ABSTRACT Nontypable Haemophilus influenzae is a common cause of otitis, sinusitis and conjunctivitis. It is the most common bacterial pathogen associated with chronic obstructive pulmonary disease (COPD). Studies have shown that nonpathogenic Haemophilus haemolyticus are often mistaken for Haemophilus influenzae due to an absent hemolytic reaction on blood agar. Distinguishing H. haemolyticus from H. influenzae is important to prevent unnecessary antibiotic use, and to understand the role of H. influenzae in clinical infections. In this study, PCR-primers for amplifying 16S rDNA sequences were used to set up a method for distinguishing H. haemolyticus from H. influenzae. The aim was to use the method for analyzing apparent H. influenzae strains, to investigate if some strains were in fact H. haemolyticus. However, because of problems with unspecific primerannealing,no conclusions could be drawn regarding misclassification of H. haemolyticus. Moraxella catarrhalis is the second most common bacterial pathogen associated with COPD. It also causes otitis and sinusitis. An important virulence factor of M. catarrhalis is the outer membrane protein Moraxella catarrhalis IgD-binding protein (MID). One part of the protein; MID764-913 , has been shown to function as an adhesin, and this part has been fragmented to further investigate its adhesive properties. The aim of this second, independent study, was to express some of these proteinfragments by cloning in E. coli. The time spent on this project was too short, and no proteins could be expressed duing this period.

The purpose of the study was to set up a method for cultivation of C. pneumoniae from infected mouse tissue in Hep2 cells. We also evaluated a new reagent, Chlamatis, which is considered to increase the detection sensitivity of the bacterium with both PCR and cultivation. All 10 serum samples treated with Chlamatis were negative for C. pneumoniae in PCR. The cultivation of tissue was found to work without problems. The yield of the bacteria was highest at the speed of 30 Hz using homogenization with TissueLyser. Mice infected with C. pneumoniae were killed at days 4, 8, 20 and 40. The highest yields of C. pneumoniae were found at days 4 and 8 using PCR with all infected mice. The results obtained with PCR and cultivation confirmed each other to a large extent. For heart tissue, PCR positive mice were found only at days 4 and 8. The number of PCR positive lung samples confirmed to a large extent the number found by cultivation, except for mice killed after 4 days and 40 days where the results differed slightly. This indicated that the optimization of the cultivation method was successful

Aim Because of the major problems that certain Vibrio specie, especially Vibrio harveyi, can cause the aquaculture industries a rapid method to identify Vibrio isolates is required. Early diagnosis of a V. harveyi infection could facilitate disease surveillance, treatment and prevention in cultured marine animals. Therefore, the use of PCR to aid in the identification of Vibrio is increasing and a way of extracting DNA in a cheap, fast and easy way is also of an important requirement to facilitate rapid diagnosis. Methods This report comprises biochemical profiling and PCR methods in the characterisation of four isolates of V. harveyi and single isolates of V. tubiashii, V. alginolyticus, V. anguillarum, V. splendidus, V. tapetis and V. parahaemolyticus. Strains were examined for adherence to a Hep-2 cell line. Four different DNA extraction methods were evaluated and compared. The detection limits and the analytical limits of two PCR methods for Vibrio were determined. Results The overall findings were that the use of a greater range of biochemical substrates than are in the API 20E is necessary to identify Vibrio strains, and that none of the strains tested adhered to Hep-2 cells. All extraction methods successfully produced DNA with the kit method giving the purest samples. RNA was a contaminant of the other techniques but this could be overcome by treating extracts with RNase. The rapid microwave extraction method gave appropriate PCR amplicons when tested. Conclusion PCR determination of the VH-sequence in combination with VHA and a distinguishable colonial morphology may be a good choice for the identifying of Vibrio harveyi.

The global increase of antibiotic resistant bacteria threatens the modern health care and challenges the therapeutic effects of available antibiotics. The b-lactam mecillinam (Mec) is an exception to this due to a stable clinical resistance prevalence resistance of approximately 3%. It is only used to treat uncomplicated urinary tract infections (UTIs), mainly caused by E. coli. Mecillinam resistance (MecR) is easily selected for in laboratory settings and linked to >40 genes, including the mrdA gene encoding the Mec target penicillin-binding protein 2. A majority of the known MecR mutations confer a severe fitness cost. Fitness is important for bacteria to survive in the bladder and clinical isolates have been shown to have high fitness. These isolates contain loss-of-function mutations in the cysB gene, which encode a positive regulator of cysteine biosynthesis. In a previous evolution experiment, fitness cost of cysB and mrdA MecR mutations was compensated and the compensatory mutations were identified. Here the compensatory mutations were reconstructed into wildtype (WT) E. coli strain MG1655, and cysB and mrdA backgrounds to study the impact of the mutations on resistance and fitness, using MIC tests and Bioscreen C assays. Our results show that the mrdA mutants only had partial fitness compensation (significantly lower fitness than WT) for all strains and all strains also increased their MecR. The low fitness is possibly an explanation for the lack of mrdA mutants outside laboratories. Of the clinically relevant cysB mutants the majority lost their resistance when increasing growth rate, some even to levels significantly higher than WT, indicating that DcysB mutations are easier to compensate for. One strain (ydjNmx2) however, had a significantly higher growth rate while remaining clinically MecR.

The Lyme disease causing spirochaete Borrelia burgdorferi sensu lato is transmitted by ticks within the genus Ixodes. These ticks are liberal host seekers and parasitise mammals, birds and reptiles. Prior to this study, the distribution of I. ricinus ticks and Lyme disease was thought to be restricted to the southern half of Sweden. On the island Norrbyskär, located in the Bothnian Gulf, there were reports of a high incidence of tick infestation on humans. To investigate the occurrence of B. burgdorferi s.l. in these ticks and to characterise presumptive isolates at the molecular level we sampled a number of I. ricinus ticks. Three different isolates were obtained from two different ticks, NBS16 from a nymph and NBS23a and NBS23b from an adult female tick. The seabird associated tick I. uriae is circumpolar distributed in both hemispheres. On the island Bonden, which house one of the largest seabird colonies in the Baltic Sea, I. uriae were collected and surveyed for spirochaetes. One isolate of B. burgdorferi s.l. was obtained. This B. burgdorferi s.l. isolate is identical to the Lyme disease Borrelia strain NBS16 isolated from Norrbyskär. To investigate the role of seabirds in the epidemiology of B. burgdorferi s.l., I. uriae were collected from seabird colonies in the southern and northern hemispheres. Borrelia DNA was extracted from the ticks and from cultured spirochaetes. Sequence analysis of the flagellin gene revealed that the DNA obtained was from B. garinii, regardless of the geographical origin of the sample. Identical fla gene fragments in ticks collected in both hemispheres indicate a transhemispheric exchange of B. garinii. A marine ecological niche and epidemiological route for Lyme disease Borrelia are proposed. The prevalence of B. burgdorferi s.l. infected ticks on migrating passerine birds was studied. A total of 22, 998 birds were caught and examined for ticks. The presence of spirochaetes in the 967 collected ticks was determined by DNA amplification by PCR on all ticks. To determine which B. burgdorferi s.l. species were present, classification was performed by DNA amplification using species-specific 16S rDNA primers and by DNA sequencing. Flagellin gene sequences of all species of B. burgdorferi s.l. previously recorded in Europe were found. B. garinii was the most prevalent. These data support the notion that passerine birds are at least partly responsible for the distribution of Lyme disease Borrelia spirochaetes in Europe. To elucidate the distribution of B. burgdorferi s.l. in subarctic regions, strains isolated from I. ricinus and I. uriae ticks found on islands in the northern Atlantic and Baltic Sea were characterised molecularly. All isolates were verified as B. garinii by 16S-rRNA gene analysis and immunoblotting using monoclonal antibodies specific for the outer surface proteins A and C. Three ribotypes (RT's) of B. garinii were found. The I. ricinus associated RT1 is phenotypically the most heterogeneous. RT2 is restricted to the islands in the northern Baltic Sea, whereas RT3 was also recovered from ticks found on islands in the North Atlantic. The heterogeneity of the B. garinii population in the Baltic Sea might be influenced by two geographically opposite directions, North Atlantic (RT3) and Euroasia (RT1). / digitalisering@umu.se

Nanoflagellates were found to be abundant in a coastal area of the northern Bothnian Sea. The maximum concentration of nanoflagellates, approximately 8000 cells ml-1, was observed in July, coinciding with a decrease in the abundance of cyanobacteria. Pigmented and non-pigmented nanoflagellates were approximately equally distributed throughout the year. Most of the identified genera are known as being phagotrophic, independent if autotrophic or not. A non-cyst-forming pigmented flagellate, Ochromonas sp., was isolated and nutritionally characterized. This chrysophycean flagellate was shown to be a mainly heterotrophic organism: Photosynthesis was too poor to support multiplication of the cells, whereas when feeding on bacteria, high growth rates were obtained. The biological function of the photosynthetic apparatus is suggested to be a survival mechanism during poor bacterial conditions. The flagellate grazed bacteria selectively, preferring cyanobacteria and large cells of heterotrophic bacteria, presumably depending on size-selective grazing. Despite higher growth rates of the bacteria in the sea during summer (July) than spring (May), heterotrophic bacteria in the sea was observed to be smaller in the summer. Nanoflagellates showed a maximum in July, and by selective grazing of large bacteria they might have caused the decrease in the average size of the bacteria and the decrease in the abundance of cyanobacteria. During the consumption of bacteria the flagellate was shown to remineralize nutrients at high rates and excrete dissolved free amino acids. Assuming the existence of a protozoan predator-prey chain of several trophic levels, it seems likely that a significant part of the nutrients fixed by primary producers is remineralized in the euphotic zone. Furthermore, data from this work indicate that flagellate activity may be a significant source of dissolved free amino acids, utilizable for the heterotrophic bacteria. / digitalisering@umu

The membrane system of a eukaryotic cell is a large and complex system handling the transport, exchange and degradation of many kinds of material. Recent research shows that double-stranded RNA (dsRNA) mediated gene silencing (RNA interference) is a membrane related process. After long dsRNA is processed to small interfering RNA (siRNA) by Dicer, the guide strand and passenger strand are separated in the RNA induced silencing complex (RISC) by Argonaute. The process of loading siRNA into RISC has been suggested to occur at the rough Endoplasmic Reticulum (rER).The components of RISC also associate with late endosomes/multivesicular bodies (MVBs). Furthermore, disturbing the balance between late endosomes/MVBs and lysosomes has been shown to affect the efficiency of silencing. We use the nematode Caenorhabditis elegans as our model organism to study two questions: how does membrane transport affect RNAi and spreading of RNAi from the recipient cells to other tissues (systemic RNAi); and how does RNA transport contribute to the multigenerational silencing induced by dsRNA (RNAi inheritance)? Using SID-5, a protein required for efficient systemic RNAi, as bait in a yeast two-hybrid (Y2H) screen, we got 32 SID-5 interacting candidate proteins. Two of these are the SNARE protein SEC-22 and the putative RNA binding protein C12D8.1. In two additional Y2H screens, we found that SID-5 interacts with multiple syntaxin SNAREs, including SYX-6, whereas SEC-22 only interacts with SYX-6. SNAREs usually function in vesicle fusion processes. We found the two SNARE proteins SEC-22 and SYX-6 to be negative regulators of RNAi and to localize to late endosomes/MVBs. In addition, loss of sid-5 leads to an endosome maturation defect. Finally, we found that the putative RNA binding protein C12D8.1 negatively regulates RNAi inheritance and that C12D8.1 mutant animals show impaired RNAi upon targeting a new gene. Taken together, the results presented in this thesis provide us with more evidence for the connection of the membrane transport system and RNAi. The identification of a putative negative regulator of RNAi inheritance further enriches this research field.

Despite the existence of a treatment, there is still not a cure for HIV-1 infection and there arearound 700 000 deaths per year from AIDS-related diseases. A major barrier for a cure is theestablishment of latent reservoirs that are impossible to distinguish from healthy cells and thuscan escape the immune system. One potential solution is called shock-and-kill strategy, whichaims to induce HIV-1 reactivation, exposing latently infected cells to the immune system andmaking them susceptible to cell death. In our lab, it was seen that when NK cells are stimulatedwith a pan-caspase inhibitor, they acquire the “shock” ability, but it is still unknown how. Inthis project, we observed that the supernatant from pan-caspase inhibitor-stimulated NK cellscan increase HIV-1 reactivation in two different latency models. Furthermore, the protein levelsof three HIV-1 suppressors were found to be increased in the same supernatant. For this reason,their effect in HIV-1 reactivation in latently infected cells was analysed. Although we did notobserve an increase in HIV-1 reactivation, the upregulation of these three proteins can be usefulin the clinical context. Since they are HIV-1 suppressors, their presence can prevent theinfection from spreading after latent cells are reactivated. Altogether, our results show that NKcells stimulated with a pan-caspase inhibitor are secreting a biological product that inducesHIV-1 reactivation. This indicates that there is a pathway in NK cells that can potentially beexploited in order for them to be able to induce HIV-1 reactivation.

The Selection during Niche AdaPtation (SNAP) hypothesis aims to explain how the gene order in bacterial chromosomes can change as the result of bacteria adapting to a new environment. It starts with a duplication of a chromosomal segment that includes some genes providing a fitness advantage. The duplication of these genes is preserved by positive selection. However, the rest of the duplicated segment accumulates mutations, including deletions. This results in a rearranged gene order. In this work, we develop a method to identify SNAP in bacterial chromosomes. The method was tested in Salmonella and Bartonella genomes. First, each gene was assigned an orthologous group (OG). For each genus, single-copy panorthologs (SCPos), the OGs that were present in most of the genomes as one copy, were targeted. If these SCPos were present twice or more in a genome, they were used to build duplicated regions within said genome. The resulting regions were visualized and their possible compatibility with the SNAP hypothesis was discussed. Even though the method proved to be effective on Bartonella genomes, it was less efficient on Salmonella. In addition, no strong evidence of SNAP was detected in Salmonella genomes.

Culex pipiens, in the family Culicidae, has emerged as one of the biggest vectors for West Nile virus. It has two bioforms, pipiens and molestus, which differ from each other regarding habitat, diapause, and prey. Pipiens prefers to bite birds, and molestus prefers to bite humans. There is to some extent hybridization between the two, which creates a bridge-vector between birds and humans. One way to study the relationships and spreading of the mosquitos is using the intracellular bacteria Wolbachia pipientis which is present in at least 99% of al Culex mosquitoes. The bacteria have two fast evolving genes, pk1 and ank2 which are suitable for this. Not only are the bacteria suitable for genetics, but it is also manipulating the reproductive system of the mosquitoes through Cytoplasmic Incompatibility, which changes structures of populations and allows for the bacteria to spread fast and efficient. We wanted to investigate levels of Wolbachia in different populations, as well as if the two bioforms prefer a prey, together with mapping the relationships between populations using the two genes. We found that Wolbachia was present in all tested mosquitoes, with higher levels of it in the abdomen than in the thorax. We also found that the theory of a preferred prey was false within the tested populations, since both bioforms preferred birds. Lastly, we could identify five different strains of Wolbachia pipientis concentrated to different locations. This study has shown that Wolbachia is present in all tested mosquitoes and is a useful tool to determine relationships within and between populations. This is important to be able to gain understanding of the spread of West Nile virus and other vector borne diseases spread by Culex pipiens mosquitoes.