ctec 2 - Novozymes) foi realizada para avaliar o efeito dos pré-tratamentos e acessibilidade à celulose no rendimento em glicose. O efeito dos pré-tratamentos foi primeiramente analisado pela quantidade de massa recuperada. Todas as frações estudadas apresentaram uma tendência em perder massa com aumento da concentração de reagente utilizado no pré-tratamento. O pré-tratamento ácido resultou em menor recuperação de massa, o que ocorreu em função da solubilização de hemicelulose. A caracterização química apontou a remoção de hemicelulose e principalmente lignina dos materiais em função do pré-tratamento e das suas condições. A deslignificação com clorito de sódio (oxidativo) resultou em remoção de lignina, chegando a quase a sua totalidade em materiais como a folha. A determinação de acessibilidade com os corantes Vermelho Congo, Direct Blue e Direct Orange indicaram que o aumento da concentração de reagentes no pré-tratamento provoca aumento de acessibilidade à celulose. Entretanto, os corantes Direct Orange e Blue foram mais precisos na determinação da acessibilidade à celulose em comparação ao Vermelho Congo. A fração de menor recalcitrância, entrenó, apresentou adsorção de 525,9 mg/g no ensaio com Vermelho congo, o Direct Orange 1333,3 mg/g e o Direct Blue 746,3 mg/g. O rendimento em glicose na hidrólise enzimática seguiu a tendência de melhora com aumento da acessibilidade. Do mesmo modo, a remoção de lignina resultou em maior rendimento em glicose na hidrólise enzimática, o entrenó deslignificado resultou na quase completa conversão da celulose em glicose. Este estudo identificou a fração externa como mais recalcitrante, e entrenó como menos recalcitrante, resultando em menor rendimento e maior de glicose na hidrólise enzimática, respectivamente. A remoção de hemicelulose e lignina por meio de pré-tratamentos influenciou diretamente na acessibilidade à celulose, resultando em melhor ação das enzimas na hidrólise enzimática de todas as frações. / The lignocellulosic biomass, such as the provided by the sugarcane, is an abundant source of raw materials for energy production. In order to better use this biomass, milling and pretreatments can be employed to alter the structure of the materials, remove lignin and hemicellulose. This effect exposes the cellulose and raises its accessibility, which is is one of the most important property to ensure enzymatic digestibility. However, the biomass generated from the sugarcane have different physicochemical characteristics, giving different responses to the pretreatments. In this context, this study aimed to verify the effects of lignin and hemicellulose removal from the sugarcane biomass (external fraction, node, internode and leaf) on cellulose accessibility. The sugarcane was fractioned in external fraction, node, internode and leaf. Each fraction was pretreated with acid (5, 10, 20 % m/m acid mass per material mass, at 121°C/30 min), alkaline (5, 10, 20, 30 % NaOH m/m) oxidative (0,5, 1, 2 ,3 h charged with 30 % sodium chlorite). The chemical composition of the samples was determined based on cellulose, hemicellulose and lignin contents. Accessibility was determined by dye adsorption of Direct Orange (external specific surface), Direct Blue (internal specific surface) and Congo Red (total surface). Enzymatic hydrolysis (15 FPU/g of biomass, Cellic Ctec 2 – Novozymes) was used to verify the effects of pretreatments and cellulose accessibility on the glucose yield. All studied fractions showed tendency to lose mass with increasing reagent concentrations used in the pretreatments. Acid pretreatment resulted in low mass recovery due to hemicellulose solubilization. Chemical composition showed hemicellulose removal and significant lignin removal from the materials due to the pretreatments and their conditions. Delignification by sodium chlorite (oxidative) resulted in lignin removal, with almost completely removal with leaf samples. Accessibility determined by Congo Red, Direct Orange and Direct Blue dyes indicated that more aggressive pretreatments improved cellulose accessibility. However, Direct Orange and Direct Blue dyes were more precise than Congo Red while evaluating cellulose accessibility. The less recalcitrant fraction, the internode, showed 525,9 mg/g of Congo Red adsorption, 1333,3 mg/g of Direct Orange and 746,3 mg/g of Direct Blue. Glucose yield during enzymatic hydrolysis improved with higher cellulose accessibility. Lignin removal resulted in higher glucose yield, with delignified internode samples showing almost complete cellulose conversion. This study identified the external fraction as the most recalcitrant and the internode as the least recalcitrant, resulting in lower glucose yield and higher glucose yield, respectively. Hemicellulose and lignin removal by the pretreatments directly influenced cellulose accessibility, resulting in better enzymatic activity across all fractions.

Conselho Nacional de Desenvolvimento CientÃfico e TecnolÃgico / A espÃcie Aspergillus niger AN 400 foi inoculada em reatores em batelada com o objetivo de remover corante vermelho do congo de meio sintÃtico e estudar a eficiÃncia do tratamento na presenÃa e ausÃncia de glicose e o efeito da imobilizaÃÃo da biomassa sobre a otimizaÃÃo do processo. Foram utilizados 84 reatores, confeccionados em vidro e vedados com tampa rosqueÃvel, e com volume Ãtil de 1,5 L, sendo o ar fornecido por mini-compressores de ar. O experimento abrangeu perÃodo de 25 dias e os reatores foram agrupados de acordo com sua respectiva funÃÃo em: 14 reatores de controle sem meio suporte; 14 reatores de controle com meio suporte; 14 reatores com biomassa fÃngica dispersa; 14 reatores com biomassa fÃngica dispersa e adiÃÃo de 1 g/L de glicose; 14 reatores com biomassa imobilizada e 14 reatores com biomassa imobilizada e adiÃÃo de 1 g/L de glicose. Os resultados obtidos mostraram que a maior eficiÃncia de remoÃÃo do corante ocorreu nos reatores contendo biomassa imobilizada, com meio com glicose (87%) e meio sem glicose (85%). A glicose, na concentraÃÃo utilizada, nÃo influenciou na eficiÃncia do processo. A remoÃÃo de matÃria orgÃnica, em termos de DQO, nÃo acompanhou a remoÃÃo do corante, o que foi atribuÃdo à provÃvel presenÃa de subprodutos da degradaÃÃo do corante e compostos excretados no meio pelos microrganismos. A imobilizaÃÃo da biomassa nas espumas de poliuretano foi determinante para a eficiÃncia do processo, uma vez que os fungos estavam estabelecidos na forma de biofilme, representando um mecanismo contra o efeito tÃxico do poluente. / The species Aspergillus niger AN 400 has been inoculated in batch in order to remove Congo Red dye from the synthetic environment and study the treatment efficiency in the presence and absence of glucose and the biomass immobilization effect on the process optimization. It has been applied 84 reactors, produced and held in a screw top container of glass, which had a useful capacity of 1,5 L, whilst the air was supplied by small compressors. The experiment lasted a period of 25 days and the reactors without support medium; 14 control reactors with dispersed fungal biomass on which was added glucose (1 g/L); 14 reactors with immobilized fungal biomass and 14 reactors with immobilized fungal biomass on which was added glucose (1 g/L). The results obtained demonstrated that the greatest efficiency in removing the dye occurred in the reactors containing immobilized biomass in a environment with glucose concentration (87%) or not (85%). The glucose considering the utilized concentration has not performed any influence on the process efficiency. The organic matter removal which was assigned to the likely presence of by products originated by the dye and compounds expelled in the environment by microorganisms. The immobilization of the biomass in the polyurethane foams was determinant to the process efficiency as fungus was in a biofilm shape, representing a mechanism against the toxic effect of the pollutant.

CoordenaÃÃo de AperfeiÃoamento de Pessoal de NÃvel Superior / Historicamente, as bactÃrias foram vistas como organismos que vivem isolados, no entanto, à claro, agora, que a grande maioria de bactÃrias existe em comunidades complexas, conhecidas como biofilmes. As bactÃrias em biofilmes se encontram aderidas a superfÃcies diversas, tanto abiÃticas como biÃticas (dente, osso, mucosa), compondo um ecossistema altamente estruturado, dinÃmico e organizado. Um exemplo de infecÃÃo que pode envolver a presenÃa formaÃÃo de biofilme à a otite - definida como inflamaÃÃo aguda ou crÃnica da orelha, podendo se estender desde o epitÃlio do conduto auditivo externo atà a orelha interna. Descrita como a doenÃa mais comum do canal auditivo externo em cÃes, possui uma etiologia multifatorial, que inclui fungos e bactÃrias, principalmente do gÃnero Staphylococcus. BactÃrias desse gÃnero sÃo comensais de pele e mucosas, mas podem atuar como patÃgenos oportunistas em condiÃÃes propÃcias e sÃo frequentemente associadas a uma ampla variedade de infecÃÃes em seres humanos e animais com vÃrios relatos de refratariedade aos tratamentos usuais. Em um biofilme, as bactÃrias podem ser dezenas de vezes mais resistentes aos antibiÃticos, quando comparadas Ãs mesmas bactÃrias em crescimento planctÃnico. O combate a infecÃÃes envolvendo bactÃrias em biofilme à um grande desafio da microbiologia mundial, que leva à busca de novas opÃÃes terapÃuticas. Com efeito, este estudo teve como objetivo avaliar o efeito inibitÃrio in vitro de seis substÃncias â trÃs agentes antimicrobianos clÃssicos, ciprofloxacina, cloranfenicol, gentamicina; e trÃs agentes antimicrobianos nÃo-clÃssicos timol, carvacrol, perÃxido de hidrogÃnio (H2O2) â contra cepas estafilocÃcicas de otite canina em crescimento planctÃnico e em biofilme. Foram avaliadas 54 cepas clÃnicas isoladas de secreÃÃo purulenta de cÃes com otite, divididas entre cinco espÃcies: S. intermedius, S. simulans, S. haemolyticus, S. epidermidis e S. lugdunensis. As 16 cepas classificadas como produtoras de biofilme (11 de S. intermedius e cinco de S. simulans), segundo resultado obtido pelo teste do Ãgar vermelho Congo e confirmaÃÃo por microscopia eletrÃnica de varredura (MEV), foram usadas em ensaios de microdiluiÃÃo em caldo para determinaÃÃo de concentraÃÃo inibitÃria mÃnima (CIM) e concentraÃÃo inibitÃria mÃnima em biofilme (CIMB). Com relaÃÃo Ãs cepas produtoras de biofilme, foram observados os seguintes resultados: os valores para ciprofloxacina foram 0,12 ≤CIM≤0,5 mcg/mL (mÃdia 0,28 mcg/mL) e 0,5≤CIMB≤8 mcg/mL (mÃdia 1,79 mcg/mL); para cloranfenicol 2≤CIM≤16 mcg/mL (mÃdia 7,41 mcg/mL) e 8≤CIMB≤32 mcg/mL (mÃdia 20,71 mcg/mL); para gentamicina 0,5≤CIM≤4 mcg/mL (mÃdia 2,09 mcg/mL) e 4≤CIMB≤64 mcg/mL (mÃdia 24,24 mcg/mL); para timol 32≤CIM≤512 mcg/mL (mÃdia 137,41 mcg/mL) e 256≤CIMB≤2048 mcg/mL (mÃdia 768 mcg/mL); carvacrol 32≤CIM≤512 mcg/mL (mÃdia 128 mcg/mL) e 256≤CIMB≤4096 mcg/mL (mÃdia 993,88 mcg/mL); e para H2O2 32≤CIM≤128 ppm (mÃdia 99,76 ppm) e 128≤CIMB≤4096 ppm (mÃdia 1874,82 ppm). Os dados obtidos apontam para o potencial terapÃutico dos seis antibiÃticos estudados no tratamento de infecÃÃes estafilocÃcicas associadas a biofilme, sendo necessÃrios novos estudos para investigar os mecanismos de aÃÃo dessas drogas sobre o biofilme, bem como o delineamento de experimentos in vivo para confirmar a significÃncia desses achados. / Historically, bacteria have been seen as isolated organisms; however, it is now clear that the vast majority of bacteria exist in complex communities known as biofilms. Bacteria in biofilms are adhered to various surfaces, both abiotic and biotic (teeth, bones, mucosa), often forming a highly dynamic ecosystem, which is structured and organized. An example of infection, which can involve the formation of biofilm is otitis - defined as an acute or chronic inflammation of the ear, which may extend from the external ear canal to the inner ear. Described as the most common disease of the external ear canal in dogs, it has a multifactorial etiology, including fungi and bacteria, especially of the genus Staphylococcus. Bacteria of this genus are commensal to skin and mucous membranes, but can act as opportunistic pathogens in favorable conditions and are often associated with a wide variety of infections in humans and animals with many reports of refractoriness to usual treatments. In biofilm, bacteria can be ten to a hundred times more resistant to antibiotics when compared to the same bacteria in planktonic growth. The struggle to fight infections involving bacterial biofilms is a major challenge of microbiology today, which, in turn, leads to the search for new therapeutic options. Thus, this study aimed to evaluate the in vitro inhibitory effect of six substances â three classic antimicrobial agents ciprofloxacin, chloramphenicol, gentamicin; and three non-classic antimicrobial agents thymol, carvacrol, hydrogen peroxide (H2O2) - against staphylococcal strains from canine otitis in planktonic growth and in biofilm. We analyzed 54 clinical strains isolated from purulent secretion of canine otitis, divided into five species: S. intermedius, S. simulans, S. haemolyticus, S.epidermidis and S. lugdunensis. The 16 strains classified as biofilm producers (11 S. intermedius and five S. simulans), according to result obtained by the Congo red agar test and confirmed by scanning electron microscopy (SEM), were used in broth microdilution assay for determination of minimum inhibitory concentration (MIC) and minimum biofilm inhibitory concentration (MBIC). With regards to the biofilm-producing strains, the following results were observed: the values for ciprofloxacin were 0,12 ≤MIC≤0,5 mcg/mL (mean 0,28 mcg/mL) and 0,5≤MBIC≤8 mcg/mL (mean 1,79 mcg/mL); for chloramphenicol 2≤MIC≤16 mcg/mL (mean 7,41 mcg/mL) and 8≤MBIC≤32 mcg/mL (mean 20,71 mcg/mL); for gentamicin 0,5≤MIC≤4 mcg/mL (mean 2,09 mcg/mL) and 4≤MBIC≤64 mcg/mL (mean 24,24 mcg/mL); for thymol 32≤MIC≤512 mcg/mL (mean 137,41 mcg/mL) and 256≤MBIC≤2048 mcg/mL (mean 768 mcg/mL); carvacrol 32≤MIC≤512 mcg/mL (mean 128 mcg/mL) and 256≤MBIC≤4096 mcg/mL (mean 993,88 mcg/mL); and for H2O2 for 32≤MIC≤128 mcg/mL (mean 99,76 ppm) and 128≤MBIC≤4096 ppm (mean 1874,82 ppm). The presented data indicates the therapeutic potential of the six antibiotics studied in the treatment of staphylococcal infections associated with biofilm, which warrants further studies to investigate the mechanisms of action of these drugs on biofilms and the design of in vivo experiments to confirm the significance of these findings.

Ansamling av amyloid beta (Aβ) i de extracellulära miljöerna är associerad till många svåra sjukdomar som Alzheimers och ålders-relaterad makuladegeneration (AMD). Amyloider karaktäriseras av att de är olösliga, toxiska mot neuron och orsakar därför svår skada. AMD är den ledande orsaken till blindhet och irreversibelt förlorande av skarp syn då Aβ manifesterar i makula. I AMD orsakar Aβ inflammatorisk aktivitet där det retinala pigmentepitelet bryts ned och ljuskänsliga fotoreceptorer dör genom apoptos. Idag lever ca 150 miljoner människor med AMD där mänga har svårt att utföra vardagliga uppgifter till följd av förlust av skarp syn. Idag är Kongo röd en av de vanligaste metoderna för att visualisera amyloider in vitro. Den patogenes som orsakas av amyloider kan analyseras med immunofluorescens och immunohistokemi. Syftet med studien var att undersöka förekomst av amyloider i samband med celldöd i näthinna från gris, undersöka den patogenes som amyloider orsakar med immunofluorescens och immunohistokemi, samt undersöka om det finns korrelation mellan amyloider och celldöd. Resultatet visade att amyloider var förekommande i näthinnan och hade orsakat celldöd och ansamling av aggresomer. Amyloider och den patologi som orsakats kunde visualiseras i det yttre lagret av näthinnan. / Deposition of amyloid beta (Aβ) in the extracellular environment are associated to some severe diseases, like Alzheimer’s disease and age-related macular degeneration (AMD). Amyloids are characterized by insolubility, toxicity towards neuron and are there-for damaging to tissues. AMD is the primary cause of blindness and irreversible loss of central vision through manifestation of Aβ in the macula. In AMD, Aβ drives an inflammatory action that degenerates the retinal pigment epithelium and cause atrophy of photoreceptors. Today ~150 million people live with AMD where many find difficulties performing everyday tasks due to loss of sharp vision. Congo red is a gold standard for visualizing amyloids in vitro and the pathogenesis caused by amyloids can be analyzed by immunofluorescence and immunohistochemistry. The purpose of this study was to show the presence of amyloids relating to cell death in pig retina, show the pathogenesis caused by amyloids by using immunofluorescence and immunohistochemistry, and investigate whether there is correlation between amyloids and cell death. The result showed that amyloids were present in the retina and caused cell death and gathering of aggresomes. Amyloids and the caused pathology could be visualized in the outer layer of the retina.

Alzheimer’s disease is an incurable neurodegenerative disorder linked to the amyloid β (Aβ) peptide, a 38-43 residue peptide. The detailed molecular disease mechanism(s) is (are) unknown, but oligomeric Aβ structures are proposed to be involved. In common for the papers in this thesis is interactions; interactions between Aβ(1-40) and selected molecules and metal ions. The purpose has been to find out more about the structural states that Aβ can adopt, in particular the β-sheet state, which probably is linked to the oligomeric structures. The methods used have been nuclear magnetic resonance (NMR), circular dichroism (CD) and fluorescence spectroscopy using Thioflavin T (ThT). Upon addition of SDS/LiDS detergent or Congo red (CR) to Aβ(1-40), the initial random coil/PII-helix state was transformed into β-sheet and, in the case of detergent, a final α-helical state. In contrast to SDS/LiDS and CR, the dimeric Affibody molecule locks monomeric Aβ(1-40) in a β-hairpin state. It was found that by truncating the flexible N-terminal end of the Affibody molecule its affinity to Aβ was improved. The aggregation of Aβ(1-40) was further studied in the presence of a β-cyclodextrin dimer by a kinetic assay using ThT. Although having a weak dissociation constant in the millimolar range, the β-cyclodextrin dimer modified the aggregation pathways of Aβ. Finally Aβ(1-40) was studied in presence of Cu2+ and Zn2+ at physiological and low pH. Cu2+ was observed to maintain its specific binding to Aβ when decreasing the pH to 5.5 while Zn2+ behaved differently. This could be of importance in the Alzheimer’s disease brain in which the environment can become acidic due to inflammation.        In conclusion the results show that Aβ(1-40) is very sensitive to its environment, responding by adopting different conformations and aggregating in aqueous solutions. The β-sheet state is induced by varying molecules with different properties, properties that govern the final Aβ state. / At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 4: Manuscript. Paper 5: Manuscript.

Protein (mis)folding into highly ordered, fibrillar structures, amyloid fibrils, is a hallmark of several, mainly neurodegenerative, disorders. The mechanism of this supra-molecular self-assembly reaction, as well as its relationship to protein folding are not well understood. In particular, the molecular origin of the metastability of the soluble state of proteins with respect to the aggregated states has not been clearly established. In this dissertation, it is demonstrated, that highly accurate kinetic experiments, using a novel biosensing method, can yield fundamental insight into the dynamics of proteins in the region of the free energy landscape corresponding to protein aggregation. First, a section on Method development describes the extension and elaboration of the previously established kinetic assay relying on quartz crystal microbalance measurements for the study of amyloid fibril elongation (Chapter 3). This methodology is then applied in order to study in great detail the origin of the various contributions to the free energy barriers separating the soluble state of a protein from its aggregated state. In particular, the relative importance of residual structure, hydrophobicity (Chapter 4) and electrostatic interactions (Chapter 5) for the total free energy of activation are discussed. In the last part of this thesis (Chapter 6), it is demonstrated that this biosensing method can also be used to study the binding of small molecules to amyloid fibrils, a very useful feature in the framework of the quest for potential inhibitors of amyloid formation. In addition, it is shown that Thioflavin T, to-date the most frequently employed fluorescent label molecule for bulk solution kinetic studies, can in the presence of potential amyloid inhibitor candidates be highly unreliable as a means to quantify the effect of the inhibitor on amyloid formation kinetics. In summary, the work in this thesis contributes to both the fundamental and the applied aspects of the field of protein aggregation.