Coming dissertations at Uppsala university
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Drivers and Components of Genetic Diversity in Boreal Forest Trees : The Role of Hybridization and Gene Copy Number Variation in the Evolution of Norway and Siberian Spruce
Link: http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-543181
The genetic diversity that underpins biodiversity is shaped by a combination of evolutionary forces, including mutation, migration, genetic drift, and natural selection. The advent of sequencing technologies has enabled genetic studies to be scaled up, both in terms of the number of individuals and the number and types of genetic markers considered. In particular it has shown that structural variation captures more genetic diversity than single nucleotide polymorphisms. Extensive population genomics studies across species ranges have also revealed much more permissive boundaries between species than previously thought. A comprehensive understanding of the origins of genetic diversity and the factors that shape it would therefore require large-scale studies spanning a range of biological levels and scales, from individual genomes to whole populations, and from point mutations to large structural variations. We have addressed these questions in the case of Norway spruce (Picea abies) and Siberian spruce (Picea obovata), two boreal forest tree species with continental ranges.
In Paper I, we used genome-wide SNPs to show that extensive gene flow exists between Norway spruce and Siberian spruce, and we used coalescent simulations to reveal the occurrence of repeated hybridization events between the two species across glacial cycles. These events had a profound impact on the evolutionary trajectories of both species, and a large hybrid zone now extends from northwestern Europe to the southern Urals. Paper II is an eco-evolutionary study in which we demonstrated the role of hybridization in expanding both the species' ecological niche breadth and their resilience to climate change. In Paper III, we investigated patterns of adaptation at two different geographical scales (a latitudinal cline across Sweden and a longitudinal cline across both species' ranges), focusing on the role of gene copy number variations (gCNVs). We showed that a significant proportion of genes have copy number variations and that they are distributed across the genome. These gCNVs are associated with responses to abiotic and biotic stresses, including drought tolerance, temperature regulation and immune responses. Genotype-environment association also revealed that gCNVs play an important role in adaptation along environmental gradients, probably because of the quantitative response they allow. Importantly, we did not detect these candidate genes with conventional methods using SNP data. This work on gCNVs was made possible by the development of a comprehensive framework for detecting CNVs from single nucleotide polymorphism (SNP) data, presented in Paper IV. Paper V further extends the method under a composite likelihood ratio framework to be used with whole genome resequencing data.
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Active vs. Passive : The Role of Ceramic Particles in Solid Composite Polymer Electrolytes for Lithium Batteries
Link: http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-543243
Since the state-of-the-art Li-ion batteries are close to reaching their theoretical limit in energy density, it becomes crucial to develop next-generation batteries that enable better safety, higher energy density, and longer lifetime. One such next-generation technology is solid-state batteries, employing solid-state electrolytes. Both polymer and inorganic electrolytes are well-explored in this context. While polymers are flexible and easily processable, their ionic conductivities are generally insufficient. Inorganic ceramics can be good ionic conductors, but display interfacial issues. Therefore, combining polymeric and ceramic material in composites polymer electrolytes (CPEs) can – in principle – be beneficial to merge the advantages of both categories. However, it is still unclear how to best construct such systems, and how the ions are actually transported in them.
This thesis explores ionic transport in CPEs, both with ion-conducting (“active”) and non-ion-conducting (“passive”) ceramic fillers. The focus is on the amorphous polymer material poly(trimethylene carbonate) (PTMC), the active ceramic filler Li7La3Zr2O12 (LLZO), and the passive ceramic fillers LiAlO2 (LAO) and NaAlO2 (NAO). The ionic transport mechanism in PTMC:LLZO CPEs is determined to be dependent on two main factors: particle loading and surface chemistry. An increase in ionic conductivity up to 30 wt% of Li7La3Zr2O12 is seen due to formation of additional transport pathways along the polymer-ceramic interfaces, while higher loadings affect the ionic conductivity negatively. While this can partly be explained by particle agglomeration, the presence of Li2CO3 on the Li7La3Zr2O12 surface also contributes to retard the ionic movement along the interfaces. Therefore, boric acid treatment is explored as a strategy to enable a Li2CO3-free surface of Li7La3Zr2O12 particles, which renders improved ionic transport and battery performance. Boron-treated Li7La3Zr2O12 shows formation of LiBO2, which yields a negative zeta-potential, indicative of interactions between the ceramic particles and Li+ ions. That the surface chemistry – rather than the bulk – of the ceramic filler ultimately controls the overall transport, opens the door towards employment of passive fillers. It is shown that LiAlO2 particles can increase the ionic conductivity by one order of magnitude and the Li+ transference number to almost 1, effectively rendering the LiAlO2-based CPE a single-ion conductor. These enhanced ionic transport properties can be explained by the ability of LiAlO2 particles to promote better ion-ion separation through the attraction of negatively charged TFSI anions to the surface. This renders considerably improved battery performance, enabling cycling in Li||NMC cells. Similar effects are also seen for the analogous Na-ion battery system.
Thereby, considering that the bulk conductivity of active fillers does not contribute to the overall ionic conduction in CPEs, and that passive fillers such as LiAlO2 can greatly enhance the ionic transport because of its surface chemistry enabling greater ion-ion separation and favorable transport pathways, this thesis provides guidelines for future design of solid-state conductors for Li- and Na-batteries.
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Biochemical strategies for ligand discovery against cancer targets
Link: http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-543034
Cancer is a common disease and diagnosis frequency correlates with population age. Though many cancers can be cured today, numerous types remain difficult to treat. Treatments can evoke side effects and often don’t reach the clinic due to inefficacy. Thus, better targeted anti-cancer therapies and candidate drugs are required. This thesis focusses on initial stages of drug discovery where we sought to identify ligands specifically targeting SET and MYND domain containing protein 3 (SMYD3), and Cullin3 associated adaptor proteins: Kelch-like protein 12 (KLHL12) and 20 (KLHL20). These targets are all associated with cancer although their biological mechanisms remain elusive. The targets were challenging from a biochemical perspective, nevertheless via robust expression and purification methods, an amalgamation of biochemical techniques and computational methods were used to identify, characterize, and evolve fragment and peptide-based ligands. Sensitive multiplexed screening assays enabled selection of specific hits. A grating coupled interferometry-based biosensor assay implemented a kinetic criterion for fragment hit identification against SMYD3. Four fragments from a library containing 1056 fragments had their binding site and orientation established using X-ray crystallography. Fragment evolution based on the SMYD3 allosteric ligand diperodon encompassed a structure-affinity-relationship (SAR)-based approach, and a deconstruction-and-growth method wherein ligands with KD of 0.4-180 μM were attained. Structure prediction complemented a surface plasmon resonance (SPR) biosensor-driven approach to develop a stapled peptide ligand against the Kelch domain of KLHL20, derived from zinc finger translocation associated protein (ZFTA). This peptide had KD of 1.14 mM and alanine scanning revealed aspartate as vital for interaction. Multiplexed fragment-based SPR biosensor screening assays against the Kelch domains of KLHL12 and 20 identified 237 and 266 hits from a library containing 3000+ fragments. Hit selection was based on preference for folded protein and dose-response analysis was conducted for validation and hit reduction to 24 and 21. Hit SAR was probed using modelling and fragment analogues. NMR confirmed fragment-protein binding. All targets studied herein were concluded as poorly druggable, however using multiple experimental approaches alongside computational methodologies permitted hit identification, validation, and a further understanding of poorly druggable targets. The validated hits presented are befitting for evolution by medicinal chemistry.