| 1. |
- Bergström, Anders, 1969-
(författare)
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Oviposition strategies in butterflies and consequences for conservation
- 2005
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Oviposition strategies are an important component of life history evolution in insects. Oviposition is a complex behaviour, where females must locate suitable habitat patches, locate oviposition sites, evaluate the quality, and finally decide how many eggs to lay. In this thesis, I explore some factors that may influence oviposition strategies in female butterflies. It discusses oviposition strategies from large to fine scales and ends with a discussion on implications for conservation. In paper I we tested for local adaptations in oviposition preference and larval performance in Polyommatus icarus. The result suggests that this species is evolutionary conservative in its utilization of the tested host plants. In the second paper we investigated frequency-dependent host plant choice in Polygonia c-album and showed that females spent significantly more time, and laid more eggs, in patches with high frequency of the preferred host. The influence of nectar sources on host plant choice in P. icarus was tested in paper III, females preferred ovipositing on host plants with flowers and after feeding. In paper IV we investigated oviposition “mistakes” in P. c-album and found differences in discrimination of hosts and non-hosts. Further, we showed that P. c-album butterflies are capable of responding to host quality by increasing clutch sizes on a high ranked host (paper V). Finally, in paper VI I explored how female oviposition behaviour can influence habitat management for a threatened butterfly species, Parnassius mnemosyne, by doing an observational field study on oviposition site preferences. This thesis highlights oviposition as a stepwise process and show that female discrimination is important at a multitude of levels with implications for oviposition strategies.
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| 2. |
- Borgström, Johannes
(författare)
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Equivalences and Calculi for Formal Verification of Cryptographic Protocols
- 2008
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Security protocols are essential to the proper functioning of any distributed system running over an insecure network but often have flaws that can be exploited even without breaking the cryptography. Formal cryptography, the assumption that the cryptographic primitives are flawless, facilitates the construction of formal models and verification tools. Such models are often based on process calculi, small formal languages for modelling communicating systems. The spi calculus, a process calculus for the modelling and formal verification of cryptographic protocols, is an extension of the pi calculus with cryptography. In the spi calculus, security properties can be formulated as equations on process terms, so no external formalism is needed. Moreover, the contextual nature of observational process equivalences takes into account any attacker/environment that can be expressed in the calculus. We set out to address the problem of automatic verification of observational equivalence in an extension of the spi calculus: A channel-passing calculus with a more general expression language. As a first step, we study existing non-contextual proof techniques for a particular canonical contextual equivalence. In contrast to standard process calculi, reasoning on cryptographic processes must take into account the partial knowledge of the environment about transmitted messages. In the setting of the spi calculus, several notions of environment-sensitive bisimulation has been developed to treat this environment knowledge. We exhibit distinguishing examples between several of these notions, including ones previously believed to coincide. We then give a general framework for comparison of environment-sensitive relations, based on a comparison of the corresponding kinds of environment and notions of environment consistency. Within this framework we perform an exhaustive comparison of the different bisimulations, where every possible relation that is not proven is disproven. For the second step, we consider the question of which expression languages are suitable. Extending the expression language to account for more sophisticated cryptographic primitives or other kinds of data terms quickly leads to decidability issues. Two important problems in this area are the knowledge problem and an indistinguishability problem called static equivalence. It is known that decidability of static equivalence implies decidability of knowledge in many cases; we exhibit an expression language where knowledge is decidable but static equivalence is not. We then define a class of constructor-destructor expression languages and prove that environment consistency over any such language directly corresponds to static equivalence in a particular extension thereof. We proceed to place some loose constraints on deterministic expression evaluation, and redefine the spi calculus in this more general setting. Once we have chosen an expression language, we encounter a third problem, which is inherent in the operational semantics of message-passing process calculi: The possibility to receive arbitrary messages gives rise to infinite branching on process input. To mitigate this problem, we define a symbolic semantics, where the substitution of received messages for input variables never takes place. Instead, input variables are only subject to logical constraints. We then use this symbolic semantics to define a symbolic bisimulation that is sound and complete with respect to its concrete counterpart, extending the possibilities for automated bisimulation checkers.
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| 3. |
- Claybourn, Thomas M., 1989-
(författare)
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Biostratigraphy and Systematics of Cambrian Small Shelly Fossils from East Antarctica and South Australia
- 2021
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The remote lower Cambrian Byrd group of sedimentary rocks from East Antarctica has been studied intermittently since its discovery over a century ago. Previous insights into the trilobites and archaeocyaths indicated a close correlation to the sedimentary sequences of South Australia. The lowest unit of the Byrd Group is the fossiliferous Shackleton Limestone which overlies the Neoproterozoic metamorphic rocks of the Beardmore Group and is representative of a long period of carbonate shelf formation on a passive margin with the palaeo-Pacific. This was truncated by marine transgression and the deposition of the deeper-water calcareous siltstones of the fossiliferous Holyoake Formation. This is overlain by the Starshot Formation and all three units are cross-cut by the Douglas Conglomerate, marking the start of a collisional tectonic regime between the East Gondwana and palaeo-Pacific plates. The first systematically sampled and analysed sections through the carbonate Shackleton Limestone and argillaceous Holyoake Formation has yielded a new fauna of small primarily phosphatic and secondarily phosphatised shelly fossils. The abundant molluscs, brachiopods and tommotiids are reported here. These findings are ideal for correlating this section to the fossil biozones of South Australia, including the Dailyatia odyssei small shelly fossil Zone and the Pararaia janeae trilobite Zone. Chemostratigraphic data from three sections preserve the profiles of two major stable carbon isotope excursions: the Mingxinsi Carbon Isotope Excursion and the Archaeocyathid Extinction Carbon isotope Excursion. The combination of these two lines of evidence are a strong indicator for Cambrian Series 2, early-mid Stage 4. This is corroborated by newly described D. odyssei-P. janeae Zone small shelly fossils from the carbonate clasts from the Cambrian Stage 4 White Point Conglomerate of South Australia which bear strong similarity to the fauna of the Shackleton Limestone. Palaeobiogeographically the fauna recovered from the Byrd Group is similar to the East Gondwanan region of South Australia, with similar brachiopod assemblages to those recovered from the Xinji Formation of North China and similar molluscan assemblages to the Bastion Formation of North-East Greenland.
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| 4. |
- Hoppe, Johanna M., 1981-
(författare)
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Emotional mental imagery and the reduction of fear within the mind’s eye
- 2021
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Mental imagery refers to sensory-perceptual experiences in the absence of external sensory input. Emotional mental imagery (i.e., imagery with emotional content) is a key feature in many mental disorders, such as the image-based intrusive memories of trauma in posttraumatic stress disorder (PTSD). However, mental imagery can also be a vehicle for emotional change. In imaginal exposure, fear-provoking events are revisited using mental imagery. Imaginal exposure is a core component in evidence-based therapies for anxiety and PTSD. Treatment development is needed, as effects are many times insufficient, accessibility is low, and the treatment is not well-tolerated by some patients. The aim of this thesis was to increase knowledge of underlying mechanisms of imaginal exposure and improve our understanding of emotional mental imagery. The thesis explored the neural underpinnings of imaginal exposure and investigated mechanisms that could enhance its effectiveness, accessibility and tolerability. To further our knowledge of intrusive memories in PTSD (i.e., involuntary mental imagery), the characteristics of trauma memory hotspots (worst moments) collected within the first hours after trauma were explored. Study I demonstrated that imaginal exposure to mental imagery of phobic (vs. neutral) stimuli robustly activated emotion-processing brain areas. Study I also revealed that a brief 10-minute session of imaginal exposure was associated with reduced fear one week later. Study II investigated the link between vividness (clarity and liveliness) of mental imagery during imaginal exposure and reduction of fear using an experimental analogue of imaginal exposure (imaginal extinction). No evidence was found that high imagery vividness during imaginal extinction was associated with better long-term reduction in physiological fear responses than lower vividness. Study III revealed that hotspots collected soon after trauma are expressed as motion-rich sensory-perceptual experiences (mental imagery) with little detail on emotion/cognition. The contributions of this thesis involve demonstrating that mental imagery has the power to elicit emotional responses at subjective, physiological and neural levels and suggesting new avenues for treatment development. Future studies should explore the benefits of briefer imaginal exposure sessions to improve the effectiveness and accessibility of imaginal exposure. Future studies should also examine if fear reduction can be obtained with less vivid imaginal exposure, which could help attenuate distress and thereby make imaginal exposure tolerable for more patients. Lastly, the dynamic and visuospatial nature of newly formed trauma memory hotspots may help elucidate mechanisms through which tasks conducted posttrauma can prevent intrusive memories.
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| 5. |
- Jimenez-Gonzalez, Alejandro
(författare)
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Stolen genes, a shortcut to success : Evolution of metabolic and detoxification capacities in Diplomonads
- 2020
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Parasites do not represent a single evolutionary lineage meaning that they have evolved several times. The changes that parasites have undergone to adapt to such a lifestyle are not entirely understood. This thesis focuses on the study of diplomonads (Fornicata, Metamonada), a group of host-associated or free-living protists, to better understand how they adapted to different environments and hosts.Diplomonads, and close relatives, are found in low-oxygen environments. However, some species can withstand fluctuating levels of oxygen. In a first study, we reconstructed the oxygen detoxification pathway of Fornicata and study its evolution. Comparative genomics showed that Fornicata shares a common pathway with lineage-specific modifications. Phylogenetic analyses showed a pathway in a constant change where proteins have been gained and lost.In a second study, the Giardia muris genome was sequenced and compared to the genome of G. intestinalis WB. We reconstructed the metabolic capacities of both species. Our analyses showed that the observed differences are the result of gene acquisitions or differential losses that can be explained based on differences in the environment of the hosts.Considering what we observed in the two previous studies, we reconstructed the metabolic capacities of four diplomonads. Using cluster analysis, we reconstructed the putative metabolism of the last Diplomonadida common ancestor. Our analyses suggested that this ancestor was, most likely, an obligate host-associated organism. However, we identified that traits associated with parasitic diplomonads evolved in a free-living ancestor.In the last study, we analyzed the genome of Hexamita inflata, a free-living, diplomonad. Our analyses showed that Trepomonas sp. PC1 and H. inflata acquired important genes for the adaptation to a secondary free-living in a common ancestor. However, our analyses also showed independent adaptations. The synthesis of glutathione and the acquisition of glutathione peroxidase, most likely, allow H. inflata to detoxify higher levels of oxygen and arsenic than other diplomonads.In conclusion, this thesis highlights the value of metabolic analyses to identify how microbial eukaryotes interact with their environment. The phylogenetic approach shows that the acquisition of genes and differential losses have been important processes in the adaptation of different hosts and environments.
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| 6. |
- Johansson, Henrik A. B., 1979-
(författare)
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Ionization and Fragmentation of Complex Molecules and Clusters : Biomolecules and Polycyclic Aromatic Hydrocarbons
- 2011
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- This work deals with ionization and fragmentation of biomolecules and polycyclic aromatic hydrocarbon (PAH) molecules. They are studied in the gas phase both as isolated molecules and as weakly bound clusters. The purpose of the experimental and theoretical investigations are to elucidate charge and energy transfer and related redistribution processes, as well as fragmentation behaviors. The first part of this thesis presents results from studies on biomolecular ions, in particular nucleotides and peptides, which are primarily examined in electron capture induced dissociation processes. These investigations are relevant for the better understanding of radiation damage to DNA and processes involved in the sequencing of proteins. It is found that the immediate environment have a decisive influence on the fragmentation behaviors. Evaporation of surrounding molecules protect the biomolecules, but their effect on the electronic structure may also enhance or suppress different fragmentation channels. In the second part of the thesis, results from studies on PAH molecules are presented. Experimentally, their properties are mainly probed through collisions with atomic ion projectiles having kilo-electronvolt kinetic energies. As a widespread pollutant on Earth, and as a family of abundant molecules in space, PAHs are not only relevant from an environmental and health perspective, but they are also important for the understanding of the universe. The present results relate to the stabilities of these molecules, both in isolated form and in clusters, when heated or multiply ionized. It is found to be easier to remove several electrons from clusters of PAH molecules than from isolated PAHs, and fission processes determine their ultimate stabilities. Heated low-charge state clusters of PAHs undergo long evaporation sequences once these have started. For isolated and heated PAHs, internal structural rearrangements are demonstrated to be important in the fragmentation processes.
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| 7. |
- Kehrein, Kirsten, 1984-
(författare)
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Organization of mitochondrial gene expression in yeast : Specific features of organellar protein synthesis
- 2014
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Mitochondria contain their own genetic system, encoding key subunits of the oxidative phosphorylation system. These subunits are expressed by an organelle-specific gene expression machinery. This work revealed a number of fundamental aspects of mitochondrial gene expression and provides evidence that this process is organized in a unique and organelle-specific manner which likely evolved to optimize protein synthesis and assembly in mitochondria. Most importantly, improving the experimental handling of ribosomes we could show that mitochondrial ribosomes are organized in large assemblies that we termed MIOREX complexes. Ribosomes present in these complexes organize gene expression by recruiting multiple factors required for post-transcriptional steps. In addition, we could reveal mechanisms by which ribosome-interactor complexes modulate and coordinate the expression and assembly of the respiratory chain subunits. For example we showed that the Cbp3-Cbp6 complex binds to the ribosome in proximity to the tunnel exit to coordinate synthesis and assembly of cytochrome b. This location perfectly positions Cbp3-Cbp6 for direct binding to newly synthesized cytochrome b and permits Cbp3-Cbp6 to establish a feedback loop that allows modulation of cytochrome b synthesis in response to assembly efficiency. Likewise the interaction of the membrane-anchor proteins Mba1 and Mdm38 with the tunnel exit region enables them to participate in the translation of the two intron-encoding genes COX1 and COB in addition to their role in membrane insertion. In summary, work presented in this thesis shows that mitochondrial gene expression is a highly organized and regulated process. The concepts and technical innovations will facilitate the elucidation of many additional and important aspects and therefore contribute to the general understanding of how proteins are synthesized in mitochondria.
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| 8. |
- Nordblad, Erik, 1981-
(författare)
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Opening New Radio Windows and Bending Twisted Beams
- 2011
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- In ground based high frequency (HF) radio pumping experiments, absorption of ordinary (O) mode pump waves energises the ionospheric plasma, producing optical emissions and other effects. Pump-induced or natural kilometre-scale field-aligned density depletions are believed to play a role in self-focussing phenomena such as the magnetic zenith (MZ) effect, i.e., the increased plasma response observed in the direction of Earth's magnetic field. Using ray tracing, we study the propagation of ordinary (O) mode HF radio waves in an ionosphere modified by density depletions, with special attention to transmission through the radio window (RW), where O mode waves convert into the extraordinary (X, or Z) mode. The depletions are shown to shift the position of the RW, or to introduce RWs at new locations. In a simplified model neglecting absorption, we estimate the wave electric field strength perpendicular to the magnetic field at altitudes normally inaccessible. This field could excite upper hybrid waves on small scale density perturbations. We also show how transmission and focussing combine to give stronger fields in some directions, notably at angles close to the MZ, with possible implications for the MZ effect. In a separate study, we consider electromagnetic (e-m) beams with helical wavefronts (i.e., twisted beams), which are associated with orbital angular momentum (OAM). By applying geometrical optics to each plane wave component of a twisted nonparaxial e-m Bessel beam, we calculate analytically the shift of the beam's centre of gravity during propagation perpendicularly and obliquely to a weak refractive index gradient in an isotropic medium. In addition to the so-called Hall shifts expected from paraxial theory, the nonparaxial treatment reveals new shifts in both the transverse and lateral directions. In some situations, the new shifts should be significant also for nearly paraxial beams.
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| 9. |
- Pashkevich, Natallia, 1983-
(författare)
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Information Worker Productivity Enabled by IT System Usage : A Complementary-Based Approach
- 2016
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Assessing the conditions of productivity of individual workers who process information and use IT has been a concern for many researchers. Prior studies have applied different theoretical foundations to study the relationship between IT use and productivity at individual level in post adoption scenarios and have provided mixed results. In the last decades, the proposition that there is a need for a set of factors to be changed in a synchronized fashion when using an IT system has received particular attention. Very little, however, is known about the configurations of these factors at individual level. To investigate this gap, we have designed a new research model of an information worker’s individual productivity when a more aligned IT system is used in a synchronized manner with both individual and organizational factors. The formulated research model is grounded on the complementarity theory, functioning here as a meta-theory guiding the linking of productivity theory, Kirton’s adaption-innovation theory, and several theoretical bodies on the structure of production processes and human resource management. The formulated model was tested in two empirical studies – a longitudinal quasi-randomized field experiment and an online experiment – conducted to investigate configurations of complementary factors that increase productivity when a new, more aligned IT system is used.Overall, the two studies shed important light on configurations of complementary factors and the improvement of the research design to study their impact on IT-enabled productivity. The obtained results contribute to the research that focuses on individual information worker IT-enabled productivity as well as research that rests on the complementarity theory with new configurations of complementary factors that, when matched correctly, can increase individual productivity of information workers. Eventually, the studies presented here advocate that further research is needed to increase our in-depth understanding of complementary factors and their impact on individual IT-enabled productivity of information workers.
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| 10. |
- Sellberg, Jonas A., 1985-
(författare)
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X-ray scattering and spectroscopy of supercooled water and ice
- 2014
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- This thesis presents experimental studies of water and ice at near-atmospheric pressures using intense x-rays only accessible at synchrotrons and free-electron lasers. In particular, it focuses on the deeply supercooled, metastable state and its implications on ice nucleation.The local structure of the liquid phase was studied by x-ray scattering over a wide temperature range extending from 339 K down to 227 K. In order to be able to study the deeply supercooled liquid, micron-sized water droplets were evaporatively cooled in vacuum and probed by ultrashort x-ray pulses. This is to date the lowest temperature at which measurements of the structure have been performed on bulk liquid water cooled from room temperature. Upon deep supercooling, the structure evolved toward that of a low-density liquid with local tetrahedral coordination. At ~230 K, where the low-density liquid structure started to dominate, the number of droplets containing ice nuclei increased rapidly. The estimated nucleation rate suggests that there is a “fragile-to-strong” transition in the dynamics of the liquid below 230 K, and its implications on water structure are discussed.Similarly, the electronic structure of deeply supercooled water was studied by x-ray emission spectroscopy down to 222 K, but the spectral changes expected from the structural transformation remained absent and explanations are discussed. At high fluence, the non-linear dependence of the x-ray emission yield indicated that there were high valence hole densities created during the x-ray pulse length due to Auger cascades, resulting in reabsorption of the x-ray emission.Finally, the hydrogen-bonded network in water was studied by x-ray absorption spectroscopy and compared to various ices. It was found that the pre-edge absorption cross-section, which is associated with distorted hydrogen bonds, could be minimized for crystalline ice grown on a hydrophobic BaF2(111) surface with low concentration of nucleation centers.
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