Design of a tool to study the fate of Chlamydia trachomatis infected cells

Chlamydia trachomatis has a unique obligate intracellular developmental cycle that ends by the lysis of the cell and/or the extrusion of the bacteria in order to allow for re-infections. While Chlamydia trachomatis infections are often asymptomatic the diagnosis of Chlamydia trachomatis is usually late, occurring after manifestation of persistency. Investigations on the consequences of long-term infections and the molecular mechanisms behind it will reveal light to what extent bacteria can modulate host cell function and what the ultimate fate of host cells after clearance of an infection is. Such studies on the host cell fate could be greatly facilitated if the infected cells become permanently marked during and after the infection. Therefore, this project intends to develop a new genetic tool that would allow permanently labeling of Chlamydia trachomatis host cells. The plan was to generate a Chlamydia trachomatis strain that encodes a recombinant CRE recombinase, fused to a secretory effector function of the Chlamydia type 3 secretion system (T3SS). Upon translocation into the host cell, this recombinant CRE enzyme could then, owing to its site-specific recombination function, switch a reporter gene contained in the host cell genome. To this end, the reporter line carried a membrane-tagged tdTomato (mT) gene flanked by two LoxP sequences followed by a GFP gene. The translocation of the recombinant CRE recombinase into this cell line was designed to trigger the recombination of the LoxP sites whereby the cells would turn from red fluorescence to green as an irreversible label of the infected cells. Successful execution of this mechanism would allow to draw a direct link between Chlamydia trachomatis infection and the subsequent fate of the infected cell.

Larvicidal activity of oil-resin fractions from the Brazilian medicinal plant Copaifera reticulata Ducke (Leguminosae-Caesalpinoideae) against Aedes aegypti (Diptera, Culicidae)

Oil-resin fractions from Copaifera reticulata Ducke (Leguminosae-Caesalpinoideae) were evaluated for larvicidal activity on third larval instars of Aedes aegypti, in searching for alternative control methods for this mosquito. The bioactive fractions were chemically monitored by thin-layer chromatography, ¹H and 13C nuclear magnetic resonance and mass spectrometry. Bioassays were performed using five repetitions, at a temperature of 28 ± 1°C, relative humidity of 80 ± 5% and light and dark cycles of 12h. Mortality was indicated by darkening of the cephalic capsule after 24h of exposure of the larvae to the solutions. The most active fractions were CRM1-4 (sesquiterpenes) and CRM5-7 (labdane diterpenes), which showed LC50 values of 0.2 and 0.8ppm, respectively.

Gold nanoparticles for plasmid delivery

Gene therapy presents an ideal strategy for the treatment of genetic as well as acquired diseases, such as cancer and typically involves the insertion of a functioning gene into cells to correct a cellular dysfunction or to provide a new cellular function. Gene delivery vectors are based in two models: viral and non-viral. Viral vectors have high transfection efficiency but their major barrier is immunogenicity. Since the non-viral vectors have no immunogenicity, these have been widely studied. Gold nanoparticles have been proposed as optimal delivery systems of genetic material, due their small size, high surface-to-volume ratio and the ability to be functionalized with multiple molecules. In the present work, an AuNP-based formulation was developed to deliver a plasmid in a colorectal cancer cell line, containing as reporter gene the gene encoding to EGFP. The delivery system resulted from the functionalization of 14 nm AuNP with a PEG layer (4300114 PEG chains/AuNP), which increases stability and biocompatibility of AuNPs; quaternary ammonium groups which provide positive charges that allow electrostatic binding of plasmid, which is considered the therapeutic agent to be transported into cells. The system developed was characterized by UV-vis spectroscopy, DLS, TEM and by electrophoretic mobility, yielding a formulation with 113.5 nm.Transfection efficiency of the formulation developed was evaluated through PCR and through EGFP expression by fluorescence microscopy and fluorescence spectroscopy. The internalization was observed 3h post transfection; however a low level of EGFP expression was achieved. After 24h of incubation, EGFP expression increases just 3 times compared to non-transfected cells. The commercial system (Lipofectamine) expressed EGFP 5 times more than the system developed AuNP@PEG@R4N+@pEGFP. This difference could be related to lower translocation to the nucleus.

Application of NMR RDC’s, relaxation and self-diffusion for the study of dynamic processes of small molecules in solution

Spin-lattice Relaxation, self-Diffusion coefficients and Residual Dipolar Couplings (RDC’s) are the basis of well established Nuclear Magnetic Resonance techniques for the physicochemical study of small molecules (typically organic compounds and natural products with MW < 1000 Da), as they proved to be a powerful and complementary source of information about structural dynamic processes in solution. The work developed in this thesis consists in the application of the earlier-mentioned NMR techniques to explore, analyze and systematize patterns of the molecular dynamic behavior of selected small molecules in particular experimental conditions. Two systems were chosen to investigate molecular dynamic behavior by these techniques: the dynamics of ion-pair formation and ion interaction in ionic liquids (IL) and the dynamics of molecular reorientation when molecules are placed in oriented phases (alignment media). The application of NMR spin-lattice relaxation and self-diffusion measurements was applied to study the rotational and translational molecular dynamics of the IL: 1-butyl-3-methylimidazolium tetrafluoroborate [BMIM][BF4]. The study of the cation-anion dynamics in neat and IL-water mixtures was systematically investigated by a combination of multinuclear NMR relaxation techniques with diffusion data (using by H1, C13 and F19 NMR spectroscopy). Spin-lattice relaxation time (T1), self-diffusion coefficients and nuclear Overhauser effect experiments were combined to determine the conditions that favor the formation of long lived [BMIM][BF4] ion-pairs in water. For this purpose and using the self-diffusion coefficients of cation and anion as a probe, different IL-water compositions were screened (from neat IL to infinite dilution) to find the conditions where both cation and anion present equal diffusion coefficients (8% water fraction at 25 ºC). This condition as well as the neat IL and the infinite dilution were then further studied by 13C NMR relaxation in order to determine correlation times (c) for the molecular reorientational motion using a mathematical iterative procedure and experimental data obtained in a temperature range between 273 and 353 K. The behavior of self-diffusion and relaxation data obtained in our experiments point at the combining parameters of molar fraction 8 % and temperature 298 K as the most favorable condition for the formation of long lived ion-pairs. When molecules are subjected to soft anisotropic motion by being placed in some special media, Residual Dipolar Couplings (RDCs), can be measured, because of the partial alignment induced by this media. RDCs are emerging as a powerful routine tool employed in conformational analysis, as it complements and even outperforms the approaches based on the classical NMR NOE or J3 couplings. In this work, three different alignment media have been characterized and evaluated in terms of integrity using 2H and 1H 1D-NMR spectroscopy, namely the stretched and compressed gel PMMA, and the lyotropic liquid crystals CpCl/n-hexanol/brine and cromolyn/water. The influence that different media and degrees of alignment have on the dynamic properties of several molecules was explored. Different sized sugars were used and their self-diffusion was determined as well as conformation features using RDCs. The results obtained indicate that no influence is felt by the small molecules diffusion and conformational features studied within the alignment degree range studied, which was the 3, 5 and 6 % CpCl/n-hexanol/brine for diffusion, and 5 and 7.5 % CpCl/n-hexanol/brine for conformation. It was also possible to determine that the small molecules diffusion verified in the alignment media presented close values to the ones observed in water, reinforcing the idea of no conditioning of molecular properties in such media.

Late onset sepsis and intestinal bacterial colonization in very low birth weight infants receiving long-term parenteral nutrition

INTRODUCTION: The purpose of this study was to establish the late onset sepsis (LOS) rate of our service, characterize the intestinal microbiota and evaluate a possible association between gut flora and sepsis in surgical infants who were receiving parenteral nutrition (PN). METHODS: Surveillance cultures of the gut were taken at the start of PN and thereafter once a week. Specimens for blood culture were collected based on clinical criteria established by the medical staff. The central venous catheter (CVC) tip was removed under aseptic conditions. Standard laboratory methods were used to identify the microorganisms that grew on cultures of gut, blood and CVC tip. RESULTS: 74 very low birth weight infants were analyzed. All the infants were receiving PN and antibiotics when the gut culture was started. In total, 21 (28.4%) infants experienced 28 episodes of LOS with no identified source. Coagulase negative staphylococci were the most common bacteria identified, both in the intestine (74.2%) and blood (67.8%). All infections occurred in patients who received PN through a central venous catheter. Six infants experienced episodes of microbial translocation. CONCLUSIONS: In this study, LOS was the most frequent episode in neonates receiving parenteral nutrition who had been submitted to surgery; 28.6% of this infection was probably a gut-derived phenomenon and requires novel strategies for prevention.

Technical optimization of the synthesis of flavours

The goal of this thesis is the investigation and optimization of the synthesis of potential fragrances. This work is projected as collaboration between the University of Applied Sciences in Merseburg and the company Miltitz Aromatics GmbH in Bitterfeld‐Wolfen (Germany). Flavoured compounds can be synthesized in different ways and by various methods. In this work, methods like the phase transfer catalysis and the Cope‐rearrangement were investigated and applied, for getting a high yield and quantity of the desired substances and without any by‐products or side reactions. This involved the study of syntheses with different process parameters such as temperature, solvent, pressure and reaction time. The main focus was on Cope‐rearrangement, which is a common method in the synthesis of new potential fragrance compounds. The substances synthesized in this work have a hepta‐1,5‐diene‐structure and that is why they can easily undergo this [3,3]‐sigma tropic rearrangement. The lead compound of all research was 2,5‐dimethyl‐2‐vinyl‐4‐hexenenitrile (Neronil). Neronil is synthesized by an alkylation of 2‐methyl‐3‐butenenitrile with prenylchloride under basic conditions in a phase‐transfer system. In this work the yield of isolated Neronil is improved from about 35% to 46% by according to the execution conditions of the reaction. Additionally the amount of side product was decreased. This synthesized hexenenitrile involved not only the aforementioned 1,5‐diene‐structure, but also a cyano group, that makes this structure a suitable base for the synthesis of new potential fragrance compounds. It was observed that Neronil can be transferred into 2,5‐dimethyl‐2‐vinyl‐4‐hexenoic acid by a hydrolysis under basic conditions. After five hours the acid can be obtained with a yield of 96%. The following esterification is realized with isobutanol to produce 2,5‐dimethyl‐2‐vinyl‐4‐hexenoic acid isobutyl ester with quantitative conversion. It was observed that the Neronil and the corresponding ester can be converted into the corresponding Cope‐product, with a conversion of 30 % and 80%. Implementing the Cope‐rearrangement, the acid was heated and an unexpected decarboxylated product is formed. To achieve the best verification of reaction development and structure, scrupulous analyses were done using GC‐MS, 1H‐NMR and 13C‐ NMR.

Histological and endoscopic features of the stomachs of patients with Chagas disease in the era of Helicobacter pylori

Introduction Most studies that have evaluated the stomachs of patients with Chagas disease were performed before the discovery of Helicobacter pylori and used no control groups. This study compared the gastric features of chagasic and non-chagasic patients and assessed whether gastritis could be associated with Chagas disease. Methods Gastric biopsy samples were taken from patients who underwent endoscopy for histological analysis according to the Updated Sydney System. H. pylori infection was assessed by histology, 16S ribosomal ribonucleic acid (rRNA) polymerase chain reaction (PCR), serology and the 13C-urea breath test. Patients were considered H. pylori-negative when all of these diagnostic tests were negative. Clinical and socio-demographic data were obtained by reviewing medical records and using a questionnaire. Results The prevalence of H. pylori infection (70.3% versus 71.7%) and chronic gastritis (92.2% versus 85%) was similar in the chagasic and non-chagasic groups, respectively; such as peptic ulcer, atrophy and intestinal metaplasia. Gastritis was associated with H. pylori infection independent of Chagas disease in a log-binomial regression model. However, the chagasic H. pylori-negative patients showed a significantly higher grade of mononuclear (in the corpus) and polymorphonuclear (PMN) (in the antrum) cell infiltration. Additionally, the patients with the digestive form of Chagas disease showed a significantly lower prevalence of corpus atrophy than those with other clinical forms. Conclusions The prevalence of H. pylori infection and of gastric histological and endoscopic features was similar among the chagasic and non-chagasic patients. Additionally, this is the first controlled study to demonstrate that H. pylori is the major cause of gastritis in patients with Chagas disease.

Development of human central nervous system 3D in vitro models for preclinical research

Neurological disorders are a major concern in modern societies, with increasing prevalence mainly related with the higher life expectancy. Most of the current available therapeutic options can only control and ameliorate the patients’ symptoms, often be-coming refractory over time. Therapeutic breakthroughs and advances have been hampered by the lack of accurate central nervous system (CNS) models. The develop-ment of these models allows the study of the disease onset/progression mechanisms and the preclinical evaluation of novel therapeutics. This has traditionally relied on genetically engineered animal models that often diverge considerably from the human phenotype (developmentally, anatomically and physiologically) and 2D in vitro cell models, which fail to recapitulate the characteristics of the target tissue (cell-cell and cell-matrix interactions, cell polarity). The in vitro recapitulation of CNS phenotypic and functional features requires the implementation of advanced culture strategies that enable to mimic the in vivo struc-tural and molecular complexity. Models based on differentiation of human neural stem cells (hNSC) in 3D cultures have great potential as complementary tools in preclinical research, bridging the gap between human clinical studies and animal models. This thesis aimed at the development of novel human 3D in vitro CNS models by integrat-ing agitation-based culture systems and a wide array of characterization tools. Neural differentiation of hNSC as 3D neurospheres was explored in Chapter 2. Here, it was demonstrated that human midbrain-derived neural progenitor cells from fetal origin (hmNPC) can generate complex tissue-like structures containing functional dopaminergic neurons, as well as astrocytes and oligodendrocytes. Chapter 3 focused on the development of cellular characterization assays for cell aggregates based on light-sheet fluorescence imaging systems, which resulted in increased spatial resolu-tion both for fixed samples or live imaging. The applicability of the developed human 3D cell model for preclinical research was explored in Chapter 4, evaluating the poten-tial of a viral vector candidate for gene therapy. The efficacy and safety of helper-dependent CAV-2 (hd-CAV-2) for gene delivery in human neurons was evaluated, demonstrating increased neuronal tropism, efficient transgene expression and minimal toxicity. The potential of human 3D in vitro CNS models to mimic brain functions was further addressed in Chapter 5. Exploring the use of 13C-labeled substrates and Nucle-ar Magnetic Resonance (NMR) spectroscopy tools, neural metabolic signatures were evaluated showing lineage-specific metabolic specialization and establishment of neu-ron-astrocytic shuttles upon differentiation. Chapter 6 focused on transferring the knowledge and strategies described in the previous chapters for the implementation of a scalable and robust process for the 3D differentiation of hNSC derived from human induced pluripotent stem cells (hiPSC). Here, software-controlled perfusion stirred-tank bioreactors were used as technological system to sustain cell aggregation and dif-ferentiation. The work developed in this thesis provides practical and versatile new in vitro ap-proaches to model the human brain. Furthermore, the culture strategies described herein can be further extended to other sources of neural phenotypes, including pa-tient-derived hiPSC. The combination of this 3D culture strategy with the implemented characterization methods represents a powerful complementary tool applicable in the drug discovery, toxicology and disease modeling.

Synthesis and characterization of novel 4H-pyran-4-ylidene indole-based heterocyclic systems for several optical applications

The development of organic materials displaying high two-photon absorption (TPA) has attracted much attention in recent years due to a variety of potential applications in photonics and optoelectronics, such as three-dimensional optical data storage, fluorescence imaging, two-photon microscopy, optical limiting, microfabrication, photodynamic therapy, upconverted lasing, etc. The most frequently employed structural motifs for TPA materials are donor–pi bridge–acceptor (D–pi–A) dipoles, donor–pi bridge–donor (D–pi–D) and acceptor–pi bridge-acceptor (A–pi–A) quadrupoles, octupoles, etc. In this work we present the synthesis and photophysical characterization of quadrupolar heterocyclic systems with potential applications in materials and biological sciences as TPA chromophores. Indole is a versatile building block for the synthesis of heterocyclic systems for several optoelectronic applications (chemosensors, nonlinear optical, OLEDs) due to its photophysical properties and donor electron ability and 4H-pyran-4-ylidene fragment is frequently used for the synthesis of red light-emitting materials. On the other hand, 2-(2,6-dimethyl-4H-pyran-4-ylidene)malononitrile (1) and 1,3-diethyl-dihydro-5-(2,6-dimethyl-4H-pyran-4-ylidene)-2-thiobarbituric (2) units are usually used as strong acceptor moieties for the preparation of π-conjugated systems of the push-pull type. These building blocks were prepared by Knoevenagel condensation of the corresponding ketone precursor with malononitrile or 1,3-diethyl-dihydro-2-thiobarbituric acid. The new quadrupolar 4H-pyran-4-ylidene fluorophores (3) derived from indole were prepared through condensation of 5-methyl-1H-indole-3-carbaldehyde with the acceptor precursors 1 and 2, in the presence of a catalytical amount of piperidine. The new compounds were characterized by the usual spectroscopic techniques (UV-vis., FT-IR and multinuclear NMR - 1H, 13C).

Dinâmica do ecótono floresta-campo no sul do estado do Amazonas no Holoceno, através de estudos isotópicos e fitossociológicos

Com o emprego dos isótopos do carbono (12C, 13C, 14C) da matéria orgânica do solo (MOS) e das plantas, é apresentado um estudo comparativo entre perfis orgânicos de solos formados em depressões de áreas cobertas por ecossistemas de campos e florestas ao sul do estado do Amazonas, visando o entendimento da dinâmica da paleovegetação. A dinâmica da vegetação atual na região foi avaliada utilizando-se estudos fitossociológicos e caracterizações botânica e isotópica (delta13C) das espécies de plantas presentes em duas bordas floresta-campo. Teores de carbono orgânico total foram superiores nas camadas superficiais no campo, quando comparados com a floresta. Dados de delta13C associados à cronologia do 14C indicaram predomínio de plantas C3 no início do Holoceno em ambos os ecótonos. Entre aproximadamente 7.000-3.000 anos AP verificou-se a influência crescente de plantas C4, indicando regressão da floresta com possível presença de um clima mais seco. A partir de aproximadamente 3.000 anos AP os dados sugeriram expansão da floresta provavelmente relacionada ao retorno a um clima mais úmido. A presença de algumas espécies características da borda, como a Sclerolobium paniculatum e Himatanthus sucuuba, nos campos, sugere o atual avanço da floresta sobre os mesmos. Estas espécies estariam sendo as bioindicadoras desse avanço.

Origem e dinâmica da deposição dos sedimentos superficiais na Várzea do Lago Grande de Curuai, Pará, Brasil

Este estudo tem por objetivo caracterizar os sedimentos superficiais de um sistema de Várzea do Rio Amazonas, quanto a sua granulometria e ao seu teor orgânico, assim como compreender a origem e a hidrodinâmica destes sedimentos. 51 amostras de sedimento superficial foram coletadas na Várzea do Lago Grande de Curuai, localizada na margem direita do Rio Amazonas à aproximadamente 850km da foz. A granulometria, o teor em carbono orgânico e nitrogênio total, a razão entre o carbono e o nitrogênio (C/N), assim como o isótopo estável do carbono (δ13C) e do nitrogênio (δ15N) foram utilisados para este fim. Este estudo colocou em evidência que os sedimentos da várzea são finos, caracterizados principalmente pela presença de silte (médio à fino), seguido de argila e tem como principal fonte o Rio Amazonas e a Formação Alter do Chão. A presença de areia é pequena e extremamente localizada, próxima as áreas de deságue dos igarapés de terra firme que representam sua maior fonte. O teor de matéria orgânica nestes sedimentos varia entre 1,5 à 37% de carbono. Os resultados do isótopo do carbono (13C) e da razão C/N evidenciam a presença de matéria orgânica composta por diferentes fontes: material orgânico terrígeno, macrofítico, solos, material orgânico transportado pelo rio, e um componente fitoplanctônico.

Triterpenos das folhas de Minquartia guianensis Aubl. (Olacaceae)

Este artigo descreve o isolamento dos triterpenos lupeol, taraxerol, lupen-3-ona e esqualeno obtido do extrato diclorometânico das folhas da espécie Minquartia guianensis Aubl., pertencente à família Olacaceae. Estes terpenóides foram isolados através de técnicas cromatográficas e identificados utilizando Ressonância Magnética Nuclear (RMN) de ¹H e de 13C. Na literatura disponível, este é o primeiro relato destes triterpenos em M. guianensis.

Reconstituição paleoambiental do Lago Santa Ninha, Várzea do Lago Grande de Curuai, Pará, Brasil

Este estudo teve por objetivo reconstituir as mudanças paleoambientais e paleohidrológicas no baixo Amazonas. Um testemunho de sedimento foi coletado no Lago Santa Ninha, na várzea do Lago Grande de Curuai, localizada na margem direita do Rio Amazonas a aproximadamente 850 km da foz. O teor de água, a granulometria, as datações com carbono 14, os conteúdos de carbono orgânico e nitrogênio total e o isótopo estável do carbono (δ13C) foram utilizados para determinar os processos sedimentares a que o meio esteve submetido. O testemunho estudado possui 270 cm de comprimento que corresponde a um período de 5600 anos cal AP. Este estudo colocou em evidência diferentes ambientes sedimentares: na base do testemunho até 4900 anos cal AP há uma vegetação inundada que foi gradualmente substituida por bancos de gramíneas e por uma planicie com secas sazonais em 4000 anos cal AP até alcançar, desde 600 anos AP as condições atuais deste lago. Estas alterações podem ter ocorrido em decorrência de mudanças no ciclo hidrológico do Rio Amazonas que, por sua vez, também são reflexos de alterações climáticas.

Constituintes químicos, fenóis totais e atividade antioxidante de Sterculia striata St. Hil. et Naudin

A investigação fitoquímica das cascas do caule de Sterculia striata St. Hil. et Naudin, através de métodos cromatográficos, conduziu ao isolamento dos esteróides sitosterol, estigmasterol e sitosterol-3-O-β-D-glicopiranosídeo, além de quatro triterpenóides pentacíclicos, o lupeol, 3-β-O-acil lupeol, lupenona e ácido betulínico. As estruturas desses compostos foram identificadas por análise dos espectros de RMN ¹H e 13C e comparações com dados da literatura. Para determinação do teor de fenóis totais do extrato etanólico de S. striata utilizou-se o reativo Folin Ciocalteu, enquanto na avaliação da atividade antioxidante empregou-se o radical livre DPPH. Este é o primeiro trabalho descrevendo o estudo químico com as cascas do caule desta espécie.

Impacto da conversão floresta - pastagem nos estoques e na dinâmica do carbono e substâncias húmicas do solo no bioma Amazônico

O presente estudo avaliou as consequências do desmatamento e a utilização do solo com Brachiaria brizantha em relação ao estoque e dinâmica de C e frações húmicas em duas floresta-pastagem no Acre. A primeira localizada sequências município de Rio Branco em área de Floresta Aberta com bambu e palmeira e duas pastagens de B. brizantha de 3 e 10 anos com predomínio de Argissolo Vermelho-Amarelo alítico plíntico. O segundo situado no município de Senador Guiomard em área de Floresta Densa e pastagem de B. brizantha de 20 anos em Latossolo Vermelho-Amarelo distrófico. Em cada local foram coletadas, em triplicata, amostras de solos nas profundidades de 0-5, 5-10, 10-20 e 20-40 cm. Nestas amostras foram avaliadas as características físico-químicas, o C das substâncias húmicas e da matéria orgânica leve, e a composição isotópica do solo e das respectivas frações orgânicas até 1 m de profundidade, determinando o percentual de C derivado da pastagem e da floresta. Houve incremento nos estoques de C do solo e nos valores de δ13C do solo com o tempo de utilização da pastagem, em ambas as sucessões. A porcentagem de C derivado de pastagem foi expressiva na camada superficial do sistema com 20 anos de uso, com proporções que chegaram a 70% do C total. Os valores de δ13C para os ácidos húmicos variaram de -12,19 a -17,57 ‰, indicando maior proporção de C derivado da pastagem. A estabilidade estrutural da MOS, inferida pela relação humina com as frações ácido fúlvico e ácido húmico (HUM/FAF+FAH), tenderam a diminuir nos ecossistemas de pastagem quando comparada com as florestas naturais.