The uncertain consequences of transferring bacterial strains between laboratories - rpoS instability as an example

Abstract Background Microbiological studies frequently involve exchanges of strains between laboratories and/or stock centers. The integrity of exchanged strains is vital for archival reasons and to ensure reproducible experimental results. For at least 50 years, one of the most common means of shipping bacteria was by inoculating bacterial samples in agar stabs. Long-term cultures in stabs exhibit genetic instabilities and one common instability is in rpoS. The sigma factor RpoS accumulates in response to several stresses and in the stationary phase. One consequence of RpoS accumulation is the competition with the vegetative sigma factor σ70. Under nutrient limiting conditions mutations in rpoS or in genes that regulate its expression tend to accumulate. Here, we investigate whether short-term storage and mailing of cultures in stabs results in genetic heterogeneity. Results We found that samples of the E. coli K-12 strain MC4100TF exchanged on three separate occasions by mail between our laboratories became heterogeneous. Reconstruction studies indicated that LB-stabs exhibited mutations previously found in GASP studies in stationary phase LB broth. At least 40% of reconstructed stocks and an equivalent proportion of actually mailed stock contained these mutations. Mutants with low RpoS levels emerged within 7 days of incubation in the stabs. Sequence analysis of ten of these segregants revealed that they harboured each of three different rpoS mutations. These mutants displayed the classical phenotypes of bacteria lacking rpoS. The genetic stability of MC4100TF was also tested in filter disks embedded in glycerol. Under these conditions, GASP mutants emerge only after a 3-week period. We also confirm that the intrinsic high RpoS level in MC4100TF is mainly due to the presence of an IS1 insertion in rssB. Conclusions Given that many E. coli strains contain high RpoS levels similar to MC4100TF, the integrity of such strains during transfers and storage is questionable. Variations in important collections may be due to storage-transfer related issues. These results raise important questions on the integrity of bacterial archives and transferred strains, explain variation like in the ECOR collection between laboratories and indicate a need for the development of better methods of strain transfer.

Mechanisms of ring chromosome formation, ring instability and clinical consequences

Background The breakpoints and mechanisms of ring chromosome formation were studied and mapped in 14 patients. Methods Several techniques were performed such as genome-wide array, MLPA (Multiplex Ligation-Dependent Probe Amplification) and FISH (Fluorescent in situ Hybridization). Results The ring chromosomes of patients I to XIV were determined to be, respectively: r(3)(p26.1q29), r(4)(p16.3q35.2), r(10)(p15.3q26.2), r(10)(p15.3q26.13), r(13)(p13q31.1), r(13)(p13q34), r(14)(p13q32.33), r(15)(p13q26.2), r(18)(p11.32q22.2), r(18)(p11.32q21.33), r(18)(p11.21q23), r(22)(p13q13.33), r(22)(p13q13.2), and r(22)(p13q13.2). These rings were found to have been formed by different mechanisms, such as: breaks in both chromosome arms followed by end-to-end reunion (patients IV, VIII, IX, XI, XIII and XIV); a break in one chromosome arm followed by fusion with the subtelomeric region of the other (patients I and II); a break in one chromosome arm followed by fusion with the opposite telomeric region (patients III and X); fusion of two subtelomeric regions (patient VII); and telomere-telomere fusion (patient XII). Thus, the r(14) and one r(22) can be considered complete rings, since there was no loss of relevant genetic material. Two patients (V and VI) with r(13) showed duplication along with terminal deletion of 13q, one of them proved to be inverted, a mechanism known as inv-dup-del. Ring instability was detected by ring loss and secondary aberrations in all but three patients, who presented stable ring chromosomes (II, XIII and XIV). Conclusions We concluded that the clinical phenotype of patients with ring chromosomes may be related with different factors, including gene haploinsufficiency, gene duplications and ring instability. Epigenetic factors due to the circular architecture of ring chromosomes must also be considered, since even complete ring chromosomes can result in phenotypic alterations, as observed in our patients with complete r(14) and r(22).

A swirler stabilized combustion chamber for a micro-gas turbine fuelled with natural gas

Micro-gas turbines are a good alternative for on-site power generation, since their operation is very reliable. The possibility of operating with various fuels increases versatility and, as a result, the usage of these devices. Focusing on a performance improvement of a tri-fuel low-cost micro-gas turbine, this work presents investigations of the inner flow of its combustion chamber. The aim of this analysis was the characterization of the flame structure by the temperature field of the chamber inner flow. The chamber was fuelled with natural gas. In the current chamber, a swirler and a reversed flow configuration were utilized to provide flame stabilization. The inner flow investigations were done with numerical analysis, which were compared to experimental data. The analysis of the inner flow was done with numerical simulations, which used the RSM turbulence model. A β-PDF equilibrium model was adopted to account for the turbulent combustion process. Different models of heat transfer were compared. Thermal radiation and specially heat conduction in the liner walls played significant roles on results.

Numerical simulation of an ethanol turbulent spray flame with RANS and diffusion combustion model

A detailed numerical simulation of ethanol turbulent spray combustion on a rounded jet flame is pre- sented in this article. The focus is to propose a robust mathematical model with relatively low complexity sub- models to reproduce the main characteristics of the cou- pling between both phases, such as the turbulence modulation, turbulent droplets dissipation, and evaporative cooling effect. A RANS turbulent model is implemented. Special features of the model include an Eulerian– Lagrangian procedure under a fully two-way coupling and a modified flame sheet model with a joint mixture fraction– enthalpy b -PDF. Reasonable agreement between measured and computed mean profiles of temperature of the gas phase and droplet size distributions is achieved. Deviations found between measured and predicted mean velocity profiles are attributed to the turbulent combustion modeling adopted

A study on the fluid dynamics of domestic Gas burners

Domestic gas burners are investigated experimentally and numerically in order to further understand the fluid dynamics processes that drive the cooking appliance performances. In particular, a numerical simulation tool has been developed in order to predict the onset of two flame instabilities which may deteriorate the performances of the burner: the flame back and flame lift. The numerical model has been firstly validated by comparing the simulated flow field with a data set of experimental measurements. A prediction criterion for the flame back instability has been formulated based on isothermal simulations without involving the combustion modelization. This analysis has been verified by a Design Of Experiments investigation performed on different burner prototype geometries. On the contrary, the formulation of a prediction criterion regarding the flame lift instability has required the use of a combustion model in the numerical code. In this analysis, the structure and aerodynamics of the flame generated by a cooking appliance has thus been characterized by experimental and numerical investigations, in which, by varying the flow inlet conditions, the flame behaviour was studied from a stable reference case toward a complete blow-out.

Experimental analysis of coaxial jets: instability, flow and mixing characterization

The velocity and mixing field of two turbulent jets configurations have been experimentally characterized by means of cold- and hot-wire anemometry in order to investigate the effects of the initial conditions on the flow development. In particular, experiments have been focused on the effect of the separation wall between the two streams on the flow field. The results of the experiments have pointed out that the wake behind a thick wall separating wall has a strong influence on the flow field evolution. For instance, for nearly unitary velocity ratios, a clear vortex shedding from the wall is observable. This phenomenon enhances the mixing between the inner and outer shear layer. This enhancement in the fluctuating activity is a consequence of a local absolute instability of the flow which, for a small range of velocity ratios, behaves as an hydrodynamic oscillator with no sensibility to external perturbations. It has been suggested indeed that this absolute instability can be used as a passive method to control the flow evolution. Finally, acoustic excitation has been applied to the near field in order to verify whether or not the observed vortex shedding behind the separating wall is due to a global oscillating mode as predicted by the theory. A new scaling relationship has been also proposed to determine the preferred frequency for nearly unitary velocity ratios. The proposed law takes into account both the Reynolds number and the velocity ratio dependence of this frequency and, therefore, improves all the previously proposed relationships.

Modeling hydrothermal system: deriving observables and hydrothermal instability in volcanic and non-volcanic setting

Hydrothermal fluids are a fundamental resource for understanding and monitoring volcanic and non-volcanic systems. This thesis is focused on the study of hydrothermal system through numerical modeling with the geothermal simulator TOUGH2. Several simulations are presented, and geophysical and geochemical observables, arising from fluids circulation, are analyzed in detail throughout the thesis. In a volcanic setting, fluids feeding fumaroles and hot spring may play a key role in the hazard evaluation. The evolution of the fluids circulation is caused by a strong interaction between magmatic and hydrothermal systems. A simultaneous analysis of different geophysical and geochemical observables is a sound approach for interpreting monitored data and to infer a consistent conceptual model. Analyzed observables are ground displacement, gravity changes, electrical conductivity, amount, composition and temperature of the emitted gases at surface, and extent of degassing area. Results highlight the different temporal response of the considered observables, as well as the different radial pattern of variation. However, magnitude, temporal response and radial pattern of these signals depend not only on the evolution of fluid circulation, but a main role is played by the considered rock properties. Numerical simulations highlight differences that arise from the assumption of different permeabilities, for both homogeneous and heterogeneous systems. Rock properties affect hydrothermal fluid circulation, controlling both the range of variation and the temporal evolution of the observable signals. Low temperature fumaroles and low discharge rate may be affected by atmospheric conditions. Detailed parametric simulations were performed, aimed to understand the effects of system properties, such as permeability and gas reservoir overpressure, on diffuse degassing when air temperature and barometric pressure changes are applied to the ground surface. Hydrothermal circulation, however, is not only a characteristic of volcanic system. Hot fluids may be involved in several mankind problems, such as studies on geothermal engineering, nuclear waste propagation in porous medium, and Geological Carbon Sequestration (GCS). The current concept for large-scale GCS is the direct injection of supercritical carbon dioxide into deep geological formations which typically contain brine. Upward displacement of such brine from deep reservoirs driven by pressure increases resulting from carbon dioxide injection may occur through abandoned wells, permeable faults or permeable channels. Brine intrusion into aquifers may degrade groundwater resources. Numerical results show that pressure rise drives dense water up to the conduits, and does not necessarily result in continuous flow. Rather, overpressure leads to new hydrostatic equilibrium if fluids are initially density stratified. If warm and salty fluid does not cool passing through the conduit, an oscillatory solution is then possible. Parameter studies delineate steady-state (static) and oscillatory solutions.

Dynamic stabilization of Rayleigh-Taylor instability of ablation fronts in inertial confinement fusion

One of the most important problems in inertial confinement fusion is how to find a way to mitigate the onset of the Rayleigh-Taylor instability which arises in the ablation front during the compression. In this thesis it is studied in detail the possibility of using for such a purpose the well-known mechanism of dynamic stabilization, already applied to other dynamical systems such as the inverted pendulum. In this context, a periodic acceleration superposed to the background gravity generates a vertical vibration of the ablation front itself. The effects of different driving modulations (Dirac deltas and square waves) are analyzed from a theoretical point of view, with a focus on stabilization of ion beam driven ablation fronts, and a comparison is made, in order to look for optimization.

Development of control-oriented models of Dual Clutch Transmission systems

A control-oriented model of a Dual Clutch Transmission was developed for real-time Hardware In the Loop (HIL) applications, to support model-based development of the DCT controller. The model is an innovative attempt to reproduce the fast dynamics of the actuation system while maintaining a step size large enough for real-time applications. The model comprehends a detailed physical description of hydraulic circuit, clutches, synchronizers and gears, and simplified vehicle and internal combustion engine sub-models. As the oil circulating in the system has a large bulk modulus, the pressure dynamics are very fast, possibly causing instability in a real-time simulation; the same challenge involves the servo valves dynamics, due to the very small masses of the moving elements. Therefore, the hydraulic circuit model has been modified and simplified without losing physical validity, in order to adapt it to the real-time simulation requirements. The results of offline simulations have been compared to on-board measurements to verify the validity of the developed model, that was then implemented in a HIL system and connected to the TCU (Transmission Control Unit). Several tests have been performed: electrical failure tests on sensors and actuators, hydraulic and mechanical failure tests on hydraulic valves, clutches and synchronizers, and application tests comprehending all the main features of the control performed by the TCU. Being based on physical laws, in every condition the model simulates a plausible reaction of the system. The first intensive use of the HIL application led to the validation of the new safety strategies implemented inside the TCU software. A test automation procedure has been developed to permit the execution of a pattern of tests without the interaction of the user; fully repeatable tests can be performed for non-regression verification, allowing the testing of new software releases in fully automatic mode.

A numerical methodology for the multi-objective optimization of the DI Diesel engine combustion

DI Diesel engine are widely used both for industrial and automotive applications due to their durability and fuel economy. Nonetheless, increasing environmental concerns force that type of engine to comply with increasingly demanding emission limits, so that, it has become mandatory to develop a robust design methodology of the DI Diesel combustion system focused on reduction of soot and NOx simultaneously while maintaining a reasonable fuel economy. In recent years, genetic algorithms and CFD three-dimensional combustion simulations have been successfully applied to that kind of problem. However, combining GAs optimization with actual CFD three-dimensional combustion simulations can be too onerous since a large number of calculations is usually needed for the genetic algorithm to converge, resulting in a high computational cost and, thus, limiting the suitability of this method for industrial processes. In order to make the optimization process less time-consuming, CFD simulations can be more conveniently used to generate a training set for the learning process of an artificial neural network which, once correctly trained, can be used to forecast the engine outputs as a function of the design parameters during a GA optimization performing a so-called virtual optimization. In the current work, a numerical methodology for the multi-objective virtual optimization of the combustion of an automotive DI Diesel engine, which relies on artificial neural networks and genetic algorithms, was developed.

Development of a method for plasma - induced combustion of intermediate to low-level radioactive waste

This work demonstrates that the plasma - induced combustion of intermediate to low-level radioactive waste is a suitable method for volume reduction and stabilization. Weaknesses of existing facilities can be overcome with novel developments. Plasma treatment of LILW has a high economical advantage by volume reduction for storage in final repositories.

Morphological instability analysis of a misfit strained core-shell nanowire for the growth of quantum dots

Nell'ambito delle nanostrutture, un ruolo primario è svolto dai punti quantici. In questo lavoro siamo interessati all'analisi teorica del processo di creazione dei punti quantici: esso può avvenire per eteroepitassia, in particolare secondo il metodo studiato da Stranski-Krastanov. Un film di Germanio viene depositato su un substrato di Silicio in modo coerente, cioè senza dislocazioni, e, a causa del misfit tra le maglie dei due materiali, c'è un accumulo di energia elastica nel film. A una certa altezza critica questa energia del film può essere ridotta se il film si organizza in isole (punti quantici), dove la tensione può essere rilassata lateralmente. L'altezza critica dipende dai moduli di Young (E, υ), dal misfit tra le maglie (m) e dalla tensione superficiali (γ). Il trasporto di materiale nel film è portato avanti per diffusione superficiale. Il punto focale nell'analisi delle instabilità indotte dal misfit tra le maglie dei materiali è la ricerca delle caratteristiche che individuano il modo di crescita più rapido dei punti quantici. In questo lavoro siamo interessati ad un caso particolare: la crescita di punti quantici non su una superficie piana ma sulla superficie di un nanofilo quantico a geometria cilindrica. L'analisi delle instabilità viene condotta risolvendo le equazioni all'equilibrio: a tal fine sono state calcolate le distribuzioni del tensore delle deformazioni e degli sforzo di un nanofilo core-shell con una superficie perturbata al primo ordine rispetto all'ampiezza della perturbazione. L'analisi è stata condotta con particolari condizioni al contorno ed ipotesi geometriche, e diverse scelte dello stato di riferimento del campo degli spostamenti. Risolto il problema elastico, è stata studiata l'equazione dinamica di evoluzione descrivente la diffusione di superficie. Il risultato dell'analisi di instabilità è il tasso di crescita in funzione del numero d'onda q, con diversi valori del raggio del core, spessore dello shell e modo normale n, al fine di trovare il più veloce modo di crescita della perturbazione.

Fingering instability down the outside of a vertical cylinder

We present an experimental and numerical study examining the dynamics of a gravity-driven contact line of a thin viscous film traveling down the outside of a vertical cylinder of radius R. Experiments on cylinders with radii ranging between 0.159 and 3.81 cm show that the contact line is unstable to a fingering pattern for two fluids with differing viscosities, surface tensions, and wetting properties. The dynamics of the contact line is studied and results are compared to previous studies of inclined plane experiments in order to understand the influence substrate curvature plays on the fingering pattern. A lubrication model is derived for the film height in the limit that ε = H/R≪1, where H is the upstream film thickness, and in terms of a Bond number ρgR3/(γH), and the linear stability of the contact line is analyzed using traveling wave solutions. Curvature controls the capillary ridge height of the traveling wave and the range of unstable wavelength when ε = O(10-1), whereas the shape and stability of the contact line converge to the behavior one observes on a vertical plane when ε ≤ O(10-2). The most unstable wave mode, cutoff wave mode for neutral stability, and maximum growth rate scale as 0.45 where = ρgR2/γ ≥ 1.3, and the contact line is unstable to fingering when ≥ 0.56. Using the experimental data to extrapolate outside the range of validity of the thin film model, we estimate the contact line is stable when <0.56. Agreement is excellent between the model and the experimental data for the wave number (i.e., number of fingers) and wavelength of the fingering pattern that forms along the contact line.