| 31. |
- Zorzet, Anna, 1977-
(författare)
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Mechanisms of Adaptation to Deformylase Inhibitors
- 2010
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Antibiotic resistance is a growing problem on a global scale. Increasing numbers of bacteria resistant toward one or multiple antibiotics could return us to the high mortality rates for infectious diseases of the pre-antibiotic era. The need for development of new classes of antibiotics is great as is increased understanding of the mechanisms underlying the development of antibiotic resistance. We have investigated the emergence of resistance to peptide deformylase inhibitors, a new class of antibiotics that target bacterial protein synthesis. The fitness of resistant mutants as well as their propensity to acquire secondary compensatory mutations was assessed in order to gain some insight into the potential clinical risk of resistance development. Most of this work was done in the bacterium Salmonella typhimurium, due to the availability of excellent genetic tools to study these phenomena. In addition, we have studied the bacterium Staphylococcus aureus as peptide deformylase inhibitors have been shown to have the greatest effect on Gram-positive organisms. In the course of this work we also examined the mechanistic aspects of translation initiation. Using a cell-free in vitro translation system we studied the effects of various components on translation initiation. These results have been combined with results obtained from resistant and compensated bacterial strains in vivo to gain new insights into the mechanisms of translation initiation.
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| 32. |
- B. Moreno, Anaísa
(författare)
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Evolution and host-specific adaptations of Legionella pneumophila
- 2022
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- How bacteria evolve pathogenic traits is shaped by their communities and environments. Legionella pneumophila is ubiquitous in aquatic habitats, where it persists by replicating within a broad range of protozoan hosts. Using the same mechanisms, L. pneumophila may also accidentally infect humans, causing a severe pneumonia known as Legionnaires’ disease. As hosts, humans are evolutionary dead-ends, resulting in the loss of human-specific adaptations after infection. This thesis aims to identify and characterise these host adaptations.In Paper I, we study the in-patient evolution of L. pneumophila. We collected a large set of strains from sporadic infections and outbreaks, pairing clinical isolates with their respective environmental sources. Using comparative genomic analyses, we identified two genes individually mutated in three independent infections. One gene encoded an outer membrane protein, a homolog from the OmpP1/FadL family, and the other an EAL domain-containing protein. These results suggest that convergent evolution may be at play and that these mutations are potential candidates for human-specific host adaptations.In Paper II, we investigate host adaptation and the selective pressures that drive it using a long-term experimental evolution approach. We passaged L. pneumophila in Acanthamoeba castellanii and U937 macrophages, separately and in alternation, for over 800 generations. We found 49 fixed mutations across the 18 evolved populations: two distinct mutations in RpsL, which confers streptomycin resistance, as well as two additional mutations, each consistently associated with one of the former, in the chaperonin GroES or in RpsD, a known compensatory mutation. Mutations in the lipopolysaccharide synthesis operon were observed only in lineages passaged in A. castellanii, whilst mutations in LerC were fixed in six lineages passaged in U937, making these candidate mutations for host-specific adaptations.In Paper III, we shift focus to A. castellanii, a natural host of L. pneumophila. We describe a novel method for high-efficiency transfection of this amoeba with a cationic polymer. Using a systematic approach to test different parameters, we found that widely available and inexpensive polyethylenimines can be used to transfect A. castellanii at a much greater efficiency than the currently used reagents.In conclusion, these studies suggest that although L. pneumophila can infect humans, it is sub-optimally adapted for it, and offer potential determinants of host-specificity in L. pneumophila.
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| 33. |
- Brabie, Dan, 1975-
(författare)
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On Derailment-Worthiness in Rail Vehicle Design : Analysis of vehicle features influencing derailment processes and consequences
- 2007
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- This thesis aims at systematically studying the possibilities of minimizing devastating consequences of high-speed rail vehicle derailments by appropriate measures and features in the train design including the running gear. Firstly, an empirical database is established containing as much relevant information as possible of past incidents and accidents that have occurred at substantial running speeds due to mechanical failure close to the interface between the running gear and the track. Other causes that ultimately brought the train in a derailed condition are also covered. Although various accidental circumstances make each derailment a unique event, certain patterns appear to emerge which lead to several critical vehicle parameters capable of influencing the outcome of a derailment or preventing a derailment to occur. Secondly, the possibility of preventing wheel climbing derailments after an axle journal failure is studied by implementing mechanical restrictions between wheelsets and bogie frame. In this respect, a multi body system (MBS) computer model is developed to account for such an axle failure condition, which is successfully validated on the basis of two authentic passenger car events. In order to study the overall post-derailment vehicle behaviour, in particular the wheelsets’ vertical motion and lateral deviation on sleepers, a comprehensive MBS post-derailment module is developed and implemented in the commercially available software GENSYS. The model detects wheel-sleeper impact conditions and applies valid force resultants calculated through linear interpolation based on a pre-defined look-up table. The table was constructed through exhaustive finite element (FE) wheel to concrete sleeper impact simulations utilising the commercially available software LS-DYNA. The MBS post-derailment module has been validated successfully in several stages, including a correct prediction of the derailing wheelset’s trajectory over ten consecutive sleepers in comparison with an authentic passenger vehicle derailment event. An extensive simulation analysis on the feasibility of utilizing alternative substitute guidance mechanisms attached to the running gear on rail vehicles is presented, as means of minimizing the lateral deviation. Three low-reaching guidance mechanisms attached onto the running gear (bogie frame, brake disc and axle journal box) are analysed in terms of geometrical parameters for a successful engagement with the rail in order to prevent large lateral deviations after twelve different derailment scenarios. Three conventional coupled passenger trailing cars are investigated in terms of lateral deviation and vehicle overturning tendency after derailments on tangent and curved track. This is performed as a function of various vehicle design features and parameters such as: maximum centre coupler yaw angle, carbody height of centre of gravity, coupler height and additional running gear features. In a similar manner, the articulated train concept is investigated in terms of the post-derailment vehicle behaviour as a function of different inter-carbody damper characteristics and running gear features.
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| 34. |
- Edstedt, Lars, 1981-
(författare)
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Mellan åtal och dom : Om underlaget och ramarna för rättens bedömning av frågorna om skuld, rubricering och påföljd
- 2024
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Between Indictment and Judgment. On the Basis for and the Limits of the Court’s Assessmentof Questions Concerning Guilt, Legal Qualification and Sentence.This study concerns the relationship between the indictment and the judgment in Swedish criminal procedure. Three central aspects of the criminal judgment are covered: The question of the accused’s guilt (the alleged criminal act in the indictment), the legal qualification of the offence and the sentence. The rule governing this relationship, between indictment and judgment, can be found in Chapter 30 paragraph 3 of the Swedish Code of Judicial Procedure. The requirements on the contents of the indictment are carefully examined, as well as other procedural acts, by the accused and by the court itself through its direction of the proceedings, that can have an effect on the limits of the court’s examination of criminal cases.Two questions of paramount importance are covered in-depth: How detailed must the indictment be (and what are the consequences of vagueness in the indictment)? And how should the principle that the court is bound by the indictment be interpreted? It is argued that a flexible standard for the indictment should be applied, allowing different legal consequences for varying deficiencies. With regard to the court being bound by the indictment, is argued that the theory of literary interpretation of the indictment is flawed, and that the demands of the principle of contradictory proceedings should determine the boundaries of the criminal act in the indictment.The study also contains a comprehensive examination of the case-law of the European Court of Human Rights concerning the right of the accused to be informed of the natureand cause of the accusation, contained in Article 6 § 3 (a) of the European Convention of Human Rights.The material rules of immediate interest are explored against the backdrop of a lengthy investigation into their historical and ideological underpinnings. The history of Swedish criminal procedure is described, as well as various theoretical developments. In particular, the question if Swedish criminal procedure should best be described as inquisitorial or accusatorial/adversarial and questions concerning the function of criminal procedure are investigated.
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| 35. |
- Gullberg, Erik, 1980-
(författare)
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Selection of Resistance at very low Antibiotic Concentrations
- 2014
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The extensive medical and agricultural use and misuse of antibiotics during the last 70 years has caused an enrichment of resistant pathogenic bacteria that now severely threatens our capacity to efficiently treat bacterial infections. While is has been known for a long time that high concentrations of antibiotics can select for resistant mutants, less is known about the lower limit at which antibiotics can be selective and enrich for resistant bacteria.In this thesis we investigated the role of low concentrations of antibiotics and heavy metals in the enrichment and evolution of antibiotic resistance. Selection was studied using Escherichia coli and Salmonella enterica serovar Typhimurium LT2 with different resistance mutations, different chromosomal resistance genes as well as large conjugative multidrug resistance plasmids. Using very sensitive competition experiments, we showed that antibiotic and heavy metal levels more than several hundred-fold below the minimal inhibitory concentration of susceptible bacteria can enrich for resistant bacteria. Additionally, we demonstrated that subinhibitory levels of antibiotics can select for de novo resistant mutants, and that these conditions can select for a new spectrum of low-cost resistance mutations. The combinatorial effects of antibiotics and heavy metals can cause an enrichment of a multidrug resistance plasmid, even if the concentration of each compound individually is not high enough to cause selection.These results indicate that environments contaminated with low levels of antibiotics and heavy metals such as, for example, sewage water or soil fertilized with sludge or manure, could provide a setting for selection, enrichment and transfer of antibiotic resistance genes. This selection could be a critical step in the transfer of resistance genes from environmental bacteria to human pathogens.
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| 36. |
- Lundin, Erik
(författare)
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Evolution of New Genes and Functions
- 2018
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- To answer major evolutionary questions, we need a better understanding of the effects of mutations on specific functions and organism fitness. The aim of this thesis was to elucidate how new functions evolve and potential trade-offs with the original function.Paper I identified a bimodal distribution of fitness effects of mutations in Salmonella enterica HisA protein. Most mutations negatively affected protein function but the effect was masked at high gene expression. Expression levels and the extent to which the studied protein limited growth were important in determining the fitness effects of mutations. No fitness prediction tool was satisfactorily alone but in combination predictions were improved.In Paper II, S. enterica HisA was evolved to acquire TrpF activity. Numerous pathways towards improved TrpF activity were examined and several improvement mechanisms were identified. Improved TrpF activity extensively reduced the original activity, generalist enzymes were rare and restoring original activity after an initial loss was difficult. Furthermore, expression levels had a major impact on the shape of the trade-off curve.In Paper III, adaptation during serial passage of Escherichia coli and S. enterica under laboratory conditions were examined. Adaptive mutations were identified in four different laboratory media and their fitness effects were determined. Little overlap in mutation spectra was found in the different media and species suggesting that adaptation was media-specific. Furthermore, media adaptation mutations reduced the accuracy of fitness assays and the use of pre-adapted strains improved the sensitivity of fitness assays 10-fold.Paper IV examined evolution of novel metabolic capabilities in S. enterica by analyzing growth on 124 non-native carbon sources. Growth was observed on 25 compounds and for five of these, the causative mutation was identified. Increased gene expression of cryptic genes was a major mechanism for acquiring the novel phenotypes.In conclusion, my results show that in most cases many types of mutations can improve a function and allow adaptive evolution but this often is associated with a trade-off and loss in other abilities. Increased gene expression was a major mechanism by which bacteria could compensate for loss of an activity as well as acquire new metabolic capabilities.
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| 37. |
- Lövgren, Mattias, 1974-
(författare)
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Accessory factors for ribosomal assembly
- 2004
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The assembly of ribosomal RNA (rRNA) and ribosomal proteins (r-proteins) into ribosomal subunits (30S and 50S) is a complex process. Transcription of rRNA requires antitermination proteins and the primary transcripts are processed by ribonucleases. R-proteins and rRNAs are chemically modified, the r-proteins bind to the rRNAs and the formed RNA-protein complexes are folded into mature ribosomal subunits. All these processes are well-coordinated and overlapping. Non-ribosomal factors are required for proper assembly and maturation of the ribosomal subunits. Two of these factors are the RimM and RbfA proteins, which bind to 30S subunits and are important for efficient processing of 16S rRNA. Lack of either RimM or RbfA results in a reduced amount of polysomes and a lower growth rate. An increased amount of RbfA can partially compensate for deficiencies shown by a RimM lacking mutant.Here, mutations that alter phylogenetically conserved amino acids in RimM have been constructed. One of these (rimM120), which resulted in the replacement of two adjacent tyrosines by alanines, reduced the growth rate three-fold and also decreased the processing efficiency of 16S rRNA. The RimM120 mutant protein showed a much reduced binding to the 30S subunits. Suppression of the rimM120 mutant was achieved by increased amount of the RimM120 protein, by overexpression of rbfA, or by mutations that changed r-protein S19 or 16S rRNA. A variant of r-protein S13, which was previously isolated as a suppressor to a deletion of rimM (∆rimM), suppressed also the rimM120 mutation. The wild-type RimM protein, but not the RimM120 protein, was shown to bind r-protein S19 in the 30S subunits. The changes in S13, S19 and 16S rRNA that compensated for the deficiencies shown by the rimM mutants are all located within a small region of the head of the 30S subunit, suggesting that this region is the likely target for the RimM action.To isolate RbfA variants that show reduced association with the 30S subunits, phylogenetically conserved, surface exposed amino acid residues of RbfA were changed to alanines or, in some instances, to amino acids of the opposite charge to that in the wild-type protein. Alterations of F5, R31, D46 and D100 had the largest effect on growth.Mutations in the metY-nusA-infB operon, isolated as suppressors to the ∆rimM mutant, were shown to increase the amounts of RbfA. In a ∆rimM mutant, all RbfA protein was found associated with the 30S subunits and no free RbfA was detected.The RlmB protein was shown to be the methyltransferase responsible for the formation of Gm2251 in 23S rRNA in Escherichia coli. Unlike a Saccharomyces cerevisiae mutant that lacks the orthologue to RlmB, Pet56p, which methylates mitochondrial rRNA, a ∆rlmB mutant did not show any defects in ribosomal assembly.
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| 38. |
- Malmgren, Mike
(författare)
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Managing Risks in Business Critical Outsourcing : A Perspective from the Outsourcer and the Supplier
- 2010
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Companies are increasingly outsourcing business critical activities to suppliers of outsourcing services. As the complexity and business criticality of the outsourced activities increases, the risk of poor performance increases. This thesis studies large scale outsourcing in the telecom industry where a recent trend is to transfer the development, operation and maintenance of the telecom infrastructure to telecom equipment suppliers. The significance of this type of outsourcing is that the outsourced activity is the revenue generating part of the telecom operators business.Part 1 discusses the purpose and research questions followed by the theoretical underpinning in the research. The research strategy is to study the outsourcing relationship in three distinct stages of its development and the theoretical underpinning applies transaction costs analysis in the Scoping & Search stage and Das &Teng’s (2001) framework of trust and control for managing risks in the Negotiation and Transition stages. This design is in response to calls for a more detailed understanding of how organizations manage risks, it therefore takes the perspective of both the outsourcer and the supplier in the research.Part 2 is a multiple case study of telecom operators in Holland, Sweden and Australia where the supplier in all three cases is Ericsson Global Services organization. The study is further supplemented by mini-cases of large scale IS/IT infrastructure outsourcing.Part 3 has three main parts. Firstly, a cross case analysis of the cases in Part 2; secondly, a discussion of the findings linked to the research questions resulting in a set of propositions. The third and final part covers additional insights and learnings from studying business critical outsourcing and suggestions for further research.The main contributions in the research can be summarised as:Physical asset specificity follows transaction costs logic, however human asset specificity is largely ignored by both outsourcer and supplierBusiness critical outsourcing by its nature faces a limited market for capable suppliers. This results in single-source negotiations followed by a cooperative stance and open book negotiations.Das & Teng’s (2001) framework for management of risks has been found to have specific directions, some bi-directional and others uni-directional. Furthermore, different dimensions in the framework operate at different managerial levels. Goodwill trust-building operate at the corporate executive level, competence trust-building, output and behavioural control at the level of the negotiation team, and the research indicates that the social control dimension is not applied in business critical outsourcing negotiations.A further finding is that goodwill trust-building precedes all other dimensions of trust and control, and is a pre-requisite for establishing a cooperative stance in the negotiations.
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| 39. |
- Nordigården, Daniel, 1978-
(författare)
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Outsourcing in the Wood Product Manufacturing Sector A Combined Customer and Supplier Perspective
- 2007
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Outsourcing can be defined as transferring an activity from internal to external control. This thesis studies outsourcing in the wood product manufacturing (WPM) sector from both a customer and supplier perspective. The research design is a multiple case study approach, and it is based on six Scandinavian companies in the door, floor and window industries and one larger supplier of raw material. This study provides an understanding of driving forces for outsourcing in a different context than previously studied and has identified cost reduction in combination with reallocating resources from non-core activities as main driving forces. Compared to several other industrial sectors, outsourcing strategies for the WPM firms have little to do with accessing external sources’ capabilities.In the literature, there is often a main focus on the strategic level of outsourcing, however, such heavy resource-based focus in terms of a core competence approach in the formulation of outsourcing strategies at the customer side risks forgetting that components can still be vulnerable to supplier failure. Here, more focus needs to be put on the operational level when considering outsourcing. This thesis illustrates customers considering outsourcing where there are not any given outsourcing supplier partners developed. At the same time, for the supplier side, forward integration and specialising by taking over outsourcing is complicated by an initial divergent production flow of sawn timber. When not all contexts have developed supplier markets for directly managing outsourcing, it should not be assumed that general outsourcing models are directly applicable. In general, the question of whether or not to outsource seems too complex to simply be considered as either “in or out”. A company needs safeguards when conducting outsourcing and in a situation where there is a non-developed supplier market, parallel in-house production becomes an alternative.
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| 40. |
- Olofsson, Sara K., 1977-
(författare)
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Relation Between Drug Exposure and Selection of Antibiotic Resistant Bacteria
- 2006
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The worldwide increase in antibiotic resistance is a concern for public health. When the appropriate antibiotic dosage is determined, the priorities are efficacy and toxicity. The aim of this thesis was to gain knowledge about the most efficient dosing regimens in order to minimize the emergence and selection of antibiotic-resistant mutants. We also wanted to assess the impact of antibiotic selective pressure and host to host transmission for the dissemination of resistance. Escherichia coli bacteria with different levels of cefotaxime susceptibility were competed in an in vitro kinetic model, demonstrating a complex selection of low-level resistance influenced e.g. by the time duration of selective concentrations and the rise of new mutants. We also constructed a mathematical model incorporating biologically relevant parameters and showed its usefulness when assessing the risks of resistance development. When E. coli populations with pre-existing fluoroquinolone-resistant mutants were exposed to simulated serum concentrations, several currently used doses of fluoroquinolones clearly enhanced the development and selection of resistance. The mutant prevention concentration (MPC) was measured for several E. coli isolates with different fluoroquinolone susceptibilities, and because of fluctuating antibiotic concentrations in the human body, the pharmacokinetics was considered when evaluating MPC. Results indicate that the area under the serum concentration time curve in relation to the MPC may be a useful predictor for emergence of resistance. In the commensal flora of healthy human couples we noted a high frequency of trimethoprim-resistant E. coli. There was also an extensive sharing and transmission of E. coli clones. Treating the female with trimethoprim reduced the number of intestinal E. coli which might have facilitated the transmission from the male partner. These findings suggest that the rate of transmission is high and effectively contributes to the spread of both susceptible and antibiotic-resistant E. coli in intrafamilial settings.
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