Étude structurale et fonctionnelle du canal potassium dépendant du voltage KvAP

Les canaux ioniques dépendants du voltage sont responsables de l'initiation et de la propagation des potentiels d'action dans les cellules excitables. De nombreuses maladies héréditaires (channelopathies) sont associées à un contrôle défectueux du voltage par ces canaux (arythmies, épilepsie, etc.). L’établissement de la relation structure-fonction exacte de ces canaux est donc crucial pour le développement de nouveaux agents thérapeutiques spécifiques. Dans ce contexte, le canal procaryote dépendant du voltage et sélectif au potassium KvAP a servi de modèle d’étude afin d’approfondir i) le processus du couplage électromécanique, ii) l’influence des lipides sur l’activité voltage-dépendante et iii) l’inactivation de type closed-state. Afin de pallier à l’absence de données structurales dynamiques du côté cytosolique ainsi que de structure cristalline dans l’état fermé, nous avons mesuré le mouvement du linker S4-S5 durant le gating par spectroscopie de fluorescence (LRET). Pour ce faire, nous avons utilisé une technique novatrice du contrôle de l’état conformationnel du canal en utilisant les lipides (phospholipides et non phospholipides) au lieu du voltage. Un modèle dans l’état fermé a ainsi été produit et a démontré qu’un mouvement latéral modeste de 4 Å du linker S4-S5 est suffisant pour mener à la fermeture du pore de conduction. Les interactions lipides - canaux jouent un rôle déterminant dans la régulation de la fonction des canaux ioniques mais ne sont pas encore bien caractérisées. Nous avons donc également étudié l’influence de différents lipides sur l’activation voltage - dépendante de KvAP et mis en évidence deux sites distincts d’interactions menant à des effets différents : au niveau du senseur de voltage, menant au déplacement de la courbe conductance-voltage, et du côté intracellulaire, influençant le degré de la pente de cette même courbe. Nous avons également démontré que l’échange de lipides autour de KvAP est extrêmement limité et affiche une dépendance à l’état conformationnel du canal, ne se produisant que dans l’état ouvert. KvAP possède une inactivation lente particulière, accessible depuis l'état ouvert. Nous avons étudié les effets de la composition lipidique et de la température sur l'entrée dans l'état inactivé et le temps de récupération. Nous avons également utilisé la spectroscopie de fluorescence (quenching) en voltage imposé afin d'élucider les bases moléculaires de l’inactivation de type closed-state. Nous avons identifié une position à la base de l’hélice S4 qui semble impliquée à la fois dans le mécanisme responsable de ce type d'inactivation et dans la récupération particulièrement lente qui est typique du canal KvAP.

Le rôle de l’Oxygénation Extracorporelle par Membrane (ECMO) dans la réanimation cardio-pulmonaire

Rapport de stage présenté à la Faculté de médecine en vue de l'obtention du grade de Maître ès sciences appliquées (M.Sc.A.) en génie biomédical, option génie clinique.

A PVC plasticized membrane sensor for nickel ions

A new PVC membrane sensor, which is highly selective towards Ni (II) ions, has been developed using a thiophene-derivative Schiff base as the ionophore. The best performance was exhibited by the membrane having the composition percentage ratio of 5:3:61:31 (ionophore:NaTPB:DBP:PVC) (w=w), where NaTPB is the anion excluder, sodium tetraphenylborate and DBP is the plasticizing agent (dibutyl phthalate). The membrane exhibited a good Nernstian response for nickel ions over the concentration range of 1.0 10 1– 5.0 10 6M (limit of detection is 1.8 10 6 M) with a slope of 29.5 1.0mV per decade of activity. It has a fast response time of<20 s and can be used for a period of 4 months with good reproducibility. The sensor is suitable for use in aqueous solutions of a wide pH range of 3.2–7.9. The sensor shows high selectivity to nickel ions over a large number of mono-, bi- and trivalent cations. It has been successfully used as an indicator electrode in the potentiometric titration of nickel ions against EDTA and also for direct determination of nickel content in real samples – wastewater samples from electroplating industries and Indian chocolates.

A PVC Plasticized Membrane Sensor for Nickel Ions

A new PVC membrane sensor, which is highly selective towards Ni (II) ions, has been developed using a thiophene-derivative Schiff base as the ionophore. The best performance was exhibited by the membrane having the composition percentage ratio of 5:3:61:31 (ionophore:NaTPB:DBP:PVC) (w=w), where NaTPB is the anion excluder, sodium tetraphenylborate and DBP is the plasticizing agent (dibutyl phthalate). The membrane exhibited a good Nernstian response for nickel ions over the concentration range of 1.0 10 1– 5.0 10 6M (limit of detection is 1.8 10 6 M) with a slope of 29.5 1.0mV per decade of activity. It has a fast response time of<20 s and can be used for a period of 4 months with good reproducibility. The sensor is suitable for use in aqueous solutions of a wide pH range of 3.2–7.9. The sensor shows high selectivity to nickel ions over a large number of mono-, bi- and trivalent cations. It has been successfully used as an indicator electrode in the potentiometric titration of nickel ions against EDTA and also for direct determination of nickel content in real samples – wastewater samples from electroplating industries and Indian chocolates.

Biochemical Investigations on the Stability of Biological Membranes

In this project, an attempt has been made to study the stability of erythrocyte and lysosomal membranes biochemically. Erythrocytes were chosen for the study because of their ready availability and relative simplicity. Biological membranes forming closed boundaries between compartments of varying composition consist mainly of proteins and lipids. They are asymmetric, fluid structures that are thermodynamically stable and metabolically active. Normal cellular function begins with normal membrane structure and any variation in it may upset the normal functions. The degree of fluidity of a membrane depends on the chain length of its lipids and degree of unsaturation of constituent fatty acids. In response to environmental changes, many cells can regulate composition of their membranes to maintain the overall semi fluid environment necessary for many membrane associated functions. The assembly and Maintenance of membrane structures in cells is a dynamic process. The components are not only synthesized and inserted into a growing membrane but are also continuously degraded at a slower rate. This turnover process varies with each individual molecule.Lysosomes are important in the catabolic processes occurring in the cell. Lysosomes contain hydrolytic enzymes and are stable under normal conditions. In certain pathological conditions, the lysosomal membrane may rupture, releasing the hydrolytic enzymes into the cell and digestion of cell takes place as a whole. This is very dangerous. In normal life processes of multi cellular organisms, lysosomes rupture following the death of a cell and it may have some value as a built in mechanism for selfremoval of dead cells.An attempt has also been made in this project towards developing lysosome membrane stability as an index of fish spoilage during storage. Different membranes within the cell and between cells have different compositions as reflected in the ratio of protein to lipid. The difference is not surprising given the very different functions of membranes

PVC Supported Liquid Membrane and Carbon Paste Potentiometric Sensors Incorporating a Mn(III)-Porphyrin for the Direct Determination of Undissociated Paracetamol

PVC supported liquid membrane and carbon paste potentiometric sensors incorporating an Mn(III)-porphyrin complex as a neutral host molecule were developed for the determination of paracetamol. The measurements were carried out in solution at pH 5.5. Under such conditions paracetamol exists as a neutral molecule. The mechanism of molecular recognition between the Mn(III)-porphyrin and paracetamol, leading to potentiometric signal generation, is discussed.The sensitivity and selectivity toward paracetamol of carbon paste and polymeric liquid membrane electrodes incorporating an Mn(III)-porphyrin host were compared. The applicability of these sensors to the direct determination of paracetamol was checked by performing a recovery test in human plasma.

Biochemical Studies on the Protective Effect of Taurine on Experimentally Induced Myocardial infarction in Rats

The present study indicate that prior administration of taurine is effective in minimizing all the deleterious effects induced by isoproterenol, thereby justifying its use as a potent cytoprotective agent. The overall cardioprotective effect of taurine is probably related to its antioxidant property evidenced by its ability to reduce lipid peroxidation and to maintain the activities of free radical enzymes and nonenzymatic antioxidants, its membrane stabilizing action and to its hypolipidemic property.

Biochemical Studies on the Protective Effect of Taurine on Experimentally Induced Fulminat Hepatic Failure in Rats

Fulminant hepatic failure (FHF) is a dramatic and challenging syndrome in clinical medicine. Although an uncommon disorder, it is usually fatal and occurs in previously healthy person. While the causes of FHF remain unclear, viral hepatitis and drug-induced liver injury account for the majority of cases. Hepatitis E causes large-scale epidemics of hepatitis in the Indian subcontinent, involving hundreds of thousands of cases with high mortality. FHF is associated with several clinical features like jaundice, shrunken liver, easy bruising, low levels of serum proteins, fatigue, multi-organ failure etc and metabolic derangements like hypoglycemia, hyperlipidemia, hyponatremia, defective protein synthesis, reduced energy production, decreased rate of urea production etc. These disturbances are predominantly attributed to oxidative stress, membrane destabilization and osmolytic imbalances. The options available for these patients are quite minimal with liver transplantation being one of them. But the procedure is ridden with issues causing it to find less favor among the patients and the caregivers. Use of hepatoprotective and cytoprotective drugs, is being considered to be a more acceptable alternative as a strategy to enhance liver regeneration. In this regard use of taurine a naturally occurring amino acid that plays a crucial role in many physiological processes would prove to be effective. In the present study, hepatoprotective effect of taurine on a rat model of induced FHF was studied. Taurine supplementation has effectively counteracted the metabolic and structural aberrations in the liver caused by D-galactosamine intoxication.

Aqueous Sol-gel Process for Nanocrystalline Photocatalytic Titania, Transparent Functional Coatings and Ceramic Membrane

The present thesis develops from the point of view of titania sol-gel chemistry and an attempt is made to address the modification of the process for better photoactive titania by selective doping and also demonstration of utilization of the process for the preparation of supported membranes and self cleaning films.A general introduction to nanomaterials, nanocrystalline titania and sol-gel chemistry are presented in the first chapter. A brief and updated literature review on sol-gel titania, with special emphasis on catalytic and photocatalytic properties and anatase to rutile transformation are covered. Based on critical assessment of the reported information the present research problem has been defined.The second chapter describes a new aqueous sol-gel method for the preparation of nanocrystalline titania using titanyl sulphate as precursor. This approach is novel since no earlier work has been reported in the same lines proposed here. The sol-gel process has been followed at each step using particle size, zeta potential measurements on the sol and thermal analysis of the resultant gel. The prepared powders were then characterized using X-ray diffraction, FTIR, BET surface area analysis and transmission electron microscopy.The third chapter presents a detailed discussion on the physico-chemical characterization of the aqueous sol-gel derived doped titania. The effect of dopants such as tantalum, gadolinium and ytterbium on the anatase to rutile phase transformation, surface area as well as their influence on photoactivity is also included. The fourth chapter demonstrates application of the aqueous sol-gel method in developing titania coatings on porous alumina substrates for controlling the poresize for use as membrane elements in ultrafiltration. Thin coatings having ~50 nm thickness and transparency of ~90% developed on glass surface were tested successfully for self cleaning applications.

Characterization of Lipid Droplets and Functional Analysis of Lipid Droplet-Associated Proteins in Dictyostelium discoideum

Lipid droplets (LDs) are the universal storage form of fat as a reservoir of metabolic energy in animals, plants, bacteria and single celled eukaryotes. Dictyostelium LD formation was investigated in response to the addition of different nutrients to the growth medium. LDs were induced by adding exogenous cholesterol, palmitic acid (PA) as well as growth in bacterial suspension, while glucose addition fails to form LDs. Among these nutrients, PA addition is most effective to stimulate LD formation, and depletion of PA from the medium caused LD degradation. The neutral lipids incorporated into the LD-core are composed of triacylglycerol (TAG), steryl esters, and an unknown neutral lipid (UKL) species when the cells were loaded simultaneously with cholesterol and PA. In order to avoid the contamination with other cellular organelles, the LD-purification method was modified. The isolated LD fraction was analysed by mass spectrometry and 100 proteins were identified. Nineteen of these appear to be directly involved in lipid metabolism or function in regulating LD morphology. Together with a previous study, a total of 13 proteins from the LD-proteome were confirmed to localize to LDs after the induction with PA. Among the identified LD-proteins, the localization of Ldp (lipid droplet membrane protein), GPAT3 (glycerol-3-phosphate acyltransferase 3) and AGPAT3 (1-acylglycerol-3-phosphate-acyltransferase 3) were further verified by GFP-tagging at the N-termini or C-termini of the respective proteins. Fluorescence microscopy demonstrated that PA-treatment stimulated the translocation of the three proteins from the ER to LDs. In order to clarify DGAT (diacylglycerol acyltransferase) function in Dictyostelium, the localization of DGAT1, that is not present in LD-proteome, was also investigated. GFP-tagged DGAT1 localized to the ER both, in the presence and absence of PA, which is different from the previously observed localization of GFP-tagged DGAT2, which almost exclusively binds to LDs. The investigation of the cellular neutral lipid level helps to elucidate the mechanism responsible for LD-formation in Dictyostelium cells. Ldp and two short-chain dehydrogenases, ADH (alcohol dehydrogenase) and Ali (ADH-like protein), are not involved in neutral lipid biosynthesis. GPAT, AGPAT and DGAT are three transferases responsible for the three acylation steps of de novo TAG synthesis. Knock-out (KO) of AGPAT3 and DGAT2 did not affect storage-fat formation significantly, whereas cells lacking GPAT3 or DGAT1 decreased TAG and LD accumulation dramatically. Furthermore, DGAT1 is responsible for the accumulation of the unknown lipid UKL. Overexpression of DGAT2 can rescue the reduced TAG content of the DGAT1-KO mutant, but fails to restore UKL content in these cells, indicating that of DGAT1 and DGAT2 have overlapping functions in TAG synthesis, but the role in UKL formation is unique to DGAT1. Both GPAT3 and DGAT1 affect phagocytic activity. Mutation of GPAT3 increases it but a DGAT1-KO decreases phagocytosis. The double knockout of DGAT1 and 2 also impairs the ability to grow on a bacterial lawn, which again can be rescued by overexpression of DGAT2. These and other results are incorporated into a new model, which proposes that up-regulation of phagocytosis serves to replenish precursor molecules of membrane lipid synthesis, whereas phagocytosis is down-regulated when excess fatty acids are used for storage-fat formation.  

Facilitating folding of outer membrane proteins, roles of the periplasmic chaperone Skp and the outer membrane lipoprotein BamD

This thesis describes several important advancements in the understanding of the assembly of outer membrane proteins of Gram-negative bacteria like Escherichia coli. A first study was performed to identify binding regions in the trimeric chaperone Skp for outer membrane proteins. Skp is known to facilitate the passage of unfolded outer membrane proteins (OMPs) through the periplasm to the outer membrane (OM). A gene construct named “synthetic chaperone protein (scp)” gene was used to express a fusion protein (Scp) into the cytoplasm of E. coli. The scp gene was used as a template to design mutants of Scp suitable for structural and functional studies using site-directed spectroscopy. Fluorescence resonance energy transfer (FRET) was used to identify distances in Skp-OmpA complexes that separate regions in Scp and in outer membrane protein A (OmpA) from E. coli. For this study, single cysteine (Cys) mutants and single Cys - single tryptophan (Trp) double mutants of Scp were prepared. For FRET experiments, the cysteines were labeled with the tryptophan fluorescence energy acceptor IAEDANS. Single Trp mutants of OmpA were used as fluorescence energy donors. In the second part of this thesis, the function of BamD and the structure of BamD-Scp complexes were examined. BamD is an essential component of the β-barrel assembly machinery (BAM) complex of the OM of Gram-negative bacteria. Fluorescence spectroscopy was used to probe the interactions of BamD with lipid membranes and to investigate the interactions of BamD with possible partner proteins from the periplasm and from the OM. A range of single cysteine (Cys) and single tryptophan (Trp) mutants of BamD were prepared. A very important conclusion from the extensive FRET study is that the essential lipoprotein BamD interacts and binds to the periplasmic chaperone Skp. BamD contains tetratrico peptide repeat (TPR) motifs that are suggested to serve as docking sites for periplasmic chaperones such as Skp.

"A Sequence in Subdomain 2 of DBL1a of Plasmodium falciparum Erythrocyte Membrane Protein 1 Induces Strain Transcending Antibodies"

Immunity to severe malaria is the first level of immunity acquired to Plasmodium falciparum. Antibodies to the variant antigen PfEMP1 (P. falciparum erythrocyte membrane protein 1) present at the surface of the parasitized red blood cell (pRBC) confer protection by blocking microvascular sequestration. Here we have generated antibodies to peptide sequences of subdomain 2 of PfEMP1-DBL1a previously identified to be associated with severe or mild malaria. A set of sera generated to the amino acid sequence KLQTLTLHQVREYWWALNRKEVWKA, containing the motif ALNRKE, stained the live pRBC. 50% of parasites tested (7/14) were positive both in flow cytometry and immunofluorescence assays with live pRBCs including both laboratory strains and in vitro adapted clinical isolates. Antibodies that reacted selectively with the sequence REYWWALNRKEVWKA in a 15-mer peptide array of DBL1a-domains were also found to react with the pRBC surface. By utilizing a peptide array to map the binding properties of the elicited anti-DBL1a antibodies, the amino acids WxxNRx were found essential for antibody binding. Complementary experiments using 135 degenerate RDSM peptide sequences obtained from 93 Ugandan patient-isolates showed that antibody binding occurred when the amino acids WxLNRKE/D were present in the peptide. The data suggests that the ALNRKE sequence motif, associated with severe malaria, induces strain-transcending antibodies that react with the pRBC surface

A sequence in subdomain 2 of DBL1 alpha of plasmodium falciparum erythrocyte membrane protein 1 induces strain transcending antibodies

Immunity to severe malaria is the first level of immunity acquired to Plasmodium falciparum. Antibodies to the variant antigen PfEMP1 (P. falciparum erythrocyte membrane protein 1) present at the surface of the parasitized red blood cell (pRBC) confer protection by blocking microvascular sequestration. Here we have generated antibodies to peptide sequences of subdomain 2 of PfEMP1-DBL1 alpha previously identified to be associated with severe or mild malaria. A set of sera generated to the amino acid sequence KLQTLTLHQVREYWWALNRKEVWKA, containing the motif ALNRKE, stained the live pRBC. 50% of parasites tested (7/14) were positive both in flow cytometry and immunofluorescence assays with live pRBCs including both laboratory strains and in vitro adapted clinical isolates. Antibodies that reacted selectively with the sequence REYWWALNRKEVWKA in a 15-mer peptide array of DBL1 alpha-domains were also found to react with the pRBC surface. By utilizing a peptide array to map the binding properties of the elicited anti-DBL1 alpha antibodies, the amino acids WxxNRx were found essential for antibody binding. Complementary experiments using 135 degenerate RDSM peptide sequences obtained from 93 Ugandan patient-isolates showed that antibody binding occurred when the amino acids WxLNRKE/D were present in the peptide. The data suggests that the ALNRKE sequence motif, associated with severe malaria, induces strain-transcending antibodies that react with the pRBC surface.

Polimorfismos del gen Butirilcolinesterasa responsables de reacciones adversas en pacientes consumidores de “cocaína”

La butirilcolinesterasa humana (BChE; EC 3.1.1.8) es una enzima polimórfica sintetizada en el hígado y en el tejido adiposo, ampliamente distribuida en el organismo y encargada de hidrolizar algunos ésteres de colina como la procaína, ésteres alifáticos como el ácido acetilsalicílico, fármacos como la metilprednisolona, el mivacurium y la succinilcolina y drogas de uso y/o abuso como la heroína y la cocaína. Es codificada por el gen BCHE (OMIM 177400), habiéndose identificado más de 100 variantes, algunas no estudiadas plenamente, además de la forma más frecuente, llamada usual o silvestre. Diferentes polimorfismos del gen BCHE se han relacionado con la síntesis de enzimas con niveles variados de actividad catalítica. Las bases moleculares de algunas de esas variantes genéticas han sido reportadas, entre las que se encuentra las variantes Atípica (A), fluoruro-resistente del tipo 1 y 2 (F-1 y F-2), silente (S), Kalow (K), James (J) y Hammersmith (H). En este estudio, en un grupo de pacientes se aplicó el instrumento validado Lifetime Severity Index for Cocaine Use Disorder (LSI-C) para evaluar la gravedad del consumo de “cocaína” a lo largo de la vida. Además, se determinaron Polimorfismos de Nucleótido Simple (SNPs) en el gen BCHE conocidos como responsables de reacciones adversas en pacientes consumidores de “cocaína” mediante secuenciación del gen y se predijo el efecto delos SNPs sobre la función y la estructura de la proteína, mediante el uso de herramientas bio-informáticas. El instrumento LSI-C ofreció resultados en cuatro dimensiones: consumo a lo largo de la vida, consumo reciente, dependencia psicológica e intento de abandono del consumo. Los estudios de análisis molecular permitieron observar dos SNPs codificantes (cSNPs) no sinónimos en el 27.3% de la muestra, c.293A>G (p.Asp98Gly) y c.1699G>A (p.Ala567Thr), localizados en los exones 2 y 4, que corresponden, desde el punto de vista funcional, a la variante Atípica (A) [dbSNP: rs1799807] y a la variante Kalow (K) [dbSNP: rs1803274] de la enzima BChE, respectivamente. Los estudios de predicción In silico establecieron para el SNP p.Asp98Gly un carácter patogénico, mientras que para el SNP p.Ala567Thr, mostraron un comportamiento neutro. El análisis de los resultados permite proponer la existencia de una relación entre polimorfismos o variantes genéticas responsables de una baja actividad catalítica y/o baja concentración plasmática de la enzima BChE y algunas de las reacciones adversas ocurridas en pacientes consumidores de cocaína.