The C-4-Dicarboxylate carriers DcuB and DctA of Escherichia coli: function as cosensors and topology

Das fakultativ anaerobe Enterobakterium Escherichia coli nutzt C4-Dicarboxylate sowohl unter aeroben als auch anaeroben Bedingungen als Kohlenstoff- und Energiequelle. Die Aufnahme der C4-Dicarboxylaten und die Energiekonservierung mittels Fumaratatmung wird durch das Zweikomponentensystem DcuSR reguliert. Die Sensorhistidinkinase DcuS und der nachgeschaltete Responseregulator DcuR aktivieren bei Verfügbarkeit von C4-Dicarboxylaten die Expression der Gene für den Succinat Transporter DctA, den anaeroben Fumarat/Succinat Antiporter DcuB, die Fumarase B sowie die Fumaratreduktase FrdABCD. Die Transportproteine DctA und DcuB wiederum regulieren die Expression der DcuSR-abhängigen Gene negativ. Fehlen von DctA oder DcuB resultiert bereits ohne Effektor in einer maximalen Expression von dctA bzw. dcuB. Durch gerichtete und ungerichtete Mutagenese wurde gezeigt, dass die Transportfunktion des Carriers DcuB unabhängig von seiner regulatorischen Funktion ist. DcuB kann daher als Cosensor des DcuSR Systems angesehen werden.rnUnter Verwendung von Reportergenfusionen von C-terminal verkürzten Konstrukten von DcuB mit der Alkalischen Phosphatase und der β-Galactosidase wurde die Topologie des Multitransmembranproteins DcuB bestimmt. Zusätzlich wurde die Zugänglichkeit bestimmter Aminosäurereste durch chemische Modifikation mit membran-durchlässigen und membran-undurchlässigen Thiolreagenzien untersucht. Die erhaltenen Ergebnisse deuten auf die Existenz eines tief in die Membran reichenden, hydrophilen Kanal hin, welcher zum Periplasma hin geöffnet ist. Mit Hilfe der Topologie-Studien, des Hydropathie-Blots und der Sekundärstruktur-Vorhersage wurde ein Modell des Carriers erstellt. DcuB besitzt kurze, periplasmatisch liegende Proteinenden, die durch 12 Transmembranhelices und zwei große hydrophile Schleifen jeweils zwischen TM VII/VIII und TM XI/XII verbunden sind. Die regulatorisch relevanten Reste K353, T396 und D398 befinden sich innerhalb von TM XI sowie auf der angrenzenden cytoplasmatischen Schleife XI-XII. Unter Berücksichtigung der strukturellen und funktionellen Aspekte wurde ein Regulationsmodell erstellt, welches die gemeinsam durch DcuB und DcuS kontrollierte C4-Dicarboxylat-abhängige Genexpression darstellt. rnDer Effekt von DctA und DcuSR auf die Expression einer dctA´-´lacZ Reportergenfusion und auf die aerobe C4-Dicarboxylat-Aufnahme wurde untersucht. In-vivo FRET-Messungen weisen auf eine direkte Wechselwirkung zwischen dem Carrier DctA und dem Sensor DcuS hin. Dieses Ergebnis stützt die Theorie der Regulation von DcuS durch C4-Dicarboxylate und durch die Cosensoren DctA bzw. DcuB mittels direkter Protein-Protein Interaktion.rn

Costruzione di chimere molecolari dell'enzima Integrasi di HIV con attività idrolizzante delle LTR virali.

La Sindrome da Immunodeficienza Acquisita (AIDS o SIDA) causata da HIV-1 (Virus dell'Immunodeficienza umana) è caratterizzata dalla graduale compromissione del sistema immunitario del soggetto colpito. Le attuali terapie farmacologiche, purtroppo, non riescono a eliminare l'infezione a causa della comparsa di continui ceppi resistenti ai farmaci, e inoltre questi trattamenti non sono in grado di eliminare i reservoir virali latenti e permettere l'eradicazione definitiva del virus dall’organismo. E' in questo ambito che si colloca il progetto a cui ho lavorato principalmente in questi anni, cioè la creazione di una strategia per eradicare il provirus di HIV integrato nel genoma della cellula ospite. L'Integrasi di HIV-1 è un enzima che media l'integrazione del cDNA virale nel genoma della cellula ospite. La nostra idea è stata, quindi, quella di associare all'attività di legame dell'IN stessa, un'attività catalitica. A tal fine abbiamo creato una proteina chimerica costituita da un dominio DNA-binding, dato dall'Integrasi, e da un dominio con attività nucleasica fornito dall'enzima FokI. La chimera ottenuta è stata sottoposta a mutagenesi random mediante UV, ed è stata oggetto di selezione in vivo, al fine di ottenere una chimera capace di riconoscere, specificamente le LTR di HIV-1, e idrolizzare i siti di inserzione. Questo lavoro porterà a definire pertanto se l'IN di HIV può essere riprogrammata a catalizzare una nuova funzione mediante la sostituzione dell'attività del proprio dominio catalitico con quello di FokI.

PAS c als signaltransduzierende Domäne des Sensorproteins DcuS von Escherichia coli

Bakterien besitzen membranintegrierte Sensoren für die Reaktion auf verändernde Umweltbedingungen.rnViele der Sensoren sind Zweikomponenten-Systeme bestehend aus einer Sensorhistidinkinase und einem Responseregulator der die zellulare Antwort auslöst. DcuS, der C4-Dicarboxylat-Sensor von DcuS ist eine membranintegrierte Histidin-Kinase. DcuS ist ein Multidomänen-Protein mit einer sensorischen periplasmatischen PASP (Per-Arnt-Sim) Domäne, zwei Transmembranhelices, eine cytoplasmatische PASC-Domäne und eine C-terminale Kinase-Domäne. PAS-Domänen sind ubiquitäre Signalmodule die in allen Reichen des Lebens zu finden sind. PAS-Domänen detektieren eine Vielfalt von Reizen wie Licht, Sauerstoff, Redoxpotential und verschiedene kleine Moleküle so wie die Modulation von Protein-Protein Interaktionen. PAS-Domänen sind strukturell homolog und besitzen eine charakteristische α/β-Faltung. Eine große Anzahl der sensorischen PAS-Domänen wurden identifiziert, aber viele der PAS-Domänen besitzen keinen apparenten Cofaktor und die Funktion ist unbekannt.rnEine Kombination aus gerichteter und ungerichteter Mutagenese, Protein-Protein-Interaktionsstudien und Festkörper-NMR (ssNMR) Experimente mit strukturellem Modelling wurde zur Untersuchung der Struktur und Funktion der cytoplasmatischen PAS-Domäne des membranintegrierten Sensors DcuS verwendet. Die Experimente zeigen, dass PASC eine wichtige Rolle in die Signaltransduktion von PASP zur C-terminalen Histidin-Kinase von DcuS spielt.rn

Implementazione di un codice di calcolo random close per un propellente solido

L’impacchettamento risulta essere importante in molti settori industriali, come il settore minerario, farmaceutico e soprattutto il settore spaziale, in quanto permette di massimizzare il grado di riempimento del propellente solido di un razzo ottenendo prestazioni migliori e notevoli vantaggi economici. Il lavoro di tesi presentato nel seguente elaborato consiste nello studio dell’impacchettamento casuale, in particolare il caso Random Close Packing, di un propellente solido; per fare ciò è stato implementato un codice in ambiente C++ presso l’hangar della Scuola di Ingegneria ed Architettura con sede a Forlì. L’obiettivo principale era quello di trovare la granulometria delle particelle di perclorato di ammonio e delle particelle di alluminio tali da minimizzare gli spazi lasciati vuoti dalle particelle stesse.

Study of the genes involved in Naphthenic acids (NAs) degradation by Rhodococcus spp.

Naphthenic acids (NAs) are an important group of organic pollutants mainly found in hydrocarbon deposits. Although these compounds are toxic, recalcitrant, and persistent in the environment, we are just learning the diversity of microbial communities involved in NAs- degradation and the mechanisms by which NAs are biodegraded. Studies have shown that naphthenic acids are susceptible to biodegradation, which decreases their concentration and reduces toxicity. Nevertheless, little is still known about their biodegradability. The present PhD Thesis’s work is aimed to study the biodegradation of simple model NAs using bacteria strains belonging to the Rhodococcus genus. In particular, Rh. sp. BCP1 and Rh. opacus R7 were able to utilize NAs such as cyclohexane carboxylic acid and cyclopentane carboxylic acid as the sole carbon and energy sources, even at concentrations up to 1000 mg/L. The presence of either substituents or longer carboxylic acid chains attached to the cyclohexane ring negatively affected the growth by pure bacterial cultures. Moreover, BCP1 and R7 cells incubated in the presence of CHCA or CPCA show a general increase of saturated and methyl-substituted fatty acids in their membrane, while the cis-mono-unsaturated ones decrease, as compared to glucose-grown cells. The observed lipid molecules modification during the growth in the presence of NAs is suggested as a possible mechanism to decrease the fluidity of the cell membrane to counteract NAs toxicity. In order to further evaluate this toxic effect on cell features, the morphological changes of BCP1 and R7 cells were also assessed through Transmission Electron Microscopy (TEM), revealing interesting ultrastructural changes. The induction of putative genes, and the construction of a random transposon mutagenesis library were also carried out to reveal the mechanisms by which these Rhodococcus strains can degrade toxic compounds such as NAs.

Random lattice models

This thesis deals with three different physical models, where each model involves a random component which is linked to a cubic lattice. First, a model is studied, which is used in numerical calculations of Quantum Chromodynamics.In these calculations random gauge-fields are distributed on the bonds of the lattice. The formulation of the model is fitted into the mathematical framework of ergodic operator families. We prove, that for small coupling constants, the ergodicity of the underlying probability measure is indeed ensured and that the integrated density of states of the Wilson-Dirac operator exists. The physical situations treated in the next two chapters are more similar to one another. In both cases the principle idea is to study a fermion system in a cubic crystal with impurities, that are modeled by a random potential located at the lattice sites. In the second model we apply the Hartree-Fock approximation to such a system. For the case of reduced Hartree-Fock theory at positive temperatures and a fixed chemical potential we consider the limit of an infinite system. In that case we show the existence and uniqueness of minimizers of the Hartree-Fock functional. In the third model we formulate the fermion system algebraically via C*-algebras. The question imposed here is to calculate the heat production of the system under the influence of an outer electromagnetic field. We show that the heat production corresponds exactly to what is empirically predicted by Joule's law in the regime of linear response.

Crystallization and morphology of the PLLA phase within random poly (L-lactide-ran-ɛ-caprolactone)

This work has mainly focused on the poly (L-lactide) (PLLA) which is a material for multiple applications with performances comparable to those of petrochemical polymers (PP, PS, PET, etc. ...), readily recyclable and also compostable. However, PLLA has certain shortcomings that limit its applications. It is a brittle, hard polymer with a very low elongation at break, hydrophobic, exhibits low crystallization kinetics and takes a long time to degrade. The properties of PLLA may be modified by copolymerization (random, block, and graft) of L-lactide monomers with other co-monomers. In this thesis it has been studied the crystallization and morphology of random copolymers poly (L-lactide-ran-ε-caprolactone) with different compositions of the two monomers since the physical, mechanical, optical and chemical properties of a material depend on this behavior. Thermal analyses were performed by differential scanning calorimetry (DSC) and thermogravimetry (TGA) to observe behaviors due to the different compositions of the copolymers. The crystallization kinetics and morphology of poly (L-lactide-ran-ε-caprolactone) was investigated by polarized light optical microscopy (PLOM) and differential scanning calorimetry (DSC). Their thermal behavior was observed with crystallization from melt. It was observed that with increasing amounts of PCL in the copolymer, there is a decrease of the thermal degradation. Studies on the crystallization kinetics have shown that small quantities of PCL in the copolymer increase the overall crystallization kinetics and the crystal growth rate which decreases with higher quantities of PCL.

Studio e implementazione di un modello random-close per propellenti solidi

L'obiettivo di questo lavoro di tesi è quello di implementare un codice di calcolo, attraverso l'algoritmo di Lubachevsky-Stillinger, in modo da poter prevedere la frazione volumetrica occupata dalle particelle solide che costituiscono il grain negli endoreattori a propellente solido. Particolare attenzione verrà rivolta al problema dell'impacchettamento sferico random (Random-Close Packing) che tale algoritmo cerca di modellare, e le ipotesi per cui tale modellazione può essere applicata al tipo di problema proposto. Inoltre saranno descritte le procedure effettuate per l'ottenimento dei risultati numerici delle simulazioni e la loro motivazione, oltre ai limiti del modello utilizzato e alle migliorie apportate per un'esecuzione più efficiente e veloce.

Progetto vhdl di un nucleo di calcolo per misure di impedenza basate su segnali pseudo-random

In questo elaborato si affronta il progetto di un nucleo di calcolo per misure d'impedenza sulla pelle tramite l'utilizzo di segnali pseudo-random. La misura viene effettuata applicando il segnale casuale all'impedenza per ottenere la risposta impulsiva tramite un'operazione di convoluzione. Il nucleo di calcolo è stato implementato in VHDL.

Fluctuation properties in random walks on networks and simple integrate and fire models

In questa tesi si è studiato l’insorgere di eventi critici in un semplice modello neurale del tipo Integrate and Fire, basato su processi dinamici stocastici markoviani definiti su una rete. Il segnale neurale elettrico è stato modellato da un flusso di particelle. Si è concentrata l’attenzione sulla fase transiente del sistema, cercando di identificare fenomeni simili alla sincronizzazione neurale, la quale può essere considerata un evento critico. Sono state studiate reti particolarmente semplici, trovando che il modello proposto ha la capacità di produrre effetti "a cascata" nell’attività neurale, dovuti a Self Organized Criticality (auto organizzazione del sistema in stati instabili); questi effetti non vengono invece osservati in Random Walks sulle stesse reti. Si è visto che un piccolo stimolo random è capace di generare nell’attività della rete delle fluttuazioni notevoli, in particolar modo se il sistema si trova in una fase al limite dell’equilibrio. I picchi di attività così rilevati sono stati interpretati come valanghe di segnale neurale, fenomeno riconducibile alla sincronizzazione.

Mission synthesis of sine-on-random excitations for accelerated vibration qualification testing

In most real-life environments, mechanical or electronic components are subjected to vibrations. Some of these components may have to pass qualification tests to verify that they can withstand the fatigue damage they will encounter during their operational life. In order to conduct a reliable test, the environmental excitations can be taken as a reference to synthesize the test profile: this procedure is referred to as “test tailoring”. Due to cost and feasibility reasons, accelerated qualification tests are usually performed. In this case, the duration of the original excitation which acts on the component for its entire life-cycle, typically hundreds or thousands of hours, is reduced. In particular, the “Mission Synthesis” procedure lets to quantify the induced damage of the environmental vibration through two functions: the Fatigue Damage Spectrum (FDS) quantifies the fatigue damage, while the Maximum Response Spectrum (MRS) quantifies the maximum stress. Then, a new random Power Spectral Density (PSD) can be synthesized, with same amount of induced damage, but a specified duration in order to conduct accelerated tests. In this work, the Mission Synthesis procedure is applied in the case of so-called Sine-on-Random vibrations, i.e. excitations composed of random vibrations superimposed on deterministic contributions, in the form of sine tones typically due to some rotating parts of the system (e.g. helicopters, engine-mounted components, …). In fact, a proper test tailoring should not only preserve the accumulated fatigue damage, but also the “nature” of the excitation (in this case the sinusoidal components superimposed on the random process) in order to obtain reliable results. The classic time-domain approach is taken as a reference for the comparison of different methods for the FDS calculation in presence of Sine-on-Random vibrations. Then, a methodology to compute a Sine-on-Random specification based on a mission FDS is presented.

On the recurrence of random walks in Lévy random environments

This thesis investigates one-dimensional random walks in random environment whose transition probabilities might have an infinite variance. The ergodicity of the dynamical system ''from the point of view of the particle'' is proved under the assumptions of transitivity and existence of an absolutely continuous steady state on the space of the environments. We show that, if the average of the local drift over the environments is summable and null, then the RWRE is recurrent. We provide an example satisfying all the hypotheses.

Stationary states in random walks on networks

In this thesis we dealt with the problem of describing a transportation network in which the objects in movement were subject to both finite transportation capacity and finite accomodation capacity. The movements across such a system are realistically of a simultaneous nature which poses some challenges when formulating a mathematical description. We tried to derive such a general modellization from one posed on a simplified problem based on asyncronicity in particle transitions. We did so considering one-step processes based on the assumption that the system could be describable through discrete time Markov processes with finite state space. After describing the pre-established dynamics in terms of master equations we determined stationary states for the considered processes. Numerical simulations then led to the conclusion that a general system naturally evolves toward a congestion state when its particle transition simultaneously and we consider one single constraint in the form of network node capacity. Moreover the congested nodes of a system tend to be located in adjacent spots in the network, thus forming local clusters of congested nodes.

Atlas-Based Segmentation of Brain Tumor Images Using a Markov Random Field-Based Tumor Growth Model and Non-Rigid Registration

We propose a new and clinically oriented approach to perform atlas-based segmentation of brain tumor images. A mesh-free method is used to model tumor-induced soft tissue deformations in a healthy brain atlas image with subsequent registration of the modified atlas to a pathologic patient image. The atlas is seeded with a tumor position prior and tumor growth simulating the tumor mass effect is performed with the aim of improving the registration accuracy in case of patients with space-occupying lesions. We perform tests on 2D axial slices of five different patient data sets and show that the approach gives good results for the segmentation of white matter, grey matter, cerebrospinal fluid and the tumor.