| 1. |
- Meyer, René, et al.
(författare)
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Heterogeneous kinetics of AKT signaling in individual cells are accounted for by variable protein concentration
- 2012
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Ingår i: Frontiers in Physiology. - : Frontiers Media SA. - 1664-042X. ; 3:451
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Tidskriftsartikel (refereegranskat)abstract
- In most solid cancers, cells harboring oncogenic mutations represent only a sub-fraction of the entire population. Within this sub-fraction the expression level of mutated proteins can vary significantly due to cellular variability limiting the efficiency of targeted therapy. To address the causes of the heterogeneity, we performed a systematic analysis of one of the most frequently mutated pathways in cancer cells, the phosphatidylinositol 3 kinase (PI3K) signaling pathway. Among others PI3K signaling is activated by the hepatocyte growth factor (HGF) that regulates proliferation of hepatocytes during liver regeneration but also fosters tumor cell proliferation. HGF mediated responses of PI3K signaling were monitored both at the single cell and cell population level in primary mouse hepatocytes and in the hepatoma cell line Hepa1_6. Interestingly, we observed that the HGF mediated AKT responses at the level of individual cells is rather heterogeneous. However, the overall average behavior of the single cells strongly resembled the dynamics of AKT activation determined at the cell population level. To gain insights into the molecular cause for the observed heterogeneous behavior of individual cells, we employed dynamic mathematical modeling in a stochastic framework. Our analysis demonstrated that intrinsic noise was not sufficient to explain the observed kinetic behavior, but rather the importance of extrinsic noise has to be considered. Thus, distinct from gene expression in the examined signaling pathway fluctuations of the reaction rates has only a minor impact whereas variability in the concentration of the various signaling components even in a clonal cell population is a key determinant for the kinetic behavior.
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| 2. |
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| 3. |
- Bodvard, Kristofer, 1981, et al.
(författare)
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Continuous light exposure causes cumulative stress that affects the localization oscillation dynamics of the transcription factor Msn2p.
- 2011
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Ingår i: Biochimica et biophysica acta. - : Elsevier BV. - 0006-3002. ; 1813:2, s. 358-366
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Tidskriftsartikel (refereegranskat)abstract
- Light exposure is a potentially powerful stress factor during in vivo optical microscopy studies. In yeast, the general transcription factor Msn2p translocates from the cytoplasm to the nucleus in response to illumination. However, previous time-lapse fluorescence microscopy studies of Msn2p have utilized a variety of discrete exposure settings, which makes it difficult to correlate stress levels and illumination parameters. We here investigate how continuous illumination with blue light, corresponding to GFP excitation wavelengths, affects the localization pattern of Msn2p-GFP in budding yeast. The localization pattern was analyzed using a novel approach that combines wavelet decomposition and change point analysis. It was found that the Msn2p nucleocytoplasmic localization trajectories for individual cells exhibit up to three distinct and successive states; i) Msn2p localizes to the cytoplasm; ii) Msn2p rapidly shuttles between the cytoplasm and the nucleus; iii) Msn2p localizes to the nucleus. Many cells pass through all states consecutively at high light intensities, while at lower light intensities most cells only reach states i) or ii). This behaviour strongly indicates that continuous light exposure gradually increases the stress level over time, presumably through continuous accumulation of toxic photoproducts, thereby forcing the cell through a bistable region corresponding to nucleocytoplasmic oscillations. We also show that the localization patterns are dependent on protein kinase A (PKA) activity, i.e. yeast cells with constantly low PKA activity showed a stronger stress response. In particular, the nucleocytoplasmic oscillation frequency was found to be significantly higher for cells with low PKA activity for all light intensities.
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| 4. |
- Kvarnström, Mats, 1974, et al.
(författare)
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Brownian dynamics simulations in hydrogels using an adaptive time-stepping algorithm
- 2009
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Ingår i: Physical Review E. - 2470-0045 .- 2470-0053. ; 79:1, s. 16102-
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Tidskriftsartikel (refereegranskat)abstract
- The adaptive time-stepping algorithm for Brownian simulation of solute diffusion in three-dimensional complex geometries previously developed by the authors of this paper was applied to heterogeneous three-dimensional polymer hydrogel structures. The simulations were performed on reconstructed three-dimensional hydrogels. The obstruction effect from the gel strands on water and diffusion of dendrimers with different sizes were determined by simulations and compared with experimental nuclear magnetic resonance diffusometry data obtained from the same material. It was concluded that obstruction alone cannot explain the observed diffusion rates, but an interaction between the dendrimers and the gel strands should be included in the simulations. The effect of a sticky-wall interaction potential with geometrically distributed residence times on the diffusion rate has been studied. It was found that sticky-wall interaction is a possible explanation for the discrepancy between simulated and experimental diffusion data for dendrimers of different sizes diffusing in hydrogels.
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| 5. |
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| 6. |
- Kvarnström, Mats, 1974, et al.
(författare)
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Estimation of centres and radial intensity profiles of spherical nano-particles in digital microscopy
- 2007
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Ingår i: Biometrical Journal. - : Wiley. - 0323-3847 .- 1521-4036. ; 49:2, s. 300-311
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Tidskriftsartikel (refereegranskat)abstract
- Control of the microscopic characteristics of colloidal systems is critical in a wealth of application areas, ranging from food to pharmaceuticals. To assist in estimating these characteristics, we present a method for estimating the positions of spherical nano-particles in digital microscopy images. The radial intensity profiles of particles, which depend on the distances of the particles from the focal plane of the light microscope and have no closed functional form, are modelled using a local quadratic kernel estimate. We also allow for the case where pixel values are censored at an upper limit of 255. Standard errors of centre estimates are obtained using a sandwich estimator which takes into account spatial autocorrelation in the errors. The approach is validated by a simulation study.
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| 7. |
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| 8. |
- Kvarnström, Mats, 1974, et al.
(författare)
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Image analysis algorithms for cell contour recognition in budding yeast
- 2008
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Ingår i: Optics Express. - 1094-4087 .- 1094-4087. ; 16:17, s. 12943-12957
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Tidskriftsartikel (refereegranskat)abstract
- Quantification of protein abundance and subcellular localization dynamics from fluorescence microscopy images is of high contemporary interest in cell and molecular biology. For large-scale studies of cell populations and for time-lapse studies, such quantitative analysiscan not be performed effectively without some kind of automated image analysis tool. Here, we present fast algorithms for automatic cell contour recognition in bright field images, optimized to the model organismbudding yeast (Saccharomyces cerevisiae). The cell contours can be used to effectively quantify cell morphology parameters as well as protein abundance and subcellular localization from overlaid fluorescence data.
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| 9. |
- Kvarnström, Mats, 1974, et al.
(författare)
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Laplace moving average model for multi-axial responses applied to fatigue analysis of a cultivator
- 2013
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Ingår i: Probabilistic Engineering Mechanics. - : Elsevier BV. - 0266-8920 .- 1878-4275. ; 34, s. 12-25
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Tidskriftsartikel (refereegranskat)abstract
- Modeling of loads on a vehicle through Laplace moving averages is extended to the multivariate setting and efficient methods of computing the damage indexes are discussed. Multivariate Laplace moving averages are used as statistical models of multi-axial loads represented by forces and moments measured at some locations of a cultivator. As opposed to models based on the Gaussian distribution, these models account explicitly for transients that have a common origin—vibrations that can be caused by large obstacles encountered by a cultivator or a vehicle driving into potholes. The model is characterized by a low number of parameters accounting for fundamental characteristics of multivariate signals: the covariance matrix representing size of loads and their mutual dependence, the excess kurtosis that in the model is related to relative size of transients, and the time scale that accounts for the vehicle speed. These parameters can be used to capture diversity of environmental conditions in which the vehicle operates. Distributions of parameter values that are specific to a given market or encountered by specific customers can be then used to describe the long term loading. The model is validated by analysis of the resulting damage index. It is shown that the parameters enter this index in a multiplicative and explicit manner and, for a given damage exponent, only the factor representing dependence on the kurtosis has to be obtained through regression approximation based on Monte Carlo simulations. An example of actual cultivator data is used to illustrate the accuracy of damage and fatigue life prediction.
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