Molecular architecture of fur binding to iron-induced and - repressed genes in Helicobacter pylori

The ferric uptake regulator protein Fur regulates iron-dependent gene expression in bacteria. In the human pathogen Helicobacter pylori, Fur has been shown to regulate iron-induced and iron-repressed genes. Herein we investigate the molecular mechanisms that control this differential iron-responsive Fur regulation. Hydroxyl radical footprinting showed that Fur has different binding architectures, which characterize distinct operator typologies. On operators recognized with higher affinity by holo-Fur, the protein binds to a continuous AT-rich stretch of about 20 bp, displaying an extended protection pattern. This is indicative of protein wrapping around the DNA helix. DNA binding interference assays with the minor groove binding drug distamycin A, point out that the recognition of the holo-operators occurs through the minor groove of the DNA. By contrast, on the apo-operators, Fur binds primarily to thymine dimers within a newly identified TCATTn10TT consensus element, indicative of Fur binding to one side of the DNA, in the major groove of the double helix. Reconstitution of the TCATTn10TT motif within a holo-operator results in a feature binding swap from an holo-Fur- to an apo-Fur-recognized operator, affecting both affinity and binding architecture of Fur, and conferring apo-Fur repression features in vivo. Size exclusion chromatography indicated that Fur is a dimer in solution. However, in the presence of divalent metal ions the protein is able to multimerize. Accordingly, apo-Fur binds DNA as a dimer in gel shift assays, while in presence of iron, higher order complexes are formed. Stoichiometric Ferguson analysis indicates that these complexes correspond to one or two Fur tetramers, each bound to an operator element. Together these data suggest that the apo- and holo-Fur repression mechanisms apparently rely on two distinctive modes of operator-recognition, involving respectively the readout of a specific nucleotide consensus motif in the major groove for apo-operators, and the recognition of AT-rich stretches in the minor groove for holo-operators, whereas the iron-responsive binding affinity is controlled through metal-dependent shaping of the protein structure in order to match preferentially the major or the minor groove.

Second law analysis and simulation techniques for the energy optimization of buildings

The research activity described in this thesis is focused mainly on the study of finite-element techniques applied to thermo-fluid dynamic problems of plant components and on the study of dynamic simulation techniques applied to integrated building design in order to enhance the energy performance of the building. The first part of this doctorate thesis is a broad dissertation on second law analysis of thermodynamic processes with the purpose of including the issue of the energy efficiency of buildings within a wider cultural context which is usually not considered by professionals in the energy sector. In particular, the first chapter includes, a rigorous scheme for the deduction of the expressions for molar exergy and molar flow exergy of pure chemical fuels. The study shows that molar exergy and molar flow exergy coincide when the temperature and pressure of the fuel are equal to those of the environment in which the combustion reaction takes place. A simple method to determine the Gibbs free energy for non-standard values of the temperature and pressure of the environment is then clarified. For hydrogen, carbon dioxide, and several hydrocarbons, the dependence of the molar exergy on the temperature and relative humidity of the environment is reported, together with an evaluation of molar exergy and molar flow exergy when the temperature and pressure of the fuel are different from those of the environment. As an application of second law analysis, a comparison of the thermodynamic efficiency of a condensing boiler and of a heat pump is also reported. The second chapter presents a study of borehole heat exchangers, that is, a polyethylene piping network buried in the soil which allows a ground-coupled heat pump to exchange heat with the ground. After a brief overview of low-enthalpy geothermal plants, an apparatus designed and assembled by the author to carry out thermal response tests is presented. Data obtained by means of in situ thermal response tests are reported and evaluated by means of a finite-element simulation method, implemented through the software package COMSOL Multyphysics. The simulation method allows the determination of the precise value of the effective thermal properties of the ground and of the grout, which are essential for the design of borehole heat exchangers. In addition to the study of a single plant component, namely the borehole heat exchanger, in the third chapter is presented a thorough process for the plant design of a zero carbon building complex. The plant is composed of: 1) a ground-coupled heat pump system for space heating and cooling, with electricity supplied by photovoltaic solar collectors; 2) air dehumidifiers; 3) thermal solar collectors to match 70% of domestic hot water energy use, and a wood pellet boiler for the remaining domestic hot water energy use and for exceptional winter peaks. This chapter includes the design methodology adopted: 1) dynamic simulation of the building complex with the software package TRNSYS for evaluating the energy requirements of the building complex; 2) ground-coupled heat pumps modelled by means of TRNSYS; and 3) evaluation of the total length of the borehole heat exchanger by an iterative method developed by the author. An economic feasibility and an exergy analysis of the proposed plant, compared with two other plants, are reported. The exergy analysis was performed by considering the embodied energy of the components of each plant and the exergy loss during the functioning of the plants.

An New Energetic Approach to the Modeling of Human Joint Kinematics: Application to the Ankle

The objective of this dissertation is to develop and test a predictive model for the passive kinematics of human joints based on the energy minimization principle. To pursue this goal, the tibio-talar joint is chosen as a reference joint, for the reduced number of bones involved and its simplicity, if compared with other sinovial joints such as the knee or the wrist. Starting from the knowledge of the articular surface shapes, the spatial trajectory of passive motion is obtained as the envelop of joint configurations that maximize the surfaces congruence. An increase in joint congruence corresponds to an improved capability of distributing an applied load, allowing the joint to attain a better strength with less material. Thus, joint congruence maximization is a simple geometric way to capture the idea of joint energy minimization. The results obtained are validated against in vitro measured trajectories. Preliminary comparison provide strong support for the predictions of the theoretical model.