<div>Biological dynamics have been studied by many methods. Fluorescence dynamic microscopy and optical coherence tomography provided fundamental understandings of biological systems. However, their high NA optics only represent local characteristics. Biodynamic imaging (BDI) technique implements a low NA optics and acquires the statistical average of Doppler shifts that occurred by dynamic light scattering with biological dynamic subsystems provided globally averaged dynamic characteristics. </div><div>BDI is used for this study to investigate biomedical applications. The chemotherapy efficacy measurement by BDI demonstrated a good agreement between the Doppler spectral phenotypes and the preclinical outcomes. Also, dynamic responses of microbiomes by chemical stimuli demonstrated featured Doppler characteristics. The bacterial infection of epithelial spheroids showed consistent spectral responses and antibiotic-resistant E. coli infection treatment with a sensitive and resistive antibiotic showed a dramatic contrast. Furthermore, the phase-sensitive characteristics of BDI provided a clue to understanding the characteristics of the random process of biological systems. Levy-like heavy-tailed probability density functions are demonstrated and </div><div>the shape changed by infection will be discussed. </div>

Magister Chirurgiae Dentium - MChD / When faced with a failing or failed root treatment, the dentist must decide whether the tooth can be retreated and saved or extracted. The dentist's decision to retreat is often based on the x-ray presenting a failing root treatment. The dentist must be aware that there might be a number of factors that have contributed to the failure and which may preclude, following retreatment, a successful long term clinical function. The current study has been made to determine those factors that may influence the prognosis in order to assist the clinician in advising the patient of the best course of treatment. A literature review was made to determine and identify these factors and explain their relevance and influence on the healing process. The current study included identifying the factors described in the literature review and noting their influence on the prognosis following non-surgical retreatment. Retreatment of failed root treated teeth requires special knowledge and skill from the clinician in order to correct and manage the case. The current study was made in a clinical setting and compared results of retreatment with two types of rotary files on the market: progressive or variable taper (Pro Taper) with constant non-ISO 06 taper (K3). Clinical signs and symptoms were noted at the patient's presentation and following recalls at 1, 4 months and 1 year. The results were recorded and statistically analysed and the results were discussed. The results showed that out of 81 patients 10cases of retreatment were considered to have failed and 68 cases were considered to have been successful. Three patients did not return for their assessments and were therefore not considered in further results. There was a statistically significant (p<0.1 0) recording of deep periodontal pockets associated with teeth with failing root treatments (40%) and (13%) in the "Success" group. The two estimated proportions of "Sinus" present (60%) in the "Failure" group and 10% in the 'Success' group were significantly different (p<0.01). "Sinus present" in the "Success group" means in the initial clinical assessment before retreatment was initiated. The presence of a sinus at the One Year follow up signified a failure of the root retreatment (p<0.001). The two estimated proportions of "Occlusion" present (80% and 99%) in the "Failure" and "Success" group were significantly different (p<0.05). Therefore, teeth in "occlusion" were more within the "Success" group. 70% of those teeth that failed had pretreatment apical rarefactions of greater than 6mm diameter; whereas 76.5% of successful retreatments had areas less than 6mm diameter. The differences were significant according to Fisher's Exact Test (p<0.01). 44% of failed cases had areas of rarefaction described as "diffuse"; and 56% of failed cases had areas that were described as "well-defined". 95% of cases that were successful had areas described as "diffuse" and the rest were "welldefined". The differences between the success and failure categories were statistically significant (p<0.0 1). The two estimated proportions of "Post present" (0% and 31%) in the "Failure" and "Success" groups were significantly different (p<0.1 0). Therefore, the "Post was present" in many more cases within the "Success" group than in the "Failure" group. There was no difference between the Median "Crown/Root" ratios of the "Failure" (Median = 0.595) or "Success" groups (Median = 0.662) (Wilcoxon Test, p>O.10). Teeth with longer roots tend to lead to failure, however there was a considerable overlap between the distributions. Therefore the finding is that the Median length of the roots of the "Failures" is longer than that of the "Successes". (Wilcoxon Rank Sum Test, p-value = 0.0628). The results also indicated that previous short root filling preparation contributes to the final success of retreatment (Fisher Exact Test, p<0.05). There was a significant difference between the distribution of the "Failure" and "Success" (88.2%) groups (Fisher Exact Test, p<O.OI) in those cases with initial short obturated fillings. When comparing the outcome following the use of the two types of rotary files it was found that the "Successes" with K3 File (35 out of 41) was 85%; and with Protaper File (32 out of 36) 89%. The "Success" rate certainly was not different between the two file types. The conclusions drawn from the current study was not significantly different from those in the literature review and the overall results were of a similar nature with some minor changes. However it is clear that non-surgical root retreatment offers a good prognosis and should be included as an option for failed or failing root treatment.

La méthylation de l'ADN est une marque épigénétique importante chez les mammifères. Malgré le fait que la méthylation de la cytosine en 5' (5mC) soit reconnue comme une modification épigénétique stable, il devient de plus en plus reconnu qu'elle soit un processus plus dynamique impliquant des voies de méthylation et de déméthylation actives. La dynamique de la méthylation de l'ADN est désormais bien caractérisée dans le développement et dans le fonctionnement cellulaire des mammifères. Très peu est cependant connu concernant les implications régulatrices dans les réponses immunitaires. Pour se faire, nous avons effectué des analyses du niveau de transcription des gènes ainsi que du profilage épigénétique de cellules dendritiques (DCs) humaines. Ceux-ci ont été faits avant et après infection par le pathogène Mycobacterium tuberculosis (MTB). Nos résultats fournissent le premier portrait génomique du remodelage épigénétique survenant dans les DCs en réponse à une infection bactérienne. Nous avons constaté que les changements dans la méthylation de l'ADN sont omniprésents, identifiant 3,926 régions différentiellement méthylées lors des infections par MTB (MTB-RDMs). Les MTB-RDMs montrent un chevauchement frappant avec les régions génomiques marquées par les histones associées avec des régions amplificatrices. De plus, nos analyses ont révélées que les MTB-RDMs sont activement liées par des facteurs de transcription associés à l'immunité avant même d'être infecté par MTB, suggérant ces domaines comme étant des éléments d'activation dans un état de dormance. Nos données suggèrent que les changements actifs dans la méthylation jouent un rôle essentiel pour contrôler la réponse cellulaire des DCs à l'infection bactérienne. / DNA methylation is an important epigenetic mark in mammals. Although methylation at the 5’ position of cytosine (5mC) is recognized as a stable epigenetic modification, it is becoming increasingly viewed as a more dynamic process that involves both active methylation and demethylation pathways. While the dynamics of DNA methylation has been well characterized in mammalian development and normal cellular function, little is known about its regulatory implications in immune responses. To that end, we performed comprehensive transcriptional and epigenetic profiling of primary dendritic cell (DC) samples from humans, before and after infection with Mycobacterium tuberculosis (MTB). Our results provide the first complete genomic portrait of the extensive epigenetic remodeling occurring in primary DCs in response to a bacterial infection. We found that active changes in DNA methylation are pervasive, identifying 3,926 MTB-induced differentially methylated regions (MTB-DMRs). MTB-DMRs show a striking overlap with genomic regions marked by histones associated with enhancer activity. ATAC-seq footprinting analysis revealed that regions that change methylation were actively bound by immune-related TFs prior to MTB-infection suggesting that these domains are likely to represent enhancer elements in a poised state. Our data suggests that active changes in DNA methylation play an essential and previously unappreciated role at controlling of the regulatory programs engaged by DCs in response to a bacterial infection.

In der vorliegenden Arbeit wurde der Einfluss von Prä- und Probiotika auf bakterielle Translokation (BT) und postoperative Infektionen nach großen viszeralchirurgischen Eingriffen untersucht. Dabei wurde aus methodischen Gründen zunächst BT nach Leber- (LR) und Colonresektion (CR) allein oder in Kombination experimentell im Rattenmodell quantifiziert und deren potentielle Pathomechanismen untersucht. Anschließend wurde der Einfluss von einzelnen Probiotika und einer Kombination verschiedener Probiotika und Präbiotika auf die Inzidenz bakterieller Infektionen nach Lebertransplantation (LTX) und pyloruserhaltender Pankreaskopfresektion (PPPD) in zwei prospektiv randomisierten klinischen Studien analysiert. Im experimentellen Teil der Untersuchungen wurde BT nach LR vor allem in Leber und Milz, nach CR hauptsächlich in mesenterialen Lymphknoten (MLK) und Milz nachgewiesen. Kombination von LR und CR führte zu einer Potenzierung der BT, parallel zum Ausmaß der LR. Durch Gabe von Probiotika wurde die Konzentration von Bakterien in den MLK signifikant gesenkt. Tiere mit einer hohen coecalen Laktobazillenkonzentration hatten eine signifikant niedrigere bakterielle Konzentration in allen untersuchten Organen als Tiere mit weniger Laktobazillen. CR führten zu einer Zunahme der coecalen gramnegativen Bakterienkonzentration und zu einer Abnahme der Laktobazillen. Histologische Veränderungen der Darmmukosa wurden nicht beobachtet. Die parazelluläre Permeabilität für Ionen, nicht aber für die höhermolekulare Laktulose war im Colon in allen Gruppen im Vergleich zur Kontrollgruppe erhöht. Probiotika beeinflussten die Zusammensetzung der coecalen Flora und damit auch die BT. In der ersten klinischen Studie verminderte postoperative orale Gabe von Laktobazillus plantarum und einer ballaststoffhaltigen Ernährungslösung die Inzidenz von bakteriellen Infektionen nach LTX im Vergleich zu selektiver Darmdekontamination und ballaststofffreier Ernährung signifikant. Die Gabe von Ballaststoffen und hitzeinaktivierten Laktobazillen führte zwar auch zu einer geringen Reduktion der Infektionen; diese war jedoch nicht signifikant. In der Mehrzahl wurden enteropathogene Bakterien isoliert. Die zweite klinische Studie untersuchte den Einfluss einer Kombination von vier verschiedenen Milchsäurebakterien und vier Präbiotika auf die Inzidenz bakterieller Infektionen nach LTX und PPPD. Im Vergleich zu Präbiotika und Placebo kam es zu einer deutlichen Verminderung der Infekte, die nach LTX auch signifikant war. In beiden Studien wurde die enterale Ernährung gut vertragen mit relativ wenig Nebenwirkungen. BT tritt somit sehr häufig auch nach kleineren viszeralchirurgischen Eingriffen auf und hat organspezifisch verschiedene Ursachen. Probiotika konnten sowohl tierexperimentell die BT vermindern als auch klinisch die Inzidenz bakterieller Infektionen nach großen viszeralchirurgischen Eingriffen senken. Da sie leicht zu verabreichen sind und wenig Nebenwirkungen verursachen, könnten sie breit eingesetzt werden. / In the present study, the impact of pre- and probiotics on bacterial translocation (BT) and postoperative bacterial infection rates was assessed. Due to methodological reasons, we first quantified BT following single liver (LR) and colon resection (CR) or a combination of both and analysed potential pathogenic mechanisms for BT. Then, we performed two prospective randomised clinical studies to analyse the influence of a single probiotic strain and a combination of different pre- and probiotics on the incidence of bacterial infections in patients with liver transplantation (OLT) or pylorus preserving partial pancreatoduodenectomy (PPPD). In the rat model, BT after LR mainly occurred in the liver and spleen, after CR mainly in the mesenteric lymph nodes (MLN) and spleen. BT was increased in the animals with combined operation, in parallel to the extent of liver resection. Probiotics significantly decreased the bacterial concentration in the MLN. Animals with a high cecal concentration of lactobacilli had significantly less BT than the others. CR led to an increase of cecal gramnegative bacterial concentrations and to a decrease of lactobacilli. No histological changes were observed in the intestine. Paracellular permeability for ions, but not for the larger molecule lactulose, was increased in the colon in all groups compared to the sham group. Probiotics had an influence on cecal bacterial concentration. In the first clinical study, postoperative oral administration of Lactobacillus plantarum and a fibre-enriched enteral diet significantly decreased bacterial infection rates after OLT compared to selective bowel decontamination and a fibre-free diet. Fibre and heat-inactivated Lactobacillus also led to a slight, but not significant decrease of infections. Mainly gut-derived bacteria were isolated. The second clinical study analysed the influence of a combination of four different lactic acid bacteria and fibres on bacterial infection rates after OLT and PPPD. Compared to fibres and placebo, infection rates were significantly lower after OLT and markedly lower after PPPD. In both studies, the study substances were well tolerated without serious side effects. BT even occurs following minor abdominal surgery and is caused by different mechanisms related to the kind of operation. Probiotics were able to diminish BT in the rat model as well as to decrease bacterial infection rates following major abdominal surgery in the clinical studies. As they are easy to administer and do not cause severe side effects, they could be useful in clinical practice.

A meningite bacteriana no período neonatal é uma doença grave, associada à mortalidade elevada e seqüelas em cerca de 12 a 29% dos sobreviventes. Nos recém-nascidos com peso ao nascimento < 2500 g, o risco de adquirir meningite é três vezes superior àqueles com peso >= 2500 g e, entre neonatos de muito baixo peso (< 1500 g), o risco é 17 vezes maior. Objetivo: Geral: descrever o quadro clínico e as complicações da meningite bacteriana em dois grupos de recém-nascidos, considerados de acordo com o peso de nascimento (= 2500 g). Específico: descrever e comparar os agentes etiológicos, a freqüência de sinais e sintomas neurológicos e de complicações, a mortalidade e a duração do tratamento nos dois grupos. Métodos: Estudo observacional de 87 recém-nascidos com meningite bacteriana, admitidos na Unidade de Cuidados Intensivos Neonatais do Instituto da Criança do Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, no período de 11 anos (janeiro de 1994 a dezembro de 2004). Os dados foram obtidos através da análise de prontuários. Na análise estatística foram utilizados o teste exato de Fisher e teste não paramétrico de Mann Whitney. Resultados: Foram identificadas bactérias no líquor em 39% dos pacientes, sendo 50% bactérias Gram-positivas e 50% Gram-negativas. A maioria dos neonatos apresentou sinais e sintomas inespecíficos: febre (63,2%), irritabilidade (31%), letargia (26,4%). Os achados neurológicos ocorreram em 35,3% dos casos. As complicações ocorreram em 48,2% dos neonatos, principalmente convulsões (23%), hemorragia intracraniana (14,9%) e hidrocefalia (13,8%) com mortalidade de 11,5 %. Na comparação entre evolução clínica e peso de nascimento observou-se associação entre peso >= 2500 g e convulsão (p=0,047), peso >= 2500 g e fontanela abaulada (p=0,019), bactéria no LCR e complicações (p=0,008) e bactéria no LCR e óbitos (p=0,043). Conclusões: Os agentes etiológicos mais freqüentemente identificados no LCR foram as enterobactérias (41%), seguidas de Streptococcus B (17,5%), Streptococcus não B (17,5%), Staphylococcus aureus (11,7%), Neisseria meningitidis (8,8%) e Enterococcus faecalis (3,0%), não havendo diferença entre tipo de bactérias e peso de nascimento. Os sinais e sintomas predominantes foram inespecíficos, com achados neurológicos em 35% dos casos. A freqüência maior de sintomas neurológicos nos recém-nascidos com peso >= 2500 g, sugere maior grau de maturidade do sistema nervoso central nestas crianças. Embora a mortalidade tenha sido inferior à observada em estudos anteriores no mesmo Serviço, a freqüência de complicações foi alta, independentemente do peso de nascimento. A presença de bactéria no LCR associou-se à maior freqüência de convulsões e mortalidade. A necessidade de manutenção do tratamento por tempo mais prolongado nos recém-nascidos de baixo peso sugere maior gravidade da doença neste grupo de neonatos. / Bacterial meningitis in the neonatal period is a severe disease, associated to elevated mortality and sequelae in around 12 to 29% of the survivors. Newborns whose birth weight is < 2,500g have a 3-fold increase in the risk of acquiring meningitis when compared to those whose weight is >= 2,500; among those with very low birth weight (< 1,500g), the risk increases 17-fold. Objectives: General: to describe the clinical picture and the complications of bacterial meningitis in two groups of newborns, considered according to birth weight (< 2,500g or >= 2,500g). Specific: to describe and compare the etiological agents, the frequency of neurological signs and symptoms and complications, mortality rate and duration of treatment in both groups. Methods: Observational study of 87 newborns with bacterial meningitis, admitted at the Neonatal Intensive Care Unit (NICU) of Instituto da Criança of Hospital das Clínicas of the University of São Paulo School of Medicine, during an 11-year period (January 1994 to December 2004). The data were obtained through the analysis of hospital files. Statistical analysis was carried out with Fisher\'s exact test and the non-parametric Mann Whitney test. Results: Bacteria were identified in the cerebrospinal fluid (CSF) of 39% of the patients, with 50% of them being Gram-positive and 50%, Gram-negative. Most neonates presented unspecific signs and symptoms: fever (63.2%), irritability (31%), and lethargy (26.4%). The neurological findings occurred in 35.3% of the cases. Complications occurred in 48.2% of the neonates, and were mainly seizures (23%), intracranial hemorrhage (14.9%) and hydrocephalus (13.8%) with a mortality rate of 11.5%. At the comparison between clinical evolution and birth weight, associations between weight >= 2,500g and seizures (p=0.047), weight >= 2,500g and concave fontanel (p=0.019), bacteria in the CSF and complications (p=0.008) and bacteria in the CSF and death (p=0.043) were observed. Conclusions: The etiological agents most often identified in the CSF were enterobacteria (41%), followed by B Streptococcus (17.5%), non-B Streptococcus (17.5%), Staphylococcus aureus (11.7%), Neisseria meningitidis (8.8%) and Enterococcus faecalis(3.0%), with no statistical difference between the type of bacteria and birth weight. The predominant signs and symptoms were unspecific, with neurological findings in 35% of the cases. The higher frequency of neurological signs and symptoms in newborns with birth weight >= 2,500g suggest a higher degree of central nervous system maturity in these infants. Although the mortality was lower than that observed in previous studies at the same Service, the frequency of complications was high, regardless of birth weight. The presence of bacteria in the CSF was associated to a higher frequency of seizures and mortality. The need for prolonged treatment in newborns with low birth weight suggests higher disease severity in this group of neonates.

A meningite bacteriana no período neonatal é uma doença grave, associada à mortalidade elevada e seqüelas em cerca de 12 a 29% dos sobreviventes. Nos recém-nascidos com peso ao nascimento < 2500 g, o risco de adquirir meningite é três vezes superior àqueles com peso >= 2500 g e, entre neonatos de muito baixo peso (< 1500 g), o risco é 17 vezes maior. Objetivo: Geral: descrever o quadro clínico e as complicações da meningite bacteriana em dois grupos de recém-nascidos, considerados de acordo com o peso de nascimento (= 2500 g). Específico: descrever e comparar os agentes etiológicos, a freqüência de sinais e sintomas neurológicos e de complicações, a mortalidade e a duração do tratamento nos dois grupos. Métodos: Estudo observacional de 87 recém-nascidos com meningite bacteriana, admitidos na Unidade de Cuidados Intensivos Neonatais do Instituto da Criança do Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, no período de 11 anos (janeiro de 1994 a dezembro de 2004). Os dados foram obtidos através da análise de prontuários. Na análise estatística foram utilizados o teste exato de Fisher e teste não paramétrico de Mann Whitney. Resultados: Foram identificadas bactérias no líquor em 39% dos pacientes, sendo 50% bactérias Gram-positivas e 50% Gram-negativas. A maioria dos neonatos apresentou sinais e sintomas inespecíficos: febre (63,2%), irritabilidade (31%), letargia (26,4%). Os achados neurológicos ocorreram em 35,3% dos casos. As complicações ocorreram em 48,2% dos neonatos, principalmente convulsões (23%), hemorragia intracraniana (14,9%) e hidrocefalia (13,8%) com mortalidade de 11,5 %. Na comparação entre evolução clínica e peso de nascimento observou-se associação entre peso >= 2500 g e convulsão (p=0,047), peso >= 2500 g e fontanela abaulada (p=0,019), bactéria no LCR e complicações (p=0,008) e bactéria no LCR e óbitos (p=0,043). Conclusões: Os agentes etiológicos mais freqüentemente identificados no LCR foram as enterobactérias (41%), seguidas de Streptococcus B (17,5%), Streptococcus não B (17,5%), Staphylococcus aureus (11,7%), Neisseria meningitidis (8,8%) e Enterococcus faecalis (3,0%), não havendo diferença entre tipo de bactérias e peso de nascimento. Os sinais e sintomas predominantes foram inespecíficos, com achados neurológicos em 35% dos casos. A freqüência maior de sintomas neurológicos nos recém-nascidos com peso >= 2500 g, sugere maior grau de maturidade do sistema nervoso central nestas crianças. Embora a mortalidade tenha sido inferior à observada em estudos anteriores no mesmo Serviço, a freqüência de complicações foi alta, independentemente do peso de nascimento. A presença de bactéria no LCR associou-se à maior freqüência de convulsões e mortalidade. A necessidade de manutenção do tratamento por tempo mais prolongado nos recém-nascidos de baixo peso sugere maior gravidade da doença neste grupo de neonatos. / Bacterial meningitis in the neonatal period is a severe disease, associated to elevated mortality and sequelae in around 12 to 29% of the survivors. Newborns whose birth weight is < 2,500g have a 3-fold increase in the risk of acquiring meningitis when compared to those whose weight is >= 2,500; among those with very low birth weight (< 1,500g), the risk increases 17-fold. Objectives: General: to describe the clinical picture and the complications of bacterial meningitis in two groups of newborns, considered according to birth weight (< 2,500g or >= 2,500g). Specific: to describe and compare the etiological agents, the frequency of neurological signs and symptoms and complications, mortality rate and duration of treatment in both groups. Methods: Observational study of 87 newborns with bacterial meningitis, admitted at the Neonatal Intensive Care Unit (NICU) of Instituto da Criança of Hospital das Clínicas of the University of São Paulo School of Medicine, during an 11-year period (January 1994 to December 2004). The data were obtained through the analysis of hospital files. Statistical analysis was carried out with Fisher\'s exact test and the non-parametric Mann Whitney test. Results: Bacteria were identified in the cerebrospinal fluid (CSF) of 39% of the patients, with 50% of them being Gram-positive and 50%, Gram-negative. Most neonates presented unspecific signs and symptoms: fever (63.2%), irritability (31%), and lethargy (26.4%). The neurological findings occurred in 35.3% of the cases. Complications occurred in 48.2% of the neonates, and were mainly seizures (23%), intracranial hemorrhage (14.9%) and hydrocephalus (13.8%) with a mortality rate of 11.5%. At the comparison between clinical evolution and birth weight, associations between weight >= 2,500g and seizures (p=0.047), weight >= 2,500g and concave fontanel (p=0.019), bacteria in the CSF and complications (p=0.008) and bacteria in the CSF and death (p=0.043) were observed. Conclusions: The etiological agents most often identified in the CSF were enterobacteria (41%), followed by B Streptococcus (17.5%), non-B Streptococcus (17.5%), Staphylococcus aureus (11.7%), Neisseria meningitidis (8.8%) and Enterococcus faecalis(3.0%), with no statistical difference between the type of bacteria and birth weight. The predominant signs and symptoms were unspecific, with neurological findings in 35% of the cases. The higher frequency of neurological signs and symptoms in newborns with birth weight >= 2,500g suggest a higher degree of central nervous system maturity in these infants. Although the mortality was lower than that observed in previous studies at the same Service, the frequency of complications was high, regardless of birth weight. The presence of bacteria in the CSF was associated to a higher frequency of seizures and mortality. The need for prolonged treatment in newborns with low birth weight suggests higher disease severity in this group of neonates.

Endotoxin or Lipopolysaccharide (LPS) is the invariant structural component of gram negative bacterial outer membranes and is the chief causative factor of Sepsis or endotoxic shock. Sepsis is a syndrome that has very high mortality rates even in this age of excellent therapeutics and critical patient care. The treatment for sepsis till date remains nonspecific and supportive due to lack of effective anti-endotoxic drugs. Sepsis is initiated when the circulating bacteria shed LPS from their cell envelopes. Shed LPS aggregates are recognized by LPS binding proteins and receptors, which activate the host's immune system. Uncontrolled and excessive stimulation of the host's immune system precipitates endotoxic shock which in advanced cases involving multiple system organ failure inevitably lead to patient's death. Many strategies have been tested out to combat this deadly affliction. One of the attractive clinical modalities in sepsis treatment is the use of peptides as LPS sequestering anti-endotoxic drugs. A classical peptide antibiotic of this class is Polymyxin B (PMB) a cyclic cationic acylated molecule, that recognizes LPS with a very high affinity. This thesis describes kinetics and thermodynamics of PMB-LPS interactions and applies these parameters over a framework of different models so as to gain insights into the structure-function relationships that govern the interactions of this peptide with endotoxin(s). Classical biophysical techniques like fluorescence, circular dichroism spectroscopy, stopped flow kinetics, titration calorirnetry (ITC) and the relatively new technique of Surface Plasmon Resonance (SPR) have been employed to dissect out the mechanism of the range of non-covalent forces that are involved in peptide-endotoxin recognition. Certain proteins that exhibit LPS binding activity have also been studied to gains insight about their mode of action. Implications of these studies for designing peptides that have better anti-endotoxic properties are also highlighted. The first chapter introduces and highlights the clinical features of sepsis. It also attempts to shed light on the LPS mediated signal transduction pathway that leads to endotoxic shock. This chapter also briefly explains the roles of many LPS receptors that are present in the human system and their specific roles in the signal transduction pathways. The second part of this chapter deals with the role of cationic peptides as anti-endotoxic drugs. Certain key functional aspects of these peptides, which impart in them, the desirable property of LPS recognition have also been discussed The second chapter describes the kinetic studies undertaken to unravel the exact mechanism of LPS-PMB interaction. The studies reveal that PMB recognizes LPS in a biphasic manner, with the second, unimolecular isomerization step of the reaction being the rate-limiting step. The initial reaction is shown to be influenced by the presence of salt in the reaction medium. The dissociation phase of this interaction also shows a biphasic pattern. These data allow us to speculate upon the exact mechanism by which PMB is able to recognize LPS. The studies also shed light on some structural aspects that govern and confer such high LPS binding activity to PMB. Based on these a model has been proposed to explain this recognition (C.J. Thomas et al, 1998). The second chapter discuses the mode of action of various PMB analogs. These analogs have been chosen in terms of their mode of action as well as their structural similarly to PMB. The affinities of these analogs to LPS and lipid A were quantified using the Surface plasmon resonance (SPR) method. SPR, a technique that relies on the quantification of change in mass during a binary binding process occurring between an immobilized entity and a flowing ligand, is a rapid and sensitive method to measure biologically relevant interactions. SPR studies provide us with the binding constants and thermodynamic parameters that allow evaluation of the affinities of these peptides towards LPS (C.J.Thomas and A.Surolia, 1999). The third chapter discusses a hitherto unknown mode by which PMB acts on a LPS lamellae. The results of this study wherein the binding affinities of PMB and its analogs were performed on monolayers and tethered liposomes, show that PMB is able to remove specifically LPS or lipid A from monolayers or bilayer assemblies such as tethered liposomes. The exact mode of action of PMB is deciphered in the light of these new studies, which allow us to posit on the observed efficacy of PMB in neutralizing the endotoxin as compared to peptides with nearly similar affinities for LPS (C.J Thomas et al 1999). In the fourth chapter a series of 23 residue peptides, based on the sequence corresponding to the anti-sense strand of magainin gene have been synthesized. Magainin an amphiphilic helical peptide obtained from frog skins plays a vital role in the innate immune defense mechanisms of these organisms. It also exhibits LPS binding activity that makes it an attractive target as an anti-endotoxic drug. Biochemical and biophysical characterization of these peptides reveal that they have the tendency to perturb both the inner and the outer membranes of E.coli. The peptides are amphiphilic and have helical structure in a membrane bound environment. Three of the peptides tested have high affinities for lipid A that approach the values shown by PMB. The kinetic parameters obtained by stopped flow and SPR studies in conjunction with the therrnodynamic parameters obtained using ITC studies allow us to highlight the key structural features that need to be exhibited by peptides that are designed to be LPS recognizers. The studies also project the fact that ionic forces play an important role in the initial recognition of LPS by these peptides. Fortification of the might of these ionic charges increases affinity for LPS where as the hydrophobic residues that interact at the next phase of binding are more amenable to disruptions in contiguity. These factors are discussed using the helical wheel diagram that shows the clear amphiphilicity displayed by these peptides. (C.J Thomas et al Manuscript under preparation, 2000) Chapter six discusses the mode of action of certain LPS binding proteins. Limulus anti endotoxic factor (LALF) plays a vital role in the innate immune based defense systems of the horseshoe crab. Galectin-3 is a metal ion independent, galactosc binding Icctin of human origin with unknown functions. Both these phylogcntically-unrclatcd proteins exhibit LPS/lipid A recognizing properties. ITC and SPR studies have been used to determine the binding constants displayed by these proteins for lipid A. LALF bind to lipid A with very high affinity than compared to Galectin-3 and is also able to take away selectively lipid A from both monolayers and tethered liposomes. Galectin-3 does not show this property of LALF, which might account for its lowered affinities. Also structurally LALF has amphiphilic nature that confers high lipid A binding activity, which is clearly lacking in Galectin-3. These studies in conjunction with the knowledge gained from the study of LPS-PMB interaction stress on the importance of amphiphilicity in LPS recognition. (C.J Thomas et al Manuscript under preparation, 2000). The final chapter is a general discussion that attempts to collate all these kinetic and thermodynamic observations in the pursuit of designing small easily manipulatable peptides that exhibit high LPS binding activity. These studies are aimed to act as rough guidelines to the design of LPS sequestering peptides that might have better therapeutic and pharmacokinetic properties. The appendix to the main body of work presented in thesis are two pieces of work pertaining to the elucidation the kinetics and mechanism of sugar lectin interactions, when sugars are presented as glycolipids in monolayers or bilaycrs liposomes. Mode of the presentation of sugars at cell-surfaces in the form of glycolipids as ligands influence their recognition by macromolecular receptors like lectins. Appendix 1 is a study of the mode of action of Ulex europeus I lectin binding to H-fucolipid containing tethered liposomes, by SPR. Fucosylated sugars are often used as key markers in histochemical analysis of malignant cancerous tissues. Ulex lectin plays a vital role as a marker for identification of these tissues. The kinetics and thermodynamic parameters that are obtained in this study throw some light on the mode of recognition of glycolipid receptor by Ulex europeus I lectin (C.J Thomas and A. Surolia 2000). Appendix 2 is a study, that attempts to quantify the initial kinetic parameters that correlate the recognition of glycolipid receptors with their inclination at the membrane surface and the influence of charge on them by soyabean agglutinin (SBA), Abrus agglutinin I and II. Studies on the soyabean agglutinin-globoside interaction highlights the divalent cation mediated reorientation of these receptors on their accessibility and recognition to the agglutinin. The divalent cations are speculated to orient the oligosaccharide head groups in a spatial geometry that allows a heightened kinetics of their interaction by SBA. These studies reveal that the reorganization of the binding pocket of a lectin can also have a profound influence on ihc rates of recognition of a glycospingolipid ligand by a lectin as exemplified by Abrus agglutinin II- GM1 interactions (C.J Thomas ct al, Manuscript under preparation).

No description available.

Les molécules classiques du complexe majeur d’histocompatibilité de classe II (CMHII) sont des glycoprotéines de surface spécialisées dans la présentation de peptides, principalement dérivés de pathogènes extracellulaires, aux récepteurs des lymphocytes T CD4+ afin d’initier la réponse immunitaire adaptative. Elles sont encodées, avec celles du CMH de classe I, par les gènes les plus polymorphiques identifiés jusqu’à maintenant, avec plusieurs loci et une grande diversité allélique à chacun d’eux. De plus, le polymorphisme des gènes du CMHII n’est pas limité qu’aux séquences codantes. Il est également observé dans les promoteurs où on a démontré ses effets sur le niveau d’expression des gènes. La variation de la régulation d’un gène est considérée comme un facteur important et pour laquelle des modifications morphologiques, physiologiques et comportementales sont observées chez tous les organismes. Des séquences d’ADN répétées impliquées dans cette régulation ont été identifiées dans les régions non-codantes des génomes. D’un autre côté, la sélection par les pathogènes permettrait l’évolution et le maintien du polymorphisme des gènes du CMH chez les vertébrés. À ce sujet, plusieurs études ont montré l’implication de différents allèles du CMH dans la résistance ou la susceptibilité aux maladies. Cette étude avait pour objectifs de caractériser le polymorphisme du gène MHIIb chez l’omble de fontaine (Salvelinus fontinalis) et de documenter ses effets au niveau de la survie conférée par des allèles et/ou génotypes particuliers lors d’une infection, ainsi que sur la variation du niveau d’expression du gène dans différentes conditions. Dans une première partie, nous avons identifié un total de 6 allèles du gène MHIIb, désignés Safo-DAB*0101 à Safo-DAB*0601, qui montrent une grande similarité avec les séquences codantes provenant de poissons téléostéens et de l’humain. L’analyse des séquences du domaine b1 a permis de détecter l’effet d’une pression sélective positive pour maintenir le polymorphisme dans cette région de la molécule. Quatre de ces allèles ont été testés lors d’une expérience d’infection avec le pathogène Aeromonas salmonicida afin d’évaluer l’effet qu’ils pouvaient avoir sur la survie des poissons. Nous avons trouvé que l’allèle DAB*0101 était significativement associé à la résistance à la furonculose. En plus d’avoir été identifié chez les individus homozygotes pour cet allèle, l’effet a également été remarqué au niveau de la survie les poissons de génotype DAB*0101/*0201. À l’opposé, les facteurs de risque élevé obtenus pour les génotypes DAB*0201/*0301 et DAB*0301/*0401 suggèrent plutôt une association à la susceptibilité. Étant donné la faible fréquence à laquelle l’allèle DAB*0101 a été retrouvé dans la population, le modèle de la sélection dépendante de la fréquence pourrait expliquer l’avantage conféré par ce dernier et souligne l’importance de ce mécanisme pour le maintien du polymorphisme du gène MHIIb chez l’omble de fontaine. Dans une seconde partie, nous avons rapporté la présence d’un minisatellite polymorphique formé d’un motif de 32 nucléotides dans le second intron du gène MHIIb, et pour lequel un nombre exclusif de répétitions du motif a été associé à chaque allèle (69, 27, 20, 40, 19 et 25 répétitions pour les allèles DAB*0101 à DAB*0601 respectivement). L’expression relative de quatre allèles a été évaluée dans des poissons hétérozygotes aux températures de 6 ºC et 18 ºC. Les résultats indiquent que les allèles possédant un long minisatellite montrent une réduction de l’expression du gène d’un facteur 1,67 à 2,56 par rapport aux allèles qui en contiennent un court. De même, des allèles qui incluent des minisatellites de tailles similaires n’affichent pas de différence significative au niveau de l’abondance du transcrit aux deux températures. De plus, l’effet répressif associé aux longs minisatellites est amplifié à la température de 18 ºC dans des poissons de trois génotypes différents. Nous avons finalement observé une augmentation significative par un facteur 2,08 de l’expression totale du gène MHIIb à la température de 6 ºC. Ces résultats appuient l’implication des séquences d’ADN répétées dans la régulation de l’activité transcriptionnelle d’un gène et suggèrent qu’un minisatellite sensible aux différences de températures pourrait être soumis aux forces sélectives et jouer un rôle important dans l’expression de gènes et l’évolution des organismes poïkilothermes. / Classical major histocompatibility complex class II (MHCII) molecules are cell-surface glycoproteins specialized in the presentation of peptides, mainly derived from extracellular pathogens, to the antigen receptors of CD4+ T cells in the adaptive immune system. They are encoded, with those of the MHC class I, by the most polymorphic genes known to date, with multiple loci and high allelic diversity at each one. Moreover, the polymorphism within MHCII genes is not restricted to coding sequences. It has also been observed in promoters where it was shown to affect the expression level of the genes. Variation in gene regulation is believed to be an important factor from which modification in morphology, physiology or behaviour can be observed in all organisms. Repeated DNA sequences with functional roles in this regulation have been identified within the non-coding parts of the genomes. On the other hand, pathogen-driven selection is also believed to be important in the evolution and maintenance of the polymorphism of the MHC genes in vertebrates. Studies have shown the implication of different MHC alleles in disease resistance or susceptibility. In this study, our aims were to characterize the polymorphism of the MHIIb gene in brook charr (Salvelinus fontinalis), to document its effects on the survival conferred by specific alleles and/or genotypes following an infection and on the variation of the expression level of the gene in different environmental conditions. In a first part, we identified a total of 6 MHIIb alleles, designated Safo-DAB*0101 to Safo-DAB*0601, showing a high similarity to coding sequences from teleost fish and human. Analysis of the b1 domain sequences indicates the effect of a positive selection pressure to select polymorphic mutations in that region of the molecule. Four of these alleles were tested in a challenge experiment against the pathogen Aeromonas salmonicida to evaluate their effect on fish survival. We found that one allele, DAB*0101, was significantly associated with resistance to furonculosis. In addition to homozygotes for this allele, its resistance effect was also detected in the heterozygote individuals of the DAB*0101/*0201 genotype. In contrast, other allelic combinations, namely heterozygous genotypes DAB*0201/*0301 and DAB*0301/*0401 were significantly associated with increased susceptibility. Given that its frequency was relatively low in the population, the negative frequency dependant selection hypothesis could explain the advantage associated with the allele DAB*0101 over the other alleles and highlight the importance of this mechanism to sustain variation at the MHC in brook charr. In a second part, we reported the identification of a polymorphic minisatellite formed of a 32 nucleotides motif in the second intron of MHIIb gene, and for which distinctive repeat numbers of the motif were associated to each alleles (69, 27, 20, 40, 19 and 25 repeats for the DAB*0101 to DAB*0601 alleles respectively). Relative expression levels of four alleles were determined in heterozygous fish at temperature of 18 ºC and 6 ºC. Results indicate that alleles carrying the longest minisatellite showed a 1.67 to 2.56-fold reduction in the transcript expression relatively to the shortest one. In contrast, no significant differences were seen in the expression levels between alleles with comparable minisatellite length at both temperatures. Furthermore, the repressive activity associated to the longest minisatellite was more effective at temperature of 18 ºC in fish from three different genotypes. We finally observed a significant 2.08-fold up-regulation of the total MHII transcript amount at 6 ºC. The results support the implication of repeated DNA sequences in the regulation of the gene transcriptional activity and suggest that a temperature-sensitive minisatellite could potentially be submitted to selective forces and therefore play an important role in gene expression and evolution in ectothermic organisms.

Les molécules classiques du complexe majeur d’histocompatibilité de classe II (CMHII) sont des glycoprotéines de surface spécialisées dans la présentation de peptides, principalement dérivés de pathogènes extracellulaires, aux récepteurs des lymphocytes T CD4+ afin d’initier la réponse immunitaire adaptative. Elles sont encodées, avec celles du CMH de classe I, par les gènes les plus polymorphiques identifiés jusqu’à maintenant, avec plusieurs loci et une grande diversité allélique à chacun d’eux. De plus, le polymorphisme des gènes du CMHII n’est pas limité qu’aux séquences codantes. Il est également observé dans les promoteurs où on a démontré ses effets sur le niveau d’expression des gènes. La variation de la régulation d’un gène est considérée comme un facteur important et pour laquelle des modifications morphologiques, physiologiques et comportementales sont observées chez tous les organismes. Des séquences d’ADN répétées impliquées dans cette régulation ont été identifiées dans les régions non-codantes des génomes. D’un autre côté, la sélection par les pathogènes permettrait l’évolution et le maintien du polymorphisme des gènes du CMH chez les vertébrés. À ce sujet, plusieurs études ont montré l’implication de différents allèles du CMH dans la résistance ou la susceptibilité aux maladies. Cette étude avait pour objectifs de caractériser le polymorphisme du gène MHIIb chez l’omble de fontaine (Salvelinus fontinalis) et de documenter ses effets au niveau de la survie conférée par des allèles et/ou génotypes particuliers lors d’une infection, ainsi que sur la variation du niveau d’expression du gène dans différentes conditions. Dans une première partie, nous avons identifié un total de 6 allèles du gène MHIIb, désignés Safo-DAB*0101 à Safo-DAB*0601, qui montrent une grande similarité avec les séquences codantes provenant de poissons téléostéens et de l’humain. L’analyse des séquences du domaine b1 a permis de détecter l’effet d’une pression sélective positive pour maintenir le polymorphisme dans cette région de la molécule. Quatre de ces allèles ont été testés lors d’une expérience d’infection avec le pathogène Aeromonas salmonicida afin d’évaluer l’effet qu’ils pouvaient avoir sur la survie des poissons. Nous avons trouvé que l’allèle DAB*0101 était significativement associé à la résistance à la furonculose. En plus d’avoir été identifié chez les individus homozygotes pour cet allèle, l’effet a également été remarqué au niveau de la survie les poissons de génotype DAB*0101/*0201. À l’opposé, les facteurs de risque élevé obtenus pour les génotypes DAB*0201/*0301 et DAB*0301/*0401 suggèrent plutôt une association à la susceptibilité. Étant donné la faible fréquence à laquelle l’allèle DAB*0101 a été retrouvé dans la population, le modèle de la sélection dépendante de la fréquence pourrait expliquer l’avantage conféré par ce dernier et souligne l’importance de ce mécanisme pour le maintien du polymorphisme du gène MHIIb chez l’omble de fontaine. Dans une seconde partie, nous avons rapporté la présence d’un minisatellite polymorphique formé d’un motif de 32 nucléotides dans le second intron du gène MHIIb, et pour lequel un nombre exclusif de répétitions du motif a été associé à chaque allèle (69, 27, 20, 40, 19 et 25 répétitions pour les allèles DAB*0101 à DAB*0601 respectivement). L’expression relative de quatre allèles a été évaluée dans des poissons hétérozygotes aux températures de 6 ºC et 18 ºC. Les résultats indiquent que les allèles possédant un long minisatellite montrent une réduction de l’expression du gène d’un facteur 1,67 à 2,56 par rapport aux allèles qui en contiennent un court. De même, des allèles qui incluent des minisatellites de tailles similaires n’affichent pas de différence significative au niveau de l’abondance du transcrit aux deux températures. De plus, l’effet répressif associé aux longs minisatellites est amplifié à la température de 18 ºC dans des poissons de trois génotypes différents. Nous avons finalement observé une augmentation significative par un facteur 2,08 de l’expression totale du gène MHIIb à la température de 6 ºC. Ces résultats appuient l’implication des séquences d’ADN répétées dans la régulation de l’activité transcriptionnelle d’un gène et suggèrent qu’un minisatellite sensible aux différences de températures pourrait être soumis aux forces sélectives et jouer un rôle important dans l’expression de gènes et l’évolution des organismes poïkilothermes. / Classical major histocompatibility complex class II (MHCII) molecules are cell-surface glycoproteins specialized in the presentation of peptides, mainly derived from extracellular pathogens, to the antigen receptors of CD4+ T cells in the adaptive immune system. They are encoded, with those of the MHC class I, by the most polymorphic genes known to date, with multiple loci and high allelic diversity at each one. Moreover, the polymorphism within MHCII genes is not restricted to coding sequences. It has also been observed in promoters where it was shown to affect the expression level of the genes. Variation in gene regulation is believed to be an important factor from which modification in morphology, physiology or behaviour can be observed in all organisms. Repeated DNA sequences with functional roles in this regulation have been identified within the non-coding parts of the genomes. On the other hand, pathogen-driven selection is also believed to be important in the evolution and maintenance of the polymorphism of the MHC genes in vertebrates. Studies have shown the implication of different MHC alleles in disease resistance or susceptibility. In this study, our aims were to characterize the polymorphism of the MHIIb gene in brook charr (Salvelinus fontinalis), to document its effects on the survival conferred by specific alleles and/or genotypes following an infection and on the variation of the expression level of the gene in different environmental conditions. In a first part, we identified a total of 6 MHIIb alleles, designated Safo-DAB*0101 to Safo-DAB*0601, showing a high similarity to coding sequences from teleost fish and human. Analysis of the b1 domain sequences indicates the effect of a positive selection pressure to select polymorphic mutations in that region of the molecule. Four of these alleles were tested in a challenge experiment against the pathogen Aeromonas salmonicida to evaluate their effect on fish survival. We found that one allele, DAB*0101, was significantly associated with resistance to furonculosis. In addition to homozygotes for this allele, its resistance effect was also detected in the heterozygote individuals of the DAB*0101/*0201 genotype. In contrast, other allelic combinations, namely heterozygous genotypes DAB*0201/*0301 and DAB*0301/*0401 were significantly associated with increased susceptibility. Given that its frequency was relatively low in the population, the negative frequency dependant selection hypothesis could explain the advantage associated with the allele DAB*0101 over the other alleles and highlight the importance of this mechanism to sustain variation at the MHC in brook charr. In a second part, we reported the identification of a polymorphic minisatellite formed of a 32 nucleotides motif in the second intron of MHIIb gene, and for which distinctive repeat numbers of the motif were associated to each alleles (69, 27, 20, 40, 19 and 25 repeats for the DAB*0101 to DAB*0601 alleles respectively). Relative expression levels of four alleles were determined in heterozygous fish at temperature of 18 ºC and 6 ºC. Results indicate that alleles carrying the longest minisatellite showed a 1.67 to 2.56-fold reduction in the transcript expression relatively to the shortest one. In contrast, no significant differences were seen in the expression levels between alleles with comparable minisatellite length at both temperatures. Furthermore, the repressive activity associated to the longest minisatellite was more effective at temperature of 18 ºC in fish from three different genotypes. We finally observed a significant 2.08-fold up-regulation of the total MHII transcript amount at 6 ºC. The results support the implication of repeated DNA sequences in the regulation of the gene transcriptional activity and suggest that a temperature-sensitive minisatellite could potentially be submitted to selective forces and therefore play an important role in gene expression and evolution in ectothermic organisms.