For applications from biosensor generation to synthetic biology, the ability to accurately and quantitatively generate input-output data from biological systems over a wide dynamic range is becoming increasingly important. This study has demonstrated that a simple approach utilising multiple promoters, recognising the same transcriptional activator but with differing affinities, linked to compatible reporter genes can achieve this goal. This simple system highlights that even for complex promoters with multiple binding sites we can use the ratio of two reporters to obtain accurate and reproducible input-output data for reporters contained on a high copy number plasmid without the need for any background subtraction or accurate determination of cell number. It has also demonstrated that the precise promoter strengths are not too crucial to the design, provided they are significantly different, as taking the ratio of either the high affinity/low affinity or medium affinity/low affinity channels give similar improvements over any single channel alone. The modularity of this system means that it should be possible to exchange the IPTG inducible promoter and hence place the ntrC* gene under the regulation of any environmentally important promoter. It should also be possible to simply construct different strength promoters for the same transcriptional activator by standard DNA synthesis techniques, therefore allowing direct ratiometric detection of specific active transcription factors. Finally, there is considerable interest in the biosensor field in the use of immobilised cells for field based applications. In these cases, determining the exact number of viable cells present at the time of use may be problematic and obtaining high signal levels may also be essential. In this regard, the use of ratiometric reporters from constructs on high copy number plasmids could alleviate many of these potential problems and significantly simplify the required biosensor detection equipment.

A ratiometric laser induced fluorescence (LIF) thermometry applied to micro-scale temperature measurement for natural convection flows. To eliminate incident light non-uniformity and imperfection of recording device, two fluorescence dyes are used: one is temperature sensitive fluorescence dye (Rhodamine B) and another is relatively temperature insensitive fluorescence dye (Rhodamine 110). Accurate and elaborate calibration for intensity ratio verses temperature obtained using an isothermal cuvette, which was controlled by two thermo-bathes. 488nm Ar-ion laser used for incident light and two filter sets used for separating each fluorescence emission. Thermally stratified filed of 10mm channel with micro-scale resolution measured within 1.3?C uncertainty of liner prediction with 23?m x 23?m spatial resolution. Natural convection flows at 10mm channel also observed. The several difficulties for applying to heated evaporating meniscus were identified and a few resolutions were suggested.

Research in the field of molecular neuroscience contributes a better perception of the events that trigger neurodegeneration. At the forefront of this work is the study of intracellular calcium as a consequence of mitochondrial dumping and NMDA receptor activation by glutamate. Increased intracellular calcium presages excitotoxicity with ultimate apoptosis of the cell. Among the many disorders involving this sequence is depression, a disorder that in and of itself is a risk factor for neurodegenerative disorders such as Alzheimer disease. The successful use of anti-depressants to alleviate the depressive state leads to the question about whether these pharmacological agents, as part of their effect to ameliorate depression, might have an effect on intracellular calcium. Until now, this has not been explored directly but such exploration was initiated with this thesis. As a model for astrocytes and neurons, two cell lines, C6 and SH-SY5Y were used. These were differentiated with all-trans retinoic acid into astrocyte-like and neuron-like cells. Graphic imaging of intracellular calcium by ratiometrics is not new, but what is new is using this technique to evaluate the effect of the antidepressants mirtazapine and citalopram on intracellular calcium fluxes induced by glutamate. Furthermore, comparing the ratiometric intracellular calcium flux in the presence of mirtazapine and citalopram to that of known NMDA blockers was also done for the first time. Also studied were the acute and chronic effects of mirtazapine and citalopram on cell viability. The antidepressant agents, mirtazapine and citalopram, were chosen for this study. Mirtazapine blocks the adrenergic and serotonergic inhibitory autoreceptors which results in the increased release of these neurotransmitters and increases their concentration in the synapse. And it also has been shown to have an anti-oxidant and a calcium modulatory effect. Citalopram has the highest degree of serotonin reuptake selectivity of all the selective serotonin reuptake inhibitors. The ratiometric studies found that mirtazapine and citalopram reduce the effect of glutamate-induced increase in relative [Ca2+]i by either a direct or indirect action on NMDA receptors. This effect is not similar to the NMDA blockers memantine and AP5. The supporting evidence is that CCCP, which normally releases calcium from mitochondria, has no effect in cells treated with acute mirtazapine or citalopram. This indicates that no calcium entered the cell – and subsequently none was taken up by mitochondria – in response to glutamate. However, these observations were with a limited number of cells and, therefore, these results will have to be verified by different techniques by different laboratories. In microplate studies, all drugs studied reduced cell viability but the mechanism behind this reduced viability remains to be determined. This may be due to mutations in enzymatic expression, uptake of drug through the cell membrane, or other perturbations. The reduction in cell viability induced by acute glutamate was attenuated by pretreatment with mirtazapine or citalopram. Moreover, chronic treatment of the cells with mirtazapine or citalopram for 10 weeks before acute treatment with glutamate either attenuated the effect on viability or reversed it. Based on this present study, mirtazapine and citalopram may be useful as neuroprotective agents to alleviate not only depression but also to reduce cell death in neurodegenerative diseases, trauma and stroke.

The pH of tumors and surrounding tissues is a key biophysical property of the tumor microenvironment that affects how a tumor survives and how it invades the surrounding space of normal tissue. Research into tumorigenesis and tumor treatment is greatly dependent on accurate, precise, and reproducible measurements. Optical imaging is generally regarded as the best choice for non-invasive and high spatial resolution measurements. Ratiometric fluorescence imaging and fluorescence lifetime imaging microscopy (FLIM) are two primary ways for measuring tumor pH.pH measurements in a window chamber animal model using a ratiometric fluorescence imaging technique is demonstrated in this dissertation. The experimental setup, imaging protocols, and results are presented. A significantly varying bias was consistently observed in the measured pH. A comprehensive analysis on the possible error sources accounting for this bias is carried out. The result of analysis reveals that accuracy of ratiometric method is most likely limited by biological and physiological factors.FLIM is a promising alternative because the fluorescence lifetime is insensitive to the biological and physiological factors. Photon noise is the predominant error source of FLIM. The Fisher information matrix and the Cramér-Rao lower bound are used to calculate the lowest possible variance of estimated lifetime for time-domain (TD) FLIM. A statistical analysis of frequency-domain (FD) FLIM using homodyne lock-in detection is also performed and the probability density function of the estimated lifetime is derived. The results allow the derivation of the optimum experimental parameters, which yields the lowest variance of the estimated lifetime in a given period of imaging time. The analyses of both TD and FD-FLIM agree with results of corresponding Monte Carlo simulations.

The importance of sensing Nitric Oxide (NO) in physiology and medicine has led us to explore the reactivity of NO with organometallic Re dyes. Rhenium complexes were synthesized with the ability to react with NO and sense it under physiological conditions. Fluorescent 1,10-phenantroline complexes (phen)Re(PPh3)(CO)2OSO2CF3 (1) and (phen)Re(CH3CN)(CO)2OSO2CF3 (3) can sense NO in the range of 10 - 150 mM showing a decrease in fluorescence response at 514 nm and 532 nm respectively, upon NO-donor addition (lexc = 360 nm). (phen)Re(THF)(CO)2OSO2CF3 (2) showed a ratiometric response with a decrease in fluorescence intensity at 585 nm and an increase at 445 nm. These complexes were characterized by FT-IR, 1H-NMR, 13C-NMR, and 19F‑NMR. The quantum yields (F) and lifetimes (t) were also determined. On the basis of 19F‑NMR and 1H-NMR spectroscopic evidence, the proposed mechanism of action involves dissociation of CF3SO3- (abbreviated as OTf-) together with PPh3, (for 1), THF (for 2), or CH3CN (for 3). Fluorescence microscopy showed that 1 permeates through the cell membrane of rat aortic endothelial cells (RAOEC) and 2 gives increase in cell fluorescence response at 450 nm when exogenous NO is added to RAOEC. The Re complexes of dppz (dppz = 2,2’-dipyrido[3,2-a:2,3’-c]phenazine) (dppz)Re(THF)(CO)2OSO2CF3 (A2) and (dppz)Re(CH3CN)(CO)2OSO2CF3) (A3) were synthesized using the same methods as for complexes 1 and 3. Even though the dppz complexes exhibited similar behavior than the phenanthroline analogs, the signal changes were small and the results were inconclusive. The a-Diimine Re complexes of Xy-DAD (XyDAD = 1,4-bis-[2,6-dimethylphenyl]-1,4-diazo-1,3-butadiene) (Xy-DAD)Re(THF)(CO)2OSO2CF3 (8) and (Xy-DAD)Re(CH3CN)(CO)2OSO2CF3 (9) showed reactivity with NO and CN- with a response in the visible range of the absorption spectrum. These diazadiene (DAD) complexes showed decreased reactivity with NO and CN- in the presence of oxidants. The i-PrDAD complexes (i-PrDAD = 1,4‑bis-[2,6-diisopropylphenyl]-1,4-diazo-1,3-butadiene) (i‑Pr‑DAD)Re(THF)(CO)2OTf (10) and (i‑Pr‑DAD)Re(CH3CN)(CO)2OTf (11) exhibited similar behavior with the Xy-DAD analogs, but the spectral changes were much smaller and the results were inconclusive. The ESI-MS Mass Spectrometry studies of the phenanthroline complexes 1, and 2, after reaction with NO-donor showed that 1 and 2 react with NO to give [Re(CO)2(NO)2S2]+ species, while (phen)Re(CO)3Cl and (phen)Re(CO)3OSO2CF3 do not show any metal-NO containing products, which is consistent with the fluorescence studies.

The H+-ATPase rich (HR) cells of zebrafish larvae are a sub-type of ion-transporting cell located on the yolk sac epithelium that are responsible for Na+ uptake and H+ extrusion. Current models of HR cell ion transport mechanisms in zebrafish larvae are well established, but little is known about the involvement of the various ion transport pathways in regulating intracellular acid-base status. In the present study, a ratiometric imaging technique using the pH indicator dye BCECF was developed to monitor intracellular pH (pHi) continuously in larval zebrafish HR cells in vivo. Initial validation experiments demonstrated that HR cells subjected to respiratory acidosis (1% CO2) or metabolic alkalosis (20 mM NH4Cl) exhibited changes in BCECF 513/438 emission ratios which were consistent with the expected effects of these treatments on pHi. Subsequent experiments focussed on the involvement of the two principal apical membrane acid excretory pathways, the Na+/H+ exchanger (isoform NHE3b; zslc9a3.2) and the H+-ATPase (atpv1aa) in pHi regulation. Additionally, the role of HR cell carbonic anhydrase (“CA2-like a”) was investigated because of its presumed role in providing H+ for Na+/H+ exchange and H+-ATPase. To do so, relative HR cell pHi changes were monitored during acid-base challenges in shams and in fish experiencing morpholino gene knockdown of either NHE3b, H+-ATPase or “CA2-like a”. The temporal pattern and extent of intracellular acidification during exposure of fish to 1% CO2 and the extent of post-CO2 alkalization were altered markedly in fish experiencing knockdown of “CA2-like a”, NHE3b or H+-ATPase. Although there were slight differences among the three knockdown experiments, the typical response was a greater degree of intracellular acidification during CO2 exposure and a reduced capacity to restore pHi to baseline levels post-hypercapnia. Knockdown of “CA2-like a”, although presumed to limit H+ availability to NHE3b and H+-ATPase, yielded qualitatively similar results to knockdown of either single H+ excretory pathway. The metabolic alkalosis and subsequent acidification associated with NH4Cl exposure and its washout were largely unaffected by gene knockdown. Overall, the results suggest markedly different mechanisms of intracellular acid-base regulation in zebrafish HR cells depending on the nature of the acid-base disturbance.

The use of spectrofluorometers to examine nanomaterials is quite popular using either fluorescence or synchronous measurements. However, understanding how a material’s optical properties can influence spectral acquisition are of great importance to accurately characterize nanomaterials. This dissertation presents a series of computational and experimental studies aimed at enhancing the quantitative understanding of nanoparticle interactions with matter and photons. This allows for more reliable spectrofluorometer based acquisition of nanoparticle containing solutions. Chapter I presents a background overview of the works described in this dissertation. Correction of the gold nanoparticle (AuNP) inner filter effect (IFE) on fluorophore fluorescence using PEGylated AuNPs as an external reference method is demonstrated in Chapter II. The AuNP IFE is corrected to quantify tryptophan fluorescence for surface adsorbed proteins. We demonstrate that protein adsorption onto AuNPs will only induce ~ 20% tryptophan fluorescence reduction instead of the commonly assumed 100% reduction. Using water Raman intensities to determine the effective path lengths of a spectrofluorometer for correction of fluorophore fluorescence is discussed in Chapter III. Using Ni(NO3)2 and K2Cr2O7 as Raman IFE references, the excitation and emission path lengths are found to exhibit chromophore and fluorophore independence, however path lengths are spectrofluorometer dependent. Finally, ratiometric resonance synchronous spectroscopy (R2S2) is discussed in Chapter IV. Using a combination of UV-vis and R2S2 spectroscopy, the optical cross sections of a wide range of nanomaterials were determined. Also on-resonance fluorescence in solution is demonstrated for the first time. The nanoparticles discussed range from photon absorbers, scatterers, simultaneous photon absorbers and scatterers, all the way to simultaneous photon absorbers, scatterers, and emitters.

Arsenic contamination of groundwater remains a serious health concern in many areas of the world. Developing countries such as Bangladesh and Nepal are particularly affected because access to high quality water infrastructure is low. Since the 1970s, most water in these countries is sourced from shallow tube wells installed to reduce the spread of diseases associated with poor water hygiene. In this goal they were successful, however by the mid 1990s it became apparent that many of these wells were contaminated by arsenic and that these countries’ rural poor were being slowly poisoned. No simple, cheap, and reliable test for arsenic exists, and efforts to mitigate arsenic contamination have been severely limited by this over the past two decades. Government backed well-testing efforts using commercially available field kits have many issues with reliability, safety, rigour, and transparency, and have lost their urgency over the past decade, while the expensive field test kits remain out of the reach of most ordinary people in these areas. Synthetic Biology offers the technology to develop a new class of biosensor by exploiting bacteria’s natural ability to sense and respond to levels of arsenic considerably lower than commercially available kits which are based on analytical chemistry. In order to reach this goal, we must first develop our understanding of the natural response to arsenic in our chosen host, B. subtilis. Although we have a reasonably good qualitative understanding of the operon responsible for arsenic sensing, very little quantitative analysis has been carried out, and a robust system for ratiometric characterisation has not been established in the bacteria. In this work, a robust platform for rapid ratiometric characterisation is established in B. subtilis. A rigorous mathematical model of the ars operon is developed and analysed before being verified experimentally. This new knowledge is then used to explore synthetic permutations to the natural system aimed at improving the sensor properties of the system. Finally, a biological architecture for an easily tunable biosensor with good characteristics is recommended.

Chez les eucaryotes supérieurs, la progression ordonnée du cycle cellulaire est régie par une dizaine de kinases Cdk-cyclines. Les altérations génétiques ou épigénétiques impliquant des oncogènes ou des gènes codant pour des suppresseurs de tumeurs sont souvent associées à l'expression ou l'activation aberrante des Cdks, favorisant ainsi la prolifération cellulaire incontrôlée et notamment le développement de cancers. Malgré la pertinence oncogénique et thérapeutique de ces protéines, leur détection est restée jusqu'à présent limitée à des méthodes indirectes et invasives. Dans ce contexte, mes travaux de thèse ont permis de développer un biosenseur peptidique fluorescent permettant de reconnaître spécifiquement les Cdk-cyclines. Associé à une stratégie de vectorisation non invasive basée sur l'utilisation de peptides vecteurs pénétrants, le biosenseur a été délivré efficacement dans les cellules. La mise au point d'une quantification ratiométrique du signal a par ailleurs permis d'évaluer l'abondance relative des Cdk-cyclines endogènes. Deux variants plus spécifiques de certains complexes ont pu être développés. Enfin, d'autres versions du biosenseur ont quant à elles permis d'évaluer sa biodistribution in vivo et de mettre au point un essai cellulaire en vue d'un criblage de petites molécules ayant un effet sur l'abondance relative des Cdk-cyclines. / Cdk-cyclins represent key regulators of cell cycle progression among superior eukaryotes. Genetic and epigenetic alterations involving oncogenes or tumor suppressor genes are often associated with aberrant expression or activation of Cdks, leading to the sustained proliferation of cells and by the way to the development of cancers. Despite the oncogenic and therapeutic relevance of these proteins, their detection has so far remained limited to indirect and invasive methods. My Ph.D. thesis work aimed in this context at developing peptidic fluorescent biosensors that specifically recognize Cdk-cyclins. Combined to cell-penetrating peptides, the biosensor was efficiently delivered into cells. Following the development of the signal ratiometric quantification, the relative abundance of endogenous Cdk-cyclins was directly evaluated in living cells. Two other variants, that are more specific towards specific Cdk-cyclin complexes, were also designed. Finally, the development of novel versions of the biosensor allowed us to evaluate its biodistribution in vivo and to set up a cell-based assay to screen small molecules having an effect on Cdk-cyclin relative abundance.

The diploma thesis deals with the evaluation of the economic situation of the company ABC, in the years 2012 to 2019. The first, theoretical part of the thesis describes financial indicators, regression and correlation analysis and time series. The practical part of the diploma thesis contains calculations of financial indicators, some of them are selected for statistical analysis, which further serves as a prediction of development in the next two years. The practical part also compares the results with the industry average. The last part of the work contains proposals that lead to the improvement of the financial situation of the selected company.