| 1. |
- Dyrhage, Karl
(författare)
-
Multi-omics investigation into bacterial evolution
- 2022
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The focus of this thesis is the investigation of the evolution and cellular processes of Tuwongella immobilis and Apilactobacillus kunkeei, two bacterial species with different levels of genomic and cellular complexity, using a multi-omics approach.In the first study we examined the proteome of T. immobilis with LC-MS/MS after fractionation by differential solubilisation, yielding fractions corresponding to the cytoplasm, inner membrane, and outer membrane. The experiment was repeated with Escherichia coli and the results were compared. T. immobilis had five times as many predicted cytoplasmic proteins in the most hydrophobic fraction as E. coli. Among these are innovations in the Planctomycetota lineage and protein families that have undergone recent paralogisation followed by domain shuffling, including many enzymes related to information processing.The remaining three studies dealt with honeybee symbiont A. kunkeei. In the first of these, we sequenced and compared the chromosomal and extrachromosomal content of 102 novel A. kunkeei strains. We found that A. kunkeei has an open pangenome and an active set of transposable elements. Within the population we discovered three plasmids between 19.5 and 32.9 kb, one of which codes for enzymes involved in the synthesis of the antimicrobial compound kunkecin A which inhibits growth of the bee pathogen Melisococcus plutonius.In the next study we collected transcriptomic, proteomic, and metabolomic data from two growth phases from A. kunkeei strain A1401 and mapped the results to a metabolic pathway model. Enzymes involved in fermentation of fructose were highly expressed during the exponential growth phase. Enzymes involved in UMP biosynthesis were upregulated during stationary phase, as were protein involved in stress response and detoxification.The last study concerned the secretome of A. kunkeei. We characterised two types of extracellular particles from A. kunkeei strains A1401 and A0901. One type of particle was found to be proteinaceous, while the other type constituted membrane vesicles containing RNA. Comparison of transcriptomic data from the membrane vesicles and whole cells showed that the packing of the RNA was largely untargeted, but with a bias towards highly expressed mRNAs. We suggest that the cell uses membrane vesicles as a mechanism to get rid of superfluous mRNAs after rapid-response overexpression.Together these studies provide insights into the processes driving evolution in T. immobilis and A. kunkeei, and generate several testable hypotheses for future studies.
|
|
| 2. |
- Ancillotti, Mirko, 1981-
(författare)
-
Antibiotic Resistance: A Multimethod Investigation of Individual Responsibility and Behaviour
- 2021
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The rapid development of antibiotic resistance is directly related to how antibiotics are used in society. The international effort to decrease and optimise the use of antibiotics should be sustained by the development of policies that are sensitive to social and cultural contexts.The overarching aim of the thesis was to explore and discuss the Swedish public’s beliefs, values and preferences influencing engagement in judicious antibiotic behaviour.Study I explored through focus group discussions lay people’s perceptions and beliefs about antibiotics and antibiotic resistance. The Health Belief Model was used to identify factors that could promote or hinder engagement in judicious antibiotic behaviour. Participants found antibiotic resistance to be a serious problem but were not equally worried about being affected by it. There was a tension between individual and collective reasons for engaging in judicious behaviour.Study II explored lay people’s views on the moral challenges posed by antibiotic resistance through focus group discussions. Participants identified in the decreasing availability of effective antibiotics a problem of justice, which involves individual as well as collective moral responsibility. Different levels of policy demandingness were discussed in light of these results.Study III investigated, through an online Discrete Choice Experiment, public preferences regarding antibiotic treatment and the relative weight of antibiotic resistance in decision-making. Public behaviour may be influenced by concerns over the rise of antibiotic resistance. Therefore, stressing individual responsibility for antibiotic resistance in clinical and societal communication may affect personal decision-making.Study IV clarified the notions of collective and individual moral responsibility for antibiotic resistance and suggested a virtue-based account thereof. While everyone is morally responsible for minimising his/her own contribution to antibiotic resistance, individuals do or do not engage in judicious antibiotic behaviour with different degrees of voluntariness.The findings suggest that people could change their behaviour due to concerns over their own contribution to antibiotic resistance. Effective health communication should be developed from an appraisal of people’s attitudes, beliefs and social norms that influence antibiotic resistance related behaviours. Policy demandingness should take into account socioeconomic factors characterising local realities.
|
|
| 3. |
- Hou, Xiao-Qing, et al.
(författare)
-
Functional Evolution of a Bark Beetle Odorant Receptor Clade Detecting Monoterpenoids of Different Ecological Origins
- 2021
-
Ingår i: Molecular biology and evolution. - : Oxford University Press. - 0737-4038 .- 1537-1719. ; 38:11, s. 4934-4947
-
Tidskriftsartikel (refereegranskat)abstract
- Insects detect odors using an array of odorant receptors (ORs), which may expand through gene duplication. How and which new functions may evolve among related ORs within a species remain poorly investigated. We addressed this question by functionally characterizing ORs from the Eurasian spruce bark beetle Ips typographus, in which physiological and behavioral responses to pheromones, volatiles from host and nonhost trees, and fungal symbionts are well described. In contrast, knowledge of OR function is restricted to two receptors detecting the pheromone compounds (S)-(-)-ipsenol (ItypOR46) and (R)-(-)-ipsdienol (ItypOR49). These receptors belong to an Ips-specific OR-lineage comprising seven ItypORs. To gain insight into the functional evolution of related ORs, we characterized the five remaining ORs in this Glade using Xenopus oocytes. Two receptors responded primarily to the host tree monoterpenes (+)-3-carene (ItypOR25) and p-cymene (ItypOR27). Two receptors responded to oxygenated monoterpenoids produced in larger relative amounts by the beetle-associated fungi, with ItypOR23 specific for (+)-trans-(1R, 4S)-4-thujanol, and ItypOR29 responding to (+)-isopinocamphone and similar ketones. ItypOR28 responded to the pheromone E-myrcenol from the competitor Ips duplicatus. Overall, the OR responses match well with those of previously characterized olfactory sensory neuron classes except that neurons detecting E-myrcenol have not been identified. The characterized ORs are under strong purifying selection and demonstrate a shared functional property in that they all primarily respond to monoterpenoids. The variation in functional groups among OR ligands and their diverse ecological origins suggest that neofunctionalization has occurred early in the evolution of this OR-lineage following gene duplication.
|
|
| 4. |
- Jagdmann, Jennifer, 1993-
(författare)
-
Antibiotic resistance in the pan-genome of E. coli
- 2022
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The pan-genome of a species is made up of all gene families that can be included in any individual isolate of the species. Escherichia coli (E. coli) has an open pan-genome including at least 128000 gene families, while only about half of the genes found in each individual isolate are common to all isolates. This indicates a great intraspecies genetic diversity that is not often considered when studying antibiotic resistance. This thesis uses a comparatively large collection of isolates to include more intraspecies genetic diversity and assess its impact on resistance.One angle of this approach was to study the impact of the pan-genome on spontaneous resistance development. For this, we compared the development of resistance to several antibiotics in a 35-strain collection of E. coli isolates. We found that frequencies of resistant mutants varied greatly between strains, that this variation was largely independent from the initial resistance level of the isolates, and that an isolate’s frequency of mutants for one antibiotic was a poor predictor of the mutant frequencies for other antibiotics. In conclusion, there was a clear impact of genetic diversity on spontaneous antibiotic resistance development. Using this approach, we observed a previously undescribed pattern of resistance development for tigecycline, a last-line antibiotic, via amplifications of a known efflux pump. In addition, we found a mutated allele of the pump with a reduced level of induction that did not allow for resistance development through amplifications. We showed that a fitness advantage at low antibiotics concentrations and clonal spread were likely contributing to the high occurrence of the mutated pump among E. coli isolates. While this efflux pump is common and well-studied, the lack of pre-existing knowledge of the mutated allele highlights the value of including many isolates in studies of antibiotic resistance. Another angle of this thesis was to determine whether intraspecies genetic diversity also impacts plasmid-borne resistance. For this, we transferred several multiresistance plasmids into a collection of E. coli hosts and characterized the plasmid-host combinations. We observed strain- and plasmid-dependent variations in resistance as well as inconsistencies in the clinical resistance categorization of different hosts with the same plasmid.In conclusion, this work reveals the impact of intraspecies genetic diversity on the development of antibiotic resistance, both through spontaneous mutations and the acquisition of resistance plasmids, highlighting the need to include intraspecies genetic diversity in studies of antibiotic resistance.
|
|
| 5. |
- Karlsson, Johan, 1990-
(författare)
-
Essays on Family Firms and Firm Growth Barriers
- 2020
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- This thesis concerns the implications of family ownership and perceived growth barriers for firm decision-making and performance. The first article examines the inclusion of family business in economics doctoral programs in the United States and Sweden, as well as the views of professors and textbook authors and research on family business. It is found that family business is not included in the examined curricula. Furthermore, professors and authors do not publish research on family business and generally do not see a need to incorporate it into economic theory. The article concludes by discussing the causes of this omission, as well as strategies to overcome them in order to further our understanding of economic action. The second article presents a novel strategy for identifying domiciled family firms using total population data. By applying this strategy to Swedish data, family firms are found to contribute to one-third of Swedish employment and gross domestic product, and a significant share of Sweden’s largest firms are family-owned. In general, family firms are found to be smaller than their non-family equivalents, although they are more profitable. Meanwhile, differences between family firms and nonfamily firms are found to diminish with firm size. The third article examines whether family firms have a comparative employment growth advantage over nonfamily firms in regions with relatively low population density. As a group, family firms are found to be the main source of job creation in rural regions, largely as a result of their large numbers. Nevertheless, the average family firm is found to grow more slowly than the average non-family firm. Meanwhile, in line with the study’s conjecture, this difference is found to decrease across the urban-rural context, i.e., across metropolitan, urban and rural regions. The fourth paper examines the representation of women in top management teams1 in family firms and non-family firms. Moreover, the share of women in a firm’s top management team is found to be positively associated with the additional appointment of female managers. Lastly, kinship bonds between the owning families and prospective managers are found to be positively associated with the appointment of women on top management teams. The fifth paper aims to capture the relationship between perceived growth barriers and firm size, which is achieved by developing a novel data-driven strategy for identifying firm size groups. It is found that smaller firms typically face accessibility constraints on equity financing, whereas larger firms generally face barriers related to competition and accessibility to qualified staff. These results are benchmarked against those using prevailing strategies for measuring firm size, whereby it is suggested that there may be a need for methodological rethinking in the field regarding its treatment of firm size.
|
|
| 6. |
- B. Moreno, Anaísa
(författare)
-
Evolution and host-specific adaptations of Legionella pneumophila
- 2022
-
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.
|
|
