High-throughput sequencing of small RNA transcriptomes reveals critical biological features targeted by microRNAs in cell models used for squamous cell cancer research

Abstract Background The implication of post-transcriptional regulation by microRNAs in molecular mechanisms underlying cancer disease is well documented. However, their interference at the cellular level is not fully explored. Functional in vitro studies are fundamental for the comprehension of their role; nevertheless results are highly dependable on the adopted cellular model. Next generation small RNA transcriptomic sequencing data of a tumor cell line and keratinocytes derived from primary culture was generated in order to characterize the microRNA content of these systems, thus helping in their understanding. Both constitute cell models for functional studies of microRNAs in head and neck squamous cell carcinoma (HNSCC), a smoking-related cancer. Known microRNAs were quantified and analyzed in the context of gene regulation. New microRNAs were investigated using similarity and structural search, ab initio classification, and prediction of the location of mature microRNAs within would-be precursor sequences. Results were compared with small RNA transcriptomic sequences from HNSCC samples in order to access the applicability of these cell models for cancer phenotype comprehension and for novel molecule discovery. Results Ten miRNAs represented over 70% of the mature molecules present in each of the cell types. The most expressed molecules were miR-21, miR-24 and miR-205, Accordingly; miR-21 and miR-205 have been previously shown to play a role in epithelial cell biology. Although miR-21 has been implicated in cancer development, and evaluated as a biomarker in HNSCC progression, no significant expression differences were seen between cell types. We demonstrate that differentially expressed mature miRNAs target cell differentiation and apoptosis related biological processes, indicating that they might represent, with acceptable accuracy, the genetic context from which they derive. Most miRNAs identified in the cancer cell line and in keratinocytes were present in tumor samples and cancer-free samples, respectively, with miR-21, miR-24 and miR-205 still among the most prevalent molecules at all instances. Thirteen miRNA-like structures, containing reads identified by the deep sequencing, were predicted from putative miRNA precursor sequences. Strong evidences suggest that one of them could be a new miRNA. This molecule was mostly expressed in the tumor cell line and HNSCC samples indicating a possible biological function in cancer. Conclusions Critical biological features of cells must be fully understood before they can be chosen as models for functional studies. Expression levels of miRNAs relate to cell type and tissue context. This study provides insights on miRNA content of two cell models used for cancer research. Pathways commonly deregulated in HNSCC might be targeted by most expressed and also by differentially expressed miRNAs. Results indicate that the use of cell models for cancer research demands careful assessment of underlying molecular characteristics for proper data interpretation. Additionally, one new miRNA-like molecule with a potential role in cancer was identified in the cell lines and clinical samples.

Sviluppo di modelli motore e veicolo per l'analisi di strategie di controllo in applicazioni Software e Hardware In the Loop

This work describes the development of a simulation tool which allows the simulation of the Internal Combustion Engine (ICE), the transmission and the vehicle dynamics. It is a control oriented simulation tool, designed in order to perform both off-line (Software In the Loop) and on-line (Hardware In the Loop) simulation. In the first case the simulation tool can be used in order to optimize Engine Control Unit strategies (as far as regard, for example, the fuel consumption or the performance of the engine), while in the second case it can be used in order to test the control system. In recent years the use of HIL simulations has proved to be very useful in developing and testing of control systems. Hardware In the Loop simulation is a technology where the actual vehicles, engines or other components are replaced by a real time simulation, based on a mathematical model and running in a real time processor. The processor reads ECU (Engine Control Unit) output signals which would normally feed the actuators and, by using mathematical models, provides the signals which would be produced by the actual sensors. The simulation tool, fully designed within Simulink, includes the possibility to simulate the only engine, the transmission and vehicle dynamics and the engine along with the vehicle and transmission dynamics, allowing in this case to evaluate the performance and the operating conditions of the Internal Combustion Engine, once it is installed on a given vehicle. Furthermore the simulation tool includes different level of complexity, since it is possible to use, for example, either a zero-dimensional or a one-dimensional model of the intake system (in this case only for off-line application, because of the higher computational effort). Given these preliminary remarks, an important goal of this work is the development of a simulation environment that can be easily adapted to different engine types (single- or multi-cylinder, four-stroke or two-stroke, diesel or gasoline) and transmission architecture without reprogramming. Also, the same simulation tool can be rapidly configured both for off-line and real-time application. The Matlab-Simulink environment has been adopted to achieve such objectives, since its graphical programming interface allows building flexible and reconfigurable models, and real-time simulation is possible with standard, off-the-shelf software and hardware platforms (such as dSPACE systems).

Multi-level models and infrastructures for simulating biological system development

The hierarchical organisation of biological systems plays a crucial role in the pattern formation of gene expression resulting from the morphogenetic processes, where autonomous internal dynamics of cells, as well as cell-to-cell interactions through membranes, are responsible for the emergent peculiar structures of the individual phenotype. Being able to reproduce the systems dynamics at different levels of such a hierarchy might be very useful for studying such a complex phenomenon of self-organisation. The idea is to model the phenomenon in terms of a large and dynamic network of compartments, where the interplay between inter-compartment and intra-compartment events determines the emergent behaviour resulting in the formation of spatial patterns. According to these premises the thesis proposes a review of the different approaches already developed in modelling developmental biology problems, as well as the main models and infrastructures available in literature for modelling biological systems, analysing their capabilities in tackling multi-compartment / multi-level models. The thesis then introduces a practical framework, MS-BioNET, for modelling and simulating these scenarios exploiting the potential of multi-level dynamics. This is based on (i) a computational model featuring networks of compartments and an enhanced model of chemical reaction addressing molecule transfer, (ii) a logic-oriented language to flexibly specify complex simulation scenarios, and (iii) a simulation engine based on the many-species/many-channels optimised version of Gillespie’s direct method. The thesis finally proposes the adoption of the agent-based model as an approach capable of capture multi-level dynamics. To overcome the problem of parameter tuning in the model, the simulators are supplied with a module for parameter optimisation. The task is defined as an optimisation problem over the parameter space in which the objective function to be minimised is the distance between the output of the simulator and a target one. The problem is tackled with a metaheuristic algorithm. As an example of application of the MS-BioNET framework and of the agent-based model, a model of the first stages of Drosophila Melanogaster development is realised. The model goal is to generate the early spatial pattern of gap gene expression. The correctness of the models is shown comparing the simulation results with real data of gene expression with spatial and temporal resolution, acquired in free on-line sources.

Genetic Manipulation, Gene Silencing and Biomarker Development in Multiple Experimental Models.

The thesis is set in three different parts, according to the relative experimental models. First, the domestic pig (Sus scrofa) is part of the study on reproductive biotechnologies: the transgenesis technique of Sperm Mediated Gene Transfer is widely studied starting from the quality of the semen, through the study of multiple uptakes of exogenous DNA and lastly used in the production of multi-transgenic blastocysts. Finally we managed to couple the transgenesis pipeline with sperm sorting and therefore produced transgenic embryos of predetermined sex. In the second part of the thesis the attention is on the fruit fly (Drosophila melanogaster) and on its derived cell line: the S2 cells. The in vitro and in vivo models are used to develop and validate an efficient way to knock down the myc gene. First an efficient in vitro protocol is described, than we demonstrate how the decrease in myc transcript remarkably affects the ribosome biogenesis through the study of Polysome gradients, rRNA content and qPCR. In vivo we identified two optimal drivers for the conditional silencing of myc, once the flies are fed with RU486: the first one is throughout the whole body (Tubulin), while the second is a head fat body driver (S32). With these results we present a very efficient model to study the role of myc in multiple aspects of translation. In the third and last part, the focus is on human derived lung fibroblasts (hLF-1), mouse tail fibroblasts and mouse tissues. We developed an efficient assay to quantify the total protein content of the nucleus on a single cell level via fluorescence. We coupled the protocol with classical immunofluorescence so to have at the same time general and particular information, demonstrating that during senescence nuclear proteins increase by 1.8 fold either in human cells, mouse cells and mouse tissues.

Origin and Nature of Radio-Loud Broad Absorption Line Quasars

The origin of Broad Absorption Line Quasars (BAL QSOs) is still an open issue. Accounting for ~20% of the QSO population, these objects present broad absorption lines in their optical spectra generated from outflows with velocities up to 0.2 c. Nowadays, the hypotheses about their nature are principally related to orientation or evolutionary scenarios. In the first one, absorption lines are produced by outflows originated by the accretion disk, basically present in all QSOs, but seen only when they intercept the line of sight. In the second hypothesis, BAL QSOs would be young or recently re-fueled QSOs, still ejecting their dust cocoon. In this case orientation would not play a role, since the absorption features would be produced by spherically ejected matter. In this work we present the results of a multi-frequency study of a Radio-Loud BAL QSO sample, and a comparison sample of Radio-Loud non-BAL QSOs. We performed observations from radio to Near-Infrared, aiming at collecting useful informations about the orientation, the age, and the morphologies of these objects. Various techniques have been applied, including local and continental radio interferometry, single dish observations and spectroscopy. The comparison with the non-BAL QSO sample allows us to conclude that no particular orientation is present in BAL QSOs. Moreover, various morphologies and ages can be found, analogously to "normal" QSOs. Thus, the solution to this astrophysical problem seems not to reside in a peculiarity of the BAL QSO subclass with respect to non-BAL QSOs, since both the studied models do not completely explain the observed characteristics. Further experiments with future instrumentation will allow us to underline useful differences and test the physical conditions in BAL QSOs.

Conditional and transgenic mouse models as tools to study the role of TGFbeta, BMP signaling in skeletal development

Die TGFbeta/BMP Signaltransduktionskaskade ist wichtig für viele Entwicklungsprozesse fast aller embryonaler sowie extraembryonaler Gewebe und sie ist ebenso essentiell bei der Aufrechterhaltung der Homöostase im adulten Organismus. In vielen Mausmodellen und Zellkulturversuchen wurde gezeigt, dass Liganden dieses Signalweges in verschiedene Stadien der Knorpel- und Knochenentwicklung involviert sind. BMPs sind beispielsweise maßgeblich an der frühen Kondensation und Bildung des Knorpels und später an Proliferation und Hypertrophie der Chondrozyten beteiligt. BMPs können ektopisch Knochenbildung auslösen und das Expressionsmuster der Liganden und spezifischen Rezeptoren in der Wachstumsfuge lässt auf eine wichtige Rolle der BMPs in der Wachstumsfuge schließen. Der gezielte knock out der BMP-Rezeptoren Bmpr1a und Bmpr1b in proliferierenden Chondrozyten führt zur Ausbildung einer generellen Chondrodysplasie. Smad1, Smad5 und Smad8 sind die Mediatoren der BMP-Signalkaskade. Im Rahmen der vorliegenden Arbeit sollte die Rolle und Funktion der Smad1- und Smad5-Proteine in der Wachstumsfuge untersucht werden. Hierzu wurden konditionale Smad1-knock out-Mäuse mit einer transgenen Mauslinie gekreuzt, die die Cre-Rekombinase spezifisch in proliferierenden Chondrozyten exprimiert. Diese Mäuse wurden mit und ohne heterozygotem Smad5-Hintergrund charakterisiert. Bei einem knock out von Smad1 allein konnte ein leichte Verkürzung der Wachstumsfuge beobachtet werden, wobei prähypertrophe und hypertrophe Zone gleichermaßen betroffen waren. Dieser Phänotyp war verstärkt in Mäusen mit zusätzlichem heterozygotem Smad5-Hintergrund. Eine Verringerung der Proliferationsrate konnte zusammen mit einer verminderten Ihh-Expression nachgewiesen werden. Zusätzlich konnte anhand von Röntgenaufnahmen eine Dysorganisation der nasalen Region und ein fehlendes nasales Septum beobachtet werden. Produktion und Mineralisation der extrazellulären Matrix waren nicht beeinträchtigt. Um die Rolle der BMP- und TGFbeta-Signalkaskaden während der endochondralen Ossifikation zu vergleichen, wurden transgene Mäuse generiert, in denen die TGFbeta-Signalkaskade spezifisch in proliferierenden Chondrozyten gestört war. Zwei Mauslinien, die ähnliche Phänotypen zeigten, wurden untersucht. Esl1 ist ein TGFbeta-bindendes Protein, von dem man annimmt, dass es die TGFbeta-Signalkaskade inhibieren kann. Esl1-knock out-Mäuse sind kleiner als Wildtypmäuse und die Überexpression von Esl1 in proliferierenden Chondrozyten führt zu einer Verlängerung der Wachstumsfuge und einer verstärkten Proliferationsrate. Knorpelmarker, wie Col2a1 und Sox9 sind in diesen Mäusen herunterreguliert, während Col10a1 und Ihh als Marker für die hypertrophe und prähypertrophe Zone herunterreguliert waren. Dies führt zu der Annahme, dass mehr Zellen in die terminale Differenzierung eintreten. Bei transgenen Mäusen, in denen ein dominant-negativer (dn) TGFbeta-Rezeptor in proliferierenden Chondrozyten überexprimiert wurde, konnte eine verlängerte prähypertrophe Zone, eine erhöhte Ihh-Expression, sowie eine verstärkte Proliferationsrate beobachtet werden. Zusätzlich konnte in homozygoten Tieren ein craniofacialer Phänotyp beschrieben werden, der zu Problemen bei der Nahrungsaufnahme und damit zu einer starken Wachstumsbeeinträchtigung führte. Die BMP- und TGFbeta-Signalkaskaden haben möglicherweise antagonistische Effekte in der Wachstumsfuge. Während der Ausfall von BMP in proliferierenden Chondrozyten aufgrund einer gesunkenen Proliferationsrate zu einer Verkürzung der Wachstumsfuge führte, kann man in Mäusen mit einer Störung der TGFbeta-Signalkaskade eine verstärkte Proliferation in einer daher verlängerten Wachstumsfuge beobachten. Ein weiteres Ziel dieser Arbeit war die Generation einer transgenen Mauslinie, die die Cre-Rekombinase spezifisch in hypertrophen Chondrozyten exprimiert. Promoterstudien mit transgenen Mäusen weisen darauf hin, dass ein putatives AP1-Element, etwa 4 kb vor dem ersten Exon des Col10a1 gelegen, wichtig für die spezifische Expression in hypertrophen Chondrozyten ist. Ein Konstrukt, dass vier Kopien dieses Elements und den basalen Promoter enthält, wurde benutzt, um die Cre-Rekombinase spezifisch zu exprimieren. Diese Mauslinie befindet sich in der Testphase und erste Daten deuten auf eine spezifische Expression der Cre-Rekombinase in hypertrophen Chondrozyten hin.

Designing Electricity Auctions in the Presence of Transmission Constraints

This paper analyzes the effect that different designs in the access to fnancial transmission rights has on spot electricity auctions. In particular, I characterize the equilibrium in the spot electricity market when financial transmission rights are assigned to the grid operator and when financial transmission rights are assigned to the firm that submits the lowest bid in the spot electricity auction. When financial transmission rights are assigned to the grid operator, my model, in contrast with the models available in the literature, works out the equilibrium for any transmission capacity. Moreover, I have found that an increase in transmission capacity not only increases competition between markets but also within a single market. When financial transmission rights are assigned to the firm that submits the lowest bid in the spot electricity auction, firms compete not only for electricity demand, but also for transmission rights and the arbitrage profits derived from its hold. I have found that introduce competition for transmission rights reduces competition in spot electricity auctions.

Kinematics of local and high-z galaxies through 3D modeling of emission-line datacubes

The kinematics is a fundamental tool to infer the dynamical structure of galaxies and to understand their formation and evolution. Spectroscopic observations of gas emission lines are often used to derive rotation curves and velocity dispersions. It is however difficult to disentangle these two quantities in low spatial-resolution data because of beam smearing. In this thesis, we present 3D-Barolo, a new software to derive the gas kinematics of disk galaxies from emission-line data-cubes. The code builds tilted-ring models in the 3D observational space and compares them with the actual data-cubes. 3D-Barolo works with data at a wide range of spatial resolutions without being affected by instrumental biases. We use 3D-Barolo to derive rotation curves and velocity dispersions of several galaxies in both the local and the high-redshift Universe. We run our code on HI observations of nearby galaxies and we compare our results with 2D traditional approaches. We show that a 3D approach to the derivation of the gas kinematics has to be preferred to a 2D approach whenever a galaxy is resolved with less than about 20 elements across the disk. We moreover analyze a sample of galaxies at z~1, observed in the H-alpha line with the KMOS/VLT spectrograph. Our 3D modeling reveals that the kinematics of these high-z systems is comparable to that of local disk galaxies, with steeply-rising rotation curves followed by a flat part and H-alpha velocity dispersions of 15-40 km/s over the whole disks. This evidence suggests that disk galaxies were already fully settled about 7-8 billion years ago. In summary, 3D-Barolo is a powerful and robust tool to separate physical and instrumental effects and to derive a reliable kinematics. The analysis of large samples of galaxies at different redshifts with 3D-Barolo will provide new insights on how galaxies assemble and evolve throughout cosmic time.

Comparative study of the different models for the calculation of BLEVEs overpressure effects

The BLEVE, acronym for Boiling Liquid Expanding Vapour Explosion, is one of the most dangerous accidents that can occur in pressure vessels. It can be defined as an explosion resulting from the failure of a vessel containing a pressure liquefied gas stored at a temperature significantly above its boiling point at atmospheric pressure. This phenomenon frequently appears when a vessel is engulfed by a fire: the heat causes the internal pressure to raise and the mechanical proprieties of the wall to decrease, with the consequent rupture of the tank and the instantaneous release of its whole content. After the breakage, the vapour outflows and expands and the liquid phase starts boiling due to the pressure drop. The formation and propagation of a distructive schock wave may occur, together with the ejection of fragments, the generation of a fireball if the stored fluid is flammable and immediately ignited or the atmospheric dispersion of a toxic cloud if the fluid contained inside the vessel is toxic. Despite the presence of many studies on the BLEVE mechanism, the exact causes and conditions of its occurrence are still elusive. In order to better understand this phenomenon, in the present study first of all the concept and definition of BLEVE are investigated. A historical analysis of the major events that have occurred over the past 60 years is described. A research of the principal causes of this event, including the analysis of the substances most frequently involved, is presented too. Afterwards a description of the main effects of BLEVEs is reported, focusing especially on the overpressure. Though the major aim of the present thesis is to contribute, with a comparative analysis, to the validation of the main models present in the literature for the calculation and prediction of the overpressure caused by BLEVEs. In line with this purpose, after a short overview of the available approaches, their ability to reproduce the trend of the overpressure is investigated. The overpressure calculated with the different models is compared with values deriving from events happened in the past and ad-hoc experiments, focusing the attention especially on medium and large scale phenomena. The ability of the models to consider different filling levels of the reservoir and different substances is analyzed too. The results of these calculations are extensively discussed. Finally some conclusive remarks are reported.

Transmission dynamics of Chlamydia trachomatis affect the impact of screening programmes

To assess the impact of screening programmes in reducing the prevalence of Chlamydia trachomatis, mathematical and computational models are used as a guideline for decision support. Unfortunately, large uncertainties exist about the parameters that determine the transmission dynamics of C. trachomatis. Here, we use a SEIRS (susceptible-exposed-infected-recovered-susceptible) model to critically analyze the turnover of C. trachomatis in a population and the impact of a screening programme. We perform a sensitivity analysis on the most important steps during an infection with C. trachomatis. Varying the fraction of the infections becoming symptomatic as well as the duration of the symptomatic period within the range of previously used parameter estimates has little effect on the transmission dynamics. However, uncertainties in the duration of temporary immunity and the asymptomatic period can result in large differences in the predicted impact of a screening programme. We therefore analyze previously published data on the persistence of asymptomatic C. trachomatis infection in women and estimate the mean duration of the asymptomatic period to be longer than anticipated so far, namely 433 days (95% CI: 420-447 days). Our study shows that a longer duration of the asymptomatic period results in a more pronounced impact of a screening programme. However, due to the slower turnover of the infection, a substantial reduction in prevalence can only be achieved after screening for several years or decades.

Laboratory-based ROTEM(®) analysis: implementing pneumatic tube transport and real-time graphic transmission

ROTEM(®) is considered a helpful point-of-care device to monitor blood coagulation. Centrally performed analysis is desirable but rapid transport of blood samples and real-time transmission of graphic results are an important prerequisite. The effect of sample transport through a pneumatic tube system on ROTEM(®) results is unknown. The aims of the present work were (i) to determine the influence of blood sample transport through a pneumatic tube system on ROTEM(®) parameters compared to manual transportation, and (ii) to verify whether graphic results can be transmitted on line via virtual network computing using local area network to the physician in charge of the patient.

America's Shifting Color Line? Reexamining Determinants of Latino Racial Self-Identification

Objectives. Latinos are the nation's largest minority group and will double in size by 2050. Their size coupled with the fact that Latinos do not constitute a separate race raises questions about Latinos' incorporation into the U. S. racial hierarchy. This article explores patterns of Latino racial identity formation, examining the determinants of racial identity. Methods. Using the 2006 Latino National Survey, I estimate multinomial logit and ordered probit models of identification choices. Results. Latino racial identity is strongly associated with several factors, including socioeconomic status, measures of perceived discrimination and commonality, and measures of acculturation/assimilation. Most Latinos have a broader, more complex understanding of race. Furthermore, some Latinos do believe that they occupy a unique position in the racial hierarchy. Conclusions. The results suggest that the color line W. E. DuBois argued has long divided our nation may eventually shift.

Antiretroviral therapy for prevention of HIV transmission in HIV-discordant couples

Antiretroviral drugs have been shown to reduce risk of mother-to-child transmission of human immunodeficiency virus (HIV) and are also widely used for post-exposure prophylaxis for parenteral and sexual exposures. Observational data, ecological studies and models suggest that sexual transmission may be lower in couples in which one partner is infected with HIV and the other is not and the infected partner is on antiretroviral therapy (ART).

Antiretroviral therapy for prevention of HIV transmission in HIV-discordant couples

Antiretroviral drugs have been shown to reduce risk of mother-to-child transmission of human immunodeficiency virus (HIV) and are also widely used for post-exposure prophylaxis for parenteral and sexual exposures. Observational data, ecological studies and models suggest that sexual transmission may be lower in couples in which one partner is infected with HIV and the other is not and the infected partner is on antiretroviral therapy (ART).

Mean CD4 cell count changes in patients failing a first-line antiretroviral therapy in resource-limited settings

Background Changes in CD4 cell counts are poorly documented in individuals with low or moderate-level viremia while on antiretroviral treatment (ART) in resource-limited settings. We assessed the impact of on-going HIV-RNA replication on CD4 cell count slopes in patients treated with a first-line combination ART. Method Naïve patients on a first-line ART regimen with at least two measures of HIV-RNA available after ART initiation were included in the study. The relationships between mean CD4 cell count change and HIV-RNA at 6 and 12 months after ART initiation (M6 and M12) were assessed by linear mixed models adjusted for gender, age, clinical stage and year of starting ART. Results 3,338 patients were included (14 cohorts, 64% female) and the group had the following characteristics: a median follow-up time of 1.6 years, a median age of 34 years, and a median CD4 cell count at ART initiation of 107 cells/μL. All patients with suppressed HIV-RNA at M12 had a continuous increase in CD4 cell count up to 18 months after treatment initiation. By contrast, any degree of HIV-RNA replication both at M6 and M12 was associated with a flat or a decreasing CD4 cell count slope. Multivariable analysis using HIV-RNA thresholds of 10,000 and 5,000 copies confirmed the significant effect of HIV-RNA on CD4 cell counts both at M6 and M12. Conclusion In routinely monitored patients on an NNRTI-based first-line ART, on-going low-level HIV-RNA replication was associated with a poor immune outcome in patients who had detectable levels of the virus after one year of ART.