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Coming dissertations at Uppsala university

  • Bound to the past: Historical contingency in aquatic microbial metacommunities Author: Máté Vass Link: Publication date: 2020-01-16 12:24

    The composition of ecological communities differs due to a combination of different processes, which includes selection by local environmental conditions, dispersal from the regional species pool and random events. Additionally, historical processes such as past dispersal events may leave their imprint on communities as well, resulting in historically contingent communities. However, in most ecological studies the existence and the effect of historical processes remained hidden, even though they could be important predictors of contemporary variations in ecological communities.

    This thesis focuses on how historical processes could influence aquatic microbial metacommunities by investigating when and where history matters, and which factors may regulate historical contingency.

    Using null model approaches, evidence for historical contingency was found in natural ecosystems, more specifically rock pool metacommunities, and appeared to be more likely to influence bacterial than microeukaryotic communities.

    The thesis further used an outdoor mesocosm experiment to test how ecosystem-sized induced differences in environmental fluctuations influenced community assembly processes along a disturbance gradient. This study did, however, not provide strong and clear evidence for the importance of historical contingency.

    In the face of climate change, results from a laboratory experiment showed that historical contingencies might be strengthened with warming. Specifically, warming increased the resistance of local communities against invasion by decreasing the establishment success of migrant species. Hence, temperature-dependent historical contingency was found in aquatic bacterial communities, although its persistence differed between local communities and the degree of invasion they were exposed to.

    Taken together, this thesis suggests that historical processes can leave their imprint on aquatic microbial communities, even though their importance is highly context dependent. Future studies, should therefore consider historical contingency, or in other words, the legacy of the past as a potentially important mechanism that can contribute to the spatial diversity of microbial communities.  

  • Towards atomically resolved magnetic measurements in the transmission electron microscope : A study of structure and magnetic moments in thin films Author: Hasan Ali Link: Publication date: 2020-01-15 09:09

    The magnetic properties of thin metallic films are significantly different from the bulk properties due to the presence of interfaces. The properties shown by such thin films are influenced by the atomic level structure of the films and the interfaces. Transmission electron microscope (TEM) has the potential to analyse the structure and the magnetic properties of such systems with atomic resolution. In this work, the TEM is employed to characterize the structure of the Fe/V and Fe/Ni multilayers and the technique of electron magnetic circular dichroism (EMCD) is developed to obtain the quantitative magnetic measurements with high spatial resolution.

    From TEM analysis of short period Fe/V  multilayers, a coherent superlattice structure is found. In short period Fe/Ni multilayer samples with different repeat frequency, only the TEM technique could verify the existence of the multilayer structure in the thinnest layers. The methods of scanning TEM imaging and electron energy loss spectroscopy (EELS) results were used and refined to determine interdiffusion at the interfaces. The confirmation of the multilayer structure helped to explain the saturation magnetization of these samples.

    Electron magnetic circular dichroism (EMCD) has the potential to quantitatively measure the magnetic moments of the materials with atomic resolution, but the technique presents several challenges. First, the EMCD measurements need to acquire two EELS spectra at two different scattering angles. These spectra are mostly acquired one after the other which makes it difficult to guaranty the identical experimental conditions and the spatial registration between the two acquisitions. We have developed a technique to simultaneously acquire the two angle-resolved EELS spectra in a single acquisition. This not only ensures the accuracy of the measurements but also improves the signal to noise ratio as compared to the previously used methods. The second important question is the effect of crystal orientations on the measured EMCD signals, considering the fact that the crystal orientation of a real crystal does not remain the same in the measured area. We developed the methodology to simultaneously acquire the EMCD signals and the local crystal orientations with high precision and experimentally showed that the crystal tilt significantly changes the magnetic signal. The third challenge is to obtain EMCD measurements with atomic resolution  which is hampered by the need of high beam convergence angles. We further developed the simultaneous acquisition technique to obtain the quantitative EMCD measurements with beam convergence angles corresponding to atomic size electron probes. 

  • Computational Modeling of the Structure, Function and Dynamics of Biomolecular Systems Author: Yashraj Kulkarni Link: Publication date: 2020-01-14 10:38

    Proteins are a structurally diverse and functionally versatile class of biomolecules. They perform a variety of life-sustaining biological processes with utmost efficiency. A profound understanding of protein function requires knowledge of its structure. Experimentally determined protein structures can serve as a starting point for computer simulations in order to study their dynamic behavior at a molecular level. In this thesis, computational methods have been used to understand structure-function relationships in two classes of proteins - intrinsically disordered proteins (IDP) and enzymes.

    Misfolding and subsequent aggregation of the amyloid beta (Aβ) peptide, an IDP, is associated with the progression of Alzheimer’s disease. Besides enriching our understanding of structural dynamics, computational studies on a medically relevant IDP such as Aβ can potentially guide therapeutic development. In the present work, binding interactions of the monomeric form of this peptide with biologically relevant molecular species such as divalent metal ions (Zn2+, Cu2+, Mn2+) and amphiphilic surfactants were characterized using long timescale molecular dynamics (MD) simulations. Among the metal ions, while Zn2+ and Cu2+ maintained coordination to a well-defined binding site in Aβ, Mn2+-binding was observed to be comparatively weak and transient. Surfactants with charged headgroups displayed strong binding interaction with Aβ. Complemented by biophysical experiments, these studies provided a multifaceted perspective of Aβ interactions with the partner molecules.

    Triosephosphate isomerase (TIM), a highly evolved and catalytically proficient enzyme, was studied using empirical valence bond (EVB) calculations to obtain deeper insights into the catalytic reaction mechanism. Multiple structural features of TIM such as the flexible loop and preorganized active site residues were investigated for their role in enzyme catalysis. The effect of substrate binding was also studied using truncated substrates. Finally, using enhanced sampling methods, dynamic behavior of the catalytically important loop 6 was characterized. The importance of structural stability and flexibility on protein function was illustrated by the work presented in this thesis, thus furthering our scientific understanding of proteins at a molecular level.