Guided Migration and Collective Behavior: Cell Dynamics during Cancer Progression

This dissertation focuses on gaining understanding of cell migration and collective behavior through a combination of experiment, analysis, and modeling techniques. Cell migration is a ubiquitous process that plays an important role during embryonic development and wound healing as well as in diseases like cancer, which is a particular focus of this work. As cancer cells become increasingly malignant, they acquire the ability to migrate away from the primary tumor and spread throughout the body to form metastatic tumors. During this process, changes in gene expression and the surrounding tumor environment can lead to changes in cell migration characteristics. In this thesis, I analyze how cells are guided by the texture of their environment and how cells cooperate with their neighbors to move collectively. The emergent properties of collectively moving groups are a particular focus of this work as collective cell dynamics are known to change in diseases such as cancer. The internal machinery for cell migration involves polymerization of the actin cytoskeleton to create protrusions that---in coordination with retraction of the rear of the cell---lead to cell motion. This actin machinery has been previously shown to respond to the topography of the surrounding surface, leading to guided migration of amoeboid cells. Here we show that epithelial cells on nanoscale ridge structures also show changes in the morphology of their cytoskeletons; actin is found to align with the ridge structures. The migration of the cells is also guided preferentially along the ridge length. These ridge structures are on length scales similar to those found in tumor microenvironments and as such provide a system for studying the response of the cells' internal migration machinery to physiologically relevant topographical cues. In addition to sensing surface topography, individual cells can also be influenced by the pushing and pulling of neighboring cells. The emergent properties of collectively migrating cells show interesting dynamics and are relevant for cancer progression, but have been less studied than the motion of individual cells. We use Particle Image Velocimetry (PIV) to extract the motion of a collectively migrating cell sheet from time lapse images. The resulting flow fields allow us to analyze collective behavior over multiple length and time scales. To analyze the connection between individual cell properties and collective migration behavior, we compare experimental flow fields with the migration of simulated cell groups. Our collective migration metrics allow for a quantitative comparison between experimental and simulated results. This comparison shows that tissue-scale decreases in collective behavior can result from changes in individual cell activity without the need to postulate the existence of subpopulations of leader cells or global gradients. In addition to tissue-scale trends in collective behavior, the migration of cell groups includes localized dynamic features such as cell rearrangements. An individual cell may smoothly follow the motion of its neighbors (affine motion) or move in a more individualistic manner (non-affine motion). By decomposing individual motion into both affine and non-affine components, we measure cell rearrangements within a collective sheet. Finally, finite-time Lyapunov exponent (FTLE) values capture the stretching of the flow field and reflect its chaotic character. Applying collective migration analysis techniques to experimental data on both malignant and non-malignant human breast epithelial cells reveals differences in collective behavior that are not found from analyzing migration speeds alone. Non-malignant cells show increased cooperative motion on long time scales whereas malignant cells remain uncooperative as time progresses. Combining multiple analysis techniques also shows that these two cell types differ in their response to a perturbation of cell-cell adhesion through the molecule E-cadherin. Non-malignant MCF10A cells use E-cadherin for short time coordination of collective motion, yet even with decreased E-cadherin expression, the cells remain coordinated over long time scales. In contrast, the migration behavior of malignant and invasive MCF10CA1a cells, which already shows decreased collective dynamics on both time scales, is insensitive to the change in E-cadherin expression.

Guided Migration and Collective Behavior: Cell Dynamics during Cancer Progression

This dissertation focuses on gaining understanding of cell migration and collective behavior through a combination of experiment, analysis, and modeling techniques. Cell migration is a ubiquitous process that plays an important role during embryonic development and wound healing as well as in diseases like cancer, which is a particular focus of this work. As cancer cells become increasingly malignant, they acquire the ability to migrate away from the primary tumor and spread throughout the body to form metastatic tumors. During this process, changes in gene expression and the surrounding tumor environment can lead to changes in cell migration characteristics. In this thesis, I analyze how cells are guided by the texture of their environment and how cells cooperate with their neighbors to move collectively. The emergent properties of collectively moving groups are a particular focus of this work as collective cell dynamics are known to change in diseases such as cancer. The internal machinery for cell migration involves polymerization of the actin cytoskeleton to create protrusions that---in coordination with retraction of the rear of the cell---lead to cell motion. This actin machinery has been previously shown to respond to the topography of the surrounding surface, leading to guided migration of amoeboid cells. Here we show that epithelial cells on nanoscale ridge structures also show changes in the morphology of their cytoskeletons; actin is found to align with the ridge structures. The migration of the cells is also guided preferentially along the ridge length. These ridge structures are on length scales similar to those found in tumor microenvironments and as such provide a system for studying the response of the cells' internal migration machinery to physiologically relevant topographical cues. In addition to sensing surface topography, individual cells can also be influenced by the pushing and pulling of neighboring cells. The emergent properties of collectively migrating cells show interesting dynamics and are relevant for cancer progression, but have been less studied than the motion of individual cells. We use Particle Image Velocimetry (PIV) to extract the motion of a collectively migrating cell sheet from time lapse images. The resulting flow fields allow us to analyze collective behavior over multiple length and time scales. To analyze the connection between individual cell properties and collective migration behavior, we compare experimental flow fields with the migration of simulated cell groups. Our collective migration metrics allow for a quantitative comparison between experimental and simulated results. This comparison shows that tissue-scale decreases in collective behavior can result from changes in individual cell activity without the need to postulate the existence of subpopulations of leader cells or global gradients. In addition to tissue-scale trends in collective behavior, the migration of cell groups includes localized dynamic features such as cell rearrangements. An individual cell may smoothly follow the motion of its neighbors (affine motion) or move in a more individualistic manner (non-affine motion). By decomposing individual motion into both affine and non-affine components, we measure cell rearrangements within a collective sheet. Finally, finite-time Lyapunov exponent (FTLE) values capture the stretching of the flow field and reflect its chaotic character. Applying collective migration analysis techniques to experimental data on both malignant and non-malignant human breast epithelial cells reveals differences in collective behavior that are not found from analyzing migration speeds alone. Non-malignant cells show increased cooperative motion on long time scales whereas malignant cells remain uncooperative as time progresses. Combining multiple analysis techniques also shows that these two cell types differ in their response to a perturbation of cell-cell adhesion through the molecule E-cadherin. Non-malignant MCF10A cells use E-cadherin for short time coordination of collective motion, yet even with decreased E-cadherin expression, the cells remain coordinated over long time scales. In contrast, the migration behavior of malignant and invasive MCF10CA1a cells, which already shows decreased collective dynamics on both time scales, is insensitive to the change in E-cadherin expression.

Experimental characterization of wingtip vortices using smoke flow visualizations

In order to predict the axial development of the wingtip vortices strength an accurate theoretical model is required. Several experimental techniques have been used to that end, e.g. PIV or hotwire anemometry, but they imply a significant cost and effort. For this reason, we have carried out experiments using the smoke-wire technique to visualize smoke streaks in six planes perpendicular to the main stream flow direction. Using this visualization technique, we obtained quantitative information regarding the vortex velocity field by means of Batchelor's model~\cite{batchelor}, which only depends on two free parameters, i.e. the vortex strength, $S$, and the virtual origin, $z_0$. Results for two chord based Reynolds numbers have been compared with those provided by del Pino et at. (2011), finding good agreement.

Teste do bulbo molhado para o plantio de cana-de-açúcar com irrigação localizada.

No Submédio do Vale do São Francisco, o sistema de cultivo da cana-de-açúcar (Saccharum spp.) é baseado no fornecimento da água durante todo o seu ciclo. Nesta região, a irrigação na cana-de-açúcar tem sido feita por sulcos, aspersão (pivô central e linear) e por gotejamento subsuperficial, os quais proporcionam índices variáveis de eficiência no uso de água pela cultura. Dentre eles, o gotejamento subsuperficial é o mais eficiente, uma vez que disponibiliza água próximo ao sistema radicular e facilita a automação do sistema para irrigação e fertirrigação durante o ciclo da cultura.

Aplicação de modelo agrometeorológico espectral no perímetro irrigado da bacia do São Francisco, utilizando imagens RAPIDEYE.

O objetivo do trabalho foi aplicar o modelo SAFER (Simple Algorithm For Evapotranspiration Retrieving) com a finalidade de analisar os parâmetros biofísicos na área do Perímetro Irrigado de Jaíba, na Bacia do São Francisco. Foram obtidos dados meteorológicos e imagens do satélite RapidEye (resolução de 5m), referente aos dias 26 de junho de 2013 e 29 de abril de 2014. Os valores médios diários do Índice de Vegetação por Diferença Normalizada (NDVI) foram 0,29±0,16 e 0,43±0,18, para 2013 e 2014, respectivamente. Na imagem de 2013 foram observados valores superiores de temperatura da superfície (Ts) (303,08±2,26 K) aos observados em 2014 (296,14±2,32 K). A evapotranspiração (ET) média diária de toda a cena de 2013 foi 0,43±0,96 mm e valor máximo de 6,11. Em 2014, os valores de ET médios diários foram de 2,19±2,01mm. Conforme estudos anteriores, a caatinga converte a maior parte da energia disponível em calor sensível (H), enquanto as culturas irrigadas apresentam altos valores de ET. Com imagens de alta resolução espacial, sem a banda termal, foi possível obter os parâmetros biofísicos da superfície possibilitando o monitoramento em nível de pivô central e talhões de culturas irrigadas, auxiliando o uso racional da água em tempos de deficiência hídrica.

Experimental determination of burning velocity in metal dust explosions

The modeling of metal dust explosion phenomenon is important in order to safeguard industries from potential accidents. A key parameter of these models is the burning velocity, which represents the consumption rate of the reactants by the flame front, during the combustion process. This work is focused on the experimental determination of aluminium burning velocity, through an alternative method, called "Direct method". The study of the methods used and the results obtained is preceded by a general analysis on dust explosion phenomenon, flame propagation phenomenon, characteristics of the metals combustion process and standard methods for determining the burning velocity. The “Direct method” requires a flame propagating through a tube recorded by high-speed cameras. Thus, the flame propagation test is carried out inside a vertical prototype made of glass. The study considers two optical technique: the direct visualization of the light emitted by the flame and the Particle Image Velocimetry (PIV) technique. These techniques were used simultaneously and allow the determination of two velocities: the flame propagation velocity and the flow velocity of the unburnt mixture. Since the burning velocity is defined by these two quantities, its direct determination is done by substracting the flow velocity of the fresh mixture from the flame propagation velocity. The results obtained by this direct determination, are approximated by a linear curve and different non-linear curves, which show a fluctuating behaviour of burning velocity. Furthermore, the burning velocity is strongly affected by turbulence. Turbulence intensity can be evaluated from PIV technique data. A comparison between burning velocity and turbulence intensity highlighted that both have a similar trend.

Caratterizzazione fluidodinamica di un digestore anaerobico modello tramite tecniche di diagnostica ottica

L’aumento del consumo di energia globale e le problematiche legate all’inquinamento stanno rendendo indispensabile lo spostamento verso fonti di energia rinnovabile. La digestione anaerobica rappresenta una possibile soluzione in quanto permette di produrre biogas da biomassa organica di scarto ma, l’ottimizzazione del processo risulta difficoltosa a causa delle numerose variabili chimiche, biologiche, fisiche e geometriche correlate. Nel presente elaborato, concentrandosi sulle problematiche relative alla miscelazione interna, è stata investigata la fluidodinamica interna di un reattore modello ottenuto tramite scale-down di un digestore anaerobico industriale che presentava problemi di sedimentazione di sostanza solida sul fondo del reattore. Tramite tecniche di diagnostica ottiche, è stato studiato il movimento del fluido, prima utilizzando acqua demineralizzata e poi una soluzione di gomma di xantano come fluido di processo, al fine di studiare il campo di moto medio interno al reattore. Le tecniche utilizzate sono la Particle Image Velocimetry (PIV) e la Planar Laser Induced Fluorescence (PLIF). Al fine di rendere il sistema investigato il più rappresentativo possibile del digestore industriale, è stato utilizzato come fluido di processo per alcune delle prove raccolte, una soluzione acquosa 1,0g/kg di gomma di xantano, le cui proprietà reologiche sono state investigate grazie ad un Reometro Anton Paar MCR 301.

Caratterizzazione fluidodinamica di reattori agitati meccanicamente tramite tecniche di diagnostica ottica: effetto del comportamento reologico delle fasi.

Il lavoro di tesi si è posto l'obiettivo di studiare il comportamento fluidodinamico di un reattore agitato meccanicamente, scale-down di un digestore anaerobico per la produzione di biogas, attraverso tecniche di diagnostica ottica. Le tecniche utilizzate sono state la Particle Image Velocimetry, PIV, e la Planar Laser Induced Fluorescence, PLIF. Le prove sono iniziate utilizzando acqua all’interno del reattore e sono proseguite utilizzando una soluzione di acqua e Carbometilcellulosa (CMC) a concentrazione di CMC progressivamente crescente per aumentare la viscosità apparente della soluzione non newtoniana con lo scopo di simulare il più realisticamente possibile la viscosità del contenuto reale del digestore. Tutte le diverse soluzioni sono state indagate per diverse velocità e diversi sensi di rotazione. Le prove di diagnostica ottica sono state progressivamente affiancate da prove al reometro di campioni di soluzione per il calcolo della viscosità apparente. La PIV ha fornito la misura del campo di moto di un piano, è stato scelto di analizzare un piano verticale. Il metodo di diagnostica ottica ho previsto l’utilizzo di quattro componenti: una sezione per il test otticamente trasparente contenente la soluzione inseminata con piccole particelle di tracciante (particelle di argento e vetro cavo) che seguono il flusso, una sorgente di illuminazione pulsata (laser), un dispositivo di registrazione (una telecamera digitale ad alta definizione) ed un software per la cross-correlazione delle immagini acquisite (DynamicStudio). La PLIF è stata implementata per lo studio del tempo caratteristico di miscelazione nel reattore. La strumentazione utilizzata è stata la stessa della PIV con un tracciante diverso a base di Rodhamina-6G. Lo studio ha riguardato il tempo necessario all’omogeneizzazione del tracciante mediante un’analisi del coefficiente di variazione, CoV, delle immagini acquisite.

Experimental analysis of the aerodynamic and mixing performance of a ventilation device

Numerous types of acute respiratory failure are routinely treated using non-invasive ventilatory support (NIV). Its efficacy is well documented: NIV lowers intubation and death rates in various respiratory disorders. It can be delivered by means of face masks or head helmets. Currently the scientific community’s interest about NIV helmets is mostly focused on optimising the mixing between CO2 and clean air and on improving patient comfort. To this end, fluid dynamic analysis plays a particularly important role and a two- pronged approach is frequently employed. While on one hand numerical simulations provide information about the entire flow field and different geometries, they exhibit require huge temporal and computational resources. Experiments on the other hand help to validate simulations and provide results with a much smaller time investment and thus remain at the core of research in fluid dynamics. The aim of this thesis work was to develop a flow bench and to utilise it for the analysis of NIV helmets. A flow test bench and an instrumented mannequin were successfully designed, produced and put into use. Experiments were performed to characterise the helmet interface in terms of pressure drop and flow rate drop over different inlet flow rates and outlet pressure set points. Velocity measurements by means of Particle Image Velocimetry were performed. Pressure drop and flow rate characteristics from experiments were contrasted with CFD data and sufficient agreement was observed between both numerical and experimental results. PIV studies permitted qualitative and quantitative comparisons with numerical simulation data and offered a clear picture of the internal flow behaviour, aiding the identification of coherent flow features.

Characterization Of Single Use Reactor Used For The Manufacturing Of Formulated Products Within The Pharmaceutical Industry

Mixing is a fundamental unit operation in the pharmaceutical industry to ensure consistent product quality across different batches. It is usually carried out in mechanically stirred tanks, with a large variety of designs according to the process requirements. A key aspect of pharmaceutical manufacturing is the extensive and meticulous cleaning of the vessels between runs to prevent the risk of contamination. Single-use reactors represent an increasing trend in the industry since they do not require cleaning and sterilization, reducing the need for utilities such as steam to sterilize equipment and the time between production batches. In contrast to traditional stainless steel vessels, single-use reactors consist of a plastic bag used as a vessel and disposed of after use. This thesis aims to characterize the fluid dynamics features and the mixing performance of a commercially available single-use reactor. The characterization employs a combination of various experimental techniques. The analysis starts with the visual observation of the liquid behavior inside the vessel, focusing on the vortex shape evolution at different impeller speeds. The power consumption is then measured using a torque meter to quantify the power number. Particle Image Velocimetry (PIV) is employed to investigate local fluid dynamics properties such as mean flow field and mean and rms velocity profiles. The same experimental setup of PIV is exploited for another optical measurement technique, the Planar Laser-Induced Fluorescence (PLIF). The PLIF measurements complete the characterization of the reactor with the qualitative visualization of the turbulent flow and the quantitative assessment of the system performance through the mixing time. The results confirm good mixing performances for the single-use reactor over the investigated impeller speeds and reveal that the filling volume plays a significant role in the fluid dynamics of the system.