| 1. |
- Abdul-Hussein, Saba
(författare)
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Cellular studies of neuromuscular disorders related to the sarcomeric proteins
- 2012
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Sarcomere is the basic unit of cardiac and skeletal muscle contraction and its proper function requires an invariant organization of this structure. Mutations in sarcomeric proteins are known to cause increasing number of different cardiac and skeletal muscle diseases. The front line in research on muscle diseases is at present to define the genetic background and pathogenesis of these diseases. The potential for development of effective therapies depends on elucidation of the molecular and cellular impact of the mutations on morphological abnormalities and muscle weakness that accompany pathogenesis. In paper I we identified an unexpected skeletal muscle myopathy in an infant with fatal cardiomyopathy due to a homozygous mutation in MyBPC3. The ectopic expression of cardiac MyBPC was restricted to abnormal type 1 muscle fibres, indicating that the muscle pathology was caused by a dominate-negative effect of mutant MyBPC3. In paper II we addressed the expression profile of a panel of sarcomeric components during myogenesis, with a focus on proteins associated with a group of congenital disorders. The analyses were performed in cultured human skeletal muscle myoblasts and myotubes. We identified early expression of certain isoforms involved in congenital diseases, suggesting the possibility of an early role for these proteins as constituent of the developing contractile apparatus during myofibrillogenesis. In paper III we used human tissue-culture cells as a model to investigate the primary trigger for β-tropomyosin-related myopathies and the basis for the histological changes seen in muscle biopsies of patients. Protein localization and pathobiology caused by dominant TPM2 mutations were investigated by transfecting human myoblasts and C2C12 with WT and mutant EGFP-fusion β-TM constructs. Abnormal aggregation of β-TM variants and their localization within the thin filaments was observed in myoblasts and differentiated myotubes. We demonstrated that histopathological phenotypes associated with β-TM mutants might be accounted for the variable response to the cellular environment influenced by physiological context, in combination with the time course of expression of mutant protein rather than the alteration of amino acid itself. Our results confirmed that cell cultures of human skeletal muscle are an appropriate tool and environment closer to the reality in human skeletal muscle and more reliably mimic the disease conditions. In paper IV we identified and characterized a new human protein aggregate myopathy and cardiomyopathy associated with combined mutations in isogenes TRIM63 and TRIM54, encoding muscle specific ring finger proteins, MuRF1 and MuRF3, respectively. Our morphological and cellular investigation suggested that the disease is caused through impaired organization of the microtubule network and sarcomeric M-band proteins. The results from this study have deepened the understanding of pathogenesis of a group of sarcomeric
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| 2. |
- Abraham, Getahun Yacob
(författare)
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Education for Democracy? : Life Orientation: Lessons on Leadeship Qualities and Voting in South African Comprehensive Schools
- 2010
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- This study takes as its starting point how teachers understand, interpret and teach social development aspects of Life Orientation in South African comprehensive schools. The specific focus is on lessons on leadership qualities and voting for third grade learners in four schools, each dominated by either Black, Coloured, White or mixed groups of learners. Field work with an ethnographic approach and a qualitative strategy was used to gain access to empirical data. Policy and curriculum documents, guidelines and textbooks were used. Classroom observations in four classes and interviews with 14 third grade teachers were conducted. Theoretical concepts of construction, deconstruction and reconstruction are applied. Ulf P Lundgren’s Frame Factor Theory is used to study school organization. Basil Bernstein’s Pedagogical Devices are considered when examining the different levels of pedagogical activities. To be a teacher in South Africa one needs to attend at least two years of teacher education after completing high school. Teachers in the classes studied underwent their teacher education during apartheid years. Due to limited in-service training, they sometimes experience problems of understanding and interpreting the learning area, which they usually tackle by consulting documents, colleagues or school authorities. The learners’ understanding varied based on their family background and type of school they attended. There were enormous differences in material, financial and organisational resources between classes and schools. The resources for teaching leadership qualities and voting were not, however, different between the classes. The lessons were teacher dominated and direct transmission was used as a method. The way teachers facilitated the lesson on leadership qualities and voting varied but all showed some democratic shortcomings. Apart from answering questions, learners were neither invited nor encouraged to participate to further their understanding of the theme. Limited aspects of leadership qualities were discussed, individual leaders’ roles were emphasised and the teachers picked candidates for class leaders in three of the classes. It was also evident that the class environments were not suitable for critical or creative thinking and democratic upbringing. The schools reproduced norms, values, languages and cultures of the different groups. Officially, teachers emphasised the common national South African identity. This emphasis on national identity could disguise the injustice some groups experience in society.
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| 3. |
- Adriaenssens, Bart, 1979
(författare)
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Individual variation in behaviour: personality and performance of brown trout in the wild
- 2010
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Individuals from the same population often show very different behaviour. These differences, when consistent across time, are referred to as animal personality or behavioural syndromes. Explaining the occurrence of animal personality from an evolutionary perspective has however proven a difficult issue to tackle. This thesis studies aspects of individual behavioural variation and personality in brown trout (Salmo trutta). More specifically, I investigate (1) to what extent variation in behaviour is consistent within and across contexts, (2) environmental and genetic effects on behaviour, (3) how this affects performance in the wild, and (4) whether this understanding can be used to improve rearing methods of supplementary hatcheries. I found brown trout to express a wide variation of behaviours and provide evidence that much of this behavioural variation is associated in bigger behavioural syndromes. As a result, separate behaviours of brown trout cannot be considered as isolated units, but combine into clusters that sometimes are associated with non-behavioural measures such as body size or growth rate. Variation was further influenced by both inherited and environmental effects. First, individuals from different maternal and paternal origin differed in size, aggressiveness and response to novel prey or novel food. These results suggest that maternal and/or genetic effects influence behaviour and growth in brown trout (I). Second, reduced rearing densities in a hatchery increased the response to novel prey, food search ability in a maze and predator response (II). And third, hatchery trout were more successful foragers than wild conspecifics, yet showed less repeatable explorative behaviour across time (III). Personality traits were generally poor predictors of growth and survival upon release, suggesting that several behavioural strategies can be successful in nature. Nevertheless, in paper IV, slow exploring individuals grew faster than more bold trout. Furthermore, parr reared at reduced densities were twice as likely to survive in the stream as trout reared at high densities. In conclusion, my results contradict simple associations between risk taking behaviour and growth-mortality tradeoffs under natural conditions. This challenges the recent view that individual differences in growth strategies can explain variation in behaviour and suggests more heterogeneous links between personality and life-history in nature (V). In addition, I show that reduced rearing hatchery densities facilitate the development of adaptive behaviour in brown trout, a finding that may have implications for current rearing methods in supplementary hatcheries.
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| 4. |
- Ahlberg, Daniel, 1982
(författare)
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Asymptotics and dynamics in first-passage and continuum percolation
- 2011
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- This thesis combines the study of asymptotic properties of percolation processes with various dynamical concepts. First-passage percolation is a model for the spatial propagation of a fluid on a discrete structure; the Shape Theorem describes its almost sure convergence towards an asymptotic shape, when considered on the square (or cubic) lattice. Asking how percolation structures are affected by simple dynamics or small perturbations presents a dynamical aspect. Such questions were previously studied for discrete processes; here, sensitivity to noise is studied in continuum percolation. Paper I studies first-passage percolation on certain 1-dimensional graphs. It is found that when identifying a suitable renewal sequence, its asymptotic behaviour is much better understood compared to higher dimensional cases. Several analogues of classical 1-dimensional limit theorems are derived. Paper II is dedicated to the Shape Theorem itself. It is shown that the convergence, apart from holding almost surely and in L^1, also holds completely. In addition, inspired by dynamical percolation and dynamical versions of classical limit theorems, the almost sure convergence is proved to be dynamically stable. Finally, a third generalization of the Shape Theorem shows that the above conclusions also hold for first-passage percolation on certain cone-like subgraphs of the lattice. Paper III proves that percolation crossings in the Poisson Boolean model, also known as the Gilbert disc model, are noise sensitive. The approach taken generalizes a method introduced by Benjamini, Kalai and Schramm. A key ingredient in the argument is an extremal result on arbitrary hypergraphs, which is used to show that almost no information about the critical process is obtained when conditioning on a denser Poisson process.
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| 5. |
- Ahlberg Helgee, Ernst, 1981
(författare)
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Improving Drug Discovery Decision Making using Machine Learning and Graph Theory in QSAR Modeling
- 2010
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- During the last decade non-linear machine-learning methods have gained popularity among QSAR modelers. The machine-learning algorithms generate highly accurate models at a cost of increased model complexity where simple interpretations, valid in the entire model domain, are rare. This thesis focuses on maximizing the amount of extracted knowledge from predictive QSAR models and data. This has been achieved by the development of a descriptor importance measure, a method for automated local optimization of compounds and a method for automated extraction of substructural alerts. Furthermore different QSAR modeling strategies have been evaluated with respect to predictivity, risks and information content. To test hypotheses and theories large scale simulations of known relations between activities and descriptors have been conducted. With the simulations it has been possible to study properties of methods,risks, implementations and errors in a controlled manner since the correct answer has been known. Simulation studies have been used in the development of the generally applicable descriptor importance measure and in the analysis of QSAR modeling strategies. The use of simulations is spread in many areas, but not that common in the computational chemistry community. The descriptor importance measure developed can be applied to any machine-learning method and validations using both real data and simulated data show that the descriptor importance measure is very accurate for non-linear methods. An automated method for local optimization of compounds was developed to partly replace manual searches made to optimize compounds. The local optimization of compounds make use of the information in available data and deterministically enumerates new compounds in a space spanned close to the compound of interest. This can be used as a starting point for further compound optimization and aids the chemist in finding new compounds. An other approach to guide chemists in the process of optimizing compounds is through substructural warnings. A fast method for significant substructure extraction has been developed that extracts significant substructures from data with respect to the activity of the compound. The method is at least on par with existing methods in terms of accuracy but is significantly less time consuming. Non-linear machine-learning methods have opened up new possibilities for QSAR modeling that changes the way chemical data can be handled by model algorithms. Therefore properties of Local and Global QSAR modeling strategies have been studied. The results show that Local models come with high risks and are less accurate compared to Global models. In summary this thesis shows that Global QSAR modeling strategies should be applied preferably using methods that are able to handle non-linear relationships. The developed methods can be interpreted easily and an extensive amount of information can be retrieved. For the methods to become easily available to a broader group of users packaging with an open-source chemical platform is needed.
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| 6. |
- Ahlström, Aisling, 1976
(författare)
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Prediction of embryo viability by morphology and metabolomic profiling
- 2013
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Abstract The ultimate challenge for all in vitro fertilisation (IVF) clinics is to develop the ability to select for transfer the best single embryo first, from the patient’s cohort of embryos, thereby maximising the chance of pregnancy while the incidence of multiple pregnancies is kept to a minimum and fewer transfer cycles are required. This ambition has driven extensive research and development into methods that can be used to predict embryo viability. The aims of this thesis were to investigate two non-invasive methods; one new method of metabolomic profiling using Near Infrared (NIR) spectroscopy to analyse spent embryo culture media and the most routine method of morphological grading at the blastocyst stage. In our initial study we investigated metabolimic profiling by NIR spectroscopy and demonstrated that there were distinct differences between NIR spectral profiles of spent embryo culture media of implanting embryos and non-implanting embryos on day 5 of development. These differences were successfully used in a predictive model to calculate viability scores that were positively correlated (R2 = 0.82, P = 0.03) to implantation rates. In addition, viability scores were not related to morphology indicating that this method could be used as an adjunct to current morphological selection criteria. We also showed, by a method of cross-validation, that a predictive algorithm was accurate even when used at different clinics using different blastocyst culture media. These findings, in addition to other published studies, suggest that selection of embryos with high NIR viability scores could potentially improve implantation rates. Unfortunately, when the application of this technology was tested in a prospective randomized controlled trial (RCT) for selection of embryos on day 2 and day 5 for transfer, its use in adjunct to morphology did not significantly improve the ongoing pregnancy rate when compared to morphology alone (34.8% versus 35.6%, P = 0.97). As such, NIR spectroscopy, in its current form, did not improve selection of the most viable embryo for transfer. These results demonstrate the importance of performing RCT’s before committing to the clinical application of any new technology or treatment. We also investigated the independent predictive strength of morphological parameters used to predict blastocyst viability in both fresh and frozen-thawed cycles. We found through our retrospective studies looking at blastocyst morphology and prediction of live birth found that trophectoderm (TE) morphology was the most important predictor after fresh single blastocyst transfer cycles and one of the most important predictors after frozen thawed transfer cycles. Expansion grade was found to be the other most important predictor of live birth after frozen-thawed transfer cycles. The inner cell mass (ICM) in both studies was not shown to be one of the most significant predictors of live birth. We have shown, for the first time, the predictive strength of TE grade over ICM for selecting the best blastocyst for embryo replacement. It may be that, even though ICM is important, a strong TE layer is essential at this stage of embryo development, allowing successful hatching and implantation. Furthermore, we found that for thawed blastocysts degree of re-expansion was the most important post thaw morphological predictor of live birth. In conclusion, we have been able to show that morphology is a strong predictor of embryo viability and by understanding the predictive strength of each parameter being used in a grading system, we can better use these parameters when making our decisions. Furthermore, there is still a need for alternative methods to predict embryo viability, but these new methods should be validated in properly conducted studies before clinical implementation, as shown by the conflicting results in our two studies when testing the NIR technology platform.
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| 7. |
- Ahlström, Bodil, 1968
(författare)
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Structure, phase behavior, and dynamics of colloidal systems characterized by strong, short- and moderate-ranged attractions: a computational study
- 2010
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Attractions between colloidal particles are often so strong that non-equilibrium behavior results. However, dissolved non-adsorbing polymer can be added to give a weak attraction between particles so that equilibrium phase transitions appear at moderate polymer concentrations. At higher polymer concentrations and small polymer-colloid size ratios non-equilibrium effects like gelation occur, for which a complete understanding is lacking. Monte Carlo and Monte Carlo-like computer simulations have been used to investigate the role of many-body effects and the structures that colloidal particles adopt under influence of a polymer-induced depletion attraction. The phase diagram proves difficult to determine for these systems by direct application of the Gibbs ensemble Monte Carlo method, especially for small polymer-colloid size ratios that correspond to short-range attractions. However, a sequential equilibration scheme is shown be able to give equilibrated fluid-fluid coexistence data where usual application of the method fails. The dynamics of colloidal particles along this fluid-fluid coexistence curve is studied by a Brownian dynamics algorithm, corrected for the use of a large time step. The dynamics slows down as the particle and polymer concentrations are increased, but the systems appear to reach equilibrium for the cases studied. This is in contrast to what is found by applying mode coupling theory; it predicts glass-like transitions already at modest polymer concentrations for short-range attractive systems, which is an issue that is investigated to some extent. In addition, a number of approximate theories have been developed and tested against the results from the computer simulations.
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| 8. |
- Ahlström, Christine
(författare)
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Modelling of tolerance and rebound in normal and diseased rats
- 2011
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The development of rebound and tolerance is an important consideration when optimizing medical therapy, both with respect to drug dosing and adverse effects. By using quantitative approaches to study these processes, potential risks can be minimized. In this thesis nicotinic acid (NiAc)-induced changes in non-esterified fatty acids (NEFA) were used as a tool to investigate key determinants of tolerance and rebound in normal Sprague Dawley and in obese Zucker rats, a disease model of dyslipidaemia. The aim of the studies was to develop and challenge a model that described tolerance and rebound following different durations, rates and routes of NiAc administration. In normal rats, administration of NiAc resulted in a rapid decrease in NEFA plasma concentration, followed by rebound, the extent of which depended on both the level and duration of drug exposure. Rebound oscillations followed long duration of NiAc exposure. During constant drug exposure, increasing NEFA concentrations indicated tolerance development. The pharmacodynamic characteristics of NiAc-induced changes in NEFA differed in normal and diseased rats, with NEFA baseline concentrations being increased, rebound diminished, and tolerance develop¬ment more pronounced in the diseased animals. The non-intuitive pattern of NiAc-induced changes in NEFA was captured by a feedback model with a moderator distributed over a series of transit compartments, where the first compartment inhibited the formation of response and the last stimulated the loss of response. The model was based on mechanistic principles, mimicking the dual actions of insulin in inhibiting the hydrolysis of triglycerides to NEFA and glycerol, and stimulating the re-esterification of NEFA. In both the normal and diseased rats, the model described the pharmacodynamic characteristics adequately. The concentration-response relationship at steady state was shifted upwards and to the right, and was shallower, in diseased rats compared to normal rats. The extent of such shifts demonstrates the impact of disease at equilibrium in the system. These studies have shown that by eliciting different exposure patterns and taking into account both the washout dynamics of the administered drug and the pharmacodynamic characteristics of normal and diseased animals, a mechanistically-based feedback model was able to tease out important information about tolerance and rebound.
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| 9. |
- Ahlström, Katarina, 1966
(författare)
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Energy-metabolic aspects of ischemia and pre-treatment: studies in porcine myocardium
- 2011
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The focus of this thesis is to clarify mechanisms involved in protective pre-treatment of ischemia by carbon monoxide (CO) and ischemic preconditioning (IP), so that new pro-tective therapies can be designed. This is studied in heart muscle, where the clinical gain would ultimately be to be able to prolong the period during a threatened myocardial infarction where permanent injury can be prevented. The aim is to elucidate energy meta-bolic relations as a basis for temporary metabolic adaptation to threatened injury in heart muscle, with focus on the biological relevance of this mechanism. All studies were conducted in an open-chest, anesthetized pig model using microdialysis sampling. Methods: In anesthetized 40 kg pigs, regional myocardial ischemia was produced by transient snare-ligation of a branch of the left anterior descending coronary artery. Micro-dialysis catheters were used for local sampling of interstitial fluid in the ischemic area. In Studies 1 and 2, CO was administered before prolonged ischemia in a clinically relevant dose (5% increase in carboxyhemoglobin). In Study 2, 45Ca2+ was administered locally by microperfusate to ischemic myocardium with 45Ca2+ recovery used as a marker for intra-cellular calcium overload during ischemia. Myocardial injury markers glycerol and glut-amate (and taurine in Studies 3 and 4) were measured in microdialysate. In Studies 3 and 4, IP was performed by 4 brief transient cycles of coronary occlusion and reperfusion before a prolonged index ischemic episode was performed. In Study 3, 14C-marked adenosine was administered locally via microdialysis catheters in the heart muscle wall, and when this was metabolized during ischemia as an energy source, it was detected as 14C-marked lactate. In Study 4, a water-soluble purine nucleoside phosphorylase inhibitor was administered to heart muscle via microdialysis which was treated by IP before an index ischemia. Markers of glycolysis were measured serially before and during ischemia for Studies 1-4. Radio-labelled markers were analyzed using liquid chromatography and scintigraphy. Results: Study 1 results showed clear signs of metabolic advantage as far as glycolytic markers related to CO during myocardial ischemia. Study 2 results demonstrated no apparent energy metabolic advantage including for 45Ca2+ recovery and no diminishment of injury markers related to the single tested carbon monoxide dose during ischemia. Study 3 showed that IP led to enhanced radio-marked adenosine consumption as an energy-metabolic substrate, and that glycolytic flow (as less glucose consumption and lactate formation) was slower in IP-treated heart muscle. Study 4 showed that local purine nucleoside phosphorylase blockade inhibits adenosine utilization as an energy-metabolic substrate during ischemia, but this did not have an effect on glycolysis or injury markers during prolonged ischemia after IP. Conclusions: From Studies 1 and 2, we concluded that CO in this dose could show effects on glycolysis during ischemia but does not seem to confer cell protection during ischemia or early reperfusion, though CO protective effects in other doses or time frames cannot be ruled out. From Study 3 we concluded that there may be an immediate energy-metabolic explanation for why more IP-treated cells survive during prolonged ischemia. From Study 4 we concluded that experimental purine nucleoside phosphorylase blockade appears to allow interruption of IP-related adenosine utilization as an energy-metabolic substrate during prolonged ischemia without obvious effects on glycolysis, and that this requires further study to test if adenosine as an energy resource during ischemia is associated with protection during infarction. Key words: myocardial ischemia, preconditioning, carbon monoxide, adenosine
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| 10. |
- Ahmadpour, Doryaneh, 1973
(författare)
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Stress, Homeostasis and Robustness: Molecular and Systems Level Analysis in Yeast
- 2012
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Abstract Cells constantly encounter stress due to alterations in the external milieu or internal parameters. However, cells are robust to such changes and maintain homeostasis. Using the yeast Saccharomyces cerevisiae as a model organism, we attempted to elucidate aspects of homeostasis and robustness at both molecular and systems levels. At the molecular level, we focused on the aquaglyceroporin Fps1 and at the systems level we investigated the High Osmolarity Glycerol (HOG) pathway. Although Fps1 plays a key role in osmotic regulation and homeostasis, the mechanisms controlling Fps1 are not yet fully understood. We present evidence that Hog1 restricts the flux of glycerol and arsenite through Fps1 by phosphorylation of a residue within the N-terminal regulatory domain. This is the first report of a Mitogen Activated Protein Kinase (MAPK) regulating an aquaglyceroporin. In addition, we demonstrate that yet another MAPK, Slt2 may also be involved in regulating Fps1. It appears that Slt2 controls Fps1 by stimulating Fps1-mediated efflux. A residue within the C-terminal regulatory domain seems to be involved in controlling arsenite efflux through Fps1. Moreover, we show that in addition to the N- and C- termini, the transmembrane core of the protein also has a large effect on the transport activity of Fps1. Taken together, we speculate that phosphorylation of the termini affects the orientation of the transmembrane helices, thereby disturbing the transport activity of the protein. At the systems level we challenged the yeast HOG signal transduction pathway with systematic perturbation in the expression levels of its components under various external conditions to identify fragile nodes. We observed a high frequency of fragile nodes within the HOG pathway due to the inherent nature of signal transduction and the distribution of these fragile nodes was independent of function or location in the pathway topology. Moreover, the fragility patterns were mainly independent of the overall pathway activation status in response to different stresses. We found that the toxicity upon overexpression is at least partly due to pathway hyperactivation and can be suppressed by deletion of upstream or downstream pathway components. Furthermore, in silico analysis highlighted the impact of model structure on in silico robustness, and suggested complex formation and scaffolding as important contributors to the observed fragility patterns. Collectively, we believe that the robustness analysis can provide complementary information to dynamic data improving understanding of the operation of cellular signaling networks.
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