Natural Killer cells are a type of lymphocyte belonging to the innate immune system and they operate cell-mediated cytotoxicity and release of pro-inflammatory cytokines against cancerous cells. However, in vivo testings have shown a reduced activity of NK cells against solid tumors probably due to the negative influence of the immunosuppressive tumor microenvironment. Multicellular tumor spheroids may constitute an advantageous model in cancer biology for studying the mechanisms behind cancer immune editing since it more closely mimics the complexity of the human body compared with the 2D model counterpart. This study investigated the interaction between NK cells isolated from blood and tumor spheroids obtained from A498 renal carcinoma cells, using light-sheet microscopy imaging which allows satisfactory cell tracking in the inner layers of the spheroids. NK cells not only indeed interact with tumor spheroids, but many of them were able to penetrate the spheroids inducing some changes in the structure of the latter. NK cells were also tracked over time, displaying the migration path and calculating the speed. The fluorescence intensity of the NK cells was found reduced as soon as they penetrate the spheroid but, conversely, the speed seems to increase inside the spheroid, a possible sign of the fallibility of the tracking algorithm in this specific case. We propose solutions for more sophisticated future implementations, involving the use of marks during the experimental phase and drift corrections at the data analysis level.

Autophagy is a conserved biological stress response in mammalian cells that is responsible for clearing damaged proteins and organelles from the cytoplasm and recycling their contents via the lysosomal pathway. In cases where the stress is not too severe, autophagy acts as a survival mechanism. In cases of severe stress, it may lead to programmed cell death. Autophagy is abnormally regulated in a wide-range of diseases, including cancer. To integrate the existing knowledge about this decision process into a rigorous, analytical framework, we built a mathematical model of cell fate decision mediated by autophagy. The model treats autophagy as a gradual response to stress that delays the initiation of apoptosis to give the cell an opportunity to survive. We show that our dynamical model is consistent with existing quantitative measurements of time courses of autophagic responses to cisplatin treatment. To understand the function of this response in cancer cells we have provided a systems biology experimental framework to study dynamical aspects of autophagy in single cancer cells using live-cell imaging and quantitative uorescence microscopy. This framework can provide new insights on function of autophagic response in cancer cells. / Ph. D.

Clostridium perfringens is a spore-forming anaerobic Gram-positive rod which has gliding motility through type IV Pili (TFP). Since the discovery of TFP in Gram-positive bacteria is relatively new, more studies are required to understand the mechanism and interaction of the proteins of this machinery. Moreover, the similarities between TFP and type 2 secretion system (T2SS) suggest that C. perfringens has also a T2SS. We studied the localization of TFP ATPases, PilB1, PilB2 and PilT in Bacillus subtilis to compare the localization in an organism other than C. perfringens and which lacks any known genes similar to TFP. Unlike the case in C. perfringens, PilB1 in B. subtilis localized to the poles in the absence of PilT, with some central foci at the future division sites. Colocalization of PilB1 was also studied with PilT and the results suggested that PilB1 needs PilT to migrate from the poles to the center. Localization of PilB2 in B. subtilis, was similar to the results in C. perfringens and to the localization of PilB1 in B. subtilis. We have not been able to co-express PilB2 with PilT yet. Succeeding in this study will help us better understand the interactions between PilB proteins and PilT. In another project, we studied a von Willebrand factor Type A-Domain Containing protein (vWA) which is secreted from C. perfringens strain 13. We overexpressed and purified this protein and tested the effects on mammalian cells. We found that the vWA is probably not a toxin but since it seems to bind to macrophage membranes, we propose that the vWA could be part of a toxin complex, probably the subunit of the complex that binds to the host cells. / Master of Science

No / The hair shaft has increasing importance in bioarchaeology, since it is now possible to retrieve detailed biomolecular information on recent life history using individual fibres (e.g., on diet, drug use and DNA). Data on hair condition is an important cornerstone to ensuring that reliable information is obtained. The following study defines morphological features of degradative change in human terminal scalp hair using different microscopy techniques. Evidence of degradative change is translated into a ranked histology for assessing hair sample condition. The approach is applied to samples of cut modern scalp hair subjected to degradation under soil burial/simulated grave conditions.

Mental and neurological disorders account for a large part of the total global disease burden, yet there is a severe lack of effective treatments for reducing the associated disability and mortality. Brain dysfunctions are caused by a large variety of factors, such as pathological network connectivity, altered cellular and physiological properties, and neurotransmitter imbalances that act together or alone to result in profound behavioral impacts. Thus, there is an urgent need for integrative tools that allow an unbiased whole-brain understanding of the underlying pathophysiology of complex brain disorders. Recent advances in tissue clearing, labeling, and high-resolution light sheet microscopy, are enabling mapping and comparative analysis of large intact brain samples in normal and diseased states. However, multiple challenges remain, specifically in achieving uniform labeling of specific molecular targets in large tissues, scalable microscopy platforms for high-resolution whole-brain imaging, and multi-scale high-accuracy comparative data analysis tools. Here, I present my work in the development of a set of novel methods to address some of these challenges. The first aim focuses on developing a rapid and uniform deep tissue molecular labeling method by utilizing modified DNA aptamers to significantly reduce the staining times (e.g., less than 4 days for an intact mouse brain, as opposed to several weeks). The second aim introduces a cost-effective (~20x cheaper) and scalable light sheet fluorescence microscopy (LSFM) implementation, so-called projected Light sheet microscopy (pLSM), for rapid high-resolution imaging of large biological samples. The third aim is focused on developing a suite of large data analysis methods (suiteWB) for high-resolution whole-brain comparative phenotyping – both at the level of neuron densities and their brain-wide projection patterns. Through this pipeline, we systematically investigated the brain-wide dopaminergic modulatory pathway alterations resulting from chronic ketamine exposure. Altogether, these sets of highly integrative labeling, imaging, and analysis tools will facilitate a comprehensive understanding of the pathophysiology of complex brain disorders and the discovery of novel therapeutic targets.

Advancements in neural interfacing technologies, such as microelectrode arrays, have significantly contributed to understanding brain function and treating neurological disorders. Decoding the intricacies and functioning of neural circuits is key to further unlocking its potential. Two key approaches, electrical neural recording and optical imaging, have been the basis of stimulating and monitoring neural circuits. Despite the remarkable progress, several key issues such as reliable stimulation of neurons, closed-loop stimulation and monitoring, and undesired background fluorescence during widefield optical imaging remain challenging. After giving a brief background on electrode and microLED arrays, the dissertation delves into the design, microfabrication, and characterization of microelectrode arrays for neural electrical stimulation, recordings, and microLED arrays as a light source for improving optical microscopy. We first discuss a dense conformal electrode array for high spatial resolution stimulation in electrosensory systems. The performance metrics of the integrated system are thoroughly examined through meticulous characterization and optimization processes. Special emphasis is placed on evaluating biocompatibility, electrical properties, and spatial resolution to ensure robust and reliable neural stimulation capability. Next, we discuss a microelectrode device that combines simultaneous electrical recording and 2-photon imaging. We use an Indium Tin Oxide (ITO) material to fabricate a transparent electrode array with a design capable of single neuron recordings. The design, microfabrication, and electrooptical characterization are presented to demonstrate the device’s capability. A system integrating the array with a GRIN lens is also presented to record and image deeper into the brain tissue. Combining both the electrical and optical recordings of neuron ensembles and finding correlations can shed further light on the functioning of neural circuits. To address the problem of unwanted background fluorescence during neural cell imaging, two microLED arrays as light sources are presented. With a microstripe array, we implement optical sectioning structured illumination microscopy (OS-SIM), and with the 2D microLED array, we implemented targeted illumination to reject background fluorescence and improve contrast. We examine the capability of the microLED as a light source with luminance-current-voltage, directivity, and transient measurements. Both implementations highlight the novel non-display application of microLED to address challenges in neural imaging. This research represents a significant contribution to the burgeoning field of neural engineering, offering novel methodologies and technologies that promise to revolutionize our approach to understanding brain functions.

Calcium (Ca²⁺) influx through Caᵥ1.2 channels mediates cardiac excitation-contraction coupling, tunes cardiac action potential duration and excitability, and regulates cardiomyocytes’ (CM) gene expression. Mechanisms regulating the sub-cellular localization, trafficking, and dynamics of surface Caᵥ1.2 in ventricular CMs are poorly understood though these are critical determinants of cardiac function. To gain new insights into Caᵥ1.2 organization, dynamics, and regulation at the CM surface we generated transgenic mice expressing an αMHC controlled cardiac-specific, dihydropyridine (DHP)- resistant α₁_ᴄ construct, tagged at the N-terminus with FLAG and HA epitopes, at the C- terminus with YFP, a 13-residue bungarotoxin binding site (BBS) inserted into in the third extracellular loop of domain II, and mutations that prevent cleavage of the C-terminus. We found robust inducible expression of DHP-resistant FLAG-HA-BBS-α₁_ᴄ-YFP in the heart that targeted to dyadic junctions, generated nisoldipine-resistant Ca²⁺ currents, supported cardiac excitation-contraction coupling, and was normally up-regulated by β-adrenergic activation with isoproterenol. Incubating transgenic CMs with AlexaFluor₆₄₇-conjugated α- bungarotoxin (BTX₆₄₇) enabled selective labeling of surface BBS-tagged Caᵥ1.2 channels. We used total internal fluorescence (TIRF) microscopy to investigate the spatiotemporal organization and dynamics of surface Caᵥ1.2 channels. Similar to endogenous Caᵥ1.2, transgenic α1C-YFP forms clusters with exponentially distributed sizes at the cell surface. A flow cytometry-based optical pulse-chase assay revealed surface Caᵥ1.2 channels in adult cardiomyocytes fully turn over within two hours. Application of angiotensin II (Ang II) decreased transgenic Caᵥ1.2 surface density and this effect was blocked by the selective Ang II receptor type I (AT1R) blocker losartan. Application of losartan by itself increased Caᵥ1.2 surface density, suggesting the potential presence of constitutively active Ang II receptors in adult CMs. Our results provide new insights into spatiotemporal organization, dynamics, and regulation of Caᵥ1.2 channels in adult CMs and introduce an approach that can be widely applied to elucidate spatiotemporal dynamics of cardiac ion channels and membrane proteins.

Improved diagnosis, prognosis and disease follow-up is a fundamental procedure and a constant challenge in medicine.  Among the different molecular biomarkers, proteins are the essential regulatory component in blood; hence, by developing enhanced specific and sensitive molecular tools will gives great insight into the different processes in disease treatment.  In this thesis, we build on the proximity ligation assay to develop and apply new adaptable methods to facilitate protein detection. In paper I, I present a variant of the proximity ligation assay (we call PLARCA) using micro titer plate for detection and quantification of protein using optical density as readout in the fluorometer. PLARCA detected femtomolar levels of these proteins in patient samples, which was considerably below the detection threshold for ELISA. In paper II, we developed and adapted a new method into the in situ PLA methods for detection and identification of extracellular vesicles (EVs) using flow cytometry as readout (a method we call ExoPLA).  We identified five target proteins on the surface of the Evs and using three colors, we identified the EV using flow cytometer. In paper III, we aim to improve the efficiency of in situ PLA by creating and developing new designs and versions of the assay we called Unfold probes Through comparison of detection of protein using in situ PLA versus Unfold probes, we observed considerable decrease in non-specific signals, and also a lower detection threshold. In paper IV, we describe the development of a solid phase proximity extension (sp-PEA) assay for protein detection and quantification. We compared detection of IL-8, TNF-alpha, IL-10 and IL-6 using spPEA and PEA; spPEA demonstrations over 2 orders of magnitudes in the lower detection concentrations by decreased in background noise.

Polymer-modified bitumen (PMB) is a high-performance material for road construction and maintenance. But its storage stability and phase separation behaviour are still not sufficiently understood and need to be studied toward a more successful and sustainable application of PMB. In this thesis, the equilibrium thermodynamics and phase separation dynamics of PMB are investigated with the aim at a fundamental understanding on PMB storage stability and phase separation behaviour. The development of polymer modifiers for paving bitumen is reviewed. The phase separation process in unstable PMBs is captured by fluorescence microscopy at the storage temperature (180 °C). A coupled phase-field model of diffusion and flow is developed to simulate and predict the PMB storage stability and phase separation behaviour. The temperature dependency of PMB phase separation behaviour is modelled by introducing temperature-dependent model parameters between 140 °C and 180 °C. This model is implemented in a finite element software package and calibrated with the experimental observations of real PMBs. The results indicate that storage stability and phase separation behaviour of PMB are strongly dependent on the specific combination of the base bitumen and polymer. An unstable PMB starts to separate into two phases by diffusion, because of the poor polymer-bitumen compatibility. Once the density difference between the two phases becomes sufficiently significant, gravity starts to drive the flow of the two phases and accelerates the separation in the vertical direction. The proposed model, based on the Cahn-Hilliard equation, Flory-Huggins theory and Navier-Stokes equations, is capable of capturing the stability differences among the investigated PMBs and their distinct microstructures at different temperatures. The various material parameters of the PMBs determine the differences in the phase separation behaviour in terms of stability and temperature dependency. The developed model is able to simulate and explain the resulting differences due to the material parameters. The outcome of this study may thus assist in future efforts of ensuring storage stability and sustainable application of PMB. / Polymermodifierade bitumen (PMB) är ett högpresterande material för väganläggning och underhåll. Men PMB:s lagringsstabilitet och fassepareringsegenskaper är inte tillräckligt förstådda än och behöver studeras för en mer framgångsrik och hållbar användning av PMB. I denna avhandling studeras termodynamisk jämvikt och fasseparation av PMB med målsättning att uppnå en grundläggande förståelse av PMB:s lagringsstabilitet och fassepareringsegenskaper. Utvecklingen av polymermodifierade bitumen sammanfattas. Fasseparationsprocessen av instabil PMB:s studeras med hjälp av fluorescens mikroskopi vid lagringstemperatur (180 °C). En kopplad fas-fälts modell som beskriver diffusion och flöde har utvecklats för att simulera och förutsäga PMB:s lagringsstabilitet och fassepareringsegenskaper. Temperaturberoendet hos PMB:s fasseparation har beskrivits genom att införa temperaturberoende modellparametrar mellan 140 °C och 180 °C. Denna modell är införd i ett finit element program och kalibrerad med experimentella observationer på verkliga PMB. Resultaten indikerar att lagringsstabiliteten och fasseparationen hos PMB är starkt beroende av den specifika kombinationen av basbitumen och polymer. En instabil PMB börjar separera i två faser genom diffusion, beroende på dålig bitumen-polymer kompatibilitet. När skillnaden i densitet mellan de två faserna blir tillräckligt stor kommer gravitationen att driva flödet av de två faserna och accelerera separationen i vertikalled. Den föreslagna modellen, baserad på Cahn-Hilliards ekvation, Flory-Huggins teori och Navier-Stokes ekvation, kan beskriva stabilitetsskillnaderna mellan de undersökta PMB:erna och deras distinkta mikrostruktur vid olika temperaturer. De olika materialparametrarna hos PMB bestämmer skillnaden i fassepareringsegenskaper i termer av stabilitet och temperaturberoende. Den utvecklade modellen kan simulera och förklara de resulterande skillnaderna på grund av materialparametrarna. Resultatet av denna studie kan bidra till att säkerställa lagringsstabilitet och hållbara applikationer för PMB. / <p>QC 20161102</p>

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