Natrium-kaliumpumpen spelar en väsentlig roll i en rad fysiologiska funktioner då den upprätthåller den elektrokemiska gradienten över cellmembranet. Ytterligare så är störningar i dess funktion associerade med flera neurologiska sjukdomar. Proteinet är en heterodimer av α– och β–subenheter, ibland även associerat med en tredje γ (FXYD) subenhet, vilket gör det problematiskt att studera dess högre ordningens organisation i cellmembranet med hjälp av konventionella, relativt storskaliga inmärkiningsprober såsom antikroppar. Inkorporering av icke-kanoniska aminosyror är ett nyutvecklat och växande område som erbjuder en lösning. Genom CuAAC– och SPIEDAC–klickkonjugationsreaktioner kan organiska färgämnen (fluoroforer) snabbt och specifikt fästas i sidokedjor med motsvarande reaktiva grupper på jonpumpen, vilket skapar en liten och icke-invasiv inmärkningsprob för fluorescensmikroskopi. För att specifikt studera alla tre subenheter samtidigt krävs inmärkning med tre olika fluoroforer). Syftet med detta projekt var att lyckas med trefärgsinmärkning genom inkorporering av icke-kanoniska aminosyror, och därigenom underlätta studerandet av hur natrium-kaliumpumpens subenheter ordnar sig i cellmembranet. Transient transfekterade HEK293T-celler med membraninmärkta jonpumpar studerades med hjälp av fluorescensmikroskopi, vilket kompletterades med gelfluorescensavbildning och immunoblotting. Samtidigt gjordes proteinuttryck och tvåfärgsinmärkning av alla nonsenskodonmuterade subenheter i kombination med varandra och var synlig i proteingel, där endast α och β tidigare hade samuttryckts. α/γ parinmärkning visade sig framgångsrik när de samtransfekterades med β av vildtyp. En autofluorescenseffekt i en av färgkanalerna påverkade resultaten för mikroskopin. Trefärgsinmärkning observerades inte i gelen, och uttrycket av subenheterna (varav α var ersatt för detta experiment) var i stort sett obefintligt. Otydlighet består därmed huruvida trefärgsinmärkning eller trippelsamuttryck är möjligt med de bioortogonala translationssystemen som användes i detta projekt på jonpumpen. / Na+/K+-ATPase is an essential ion pump protein in a host of physiological functions as it maintains the electrochemical gradient across cell membranes. Additionally, its dysfunction is implicated in several neurological diseases. The protein is a heterodimer of α and β subunits, occasionally associated with a third γ (FXYD) subunit, which makes studying its higher order organization in the cell membrane difficult using conventional, relatively large scale labeling probes such as antibodies. Non-canonical amino acid incorporation is an emerging field which offers a solution. Via CuAAC and SPIEDAC click conjugation reactions, organic fluorophores can be specifically attached to the side chains of residues of the ion pump with corresponding reactive moieties, creating a small and noninvasive probe for fluorescence microscopy imaging. In order to specifically image all three subunits concurrently, three color labeling is required. The objective of this project was to achieve three color labeling via non-canonical amino acid incorporation to aid in the study of the cell membrane localization of the subunits of Na+/K+-ATPase. Fluorescence microscopy of transiently transfected and live cell labeled HEK293T cells was complemented by in gel fluorescence imaging and immunoblotting. Coexpression and two color labeling of all nonsense codon subunit mutants in combination was shown in gel, of which only α and β had previously been coexpressed. α/γ dual labeling proved successful when cotransfected with wild type β. An autofluorescent effect in one of the color channels compromised the microscopy results. Three color labeling was not observed in gel, and expression of the subunits (including a substitute for α) was middling to absent. It remains unclear whether three color labeling or triple coexpression is a possibility with the bioorthogonal translation systems used in this project.

In biology, it is common to study cultured cells (in vitro) with fluorescence time-lapse microscopy. The cells are recorded for longer period of time and can later be viewed at an accelerated speed. During the acquisition some live cells tend to migrate. This can be a problem if the cell’s migration speed is high enough to move outside the field of view (FOV) during the acquisition time. The cells that moves outside the FOV can no longer be recorded and the information about them will be lost. This thesis presents scripts that have been developed for ZEN (blue) to be able to track a specific migrating cell of interest in real-time with automated control of imaging parameters. The microscope stage position is modified on-the-fly to have the tracked cell in the center of the FOV for the whole experiment. Three different types of experiments to track migrating NK cells were performed with the scripts. The results show that the scripts were able to track one NK cell for more than 1 hour in both conventional wide-field and lattice light-sheet microscopy. The segmentation was inaccurate when one or more objects were in close proximity to the tracked cell. By applying a watershed algorithm the segmentation result can be improved in some cases. / Inom cellulär biologi är det vanligt att studera odlade celler (in vitro) med time- lapse-mikroskopi. Flertals bilder tas på cellerna under en längre tidsperiod och när experimentet är klart så kan man titta på bilderna som en video. Under förvärvet av bilderna så tenderar vissa levande celler att migrera. Ett problem som kan uppstå är om cellens migrationshastighet är tillräckligt hög för att röra sig utanför synfältet under anskaffningstiden. De celler som rör sig utanför synfältet kan inte längre avbildas och informationen om dem kommer att gå förlorad. I denna avhandling presenteras programmeringskoder som har utvecklats för ZEN (blue) som kan spåra en specifik migrerande cell i realtid med automatiserad kontroll av bildbehandlings parametrar. Mikroskopets scenposition modifieras under experimentets gång för att få den spårade cellen kontinuerligt i mitten av synfältet. Tre olika sorters experiment i kombination med programmeringskoderna utfördes för att spåra NK-celler. Resultaten visar att programmeringskoderna lyckades spåra en NK-cell i mer än 1 timme i både ett bredfältsfluorescensmikroskop och ett lattice light-sheet mikroskop. Segmenteringen var felaktig när ett eller flera objekt var i närheten av den spårade cellen. Genom att tillämpa en watershed algoritm kan segmenteringsresultatet förbättras i vissa fall.

<p dir="ltr">The beautiful complexity of our world is manifested in how macro- and even planetary-scale processes are essentially completely determined and regulated by chemical and physical transformations happening at the micro- and nanoscale. The introduction and subsequent development of optical microscopy methods have provided us with a unique opportunity to visualize, probe, and sometimes even control these processes that are too small to be seen by the human eye by their nature.</p><p dir="ltr">Among the great variety of truly impressive advances in microscopy instrumentation, two techniques stand out in their widespread and usefulness. First of them, fluorescence imaging has completely revolutionized the study of biological specimens and living systems due to its unprecedented single-molecule sensitivity and resolution combined with video-rate imaging capability. On the other hand, chemical imaging in the mid-infrared region provides an unmatched amount of chemical information enabling label-free mapping of the spatial distribution of various classes of biological molecules. However, each of these techniques falls short where the other excels. For example, despite its high resolution and sensitivity, fluorescence imaging does not carry direct chemical information and relies on labeling specificity, while infrared microscopy is diffraction-limited at the resolution of several micrometers and suffers from low penetration depth in aqueous solutions.</p><p dir="ltr">This dissertation introduces a novel imaging method designed to combine the advantages of fluorescence imaging and infrared spectroscopy. Fluorescence-detected photothermal mid-IR (F-PTIR) microscopy is presented in <b>chapter 1</b> as a technique enabling sub-diffraction chemically-specific microscopy by detecting local temperature-induced fluctuations in fluorescence intensity to inform on localized mid-infrared absorption. F-PTIR applications in targeted biological microspectroscopy (<b>chapter 1</b>) and pharmaceutical materials (<b>chapters 2 and 3</b>) analysis are demonstrated to highlight the potential of this new method. Furthermore, instrumentation developments relying on modern radiation sources such as dual-comb quantum cascade laser and synchrotron infrared radiation are shown to improve spectral acquisition speed (<b>chapter 4</b>) and spectral coverage (<b>chapter 5</b>), respectively, to extend the application range of F-PTIR.</p>

Проведено исследование цитотоксического действия синтезированных препаратов платины на нормальные клетки человека и различные линии опухолевых клеток. Выполнена оценка фрагментации ДНК методом электрофореза. Исследована целостность цитоплазматической мембраны клеток, подверженных действию препаратов платины. Выявлено наиболее перспективное соединение платины как возможный субстрат для разработки фармацевтических препаратов для лечения онкологических заболеваний. / Within the framework of this work, reviews of the literature on tumor cells and methods of combating malignant neoplasms, including those using platinum preparations, are collected. A study was made of the cytotoxic effect of the synthesized platinum preparations on normal human cells and various tumor cell lines. DNA fragmentation was studied by electrophoresis. A study was made of the integrity of the cytoplasmic membrane of cells exposed to platinum preparations. The most promising platinum compound has been identified as a possible substrate for the development of pharmaceutical preparations for the treatment of oncological diseases.

No description available.

No description available.

Die Durchflusszytometrie und Fluoreszenzmikroskopie sind zentrale Techniken zur Analyse von Zellen, Geweben und Organen. Besonders in der Immunologie werden sie zur Identifizierung und Charakterisierung von Biomolekülen mittels fluoreszenzmarkierter Antikörper verwendet. Fluoreszenzmarker müssen je nach Anwendung hohe Helligkeit, geringe Größe und minimierte Löschung des Signals aufweisen. Stark markierte Konstrukte leiden jedoch oft unter Fluoreszenzlöschung oder großen Molekularmassen. Diese Arbeit untersucht verzweigtes Polyethylenglykol (PEG) als Träger für Fluorophore. PEG-Ketten wurden als räumliche Trennmittel identifiziert und an Aminodextran gekoppelt, wodurch hochgradig multimerisierte Fluorophor-PEG-Dextran-Zwischenprodukte entstanden. Diese Konjugate, gekoppelt mit Antikörpern, zeigen hohe Fluoreszenzintensität und wurden bei der Detektion von CAR SUP-T1-Zellen erfolgreich eingesetzt. PEG-basierte Reagenzien durchdringen jedoch oft die Zellmembran nicht, was für intrazelluläre Ziele und größere Gewebe wichtig ist. Sequentielle Multiplex-Analysen sind durch unvollständige Spaltung und Restsignale problematisch. Deshalb wurden synthetische Peptide als Rückgrat für die Fluorophor-Multimerisierung untersucht. Diese Konstrukte, verbunden mit Nanokörpern, zeigten erhöhte Helligkeit und Gewebepenetration in der Lichtblattmikroskopie von Mausorganen. Zudem wurde ein dualer Entfernungsmechanismus in die REAdyelease-Technologie integriert. Basierend auf Oligonukleotiden, Disulfiden oder Peptiden in Kombination mit Aminodextran konnte eine schnellere Signalreduktion ermöglicht werden. Dies wurde in der Konfokalmikroskopie an einer Pankreastumorzelllinie demonstriert. / Flow cytometry and fluorescence microscopy are crucial for analyzing cells and tissues, especially in immunology, where immunofluorescence is used for identifying, visualizing, and characterizing biomolecules with fluorescently labeled antibodies. These labels must meet various requirements: high brightness, small size, and the ability to be rendered non-fluorescent. However, highly labeled constructs often suffer from fluorescence self-quenching or high molecular masses, limiting their effectiveness. This work demonstrates that branched polyethylene glycol (PEG) serves as an efficient fluorophore multimerization platform for protein labeling. I explored factors critical for preventing fluorophore self-quenching in multi-fluorophore systems. Fluorescent PEGs were multimerized on an amino-dextran scaffold, generating highly multimerized fluorophore-PEG-dextran intermediates. When conjugated to antibodies, these intermediates allowed bright labeling of biomarkers on cells and tissues and were successfully used in detecting CAR SUP-T1 cells. Despite their strengths, PEG-based reagents often lack deep tissue penetration, essential for intracellular targets and 3D organ imaging. To enhance tissue penetration, I designed small peptide-based backbones for fluorophore multimerization. These constructs, coupled with nanobodies, produced homogeneous fluorescent conjugates that quickly penetrated mouse organs and enabled bright staining in light-sheet microscopy. The final part of the thesis focuses on synthesizing labels for cyclic immunofluorescence. I addressed the issue of incomplete label removal by creating erasable conjugates with two release sites. Fluorescent conjugates based on oligonucleotides, disulfides, or peptides combined with amino-dextran can be rapidly erased from labeled epitopes using a dual-release approach. This method was demonstrated in confocal microscopy and used for iterative imaging of biomarkers on a sample of a pancreatic tumor cell line.

Indiana University-Purdue University Indianapolis (IUPUI) / Advancements in human genomics have simultaneously enhanced our basic understanding of the human body and ability to combat debilitating diseases. Historically, research has shown that there have been many hindrances to realizing this medicinal revolution. One hindrance, with particular regard to the kidney, has been our inability to effectively and routinely delivery genes to various loci, without inducing significant injury. However, we have recently developed a method using hydrodynamic fluid delivery that has shown substantial promise in addressing aforesaid issues. We optimized our approach and designed a method that utilizes retrograde renal vein injections to facilitate widespread and persistent plasmid and adenoviral based transgene expression in rat kidneys. Exogenous gene expression extended throughout the cortex and medulla, lasting over 1 month within comparable expression profiles, in various renal cell types without considerably impacting normal organ function. As a proof of its utility we by attempted to prevent ischemic acute kidney injury (AKI), which is a leading cause of morbidity and mortality across among global populations, by altering the mitochondrial proteome. Specifically, our hydrodynamic delivery process facilitated an upregulated expression of mitochondrial enzymes that have been suggested to provide mediation from renal ischemic injury. Remarkably, this protein upregulation significantly enhanced mitochondrial membrane potential activity, comparable to that observed from ischemic preconditioning, and provided protection against moderate ischemia-reperfusion injury, based on serum creatinine and histology analyses. Strikingly, we also determined that hydrodynamic delivery of isotonic fluid alone, given as long as 24 hours after AKI is induced, is similarly capable of blunting the extent of injury. Altogether, these results indicate the development of novel and exciting platform for the future study and management of renal injury.

The intimate relationship between the higher-order chromatin organisation and the regulation of gene expression is increasingly attracting attention in the scientific community. Thanks to high-resolution microscopy, genome-wide molecular biology tools (3C, ChIP-on-chip), and bioinformatics, detailed structures of chromatin loops, territories, and nuclear domains are gradually emerging. However, to fully reveal a comprehensive map of nuclear organisation, some fundamental questions remain to be answered in order to fit all the pieces of the jigsaw together. The underlying mechanisms, precisely organising the interaction of the different parts of chromatin need to be understood. Previous work in our lab hypothesised and verified the “transcription factory” model for the organisation of mammalian genomes. It is widely assumed that active polymerases track along their templates as they make RNA. However, after allowing engaged polymerases to extend their transcripts in tagged precursors (e.g., Br-U or Br-UTP), and immunolabelling the now-tagged nascent RNA, active transcription units are found to be clustered in nuclei, in small and numerous sites we call “transcription factories”. Previous work suggested the transcription machinery acts both as an enzyme as well as a molecular tie that maintains chromatin loops, and the different classes of polymerases are concentrated in their own dedicated factories. This thesis aims to further characterise transcription factories. Different genes are transcribed by different classes of RNA polymerase (i.e., I, II, or III), and the resulting transcripts are processed differently (e.g., some are capped, others spliced). Do factories specialise in transcribing particular subsets of genes? This thesis developed a method using replicating minichromosomes as probes to examine whether transcription occurs in factories, and whether factories specialise in transcribing particular sets of genes. Plasmids encoding the SV40 origin of replication are transfected into COS-7 cells, where they are assembled into minichromosomes. Using RNA fluorescence in situ hybridisation (FISH), sites where minichromosomes are transcribed are visualised as discrete foci, which specialise in transcribing different groups of genes. Polymerases I, II, and III units have their own dedicated factories, and different polymerase II promoters and the presence of an intron determine the nuclear location of transcription. Using chromosome conformation capture (3C), minichromosomes with similar promoters are found in close proximity. They are also found close to similar endogenous promoters and so are likely to share factories with them. In the second part of this thesis, I used RNA FISH to confirm results obtained by tiling microarrays. Addition of tumour necrosis factor alpha (TNF alpha) to human umbilical vein endothelial cells induces an inflammatory response and the transcription of a selected sub-set of genes. My collaborators used tiling arrays to demonstrate a wave of transcription that swept along selected long genes on stimulation. RNA FISH confirmed these results, and that long introns are co-transcriptionally spliced. Results are consistent with one polymerase being engaged on an allele at any time, and with a major checkpoint that regulates polymerase escape from the first few thousand nucleotides into the long gene.

Maîtriser l’impact des maladies sur les cultures est un défi majeur de l’agriculture moderne. Cette préoccupation est un aspect important de l’optimisation de la productivité, notamment en viticulture. En France, le mildiou de la vigne causé par Plasmopara viticola est une des maladies cryptogamiques responsable des épidémies les plus dévastatrices et les plus redoutées. Les traitements reposent sur l’utilisation préventive, systématique et onéreuse de composés chimiques antifongiques dont l’utilisation massive constitue un risque à la fois pour l’homme et l’environnement. La réduction de l’utilisation de fongicide implique le développement d’outils de diagnostic au champ, qui requiert la compréhension des interactions entre la plante et les agents pathogènes. Les travaux de cette thèse pluridisciplinaire ont porté sur le pathosystème Plasmopara viticola - Vitis vinifera, notamment pour répondre à l’intérêt croissant pour un outil de diagnostic en temps réel de la maladie utilisable au vignoble. Les stilbènes sont des phytoalexines impliqués dans la défense de certaines plantes supérieures vis-à-vis de stress biotiques et abiotiques. L’autofluorescence de ces composés phénoliques, dont la biosynthèse est induite dans les feuilles de vigne par P. viticola, en fait un potentiel marqueur naturel de l’infection. En effet, la faible autofluorescence bleu-verte des feuilles de vigne saines est considérablement renforcée par l’autofluorescence violet-bleue des stilbènes à la surface de feuilles de vigne infectée par P. viticola. Cette étude a montré que quelque soit le niveau de résistance du génotype, l’autofluorescence violet-bleue des stilbènes induit par l’infection est présente au niveau des parois des cellules de l’épiderme. En dehors de la concentration, la viscosité s’est révélé être la principale variable physico-chimique influençant l’intensité de l’autofluorescence des stilbènes dans les différents compartiments cellulaires des feuilles de vigne. Ceci explique la fluorescence intense des parois, particulièrement rigides, des cellules de garde (stomates) des feuilles infectées. Le suivi cinétique journalier a révélé la nature transitoire de l’autofluorescence des stilbènes lors de l’infection. La robustesse et l’intérêt de ce signal a également été validée par la mesure à différentes échelles (de la cellule à la feuille entière) et avec différentes méthodes fluorimétriques. Les résultats de ce travail ont permis des avancées sur la connaissance du rôle de composés phénoliques induits et constitutifs dans la défense contre P. viticola. En plus de la localisation de l’autofluorescence des stilbènes en surface des feuilles, la microscopie confocale couplée à la microspectrofluorimetrie a révélé différentes localisations de ces phytoalexines dans la profondeur des tissus en corrélation avec le niveau de résistance des génotypes. L’utilisation de l’autofluorescence des stilbènes comme marqueur de l’infection a permis de mettre en évidence : 1) le fait que les flavonols constitutifs des feuilles de V. vinifera retardent le développement de l’infection par P. viticola; et 2) le fait que les acides hydroxycinnamiques constitutifs ne semble pas participer à la défense contre P. viticola. Enfin, une nouvelle méthode de diagnostic non-destructive du mildiou sur feuille basée sur l’autofluorescence des stilbènes a été développée. Elle a montré une détection pré-symptomatique du mildiou sur les feuilles de vigne entières dès le premier jour après l’infection sur la face abaxiale et le troisième jour sur la face adaxiale. Cette méthode de diagnostic du mildiou a été validée au laboratoire notamment grâce à un prototype de capteur proximal développé en collaboration avec la société Force-A. La validation de la méthode au vignoble dans le cadre d’infection naturelle est la prochaine étape pour une utilisation de ce capteur optique dans le cadre de l’agriculture durable et de la sélection variétale. / Controlling the impact of diseases on crops is a major challenge of modern agriculture. This concern is an important aspect of optimizing productivity, notably in viticulture. In France, downy mildew caused by Plasmopara viticola is a fungal disease responsible for the most devastating epidemics. The preventive and systematic treatments are expensive, while the massive use of antifungal chemicals is a risk to both humans and the environment. Reducing the use of fungicide involves the development of diagnostic tools in the field, which requires understanding the interactions between plants and pathogens. The work of this multidisciplinary thesis focused on the pathosystem Plasmopara viticola - Vitis vinifera, especially to meet the growing interest in a real-time diagnostic tool of disease applicable in the vineyard. Stilbenes are phytoalexins involved in the defense of certain higher plants against biotic and abiotic stresses. The autofluorescence of these phenolic compounds, whose biosynthesis is induced in grapevine leaves by P. viticola, makes it a potential marker of natural infection. Indeed, the low blue-green autofluorescence of grapevine leaves is greatly enhanced by the violet-blue autofluorescence of stilbenes on the surface of leaves infected by P. viticola. This study showed that whatever the level of resistance in various genotypes, violet-blue autofluorescence induced by stilbene is present in the walls of epidermal cells. In addition to their concentration, viscosity proved the main physico-chemical variable affecting the intensity of the autofluorescence of stilbenes in different compartments of vine leaves. This explains the intense fluorescence of the walls, particularly rigid, of guard cells (stomata) of infected leaves. Daily monitoring revealed a kinetic with a transient rise of the autofluorescence of stilbenes during infection. The robustness and value of this signal was also validated by measuring at different levels (cellular to whole leaf) and with various fluorimetric methods (imaging, spectroscopy, proximal sensing). These results advance our understanding of the role of constitutive and induced phenolic compounds in plant defence against P. viticola. In addition to a common location of the autofluorescence of stilbenes on the leaf surface, confocal microscopy coupled with microspectrofluorometry revealed distinctive localizations of these phytoalexins in the deep tissue correlated with the level of resistance in genotypes. This aspect no doubt needs broader testing. The use of autofluorescence of stilbene as a marker of infection allowed us to ascertain that: 1) constitutive flavonols of the leaves of V. vinifera retard the development of infection by P. viticola and 2) the constitutive hydroxycinnamic acids do not seem to participate in the defence against P. viticola. Finally, a new method for the non-destructive diagnosis of leaf infection based on the autofluorescence of stilbenes has been developed. We have demonstrated a pre-symptomatic detection of downy mildew on whole grape leaves from the first day after infection on the abaxial surface and from the third day on the adaxial surface. This method of diagnosis has been validated in the laboratory thanks to a proximal sensor prototype developed in collaboration with the company Force-A. The validation of the method in the vineyard in a context of natural infections is the next step for use of this optical sensor as a tool for sustainable agriculture and for genetic screening.