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Coming dissertations at TekNat

  • Sources of variability in heterospecific social information use for breeding habitat selection : Role of genetics and personality in collared flycatchers

    Author: Jennifer Morinay
    Publication date: 2018-11-01 07:59

    All their life, individuals have to make decisions that may strongly affect their fitness. To optimize their decisions, they can use personally acquired information but also information obtained from observing other individuals (“social information”). The propensity to gather and use social information and the information meaning might depend on both individual and environmental factors. Studying what drives within- and between-individual differences in social information use should help us understand the evolutionary potential of this supposedly adaptive behaviour. The aim of my PhD was to empirically investigate sources of variability in heterospecific social information use for breeding habitat selection. I worked on a natural population of collared flycatchers (Ficedula albicollis, Gotland Island, Sweden), a passerine species shown to cue on the presence, density, reproductive investment and nest site preference of dominant titmice for settlement decisions. Using both long term and experimental data, I showed that the use of heterospecific social information, measured as the probability to copy tit nest preference, is not heritable but depends on male age and...

  • Infrared spectroscopy studies of adsorption and photochemistry on TiO2 surfaces : From single crystals to nanostructured materials

    Author: Andreas Mattsson
    Publication date: 2018-10-29 09:00

    TiO2 based photocatalysis is a green nanotechnology that can be used for removal of pollutants from water and air, as well as making synthetic fuels from water and carbon dioxide. Said photocatalysis has received major research interests during the last decades. Despite these efforts, many elementary processes that occur on the photocatalyst surface are not fully understood and, therefore, limit our ability to purposefully manufacture more efficient photocatalytic materials. The objective of this thesis is to provide new understanding at a molecular level of important adsorbate species on the TiO2 surfaces.

    Fundamental properties of adsorption and photochemistry of primarily formic acid on different TiO2 surfaces, ranging from single crystals to nanoparticles, have been studied using infrared spectroscopy. A method to simulate IR spectra have been developed and, combined with experimental data, has been proven to be a powerful tool to identify different adsorbate geometries on the surface. In the presence of oxygen, a thermally activated and irreversible reaction between formate and oxygen adatoms takes place on the single crystal rutile (110) surface to yield hydrogen...

  • Cluster Tilting for Representation-Directed Algebras

    Author: Laertis Vaso
    Publication date: 2018-10-25 15:22
  • Effects of Ubiquinone-10 on the Stability and Mechanical Properties of Lipid Membranes

    Author: Emma K. Eriksson
    Publication date: 2018-10-19 11:44

    Ubiquinones are a group of fat-soluble molecules present in many biological membranes. The most abundant version in humans, ubiquinone-10 (Q10), plays an important role in the mitochondrial respiration chain and also functions as a powerful antioxidant. Accumulating evidence suggests that Q10 also could have other functions in the membrane. The aim of this thesis has been to explore Q10’s possible role as a membrane stabilizer.

    To investigate the potential effect of Q10 in membranes, liposomes with compositions of biological relevance were used as models systems. In lipid systems mimicking that of the inner membrane of the mitochondria, Q10 was found to lower the membrane’s permeability to hydrophilic solutes, render the membrane more resistant to rupturing and promote membrane lipid order. In models mimicking the plasma membrane of E.coli, Q10 was observed to decrease the water permeability and increase the elastic resistance against membrane deformation during osmotic shock. All in all, the results suggest a general membrane stabilizing effect of Q10. The results indicate, however, that the extent of, as well as the mechanisms behind, the membrane stabilizing effects of...

  • Spatio-temporal probabilistic forecasting of solar power, electricity consumption and net load

    Author: Dennis van der Meer
    Publication date: 2018-10-18 14:58

    The increasing penetration of renewable energy sources into the electricity generating mix poses challenges to the operational performance of the power system. Similarly, the push for energy efficiency and demand response—i.e., when electricity consumers are encouraged to alter their demand depending by means of a price signal—introduces variability on the consumption side as well.

    Forecasting is generally viewed as a cost-efficient method to mitigate the adverse effects of the aforementioned energy transition because it enables a grid operator to reduce the operational risk by, e.g., unit-commitment or curtailment. However, deterministic—or point—forecasting is currently still the norm.

    This thesis focuses on probabilistic forecasting, a method with which the uncertainty ac- companying the forecast is expressed by means of a probability distribution. In this framework, the thesis contributes to the current state-of-the-art by investigating properties of probabilistic forecasts of PV power production, electricity consumption and net load at the residential and distribution level of the electricity grid.

    The thesis starts with an introduction to probabilistic...

  • Evolutionary Approaches to Sequence Alignment

    Author: Marcin Bogusz
    Publication date: 2018-10-17 10:29

    Molecular evolutionary biology allows us to look into the past by analyzing sequences of amino acids or nucleotides. These analyses can be very complex, often involving advanced statistical models of sequence evolution to construct phylogenetic trees, study the patterns of natural selection and perform a number of other evolutionary studies. In many cases, these evolutionary studies require a prerequisite of multiple sequence alignment (MSA) - a technique, which aims at grouping the characters that share a common ancestor, or homology, into columns. This information regarding shared homology is needed by statistical models to describe the process of substitutions in order to perform evolutionary inference. Sequence alignment, however, is difficult and MSAs often contain whole regions of wrongly aligned characters, which impact downstream analyses.

    In this thesis I use two broad groups of approaches to avoid errors in the alignment. The first group addresses the analysis methods without sequence alignment by explicitly modelling the processes of substitutions, and insertions and deletions (indels) between pairs of sequences using pair hidden Markov models. I describe an...

  • Population Genetics of Human Genomic Elements

    Author: Thijessen Naidoo
    Publication date: 2018-10-16 14:39

    The genomes of living organisms are composed of a multitude of functional units, which interact with each other and their environment in a highly regulated fashion, to facilitate the expression of an enduring (and evolving) phenotype. Several approaches have emerged in the effort to identify these functional units and explore their activities. In this thesis, I have taken a population genetics approach; evaluating how the distribution of genetic variation in the human genome has been shaped through the actions of natural selection on functional genomic elements. In the first paper, I interrogate a catalogue of elements derived from biochemical signatures for signals of selection; finding significant signals of purifying selection on regulatory elements, independent of linked-purifying selection. In the second paper, I explore the pseudogene class of genomic elements, and find that a large proportion of a particular subclass, transcribed duplicated pseudogenes, has experienced significant amounts of positive selection. In the third paper, I focus on protein coding genes and variants that disrupt their open reading frames. Specifically, I examine the distribution of loss-of-...

  • Exploring the diversity and evolution of giant viruses in deep sea sediments using genome-resolved metagenomics

    Author: Disa Bäckström
    Publication date: 2018-10-15 09:33

    Viruses are the most abundant biological entities on this planet, which is impressive considering that they are completely dependent on their hosts for reproduction. Recently the idea of what viruses are has changed dramatically, with the discovery of giant viruses that belong to the Nucleocytoplasmic Large DNA Viruses (NCLDV), such as Mimiviridae, Marseilleviridae, and the proposed families Pandoraviruses, and Pithoviruses. Not only are some of these viruses as large as bacteria in size, their genomes also exceed the size of some prokaryotic genomes. The evolutionary path to viral giganticism is not yet fully understood, and several opposing theories have been proposed. The more examples of giant viruses we have to study, the clearer the picture becomes. The rate of discovery, however, is limited by the low capacity of culturing. In an effort to contribute through culture-independent methods, I used genome-resolved metagenomics to retrieve genomes of 23 new members of the NCLDV from deep sea sediment samples that were taken near Loki’s Castle hydrothermal vent field. This method has previously been used to study uncultured Bacteria and Archaea, but few successful cases of...

  • Non-genetic processes in development and heredity

    Author: Willian T. A. F. Silva
    Publication date: 2018-10-10 14:50

    There is a swiftly increasing amount of empirical evidence that non-genetic factors, such as DNA methylation and small RNAs, play an important role not only in development but also in heredity and, therefore, evolutionary dynamics. One of the most interesting aspects of non-genetic processes is their responsiveness to environmental conditions, which has been shown to affect not only the phenotype and fitness of the individuals directly exposed to the stimulus, but also their offspring even when the stimulus is no longer present, indicating that the transmission of non-genetic factors across generations might work analogously to immunization against recurring conditions. In this thesis, I explored the effects and consequences of non-genetic processes in development and heredity, from both theoretical and experimental perspectives. In Article I, I created a mathematical model of DNA methylation dynamics during the maternal-to-zygotic transition, leading to the zygotic genome activation. I found that there is a developmental constraint on the transition between different cell lineages, with an increasing flexibility of active methylation and decreasing flexibility of maintenance (...

  • Computational Modeling of the Mechanisms and Selectivity of Organophosphate Hydrolases

    Author: Miha Purg
    Publication date: 2018-10-08 15:40

    Computational modeling is becoming an increasingly integral part of (bio)chemistry, providing a powerful complementary view into the dynamics, binding, and reactivity of biochemical systems. In particular, molecular simulations based on multiscale models are now regularly employed in studies of enzymatic reactions, offering invaluable mechanistic insight through the lens of molecular energy landscapes. In this thesis, I used the empirical valence bond (EVB) and related methods to study the mechanisms and selectivity of organophosphate hydrolases.

    Organophosphate hydrolases are a diverse class of enzymes capable of degrading some of the most toxic compounds known to mankind, including pesticides and chemical warfare agents. They are particularly interesting from a mechanistic and evolutionary point of view, having evolved the ability to catalyze the hydrolysis of compounds which were introduced to nature less than a century ago. Moreover, they show promise as effective organophosphate decontamination agents and a thorough understanding of their function is fundamental to the future design of efficient and selective biocatalysts. 

    As organophosphate hydrolases are...