Intracellular pH was monitored at the cytosolic surface of plasma membrane solute transporters (Na+/H+/nucleoside co-transporters, or Cl-/HCO3- exchangers), using pH-sensitive fluorescent proteins (FPs), dual emission green FP (deGFP4) and a monomeric red FP Nectarine (mNect), whose development and characterization are also reported here. Human concentrative nucleoside transporter, hCNT3, mediates Na+/H+/nucleoside co-transport. We describe a new approach to monitor H+/uridine co-transport in HEK293 cells. pH changes at the intracellular surface of hCNT3 were monitored by fusing mNect to the cytoplasmic N-terminus of hCNT3 (mNect.hCNT3) or an inactive hCNT3 mutant (mNect.hCNT3-F563C). Cells were incubated at the permissive pH for H+-coupled nucleoside transport, pH 5.5, under both Na+-free and Na+-containing conditions. In mNect.hCNT3-expressing cells (but not under negative control conditions) the rate of acidification increased in media containing 0.5 mM uridine, providing the first direct evidence for H+-coupled uridine transport. At pH 5.5, there was no significant difference in uridine transport rates (coupled H+ flux) in the presence or absence of Na+. This suggests that in acidic Na+-containing conditions, 1 Na+ and 1 H+ are transported/uridine molecule, while in acidic Na+-free conditions, 1 H+ alone is transported/uridine. In acid environments, including renal proximal tubule and intestine, H+/nucleoside co-transport may drive nucleoside accumulation by hCNT3. Microdomains, discrete regions of altered cytosolic solute concentration, are enhanced by rapid solute transport and slow diffusion rates. pH-regulatory membrane transporters, like the Cl-/HCO3- exchanger AE1, could nucleate H+ microdomains, since AE1 has a rapid transport rate and cytosolic H+ diffusion is slow. As AE1 drives Cl-/HCO3- exchange, differences in pH, near and remote from AE1, were monitored simultaneously by deGFP4 fused to AE1 (deGFP4.AE1) and mNect.hCNT3-F563C. deGFP4.AE1-mNect.hCNT3-F563C distance was varied by co-expression of different amounts of the two proteins in HEK293 cells. As the deGFP4.AE1-mNect.hCNT3-F563C distance increased, mNect.hCNT3-F563C detected the cytosolic pH change with a time delay and reduced rate of pH change, compared to deGFP4.AE1. Carbonic anhydrase activity was essential for H+ microdomain formation. H+ diffusion along the plasma membrane was 60-fold slower than to the cytosolic ER-surface. During physiological HCO3- transport, a H+ microdomain 0.3 µm in diameter develops around AE1, which will affect nearby pH-sensitive processes.

The human gammaherpesviruses EBV and KSHV realize their oncogenic potential during latent infection. The species specificity of the human gammaherpesviruses has hindered the study of latency in animal models. Murine gammaherpesvirus MHV-68 (MHV-68) may be used as a representative gammaherpesvirus for the study of latency. The goal was to establish an in vitro model of MHV-68 latency using replication defective MHV-68. ORF50 has been identified as the major viral trans-activator essential for entry into the lytic replication cycle and necessary and sufficient for reactivation of MHV-68 virus from latency. ORF50 null mutants (A50) can theoretically be used to infect cells in vitro to facilitate an analysis of virus gene expression and episome maintenance during latency. In this project A50 mutants containing the luciferase or green fluorescence protein (GFP) under OW50 promoter control were used to infect a variety of cell types. 3T3 fibroblasts are a permissive cell line and were used for an initial characterization of the ability of A50 MHV-68 to establish latency. B lymphocytes and macrophages are the major reservoirs of persistence in vivo thus the ability of A50 mutants to establish latency in NSO B and RAW macrophage cell lines was explored. Latency was readily established and maintained in 3T3 and RAW cells. The low infectability of NSO B- cells restricted the utility of this cell line in studies of latency. Examination of patterns of lytic and latent transcription in 3T3 and RAW cells coordinately infected with A50 MHV-68 revealed reactivation efficiencies of 40-60%. Following long-term passage A50 exhibited stable transcription of two latency related genes M2 and ORF73, with episomal maintenance of the viral genome, in the absence of contaminating lytic infection. The results demonstrate the utility of A50 mutants for studies of gammaherpesvirus latency in vivo.

Levels of macromolecules fluctuate both spatially and temporally in individual cells. Such heterogeneity could be exploited for bet hedging in uncertain environments, or be suppressed by negative feedback if perturbations are deleterious. For the master stress-response regulator in Escherichia coli, RpoS, both of these scenarios have been suggested. RpoS levels are also exceedingly low and controlled by the ClpXP protease, which reportedly displays extreme spatial heterogeneity. However, little is known quantitatively about RpoS dynamics. This is partly because no functional protein fusions exist, but also because the quantitative tools for studying fluctuations and localizations are limited, particularly ones that can be independently validated. Here I develop such methods and begin applying them to RpoS. Protein localization measurements increasingly rely on fluorescent protein fusions and are difficult to verify independently. I designed a non-intrusive method for validating localization patterns in live bacterial cells by exploiting post-division heterogeneity in downstream processes. Applying this assay to the ClpXP protease, widely reported to form biologically relevant foci, revealed in fact that the protease molecules are not specifically localized inside cells, as confirmed by four independent methods. I further evaluated 20+ commonly used fluorescent reporters and found that many cause severe mislocalization when fused to homo-oligomers, likely due to avidity effects. Further reinvestigating other foci-forming proteins strongly suggests that the previously reported foci were all caused by the fluorescent proteins used. For mRNAs – which are often present in low numbers per cell and major sources of non-genetic heterogeneity – existing single-cell assays have unknown accuracy: the experimental counting errors could completely over-shadow the natural variation. I therefore optimized and cross-evaluated two single-molecule mRNA detection methods. Several problems were identified and solutions discussed. I succeeded in building a functional RpoS protein fusion, and used bulk methods to show that the RpoS feedback loop is effectively not operating during exponential- phase growth. Mathematical analyses and initial experiments in a microfluidic device further suggest that the RpoS system has several unusual properties contributing towards extremely fast stress response. A stochastic analysis further suggests that the RpoS feedback loop cannot suppress spontaneous fluctuations, and preliminary experiments indicate that large deviations might indeed play important roles.

No description available.

No description available.

No description available.

Uveal melanoma is the most common primary malignant intraocular tumour in adults and despite advances in treatment of the primary tumour, the 10-year survival rate remains unchanged. The most frequent cause of death for patients of this disease is liver metastases. Removal of the primary tumour before clinical presentation of metastases, however, has no effect on patient outcome. / In order to understand the interactions between single malignant cells or sub-clinical metastases and affected organs, we have successfully developed a novel animal model of uveal melanoma. We utilized the unique properties of green fluorescent protein, a skin-flap in vivo imaging technique, and nude mice to accomplish this goal. The precision of green fluorescent protein imaging has allowed us to observe single cells interacting with organ tissues and reveal that these malignant cells are only capable of surviving in the liver.

Colleotrichum graminicola is the causal agent of anthracnose stalk rot, and is one of the most common and aggressive pathogens of maize. The goal of my Ph.D. project was to contribute to a better understanding of the biology of the interaction between C. graminicola and its host. C. graminicola produces two type of asexual spores: one is produced on the surface of infected tissues and is thought to be involved in the spread of the disease in the field. The second type of spore, oval in shape, is produced inside the infected plant tissues, and was believed to be involved in the movement of the pathogen inside the plant tissues via the vascular system. I tested this hypothesis with both cytological and molecular approaches. I used strains of C. graminicola expressing green fluorescent proteins (GFP) to inoculate wounded plants, and followed the development of the pathogen over time. This study revealed that C. graminicola is not a vascular pathogen. C. graminicola primarily moved through the rind and vascular fibers. Oval spores were produced in colonized parenchyma cells and remained dormant, and did not appear to be involved in the movement of the pathogen, at least during the early stages of the disease development. I also studied pathogen ingress in the absence of a wound. I inoculated unwounded plants with the GFP expressing strains. C. graminicola efficiently colonized the epidermis and, given enough time, penetrated and colonized the deeper parenchyma tissues, after first moving through the fibers. To further test the role of sporulation in colonization of maize tissues, I used targeted mutagenesis to disrupt a major gene known to regulate sporulation and vegetative growth in several other fungi. The gene Cgg1, orthologue of the A. nidulans fadA, was disrupted using the split marker method. The Cgg1 mutants were less pathogenic than the wildtype to wounded plants. This was associated with an apparent increase in production of spores and primary infection hyphae. This suggests that Cgg1 signaling pathway plays a role in maximizing colonization of host tissues, and that this involves negative regulation of sporulation and primary hyphae production in planta.

Diss. (sammanfattning) Stockholm : Karolinska institutet, 2007. / Härtill 4 uppsatser.

La microscopie de super-résolution PALM (microscopie de localisation après photo-activation) est un outil performant pour l'étude des cellules à l'échelle nanométrique. Dans ses applications avancées, la microscopie PALM permet l'étude quantitative et dynamique des objets et événements biologiques. Ces applications sont cependant limitées par le comportement photophysique complexe des protéines fluorescentes photoconvertibles vert à rouge (PCFPs) utilisées comme marqueurs. En particulier, les transitions répétées et stochastiques des PCFPs entre un état sombre et un état fluorescent (scintillement) ainsi que l'incomplétude de photoconversion compliquent l'extraction d'informations quantitatives.Nos travaux combinant cristallographie aux rayons X des protéines et microscopie de localisation ont permis de mettre en évidence le rôle central d'un acide aminé conservé au sein des PCFPs, l'arginine 66, dans le contrôle du scintillement et du photoblanchiment de la forme rouge de deux PCFPs populaires: mEos2 et Dendra2.D'autre part, des résultats préliminaires suggèrent que dans leur formes vertes et dans les conditions d'illumination classiques PALM, les PCFPs entrent dans un état sombre de long temps de vie ce qui ralentit la photoconversion.Nos résultats ouvrent la porte à la conception raisonnée de nouvelles PCFPs optimisées pour les applications quantitatives et dynamiques du PALM. / Super-resolution PALM microscopy (photoactivated localization microscopy) is a powerful tool to investigate the cells with nanoscopic accuracy. Advanced PALM microscopy allows to quantitatively and dynamically study biological objects and events. These applications are nevertheless limited by the complex photophysical behavior of the green-to-red photoconvertible fluorescent proteins (PCFPs) used as markers. In particular, PCFPs red forms repeated and stochastic transitions between a fluorescent and a dark state (blinking) as well as photoconversion uncompleteness complicate the extraction of quantitative information.Our study, by combining X-ray crystallography and localization microscopy, evidences that a single aminoacid well conserved among PCFPs, the arginine 66, controls the blinking and photobleaching behavior of two popular PCFPs: mEos2 and Dendra2.Preliminary results suggest that in their green forms and under PALM classical illumination conditions, PCFPs switch to a long-lived dark state resulting in a photoconversion slowing down.Our results open the door to future rational engineering of enhanced PCFPs for quantitative and dynamic PALM.