Vibrational spectroscopic and electrochemical investigations of multi-centered heme proteins in biomimetic membrane architectures

Membrane proteins play a major role in every living cell. They are the key factors in the cell’s metabolism and in other functions, for example in cell-cell interaction, signal transduction, and transport of ions and nutrients. Cytochrome c oxidase (CcO), as one of the membrane proteins of the respiratory chain, plays a significant role in the energy transformation of higher organisms. CcO is a multi centered heme protein, utilizing redox energy to actively transport protons across the mitochondrial membrane. One aim of this dissertation is to investigate single steps in the mechanism of the ion transfer process coupled to electron transfer, which are not fully understood. The protein-tethered bilayer lipid membrane is a general approach to immobilize membrane proteins in an oriented fashion on a planar electrode embedded in a biomimetic membrane. This system enables the combination of electrochemical techniques with surface enhanced resonance Raman (SERRS), surface enhanced reflection absorption infrared (SEIRAS), and surface plasmon spectroscopy to study protein mediated electron and ion transport processes. The orientation of the enzymes within the surface confined architecture can be controlled by specific site-mutations, i.e. the insertion of a poly-histidine tag to different subunits of the enzyme. CcO can, thus, be oriented uniformly with its natural electron pathway entry pointing either towards or away from the electrode surface. The first orientation allows an ultra-fast direct electron transfer(ET) into the protein, not provided by conventional systems, which can be leveraged to study intrinsic charge transfer processes. The second orientation permits to study the interaction with its natural electron donor cytochrome c. Electrochemical and SERR measurements show conclusively that the redox site structure and the activity of the surface confined enzyme are preserved. Therefore, this biomimetic system offers a unique platform to study the kinetics of the ET processes in order to clarify mechanistic properties of the enzyme. Highly sensitive and ultra fast electrochemical techniques allow the separation of ET steps between all four redox centres including the determination of ET rates. Furthermore, proton transfer coupled to ET could be directly measured and discriminated from other ion transfer processes, revealing novel mechanistic information of the proton transfer mechanism of cytochrome c oxidase. In order to study the kinetics of the ET inside the protein, including the catalytic center, time resolved SEIRAS and SERRS measurements were performed to gain more insight into the structural and coordination changes of the heme environment. The electrical behaviour of tethered membrane systems and membrane intrinsic proteins as well as related charge transfer processes were simulated by solving the respective sets of differential equations, utilizing a software package called SPICE. This helps to understand charge transfer processes across membranes and to develop models that can help to elucidate mechanisms of complex enzymatic processes.

Potential Analysis for Hypoelliptic Second Order PDEs with Nonnegative Characteristic Form

In this Thesis we consider a class of second order partial differential operators with non-negative characteristic form and with smooth coefficients. Main assumptions on the relevant operators are hypoellipticity and existence of a well-behaved global fundamental solution. We first make a deep analysis of the L-Green function for arbitrary open sets and of its applications to the Representation Theorems of Riesz-type for L-subharmonic and L-superharmonic functions. Then, we prove an Inverse Mean value Theorem characterizing the superlevel sets of the fundamental solution by means of L-harmonic functions. Furthermore, we establish a Lebesgue-type result showing the role of the mean-integal operator in solving the homogeneus Dirichlet problem related to L in the Perron-Wiener sense. Finally, we compare Perron-Wiener and weak variational solutions of the homogeneous Dirichlet problem, under specific hypothesis on the boundary datum.

Closed-loop investigation of the dynamical properties of cardiomyocyte electrophysiology by means of Dynamic clamp and Mathematical modelling

The research field of my PhD concerns mathematical modeling and numerical simulation, applied to the cardiac electrophysiology analysis at a single cell level. This is possible thanks to the development of mathematical descriptions of single cellular components, ionic channels, pumps, exchangers and subcellular compartments. Due to the difficulties of vivo experiments on human cells, most of the measurements are acquired in vitro using animal models (e.g. guinea pig, dog, rabbit). Moreover, to study the cardiac action potential and all its features, it is necessary to acquire more specific knowledge about single ionic currents that contribute to the cardiac activity. Electrophysiological models of the heart have become very accurate in recent years giving rise to extremely complicated systems of differential equations. Although describing the behavior of cardiac cells quite well, the models are computationally demanding for numerical simulations and are very difficult to analyze from a mathematical (dynamical-systems) viewpoint. Simplified mathematical models that capture the underlying dynamics to a certain extent are therefore frequently used. The results presented in this thesis have confirmed that a close integration of computational modeling and experimental recordings in real myocytes, as performed by dynamic clamp, is a useful tool in enhancing our understanding of various components of normal cardiac electrophysiology, but also arrhythmogenic mechanisms in a pathological condition, especially when fully integrated with experimental data.

Searching and retrieving in content-based repositories of formal mathematical knowledge

In this thesis, the author presents a query language for an RDF (Resource Description Framework) database and discusses its applications in the context of the HELM project (the Hypertextual Electronic Library of Mathematics). This language aims at meeting the main requirements coming from the RDF community. in particular it includes: a human readable textual syntax and a machine-processable XML (Extensible Markup Language) syntax both for queries and for query results, a rigorously exposed formal semantics, a graph-oriented RDF data access model capable of exploring an entire RDF graph (including both RDF Models and RDF Schemata), a full set of Boolean operators to compose the query constraints, fully customizable and highly structured query results having a 4-dimensional geometry, some constructions taken from ordinary programming languages that simplify the formulation of complex queries. The HELM project aims at integrating the modern tools for the automation of formal reasoning with the most recent electronic publishing technologies, in order create and maintain a hypertextual, distributed virtual library of formal mathematical knowledge. In the spirit of the Semantic Web, the documents of this library include RDF metadata describing their structure and content in a machine-understandable form. Using the author's query engine, HELM exploits this information to implement some functionalities allowing the interactive and automatic retrieval of documents on the basis of content-aware requests that take into account the mathematical nature of these documents.

Representation theorems for indefinite quadratic forms and applications

Diese Arbeit widmet sich den Darstellungssätzen für symmetrische indefinite (das heißt nicht-halbbeschränkte) Sesquilinearformen und deren Anwendungen. Insbesondere betrachten wir den Fall, dass der zur Form assoziierte Operator keine Spektrallücke um Null besitzt. Desweiteren untersuchen wir die Beziehung zwischen reduzierenden Graphräumen, Lösungen von Operator-Riccati-Gleichungen und der Block-Diagonalisierung für diagonaldominante Block-Operator-Matrizen. Mit Hilfe der Darstellungssätze wird eine entsprechende Beziehung zwischen Operatoren, die zu indefiniten Formen assoziiert sind, und Form-Riccati-Gleichungen erreicht. In diesem Rahmen wird eine explizite Block-Diagonalisierung und eine Spektralzerlegung für den Stokes Operator sowie eine Darstellung für dessen Kern erreicht. Wir wenden die Darstellungssätze auf durch (grad u, h() grad v) gegebene Formen an, wobei Vorzeichen-indefinite Koeffzienten-Matrizen h() zugelassen sind. Als ein Resultat werden selbstadjungierte indefinite Differentialoperatoren div h() grad mit homogenen Dirichlet oder Neumann Randbedingungen konstruiert. Beispiele solcher Art sind Operatoren die in der Modellierung von optischen Metamaterialien auftauchen und links-indefinite Sturm-Liouville Operatoren.

The Feynman-Kac formula and applications to PDEs

The thesis presents a probabilistic approach to the theory of semigroups of operators, with particular attention to the Markov and Feller semigroups. The first goal of this work is the proof of the fundamental Feynman-Kac formula, which gives the solution of certain parabolic Cauchy problems, in terms of the expected value of the initial condition computed at the associated stochastic diffusion processes. The second target is the characterization of the principal eigenvalue of the generator of a semigroup with Markov transition probability function and of second order elliptic operators with real coefficients not necessarily self-adjoint. The thesis is divided into three chapters. In the first chapter we study the Brownian motion and some of its main properties, the stochastic processes, the stochastic integral and the Itô formula in order to finally arrive, in the last section, at the proof of the Feynman-Kac formula. The second chapter is devoted to the probabilistic approach to the semigroups theory and it is here that we introduce Markov and Feller semigroups. Special emphasis is given to the Feller semigroup associated with the Brownian motion. The third and last chapter is divided into two sections. In the first one we present the abstract characterization of the principal eigenvalue of the infinitesimal generator of a semigroup of operators acting on continuous functions over a compact metric space. In the second section this approach is used to study the principal eigenvalue of elliptic partial differential operators with real coefficients. At the end, in the appendix, we gather some of the technical results used in the thesis in more details. Appendix A is devoted to the Sion minimax theorem, while in appendix B we prove the Chernoff product formula for not necessarily self-adjoint operators.

The Politics of Purchasing Power: Feminist Tourism and Women's Development in Nepal

My purpose in this essay is to explore how ideas about women and development are created and circulated at the moment of consumption of wares produced at a women's development project in Nepal. I analyze the project as an example of the ways that women's development is an object of material and discursive consumption. Artifacts produced and sold by Nepali women, and purchased by tourists from the "first world," become part of an international exchange of power, money, and meaning. Based on a survey of consumers and ethnographic observations, I conclude that feminist tourists forge relations with disempowered "Others" through the pleasurable activity of an alienated market transaction. Consumers of crafts produced at a women's development project assume a position of empowerment and enlightenment, ready to help out their "women" counterparts through their support of an enterprise with circular logic: within the industry of development (although not necessarily for feminist tourists themselves), at least one of the central projects of development is the development project itself. At the same time, feminist tourists locate themselves outside the oppressive structures and ideologies affecting their "third-world sisters." This is a relation of sympathy and imagined empathy, with no sense of differential location within systems of oppression. They fail to examine or articulate the global link between their own purchasing power and local living conditions of Maithil women; the connection is effectively built out of the discourse.

Imaging of salivary gland tumours

Imaging of salivary gland tumours is a major challenge for radiologists due to the great variety of differential diagnoses. This article gives a short overview on the anatomy of the salivary glands, the epidemiology of salivary gland tumours as well as the clinical presentation and the different imaging modalities including new magnetic resonance techniques such as diffusion-weighted magnetic resonance imaging, dynamic contrast-enhanced magnetic resonance imaging and magnetic resonance spectroscopy applied in the work-up of salivary gland masses. The imaging features of different tumour types and their differential diagnoses are also discussed. Finally, staging classification and treatment options are presented.

Differential GPS as a monitoring tool on Volcano Santa Ana (Illamatepec) and the Coatepeque Caldera, El Salvador

We used differential GPS measurements from a 13 station GPS network spanning the Santa Ana Volcano and Coatepeque Caldera to characterize the inter-eruptive activity and tectonic movements near these two active and potentially hazardous features. Caldera-forming events occurred from 70-40 ka and at Santa Ana/Izalco volcanoes eruptive activity occurred as recently as 2005. Twelve differential stations were surveyed for 1 to 2 hours on a monthly basis from February through September 2009 and tied to a centrally located continuous GPS station, which serves as the reference site for this volcanic network. Repeatabilities of the averages from 20-minute sessions taken over 20 hours or longer range from 2-11 mm in the horizontal (north and east) components of the inter-station baselines, suggesting a lower detection limit for the horizontal components of any short-term tectonic or volcanic deformation. Repeatabilities of the vertical baseline component range from 12-34 mm. Analysis of the precipitable water vapor in the troposphere suggests that tropospheric decorrelation as a function of baseline lengths and variable site elevations are the most likely sources of vertical error. Differential motions of the 12 sites relative to the continuous reference site reveal inflation from February through July at several sites surrounding the caldera with vertical displacements that range from 61 mm to 139 mm followed by a lower magnitude deflation event on 1.8-7.4 km-long baselines. Uplift rates for the inflationary period reach 300 mm/yr with 1σ uncertainties of +/- 26 – 119 mm. Only one other station outside the caldera exhibits a similar deformation trend, suggesting a localized source. The results suggest that the use of differential GPS measurements from short duration occupations over short baselines can be a useful monitoring tool at sub-tropical volcanoes and calderas.

Ultrasound of the pediatric female pelvis

Pelvic pain is a common indication for ultrasound examinations in female pediatric patients. Many pathological processes affect the female pelvis in childhood. Knowledge of the normal ultrasound appearance of the pelvic organs is the basis for the recognition of pathologic findings. Pelvic pain in children is a nonspecific clinical finding often prompting use of ultrasound. Other indications for pelvic ultrasound in female children include workup of cysts seen on fetal ultrasound, urogenital malformations in newborns, precocious puberty, vaginal discharge or abnormal bleeding, and amenorrhea. Knowledge of differential diagnosis for disease processes of the female pelvic organs is essential. Ultrasound is the imaging modality of choice for evaluating the pediatric female pelvis.

DISSECTION OF STRESS RESPONSE NETWORKS REGULATING MULTIPLE STRESSES IN RICE

Important food crops like rice are constantly exposed to various stresses that can have devastating effect on their survival and productivity. Being sessile, these highly evolved organisms have developed elaborate molecular machineries to sense a mixture of stress signals and elicit a precise response to minimize the damage. However, recent discoveries revealed that the interplay of these stress regulatory and signaling molecules is highly complex and remains largely unknown. In this work, we conducted large scale analysis of differential gene expression using advanced computational methods to dissect regulation of stress response which is at the heart of all molecular changes leading to the observed phenotypic susceptibility. One of the most important stress conditions in terms of loss of productivity is drought. We performed genomic and proteomic analysis of epigenetic and miRNA mechanisms in regulation of drought responsive genes in rice and found subsets of genes with striking properties. Overexpressed genesets included higher number of epigenetic marks, miRNA targets and transcription factors which regulate drought tolerance. On the other hand, underexpressed genesets were poor in above features but were rich in number of metabolic genes with multiple co-expression partners contributing majorly towards drought resistance. Identification and characterization of the patterns exhibited by differentially expressed genes hold key to uncover the synergistic and antagonistic components of the cross talk between stress response mechanisms. We performed meta-analysis on drought and bacterial stresses in rice and Arabidopsis, and identified hundreds of shared genes. We found high level of conservation of gene expression between these stresses. Weighted co-expression network analysis detected two tight clusters of genes made up of master transcription factors and signaling genes showing strikingly opposite expression status. To comprehensively identify the shared stress responsive genes between multiple abiotic and biotic stresses in rice, we performed meta-analyses of microarray studies from seven different abiotic and six biotic stresses separately and found more than thirteen hundred shared stress responsive genes. Various machine learning techniques utilizing these genes classified the stresses into two major classes' namely abiotic and biotic stresses and multiple classes of individual stresses with high accuracy and identified the top genes showing distinct patterns of expression. Functional enrichment and co-expression network analysis revealed the different roles of plant hormones, transcription factors in conserved and non-conserved genesets in regulation of stress response.

Ar-40/Ar-39 Evidence for Middle Proterozoic (1300-1500 Ma) Slow Cooling of the Southern Black Hills, South Dakota, Midcontinent, North America: Implications for Early Proterozoic P-T Evolution and Posttectonic Magmatism

Ar-40/Ar-39 total gas and plateau dates from muscovite and biotite in the southern Black Hills, South Dakota, provide evidence for a period of Middle Proterozoic slow cooling. Early Proterozoic (1600-1650 Ma) mica dates were obtained from metasedimentary rocks located in a synformal structure between the Harney Peak and Bear Mountain domes and also south of Bear Mountain. Metamorphic rocks from the dome areas and undeformed samples of the similar to 1710 Ma Harney Peak Granite (HPG) yield Middle Proterozoic mica dates (similar to 1270-1500 Ma). Two samples collected between the synform and Bear Mountain dome yield intermediate total gas mica dates of similar to 1550 Ma. We suggest two end-member interpretations to explain the map pattern of cooling ages: (1) subhorizontal slow cooling of an area which exhibits variation in mica Ar retention intervals or (2) mild folding of a Middle Proterozoic (similar to 1500 Ma) similar to 300 degrees C isotherm. According to the second interpretation, the preservation of older dates between the domes may reflect reactivation of a preexisting synformal structure (and downwarping of relatively cold rocks) during a period of approximately east-west contraction and slow uplift during the Middle Proterozoic. The mica data, together with hornblende data from the Black Hills published elsewhere, indicate that the ambient country-rock temperature at the 3-4 kbar depth of emplacement of the HPG was between 350 degrees C and 500 degrees C, suggesting that the average upper crustal geothermal gradient was 25 degrees-40 degrees C/km prior to intrusion. The thermochronologic data suggest HPG emplacement was followed by a similar to 200 m.y. period of stability and tectonic quiescence with little uplift. We propose that crust thickened during the Early Proterozoic was uplifted and erosionally(?) thinned prior to similar to 1710 Ma and that the HPG magma was emplaced into isostatically stable crust of relatively normal thickness. We speculate that uplift and crustal thinning prior to HPG intrusion was the result of differential thinning of the subcrustal lithosphere beneath the Black Hills. If so, this process would have also caused an increase in mantle heat flux across the Moho and triggered vapor-absent melting of biotite to produce the HPG magma. This scenario for posttectonic granite generation is supported, in part, by the fact that in the whole of the Black Hills, the HPG is spatially associated with the deepest exposed Early Proterozoic country rock.

Neural circuits of emotion regulation: a comparison of mindfulness-based and cognitive reappraisal strategies

Dealing with one's emotions is a core skill in everyday life. Effective cognitive control strategies have been shown to be neurobiologically represented in prefrontal structures regulating limbic regions. In addition to cognitive strategies, mindfulness-associated methods are increasingly applied in psychotherapy. We compared the neurobiological mechanisms of these two strategies, i.e. cognitive reappraisal and mindfulness, during both the cued expectation and perception of negative and potentially negative emotional pictures. Fifty-three healthy participants were examined with functional magnetic resonance imaging (47 participants included in analysis). Twenty-four subjects applied mindfulness, 23 used cognitive reappraisal. On the neurofunctional level, both strategies were associated with comparable activity of the medial prefrontal cortex and the amygdala. When expecting negative versus neutral stimuli, the mindfulness group showed stronger activations in ventro- and dorsolateral prefrontal cortex, supramarginal gyrus as well as in the left insula. During the perception of negative versus neutral stimuli, the two groups only differed in an increased activity in the caudate in the cognitive group. Altogether, both strategies recruited overlapping brain regions known to be involved in emotion regulation. This result suggests that common neural circuits are involved in the emotion regulation by mindfulness-based and cognitive reappraisal strategies. Identifying differential activations being associated with the two strategies in this study might be one step towards a better understanding of differential mechanisms of change underlying frequently used psychotherapeutic interventions.

Eigenvalue estimates for non-selfadjoint Dirac operators on the real line

We show that the non-embedded eigenvalues of the Dirac operator on the real line with complex mass and non-Hermitian potential V lie in the disjoint union of two disks, provided that the L1-norm of V is bounded from above by the speed of light times the reduced Planck constant. The result is sharp; moreover, the analogous sharp result for the Schrödinger operator, originally proved by Abramov, Aslanyan and Davies, emerges in the nonrelativistic limit. For massless Dirac operators, the condition on V implies the absence of non-real eigenvalues. Our results are further generalized to potentials with slower decay at infinity. As an application, we determine bounds on resonances and embedded eigenvalues of Dirac operators with Hermitian dilation-analytic potentials.

Thermal dependence of luminescence lifetimes and radioluminescence in quartz

During time-resolved optical stimulation experiments (TR-OSL), one uses short light pulses to separate the stimulation and emission of luminescence in time. Experimental TR-OSL results show that the luminescence lifetime in quartz of sedimentary origin is independent of annealing temperature below 500 °C, but decreases monotonically thereafter. These results have been interpreted previously empirically on the basis of the existence of two separate luminescence centers LH and LL in quartz, each with its own distinct luminescence lifetime. Additional experimental evidence also supports the presence of a non-luminescent hole reservoir R, which plays a critical role in the predose effect in this material. This paper extends a recently published analytical model for thermal quenching in quartz, to include the two luminescence centers LH and LL, as well as the hole reservoir R. The new extended model involves localized electronic transitions between energy states within the two luminescence centers, and is described by a system of differential equations based on the Mott–Seitz mechanism of thermal quenching. It is shown that by using simplifying physical assumptions, one can obtain analytical solutions for the intensity of the light during a TR-OSL experiment carried out with previously annealed samples. These analytical expressions are found to be in good agreement with the numerical solutions of the equations. The results from the model are shown to be in quantitative agreement with published experimental data for commercially available quartz samples. Specifically the model describes the variation of the luminescence lifetimes with (a) annealing temperatures between room temperature and 900 °C, and (b) with stimulation temperatures between 20 and 200 °C. This paper also reports new radioluminescence (RL) measurements carried out using the same commercially available quartz samples. Gaussian deconvolution of the RL emission spectra was carried out using a total of seven emission bands between 1.5 and 4.5 eV, and the behavior of these bands was examined as a function of the annealing temperature. An emission band at ∼3.44 eV (360 nm) was found to be strongly enhanced when the annealing temperature was increased to 500 °C, and this band underwent a significant reduction in intensity with further increase in temperature. Furthermore, a new emission band at ∼3.73 eV (330 nm) became apparent for annealing temperatures in the range 600–700 °C. These new experimental results are discussed within the context of the model presented in this paper.