Analysis of the role of the Spitzenkörper in fungal morphogenesis by computer simulation of apical branching in Aspergillus niger

High-resolution video microscopy, image analysis, and computer simulation were used to study the role of the Spitzenkörper (Spk) in apical branching of ramosa-1, a temperature-sensitive mutant of Aspergillus niger. A shift to the restrictive temperature led to a cytoplasmic contraction that destabilized the Spk, causing its disappearance. After a short transition period, new Spk appeared where the two incipient apical branches emerged. Changes in cell shape, growth rate, and Spk position were recorded and transferred to the fungus simulator program to test the hypothesis that the Spk functions as a vesicle supply center (VSC). The simulation faithfully duplicated the elongation of the main hypha and the two apical branches. Elongating hyphae exhibited the growth pattern described by the hyphoid equation. During the transition phase, when no Spk was visible, the growth pattern was nonhyphoid, with consecutive periods of isometric and asymmetric expansion; the apex became enlarged and blunt before the apical branches emerged. Video microscopy images suggested that the branch Spk were formed anew by gradual condensation of vesicle clouds. Simulation exercises where the VSC was split into two new VSCs failed to produce realistic shapes, thus supporting the notion that the branch Spk did not originate by division of the original Spk. The best computer simulation of apical branching morphogenesis included simulations of the ontogeny of branch Spk via condensation of vesicle clouds. This study supports the hypothesis that the Spk plays a major role in hyphal morphogenesis by operating as a VSC—i.e., by regulating the traffic of wall-building vesicles in the manner predicted by the hyphoid model.

Ab initio calculation of electronic coupling in the photosynthetic reaction center

We have carried out an ab initio electronic structure calculations of electron transfer couplings between chromophores in the bacterial photosynthetic reaction center. The couplings agree remarkably well with parameters obtained from recent quantum dynamical modeling of experimental data assuming an explicit intermediate mechanism. We also have computed couplings on the M-side of the reaction center and have found that the interaction of the primary donor to the M-side intermediate bacteriochlorophyll is quite small because of destructive interference of the two localized coupling matrix elements. This may explain the slow rate of electron transfer down the M-side of the reaction center.

Progress toward chemical accuracy in the computer simulation of condensed phase reactions.

We describe a procedure for the generation of chemically accurate computer-simulation models to study chemical reactions in the condensed phase. The process involves (i) the use of a coupled semiempirical quantum and classical molecular mechanics method to represent solutes and solvent, respectively; (ii) the optimization of semiempirical quantum mechanics (QM) parameters to produce a computationally efficient and chemically accurate QM model; (iii) the calibration of a quantum/classical microsolvation model using ab initio quantum theory; and (iv) the use of statistical mechanical principles and methods to simulate, on massively parallel computers, the thermodynamic properties of chemical reactions in aqueous solution. The utility of this process is demonstrated by the calculation of the enthalpy of reaction in vacuum and free energy change in aqueous solution for a proton transfer involving methanol, methoxide, imidazole, and imidazolium, which are functional groups involved with proton transfers in many biochemical systems. An optimized semiempirical QM model is produced, which results in the calculation of heats of formation of the above chemical species to within 1.0 kcal/mol (1 kcal = 4.18 kJ) of experimental values. The use of the calibrated QM and microsolvation QM/MM (molecular mechanics) models for the simulation of a proton transfer in aqueous solution gives a calculated free energy that is within 1.0 kcal/mol (12.2 calculated vs. 12.8 experimental) of a value estimated from experimental pKa values of the reacting species.

Innovative analytical strategies for the development of sensor devices and mass spectrometry methods

Il lavoro presentato in questa tesi di Dottorato è incentrato sullo sviluppo di strategie analitiche innovative basate sulla sensoristica e su tecniche di spettrometria di massa in ambito biologico e della sicurezza alimentare. Il primo capitolo tratta lo studio di aspetti metodologici ed applicativi di procedure sensoristiche per l’identificazione e la determinazione di biomarkers associati alla malattia celiaca. In tale ambito, sono stati sviluppati due immunosensori, uno a trasduzione piezoelettrica e uno a trasduzione amperometrica, per la rivelazione di anticorpi anti-transglutaminasi tissutale associati a questa malattia. L’innovazione di questi dispositivi riguarda l’immobilizzazione dell’enzima tTG nella conformazione aperta (Open-tTG), che è stato dimostrato essere quella principalmente coinvolta nella patogenesi. Sulla base dei risultati ottenuti, entrambi i sistemi sviluppati si sono dimostrati una valida alternativa ai test di screening attualmente in uso per la diagnosi della celiachia. Rimanendo sempre nel contesto della malattia celiaca, ulteriore ricerca oggetto di questa tesi di Dottorato, ha riguardato lo sviluppo di metodi affidabili per il controllo di prodotti “gluten-free”. Il secondo capitolo tratta lo sviluppo di un metodo di spettrometria di massa e di un immunosensore competitivo per la rivelazione di prolammine in alimenti “gluten-free”. E’ stato sviluppato un metodo LC-ESI-MS/MS basato su un’analisi target con modalità di acquisizione del segnale selected reaction monitoring per l’identificazione di glutine in diversi cereali potenzialmente tossici per i celiaci. Inoltre ci si è focalizzati su un immunosensore competitivo per la rivelazione di gliadina, come metodo di screening rapido di farine. Entrambi i sistemi sono stati ottimizzati impiegando miscele di farina di riso addizionata di gliadina, avenine, ordeine e secaline nel caso del sistema LC-MS/MS e con sola gliadina nel caso del sensore. Infine i sistemi analitici sono stati validati analizzando sia materie prime (farine) che alimenti (biscotti, pasta, pane, etc.). L’approccio sviluppato in spettrometria di massa apre la strada alla possibilità di sviluppare un test di screening multiplo per la valutazione della sicurezza di prodotti dichiarati “gluten-free”, mentre ulteriori studi dovranno essere svolti per ricercare condizioni di estrazione compatibili con l’immunosaggio competitivo, per ora applicabile solo all’analisi di farine estratte con etanolo. Terzo capitolo di questa tesi riguarda lo sviluppo di nuovi metodi per la rivelazione di HPV, Chlamydia e Gonorrhoeae in fluidi biologici. Si è scelto un substrato costituito da strips di carta in quanto possono costituire una valida piattaforma di rivelazione, offrendo vantaggi grazie al basso costo, alla possibilità di generare dispositivi portatili e di poter visualizzare il risultato visivamente senza la necessità di strumentazioni. La metodologia sviluppata è molto semplice, non prevede l’uso di strumentazione complessa e si basa sull’uso della isothermal rolling-circle amplification per l’amplificazione del target. Inoltre, di fondamentale importanza, è l’utilizzo di nanoparticelle colorate che, essendo state funzionalizzate con una sequenza di DNA complementare al target amplificato derivante dalla RCA, ne permettono la rivelazione a occhio nudo mediante l’uso di filtri di carta. Queste strips sono state testate su campioni reali permettendo una discriminazione tra campioni positivi e negativi in tempi rapidi (10-15 minuti), aprendo una nuova via verso nuovi test altamente competitivi con quelli attualmente sul mercato.

Calix[6]arene Derivatives as Pivotal Components of Working Devices and Molecular Machine Prototypes

This Ph.D. thesis describes the synthesis, characterization and study of calix[6]arene derivatives as pivotal components for the construction of molecular machine prototypes. Initially, the ability of a calix[6]arene wheel to supramolecularly assist and increase the rate of a nucleophilic substitution reaction was exploited for the synthesis of two constitutionally isomeric oriented rotaxanes. Then, the synthesis and characterization of several hetero-functionalised calix[6]arene derivatives and the possibility to obtain molecular muscle prototypes was reported. The ability of calix[6]arenes to form oriented pseudorotaxane towards dialkyl viologen axles was then exploited for the synthesis of two calixarene-based [2]catenanes. As last part of this thesis, studies on the electrochemical response of the threading-dethreading process of calix[6]arene-based pseudorotaxanes and rotaxanes supported on glassy carbon electrodes are reported.

Identification of the mRNA targets of tRNA-­specific regulation using genome-­wide simulation of translation

FUNDING Biotechnology and Biological Sciences Research Council (BBSRC) [BB/I020926/1 to I.S.]; BBSRC PhD studentship award [C103817D to I.S. and M.C.R.]; Scottish Universities Life Science Alliance PhD studentship award (to M.C.R. and I.S.]. Funding for open access charge: BBSRC. Conflict of interest statement. None declared.

Simulation of the cold climate event 8200 years ago by meltwater outburst from Lake Agassiz

The cold climate anomaly about 8200 years ago is investigated with CLIMBER-2, a coupled atmosphere-ocean-biosphere model of intermediate complexity. This climate model simulates a cooling of about 3.6 K over the North Atlantic induced by a meltwater pulse from Lake Agassiz routed through the Hudson strait. The meltwater pulse is assumed to have a volume of 1.6 x 10^14 m^3 and a period of discharge of 2 years on the basis of glaciological modeling of the decay of the Laurentide Ice Sheet ( LIS). We present a possible mechanism which can explain the centennial duration of the 8.2 ka cold event. The mechanism is related to the existence of an additional equilibrium climate state with reduced North Atlantic Deep Water (NADW) formation and a southward shift of the NADW formation area. Hints at the additional climate state were obtained from the largely varying duration of the pulse-induced cold episode in response to overlaid random freshwater fluctuations in Monte Carlo simulations. The model equilibrium state was attained by releasing a weak multicentury freshwater flux through the St. Lawrence pathway completed by the meltwater pulse. The existence of such a climate mode appears essential for reproducing climate anomalies in close agreement with paleoclimatic reconstructions of the 8.2 ka event. The results furthermore suggest that the temporal evolution of the cold event was partly a matter of chance.

Quantum simulation of a topological Mott insulator with Rydberg atoms in a Lieb lattice

We propose a realistic scheme to quantum simulate the so-far experimentally unobserved topological Mott insulator phase-an interaction-driven topological insulator-using cold atoms in an optical Lieb lattice. To this end, we study a system of spinless fermions in a Lieb lattice, exhibiting repulsive nearest-and next-to-nearest-neighbor interactions and derive the associated zero-temperature phase diagram within mean-field approximation. In particular, we analyze how the interactions can dynamically generate a charge density wave ordered, a nematic, and a topologically nontrivial quantum anomalous Hall phase. We characterize the topology of the different phases by the Chern number and discuss the possibility of phase coexistence. Based on the identified phases, we propose a realistic implementation of this model using cold Rydberg-dressed atoms in an optical lattice. The scheme, which allows one to access, in particular, the topological Mott insulator phase, robustly and independently of its exact position in parameter space, merely requires global, always-on off-resonant laser coupling to Rydberg states and is feasible with state-of-the-art experimental techniques that have already been demonstrated in the laboratory.

Models and methods for the direct simulation of rough and micropatterned surfaces

Friction in hydrodynamic bearings are a major source of losses in car engines ([69]). The extreme loading conditions in those bearings lead to contact between the matching surfaces. In such conditions not only the overall geometry of the bearing is relevant, but also the small-scale topography of the surface determines the bearing performance. The possibility of shaping the surface of lubricated bearings down to the micrometer ([57]) opened the question of whether friction can be reduced by mean of micro-textures, with mixed results. This work focuses in the development of efficient numerical methods to solve thin film (lubrication) problems down to the roughness scale of measured surfaces. Due to the high velocities and the convergent-divergent geometries of hydrodynamic bearings, cavitation takes place. To treat cavitation in the lubrication problem the Elrod- Adams model is used, a mass-conserving model which has proven in careful numerical ([12]) and experimental ([119]) tests to be essential to obtain physically meaningful results. Another relevant aspect of the modeling is that the bearing inertial effects are considered, which is necessary to correctly simulate moving textures. As an application, the effects of micro-texturing the moving surface of the bearing were studied. Realistic values are assumed for the physical parameters defining the problems. Extensive fundamental studies were carried out in the hydrodynamic lubrication regime. Mesh-converged simulations considering the topography of real measured surfaces were also run, and the validity of the lubrication approximation was assessed for such rough surfaces.

An Investigation of Electronic Recruitment in Germany: Toward Efficacy and Opportunities

Globalization and the spread of Information and Communication Technology (ICT), particularly Internet usage, have changed the practice of recruiting employees. The Internet has become an integral part of Human Resource (HR) talent management, and as a result, a majority of business organizations in Germany have adopted an online recruitment initiative. However, technology alone no longer provides a competitive advantage. To meet their talent requirements, business organizations have turned to recruiting alternatives such as electronic recruitment or e-recruitment, which is a form of recruitment using electronic media tools to attract, hire, and retain job seekers. In this investigation, the author examined the efficacy and opportunities of e-recruitment in medium-sized German business organizations.. The author determined that many medium-sized German companies are using the Internet to recruit online but not effectively enough to create and maintain a sustainable strategic advantage. The author concluded that several areas for improvements exist in e-recruitment processes.

Pollutant emissions during pyrolysis and combustion of waste printed circuit boards, before and after metal removal

The constant increase in the production of electronic devices implies the need for an appropriate management of a growing number of waste electrical and electronic equipment. Thermal treatments represent an interesting alternative to recycle this kind of waste, but particular attention has to be paid to the potential emissions of toxic by-products. In this study, the emissions from thermal degradation of printed circuit boards (with and without metals) have been studied using a laboratory scale reactor, under oxidizing and inert atmosphere at 600 and 850 °C. Apart from carbon oxides, HBr was the main decomposition product, followed by high amounts of methane, ethylene, propylene, phenol and benzene. The maximum formation of PAHs was found in pyrolysis at 850 °C, naphthalene being the most abundant. High levels of 2-, 4-, 2,4-, 2,6- and 2,4,6-bromophenols were found, especially at 600 °C. Emissions of PCDD/Fs and dioxin-like PCBs were quite low and much lower than that of PBDD/Fs, due to the higher bromine content of the samples. Combustion at 600 °C was the run with the highest PBDD/F formation: the total content of eleven 2,3,7,8-substituted congeners (tetra- through heptaBDD/Fs) was 7240 and 3250 ng WHO2005-TEQ/kg sample, corresponding to the sample with and without metals, respectively.

SOCIAL, EMOTIONAL, COGNITIVE, AND PHYSIOLOGICAL CORRELATES OF ELECTRONIC SOCIAL BEHAVIOR

There has been very little research that has studied the capacities that can be fostered to mitigate the risk for involvement in electronic bullying or victimization and almost no research examining positive electronic behavior. The primary goal of this dissertation was to use the General Aggression Model and Anxious Apprehension Model of Trauma to explore the underlying cognitive, emotional, and self-regulation processes that are related to electronic bullying, victimization, and prosocial behavior. In Study 1, we explored several potential interpretations of the General Aggression Model that would accurately describe the relationship that electronic self-conscious appraisal, cognitive reappraisal, and activational control may have with electronic bullying and victimization. In Study 2, we used the Anxious Apprehension Model of Trauma to explore rejection cognitions as the mediator of the relationships among emotionality (emotionality, shame, state emotion responses, and physiological arousal) and electronic bullying and victimization using structural equation modelling. In addition, we explored the role of rejection cognitions in mediating the relationship of moral disengagement with electronic bullying. In Study 3, we examined predictors of electronic prosocial behavior, such as bullying, victimization, time online, electronic proficiency, electronic self-conscious appraisals, emotionality, and self-regulation. All three studies supported the General Aggression Model as a framework to guide the study of electronic behavior, and suggest the importance of cognitive, emotional, and behavioral means of regulation in shaping electronic behavior. In addition, each study has implications for the development of high quality electronic bullying prevention and intervention research.