Diabetes is one of the most common diseases in modern time. Its connection to overweight and obesity is well established, and diet and exercise are therefore important parameters in the treatment. A commonly used biomarker to diagnose and follow disease progression in diabetics is via measurements of fasting plasma glucose, FPG. In this study, the relationship between weight loss and FPG in overweight diabetics was studied. Competing hypothesis regarding the connection between weight loss and reduced FPG was investigated by using nonlinear mixed effects modeling based on data gathered from a meta-analysis by Anderson et al (1). The hypotheses suggested that either [1] weight effected FPG directly by an intermediate effector, or [2] both weight and FPG were affected by an unknown underlying mechanism. The intermediate effector was presumed to be insulin sensitivity and the underlying mechanism the blood concentration of free fatty acids.  The data was gathered from 8 different studies, all examining the results of very low energy diets (330-909 kcal/day) in overweight type 2 diabetics. Frequent measurements of weight and FPG were provided in each study with a range of 91-321 mg/dl for baseline FPG and 93-118 kg for baseline weight. The summarized studies consisted of 13 arms with 6-62 subjects in each arm. Both hypotheses were modeled by using NONMEM 7.2. A stepwise effect was used for both weight and FPG. For hypothesis [1], an inhibitory effect affected the weight input which then affected the output for insulin sensitivity by a relative change in weight or the input for the insulin sensitivity by an absolute weight change. For hypothesis [2] the same inhibitory effect affected weight input and the input for insulin sensitivity. For both models the FPG drop was then proportional to the increase in insulin sensitivity. Hypothesis [2] had a significantly lower objective function value (OFV) than hypothesis [1] and had also better results from goodness of fit plots and VPCs. It was therefore concluded that hypothesis [2] indicated the more accurate explanation of the connection between FPG and weight loss. Moreover, a strong correlation between the caloric content of the diet and the rate of weight change was seen as a result of stepwise covariate modeling. An impact from baseline BMI on rate of change for insulin sensitivity was also seen.

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Cette thèse porte sur la modification d'électrodes par des polymères électrogénérés, capables d'immobiliser une biomolécule et/ou de fournir des propriétés de transduction électrochimique afin d'élaborer des biocapteurs à ADN faisant intervenir différents types d'interactions : ADN/protéine de réparation, hybridation et aptamère/molécule cible.Dans un premier temps, nous avons immobilisé la protéine Formamidopyrimidine ADN Glycosylase (Fpg) de D. radiodurans portant un tag histidine sur un film de poly-(pyrrole-NTA) via l'interaction NTA/Cu2+/Histidine. Dans le but d'étudier, par spectroscopie d'impédance électrochimique et SPR, l'interaction de cette protéine avec un duplex d'ADN sans lésions et un duplex d'ADN portant une lésion -oxo-guanine (8-oxo-G), car la Fpg est une protéine impliquée dans la réparation de l'ADN lorsque celui-ci comporte un site 8 (8-oxo-G).Dans un second temps, nous avons élaboré un biocapteur photoélectrochimique à partir d'un complexe multifonctionnel, (Ru(bpy-pyrrole)2(dppn)]2+) (bpy-pyrrole=4-méthyl-4'-butylpyrrole-2,2'-bipyridine, dppn=benzo[i]dipyrido-[3,2-a:2'.3'-c]phénazine) pouvant être électropolymérisé, intercalé l'ADN et photoactivé. La preuve de concept a été réalisée pour une séquence type d'ADN du VIH. Une limite de détection de 10-15 mol.L-1 et une sensibilité de 0,01 unité par décade avec une gamme de linéarité allant de 10-15 à 10-10 mol.L-1 ont été obtenue. Puis, nous avons conçu un aptacapteur pour la détection de la cocaïne à l'aide d'un aptamère double-fragment, formant une seule entité en présence de cocaïne, pouvant être immobilisée par intercalation sur le ligand dppn du métallopolymère. Ainsi une gamme de linéarité comprise entre 10-6 et 5x10-4 mol L-1 a été obtenue pour une concentration d'aptamère de 10-7 mol L-1, avec une limite de détection de l'ordre de 10-6 mol L-1. / This work focuses on the conception and optimization of impedancemetric and photoelectrochemical DNA biosensors based on the modification of electrodes with electrogenerated polymers. Different types of interactions involving DNA were studied: DNA/DNA repair protein, hybridization and aptamer/target molecule.In the first part, a poly-(pyrrole-NTA)-modified electrode was used to immobilize a protein involved in DNA repair: the Fpg (Formamidopyrimidine DNA Glycosylase) from D. radiodurans. This protein was previously tagged with histidine to be immobilized via a (NTA)Cu-histidine interaction. This protein detects and removes 8-oxo-guanine (8-oxo-G), a DNA damage caused by irradiation in double stranded DNA. We studied the behavior of this Fpg with DNA duplexes with and without 8-oxo-G nucleotide by electrochemical impedance spectroscopy and SPR.In the second part, we report the design of novel photoelectrochemical biosensor based on a multifunctional complex, (Ru(bpy-pyrrole)2(dppn)]2+) (bpy-pyrrole=4-methyl-4'-butylpyrrole-2,2'-bipyridine, dppn= benzo[i]dipyrido-[3,2-a:2'.3'-c]phenazine) exhibiting photo-sensitive, DNA-intercalating and electro-polymerizable properties. This modified electrode achieves photoelectrochemical detection on planar electrode by intercalating HIV-DNA duplexes or aptamer–cocaine complexes. The photocurrent generated through visible irradiation was correlated to the oligonucleotides concentration. Low detection limits of 10-15 mol L-1 and sensitivity of 0.01 unit per decade were measured, demonstrating excellent adequacy of these modified electrodes towards duplex HIV DNA detection. For the cocaine detection, the photelectrochemical aptasensor was based on the immobilization of a 10-7 mol L-1 double-fragment anti-cocaine aptamer and finally exhibited a linear range between 10-6 and 5x10-4 mol L-1 and a detection limit of 10-6 mol L-1.

L’ADN est une molécule dont l’intégrité est cruciale pour le bon fonctionnement de tous les organismes vivants. Cependant, il est régulièrement soumis à différents stress provenant de sources endogènes ou exogènes, et qui sont capables de générer dans sa structure des dommages de nature variée. Chaque dommage peut être reconnu par une panoplie de protéines, parmi lesquelles nous pouvons retrouver les protéines de réparation, les inhibiteurs de réparation, les facteurs de transcriptions ou encore les protéines de remodelage chromatinien. Ces protéines constituent l’interactome d’une lésion donnée.Les cyclonucléosides sont des dommages complexes de l’ADN qui ont pour particularité d’impliquer à la fois la base et le résidu de sucre, entre lesquels une liaison covalente supplémentaire est créée. La présence de cette liaison a pour conséquence de déformer la double hélice de l’ADN. Ainsi, ces lésions ne sont pas prises en charge par le système de réparation par excision de bases, comme la plupart des dommages d’oxydation, mais elles seraient plutôt reconnues par le système de réparation par excision de nucléotides, ce dernier prenant en charge les lésions volumineuses.L’objectif de cette thèse est d’étudier l’interactome des cyclonucléosides en utilisant différents modèles biologiques : eucaryotes, bactéries ou archées. En utilisant une technique de piégeage de protéines sur des sondes comportant ces lésions, nous avons effectué un screening des interactions entre les cyclonucléosides et des protéines issues d’extraits protéiques HeLa. Nous avons ainsi identifié l’influence négative des cyclonucléosides sur la reconnaissance de sa séquence cible par un facteur de transcription DREF, ainsi que sur les interactions de PARP1 avec l’ADN. Ces résultats ont été confirmés par l’usage des techniques complémentaires.Nous avons également analysé les interactions entre la glycosylase bactérienne Fpg et les cyclonucléosides : cette enzyme possède une affinité pour ces lésions, sans pourtant exercer d’activité d’excision. Cette affinité est inférieure à l’affinité de la Fpg pour les sites abasiques mais reste supérieure à son affinité pour l’ADN non-endommagé. Le rôle que pourraient jouer les cyclonucléosides dans l’ADN est alors discuté suite aux résultats obtenus.Enfin, une archée radiorésistante Thermococcus gammatolerans a été étudiée. Dans un premier temps, la formation des lésions d’oxydation simples et complexes à forte dose d’irradiation (2500 et 5000 Gy) a été évaluée. La 8-oxo-désoxyguanosine, exemple des lésions simples d’oxydation, est formée en grande quantité suite à une forte dose d’irradiation, et rapidement réparée dans les cellules remises dans des conditions optimales de culture. Les cyclonucléosides, quant à eux, ne sont pas détectés même à de très fortes doses d’irradiation, ce qui soulève des questions sur la formation de ces dommages. Ensuite, deux nouvelles glycosylases isolées de Thermococcus gammatolerans ont été étudiées : leur mécanisme d’action ainsi que leur spécificité vis-à-vis des substrats ont été élucidés.Les travaux effectués au cours de cette thèse ont contribué à la meilleure compréhension des interactions entre les cyclonucléosides et les protéines interagissant avec eux. Le développement des techniques de piégeage des protéines sur les sondes lésées, qui a constitué une partie importante des travaux, pourra également servir à étudier l’interactome d’autres lésions complexes de l’ADN. / DNA is a molecule, which integrity is crucial for correct functioning of all the living organisms. However, it is regularly submitted to different stresses coming from endogenous or exogenous sources, which are able to generate various damages in its structure. Each damage may be recognized by multiple proteins, among which one can find repair proteins, inhibitors of DNA repair, transcription factors or proteins of chromatin remodelling. All these proteins constitute the interactome of a given DNA lesion.Cyclonucleosides are complex damages of DNA, which imply the base and the sugar residue at the same time, since an additional covalent bond is generated between these two. The consequence of the presence of this bond is the deformation of the double helix. For this reason, cyclonucleosides are not recognized by the base excision repair system, as the majority of the oxidative lesions are, but rather by the nucleotide excision repair system, which takes in charge bulky lesions.The objective of this thesis is to study the interactome of the cyclonucleosides, by using different biological models: eucaryotes, bacteries and archaea. By using the technique that enables trapping of proteins on the probes holding these lesions, we realised a screening of interactions between cyclonucleosides and proteins issued from the HeLa extracts. We identified the negative influence of cyclonucleosides on the recognition of its target sequence by the transcription factor DREF, as well as on the PARP1 interactions with DNA. These results were then confirmed by complementary techniques.We have also analysed the interactions between the bacterial glycosylase Fpg and cyclonucleosides: this enzyme possesses an affinity for these lesions, without however exerting an excision activity. This affinity is lower than the Fpg affinity for abasic sites, but it is higher than its affinity for non-damaged DNA. The role that could play cyclonucleosides in DNA is discussed following these results.Finally, a radioresistant archaea Thermococcus gammatolerans was studied. First, the formation of simple and complex oxidative lesions at the high radiation doses (2500 and 5000 Gy) was evaluated. 8-oxo-deoxyguanosine, which is an example of simple oxidative lesions, is formed in great quantity at high irradiation dose, and is rapidly repaired once the cells are put in their optimal culture conditions. As for cyclonucleosides, they are not detected even at very high doses of radiation, which raises questions concerning the formation of these damages. Next, two new glycosylases isolated from Thermococcus gammatolerans were studied: their mechanism of action, as well as their specificity against the substrates, were elucidated.The work accomplished during this thesis contributed to the better understanding of the interactions between cyclonucleosides and the proteins that interact with them. Also, the development of the protein trapping techniques on the damaged probes, which constituted an important part of this work, can be applied to study the interactome of other complex DNA lesions.

Pagrindinis šio magistro baigiamojo darbo tikslas buvo apžvelgti kai kurių algoritmų ir jų kombinacijų pritaikymą daugiamačiams sekų šablonams analizuoti ir įgyvendinti algoritmą, gebantį tai atlikti. Buvo aprašyta FP-Tree medžio struktūra, kuri yra skirta kompaktiškai saugoti kritiniams (pvz., dažnai pasikartojantiems) duomenims, pateiktas FP-Growth algoritmas, galintis analizuoti tokią duomenų struktūrą ir rezultate pateikiantis visų dažnų elementų šablonų aibę. Pristatyta modifikuotų FP-Growth ir PrefixSpan algoritmų kombinacija – MD-PS-FPG algoritmas, pateikti kai kurių atliktų testavimų rezultatai, tolimesnių darbų pagrindiniai tikslai ir pan. / The main goal of this master final work was to present some of the algorithms and their combinations for the multidimensional sequence pattern mining and implement an algorithm, that is capable of doing that. FP-Tree, that is used to store critical (for example, often repeated) data, was described. FP-Growth algorithm, that can analyze FP-Tree structure and give frequent pattern set as a result, was presented. MD-PS-FPG algorithm – a combination of modified FP-Growth and PrefixSpan algorithms – was introduced. The results of some tests, further work objectives and other things were also presented.

Pharmacometrics is widely used in drug development. Models are developed to describe pharmacological measurements with data gathered from a clinical trial. The information can then be applied to, for instance, safely establish dose-response relationships of a substance. Glycated hemoglobin (HbA1c) is a common biomarker used by models within antihyperglycemic drug development, as it reflects the average plasma glucose level over the previous 8-12 weeks. There are five different nonlinear mixed-effects models that describes HbA1c-formation. They use different biomarkers such as mean plasma glucose (MPG), fasting plasma glucose (FPG), fasting plasma insulin (FPI) or a combination of those. The aim of this study was to compare their performances on a population and an individual level using model averaging (MA) and to explore if reduced trial durations and different treatment could affect the outcome. Multiple weighting methods were applied to the MA workflow, such as the Akaike information criterion (AIC), cross-validation (CV) and a bootstrap model averaging method. Results show that in general, models that use MPG to describe HbA1c-formation on a population level could potentially outperform models using other biomarkers, however, models have shown similar performance on individual level. Further studies on the relationship between biomarkers and model performances must be conducted, since it could potentially lay the ground for better individual HbA1c-predictions. It can then be applied in antihyperglycemic drug development and to possibly reduce sample sizes in a clinical trial. With this project, we have illustrated how to perform MA on the aforementioned models, using different biomarkers as well as the difference between model weights on a population and individual level.

No description available.

Objectives: The aim of this study was to determine if exposure to volatile organic compounds can lead to DNA damage and impaired DNA repair capacity. Nail cosmetics is a fast growing industry around the world where employees and clients are subjected to various chemical substances which may be harmful to their health: such as formaldehyde, toluene, acetone, xylene, ethylmethacrylate, methylmethacrylate and n–buthyl acetate. These chemicals have the potential to be harmful to their health and exposure to these chemicals should be actively controlled. Formaldehyde is classified as a human carcinogen by the IARC, whereas, toluene and xylene are group three carcinogens, classified in 1999 (not classified as carcinogenic to humans), and various studies have linked DNA damage and impaired DNA repair to the above mentioned substances. Methods: Fifteen nail technicians were monitored by means of personal air sampling, measuring formaldehyde, toluene, xylene, acetone and ethylmethacrylate exposure. Fifteen unexposed subjects were chosen and matched for age and smoking habits with the exposed group. Heparinised blood samples were obtained from each test subject with which the Comet Assay was performed on lymphocytes to determine DNA damage and repair ability. Results: Exposure to ethylmethacrylates and methylmethacrylates leads to DNA damage. Methylmethacrylate causes DNA damage by specifically targeting pyrimidine (fpg) bases. N–buthyl acetate, xylene and acetone exposure impaired DNA repair capacity. The exposed group showed signs of Class III and Class IV DNA damage, whereas the control group had little Class III damage and no indication of Class IV damage. The overall DNA repair ability of the nail technicians was slightly impaired when compared to that of the control group, which is in concurrence with previous studies. Smoking habits and age did not show significant influences on the level of DNA damage and repair when compared with the control group. Conclusion: Exposure to volatile organic compounds such as ethylmethacryale and methylmethacrylate may lead to DNA damage and altered DNA repair in some individuals, although further studies are recommended. / Thesis (M.Sc. (Occupational Hygiene))--North-West University, Potchefstroom Campus, 2011.

Objectives: The aim of this study was to determine if exposure to volatile organic compounds can lead to DNA damage and impaired DNA repair capacity. Nail cosmetics is a fast growing industry around the world where employees and clients are subjected to various chemical substances which may be harmful to their health: such as formaldehyde, toluene, acetone, xylene, ethylmethacrylate, methylmethacrylate and n–buthyl acetate. These chemicals have the potential to be harmful to their health and exposure to these chemicals should be actively controlled. Formaldehyde is classified as a human carcinogen by the IARC, whereas, toluene and xylene are group three carcinogens, classified in 1999 (not classified as carcinogenic to humans), and various studies have linked DNA damage and impaired DNA repair to the above mentioned substances. Methods: Fifteen nail technicians were monitored by means of personal air sampling, measuring formaldehyde, toluene, xylene, acetone and ethylmethacrylate exposure. Fifteen unexposed subjects were chosen and matched for age and smoking habits with the exposed group. Heparinised blood samples were obtained from each test subject with which the Comet Assay was performed on lymphocytes to determine DNA damage and repair ability. Results: Exposure to ethylmethacrylates and methylmethacrylates leads to DNA damage. Methylmethacrylate causes DNA damage by specifically targeting pyrimidine (fpg) bases. N–buthyl acetate, xylene and acetone exposure impaired DNA repair capacity. The exposed group showed signs of Class III and Class IV DNA damage, whereas the control group had little Class III damage and no indication of Class IV damage. The overall DNA repair ability of the nail technicians was slightly impaired when compared to that of the control group, which is in concurrence with previous studies. Smoking habits and age did not show significant influences on the level of DNA damage and repair when compared with the control group. Conclusion: Exposure to volatile organic compounds such as ethylmethacryale and methylmethacrylate may lead to DNA damage and altered DNA repair in some individuals, although further studies are recommended. / Thesis (M.Sc. (Occupational Hygiene))--North-West University, Potchefstroom Campus, 2011.

INTRODUCTION/OBJECTIVES: Current screening guidelines for pre-diabetes and type 2 diabetes mellitus note that there are discrepancies in diagnosing the disease using the fasting plasma glucose test, oral glucose tolerance test, and HbA1c in high-risk populations. The objective of this study is to compare the effectiveness of screening methods for type 2 diabetes mellitus (T2DM) and pre-diabetes by race/ethnicity and gender. METHODS: Secondary analyses of the National Health and Nutrition Examination Survey (NHANES, 2005-2008) were performed using SPSS 19.0. Screening outcomes were assessed and compared for a sample of n=10,566, NHW, NHB, MA, and Multiracial/other men and women. Analyses included cross tabulations, ANOVA and partial correlations to establish disease prevalence, effectiveness of screenings, and statistical significance. RESULTS: It was found that the HbA1c test is comparable in precision, and is correlated with the FPG for racial and ethnic minorities. The specificities for detecting pre-diabetes using the HbA1c were higher (64-66%) for these groups than by using the standard, FPG screening method (42-49%). There were no strong, significant differences for screening effectiveness for men versus women. DISCUSSION: This study revealed that the HbA1c test might be an effective method for screening for pre-diabetes in racial and ethnic minorities instead of the FPG test alone. Screening in high-risk populations will help delay the onset of T2DM, with increased prevention during the pre-clinical phase.