Coming dissertations at Uppsala university
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Molecular mechanism of plasmid copy number control in Yersinia
Link: http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-523712
The ability of pathogenic bacteria to cause disease depends on various virulence mechanisms. The three pathogenic species of Yersinia use a type III secretion system (T3SS) to translocate effector proteins into host cells and disrupt the immune system. This T3SS is encoded on a 70kb, low-copy, virulence plasmid. A novel mechanism of virulence was identified in Y. pseudotuberculosis, where the plasmid copy number (PCN) increases during infection. The PCN needs to be tightly regulated, as it encodes important, but costly, virulence genes. This thesis expends our understanding of PCN regulation and its importance in Yersinia virulence.
In Paper I, we demonstrate that PCN regulation as a virulence mechanism is a dynamic system capable of adapting to different host environments. We found that an increased PCN is important at the onset of infection, particularly during the colonization phase. In later stages, within different organs, the PCN decreases, suggesting a reduced need for the T3SS once the infection is established. This insight was enabled by the development of a novel method based on droplet digital PCR, allowing accurate PCN detection in sample with very little target DNA.
In Paper II, we studied the PCN regulation by YopD. We showed that YopD represses PCN through the regulation of copA transcription. This YopD-dependant PCN control is released when YopD is secreted outside the bacteria upon contact with the host cell. YopD is a multifunctional protein. It possesses different domains crucial for its different functions. We found that the domains important for T3SS regulation are also required for PCN regulation.
In Paper III, we used phenotypical approaches together with Nuclear Magnetic Resonance (NMR) method to study YmoA, a protein regulating gene expression in Yersinia in response to environmental stresses. YmoA’s ability to control gene expression requires its interaction with H-NS, a global DNA regulator. YmoA up-regulates a great number of genes, the T3SS and its effectors protein for instance. We observed that it also down-regulates many others, such as flagellar assembly genes. Our findings reveal that YmoA regulates PCN and senses temperature and osmotic stress resulting in a change of its conformation, which affects its ability to form a complex with H-NS.
In summary, the studies presented in this thesis show that PCN is a highly dynamic, tightly regulated mechanism, important for Yersinia pathogenesis.
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Surviving Birth and Thriving : Identifying infants at risk of death and disability in low- and middle-income countries
Link: http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-523713
Background: Ending preventable newborn deaths is an unfinished global health agenda. Infants surviving birth have a right to thrive and to reach their full developmental potential. The aim of this thesis was to evaluate methods for identification of infants in need of neonatal resuscitation and at risk of disability in low- and middle-income countries.
Paper I was an observational study conducted in Pokhara, Nepal, comparing the heart rate in the first 3 minutes in infants who were quietly breathing (n=54) versus crying (n=1155) immediately after birth. The median heart rate did not differ between the two groups, but both bradycardia and tachycardia were more common among non-crying but breathing newborns.
Paper II was a systematic review and meta-analysis of studies examining the incidence and outcomes of intrapartum-related neonatal encephalopathy in low- and middle-income countries. Altogether 53 articles were identified. The incidence ranged from 1.5 to 20.3 per 1000 live births (5 studies), the mean neonatal mortality was 19.3 % (45 studies, 3307 infants), and the incidence of combined outcome of death or moderate to severe disability at follow-up was 44.6 % (19 studies, 1595 children).
Paper III evaluated the feasibility of smartphone-aided remote General Movements Assessment for identification of children at risk of cerebral palsy in Kathmandu, Nepal. Children surviving birth asphyxia or neonatal seizures were filmed by parents using the NeuroMotion smartphone application at home at 3 months’ age. Altogether 31 children were enrolled, and 16 parents returned at least one video of approved technical quality. Usability of the app was good based on parental survey.
In Paper IV, individual (n=4) and group interviews (n=2) were conducted with ten mothers participating in the smartphone aided follow-up of their infants. The data were analysed using deductive qualitative content analysis. The remote follow-up was acceptable with support from the research assistants. Some participants would have preferred a face-to-face evaluation.
Conclusion: Not crying at birth is a potential indicator for need of neonatal resuscitation. Infants who survive resuscitation are at risk of intrapartum-related neonatal encephalopathy, which has persistently high burden particularly in low-income countries. All survivors of encephalopathy need follow-up and smartphone-aided remote General Movements Assessment could complement the assessments in settings similar to Kathmandu.
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Frustrated magnetism in icosahedral structures : The influence of order-disorder in quasicrystals and approximant crystals
Link: http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-524558
This work will begin with an introduction to quasicrystals (QCs) and their structure, defining the unit cell-equivalent for icosahedral quasiperiodicity: a 3D tiling based on the golden ratio and aperiodic in all three dimensions. We briefly present the cut-and-project method used to generate QCs from a higher dimension hypercrystal, and how to build the 3D Penrose tilings, composed of the two golden rhombohedra. We introduce the atomic elementary units used to understand Tsai-type icosahedral QCs and their related approximant crystals (ACs). Approximants are conventional periodic crystals with local atomic environments very similar to their QC counterparts. Two methods for synthesis of Tsai-type QCs and approximants are introduced, the self-flux method as well as a rapid quench method. We describe briefly the differences between the two methods and aspect about phase stability for QCs and ACs obtained in binary and ternary systems. Various types of structural modulations can be induced in ACs which are absent from QCs. We present a new criterion discovered during the doctoral studies, which links the structure of existing ACs to the existence of stable QC counterparts. Basic concepts of magnetism relevant to Tsai systems are then introduced, with a description of the 4f shell magnetism in lanthanide elements, how it differs from transition metal magnetism, with localized (and relatively large) magnetic moments. In intermetallic systems such as Tsai-type QCs and ACs, the main type of magnetic interaction is of RKKY type. We link their structure to the magnetic behavior and phase transition that can occur in frustrated systems: spin glass, reentrant spin glass, spin ice, etc. and how they can be related to various Tsai systems.