In situ assays of N2 fixation activity, using the acetylene reduction technique, were performed in four successional stages of a Northern Wasatch Mountain subalpine forest ecosystem, elevation 2,800 m. Emphasis was made on rhizosphere fixation in association with Antennaria microphylla and Achillea millefolium. The vegetation period was approximately 100 days. Assays were performed in Saran bags. A defined amount of propane was injected at initiation of the assay and acetylene was generated from CaC2. Samples were analyzed for ethylene and propane. Data were evaluated assuming that the ethylene production was directly proportional to the increase in the ratio of ethylene to propane in the samples. Input of N by soil free-living N2 fixers in the meadow, the aspen, the fir and the spruce was 0.5, 0.3, 0.2 and 0.3 kg N ha-1 y-1, respectively. A higher activity in the presence of plant, as compared to the soil activity, was measured in 10 of the 16 assays, however, the increase was significant at three testings only. This might indicate a contribution by rhizosphere N2 fixation, but to an extent lower than was expected and therefore not detectable with the method used Leakage of gases from the test device was not corrected for in the method used for evaluation of data. This introduces and overestimation of the obtained activities that increases exponentially with a more rapid effusion rate. Correction for effusion from a closed device can be made provided quantitative analyses of the tracer gas. To determine a small difference between enclosures with and without plants the accuracies in the effusion rates must be high. Quantitative analyses were not required for evaluation according to the method used and therefore, the obtained effusion rates have too wide standard deviations for correction of the effusion rate. It was shown that the determined effusion rates with corresponding standard deviations might obscure a low rhizosphere N2 fixation activity. Acetylene reduction assays performed in open devices can not easily be corrected for diffusion of gases. The initial very rapid diffusion from an open device leads to a vastly overestimated acetylene reduction activity, when the diffusion is not corrected for.

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No description available.

Parallel detection of antibodies with different specificity has many potential applications in epidemiological research, vaccine development and in the diagnosis of allergies, autoimmune and infectious diseases. Although ELISA-based tests are suitable for this purpose, available assays can be time consuming and require large quantities of both sample and reagents thus limiting their application for mass screening. / Revisión por pares

Despite therapeutic advances, colorectal cancer still has a 45% mortality rate, and one of the most crucial problems is the development of acquired resistance to treatment with anticancer drugs. Thus the aims of this project are to develop drug-resistant colon cancer cell lines in order to identify mechanisms of resistance for the most commonly drugs used in colorectal cancer: 5-fluorouracil, oxaliplatin, and irinotecan. Following evaluation of drug sensitivity to these agents in an initial panel of eight colorectal cancer cell lines, 3 lines (DLD-1, KM-12 and HT-29) were selected for the development of 5-FU (3 lines), oxaliplatin (2) and irinotecan (1) resistant sublines by continuous drug exposure, with resistance confirmed using the MTT assay. Consistently resistant sublines were subject to a „stable isotope labelling with amino acids in cell culture‟ (SILAC) approach and a MudPIT proteomics strategy, employing 2D LC and Orbitrap Fusion mass spectrometric analysis, to identify novel predictive biomarkers for resistance. An average of 3622 proteins was quantified for each resistant and parent cell line pair, with on average 60-70 proteins up-regulated and 60-70 down-regulated in the drug resistant sublines. The validity of this approach was further confirmed using immunodetection techniques. These studies have provided candidate proteins which can be assessed for their value as predictive biomarkers, or as therapeutic targets for the modulation of acquired drug resistance in colorectal cancer.

Rhodococcus equi is an important pathogen in foals between one to six months of age and is a major cause of death in in these animals. In addition, R. equi has recently emerged as a significant opportunistic pathogen in immunosuppressed humans, especially those infected with HIV. Despite the ability of the organism to survive stressful growth conditions, for example, exposure to elevated temperature and oxygen radicals, the role of heat shock proteins in the pathogenesis of R. equi has not been well documented. In this project we developed and optimised methods to purify the heat shock protein DnaK from R. equi, using a combination of ion-exchange and affinity chromatography. The effectiveness of the purification protocols were assessed using SDS-PAGE and Western-blotting with anti-DnaK antibodies, and the enzymic activity of the purified DnaK was verified with an ATPase assay. ATPase assays were also used to investigate the roles of other heat shock proteins in enhancing the activity of DnaK.

<p> This thesis focuses on fundamental and applied aspects of sol-gel based affinity assays for screening membrane receptor targets. Fundamental studies investigate the role of non-specific interactions between polycationic polymers and sol-gel derived monoliths prepared from sodium silicate precursors. Previous studies from our group using time-resolved fluorescence anisotropy (TRFA) have shown that both the sidechain motion (Φ1) and backbone motion (Φ2) of polycationic polymers, such as poly-D-lysine, can be measured by fitting anisotropy decays of fluorescein labeled polymers to a two component hindered rotor model. These studies demonstrated that polycationic polymers remain fairly mobile in sol-gel derived materials made from sodium silicate precursors, despite the strong electrostatic interactions between the cationic polymers and the anionic silica materials. The first objective of my work was to assess the nature of the electrostatic interactions between several polycationic polymers and a silica material made from sodium silicate using a novel two-point labeling technique with a pyranine dye to determine if previous studies were indeed correct. Our results show that the two-point labeling technique with pyranine provides a more rigid interaction between the polymer and the dye compared to the previous labeling method using fluorescein, allowing for more accurate monitoring of dynamic motions of cationic polymers in sol-gel derived materials. The dynamics of poly-D-lysine entrapped in sol-gel derived materials was indeed seen to be highly restricted, contrary to results obtained in previous studies.</p> <p> While the first project provided a framework for understanding the effect of electrostatic interactions on the dynamics of biomolecules, it also provide valuable insight into the effect of non-specific interactions between cationic species and sol-gel derived materials in general. These considerations are important when using sol-gel based affinity columns for small molecule screening. The second study outlines a competitive affinity-based screening method using mass spectrometry (MS) detection that can help reduce the effect of non-specific interactions between test compounds and the column matrix in small molecule screening applications. This technique relies on the use of a high-affinity indicator compound pre-equilibrated on column to identify weak affinity ligands in mixtures through transient spikes in the indicator signal that result from the competition between the indicator and test compounds. The results of this study demonstrate the ability to identify weak affinity ligands for the nicotinic acetylcholine receptor (nAChR) using low to sub-picomole amount of active receptor on column. The technique results in a reproducible signal output that can potentially be used to obtain quantitative data on the binding affinities of target-ligand interactions. The assay is amenable to automation and can be performed at high speeds, thereby demonstrating the potential of this technique as a high-throughput screening tool for screening membrane receptors.</p> / Thesis / Master of Science (MSc)

Yes / The present study investigated the genoprotective and genotoxic effects of myricetin bulk (10 μM) and nano forms (20 μM) in the lymphocytes from pre-cancerous, monoclonal gammopathy of unknown significance (MGUS) patients and healthy individuals using the Comet and micronucleus assays. The study also evaluated the effect of myricetin on P53 expression levels, using the Western blot technique. Results showed that throughout the in-vitro treatment, lymphocytes from the patients group had higher levels of baseline DNA damage compared to the healthy group. Myricetin in both forms induced significant DNA damage, only at higher concentrations (>40 μM). The micronucleus assay showed a significant reduction (P < 0.01) in the frequency of micronuclei in mono-nucleated cells in the patient group treated with the nano form of myricetin at the non-toxic dose of 20 μM. There was a significant increase in both gene and protein P53 levels in lymphocytes isolated from healthy individuals and pre-cancerous patients. These results suggested a protective effect of myricetin and indicated its nutritional supplement potential for protection against cancer development among patients suffering from MGUS. / This study was kindly funded by Mr Nasir Qayyum, Bradford, UK.

Les enzymes sont les catalyseurs de toutes les réactions biochimiques. Leur dérégulation peut être impliquée dans de nombreuses pathologies graves. L’étude de ces réactions est importante pour dépister les anomalies, mieux comprendre le fonctionnement des enzymes et rechercher des modulateurs de leur activité. Le présent travail de thèse présente différents types d’essais enzymatiques basés sur l’électrophorèse capillaire pour étudier la cinétique d’enzymes variées. Le mode pré-capillaire où la réaction enzymatique est effectuée à l’extérieur du capillaire et les essais homogènes en-ligne en mode discontinu où la réaction est réalisée dans le capillaire, sont appliqués. Les méthodes développées sont optimisées pour assurer un mélange optimal des réactifs et une bonne séparation électrophorétique. Les constantes cinétiques et d’inhibition (Vmax, Km et IC50) de la réaction enzymatique sont déterminées et comparées à celles obtenues par les techniques classiques. Pour les essais en-ligne, plusieurs types de mélange (par application d’un champ électrique, par diffusion longitudinale ou diffusion transversale) des créneaux de réactifs sont utilisés selon le système enzymatique étudié. Finalement, jusqu’à quatre réactifs injectés successivement dans le capillaire sont mélangés avec succès. De nombreux essais sont effectués sur des matrices complexes (cellules, extraits de plantes). Le criblage d’inhibiteurs de référence et de synthèse est réalisé sur plusieurs kinases humaines : CDK1/cycline B, CDK5/p25, DYRK1A, GSK3!, PI3K, Akt et mTOR. Les essais développés se sont avérés être simples, rapides, quantitatifs, économes en réactifs et répétables. / Enzymes catalyze all enzymatic reactions. Their deregulation can be involved in several severe diseases. The study of these reactions is important to detect anomalies, to better understand enzyme functioning and to seek modulators of their activity. This thesis presents capillary electrophoresis based enzymatic assays developed to study kinetics of various enzymes. The pre-capillary mode in which the enzymatic reaction occurs outside the capillary and the incapillary plug-plug mode of homogenous assays where the reaction is performed inside the capillary are applied. The methods developed are optimized to ensure optimum reactant mixing and a good electrophoretic separation. The kinetic and inhibition constants (Vmax, Km and IC50) of the enzymatic reaction are determined by these assays and compared to the results obtained using conventional techniques. For in-capillary assays, several mixing types (by application of an electric field, by longitudinal diffusion or transverse diffusion) of the reactant plugs are used depending on the enzymatic system studied. Finally, up to four reactants injected successively in the capillary are successfully mixed. Many assays are performed on complex matrices (cells, plant extracts). Screening of referenced and synthesized inhibitors on several human kinases: CDK1/cyclin B, CDK5/p25, DYRK1A, GSK3!, PI3K, Akt and mTOR are performed. Developed assays proved to be quantitative, simple, economic, fast and robust.

The majority of cancer research projects mainly focus on the epithelial cancer cell, while the role of the tumour stroma has been largely neglected. Conventional 2D techniques, such as well plates and other kinds of tissue culture plastic, and animal models are mainly used to broaden our understanding of how tumours arise, develop, and induce metastasis. However, there is accumulating evidence suggesting a tremendous impact of the non‐cancerous tumour stroma on carcinogenesis, while other publications illustrate the great importance of advanced 3D in vitro models for cancer research. The overall goal of this work was to investigate how cancer associated fibroblasts (CAFs; the most abundant component in the tumour stroma) and normal prostate fibroblasts (NPFs), isolated from patients diagnosed with aggressive forms of prostate cancer, contribute to angiogenesis, an important hallmark of cancer progression. For this purpose, a 3D in vitro angiogenesis co‐culture model was established. At first, two (semi‐) synthetic hydrogel platforms, gelatine methacrylate (GelMA) and star‐shaped (star)PEG‐heparin hydrogels were characterised and their physicochemical properties were compared with each other. Interestingly, GelMA gels shrank while starPEG‐heparin gels swelled in cell culture medium over the course of 24 hours. The cell concentration, in addition to the stiffness, was critical for the formation of endothelial networks, and the knowledge of swelling behaviour enabled the adjustment of initial cell density to ensure the density between both gel types was comparable. Moreover, preliminary tests with mesenchymal stem cells demonstrated that the hydrogel can be actively remodelled, as evaluated by stiffness parameters at day one and seven of incubation. Growth factors (GFs) affect cellular fate and behaviour, and storage, presentation and administration of such chemokines can be critical for certain cellular applications. Due to the high anionic charge density of heparin, starPEG‐heparin hydrogels are known to reversibly immobilise several GFs and thereby might mimic the GF reservoir of the extra cellular matrix. Thus, transport processes of GFs with low and high heparin affinity inside these hydrogels were analysed by fluorescence correlation spectroscopy and a bulk diffusion approach. Results indicated that diffusion constants were synergistically decreased with increasing size and heparin affinity of the diffusant. Next, the capability of endothelial cells (ECs) to self‐assemble and organise into 3D capillary networks was tested in GelMA, starPEG‐heparin and Matrigel hydrogels. Only starPEG‐heparin hydrogels allowed the formation of interconnected capillaries in macroscopic hydrogel samples. However, as it is widely used to test for pro‐ and anti‐angiogenic agents, the 2D Matrigel angiogenesis assay was included for subsequent co‐culture experiments of ECs and fibroblasts in order to investigate how the stromal cells influence the formation of endothelial networks. For a detailed characterisation of 3D structures, a conventionally applied 2D method (Maximum Intensity Projection for 3D reconstructed images, MIP) was compared to an optimised 3D analysing tool. As a result, it was discovered that MIP analysis did not allow for an accurate determination of 3D endothelial network parameters, and can result in misleading interpretations of the data set. Indirect co‐cultures of hydrogel‐embedded ECs with a 2D layer of fibroblasts showed that fibroblast‐derived soluble factors, including stromal cell‐derived factor 1 and interleukin 8, affected endothelial network properties. However, only co‐encapsulation of ECs and fibroblasts in starPEG‐heparin hydrogel discs revealed remarkable changes in endothelial network parameters between CAF and NPF samples. In detail, the total length and branching of the capillaries was increased. For two donor pairs, the diameter of capillaries was decreased in CAF samples compared to NPF samples, underlining the high physiological relevance of this model. In contrast, significant differences in 2D Matrigel assays were not detected between, CAF, NPF and control (ECs only) samples. In summary, a 3D angiogenesis co‐culture system was successfully developed and used to characterise stromal‐endothelial interactions in detail. The combination of advanced biomaterials (starPEG‐heparin) and 3D analysing techniques goes beyond conventional 2D in vitro cancer research, and opens new avenues for the development of more complex models to further improve the acquisition of more biologically relevant data.