Thermodynamic scaling behavior in genechips

Abstract Background Affymetrix Genechips are characterized by probe pairs, a perfect match (PM) and a mismatch (MM) probe differing by a single nucleotide. Most of the data preprocessing algorithms neglect MM signals, as it was shown that MMs cannot be used as estimators of the non-specific hybridization as originally proposed by Affymetrix. The aim of this paper is to study in detail on a large number of experiments the behavior of the average PM/MM ratio. This is taken as an indicator of the quality of the hybridization and, when compared between different chip series, of the quality of the chip design. Results About 250 different GeneChip hybridizations performed at the VIB Microarray Facility for Homo sapiens, Drosophila melanogaster, and Arabidopsis thaliana were analyzed. The investigation of such a large set of data from the same source minimizes systematic experimental variations that may arise from differences in protocols or from different laboratories. The PM/MM ratios are derived theoretically from thermodynamic laws and a link is made with the sequence of PM and MM probe, more specifically with their central nucleotide triplets. Conclusion The PM/MM ratios subdivided according to the different central nucleotides triplets follow qualitatively those deduced from the hybridization free energies in solution. It is shown also that the PM and MM histograms are related by a simple scale transformation, in agreement with what is to be expected from hybridization thermodynamics. Different quantitative behavior is observed on the different chip organisms analyzed, suggesting that some organism chips have superior probe design compared to others.</p

Altered Ca2+ and Na+ Homeostasis in Human Hypertrophic Cardiomyopathy: Implications for Arrhythmogenesis

Hypertrophic cardiomyopathy (HCM) is the most common mendelian heart disease, with a prevalence of 1/500. HCM is a primary cause of sudden death, due to an heightened risk of ventricular tachyarrhythmias that often occur in young asymptomatic patients. HCM can slowly progress toward heart failure, either with preserved or reduced ejection fraction, due to worsening of diastolic function. Accumulation of intra-myocardial fibrosis and replacement scars underlies heart failure progression and represents a substrate for sustained arrhythmias in end-stage patients. However, arrhythmias and mechanical abnormalities may occur in hearts with little or no fibrosis, prompting toward functional pathomechanisms. By studying viable cardiomyocytes and trabeculae isolated from inter-ventricular septum samples of non-failing HCM patients with symptomatic obstruction who underwent myectomy operations, we identified that specific abnormalities of intracellular Ca2+ handling are associated with increased cellular arrhytmogenesis and diastolic dysfunction. In HCM cardiomyocytes, diastolic Ca2+ concentration is increased both in the cytosol and in the sarcoplasmic reticulum and the rate of Ca2+ transient decay is slower, while the amplitude of Ca2+-release is preserved. Ca2+ overload is the consequence of an increased Ca2+ entry via L-type Ca2+-current [due to prolongation the action potential (AP) plateau], combined with a reduced rate of Ca2+-extrusion through the Na+/Ca2+ exchanger [due to increased cytosolic (Na+)] and a lower expression of SERCA. Increased late Na+ current (INaL) plays a major role, as it causes both AP prolongation and Na+ overload. Intracellular Ca2+ overload determines an higher frequency of Ca2+ waves leading to delayed-afterdepolarizations (DADs) and premature contractions, but is also linked with the increased diastolic tension and slower relaxation of HCM myocardium. Sustained increase of intracellular [Ca2+] goes hand-in-hand with the increased activation of Ca2+/calmodulin-dependent protein-kinase-II (CaMKII) and augmented phosphorylation of its targets, including Ca2+ handling proteins. In transgenic HCM mouse models, we found that Ca2+ overload, CaMKII and increased INaL drive myocardial remodeling since the earliest stages of disease and underlie the development of hypertrophy, diastolic dysfunction and the arrhythmogenic substrate. In conclusion, diastolic dysfunction and arrhythmogenesis in human HCM myocardium are driven by functional alterations at cellular and molecular level that may be targets of innovative therapies

Models of Polymer Dynamics: DNA Renaturation and Zipping.

This manuscript is structured into two main parts: an introduction on polymer physics and the analysis of a few problems of biological relevance involving polymer dynamics.The aim of the first part is to provide a brief review of the essential concepts in polymer physics. We will first cover the static properties of both ideal chains and self avoiding walks, and proceed with the fundamentals of polymer networks and polymer brushes. We will then discuss the dynamical properties of polymers by reviewing the Rouse model in some details, while we will only briefly mention the role of hydrodynamic interactions. These concepts represent the basics of polymer physics and they are extensively treated in well-known theory books. In the second chapter of the manuscript we will discuss the process of polymer translocation in some details, introducing the problem and reviewing the literature on the topic. Although we do not deal with polymer translocation directly, the analogies with the zipping dynamics (topic of chapters 5 and 6) are such to motivate a brief overview of translocation in the introductory part of this thesis.The second part of this thesis provides an exhaustive review of my research work concerning polymer physics, corresponding to the last three years of the Doctor of Philosophy. In order for this thesis to maintain its internal unity the topic I worked on during the first year of the Ph.D. is treated here only marginally. The second part of this manuscript starts with an introduction on Monte Carlo methods and proceeds to describe the lattice polymer model used in the rest of the work. The following chapters are then dedicated to the study of four different problems within the framework of DNA renaturation dynamics, using the afore-mentioned simulation techniques. Renaturation is the process by which two complementary single strands of DNA bind to form a double-helix. Renaturation is believed to proceed via two steps: the formation of an active nucleus of a few base pairs, is then followed by a rapid zipping until the double helix is formed over its full length. Chapter 4 of this thesis is devoted to the study of the dynamics of the first step, known as nucleation. DNA zipping, instead, is amply discussed in Chapters 5 and 6. Everywhere the focus is on the scaling behaviour of quantities such as characteristic rates or times as a function of the polymer length. We will show that several of the studied processes have an anomalous dynamics, i.e. power laws relating characteristic times to the polymer length are governed by exponents which are different from those of ordinary diffusion. The last chapter of this manuscript is devoted to renaturation in DNA microarrays, where the process usually takes the name of hybridization. In this case one of the DNA strands is attached to a solid surface. Finally, we will draw some conclusions in Chapter 8. Two appendices for mathematical formulas have also been included at the end of the manuscript.nrpages: 151status: publishe

Chronic migraine-like headache caused by a demyelinating lesion in the brainstem

Abstract not availabl