Bifidobacterium - Human Host Interaction: Role of Human Plasminogen

Bifidobacterium is an important genus of the human gastrointestinal microbiota, affecting several host physiological features. Despite the numerous Bifidobacterium related health-promoting activities, there is still a dearth of information about the molecular mechanisms at the basis of the interaction between this microorganism and the host. Bacterial surface associated proteins may play an important role in this interaction because of their ability to intervene with host molecules, as recently reported for the host protein plasminogen. Plasminogen is the zymogen of the trypsin-like serine protease plasmin, an enzyme with a broad substrate specificity. Aim of this thesis is to deepen the knowledge about the interaction between Bifidobacterium and the human plasminogen system and its role in the Bifidobacterium-host interaction process. As a bifidobacterial model, B. animalis subsp. lactis BI07 has been used because of its large usage in dairy and pharmaceutical preparations. We started from the molecular characterization of the interaction between plasminogen and one bifidobacterial plasminogen receptor, DnaK, a cell wall protein showing high affinity for plasminogen, and went on with the study of the impact of intestinal environmental factors, such as bile salts and inflammation, on the plasminogen-mediated Bifidobacterium-host interaction. According to our in vitro findings, by enhancing the activation of the bifidobacterial bound plasminogen to plasmin, the host inflammatory response results in the decrease of the bifidobacterial adhesion to the host enterocytes, favouring bacterial migration to the luminal compartment. Conversely, in the absence of inflammation, plasminogen acts as a molecular bridge between host enterocytes and bifidobacteria, enhancing Bifidobacterium adhesion. Furthermore, adaptation to physiological concentrations of bile salts enhances the capability of this microorganism to interact with the host plasminogen system. The host plasminogen system thus represents an important and flexible tool used by bifidobacteria in the cross-talk with the host.

Model reduction of stochastic groundwater flow and transport processes

This work presents a comprehensive methodology for the reduction of analytical or numerical stochastic models characterized by uncertain input parameters or boundary conditions. The technique, based on the Polynomial Chaos Expansion (PCE) theory, represents a versatile solution to solve direct or inverse problems related to propagation of uncertainty. The potentiality of the methodology is assessed investigating different applicative contexts related to groundwater flow and transport scenarios, such as global sensitivity analysis, risk analysis and model calibration. This is achieved by implementing a numerical code, developed in the MATLAB environment, presented here in its main features and tested with literature examples. The procedure has been conceived under flexibility and efficiency criteria in order to ensure its adaptability to different fields of engineering; it has been applied to different case studies related to flow and transport in porous media. Each application is associated with innovative elements such as (i) new analytical formulations describing motion and displacement of non-Newtonian fluids in porous media, (ii) application of global sensitivity analysis to a high-complexity numerical model inspired by a real case of risk of radionuclide migration in the subsurface environment, and (iii) development of a novel sensitivity-based strategy for parameter calibration and experiment design in laboratory scale tracer transport.

Multilevel Domain Decomposition Algorithms for Monolithic Fluid-Structure Interaction Problems with Application to Haemodynamics

Finite element techniques for solving the problem of fluid-structure interaction of an elastic solid material in a laminar incompressible viscous flow are described. The mathematical problem consists of the Navier-Stokes equations in the Arbitrary Lagrangian-Eulerian formulation coupled with a non-linear structure model, considering the problem as one continuum. The coupling between the structure and the fluid is enforced inside a monolithic framework which computes simultaneously for the fluid and the structure unknowns within a unique solver. We used the well-known Crouzeix-Raviart finite element pair for discretization in space and the method of lines for discretization in time. A stability result using the Backward-Euler time-stepping scheme for both fluid and solid part and the finite element method for the space discretization has been proved. The resulting linear system has been solved by multilevel domain decomposition techniques. Our strategy is to solve several local subproblems over subdomain patches using the Schur-complement or GMRES smoother within a multigrid iterative solver. For validation and evaluation of the accuracy of the proposed methodology, we present corresponding results for a set of two FSI benchmark configurations which describe the self-induced elastic deformation of a beam attached to a cylinder in a laminar channel flow, allowing stationary as well as periodically oscillating deformations, and for a benchmark proposed by COMSOL multiphysics where a narrow vertical structure attached to the bottom wall of a channel bends under the force due to both viscous drag and pressure. Then, as an example of fluid-structure interaction in biomedical problems, we considered the academic numerical test which consists in simulating the pressure wave propagation through a straight compliant vessel. All the tests show the applicability and the numerical efficiency of our approach to both two-dimensional and three-dimensional problems.

Flow Field–Flow Fractionation for size analysis and characterization of nanoparticles for applications in Life Sciences

Nanotechnologies are rapidly expanding because of the opportunities that the new materials offer in many areas such as the manufacturing industry, food production, processing and preservation, and in the pharmaceutical and cosmetic industry. Size distribution of the nanoparticles determines their properties and is a fundamental parameter that needs to be monitored from the small-scale synthesis up to the bulk production and quality control of nanotech products on the market. A consequence of the increasing number of applications of nanomaterial is that the EU regulatory authorities are introducing the obligation for companies that make use of nanomaterials to acquire analytical platforms for the assessment of the size parameters of the nanomaterials. In this work, Asymmetrical Flow Field-Flow Fractionation (AF4) and Hollow Fiber F4 (HF5), hyphenated with Multiangle Light Scattering (MALS) are presented as tools for a deep functional characterization of nanoparticles. In particular, it is demonstrated the applicability of AF4-MALS for the characterization of liposomes in a wide series of mediums. Afterwards the technique is used to explore the functional features of a liposomal drug vector in terms of its biological and physical interaction with blood serum components: a comprehensive approach to understand the behavior of lipid vesicles in terms of drug release and fusion/interaction with other biological species is described, together with weaknesses and strength of the method. Afterwards the size characterization, size stability, and conjugation of azidothymidine drug molecules with a new generation of metastable drug vectors, the Metal Organic Frameworks, is discussed. Lastly, it is shown the applicability of HF5-ICP-MS for the rapid screening of samples of relevant nanorisk: rather than a deep and comprehensive characterization it this time shown a quick and smart methodology that within few steps provides qualitative information on the content of metallic nanoparticles in tattoo ink samples.

Analysis and mathematical modeling of wave-structure interaction

The aim of this thesis, included within the THESEUS project, is the development of a mathematical model 2DV two-phase, based on the existing code IH-2VOF developed by the University of Cantabria, able to represent together the overtopping phenomenon and the sediment transport. Several numerical simulations were carried out in order to analyze the flow characteristics on a dike crest. The results show that the seaward/landward slope does not affect the evolution of the flow depth and velocity over the dike crest whereas the most important parameter is the relative submergence. Wave heights decrease and flow velocities increase while waves travel over the crest. In particular, by increasing the submergence, the wave height decay and the increase of the velocity are less marked. Besides, an appropriate curve able to fit the variation of the wave height/velocity over the dike crest were found. Both for the wave height and for the wave velocity different fitting coefficients were determined on the basis of the submergence and of the significant wave height. An equation describing the trend of the dimensionless coefficient c_h for the wave height was derived. These conclusions could be taken into consideration for the design criteria and the upgrade of the structures. In the second part of the thesis, new equations for the representation of the sediment transport in the IH-2VOF model were introduced in order to represent beach erosion while waves run-up and overtop the sea banks during storms. The new model allows to calculate sediment fluxes in the water column together with the sediment concentration. Moreover it is possible to model the bed profile evolution. Different tests were performed under low-intensity regular waves with an homogeneous layer of sand on the bottom of a channel in order to analyze the erosion-deposition patterns and verify the model results.

Influence of optic flow on postural control

The study of optic flow on postural control may explain how self-motion perception contributes to postural stability in young males and females and how such function changes in the old falls risk population. Study I: The aim was to examine the optic flow effect on postural control in young people (n=24), using stabilometry and surface-electromyography. Subjects viewed expansion and contraction optic flow stimuli which were presented full field, in the foveral or in the peripheral visual field. Results showed that optic flow stimulation causes an asymmetry in postural balance and a different lateralization of postural control in men and women. Gender differences evoked by optic flow were found both in the muscle activity and in the prevalent direction of oscillation. The COP spatial variability was reduced during the view of peripheral stimuli which evoked a clustered prevalent direction of oscillation, while foveal and random stimuli induced non-distributed directions. Study II was aimed at investigating the age-related mechanisms of postural stability during the view of optic flow stimuli in young (n=17) and old (n=19) people, using stabilometry and kinematic. Results showed that old people showed a greater effort to maintain posture during the view of optic flow stimuli than the young. Elderly seems to use the head stabilization on trunk strategy. Visual stimuli evoke an excitatory input on postural muscles, but the stimulus structure produces different postural effects. Peripheral optic flow stabilizes postural sway, while random and foveal stimuli provoke larger sway variability similar to those evoked in baseline. Postural control uses different mechanisms within each leg to produce the appropriate postural response to interact with extrapersonal environment. Ageing reduce the effortlessness to stabilize posture during optic flow, suggesting a neuronal processing decline associated with difficulty integrating multi-sensory information of self-motion perception and increasing risk of falls.

Aerobic biodegradation of chlorinated solvents and plastics in batch and continuous-flow bioreactors: process development, and identification of suitable chemical pre-Treatments

The purpose of the first part of the research activity was to develop an aerobic cometabolic process in packed bed reactors (PBR) to treat real groundwater contaminated by trichloroethylene (TCE) and 1,1,2,2-tetrachloroethane (TeCA). In an initial screening conducted in batch bioreactors, different groundwater samples from 5 wells of the contaminated site were fed with 5 growth substrates. The work led to the selection of butane as the best growth substrate, and to the development and characterization from the site’s indigenous biomass of a suspended-cell consortium capable to degrade TCE with a 90 % mineralization of the organic chlorine. A kinetic study conducted in batch and continuous flow PBRs and led to the identification of the best carrier. A kinetic study of butane and TCE biodegradation indicated that the attached-cell consortium is characterized by a lower TCE specific degredation rates and by a lower level of mutual butane-TCE inhibition. A 31 L bioreactor was designed and set up for upscaling the experiment. The second part of the research focused on the biodegradation of 4 polymers, with and with-out chemical pre-treatments: linear low density polyethylene (LLDPE), polyethylene (PP), polystyrene (PS) and polyvinyl chloride (PVC). Initially, the 4 polymers were subjected to different chemical pre-treatments: ozonation and UV/ozonation, in gaseous and aqueous phase. It was found that, for LLDPE and PP, the coupling UV and ozone in gas phase is the most effective way to oxidize the polymers and to generate carbonyl groups on the polymer surface. In further tests, the effect of chemical pretreatment on polyner biodegrability was studied. Gas-phase ozonated and virgin polymers were incubated aerobically with: (a) a pure strain, (b) a mixed culture of bacteria; and (c) a fungal culture, together with saccharose as a co-substrate.