Coming dissertations at Uppsala university
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Polyploidy: Phylogenetics, Role of Borrowed Alleles, Evolutionary Trajectories
Link: http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-536036
Whole genome duplication is the largest genetic mutation known to occur, giving rise to polyploids, organisms with three or more complete sets of chromosomes. Polyploidy is widespread among plant lineages and is believed to have played a major role in angiosperm evolution and diversification. While the study of polyploidy has been going on for over 100 years, many questions related to its evolutionary role remain unanswered. Polyploids can reshape the gene flow landscape within a genus but the ultimate consequences of this allelic exchange are still being unraveled. Genome duplication upends the meiotic cycle but there remains great uncertainty as to whether evolutionary solutions guiding polyploid viability are universally shared among polyploid species. At the more practical level, there is a general lack of tools needed to reconstruct the phylogenetic history of a polyploid, in particular in cases where the phylogeny is highly reticulated due to high levels of introgression from other species. In this thesis, we address all these issues.
In Paper I, we present a new heuristic method suitable for inferring the phylogenetic position of the parental species of a tetraploid, and which is based on a novel phasing technique called genomic polarization. Based on extensive testing using simulated data, we show that the use of polarized genomic sequences allows for the correct identification of both parental species of an allotetraploid with up to 97% certainty in phylogenies with moderate levels of incomplete lineage sorting (ILS), and 87% in phylogenies containing high levels of ILS.
In Paper II, we propose a novel approach to disentangle introgression from polyploidization in order to determine the mode of origin and reconstruct the reticulate phylogeny of a highly hybridized polyploid, using Betula pubescens (downy birch) as a case-study. This was achieved by combining genomic polarization with modeling of polyploidization and introgression events under the multispecies coalescent, and then using simulated annealing and an approximate Bayesian computation (ABC) rejection algorithm to optimize and evaluate competing polyploidization models. We provide evidence that B. pubescens is the outcome of an autoploid genome doubling event in the common ancestor of B. pendula and its extant sister species, B. platyphylla, that took place approximately 180,000 generations ago.
In Paper III, we make use of B. pubescens gene expression data to explore whether whole genome duplication triggers common genomic responses across autopolyploid plant species. Using results previously obtained in the Arabidopsis model system as a reference, we tested whether meiotic genes found to be under strong selection in Arabidopsis autotetraploids show biased allelic expression in B. pubescens. We identified a small group of meiotic genes in B. pubescens whose expression is constrained, strongly favoring alleles introgressed from B. humilis or B. nana, a set that includes several meiotic genes previously found to be under selection in Arabidopsis autopolyploids. These results suggest that whole genome duplication triggers similar genomic responses across flowering plants, and that the evolutionary path available to autopolyploids for regaining meiotic stability is highly conserved and dependent on a small group of core meiotic genes.
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Of MOFs and Modifications: Exploring New Depths in Single-Crystalline UiO Materials
Link: http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-535772
The climate is rapidly changing for the worse, driven by our excessive consumption of planetary resources. Our best chance at mitigating the effects of climate change is the transition to sustainable resources. The Sun represents an undepletable energy source that could easily cover our growing energy requirements. Energy is best stored in fuels, which is achieved by converting low-energy precursors to high-energy products using catalysts. To be relevant on a global scale, these catalysts have to fulfill a number of requirements, which may be met by combining heterogeneous and molecular catalysis.
Metal-organic frameworks (MOFs) are a newly emerged type of crystalline material, displaying great potential for this crucial task. MOFs are customizable, chemically well-defined and offer large internal surface areas. They can be used as heterogeneous supports for catalysts. This can be achieved by functionalizing the framework to host introduced catalysts. The distribution of the catalysts within the material strongly affects catalysis; however, assessing catalyst distribution is challenging and therefore often neglected. Also, many catalytic MOFs are limited by stability issues. This lack of fundamental understanding hinders the optimization of catalytic MOFs.
In this work, we investigate the synthesis and stability of UiO-67 (UiO = Universitetet i Oslo) thin films. We reveal how humidity affects MOF growth and present mitigation strategies to make the materials more stable and their synthesis more reproducible.
We also present the development of a Rutherford backscattering spectrometry (RBS) method that enables the elemental depth profiling of UiO single crystals. We demonstrate the potential of the method to assess the distribution of post-synthetically introduced functional groups into MOFs. The method was then improved to include lighter metals and to investigate concentration gradients. With this, we investigated the effect of the linker ratio in mixed-linker UiO-67-bpy on the diffusion and distribution of post-synthetically introduced Ni2+ cations. We show that high ratios of metal-binding linkers slow down diffusion and result in inhomogeneous cation distributions.
RBS also revealed cavities at the core of UiO-67-bpy crystals under certain synthesis conditions. We rationalized the synthesis of such hollow MOFs based on emerging literature challenging some prevalent ideas about coordination equilibria in MOFs.
The work presented in this thesis provides foundational knowledge that can be used for the design of future MOF catalysts, accelerating research within the field and hopefully contributing to the much-needed transition to sustainable energy production.
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Heterogeneous Molecular Catalysis : Experimental and Computational Considerations
Link: http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-536037
The transition towards a society free from emission of CO2 hinges on the replacement of fossil fuels by more eco-friendly alternatives. An attractive option is the H2 economy, in which fuel production and usage are enclosed in a sustainable water-to-water cycle consisting of fuel cells and solar-driven water electrolysis. A major obstacle to large-scale implementation of such a cycle is the cost and availability of catalysts that promote the associated redox reactions, including the hydrogen evolution reaction (HER). Therefore, this thesis explores the possibilities of applying molecular structures as catalysts toward the HER, and of making these catalysts industrially appealing by incorporating them into a conducting polymer directly attached to an electrode surface. If successful, the resulting materials - conducting redox polymers - would constitute efficient, selective and scalable catalytic materials made from earth-abundant elements. This work presents a thorough electrochemical characterization of conducting redox polymers aimed at catalytic applications, alongside experimental and computational mechanistic studies of metalloporphyrins employed as electrocatalysts toward the HER.