As piodermites, superficiais ou profundas, representam uma das dermatopatias caninas mais comuns no cotidiano da clínica dermatológica de cães. Dentre as classificadas como superficiais, destacam-se a foliculite bacteriana e a piodermite esfoliativa ou superficial disseminada, que representam a grande maioria dos casos. Em alguns cães, as piodermites superficiais são idiopáticas, apresentam evolução crônica e caráter recidivante. A despeito de criteriosa investigação acerca de sua possível etiologia, por vezes, não se consegue evidenciar a causa para a instalação e recorrência do quadro mórbido. Tais animais apresentam frequentes recidivas, em variáveis períodos de tempo, após o término da terapia antibiótica. Para estes caninos, na bibliografia médico-veterinária há recomendação de emprego das controvertidas imunoterapia ou de antibioticoterapia sob a forma de pulsos. Portanto, objetivou-se na casuística do Serviço de Dermatologia do Hospital Veterinário da USP, determinar as principais espécies bacterianas envolvidas, a susceptibilidade destas frente a diferentes antimicrobianos, bactericidas ou bacteriostáticos, assim como, comparar a eficácia e a segurança de três distintos protocolos terapêuticos no manejo a longo prazo, de piodermites superficiais recidivantes idiopáticas. Utilizaram-se 23 animais, de quaisquer dos sexos, de distintas raças e faixas etárias. A amostragem foi aleatoriamente disposta em três grupos de experimentação (GI, GII, G III), respectivamente submetidos à imunoterapia com bacterina comercial (Estafilin®) e às pulsoterapias de \"finais de semana\" ou em \"semanas alternadas\", empregando-se cefalexina \"per os\". O principal patógeno, em 67,6 % da totalidade de isolamentos bacterianos, foi Staphylococcus intermedius. Evidenciou-se (32,4 %), ainda, as espécies S. hyicus, S. schleiferi subespécie coagulans, S. warneri e Micrococcus sp. Segundo os antibiogramas, os fármacos mais efetivos in vitro foram a amoxicilina associada ao clavulanato de potássio, a cefalexina e o ceftiofur. Verificou-se resposta plena em percentis de, respectivamente, 50,0 %, 33,3 % e 28,6 % nos Grupos II, III e I; destarte, ao se agrupar as respostas plena e moderada evidenciaram-se valores relativos de, respectivamente, 83,3 %, 50,0 % e 42,9 %. À luz da estatística (Teste do Qui Quadrado), não se observaram quaisquer diferenças estatisticamente significativas (p > 0,05) entre os percentuais de resposta aos três protocolos empregados. Todos eles mostraram-se seguros, sem acarretar efeitos adversos farmacodérmicos. / Superficial and deep pyodermas are common canine skin disorders in the small animal dermatology practice. Among the superficial form, the bacterial folliculitis and superficial spreading pyoderma represent the great majority of cases. Some dogs are affected by idiopathic, chronic and recurrent type of superficial pyoderma. Despite a rigorous search for possible reasons for its etiology, sometimes it is not possible to determine an underlying cause for the disease recurrence. At variable time periods, these dogs show frequent recurrent episodes, after the interruption of antibiotic therapy. For these patients, the veterinary medicine literature recommends the use of the controversial immune therapy or antibiotic pulse therapy. Thus, using the University of Sao Paulo / Dermatology Service\'s casuistry the present study aimed to determine the major bacterial species responsible for pyodermas, their susceptibility to several bactericidal and bacteriostatic antibiotics as well as compare the efficacy and safety of three different therapeutics protocols for the long term management of idiopathic recurrent superficial pyoderma. A total of 23 male and female, purebred dogs from different ages were randomly allocated in three distinct experimental groups (G I, G II and G III), respectively treated with bacterin immune therapy, \"weekend\" antibiotic pulse therapy and \"week on - week off\" antibiotic pulse therapy, receiving cephalexin PO. S. intermedius was identified from 67,6 % of the totality of bacterial isolates and the remaining 32,4 % was composed of S. hyicus, S. schleiferi subspecie coagulans, S. warneri and Micrococcus sp. According to the antimicrobial susceptibility results the more effective drugs were amoxicillin plus potassium clavulanate, cephalexin and ceftioufur. In percentage values a full response of 50,0 %, 33,3 % and 28,6 % was achieved in Groups I, II and III, respectively. On the other hand, when the comparison was made considering full and moderate together the values were 83,3 %, 50,0 % and 42,9 % for Groups I, II and III, respectively. Through a statistical analysis (Qui score test) no significant difference (p > 0,05) among the response to treatment percentage values was observed for the three groups. All treatments were secure and no drug eruption side effects were observed.

Even though our understanding of mechanisms such as protein folding and molecular recognition is relatively poor, antibodies and alternative affinity proteins with entirely novel functions are today generated in a routine manner. The reason for this success is an engineering approach generally known as directed evolution. Directed evolution has provided researchers with a tool for circumventing our limited knowledge and hence the possibility to create novel molecules that by no means could have been designed today. The approach is based on construction of high-complexity combinatorial libraries from which protein variants with desired properties can be selected. Engineered proteins are already indispensable tools in nearly all areas of life science and the recent advent of mainly monoclonal antibodies as therapeutic agents has directed even more attention to the field of combinatorial protein engineering. In this thesis, I present the underlying research efforts of six original papers. The overall objective of the studies has been to develop and investigate a new staphylococcal surface display method for protein engineering and protein characterization. The technology is based on display of recombinant proteins on surface of the Gram-positive bacteria Staphylococcus carnosus. In two initial studies, two key issues were addressed in order to improve the protein engineering method in regard to affinity discrimination ability and transformation efficiency. The successful results enabled investigation of the staphylococcal display system for de novo generation of affibody molecules from large combinatorial libraries. In this study, a high-complexity protein library was for the first time displayed on surface of Gram-positive bacteria and by means of fluorescence-activated cell sorting, specific affinity proteins for tumor necrosis factor-alpha were isolated. Moreover, in following papers, the staphylococcal display method was further improved and investigated for affinity determination, soluble protein production and epitope mapping purposes in order to facilitate downstream characterizations of generated affinity proteins. Taken together, in these studies we have demonstrated that the staphylococcal display system is a powerful alternative to existing technologies for protein engineering and protein characterization. / QC 20100809

<p>QC 20150922</p>

<p>The structural plasticity conferred by conformational flexibility has increasingly been recognized as a likely determinant of function. For example, multiscale heterogeneity in the calmodulin central helix most likely helps it in binding over 100 protein targets, and a concerted motion seen in both nuclear magnetic resonance (NMR) and crystal structures of ubiquitin is proposed to underlie its functional plasticity of promiscuous binding to many different proteins with high affinity. However, flexibility is manifested in a variety of ways, depending both on the protein itself and on how it is observed. Conformational heterogeneity (the term we use for flexibility when studied by X-ray crystallography) is evident in electron density, either as fully separated peaks or as anisotropic density shapes showing fluctuation of atom groupings. Many phenomena contribute to conformational heterogeneity in crystal structures, from diverse crystal contacts to functionally relevant conformational fluctuations on a wide range of time and size scales.</p><p>In addition to ubiquitin and calmodulin, the Staphylococcus aureus virulence factor staphylococcal protein A (SpA) is an example of a highly heterogeneous protein. SpA is a major contributor to bacterial evasion of the host immune system, through high-affinity binding to host proteins such as antibodies, von Willebrand factor, and tumor necrosis factor receptor 1 (TNFR1). The protein includes five small three-helix-bundle domains (E-D-A-B-C) separated by conserved flexible linkers. Prior attempts to crystallize individual domains in the absence of a binding partner were apparently unsuccessful. There are also no previous structures of tandem domains. In this thesis, I report the high-resolution crystal structures of a single C domain (collected at both cryogenic and room temperatures), a single A domain, and two B domains connected by the conserved linker. All four apo structures exhibit extensive multiscale conformational heterogeneity, which required novel modeling protocols. Comparison of domain structures shows that helix1 orientation is especially heterogeneous, coordinated with changes in sidechain conformational networks and contacting protein interfaces.</p><p>The interaction between a SpA domain and the Fc fragment of IgG was partially elucidated previously in the crystal structure 1FC2. Although informative, the previous structure wasn't properly folded and left many substantial questions unanswered, such as a detailed description of the tertiary structure of SpA domains in complex with Fc and the structural changes that take place upon binding. In this thesis, I report the 2.3-A structure of a fully folded SpA domain in complex with Fc. My structure indicates that there are extensive structural rearrangements necessary for binding Fc, including concerted rotamer changes and coupled backbone rearrangements that lead to a difference in helix1 angle. The conformational heterogeneity of the helix1/2 interface is also eliminated in the complex, with previously poly-rotameric interfacial residues locking into single rotamer conformations. Such a loss of conformational heterogeneity upon formation of the protein-protein interface may occur in SpA and in its multiple binding partners and may be an important structural paradigm in other functionally plastic proteins.</p> / Dissertation

Directed evolution is a powerful method for engineering of specific affinity proteins such as antibodies and alternative scaffold proteins. For selections from combinatorial protein libraries, robust and high-throughput selection platforms are needed. An attractive technology for this purpose is cell surface display, offering many advantages, such as the quantitative isolation of high-affinity library members using flow-cytometric cell sorting. This thesis describes the development, evaluation and use of bacterial display technologies for the engineering of affinity proteins. Affinity proteins used in therapeutic and diagnostic applications commonly aim to specifically bind to disease-related drug targets. Angiogenesis, the formation of new blood vessels from pre-existing vasculature, is a critical process in various types of cancer and vascular eye disorders. Vascular Growth Factor Receptor 2 (VEGFR2) is one of the main regulators of angiogenesis. The first two studies presented in this thesis describe the engineering of a biparatopic Affibody molecule targeting VEGFR2, intended for therapeutic and in vivo imaging applications. Monomeric VEGFR2-specific Affibody molecules were generated by combining phage and staphylococcal display technologies, and the engineering of two Affibody molecules, targeting distinct epitopes on VEGFR2 into a biparatopic construct, resulted in a dramatic increase in affinity. The biparatopic construct was able to block the ligand VEGF-A from binding to VEGFR2-expressing cells, resulting in an efficient inhibition of VEGFR2 phosphorylation and angiogenesis-like tube formation in vitro. In the third study, the staphylococcal display system was evaluated for the selection from a single-domain antibody library. This was the first demonstration of successful selection from an antibody-based library on Gram-positive bacteria. A direct comparison to the selection from the same library displayed on phage resulted in different sets of binders, and higher affinities among the clones selected by staphylococcal display. These results highlight the importance of choosing a display system that is suitable for the intended application. The last study describes the development and evaluation of an autotransporter-based display system intended for display of Affibody libraries on E. coli. A dual-purpose expression vector was designed, allowing efficient display of Affibody molecules, as well as small-scale protein production and purification of selected candidates without the need for sub-cloning. The use of E. coli would allow the display of large Affibody libraries due to a high transformation frequency. In combination with the facilitated means for protein production, this system has potential to improve the throughput of the engineering process of Affibody molecules. In summary, this thesis describes the development, evaluation and use of bacterial display systems for engineering of affinity proteins. The results demonstrate great potential of these display systems and the generated affinity proteins for future biotechnological and therapeutic use. / <p>QC 20141203</p>

This thesis, based on five research papers, presents results from development and evaluation ofmethods for identifying the interaction site of antibodies on their antigens and the functional investigation of these in different assays. As antibodies have proven to be invaluable tools in diagnostics, therapy and basic research, the demand of characterizing these binding molecules has increased. Techniques for epitope mapping in a streamlined manner are therefore needed, particularly in high throughput projects as the Human Protein Atlas that aims to systematically generate two antibodies with separate epitopes towards all human proteins.  In paper I we describe an approach to map the epitopes of polyclonal and monoclonal antibodies for the first time using staphylococcal display. This method was combined with peptide scanning and alanine scanning using suspension bead arrays, to create a streamlined approach of highresolution characterization of epitopes recognized by antibodies as demonstrated in paper II. Single epitopes were identified for the monoclonal antibodies and several (one to five) separate epitopes scattered throughout the antigen sequence were determined for each polyclonal antibody. Further, antibodies of different species origin showed overlapping binding epitopes. In paper III we studied the epitope patterns of polyclonal antibodies generated with the same antigen in different animals. Although common epitope regions could be identified the exact epitope pattern was not repeated, as some epitopes did not reoccur in the repeated immunizations. In paper IV, a potential biomarker for colon cancer, RBM3, was investigated using validated antibodies by epitope mapping and siRNA analysis. Finally, in paper V, a method for generating epitope-specific antibodies based on affinity purification of a polyclonal antibody is described. The generated antibodies were used in several immunoassays and showed a great difference in functionality. Paired antibodies with separate epitopes were successfully generated and could be used in a sandwich assay or to validate each other in immunohistochemistry. Taken together, in these studies we have demonstrated valuable concepts for the characterization of antibody epitopes. / QC 20120111

Diss. (sammanfattning) Stockholm : Karolinska institutet, 2005. / Härtill 4 uppsatser.

Diss. (sammanfattning) Stockholm : Karolinska institutet, 2010.

As piodermites, superficiais ou profundas, representam uma das dermatopatias caninas mais comuns no cotidiano da clínica dermatológica de cães. Dentre as classificadas como superficiais, destacam-se a foliculite bacteriana e a piodermite esfoliativa ou superficial disseminada, que representam a grande maioria dos casos. Em alguns cães, as piodermites superficiais são idiopáticas, apresentam evolução crônica e caráter recidivante. A despeito de criteriosa investigação acerca de sua possível etiologia, por vezes, não se consegue evidenciar a causa para a instalação e recorrência do quadro mórbido. Tais animais apresentam frequentes recidivas, em variáveis períodos de tempo, após o término da terapia antibiótica. Para estes caninos, na bibliografia médico-veterinária há recomendação de emprego das controvertidas imunoterapia ou de antibioticoterapia sob a forma de pulsos. Portanto, objetivou-se na casuística do Serviço de Dermatologia do Hospital Veterinário da USP, determinar as principais espécies bacterianas envolvidas, a susceptibilidade destas frente a diferentes antimicrobianos, bactericidas ou bacteriostáticos, assim como, comparar a eficácia e a segurança de três distintos protocolos terapêuticos no manejo a longo prazo, de piodermites superficiais recidivantes idiopáticas. Utilizaram-se 23 animais, de quaisquer dos sexos, de distintas raças e faixas etárias. A amostragem foi aleatoriamente disposta em três grupos de experimentação (GI, GII, G III), respectivamente submetidos à imunoterapia com bacterina comercial (Estafilin®) e às pulsoterapias de \"finais de semana\" ou em \"semanas alternadas\", empregando-se cefalexina \"per os\". O principal patógeno, em 67,6 % da totalidade de isolamentos bacterianos, foi Staphylococcus intermedius. Evidenciou-se (32,4 %), ainda, as espécies S. hyicus, S. schleiferi subespécie coagulans, S. warneri e Micrococcus sp. Segundo os antibiogramas, os fármacos mais efetivos in vitro foram a amoxicilina associada ao clavulanato de potássio, a cefalexina e o ceftiofur. Verificou-se resposta plena em percentis de, respectivamente, 50,0 %, 33,3 % e 28,6 % nos Grupos II, III e I; destarte, ao se agrupar as respostas plena e moderada evidenciaram-se valores relativos de, respectivamente, 83,3 %, 50,0 % e 42,9 %. À luz da estatística (Teste do Qui Quadrado), não se observaram quaisquer diferenças estatisticamente significativas (p > 0,05) entre os percentuais de resposta aos três protocolos empregados. Todos eles mostraram-se seguros, sem acarretar efeitos adversos farmacodérmicos. / Superficial and deep pyodermas are common canine skin disorders in the small animal dermatology practice. Among the superficial form, the bacterial folliculitis and superficial spreading pyoderma represent the great majority of cases. Some dogs are affected by idiopathic, chronic and recurrent type of superficial pyoderma. Despite a rigorous search for possible reasons for its etiology, sometimes it is not possible to determine an underlying cause for the disease recurrence. At variable time periods, these dogs show frequent recurrent episodes, after the interruption of antibiotic therapy. For these patients, the veterinary medicine literature recommends the use of the controversial immune therapy or antibiotic pulse therapy. Thus, using the University of Sao Paulo / Dermatology Service\'s casuistry the present study aimed to determine the major bacterial species responsible for pyodermas, their susceptibility to several bactericidal and bacteriostatic antibiotics as well as compare the efficacy and safety of three different therapeutics protocols for the long term management of idiopathic recurrent superficial pyoderma. A total of 23 male and female, purebred dogs from different ages were randomly allocated in three distinct experimental groups (G I, G II and G III), respectively treated with bacterin immune therapy, \"weekend\" antibiotic pulse therapy and \"week on - week off\" antibiotic pulse therapy, receiving cephalexin PO. S. intermedius was identified from 67,6 % of the totality of bacterial isolates and the remaining 32,4 % was composed of S. hyicus, S. schleiferi subspecie coagulans, S. warneri and Micrococcus sp. According to the antimicrobial susceptibility results the more effective drugs were amoxicillin plus potassium clavulanate, cephalexin and ceftioufur. In percentage values a full response of 50,0 %, 33,3 % and 28,6 % was achieved in Groups I, II and III, respectively. On the other hand, when the comparison was made considering full and moderate together the values were 83,3 %, 50,0 % and 42,9 % for Groups I, II and III, respectively. Through a statistical analysis (Qui score test) no significant difference (p > 0,05) among the response to treatment percentage values was observed for the three groups. All treatments were secure and no drug eruption side effects were observed.

Submitted by Biblioteca da Faculdade de Farmácia (bff@ndc.uff.br) on 2017-04-10T17:58:31Z No. of bitstreams: 1 Marques, Leila Márcia Peres [Dissertação, 2014].pdf: 1219156 bytes, checksum: dbca893aaf472356f21637055bd0d192 (MD5) / Made available in DSpace on 2017-04-10T17:58:31Z (GMT). No. of bitstreams: 1 Marques, Leila Márcia Peres [Dissertação, 2014].pdf: 1219156 bytes, checksum: dbca893aaf472356f21637055bd0d192 (MD5) / O presente trabalho tem por objetivo caracterizar fenotípica e genotipicamente cepas de S. aureus isoladas de queijo Minas frescal (QMF), quanto a qualidade microbiológica, perfil de resistência a diferentes antimicrobianos, presença do gene de resistência a meticilina (mecA), presença de genes que codificam para enterotoxinas estafilocócicas (SE) clássicas; e para cepas resistentes a meticilina, pesquisa dos genes que codificam para a citotoxina Panton Valentine Leukocidin (PVL) e o perfil de diversidade genética, através da tipificação dos tipos SCCmec, Eletroforese em gel de campo pulsado (PFGE) e do sequenciamento da proteína estafilococócica A (SpA). Estafilococos coagulase-positivos (CoPS) foram isolados a partir de 4 amostras (13,3%) de QMF, sendo que 3 (10%) amostras estavam impróprias para consumo segundo a legislação (acima de 5,0.10² UFC/g). As 31 cepas de CoPS isoladas apresentaram a sequência gênica 16S rRNA e o gene nuc, sendo confirmadas como S. aureus. As 31 cepas S. aureus apresentaram resistência a penicilina, 21 (67,74%) a eritromicina, 12 (38,71 %) a ciprofloxacina, 4 (12,9%) a clindamicina, 4 (12,9%) a oxacilina e cefoxitina, 2 (6,45%) a rifampicina, 1 (3,23%) ao cloranfenicol e a tetraciclina. Todas as 31 cepas foram sensíveis ao trimetoprim-sulfametoxazole, gentamicina e a linezolida. Sete cepas (22,58%) carreavam o gene mecA, destas, 4 apresentaram fenótipo de resistência a meticilina, sendo classificadas como S. aureus resistentes a meticilina (MRSA), sendo todos sensíveis a vancomicina e com resistência constitutiva a clindamicina. Cinco cepas (16,1%) apresentaram resistência induzida a clindamicina. Os genes que codificam para as SE clássicas (sea/seb e seb/sec) foram encontrados em 2 isolados (6,45%) MRSA. Através da PFGE e da tipificação SpA, as cepas MRSA isoladas, apresentaram 3 diferentes perfis genotípicos. Essas cepas MRSA não apresentaram os tipos SCCmec I a V, nem os genes que codificam para PVL. Os resultados obtidos neste trabalho indicam que cepas MRSA estão sendo veiculadas através do QMF, provavelmente por manipulação humana inadequada e/ou condições higiênico-sanitárias precárias. O potencial enterotoxigênico destas bactérias indica que o QMF pode causar intoxicação alimentar, sendo um risco para a saúde pública / This study aimed to characterize genotypic and phenotypically S. aureus strains isolated from Minas frescal cheese (MFC) to evaluate the microbiological quality, resistance profile to diferent antimicrobials, the presence of methicillin resistance (mecA) gene and the presence of genes encoding classical staphylococcal enterotoxins (SE). Only for methicillin resistant S. aureus (MRSA) strains were performed the gene encoding Panton Valentine Leukocidin cytotoxin (PVL) and the genetic diversity profile through Pulsed-field gel electrophoresis (PFGE), typing of SCCmec and SpA typing. Coagulase-positive staphylococci (CoPS) were identified in four MFC samples (13.3%), and three (10%) samples showed the number of colony forming units (CFU) higher than allowed to MFC by Brazilian legislation (5,0x10² UFC/g). All the 31 CoPS strains carried the gene sequence 16S rRNA and nuc gene, and were confirmed as S. aureus. All 31 strains of S. aureus were resistant to penicillin, 21 (67.74%) to erythromycin, 12 (38.71%) to ciprofloxacin, 4 (12.9%) to clindamycin, 4 (12.9%) to oxacillin and cefoxitin, 2 (6.45%) to rifampicin, 1 (3.23%) to chloramphenicol and tetracycline. All the 31 CoPS strains were susceptible to trimethoprim-sulfamethoxazole, gentamicin and linezolid. Seven strains (22.58%) encoded mecA gene, four of them showed the methicillin resistance phenotypic, been classified as methycilin resistant S. aureus (MRSA). All MRSA isolates were susceptible to vancomycin and showed constitutive clindamycin resistance. Five strains (16.1%) showed induced clindamycin resistance. The gene encoding the classical SE (sea/seb and seb/sec) were detected in two isolates (6.45%) MRSA. Genetic analysis of MRSA strains was performed by PFGE and SpA typing showed three different profiles. The strains that showed mecA gene, did not show PVL genes coding, neither the types of SCCmec typing. The results obtained in this study showed that MRSA strains are being transmitted by MFC samples, probably due to inadequate human manipulation and/or poor and inefficient hygienic-sanitary conditions. The enterotoxigenic potential of these strains is a concern for public health due to the risk of food poisoning among the MFC consumers