DNA molecular recognition specificity : pairwise and in competition

Despite its importance in biological systems, the molecular recognition of DNA hybridization within complex, competitive environments is poorly understood. The present thesis investigates DNA hybridization in thermal equilibrium for DNA strands bound to the surface of a microarray as well as in solution in presence of one or more competitors. For the latter we employ fluorescence anisotropy and fluorescence correlation spectroscopy to determine binding affinities of two DNA strands in a pairwise manner and in presence of a single competitor. Our results reveal that there must be a non-trivial interaction between the competing strands that extends beyond simple double helix formation. This is a signature of cooperative behavior, which can lead to more complex binding phenomena than previously thought. Moreover, we find surprising differences between the results of both techniques, which we attribute to differing sensitivities to distinct microstates of double helix formation. The second part of this work is performed with surface-bound DNA and devoted to experimentally determine a sufficient number of differing bases between two sequences to avoid cross-hybridization. We construct a set of 23 non-interacting sequences with a length of 7 bases. We conclude that for systems of increasing complexity a high level of discrimination between many competitors is essential for accurate recognition.Trotz der Relevanz für biologische Systeme sind die Mechanismen molekularer Erkennung bei der Hybridisierung von DNA in komplexen Umgebungen kaum verstanden. Die vorliegende Arbeit untersucht DNA Hybridisierung im thermischen Gleichgewicht mit DNA-Strängen sowohl an die Oberfläche eines Microarrays gebunden als auch in Lösung in Gegenwart von Konkurrenten. Für letztere verwenden wir Fluoreszenzanisotropie sowie -korrelationsspektroskopie, um Bindungsaffinitäten zweier DNA-Stränge paarweise und in Anwesenheit einzelner Konkurrenten zu bestimmen. Unsere Ergebnisse zeigen, dass es nicht triviale Wechselwirkungen zwischen den beteiligten Strängen geben muss, die über die einfache Bildung einer Doppelhelix hinausgehen. Diese Beobachtung deutet auf kooperatives Verhalten hin und zeigt, dass DNA-Hybridisierung komplexer abläuft als bisher angenommen. Außerdem finden wir eine unerwartete Diskrepanz beider Methoden, die auf unterschiedliche Sensitivitäten für bestimmte Mikrozustände der gebundenen DNA zurückgeht. Im zweiten Teil der Arbeit widmen wir uns Experimenten mit oberflächengebundener DNA. Wir bestimmen eine ausreichende Anzahl sich unterscheidender Basenpaare zweier Stränge, um nicht spezifische Hybridisierung zu vermeiden, und zeigen, dass sich damit ein Satz aus 23 nicht interagierenden Strängen á 7 Basen konstruieren lässt. Wir schließen, dass für zunehmend komplexe Systeme ein hoher Diskriminierungsgrad zwischen vielen Konkurrenten unabdingbar für präzise Erkennung ist

DNA oligomer binding in competition exhibits cooperativity

Binding of two complementary DNA single strands to a double-helix, DNA hybridization, is a sequence specific molecular recognition process that plays important roles in biology and biotechnological applications. In the past much work has been devoted to understand double helix formation, however, DNA binding in complex situations often remains difficult to deal with. Here we use fluorescence anisotropy to assess the binding affinities of DNA oligonucleotide strands that compete for hybridization to the same probe molecule in thermal equilibrium. We find that the ratio of the binding constants in competition can change substantially compared to pairwise assessments. This is a signature of non-trivial interaction among the competitors: the binding microstates of each strand are affected by the presence of the other, but to a different degree. To our knowledge this type of phenomenon is not included in current equilibrium models of oligonucleotide binding. We suggest interactions beyond double helix conformations to cause the observed cooperative behavior. The cooperativity could produce more complex binding phenomena than previously thought

Evaluating the Components of Alexithymia in Patients With Obsessive-Compulsive Disorder

Background: This study aimed to evaluate the differences in alexithymia components between patients with obsessive-compulsive disorder (OCD) and normal individuals.Methods: In this ex-post facto study, 23 obsessive-compulsive outpatients’ selected by available sampling method and 22 personnel of the same hospitals (Taft Comprehensive Psychiatric Hospital, Imam Ali, Shahid Rahnemoon, and Baghayipoor Clinics) were selected as a control group in 2015 in Yazd, Iran. Yale-Brown Obsessive-Compulsive and Toronto Alexithymia Scale-20 were used in this study.Results: Data were analyzed by multivariate analysis of variance (MANOVA). The results showed that patients with OCD were significantly different from the control group in the total alexithymia score (F=7.232, P=0.01). However, both groups had significant differences only in the subscale of difficulty in identifying feelings.Conclusion: It can be concluded that both groups had significant differences in the total alexithymia score and one of its subscales

Effect of health on economic growth: A panel data study of developed and developing countries

In this paper, we investigate the effect of health, such as fertility rate, total (birth per woman), life expectancy at birth, total (years) and mortality rate, under-5(per 1000 live birth), as well as capital stock on the economic growth of 16 developed countries and 14 developing countries using Panel Unit Root and Panel Data Model for the period 1990-2010. In this investigation we have found that capital stock and life expectancy have a statistically significant positive effect on economic growth in both groups of countries. Mortality rate has a statistically significant negative effect on economic growth in both groups of countries. On the other hand fertility rate has a statistically significant positive effect on economic growth in developed countries while it has a statistically significant negative effect on economic growth in developing countries. Also the study results show that the fixed effects approach is more appropriate

Effect of health on economic growth: A panel data study of developed and developing countries

In this paper, we investigate the effect of health, such as fertility rate, total (birth per woman), life expectancy at birth, total (years) and mortality rate, under-5(per 1000 live birth), as well as capital stock on the economic growth of 16 developed countries and 14 developing countries using Panel Unit Root and Panel Data Model for the period 1990-2010. In this investigation we have found that capital stock and life expectancy have a statistically significant positive effect on economic growth in both groups of countries. Mortality rate has a statistically significant negative effect on economic growth in both groups of countries. On the other hand fertility rate has a statistically significant positive effect on economic growth in developed countries while it has a statistically significant negative effect on economic growth in developing countries. Also the study results show that the fixed effects approach is more appropriate

Effect of health on economic growth: A panel data study of developed and developing countries

In this paper, we investigate the effect of health, such as fertility rate, total (birth per woman), life expectancy at birth, total (years) and mortality rate, under-5(per 1000 live birth), as well as capital stock on the economic growth of 16 developed countries and 14 developing countries using Panel Unit Root and Panel Data Model for the period 1990-2010. In this investigation we have found that capital stock and life expectancy have a statistically significant positive effect on economic growth in both groups of countries. Mortality rate has a statistically significant negative effect on economic growth in both groups of countries. On the other hand fertility rate has a statistically significant positive effect on economic growth in developed countries while it has a statistically significant negative effect on economic growth in developing countries. Also the study results show that the fixed effects approach is more appropriate

Análisis numérico de diferentes geometrías en el análisis dinámico en la plataforma de gravedad.

On Gravity platform Dynamic Response is a support structure held in place by gravity. Given that the gravity platforms are supportedby the sea bed but not attached to the ground, the motion of them is known as a rocking fluctuation. During the fluctuations, theplatform maybe overturned if the angle is large. In this study, using Ansys Aqwa hydrodynamic software and analytical methods withregard to the performance, the dynamic interaction of platform’s geometry on hydrodynamic forces have been simulated. Theobjective of this study was to analyze the hydrodynamic parameters of the sea and rocking fluctuations of gravity platforms under theimpact of regular wave’s moment considering the soil mechanics and hydrodynamic features of the structure. In order to achievethe objective the hydrodynamic forces using numerical simulations and analytical methods for one column and three hollow columnsplatforms were analyzed. Finally, responses of the platform to irregular waves were studied using numerical simulation. The resultsshowed that with the increasing of the depth, the impact of wave’s force and moment on the base of platform are reduced throughexponential relationship. The reductions are due to the effective depth that is equal to half the wave length. The results suggestthat the response of the rocking motion of gravity platform shows significant changes in relation to height and wavelength. Based onthe curves fitted to the data of the fluctuation angle, sustainability of the platform in the rocking motion can be thoroughly andcompletely investigated

Learning Lines with Ordinal Constraints

We study the problem of finding a mapping f from a set of points into the real line, under ordinal triple constraints. An ordinal constraint for a triple of points (u,v,w) asserts that |f(u)-f(v)| < |f(u)-f(w)|. We present an approximation algorithm for the dense case of this problem. Given an instance that admits a solution that satisfies (1-?)-fraction of all constraints, our algorithm computes a solution that satisfies (1-O(?^{1/8}))-fraction of all constraints, in time O(n?) + (1/?)^{O(1/?^{1/8})} n

Crude Oil-polluted Soil Induces Ultrastructural and Enzyme Activity Changes in the Shoot of Lentil

Plants are always under threat due to various biotic and abiotic stresses. They respond to such threats by an efficient antioxidative enzyme system such as catalase. The presence of petroleum in soil is a stressful environmental factor for plants. In this study, cellular and biochemical changes were investigated in the shoot of lentil grown in the crude oil-polluted soil. Transmission electron microscope micrographs showed various injuries in the level of subcellular content including nucleus, chloroplast and mitochondria. In the treated samples, catalase activity and its kinetics factors (Vmax and Km) were different from the control. In the treated, Km of the enzyme was lower than that of the control. Temperature and pH profiles of the enzyme were different in the control and treated samples. Catalase purification in both treated and control samples showed that two catalase isoforms were expressed in the treated sample in comparison to the control, in which only one type of catalase was detected