Streptococcus pyogenes is an important human pathogen. One of the most prominent virulence factors produced by S. pyogenes is SfbI, a surface adhesin composed of three domains: thioester domain (TED), proline-rich repeat domain (PRR) and fibronectin-binding repeat domain (FnBD). The structures and functions of TED and PRR and their contributions to the pathogenesis of streptococcal diseases are unknown. The interaction between PRR and its putative target, the intracellular actin cytoskeleton regulator Arp2/3, was investigated by both in vitro and in vivo studies. PRR was shown to inhibit Arp2/3-dependent actin polymerisation. The expression of PRR in HeLa cells caused disruption to the cytoskeleton of the cells. All data point towards a role of PRR in inhibiting the Arp2/3 complex but more evidence is needed to support this. The N-terminal domain of SfbI (TED) and four homologous domains from S. pyogenes, group G streptococci and Streptococcus pneumoniae were characterised by mass spectrometry, NMR spectroscopy and biochemical assays. All were shown to possess intramolecular thioester bonds, spontaneously formed between sides chains of Cys and Gln residues. Fibrinogen (Fg) was identified as the first binding target of bacterial TEDs with direct evidence that the thioester bond was involved in the interaction with Fg. A pull-down experiment using human plasma showed Fg is a specific binding partner of SfbI-TED. The binding sites were narrowed down to the thioester-forming Gln of SfbI-TED and Lys residues in the Fg-Aα chain, and binding potentially occurred via covalent isopeptide linkage. The data presented here suggest two new roles for SfbI, previously unknown in bacterial pathogenesis. The PRR may be the first bacterial inhibitor of the actin cytoskeleton acting by inhibiting the Arp2/3 complex. Thioester domains appear to be a shared common feature of surface proteins of many Gram-positive pathogens. They may form covalent crosslinks between bacteria and host tissue.

There has been significant debate, specifically within the African context, regarding the validity of using HCT data as part of routine surveillance data for the HIV epidemic. The use of HCT data in tracking the prevalence of HIV, as well as in estimating incidence rates for HIV, has been applied in some African countries, and may offer opportunities to strengthen surveillance in the Gauteng Province, South Africa. Literature suggests HCT data are biased as a result of the high proportion of repeat testers, where repeat testing may be related to high risk sexual behaviour. (1–8) It has been suggested that HCT data be separated into first-time- and repeat tester data in prevalence or incidence estimations. (9) The aim of this research was to determine if there are demographic and HIV prevalence differences between first-time- and repeat testers, as suggested in the literature. (9) Existing mobile HCT unit data was used from the Foundation for Professional Development (FPD). The data was collected in the Tshwane Metropolitan Municipality, Gauteng Province, South Africa. An observational, cross-sectional study design was applied. A systematic random sample of 400 first-time testers and 400 repeat-testers was drawn and analyzed. The findings of this study indicated an overall 10.0% (n=80) HIV prevalence rate. When compared to the Gauteng adult prevalence (15+) of 14.4%, the study prevalence is lower. (10) When looking at the characteristics of the first-time tester and repeat tester groups, there was an HIV prevalence rate of 12.5% (n=51/407, p=0.0152) in the first-time tester group, and 7.4% (n=29/393, p=0.0152) HIV prevalence rate in the repeat tester group. Although literature suggests that repeat testers are the more at risk population, the finding in this study clearly demonstrates that there is a difference in HIV prevalence between first-time- and repeat testers. When first-time/repeat tester was used as the dependent variable, it was found that females are 0.6 less times likely to be a first-time tester compared to males (OR=0.6, p=0.001). The finding of a difference in HIV prevalence between first-time- and repeat tester groups was consistent with three other studies in Ethiopia, Uganda and Kenya. In these studies, HIV prevalence in first-time testers was slightly higher than in that of repeat-testers. (3,11,12) It was found that there is a difference in the HIV and demographic profile between those who test for HIV for the first time and those who are repeat testers. The perceived risk and vulnerability to HIV plays a heavy role in motivating individuals to test once, or repeatedly. In regards to disease surveillance, this study did not prove that the population that utilises mobile HCT are representative of the Tshwane population. This study highlighted the need to better understand the sub-groups and characteristics of those who test for the first-time and those who test repeatedly for HIV. In conclusion, this study has provided evidence that there is a difference between the HIV prevalence of first-time- and repeat testers. However, there is good reason to doubt that the prevalence rate of first-time testers is genuine. Copyright / Dissertation (MSc)--University of Pretoria, 2013. / School of Health Systems and Public Health (SHSPH) / Unrestricted

Trinucleotide repeat (TNR) expansions are the cause of over 40 human neurodegenerative diseases, and are linked to DNA damage and base excision repair (BER). We explored the role of DNA damage and BER in modulating TNR instability through analysis of DNA structures, BER protein activities, and reconstitution of repair using human BER proteins and synthesized DNA containing various types of damage. We show that DNA damage and BER can modulate TNR expansions by promoting removal of a TNR hairpin through coordinated activities of BER proteins and cofactors. We found that during repair in a TNR hairpin, coordination between the 5’-flap endonuclease activity of flap endonuclease 1 (FEN1), 3’-5’ exonuclease activity of AP endonuclease 1 (APE1), and activity of DNA ligase I (LIG I) can resolve the double-flap structure produced during BER in the hairpin loop. The resolution of the double-flap structure resulted in hairpin removal and prevention or attenuation of TNR expansions and provides the first evidence that coordination among BER proteins can remove a TNR hairpin. We further explored the role of BER cofactors in modulating TNR instability and found that the repair cofactor proliferating cell nuclear antigen (PCNA) facilitates genomic stability by promoting removal of a TNR hairpin. Hairpin removal was accomplished by altering dynamic TNR structures to allow more efficient FEN1 cleavage and DNA polymerase β (pol β) synthesis and stimulating the activity of LIG I. This study provides the first evidence that a DNA repair cofactor plays an important role in modulating TNR instability. Finally, we explored the effects of sugar modifications in abasic sites on activities of BER proteins and BER efficiency during repair in a TNR tract. We found that an oxidized sugar inhibits the activities of BER enzymes, interrupting their coordination and preventing efficient repair. Inefficient repair results in accumulation of repair intermediates with DNA breaks, contributing to genomic instability. Our results indicate that DNA base lesions and BER play a crucial role in modulating TNR instability. The research presented herein provides a molecular basis for further developing BER as a target for prevention and treatment of neurodegenerative diseases caused by TNR expansion.

“Rapid repeat pregnancy”, which is common among young mothers, is the onset of pregnancy within 24 months of a previous pregnancy outcome. Teenage motherhood is associated with many economic, social, and health challenges. These challenges often become more serious and more difficult to manage after a subsequent delivery. The circumstances surrounding rapid repeat pregnancy among young mothers living in Ottawa remain unclear. This study explores the experiences, knowledge, and attitudes of young mothers towards rapid repeat pregnancy and contraception through a multi-method study. The multimethod study includes in-depth interviews with young mothers living in Ottawa who have experienced rapid repeat pregnancy and in-depth interviews with services providers who work with them. Results from the interviews indicate that young mothers often do not use post-partum contraception, actively and passively plan their pregnancies, experience violence, and have mental health and substance abuse issues. Many young mothers expressed that trying to access services, especially mental health support services, can be a long and difficult process. Key informants expressed the need for more sexpositive, youth-friendly sexual and reproductive health education. There is a need to identify and further develop youth-friendly services that young mothers feel comfortable accessing. Supporting efforts to increase adolescent mothers’ and service providers’ awareness of existing services appears warranted.

The increase of firearm-related violence has plagued Sweden, and specifically Malmö, for thirty years. This Systematic Literature Review gathered ten articles from different fields in order to discern the causes behind such an increase, the mechanisms of gun violence in a Swedish settings and the implications for Malmö on a criminological level. Results showed that a combination of factors such as the illegal importation of illicit firearms and the expansion of organized criminal groups in vulnerable territories were responsible for a shift of pattern in homicide. This change is preventing the police from properly solving homicide cases and the criminal justice system from prosecuting them. All in all, firearm violence is strongly related to gang activities in the three largest Swedish cities and the reason why Malmö is the most affected may be explained by the large number of clustered near-repeat shootings spread over three neighborhoods considered vulnerable. Actions have been taken though still require some analysis.

Introduction: Macroscopic hematuria is an important alarm symptom of cancer in theurinary tract. One single episode in patients over the age of 50 fulfills the criteria for referralto the standardized care pathway. Several patients included in the pathway with a negativeresult of the investigation will return with recurrent macroscopic hematuria for repeatinvestigation. Aim: To evaluate the diagnostic yield of repeat investigation in patients presenting withrecurrent macroscopic hematuria after a previous negative investigation and to estimate theincidence of false negative investigations in the standardized care pathway for cancer in theurinary tract. Material and Methods: A retrospective review of medical records was performed at theDepartment of Urology in Örebro County, including all patients investigated in thestandardized care pathway for cancer in the urinary tract during 2016 with a negative result ofthe investigation. Individuals with repeat investigation were identified. Results of theseinvestigations and the time interval between investigations were documented. Results: Repeat investigation was performed in 96 out of 627 patients (15.3%). Two (2.1%)were diagnosed with cancer, at a time interval from initial investigation of 4 and 27 months,respectively. Other results were benign urological conditions (n = 62) and normalinvestigations (n = 30). Conclusions: It appears that few tumors are missed when macroscopic hematuria isinvestigated in the standardized care pathway. We observed a very low number of newlydiagnosed cancers after repeat investigation of recurrent macroscopic hematuria. A moreselective approach regarding repeat investigations should be considered.

Magister Scientiae (Biodiversity and Conservation Biology) - MSc (Biodiv and Cons Biol) / Areas of high biodiversity and complex species assemblages are often difficult to manage and to set up meaningful monitoring and evaluations programmes. Mountain Fynbos is such an ecosystem and in the Cape of Good Hope (part of the Table Mountain National Park) plant biodiversity over the last five decades has been in decline. The reasons are difficult to speculate since large herbivores, altered fire regimes and even climate change could be contributors to this decline which has been quantified using fixed quadrats and standard cover-abundance estimates based on a Braun-Blanquet methodology. To provide more detailed data that has more resolution in terms of identifying ecological processes, Fixed-Point Repeat Photography has been presented as a management “solution”. However, photography remains a difficult method to standardize subjects and has certain operational limitations.

This dissertation explores the differential effects of fires and rodent communities on native and invasive desert plant communities. Chapter one examines the impacts of fire and repeat fires on fuel loads in two different Utah desert sites, one in the cool Great Basin Desert and one in the hyper-arid Mojave Desert, over the course of four years. We found that both desert sites responded with varying intensities to a single burn, but the effects of a reburn were not as pronounced. We also found that our Great Basin Desert site had a stronger response to fire than our Mojave Desert site, producing a higher plant fuel loads that could potentially exacerbate the changing fire regimes. These data can be used to help map the effects that climate change may have on fuel loads and the fire potential of these deserts. Chapter two uses a full factorial experimental design to compare the effects of rodent herbivory and fire on native versus invasive seedlings at our Mojave Desert field site. We found that rodent herbivory has a more negative impact on the survival of native seedlings than invasive seedlings. This could be because the invasives are grasses that tend to tolerate herbivory better than the native shrubs and forbs. Chapter three again uses a full factorial experimental design to assess the impacts of rodents and fire on the fate of native and invasive seeds at our field site in the Mojave Desert. We found that rodents removed seeds, and they did show preferences for some species of seed over others, but these preferences were not different between native and invasive seeds or seed mass. We propose that the preferences may be influenced by other seed traits such as water content, handling time or physical and chemical defenses. As with the seedlings in chapter two, fire did not have any impact on rodent seed preferences. These data highlight the importance of considering rodent effects on seeds used in restoration effects following wildfires.

Concussions are the injury and symptoms that can result from transmission of a biomechanical force to the brain. They represent a significant global health burden, and are the subject of a growing body of medical research. A concussion can only be definitively diagnosed by a medical professional based on symptoms, although advanced neuroimaging and biomarker-based approaches are promising future diagnostic tools. There is no treatment for concussion beyond following return-to-work or -play guidelines, which recommend avoiding strenuous physical and cognitive activities until they no longer exacerbate symptoms. Preclinical models of concussion have been used to examine pathophysiological processes underlying symptoms, which is an important step in developing tools for diagnosis and treatment. Historically the clinical translation of preclinical concussion research has been limited, and the use of anaesthesia, and preference for adult male rats may contribute to this. These means of reducing variability are justified, but preclinical research moving forward should address these limitations to translatability by including more clinically relevant subjects and avoiding anaesthesia. To this end, we developed a new preclinical model for pediatric concussion. Our awake closed head injury (ACHI) model is well-suited to this purpose because it produces a helmeted closed-head injury involving vertical and rotational displacement of the head, and does not require anaesthesia. Before the ACHI model can be used to investigate concussion mechanism, diagnosis, and treatment, it needs to be characterized to demonstrate that it produces clinically relevant neurobehavioral and pathological changes. We developed a modified neurologic assessment protocol to test neurologic function immediately after each injury. The Barnes maze, elevated plus maze, open field, and Rotarod were used to measure injury-related changes in cognition, anxiety, and motor function. The Barnes maze reversal task was used to detect more subtle cognitive impairments of executive function. Structural MRI was used to search for visible lesion, hemorrhage, or atrophy; and silver-stain histology was used to detect neurodegeneration. We determined repeated ACHI produced acute neurologic impairment with the NAP, and a mild spatial learning deficit potentially mediated impaired cognitive flexibility in the Barnes maze and reversal training. These were accompanied by neurodegeneration in the optic tract, hippocampus, and ipsilateral cortex during the first week of recovery. Thus, following the internationally recognised definition developed by the concussion in sport group, we demonstrated 1) an “impulsive” force transmitted to the head results in 2) the rapid onset of short-lived neurologic impairment that resolves spontaneously. This occurs 3) with normal structural neuroimaging, and 4) produces cognitive impairment, and LOC in a subset of cases. The ACHI model is the first in Canada to forego anaesthesia, and this is the first demonstration of neurocognitive impairment accompanied by diffuse neurodegeneration in the absence of structural MRI abnormalities after mild traumatic brain injury in juvenile male and female rats. / Graduate

Phytophthora sojae, the causal organism of stem and root rot, and <i>Soybean mosaic virus</i> (SMV) cause two of the most highly destructive diseases of soybean (<i>Glycine max</i> L. Merr). <i>P. sojae</i> can be managed either through deployment of race-specific resistance or through quantitative resistance termed partial resistance. In the current study, partial resistance to <i>P. sojae</i> was mapped in an interspecific recombinant inbred line (RIL) population of <i>Glycine max</i> by <i>Glycine soja</i>. One major quantitative trait loci (QTL) on molecular linkage group (MLG)-J (chromosome 16) and two minor QTL on MLG-I (chromosome 20) and -G (chromosome 18) were mapped using conventional molecular markers. Additionally, partial resistance to <i>P. sojae</i> was mapped in the same RIL population using single feature polymorphism (SFP) markers that further fine mapped the <i>P. sojae</i> QTL and identified potential candidate genes contributing to resistance. In a separate study, race-specific resistance was characterized in PI96983 discovering a potentially new allele of <i>Rps4</i> on MLG-G. Finally, using the newly available whole-genome shotgun sequence of soybean, <i>Rsv4</i> conferring resistance to strains of SMV known in the US, was localized to an approximately 100 kb region of sequence on chromosome 2 (MLG-D1B). Newly designed PCR-based markers permit for efficient selection of <i>Rsv4</i> by breeding programs. Identified candidate genes for <i>Rsv4</i> are discussed. Genomic resources developed in all of these studies provide breeders the tools necessary for developing durable resistance to both SMV and <i>P. sojae</i>. / Ph. D.