We have constructed a single molecule detection system with the capability to simultaneously measure many parameters, including transient fluorescence intensity, fluorescence lifetime, and photon anti-bunching behavior via the Hanbury Brown-Twiss photon-correlation technique. In addition, we apply the system to study the single DiI (1, 1 '- dioctadecyl- 3, 3 , 3 ', 3 ' - tetramethylindocarbocyanine perchlorate) molecule, to characterize the photo-physical behaviors. Cyanine dyes are the molecules that constitute of two nitrogen centers, one of which is positive charged, and is linked by a conjugated chain with odd number of carbon atoms to the other nitrogen center. Cyanine dyes are interested in the photo sensitization, optical recording media, nonlinear optics, laser dyes, and many interesting photophysical and photochemical behaviors. Among them, DiI plays an important role in single molecule fluorescence investigations. The high photo-stability, good QE, and low inter-system crossing rates, make it a pioneer for the widely investigations in single molecule studies. Our experimental goal is to understand the characteristic of the monitored single molecule by the measuring photo-physical parameters. Our results include the typical behaviors in DiI molecules: clear on-off blinking, fluorescence anti-bunching, one-step photo-bleaching, and consistent fluorescence polarization orientation. In addition, we also observed some change during measurement, which indicates the corresponding change of structure. Few molecules also exhibit non-zero probability around the zero delay time, which indicates the simultaneous existence of more than one quantum emitters in the detected region. These results demonstrate that the parameters are essential for understanding and characterizing the observed molecules in single molecule level.

Yes / This study used fluorescence excitation-emission matrices (EEMs) analysis to investigate the characteristics of natural organic matter (NOM) in treated water using okra crude extract (OCE), sabdariffa crude extract (SCE) and kenaf crude extract (KCE) as coagulants. In addition, an assessment of the impact of purified okra protein (POP), purified sabdariffa protein (PSP) and purified kenaf protein (PKP) was undertaken. The performance evaluation of these coagulants in terms of increase or decrease in dissolved organic carbon (DOC) was compared with Peak T fluorescence intensity observed at excitation wavelength 220–230 nm, and emission wavelength 340–360 nm. Fluorescence analysis of water treated with the crude extracts identified the removal of DOC in peaks A and C region whereas the increase in DOC from the protein was predominantly found in peaks T and B region. Furthermore, it was observed that the purified proteins were noted to be capable of reducing the DOC concentration in raw water where all fluorophores were not detected. The application of OCE, SCE and KCE yielded an increase in DOC of 65, 61 and 55% respectively, corresponding to increases of 65, 29 and 54% in peak T fluorescence intensities, at 100 mg/l dose. Furthermore, DOC concentration was reduced by 25, 24 and 18% using POP, PSP and PKP respectively as coagulants with corresponding decreases in fluorescence intensity of 46%, 44 and 36% in POP, PSP and PKP, at a lower dose of 0.1 mg/l. Therefore, it is clear that Peak T fluorescence intensity could be used to characterise organic matter in treated water using natural extracts to assess final water quality. / Financial support given to this research work by the Nigerian Government through the Tertiary Education Trust Fund (TETfund/AST &D/2013/2014/CE/02)

La pression rencontrée par les organismes sur Terre varie de la pression atmosphérique à 110 MPa atteinte dans la fosse la plus profonde de l'océan. Même si Escherichia. coli n’est pas naturellement résistante à la pression, elle capable d'acquérir une résistance et même supporter un choc de pression de 2 GPa (~20 000 atm). L'une des réponses intéressantes d’E. coli à un choc sous létal de pression (100 MPa) est l'induction d'une réponse SOS dépendante de RecA due à des lésions double brins de l’ADN. La pression elle-même n'est pas capable de compromettre l'intégrité covalente de l'ADN. Des criblages ont permis d’isoler des souches d’E. coli résistantes à la pression qui révèlent qu'une endonucléase de restriction (ER) de type IV, Mrr, est le seul facteur responsable du clivage de l'ADN. Cette enzyme cible uniquement l'ADN méthylé et l’expression d’une MTase étrangère, M.HhaII, est également capable d'induire une réponse SOS dans des souches de E. coli en présence de Mrr. Ici, nous démontrons en utilisant des techniques de fluctuations d’intensité de fluorescence, in vivo et in vitro que Mrr est un présent sous la forme d’un tétramère dans les cellules non stressées. La pression est capable de dissocier Mrr en dimères actifs qui peuvent lier l'ADN et cliver à certains sites cryptiques. En revanche, la MTase HhaII favorise la forme dimeric de Mrr liée à l’ADN en raison de la méthylation de nombreux sites de haute affinité. Une analyse mutationnelle et un modèle d’homologie 3D de la protéine entière révèle la base structurelle probable du changement entre la forme tétramérique inactive à la forme dimérique active. Nous avons mis en pace un système permettant de faire de la microscopie sous pression (in vitro and in vivo) et nos résultats préliminaires ont confirmé notre modèle d’activation de Mrr. / The pressure encountered by organisms on Earth varies from the atmospheric pressure to 110 MPa as reached in the deepest trench of the ocean. Although Escherichia coli is not naturally resistant to high pressure, it is capable of acquiring pressure resistance and withstanding a pressure shock up to 2 GPa (~20,000 atm). When exposed to a sub-lethal pressure shock (100 MPa) E. coli induces a RecA-dependent SOS response due to DNA double strand breaks. Pressure itself is not capable of compromising the covalent integrity of the DNA. Instead, screens for pressure-resistance E. coli mutants have revealed that a Type IV restriction endonuclease, Mrr is the only factor responsible for DNA cleavage. This enzymes targets only methylated DNA and expression of a foreign methyltransferase, M.HhaII, is also capable of inducing an SOS response in strains harboring Mrr. Here, we demonstrate using fluorescence fluctuation techniques in vivo and in vitro that Mrr is present as a tetramer in unstressed cells and that pressure dissociates Mrr into active dimers that can bind DNA and cleave at some cryptic sites. In contrast, the M.HhaII MTase pulls the Mrr tetramer-dimer equilibrium to the dimer-bound DNA form probably due to the methylation of many high-affinity sites. Mutational analysis associated with a 3D homology model of the full-length protein reveals the probable structural basis for the switch from an inactive tetramer to an active dimer. We set up a system that allows microscopy experiments (in vitro and in vivo) under pressure and preliminary results have confirmed our model of Mrr activation.

No description available.

Le travail présenté dans cette thèse est une contribution pour progresser vers des mesures thermiques plus quantitatives. Il s'agit de mesurer la température par la technique RIF de l'émission verte. Les travaux réalisés dans ce mémoire s'articulent en trois étapes. Au départ nous avons mesuré la température d'échauffement d'un cristal massif Sr0.3Cd0.7F2 codopés Er3+/Yb3+ d'épaisseur 0.3 mm. L'échauffement induit par l'excitation des ions Yb3+ à 974.4 nm a été mesurée à une distance (d) au bord de cristal, par l'émission verte des ions Er3+ excité par le laser rouge (652 nm) au bord du cristal. La seconde étape a eu pour but la mesure de la température d'échauffement du même cristal précédent, mais en dimension microscopique. Ces microparticules fluorescentes ont été fixées à l'extrémité d'une sonde thermique de Wollaston. L'échauffement des microparticules se fait par une excitation laser rouge à 652 nm ou par effet Joule en parcourant un courant électrique dans la sonde thermorésistive. La troisième étape a eu pour principal objectif la mesure de la température à l'échelle micrométrique en utilisant un microscope à force atomique (AFM) sur lequel est montée une sonde thermorésistive munie à son extrémité d'une microparticule fluorescente de Sr0.3Cd0.7F2 codopée Er3+/Yb3+ de 15 µm utilisée comme capteur de température. La technique est basée sur la variation de l'intensité de la fluorescence de la microparticule en contact avec une surface chaude. Cette nouvelle technique nous a permis d'obtenir une image cartographique de la température d'un microsystème, composé de lignes chauffantes submicroniques, chauffé par effet Joule. / The work presented in this thesis is a contribution to progress towards more quantitative thermal measurements. This is to measure the temperature by RIF technique green emission. The work in this thesis is divided into three stages. Initially we measured the temperature rise of a massive crystal Sr0.3Cd0.7F2 codoped Er3 + / Yb3 + 0.3 mm thick. The heat induced by the excitation of Yb3 + ions to 974.4 nm was measured at a distance (d) at the edge of crystal, the green emission of the Er3 + ions excited by red laser (652 nm) at the edge of the crystal.The second step was designed to measure the temperature of the heating of the same previous crystal, but in microscopic dimensions. These fluorescent microparticles were attached to the end of a thermal probe Wollaston. The temperature rise of the microparticles is by a red laser excitation at 652 nm or by Joule effect through an electric current in the probe thermorésistive.The third step was the main aim of measuring the temperature using a micrometric scale atomic force microscope (AFM) on which is mounted at its end provided with one of a fluorescent microparticle thermorésistive probe Sr0.3Cd0.7F2 codoped Er 3 + / Yb 3 + 15 microns used as a temperature sensor. The technique is based on the change in fluorescence intensity of the microparticle in contact with a hot surface. This new technique allowed us to obtain a map image of the temperature of a microsystem consisting of submicron heating lines, heated by Joule effect.

Synaptic vesicle recycling is the reuse of synaptic membrane material and proteins after vesicles have been exocytosed at the pre-synaptic terminal of a neuronal synapse. The discovery of the mechanisms by which recycling operates is a subject of active research. Within small mammalian central nervous system nerve terminals, two studied mechanisms of recovery are clathrin-mediated endocytosis and activity-dependent bulk endocytosis. Research into the comparative kinetics and mechanisms underlying these endocytosis mechanisms commonly involves time-series fluorescence microscopy of in vitro cultures. Synaptic proteins are tagged with fluorescent markers, or the synaptic vesicles are labelled with fluorescent dye. The change in fluorescence levels of individual synapses over time in response to stimuli is used to understand synaptic activity. The image analysis of these time-series images frequently requires substantial manual effort to extract the changing synaptic fluorescence intensity levels over time. This work focusses on two closely interlinked areas, the development of improved automated image analysis tools to facilitate the analysis of microscopy image data, and computational simulations to leverage the data obtained from these experiments to gain mechanistic insight into the underlying processes involved in synaptic vesicle recycling. The imaged properties of synapses within the time-series images are characterised, in terms of synapse movement during the course of an experiment. This characterisation highlights the properties which risk adding error to the extracted fluorescence intensity data, as analysis generally requires segmentation of regions of interest with fixed size and location. Where possible, protocols to optimise the manual selection of synapses in the image are suggested. The manual selection of synapses within time-series images is a common but time consuming and difficult task. It requires considerable skill on the part of the researcher to select synapses from noisy images without introducing error or bias. Automated tools for either general image segmentation or for segmentation of synapse-like puncta do exist, but have mixed results when applied to time-series experiments. This work introduces the use of knowledge of the experiment protocol into the segmentation process. The selection of synapses as they respond to known stimuli is compared against other current segmentation methods, and tools to perform this segmentation are provided. This use of synapse activity improves the quality of the segmented set of synapses over existing segmentation tools. Finally, this work builds a number of computational models, to allow published individual data points to be aggregated into a coherent view of overall synaptic vesicle recycling. The first is FM-Sim, a stochastic hybrid model of overall synapse recycling as is expected to occur during the course of an experiment. This closed system model handles the processes of exocytosis and endocytosis. It uses Bayesian inference to fit model parameters to experimental data. In particular, it uses the experimental protocol to separate the mechanisms and rates that may contribute to the observed experimental data. The second is a mathematical model of one aspect of synaptic vesicle recycling of particular interest - homoeostasis of plasma membrane integrity on the presynaptic terminal. This model provides bounds on efficiency of the studied endocytosis mechanisms at recovery of plasma membrane area during and after neuronal stimulus. Both the image analysis and the computational simulations demonstrated in this work provide useful tools and insights into current research of synaptic vesicle recycling and the role of activity-dependent bulk endocytosis. In particular, the utility of adding time-dependent experimental protocol knowledge to both the image analysis tools and the computational simulations is shown.

Health benefits related to consumption of whole grains have been attributed in part to phytochemical and micronutrient composition. Understanding the composition, structure and distribution of these components in different cereal grains is of potential importance in aiding the selection of whole grains and their processed fractions for inclusion in the diet, and as ingredients in development of new food products. The aim of this research was to characterise the chemical components in the botanical fractions of yellow corn, barley, wheat. Manual separation, a tedious and laborious technique that yields pure fractions, suitable for compositional analysis, was used to separate whole grains into pericarp, aleurone layer, germ and endosperm fractions. Component identification and quantification of tissue components was accomplished by several techniques. The study also explored the possibility of using spectral characteristics fluorescence intensity values to provide rapid estimates of the concentrations and distribution of ferulic acid (FA), a major phenolic compound in cereal grains. While composition of phenolic acids and carotenoids was similar, the distribution was significantly different (P < 0.05) among cereal types and grain fractions. Phenolic acids were concentrated in pericarp and aleurone fractions, followed by the germ and the endosperm had the lowest levels. Yellow corn exhibited the highest values. Carotenoids, lutein and zeaxanthin were concentrated in the germ and aleurone layer of wheat and barley while in yellow corn it was in the endosperm and aleurone layer. This is the first study to report on carotenoid composition of aleurone fractions. Mineral elements, thiamine and niacin were higher in wheat aleurone than in purple barley and yellow corn aleurone layers. These findings suggest that yellow corn aleurone layers have potential as a functional food ingredient despite the low micronutrient content. A positive, significant correlation (r= 0.421, p < 0.0001) was found between fluorescence intensity values and ferulic acid concentration. Thus, fluorescence intensity profiles are a promising approach for rapid assessment of FA concentration in grain in-situ. This work has provided information that would act as a database for selection of cereal fractions and guide the miller to obtain grain fractions with enriched levels of phytochemicals and micronutrients. / February 2016

Kidney bean proteins and peptides can be developed to serve as an important ingredient for the formulation of high quality foods or therapeutic products that may positively impact on body function and human health. The main goal of this thesis was to determine the in vitro structural and functional characteristics of major proteins and enzymatic protein hydrolysate of red kidney bean (Phaseolus vulgaris). Selective aammonium sulfate precipitation of the kidney bean proteins yielded 88% globulin and 7% albumin.The globulin and albumin are glycoproteins that contained ~4% and 45% carbohydrate contents, respectively. Physicochemical and functional characteristics of the globulin fraction, such as, gelation concentration, foam stability, emulsion capacity, and emulsion stability were superior to those of albumin. Reducing SDS-PAGE revealed vicilin with molecular weight of ~45 kDa as the major globulin in kidney beans. Circular dichroism spectroscopy of the purified vicilin showed reductions in α-helix, and β-pleated sheet conformations upon addition of NaCl or changes in pH. Likewise, the tertiary structures as observed from the near-UV CD spectra were also changed by shifts in pH conditions and NaCl addition. Far UV-CD showed increased β-sheet content up till 60oC from room temperature, but a steady loss in the tertiary structure as temperature was further increased; however, β-sheet structure was still detectable at 80oC. Differential scanning calorimetry thermograms showed a prominent endothermic peak with denaturation temperature at around 90oC, attributed to thermal denaturation of vicilin. Alcalase hydrolysis of kidney bean globulin produced multifunctional peptides that showed potential antihypertensive properties because of the in vitro inhibition of activities of renin and angiotensin I converting enzyme as well as the antioxidant properties. The <1 and 5-10 kDa peptide fractions exhibited highest (p<0.05) renin inhibition and the ability to scavenge 2, 2-Diphenyl-1-picrylhydrazyl free radical, inhibit peroxidation of linoleic acid and reduce Fe3+ to Fe2+. Based on this study, incorporation of kidney bean globulin as an ingredient may be useful for the manufacture of high quality food products. Likewise, the kidney bean protein hydrolysates, especially the <1 kDa fraction represent a potential source of bioactive peptides for the formulation of functional foods and nutraceuticals.

Kidney bean proteins and peptides can be developed to serve as an important ingredient for the formulation of high quality foods or therapeutic products that may positively impact on body function and human health. The main goal of this thesis was to determine the in vitro structural and functional characteristics of major proteins and enzymatic protein hydrolysate of red kidney bean (Phaseolus vulgaris). Selective aammonium sulfate precipitation of the kidney bean proteins yielded 88% globulin and 7% albumin.The globulin and albumin are glycoproteins that contained ~4% and 45% carbohydrate contents, respectively. Physicochemical and functional characteristics of the globulin fraction, such as, gelation concentration, foam stability, emulsion capacity, and emulsion stability were superior to those of albumin. Reducing SDS-PAGE revealed vicilin with molecular weight of ~45 kDa as the major globulin in kidney beans. Circular dichroism spectroscopy of the purified vicilin showed reductions in α-helix, and β-pleated sheet conformations upon addition of NaCl or changes in pH. Likewise, the tertiary structures as observed from the near-UV CD spectra were also changed by shifts in pH conditions and NaCl addition. Far UV-CD showed increased β-sheet content up till 60oC from room temperature, but a steady loss in the tertiary structure as temperature was further increased; however, β-sheet structure was still detectable at 80oC. Differential scanning calorimetry thermograms showed a prominent endothermic peak with denaturation temperature at around 90oC, attributed to thermal denaturation of vicilin. Alcalase hydrolysis of kidney bean globulin produced multifunctional peptides that showed potential antihypertensive properties because of the in vitro inhibition of activities of renin and angiotensin I converting enzyme as well as the antioxidant properties. The <1 and 5-10 kDa peptide fractions exhibited highest (p<0.05) renin inhibition and the ability to scavenge 2, 2-Diphenyl-1-picrylhydrazyl free radical, inhibit peroxidation of linoleic acid and reduce Fe3+ to Fe2+. Based on this study, incorporation of kidney bean globulin as an ingredient may be useful for the manufacture of high quality food products. Likewise, the kidney bean protein hydrolysates, especially the <1 kDa fraction represent a potential source of bioactive peptides for the formulation of functional foods and nutraceuticals.

This thesis aims to assess the possibility of the usage of various biological fixatives for fish cell and tissues samples in order to extend its storage for later flow cytometric measurement of DNA content. The model species chosen were sterlet and tench, from which three types of samples were obtained: blood and fin tissue of subadult / adult individuals and tail tissue of hatched larvae. Altogether 13 fixation methods were tested for each type of sample of both model species. Methods were chosen based upon their easy feasibility and low time-consumption. The samples were measured on flow cytometer in native state immediately after sampling and placing in physiological saline and after 1, 5 and 10 days of fixation during which they were stored in a fridge or in a freezer at -80 ?C. Their analysis was carried out simultaneously with standards native cells from tench fin tissue when investigating sterlet samples, and commercially available fixed trout erythrocytes for tench samples. A fluorochrome used was 4',6-diamidine-2'-phenylindole dihydrochloride (DAPI; with excitation/emission maxima 358 / 461 nm). Based on the evaluation of coefficients of variation (CV) of fixed samples and the changes in their fluorescence levels in comparison with native state, optimal procedures for extended storage of all types of samples from both model species are suggested.