Trapping ability on a biochip device is useful for systematic cell addressing and real-time observation of single cells analysis, however, precise control over the cell movements remains challenging. This thesis addresses the problem of controlling movement of single cells on a biochip platform by a technique called the Dielectrophoretic (DEP) force. Existing researches showed that the DEP force offers precise control of cell movements through various microelectrode designs which generate strong polarization effects i.e., DEP forces, but with the expense of damaging cell’s structure. The thesis contribute three new microelectrode designs for trapping single cells: the dipole, the quadrupole and the adaptive octupole, structured on a metal-insulator-metal (multilayer) biochip platform called the Sandwiched Insulator with Back Contact (SIBC) biochip. Cores of the study lie on the microelectrode designs that are capable of generating strong DEP holding forces, the back contact to enhance trapping of single cells and the fabrication process of creating a metal-insulator-metal structure. This thesis also presents details on the experimental setups of the trapping experiments and the numerical analysis of the microelectrode designs. The SIBC biochip comprises of the back contact on the first metal layer, the microcavity (cell trap) on the insulator layer and the three microelectrodes on the second metal layer. Together, the three microelectrodes and the back contact generate DEP forces that attract particles/single cells toward microcavities and maintain their positioning in the traps. Prior to the fabrication, profiles of the DEP force generated by the microelectrodes are studied using COMSOL3.5a software. Simulation results suggest that the DEP trapping region can be created surrounding the microcavity if the microelectrode and the back contact are connected with AC signals that have different phases. The strongest DEP force can be obtained by setting the back contact and the microelectrodes with AC signals that have 180 degree phase difference. Evaluations on the trapping functionality for the three microelectrodes were conducted using polystyrene microbeads and Ishikawa cancer cells line suspended in various medium. Trapping capability of the three microelectrodes was demonstrated through experiments with 22 percent of the Ishikawa cancer cells and 17 percent of the polystyrene microbeads were successfully trapped. With these promising results, the new microelectrode designs together with the SIBC biochip structure have huge potentials for biomedical applications particularly in the field of diagnosis and identification of diseases.

This thesis describes a novel approach for cell encapsulation in alginate gel microbeads. The main aim of the thesis was to optimise a microfluidic setup and chip to encapsulate cells in monodisperse alginate gel microbeads. A number of cytotoxicity tests were therefore carried out to determine the effect of formulations used for the production, degradation and gelation of calcium alginate gel beads. Results from these tests revealed that the formulations used had little or no significant effect on cell growth, and therefore, alginate was deemed to be a suitable cell encapsulating material for further investigations. Alginate gel microbeads were produced using hydrodynamic focusing techniques. For this purpose two different microfluidic setups were constructed. Fluids (oil, acidified oil and samples) were driven through the microfluidic setup by gravity. However, a number of drawbacks using this setup arose, such as polydispersity and reproducibility. Syringe pumps were introduced into the design of the second microfluidic setup as a means of driving fluids through the setup. In addition three different microfluidic chips were fabricated with the aim of producing the ideal alginate gel microbead. The first microfluidic chip (PMMA MC1) was fabricated from PMMA and involved producing alginate gel microbeads that were internally gelified. This chip suffered from a number of drawbacks such as continuous blockages within the microfluidic channels, which led to the development of the second microfluidic chip. This chip was also fabricated from PMMA (PMMA MC2) but in contrast to PMMA MC1, gelification occurred externally, i.e. gelation took place off chip, and in this case the alginate microdroplets were dropped into a well containing 1 mL of acidified oil. This encapsulating procedure caused immediate cell death, which indicated that the internal gelation of alginate gel microbeads was favoured. These results also indicated that the design of the microfluidic chip needed developing in order to produce the ideal microbeads that can be used for cell encapsulation. This led to the fabrication of a novel microfluidic chip (PC MC3) which was fabricated from polycarbonate (PC) and involved internal gelation of the calcium alginate gel microbeads. The combination of using the optimised microfluidic setup and PC MC3, in addition to alternations in some of the solutions used to make the alginate microbeads, resulted in the production of the desired ideal gel microbeads containing cells. Snap shots of the encapsulated cells obtained using fluorescence microscopy after 24 hours of encapsulation, revealed that the cells showed some characteristics of living cells, yet at the same time they also showed some characteristics of dead cells. These findings demonstrate the potential use of the optimised microfluidic setup and PC MC3 chip for many biological and medical applications.

High-throughput sequencing has greatly influenced the amount of data produced and biological questions asked and answered. Sequencing approaches have also enabled rapid development of related technological fields such as single-cell and spatially resolved expression profiling. The introductory parts of this thesis give an overview of the basic molecular and technological apparatus needed to analyse the transcriptome in cells and tissues. This is succeeded by a summary of present investigations that report recent advancements in RNA profiling. RNA integrity needs to be preserved for accurate gene expression analysis. A method providing a low-cost alternative for RNA preservation was reported. Namely, a low concentration of buffered formaldehyde was used for fixation of human cell lines and peripheral blood cells (Paper I). The results from bulk RNA sequencing confirmed gene expression was not negatively impacted with the preservation procedure (r2&gt;0.88) and that long-term storage of such samples was possible (r2=0.95). However, it is important to note that a small population of cells overexpressing a limited amount of genes can skew bulk gene expression analyses making them sufficient only in carefully designed studies. Therefore, gene expression should be investigated at the single cell resolution when possible. A method for high-throughput single cell expression profiling termed microarrayed single-cell sequencing was developed (Paper II). The method incorporated fluorescence-activated cell sorting, sample deposition and profiling of thousands of barcoded single cells in one reaction. After sample attachment to a barcoded array, a high-resolution image was taken which linked the position of each array barcode sequence to each individual deposited cell. The cDNA synthesis efficiency was estimated at 17.3% while detecting 27,427 transcripts per cell on average. Additionally, spatially resolved analysis is important in cell differentiation, organ development and pathological changes. Current methods are limited in terms of throughput, cost and time. For that reason, the spatial transcriptomics method was developed (Paper III). Here, the barcoded microarray was used to obtain spatially resolved expression profiles from tissue sections using the same imaging principle. The mouse olfactory bulb was profiled on a whole-transcriptome scale and the results showed that the expression correlated well (r2=0.94-0.97) as compared to bulk RNA sequencing. The method was 6.9% efficient, reported signal diffusion at ~2 μm and accurately deconvoluted layer-specific transcripts in an unbiased manner. Lastly, the spatial transcriptomics concept was applied to profile human breast tumours in three dimensions (Paper IV). Unbiased clustering revealed previously un-annotated regions and classified them as parts of the immune system, providing a detailed view into complex interactions and crosstalk in the whole tissue volume. Spatial tumour classification divulged that certain parts of the tumour clearly classified as other subtypes as compared to bulk analysis providing useful data for current practice diagnostics. The last part of the thesis discusses a look towards the future, how the presented methods could be used, improved upon or combined in translational research. / <p>QC 20170109</p>

abstract: This work demonstrated a novel microfluidic device based on direct current (DC) insulator based dielectrophoresis (iDEP) for trapping individual mammalian cells in a microfluidic device. The novel device is also applicable for selective trapping of weakly metastatic mammalian breast cancer cells (MCF-7) from mixtures with mammalian Peripheral Blood Mononuclear Cells (PBMC) and highly metastatic mammalian breast cancer cells, MDA-MB-231. The advantage of this approach is the ease of integration of iDEP structures in microfliudic channels using soft lithography, the use of DC electric fields, the addressability of the single cell traps for downstream analysis and the straightforward multiplexing for single cell trapping. These microfluidic devices are targeted for capturing of single cells based on their DEP behavior. The numerical simulations point out the trapping regions in which single cell DEP trapping occurs. This work also demonstrates the cell conductivity values of different cell types, calculated using the single-shell model. Low conductivity buffers are used for trapping experiments. These low conductivity buffers help reduce the Joule heating. Viability of the cells in the buffer system was studied in detail with a population size of approximately 100 cells for each study. The work also demonstrates the development of the parallelized single cell trap device with optimized traps. This device is also capable of being coupled detection of target protein using MALDI-MS. / Dissertation/Thesis / Ph.D. Chemistry 2013

The most common cancer form among men i prostate cancer and measurement of circulating tumor cells (CTCs) in the blood is a useful tool to evaluating the responset o treatment and progress of disease. CTC’s are cells that have detached from the original tumor and have spread in the blood sstem. In this master thesis a panel of 16 genes at single cell levels are analyzed using Reverse Transciptase Multiplexed Ligation-dependent Probe Amplification (RT-MLPA). The method uses gene specific reverse transcription primers to generate and amplify cDNA which MLPA probes are hybridized to. Correctly hybridized probes are ligated and amplified so that relative expression profiles can be calculated. One additional MLPA probe was designed to add to the existing panel. The results show that the MLPA reaction generates products from all genes in the panel when performed on synthetic MLPA prbe targets with equal concentrations. Results from totatl RNA on cell lines show that the reverse transcription and amplification of cDNA need further optimizations. When the whole assay is working it will be possible to evaluate gene expression from CTC’s that can help us understand the  progression and spread of prostate cancer in the body. / Prostatacancer är den vanligaste cancerformen hos män. Att räkna antal cirkulerade tumörceller (CTCer) i blodet är ett bra verktyg för att undersöka hur sjukdomen fortlöper och hur den svarar på behandling. CTCer är enskilda celler som brutit sig loss från originaltrumören och sprids i kroppen genom blodsystemet. I det här examensarbetet analyseras en panel bestående av 16 gener med hjälp av Reverse Transcriptase Multiplexed Ligation-dependent Probe Amplification (RT-MLPA).  Metoden bygger på att genspecifika primrar används för att syntetisera cDNA från mRNA. MLPA-prober hybridisear sedan till det amplifierade cDNAt. MLPA prober som hybridiserat korrekt ligeras och amplifieras och den relativa uttrycksnivåerna kan beräknas. Ytterligare en MLPA-probe designades för att passa in i den existerande blandningen av MLPA-prober. Resultaten viar att alla MLPA-prober ger produkter då en syntetisk DNA-templat blandning med lika koncentrationer används. Resultaten från total-RNA från cellinjer visar att omvandlingen och amplifieringen av mRNA till cDNA måste optimeras. När hela protokollet fungerar är det möjligt att undersöka genuttrycken i CTCer vilket kan underlätta förståelsen för utveckling och spridning av prostatacancer i kroppen.

Ce travail de thèse porte sur la réalisation et la validation d'un capteur pour la mesure d'impédance en cytométrie de flux associée à un dispositif microfluidique pour des cellules sanguines dans la gamme de fréquences (100 kHz-10 MHz). Un premier chapitre introduit les propriétés électriques et diélectriques des tissus vivants. Les effets de chaque élément des cellules sur l'impédance globale mesurée sont décrits, ainsi que les modèles associés. Un état de l'art, sur les mesures de l'échelle macroscopique à la mesure unitaire de cellules, est exposé dans le second chapitre. Les mesures en cytométrie de flux et l'utilisation possible des actionneurs à ondes acoustiques de surface (SAW) y sont aussi étudiées. Le troisième chapitre concerne la modélisation analytique et la simulation par la méthode des éléments finis de cellules unitaires par des microélectrodes de différentes géométries. Les résultats de cette section ont permis de déterminer les meilleures géométries, leurs sensibilités, et leurs réponses. La fabrication du capteur est étudiée dans le quatrième chapitre. Les contraintes liées à la faisabilité par les techniques de micro-fabrication et la biocompatibilité des matériaux y sont développées. Des premiers tests de validation sur les écoulements y sont effectués. Le cinquième et dernier chapitre est centré sur la mesure de cellules et particules. Des tests de calibration ont été réalisés pour déterminer le facteur de forme des électrodes et les impédances parasites. Les mesures suivantes sur des cellules et particules ont permis de valider les résultats obtenus en simulation, ainsi que la discrimination des particules testées en fonction de leurs dimensions / This thesis focuses on the implementation and validation of a microfluidic bioimpedance sensor for cytometric measures in the frequency range ( 100kHz - 10MHz ) of biological cells ( blood cells) combined with a microfluidic device. The first chapter introduces the electrical and dielectric properties of living tissues and summarizes the state of the art. The effects of each element of the cells on the overall measured impedance are described, as well as the associated models. A state of the art, on the bioimpedance macroscopic measurements unit cell is outlined in the second chapter. Measurements by flow cytometry and the possible use of surface acoustic wave (SAW) devices as actuators are also studied. The third chapter deals with analytical modeling and simulation by the finite element method of unit cells by microelectrodes of different geometries. 3D simulations were done showing the best configuration for the electrodes design. The results of this section were used to determine the best geometry, their sensibilities, and their answers. The sensor design is described in the fourth chapter. Technological constraints related to its micro- fabrication techniques feasibility and biocompatibility of materials are developed. Flows validation tests were done and are described. The fifth and final chapter focuses on the measurement of cells and particles. In a first step, calibration tests were carried out to determine the form factor of the electrodes and the parasitic impedances. Measurements on cells and particles were used to validate the results obtained in simulation, as well as discrimination based particles tested their dimensions

abstract: Measurements of different molecular species from single cells have the potential to reveal cell-to-cell variations, which are precluded by population-based measurements. An increasing percentage of researches have been focused on proteins, for its central roles in biological processes. Immunofluorescence (IF) has been a well-established protein analysis platform. To gain comprehensive insights into cell biology and diagnostic pathology, a crucial direction would be to increase the multiplexity of current single cell protein analysis technologies. An azide-based chemical cleavable linker has been introduced to design and synthesis novel fluorescent probes. These probes allow cyclic immunofluorescence staining which leads to the feasibility of highly multiplexed single cell in situ protein profiling. These highly multiplexed imaging-based platforms have the potential to quantify more than 100 protein targets in cultured cells and more than 50 protein targets in single cells in tissues. This approach has been successfully applied in formalin-fixed paraffin-embedded (FFPE) brain tissues. Multiplexed protein expression level results reveal neuronal heterogeneity in the human hippocampus. / Dissertation/Thesis / Doctoral Dissertation Chemistry 2019

Bacterial responses to environmental stresses may be easily observed and predicted under controlled laboratory conditions. However, realistic conditions encountered during manufacturing, in retail or in households may cause unpredicted responses of spoilage or pathogenic bacteria. Therefore it is essential to identify and understand the microbial dynamics under such conditions. The overall aim of the present study was to simulate the most common environmental conditions and consumer-style practices during storage or preparation of Ready-to-Eat (RTE) and Ready-to-Cook (RTC) products in the domestic environment, and predict the microbial dynamics which may deteriorate the quality or compromise the safety of these foods. Aiming to develop a unified mathematical model for the prediction of the growth of the specific spoilage microorganisms (SSOs), the spoilage pattern of three RTE acidic spreads of low pH was described in relation to microbial, physicochemical and molecular changes during storage. Results showed that the spoilage profile of the products was primarily affected by the initial pH and the storage temperature, despite the differences in their formulation. These findings enabled the assessment of two unified models (polynomial and Ratkowsky) for the prediction of the growth of lactic acid bacteria (LAB; SSOs) in such acidic spreads, using only the initial pH, the concentration of undissociated acetic acid and the storage temperature. The models were validated under realistic conditions in household refrigerators. Despite the abrupt fluctuations of the temperature during validation procedure, they both were able to adequately predict the growth of LAB in the spreads. However, the initial contamination level was proved to be necessary and crucial for the accurate prediction of microbial dynamics. The time-temperature profiles of the validation procedure revealed that the suggested storage conditions were not followed promptly and, therefore, concerns were raised on the effect of such consumer mishandlings on the safety of foods. Therefore, the responses of Salmonella spp. and Escherichia coli O157:H7 to the stresses encountered during frozen storage, thawing and cooking of ground beef, simulating typical scenarios followed by the consumers, were evaluated. The results revealed that the guidelines issued by the food safety authorities lack of some specific points that may affect the safety of the final product, such as the duration of frozen storage and the method of cooking. In particular, it was found that the heat resistance of E. coli O157:H7 was likely increased after long term frozen storage, while cooking in pan-grill did not ensure the safety of the final product, even when cooked at the suggested temperature. As shown in the first study, the initial contamination level played a significant role on the predictions of the models and further on the shelf-life of the products. Therefore, the dynamics of realistically low initial populations of Listeria monocytogenes and Salmonella Typhimurium versus higher levels of the pathogens (such those used during in vitro trials) in RTE fresh-cut salads were compared. In addition, any potential uncertainty sources for the growth potential of the pathogens in broth-based simulations were investigated. Results showed that the growth variability of low inocula is highly affected by the marginal storage temperatures, the indigenous microflora and the availability of nutrients. Because of this, growth from low populations showed the likelihood to exceed the growth derived from unrealistically high inocula, suggesting that ―fail-dangerous‖ implications may derive from such challenge tests. Data derived from this part were compared with broth-based simulations and the results showed that high uncertainty should be expected when extrapolating such predictions from low initial populations in fresh-cut salads, due to the various factors affecting the microbial growth on a real food, which are (inevitably) ignored by broth-based models. Overall, the present Thesis highlights the significant impact of consumer mishandlings on the food safety and quality of foods and contributes to the identification of unpredicted potential risk origins in the domestic environment.

Diese Arbeit entstand im Rahmen des Projektes „Molekulare Endospektroskopie“ an der Technischen Universität Dresden. Der Titel drückt aus, dass durch Kopplung von Endoskopie und Spektroskopie Gewebe auf molekularer Ebene charakterisiert wird. Infrarot- (IR-) und Raman-Spektroskopie bieten dabei besondere Vorteile, da sie zu den molekülspektroskopischen Verfahren mit dem höchsten Informationsgehalt gehören. Beide Methoden beruhen auf Molekülschwingungen, deren Spektren einen chemischen Fingerabdruck über die Zusammensetzung und Struktur der Proben liefern. Der Autor leitete eine wissenschaftliche Nachwuchsgruppe, die die Grundlagen der schwingungs-spektroskopischen Methoden zur Bildgebung von Gewebe und Zellen entwickelte und auf klinische Probleme – vor allem aus dem neuroonkologischen Bereich – anwendete. Diese kumulative Habilitationsschrift fasst vierzehn Veröffentlichungen zusammen, wobei in der letzten die Untersuchung eines Hirntumormodells von Mäusen mit einer faseroptischen Sonde beschrieben wurde. Zunächst werden verschiedene Methoden der Biophotonik verglichen, um die hier eingesetzten Techniken in diesen Kontext zu stellen. Danach werden biomedizinische Anwendungen von Fourier-Transform-Infrarot- (FTIR-) und Raman-Imaging beschrieben. Die eigenen Beiträge sind untergliedert in (i) Raman- und FTIR-Imaging in der Neuroonkologie, (ii) FTIR-mikroskopisches Imaging von Gewebedünnschnitten und (iii) Raman- und FTIR-mikroskopisches Imaging von einzelnen Zellen. Abschließend wird in den Schlussfolgerungen und dem Ausblick diskutiert, welche Rolle die molekulare Endospektroskopie als neue instrumentell-analytische Methode in der medizinischen Diagnostik übernehmen kann. / This work summarizes the results of the project “Molecular Endospectroscopy” at the Dresden University of Technology. The title expresses that tissue is characterized on the molecular level by coupling endoscopy and spectroscopy. Infrared (IR) and Raman spectroscopy offer advantages for these applications because they belong to the methods of molecular spectroscopy with the highest information content. Both methods probe molecular vibrations that provide a chemical fingerprint for the composition and structure of samples. The author was leader of a junior research group which developed vibrational spectroscopic methods for imaging of cells and tissues and applied them to clinical problems, in particular from the field of neuro-oncology. The current cumulative habilitation thesis is based on fourteen publications. The last one describes studies of a murine brain tumor model using a fiber-optic probe. In the first part various biophotonic methods are compared. Then biomedical applications of Fourier transform infrared (FTIR) and Raman imaging are reported. The papers are grouped into the chapters (i) Raman and FTIR imaging in neuro-oncology, (ii) FTIR microscopic imaging of tissue sections and (iii) Raman and FTIR microscopic imaging of single cells. It is discussed in the conclusions and outlook how molecular endospectroscopy as a new analytical tool can complement the standard diagnostic methods.

Formation of segments during vertebrate embryogenesis is regulated by a biological clock. Models and experimental data indicate that the core of this clock consists of a cell- autonomous single cell oscillator. This oscillator likely involves a genetic feedback loop of transcriptional repressors belonging to the hairy gene family. In zebrafish, three her genes, her1, hes6 and her7, have been identified as core oscillator components. The main purpose of this project was to study the molecular mechanism of the hairy gene negative feedback oscillator in single cells. To determine whether a single cell oscillator is part of the zebrafish segmentation clock, a cell dissociation protocol was established to track the expression of Her1 ex vivo. Upon dissociation, Her1 expression continued to oscillate for up to three cycles. The period of oscillations was significantly slower than that of the segmentation clock, but appears to speed up in the presence of serum. To test whether the hairy gene interactions are sufficient to generate oscillations in single cells, a protocol was established that uses synthetic biology principles to design, construct and characterize hairy gene networks in yeast. First a library of network parts, containing hairy genes, promoters and Her binding sites was generated and subsequently assembled into simple devices to test their functionality in yeast. The three core oscillator components, Her1, Hes6 and Her7, were characterized and optimized for expression in yeast. In the SWITCH-OFF assay, the Her1 protein, modified with a MigED yeast repressor domain, was found to function as a transcriptional repressor in yeast, while Hes6 with the same modification can not. The dissociation of segmentation clock cells provides the first direct evidence that single cell oscillators exist in zebrafish. In this system, oscillator dynamics can be studied without the interactions of higher level clock components. In parallel, establishing a yeast chassis for hairy gene networks provides a novel technique to directly test predicted oscillator mechanisms by constructing them ’bottom up’.