| 1. |
- 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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| 2. |
- Tapani, Sofia, 1982, et al.
(författare)
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Joint feedback analysis modeling of nonesterified fatty acids in obese zucker rats and normal sprague-dawley rats after different routes of administration of nicotinic acid
- 2014
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Ingår i: Journal of Pharmaceutical Sciences. - : Elsevier BV. - 0022-3549 .- 1520-6017. ; 103:8, s. 2571-2584
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Tidskriftsartikel (refereegranskat)abstract
- Data were pooled from several studies on nicotinic acid (NiAc) intervention of fatty acid turnover in normal Sprague-Dawley and obese Zucker rats in order to perform a joint PKPD of data from more than 100 normal Sprague-Dawley and obese Zucker rats, exposed to several administration routes and rates. To describe the difference in pharmacodynamic parameters between obese and normal rats, we modified a previously published nonlinear mixed effects model describing tolerance and oscillatory rebound effects of NiAc on nonesterified fatty acids plasma concentrations. An important conclusion is that planning of experiments and dose scheduling cannot rely on pilot studies on normal animals alone. The obese rats have a less-pronounced concentration-response relationship and need higher doses to exhibit desired response. The relative level of fatty acid rebound after cessation of NiAc administration was also quantified in the two rat populations. Building joint normal-disease models with scaling parameter(s) to characterize the "degree of disease" can be a useful tool when designing informative experiments on diseased animals, particularly in the preclinical screen. Data were analyzed using nonlinear mixed effects modeling, for the optimization, we used an improved method for calculating the gradient than the usually adopted finite difference approximation.
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| 3. |
- Tapani, Sofia, 1982
(författare)
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Stochastic modelling and analysis of early mouse development
- 2011
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The aim of this thesis is to model and describe dynamical events for biological cells using statistical and mathematical tools. The thesis includes five papers that all relate to stochastic modelling of cells. In order to understand the development and patterning of the early mammalian embryo, stochastic modelling has become a more important tool than ever. It allows for studying the processes that mediate the transition from pluripotency of the embryonic cells to their differentiation. It is still unclear whether the positions of cells determine their future fates. One alternative possibility is that cells are pre-specified at random positions and then sort according to a already set fate. Mouse embryonic cells are thought to be equivalent in their developmental properties until approaching the eight-cell stage. Some biological studies show, in comparison, that patterning can be present already at sperm entry and in the pronuclei migration. We investigate in Paper I the dynamics of the pronuclei migration by analysing their trajectories and find that not only do the pronuclei follow a noise corrupted path towards the centre of the egg but they also have some attraction to each other which affects their dynamics. Continuing in Paper II and III, we use these results to model this behaviour with a coupled stochastic differential equation model. This enables us to simulate distributions that describe the meeting plane between pronuclei which in turn can be related to the orientation of the first cleavage of the egg. Our results show that adding randomness in sperm entry point is different from the randomness added through the environment of the egg. We are also able to show that data sets with normal eggs and eggs treated with an actin growth inhibitor give rise to considerably different model dynamics, suggesting that the treatment is affecting the migration in an invasive way. Altering the pronuclei dynamics can alter the polarity of the egg and may transfer into the later axis-formation process. Invasiveness of experimental procedures is a difficult issue to handle. The alternative to invasive procedures is not appealing since it means that important developmental features may not be discovered because of individual variability and noise, leading to guesswork of the underlying mechanisms. The embryonic cells are easily affected by treatments performed to make the measuring, made by hand, easier or by the light exposure of the microscope. Treatments as such are used for example for producing flourescent proteins in membranes or slowing processes down. Paper IV and Paper V serve to analyse how light induced stress affects yeast cells and we employ a method for analysing the noisy non-stationary time series, which are a result of the yeast experiments, using wavelet decomposition.
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| 4. |
- Tapani, Sofia, 1982
(författare)
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Three dimensional mathematical modelling of pronuclei migration for the mouse
- 2009
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Licentiatavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The main question addressed in this thesis is what happens between the moment when the sperm enters the egg and the fusion of the male and the female pronuclei. Orientation of the apposing pronuclei most likely plays a decisive role in the polarity of the developing embryo. The migration and the dependence between the pronuclei have been investigated through three different measures of correlation. It was concluded that a measure based on the projection of the movement onto the axis between the pronuclei’s centres was preferred. Two mathematical models that describe the pronuclei dynamics have been constructed in the form of stochastic differential equations. The models concern pronuclei migration from the time of the sperm entry to the fusion and spatial orientation of this fusion. First, a basic model was created. This was then developed into a refined model. The methodology consists of using stacks of confocal microscopy time-lapse images of the pronuclei migration together with statistical methods to identify realistic parameters in the models. Given different angles between the sperm entry and the position of the second polar body, the final models are then used to produce distributions of orientations of the meeting positions between the pronuclei. However, the main result is the suggested models themselves which describe the main features of the migration. The basic fitted model is based on two forces of attraction. Migration is directed towards the centre but also towards the other pronucleus. Parameter values corresponding to the size of these forces are estimated from data of both eggs treated with a microtubule inhibitor and untreated eggs. The refined model is also based on centring and attraction to the other pronucleus, but the centring is modelled into two mechanisms of pushing and pulling of the microtubule exerted forces. Simulated distributions from the models could for instance be used as initial value distributions for future models of egg cleavage.
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| 5. |
- Tapani, Sofia, 1982, et al.
(författare)
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Three dimensional mathematical modelling of pronuclei migration for the mouse
- 2009
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Ingår i: Stereology and Image Analysis. Ecs10: Proceeding of the 10th European Conference of ISS., (V.Capasso et al. Ed.), The MIRIAM Project Series. - 9788874883103 ; 4, s. 1-6
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Konferensbidrag (refereegranskat)abstract
- It is still an open question when the orientation of the embryonic-abembryonic axis of the mouse embryo is laid down. The two most explicit symmetry breaking events for the egg are the extrusion of the second polar body and the sperm entry. The main question addressed in this paper is what happens between the sperm entering the egg and fusion of the two pronuclei. Orientation of the apposing pronuclei probably plays a decisive role in the polarity of the developing embryo. In order to shed some lights on this intriguing question, a mathematical model that describes the pronuclei dynamics have been constructed in the form of a stochastic differential equation. The model concerns pronuclei migration from the time of the sperm entry to the fusion and spatial orientation of this fusion. The methodology consists of using stacks of confocal microscopy time-lapse images of the pronuclei migration together with statistical methods to identify realistic parameters in the model. Given different angles between the sperm entry and the position of the second polar body, the final model is then used to produce distributions of orientations of the meeting positions between the pronuclei. However, the main result is the suggested model itself which describes the main features of the migration. The fitted model is based on two forces of attraction. Migration is directed towards the centre but also towards the other pronucleus. Parameter values corresponding to the size of these forces are estimated from data of both eggs treated with a microtubule inhibitor and untreated eggs. Simulations from the model with the different model parameters are accomplished and distributions of meeting positions are plotted. These simulated distributions could for instance be used as initial value distributions for future models of egg cleavage.
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