| 1. |
- Jing, Yujia, 1985
(author)
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Hyperthermia-responsive liposomal systems
- 2015
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Doctoral thesis (other academic/artistic)abstract
- Abstract Sophisticated liposomal systems are emerging at an increasing rate to meet the demands for multifunctional drug carriers in chemotherapies in combined with hyperthermia. For example, liposomal drug carriers for temperature-controlled drug release under hyperthermic conditions have recently been tested in clinical trials. More advanced designs of liposomes are expected to release encapsulated contents and activate hidden surface-functions in response to heat stimulus. Towards this aim, the present thesis is focused on formulating asymmetric lipid systems that can preserve functional moieties, and reactivate the targeted function as well as release the encapsulated compounds upon local heating. The design of the asymmetric liposomal systems utilizes the heat-activated transmembrane lipid diffusion during gel to liquid-crystalline phase transitions of the lipid membranes.Rational design of advanced liposomal drug-delivery systems will require understanding of the physicochemical properties of lipid membranes under, e.g., hyperthermic conditions. Here, supported lipid membranes on planar solid surfaces were used for model studies of lipid composition yielding a gel to liquid crystalline phase-transition temperature in the range 40 – 45 °C. It was found that the liposome-to-membrane formation process is not only size-dependent but also governed by temperature. Two methods of preparing supported asymmetric lipid membranes were investigated. As a proof-of-concept, the upper leaflets were either replaced or chemically transformed by enzymatic hydrolysis. The processes were monitored using surface sensitive techniques such as quartz crystal microbalance with dissipation (QCM-D) and dual polarization interferometry (DPI). The asymmetric structures were stable at a room temperature, while lipid flip-flop was induced upon increasing of the temperature. Transmembrane lipid exchange in the asymmetric structure under hyperthermic conditions was demonstrated by detecting, through streptavidin binding, biotinylated lipids appearing at the top leaflet which were first located in the lower leaflet. The protocols developed for the supported lipid systems were adapted for the preparation of asymmetric liposomes. Biotinylated asymmetric liposomes were used as a model system to demonstrate the principle of heat-activated targeting of asymmetric liposomes to streptavidin-coated surfaces. More biologically relevant interaction was utilized to replace the biotin-streptavidin function, where asymmetric cationic liposomes were binding to anionic supported membrane immobilized surfaces upon heating. The described strategies for assembly of asymmetric supported membranes provide a guide to the development of multifunctional drug carriers. The protocols used in experiments with supported membranes were readily adapted to the preparation of asymmetric liposomes. The ongoing study tests the asymmetric liposomes in vitro, which is designed to demonstrate hyperthermia treatment can enhance accumulation of liposomes in FaDu cells, and at the same time activate release of the encapsulated components. The results of in vitro tests can be used to analyze the feasibility of utilizing the asymmetric liposomes as a platform in vivo to explore further improvement in their functions upon microwave hyperthermia.
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| 2. |
- Söderlund, Zackarias
(author)
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Engineering the extracellular matrix to model diseases and orchestrate regeneration
- 2023
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Doctoral thesis (other academic/artistic)abstract
- The extracellular matrix is not only a scaffold to which cells attach, but it is also a matrix that communicates cell signals. Because of the interplay between cells and the extracellular matrix, changes in the extracellular matrix can steer cell fate. This opens up the opportunity to design and engineer the extracellular matrix to communicate changes to the cells. Thus, this thesis has focused on understanding which parameters and signals influence cells, but also on how to utilise this knowledge to engineer a completely defined extracellular matrix. The extracellular matrix can be modulated in several ways, such as cell attachment, degradation properties, porosity, stiffness as well as being easily functionalised with molecules of interest using click chemistry.Two of the papers in this thesis focus on the development of new tools for glycosaminoglycan research to get a better understanding of how this can be modulated to steer cell signalling. Glycosaminoglycans bind growth factors, which can then either act as a co-receptor to increase the potency of the growth factor or to protect the growth factors from being broken down or inactivated. The tools that we have developed open the possibility to better study the production of glycosaminoglycans from different types of cells and better understand what changes occur in glycosaminoglycan synthesis during disease.The second two papers in this thesis focus on understanding the extracellular matrix. Article number one focuses on the effect of different extracellular matrices and stretch on cells and their secretome. Article number two, which has been the focus of this thesis, utilises the new findings in the other articles about glycosaminoglycans and the extracellular matrix to create a synthetic and defined extracellular matrix. This extracellular matrix is modified with glycosaminoglycans to have a slow release of growth factors to instruct cells to differentiate both in vitro and in vivo.
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| 3. |
- Khorshidi, Mohammad Ali, 1981-
(author)
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Live Single Cell Imaging and Analysis Using Microfluidic Devices
- 2013
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Doctoral thesis (other academic/artistic)abstract
- Today many cell biological techniques study large cell populations where an average estimate of individual cells’ behavior is observed. On the other hand, single cell analysis is required for studying functional heterogeneities between cells within populations. This thesis presents work that combines the use of microfluidic devices, optical microscopy and automated image analysis to design various cell biological assays with single cell resolution including cell proliferation, clonal expansion, cell migration, cell-cell interaction and cell viability tracking. In fact, automated high throughput single cell techniques enable new studies in cell biology which are not possible with conventional techniques.In order to automatically track dynamic behavior of single cells, we developed a microwell based device as well as a droplet microfluidic platform. These high throughput microfluidic assays allow automated time-lapse imaging of encapsulated single cells in micro droplets or confined cells inside microwells. Algorithms for automatic quantification of cells in individual microwells and micro droplets are developed and used for the analysis of cell viability and clonal expansion. The automatic counting protocols include several image analysis steps, e.g. segmentation, feature extraction and classification. The automatic quantification results were evaluated by comparing with manual counting and revealed a high success rate. In combination these automatic cell counting protocols and our microfluidic platforms can provide statistical information to better understand behavior of cells at the individual level under various conditions or treatments in vitro exemplified by the analysis of function and regulation of immune cells. Thus, together these tools can be used for developing new cellular imaging assays with resolution at the single cell level.To automatically characterize transient migration behavior of natural killer (NK) cells compartmentalized in microwells, we developed a method for single cell tracking. Time-lapse imaging showed that the NK cells often exhibited periods of high motility, interrupted with periods of slow migration or complete arrest. These transient migration arrest periods (TMAPs) often overlapped with periods of conjugations between NK cells and target cells. Such conjugation periods sometimes led to cell-mediated killing of target cells. Analysis of cytotoxic response of NK cells revealed that a small sub-class of NK cells called serial killers was able to kill several target cells. In order to determine a starting time point for cell-cell interaction, a novel technique based on ultrasound was developed to aggregate NK and target cells into the center of the microwells. Therefore, these assays can be used to automatically and rapidly assess functional and migration behavior of cells to detect differences between health and disease or the influence of drugs.The work presented in this thesis gives good examples of how microfluidic devices combined with automated imaging and image analysis can be helpful to address cell biological questions where single cell resolution is necessary.
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| 4. |
- Sun, He
(author)
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Antibiotic resistance in biogas processes
- 2021
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Doctoral thesis (other academic/artistic)abstract
- Anaerobic digestion (AD) is a well-established technology that can play a key role in development of a sustainable society. In AD, organic wastes such as animal manure, food waste and crop residues are used as substrate and converted to biogas and digestate, which represent green energy and a biofertiliser. Due to intensive use of veterinary antibiotics, antibiotic residues, antibiotic-resistant bacteria (ARB), antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) enter the AD process via the substrates and end up in the digestate. Thus, digestate may represent a source of spread of antibiotic resistance. Antibiotic resistance is one of the greatest global public health challenges of our time and is predicted to cause around 300 million premature deaths by 2050, so countering its spread is critically important. However, research on the antibiotic resistance level in AD is still quite limited. This thesis contributed essential new knowledge by a) identifying ARB communities in digestates originating from food waste, crops and dairy manure; b) assessing antibiotic resistance in plant-based substrates; c) investigating phenotypic and genotypic resistance pattern and resistance transferability of isolated ARB; and d) comparing molecular and culture-dependent methods in evaluation of antibiotic resistance. Bacillus and closely-related genera such as Paenibacillus and Lysinibacillus were found to dominate the ARB community isolated from digestate, irrespective of substrate type. Most ARGs identified for these ARB were located on chromosomes, although several ARB strains had extra-chromosomal genomes. Only one was identified as a plasmid (pAMαl), which proved to be nontransferable in plasmid conjugation testing. Thus, the dominant ARB community from the digestates studied likely poses a limited risk of antibiotic resistance spread, although even plant-based substrates were found to contain variant antibiotic resistance components. Combined use of molecular and culturedependent methods was required to reveal the true antibiotic resistance situation in the AD process.
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| 5. |
- Syed, Zulfeqhar Ali
(author)
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Mucin-like proteins in Drosophila development
- 2014
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Doctoral thesis (other academic/artistic)abstract
- Mucins are large and highly glycosylated proteins and major component of the mucus that coats the lining of epithelial organs. Mucins are characterized by the presence of extended regions rich in the amino acids Proline, Threonine and Serine (PTS domain), where the Serines and Threonines are O-glycosylated to form sugar-rich mucin domains. Mucins are classified into secreted gel-forming mucins and transmembrane mucins with possible signaling functions. The amino acid sequence of the PTS domains tends to be poorly conserved between species and different mucins. The goal of this thesis was to identify and study potential mucin-like proteins in Drosophila melanogaster. We devised a simple bioinformatic approach and developed a program that can identify PTS domains based on amino acid content. We thereby identified 36 mucins and mucin-related proteins. All proteins appear to be secreted, except for two that harbor a predicted transmembrane domain. Expression analysis at different stages of the Drosophila life cycle revealed that many mucins are expressed in the larval gut, consistent with a function in mucosal barrier formation. Interestingly, some of the mucins showed dynamic expression in different tubular organs during embryogenesis. Among these was Mur96B/Tenectin (Tnc) that was further studied to dissect its role in epithelial organ development. We found that Tnc is critical for diameter expansion of the developing hindgut. Tnc forms a transient matrix that fills the hindgut lumen and drives expansion in a dose-dependent manner, presumably by generating a luminal pressure. This study revealed a new mechanism in organ development, whereby the extent of lumen volume expansion can be regulated by the accumulation of single glycoprotein. In parallel to the bioinformatic approach, we identified a Drosophila protein that shares conserved domains with human SUSD2 and the non-mucin parts of human MUC4, called Mesh. We aimed to analyze Mesh function as a means to address the roles of these domains. Mesh was found to be is expressed in the digestive tract epithelium from mid-embryogenesis and throughout larval and adult life, localizing to the apical junction belt. Mesh is required for correct organization of the Scribble-complex, a main polarity complex conserved between fly and mammals, to prevent excess expansion of apical cell surface and for microvilli organization. The results demonstrate that mucin-like proteins, containing the PTS domains or other mucin-related domains, are essential for epithelial organ development in Drosophila.
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| 6. |
- Matar, Amal
(author)
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Considering a Baby? Responsible Screening for the Future : Ethical and social implications for implementation and use of preconception expanded carrier screening in Sweden
- 2019
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Doctoral thesis (other academic/artistic)abstract
- Preconception expanded carrier screening is a novel technology that involves the offer of a screening test for many recessive diseases (via an expanded screening panel) to prospective parents, with no priori risk. Test positive couples have a number of reproductive choices; prenatal diagnosis and aborting affected fetus, IVF and preimplantation genetic diagnosis, sperm or ovum donation or simply accept the risk. The test had been piloted in studies and can potentially be implemented in Europe. Therefore, it seemed pertinent to evaluate stakeholders’ perspectives on ethical and social implications of implementing and using preconception ECS in Sweden.Two main stakeholders were examined; healthcare professionals and health policymaking experts, via a mix of qualitative methods for data collection and data analysis. In Study I, we employed in-depth interviews to collect data and content analysis to analyze it. In Studies III and IV, expert interviews were used to gather data while thematic analysis was utilized to interpret it. Furthermore, in Study II, an ethical concept namely; reproductive autonomy, was critically discussed within a setting that expects a couple to make a conjoint reproductive decision about preconception ECS, while each partner still upholds his or her individual autonomy.The main findings of the empirical studies (Studies I, III and IV) echo to a great extent the prevailing ethical and social debates associated with the novel technology. Respondents expressed concerns with reproductive autonomy, medicalization, prioritization of health resources, discrimination and long term societal changes. Furthermore, respondents emphasized the importance to observe Swedish values, such as human dignity, equality and solidarity, when assessing a preconception ECS program. In addition, they described practicalities of implementation and political considerations that are pertinent to the Swedish context. Finally, some respondents recognized the advantages of reduced suffering and decrease in fetal anomalies and abortion as a consequence of preconception ECS.Study II, proposed a notion of couple autonomy, where certain demands if met, a couple’s reproductive decision can be accepted by healthcare staff as autonomous.The findings, in this thesis, steer towards non implementation of preconception ECS in its current status within the publicly-funded healthcare system in Sweden. This is because healthcare providers and experts were of the opinion that it would not solve a medical need, threaten Swedish values and use up resources extensively.
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| 7. |
- Halling Linder, Cecilia, 1975-
(author)
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Biochemical and functional properties of mammalian bone alkaline phosphatase isoforms during osteogenesis
- 2016
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Doctoral thesis (other academic/artistic)abstract
- The human skeleton is a living and dynamic tissue that constantly is being renewed in a process called bone remodeling. Old bone is resorbed by osteoclasts and new bone is formed by osteoblasts. Bone is a composite material made up by mineral crystals in the form of hydroxyapatite (calcium and phosphate) that provides the hardness of bone, and collagen fibrils that provides elasticity and flexibility. Alkaline phosphatase (ALP) is a family of enzymes that is present in most species and catalyzes the hydrolysis of various phosphomonoesters at alkaline pH. Despite the generalized use of ALP as a biochemical marker of bone formation, the precise function of bone ALP (BALP) is only now becoming clear. Three circulating human BALP isoforms (B1, B2, and B/I) can be distinguished in healthy individuals and a fourth isoform (B1x) has been discovered in patients with chronic kidney disease and in bone tissue.Paper I. Three endogenous phosphocompounds, (i.e., inorganic pyrophosphate (PPi), pyridoxal 5′-phosphate (PLP) and phosphoethanolamine (PEA)), have been suggested to serve as physiological substrates for BALP. The BALP isoforms display different catalytic properties towards PPi and PLP, which is attributed to their distinct N-linked glycosylation patterns. The catalytic activity, using PEA as substrate, was barely detectable for all BALP isoforms indicating that PEA is not a physiological substrate for BALP.Paper II. Mouse serum ALP is frequently measured and interpreted in mammalian bone research. However, little is known about the circulating ALPs in mice and their relation to human ALP. We characterized the circulating and tissue-derived mouse ALP isozymes and isoforms from mixed strains of wild-type and knockout mice. All four BALP isoforms (B/I, B1x, B1, and B2) were identified in mouse serum and bone tissues, in good correspondence with those found in human bones. All mouse tissues, except liver, contained significant ALP activities. This is a notable difference as human liver contains vast amounts of ALP.Paper III. The objective of this study was to investigate the binding properties of human collagen type I to human BALP, including the two BALP isoforms B1 and B2, together with ALP from human liver, human placenta and E. coli. A surface plasmon resonance-based analysis showed that BALP binds stronger to collagen type I in comparison with ALPs expressed in non-mineralizing tissues. The B2 isoform binds significantly stronger to collagen type I in comparison with the B1 isoform, indicating that glycosylation differences in human ALPs are of crucial importance for protein–protein interactions with collagen type I.Paper IV. Tartrate-resistant acid phosphatase (TRAP) is highly expressed in osteoclasts and frequently used as a marker of bone resorption. Intriguingly, recent studies show that TRAP is also expressed in osteoblasts and osteocytes. TRAP displays enzymatic activity towards the endogenous substrates for BALP, i.e., PPi and PLP. Both TRAP and BALP can alleviate the inhibitory effect of osteopontin on mineralization by dephosphorylation, which suggests a novel role for TRAP in skeletal mineralization.
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| 8. |
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| 9. |
- André, Oscar
(author)
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Data-driven microscopy: placing high-fidelity data in a population-wide context
- 2023
-
Doctoral thesis (other academic/artistic)abstract
- Mikroskopi är idag ett fundamentalt verktyg inom forskning, där det tillåter oss att skåda in och utforska våra prover i hög detalj. Mycket utav utvecklingen av nya mikroskopimetoder har strävat efter att öka den detaljnivå vi kan uppnå. Samtidigt har utvecklingen inom hårdvara, med tillgång till bättre och mer kraftfulla instrument, lett till utveckligen av metoder där fokuset är att studera en hel population av celler. Till skillnad från när vi studerar ett fåtal celler i hög detalj, tillåter det oss att sätta perspektiv på det vi ser. Det ger oss en förmåga att säga vad det normala beteendet som man kan förvänta sig är, och vilka celler som sticker ut i en population. Med andra ord, vad som är intressant.Samtidigt finns det ett stort intresse av att veta hur varje individuell cell beter sig. Varje cell är, precis som oss människor, unik. De har olika historia, olika ålder och befinner sig i olika tillstånd. Precis som våra celler i kroppen är unika, är även de cellerna som kan orsaka sjukdom unika. För att förstå varför vissa personer är mer känsliga mot sjukdom, och hur en infektion svarar på våra behandlingar behövs en förståelse och an förmåga att studera celler på individuell nivå, samtidigt som vi bibehåller ett perspektiv utifrån populations-nivå.Denna brist på perspektiv har länge varit ett problem inom mikroskopi. Den vanliga lösningen på detta problem är att vi, som människor, kan tolka en bild och peka på vad det är som är intressant eller inte. Vi är, trots allt, extremt duktiga på att tolka visuell information. Men detta är inte en helt felfri lösning. Som människor kan vi vara relativt okonsekventa, vi tolkar oftast utifrån hur vi vill att datan ser ut. Med andra ord, vi saknar förmågan att vara objektiva i vår metodik för att samla in bilder i hög detalj.Min avhandling har till stor del handlat om att utveckla ett verktyg som tillåter oss att sätta perspektiv på det vi studerar med mikroskopi. Detta har lett till Arbete 1, där vi presenterar en allmän strategi (data-styrd mikroskopi) för hur vi kan arbeta med mikroskopi för att samla in data på en hel population, samtidigt som vi kan samla in data med hög detalj på relevanta fynd i populationen. Vi presenterar även här en teknisk lösning, och utför metoden i tre olika scenarion: ett för att studera en population av celler mer allmänt, ett för att fånga det ögonblick som bakterier infekterar mänskliga celler, och ett där vi studerar och fångar in data på relevanta (från ett populations-kontext) cancerceller och följer dem över tid. Denna metod tillåter oss att samla in data i hög detalj på ett objektivt sätt, och att sätta perspektiv på det vi studerar.I Arbete 2 har vi vidare utvecklat på vår metod, där vi försöker lösa problemet att hitta en och samma cell i flera olika mikroskop. Eftersom vi, genom mikroskopi, jobbar på en så ofantligt liten skala, är det oftast väldigt svårt att orientera sig och hitta rätt inom ett prov. Det är lite som att spela På spåret och gissa vart man är, fast utan alla ledtrådar man får på varje nivå. Eftersom vi har tillgång till data på en hel population, så utgick vi från att det borde finnas samband mellan celler och deras grannar i ett prov som är unika för just dem. Genom att använda sig av dessa unika samband kom vi fram med en lösning där vi snabbt kan kalibrera ett prov på ett nytt mikroskop. Det öppnar dörrarna för oss forskare att återanvända prov, att lättare justera provet med nya markörer (för det vi vill visualisera inom cellerna), och att kunna tolka ett prov med data insamlat från flera system.COVID-19 pandemin var en stor omställning för samhället och vården. Likväl var det en stor omställning för många forskningslabb, där en kapplöpning startade för att så snabbt som möjligt förstå sig på hur viruset fungerar och hur vårt immunförsvar svarar på dess infektion. Det var i detta kontext som mitt tredje arbete utfördes. Genom den erfarenhet jag samlat på mig inom mikroskopi och att analysera bilder på stora dataset, bidrog jag med hjälp för att studera hur framtagna antikroppar kan förhindra bindningen av virus-lika partiklar till celler. Antikroppar är ett protein som immunförsvaret producerar i respons mot en patogen. En bättre förståelse kring hur antikroppar verkar, och vad skillnaden mellan en bra och en dålig antikropp är kan leda till framtagningen av bättre vaccin-program och behandlingar inom sjukvården.I Arbete 4 medverkade jag i ett arbete där bakterien Streptococcus pyogenes var i fokus. S. pyogenes enda värd är människor, och ansvarar för över 600 miljoner infektionsfall per år globalt. På bakteriens yta dominerar ett protein, M-proteinet, ett multi-funktionellt protein som bakterien (bland annat) använder sig för att binda till ytor och förhindra immunförsvarets förmåga att göra sig av med bakterien. I arbetet upptäckte vi att fibronektin binder till bakterien (specifikt M-proteinet) olika mycket beroende på mängden antikroppar som finns i miljön. Fibronektin är ett protein som vi människor producerar, och bidrar (bland annat) till att skapa den miljön som celler befinner sig i. Mängden fibronektin varierar beroende på var i kroppen man kollar. Till exempel, i saliv har du en relativt låg mängd fibronektin jämfört med i blodet. Detta ledde till hypotesen att bakterien är special-anpassad för olika miljöer i dess förmåga att undkomma immunförsvaret. En bättre förståelse kring hur bakterien är anpassad till våra olika miljöer och dess infektionsförlopp kan leda till bättre och mer anpassade behandlingar inom sjukvården.
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| 10. |
- Cavallaro, Sara, 1992-
(author)
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Development of Techniques for Characterization, Detection and Protein Profiling of Extracellular Vesicles
- 2021
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Doctoral thesis (other academic/artistic)abstract
- Nanosized extracellular vesicles (EVs, ∼30-2000 nm) have emerged as important mediators of intercellular communication, offering opportunities for both diagnostics and therapeutics. In particular, small EVs generated from the endolysosomal pathway (∼30-150 nm), referred to as exosomes, have attracted interest as a suitable biomarker for cancer diagnostics and treatment monitoring based on minimally invasive liquid biopsies. This is because exosomes carry valuable biological information (proteins, lipids, genetic material, etc.) reflecting their cells of origin. Using EVs as biomarkers or drug delivery agents in clinical applications requires a full understanding of their cellular origin, functions, and biological relevance. However, due to their small size and very high heterogeneity in molecular and physical features, the analysis of these vesicles is challenged by the limited detection ranges and/or accuracy of the currently available techniques. To overcome some of these challenges, this thesis focuses on developing different techniques for characterization, detection and protein profiling of EVs at both bulk and single particle levels. Specifically, the three methods investigated are scanning electron microscopy, electrokinetic sensing, and combined fluorescence - atomic force microscopy. First, a protocol for scanning electron microscopy imaging of EVs was optimized to improve the throughput and image quality of the method while preserving the shape of the vesicles. Application of the developed protocol for analysis of EVs from human serum showed the possibility to use scanning electron microscopy for morphological analysis and high-resolution size-based profiling of EVs over their entire size range. Comparison with nanoparticle tracking analysis, a commonly used technique for EV size estimation, showed a superior sensitivity of scanning electron microscopy for particles smaller than 70-80 nm. Moreover, the study showed process steps that can generate artifacts resembling sEVs and ways to minimize them. Secondly, a novel label-free electrokinetic sensor based on streaming current was developed, optimized and multiplexed for EV protein analysis at a bulk level. Using multiple microcapillary sensors functionalized with antibodies, the method showed the capacity for multiplexed detection of different surface markers on small EVs from non-small-cell lung cancer cells. The device performance in the multichannel configuration remained similar to the single-channel one in terms of noise, detection sensitivity, and reproducibility. The application of the technique for analysis of EVs isolated from lung cancer patients with different genomic alterations and after different applied treatments demonstrated the prospect of using EVs from liquid biopsies as a source of biomarker for cancer monitoring. Moreover, the results held promise for the application of the developed method in clinical settings. Finally, to increase the understanding of EV subpopulations and heterogeneity, a platform combining fluorescence and atomic force microscopy was developed for multiparametric analysis of EVs at a single particle level. The use of a precise spot identification approach and an efficient vesicle capture protocol allowed to study and correlate for the first time the membrane protein composition, size and mechanical properties (Young modulus) on individual small EVs. The application of the technique to vesicles isolated from different cell lines identified both common and cell line-specific EV subpopulations bearing distinct distributions of the analyzed parameters. For example, a sEV population co-expressing all the three analyzed proteins in relatively high abundance, yet having average diameters of <100 nm and relatively low Young moduli was found in all cell lines. The obtained results highlighted the possibility of using the developed platform to help decipher unsolved questions regarding EV biology.
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