Human papillomavirus type 16 (HPV-16) is the major cause of cervical cancer. HPV-16 gene expression is tightly linked to the differentiation programme of the infected epithelium. Expression of the late genes, L1 and L2, encoding the capsid proteins, is delayed until the more terminally differentiated cells. Successful inhibition of HPV-16 late gene expression early in the viral life cycle is essential for persistence of infection, the highest risk factor for cervical cancer. The goal of this thesis was to identify regulatory RNA elements and cellular factors that influence RNA processing events, such as alternative splicing and polyadenylation, during late gene expression. For this purpose, transfection of plasmids containing almost the full-length HPV-16 genome into HeLa cells, followed by RNA analysis, was employed. An exonic splicing enhancer (ESE) was identified that firmly supported the use of the E4 3’ splice site. A key regulator of HPV-16 gene expression, the E4 ESE was required for early mRNA splicing and polyadenylation, as well as for inhibition of premature late gene expression. The early polyadenylation signal (pAE) is also an important block of premature late gene expression. An upstream polyadenylation element (USE) was identified in the early 3’ untranslated region that enhanced polyadenylation at pAE, and interacted specifically with the cellular factors CstF-64, hnRNP C1/C2, PTB and hFip1. With the help of adenoviral E4orf4, a protein which causes dephosphorylation of SR proteins, we found that overexpression of SRp30c activated HPV-16 late gene expression by an exon skipping mechanism, and that SRp30c may interfere with early mRNA terminal exon definition. This work identified a crucial splicing enhancer, as well as a number of cellular proteins binding to an USE in the early region of HPV-16. Furthermore, the cellular splicing factor SRp30c was shown to play a role in the regulation of HPV-16 late gene expression.

Pathogenic organisms are transmitted to the host organism through all possible connected pathways, and cause a myriad of diseases states. Commonly occurring curable infectious diseases still impose the greatest health impacts on a worldwide perspective. The Bill & Melinda Gates Foundation partnered with RAND Corporation to form the Global Health Diagnostics Forum, with the goal of establishing and interpreting mathematical models for what effects a newly introduced point-of-care pathogen diagnostic would have in developing countries. The results were astonishing, with potentially millions of lives to be saved on an annual basis. Golden standard for diagnostics of pathogenic bacteria has long been cultureable medias. Environmental biologists have estimated that less than 1% of all bacteria are cultureable. Genomic-based approaches offer the potential to identify all microbes from all the biological kingdoms. Nucleic acid based pathogen diagnostics has evolved significantly over the past decades. Novel technologies offer increased potential in sensitivity, specificity, decreased costs and parallel sample management. However, most methods are confined to core laboratory facilities. To construct an ultimate nucleic acid based diagnostic for use in areas of need, potential frontline techniques need to be identified and combined. The research focus of this doctoral thesis work has been to develop and apply nucleic acid based methods for pathogen diagnostics. Methods and assays were applied to the two distinct systems i) screening for antibiotic resistance mutations in the bacterial pathogen Neisseria gonorrhoeae, and ii) genotype determination of the cancer causative Human Papillomavirus (HPV). The first part of the study included development of rapid, direct and multiplex Pyrosequencing nucleic acid screenings. With improved methodology in the sample preparation process, we could detect an existence of multiple co-infecting HPV genotypes at greater sensitivities than previously described, when using the same type of methodology. The second part of the study focused on multiplex nucleic acid amplification strategies using Molecular Inversion Probes with end-step Pyrosequencing screening. The PathogenMip assay presents a complete detection schematic for virtually any known pathogenic organism. We also introduce the novel Connector Inversion Probe, a padlock probe capable of complete gap-fill reactions for multiplex nucleic acid amplifications. / Patogena organismer smittas till värd organismen genom alla möjliga kontaktnätverk och skapar en mångfald olika sjukdomstillstånd. Dock är det fortfarande vanligt förekommande behandlingsbara infektiösa sjukdomar som orsakar den största hälsoförlusten, sett från ett globalt perspektiv. Bill och Melinda Gates Stiftelsen samarbetade med RAND kooperation för att forma “The Global Health Diagnostics Forum”. Deras mål var att etablera och analysera matematiska modeller för vilka effekter en ny diagnostisk metod utrustat för fältarbete skulle ha i utvecklingsländer. Resultaten var häpnadsveckande, med potentiellt miljoner av liv som skulle kunna räddas på en årlig basis. Den etablerade standarden för diagnostik av patogena bakterier har länge varit kultiveringsmedia baserad. Miljö specialiserade biologer har estimerat att mindre än 1 % av alla bakterie arter går att kultivera. Dock erbjuder genetiska analyser potentialen att kunna identifiera alla mikrober från alla de biologiska rikena. Nukleinsyrebaserade diagnostiska metoder har märkbart förbättrats över de senaste årtionden. Nya tekniker erbjuder utökad sensitivitet, selektivitet, sänkta kostnader och parallella analyser av patient prover. Dock är de flesta metoderna begränsade till standardiserade laboratoriemiljöer. För att konstruera en väl fungerande diagnostisk fältutrustning för användning i problem områden, behöver världsledande tekniker identifieras och kombineras. Fokuseringsområdet för denna doktorsavhandling har varit att utveckla och utföra nukleinsyrebaserade metoder för patogen diagnostik. Metoder och experimentella utförande applicerades på två distinkta system i) sökning av antibiotika resistens relaterade mutationer i den patogena bakterien Neisseria gonorrhoeae och ii) genotypning av det cancer orsakande Humana Papillomaviruset (HPV). Den första delen av studien inriktade sig mot utveckling av snabba, direkta och multiplexa Pyrosekvenserings baserade nukleinsyreanalyser. Med förbättrad provprepareringsmetodologi kunde vi detektera multipla HPV infektioner med högre sensitivitet än vad tidigare beskrivits med liknande metodologi. Den andra delen av studien fokuserades på multiplexa nukleinsyre amplifikationer med “Molecular Inversion Probe” tekniken med sista steg Pyrosekvenserings analys. “PathogenMip assay” erbjuder ett komplett detektionsprotokoll för alla kända patogena organismer. Vi introducerar även den nya “Connector Inversion Probe”, en “Padlock Probe” kapabel att genomföra kompletta gap fyllningar för multiplex nukleinsyre amplifiering. / QC 20100624

Developments within the field of genetic analysis have during the last decade become enormous. Advances in DNA sequencing technology have increased throughput from a thousand bases to over a billion bases in a day and decreased the cost thousandfold per base. Nevertheless, to sequence complex genomes like the human is still very expensive and efforts to attain even higher throughputs for less money are undertaken by researchers and companies. Genotyping systems for single nucleotide polymorphism (SNP) analysis with whole genome coverage have also been developed, with low cost per SNP. There is, however, a need for genotyping assays that are more cost efficient per sample with considerably higher accuracy. This thesis is focusing on a technology, based on competitive allele-specific extension and microarray detection, for genetic analysis. To increase specificity in allele-specific extension (ASE), a nucleotide degrading enzyme, apyrase, was introduced to compete with the polymerase, only allowing the fast, perfect matched primer extension to occur. The aim was to develop a method for analysis of around twenty loci in hundreds of samples in a high-throughput microarray format. A genotyping method for human papillomavirus has been developed, based on a combination of multiplex competitive hybridization (MUCH) and apyrase-mediated allele-specific extension (AMASE). Human papillomavirus (HPV), which is the causative agent in cervical cancer, exists in over a hundred different types. These types need to be determined in clinical samples. The developed assay can detect the twenty-three most common high risk types, as well as semi-quantifying multiple infections, which was demonstrated by analysis of ninety-two HPV-positive clinical samples. More stringent conditions can be obtained by increased reaction temperature. To further improve the genotyping assay, a thermostable enzyme, protease, was introduced into the allele-specific extension reaction, denoted PrASE. Increased sensitivity was achieved with an automated magnetic system that facilitates washing. The PrASE genotyping of thirteen SNPs yielded higher conversion rates, as well as more robust genotype scoring, compared to ASE. Furthermore, a comparison with pyrosequencing, where 99.8 % of the 4,420 analyzed genotypes were in concordance, indicates high accuracy and robustness of the PrASE technology. Single cells have also been analyzed by the PrASE assay to investigate loss of alleles during skin differentiation. Single cell analysis is very demanding due to the limited amounts of DNA. The multiplex PCR and the PrASE assay were optimized for single cell analysis. Twenty-four SNPs were genotyped and an increased loss of genetic material was seen in cells from the more differentiated suprabasal layers compared to the basal layer. / QC 20100714

Human papillomavirus (HPV) is widespread in the population and an important concern for public health. HPV-associated benign and cancerous disease is vaccine preventable yet vaccine uptake has been suboptimal. Adolescents are the primary target for vaccination yet their perspective has been inadequately examined. Ontario provides population-based preventive HPV vaccination to adolescent girls yet in the program’s first 2 years only approximately half of eligible girls received it. Effective strategies to improve vaccine uptake are needed. This thesis proposes a theory and ethics-based model to guide health promotion planning for HPV vaccination. Adopting an adolescent perspective, the model is applied and comprises: 1) a systematic review to identify barriers and facilitators to HPV vaccination from the viewpoint of young females; 2) GIS uses for communicating geospatial health information regarding vaccination; and 3) a roadmap for the future including recommendations for guiding principles, research, intervention development, and health policy.

Background: Several studies have shown there has been significant lack of knowledge about women who have sex with women cross infect each other with STIs. It has been less likely that women who have sex with women visit health care than heterosexuals, they often felt badly treated, invisible and did not always know where to turn in case of an STI. Objective: The objective was to examine if STI information from Kalmar and Växjö county websites and GCK-summit, targeted women who have sex with women. Method: With a queer theoretical perspective a critical discourse analysis was made by STI information on the internet. Results: Women who have sex with women have been excluded in the STI information currently available through Kalmar and Växjö county websites. The public notices for screening tests have not been designed in such way it includes women who have sex with women. Women who have sex with women have been an obscure group. Conclusion: The conclusion was that women who have sex with women have not been included in the STI information available on the internet within the county councils of Kalmar and Kronoberg.

<p>The ability to determine nucleic acid sequences is one ofthe most important platforms for the detailed study ofbiological systems. Pyrosequencing technology is a relativelynovel DNA sequencing technique with multifaceted uniquecharacteristics, adjustable to different strategies, formatsand instrumentations. The aims of this thesis were to improvethe chemistry of the Pyrosequencing technique for increasedread-length, enhance the general sequence quality and improvethe sequencing performance for challenging templates. Improvedchemistry would enable Pyrosequencing technique to be used fornumerous applications with inherent advantages in accuracy,flexibility and parallel processing.</p><p>Pyrosequencing technology, at its advent, was restricted tosequencing short stretches of DNA. The major limiting factorwas presence of an isomer of dATPaS, a substitute for thenatural dATP, which inhibited enzyme activity in thePyrosequencing chemistry. By removing this non-functionalnucleotide, we were able to achieve DNA read-lengths of up toone hundred bases, which has been a substantial accomplishmentfor performance of different applications. Furthermore, the useof a new polymerase, called Sequenase, has enabled sequencingof homopolymeric T-regions, which are challenging for thetraditional Klenow polymerase. Sequenase has markedly madepossible sequencing of such templates with synchronizedextension.</p><p>The improved read-length and chemistry has enabledadditional applications, which were not possible previously.DNA sequencing is the gold standard method for microbial andvial typing. We have utilized Pyrosequencing technology foraccurate typing ofhuman papillomaviruses, and bacterial andfungal identification with promising results.</p><p>Furthermore, DNA sequencing technologies are not capable oftyping of a sample harboring a multitude of species/types orunspecific amplification products. We have addressed theproblem of multiple infections/variants present in a clinicalsample by a new versatile method. The multiple sequencingprimer method is suited for detection and typing of samplesharboring different clinically important types/species(multiple infections) and unspecific amplifications, whicheliminates the need for nested PCR, stringent PCR conditionsand cloning. Furthermore, the method has proved to be usefulfor samples containing subdominant types/species, and sampleswith low PCR yield, which avoids reperforming unsuccessfulPCRs. We also introduce the sequence pattern recognition whenthere is a plurality of genotypes in the sample, whichfacilitates typing of more than one target DNA in the sample.Moreover, target specific sequencing primers could be easilytailored and adapted according to the desired applications orclinical settings based on regional prevalence ofmicroorganisms and viruses.</p><p>Pyrosequencing technology has also been used forclone-checking by using preprogrammed nucleotide additionorder, EST sequencing and SNP analysis, yielding accurate andreliable results.</p><p><b>Keywords:</b>apyrase, bacterial identification, dATPaS, ESTsequencing, fungal identification, human papillomavirus (HPV),microbial and viral typing, multiple sequencing primer method,Pyrosequencing technology, Sequenase, single-strandedDNA-binding protein (SSB), SNP analysis</p>

Non-melanoma skin cancer (NMSC), comprised of basal cell carcinoma (BCC) and squamous cell carcinoma (SCC), is the most common cancer in Caucasians. Ultraviolet radiation (UVR) exposure is the most important environmental risk factor for both BCC and SCC development. However, the precise relationship between UVR and the risk of NMSC is complex, and the relationship may differ by skin cancer type. It has been hypothesized that intermittent patterns and childhood sunlight exposure are important for BCC while continuous (chronic) and lifelong (i.e. childhood and adulthood) sunlight exposure is important for SCC. Epidemiologic studies have demonstrated that cutaneous human papillomavirus (HPV) infection may also be a risk factor for developing NMSC. However, the pathway by which cutaneous HPV is associated with NMSC remains unclear. It is hypothesized that UVR exposure may interact synergistically with cutaneous HPV in NMSC development. The goal of the research study was to evaluate the relationship between levels of sunlight exposure and BCC and SCC and to investigate differences in sunlight-associated BCC and SCC risk by genus-specific cutaneous HPV serostatus. To address these goals, we conducted a clinic based case-control study of histologically confirmed BCC and SCC cases recruited from a university dermatology clinic and controls with no history of cancer and screened negative for current skin cancer. Logistic regression was used to calculate odds ratios (OR) and 95% confidence intervals (CI) for the associations between measures of sunlight exposure and BCC and SCC. Multiplicative interactions were tested by placing an interaction term for the product of genus-specific HPV seroreactivity and sunlight related factors in the logistic regression models. Measures of both intermittent and continuous patterns of sunlight exposure were associated with both types of skin cancer (i.e. BCC and SCC). Specifically, history of blistering sunburn (a marker of intermittent sunlight exposure) and occupational sunlight exposure (i.e. having a job in the sun for at least 3 months for >10 years) were both associated with BCC and SCC. The major differences in patterns of sunlight exposure between BCC and SCC were observed for sunlight exposure in one's thirties. Additionally, sunlight exposure in one's twenties was associated with SCC, regardless of pattern of exposure; similar associations were not observed for BCC. Measures of timing of sunlight exposure consistently demonstrated that childhood/adolescent sunlight exposure was more important for SCC than BCC. These included number of moles on the forearms and entire body (measure of increased childhood sunlight exposure), and younger age at first and tanning bed use. Younger age at first blistering sunburn was statistically significantly associated with both BCC and SCC. NMSC cases were more likely to be seropositive for cutaneous HPV antibodies compared to controls. Compared to tanning, having a propensity to sun burn (p=0.006), or poor tanning ability (p=0.003) were significantly associated with a higher seroprevalence to genus beta HPV types within SCC cases. Statistically significant interactions were observed between poor tanning ability and genus-specific seropositivity with NMSC. Specifically, the associations between poor tanning ability and BCC (p interaction=0.02) and SCC (p interaction=0.01) were significantly stronger among individuals that were seropositive for antibodies to genus alpha HPV types. Similarly, the association between poor tanning ability and SCC was stronger among those seropositive for genus beta HPV types (p interaction=0.001). No additional significant interactions were observed for BCC or SCC between cutaneous sensitivity, history of blistering sunburn, or cumulative sunlight exposure and genus-specific seroreactivity. In conclusion, associations with patterns of sunlight exposure appeared to be similar between BCC and SCC cases. With the exception of age at first blistering sunburn, factors measuring timing of sunlight exposure demonstrated stronger and statistically significant relationships with SCC. Additionally, of the sunlight related factors measured, only the associations between poor tanning ability and BCC and SCC were significantly modified by HPV seropositivity to types in genera alpha or beta.

The overall aim of this thesis was to examine beliefs about human papillomavirus (HPV) prevention, especially vaccination, among parents, immigrant women, adolescents and school nurses, and to promote primary prevention among adolescents. The methods used in the thesis were focus group interviews, individual interviews, a web-based questionnaire, and finally, a randomised controlled intervention study. The immigrant women were largely in favour of HPV prevention, although barriers, such as logistic difficulties, and cultural or gender norms were found. Parents’ decision concerning vaccination of their daughters depended on several factors. Regardless of their final choice, they made the decision they believed was in the best interest of their daughter. The benefits outweighed the risks for parents choosing to vaccinate while parents declining made the opposite judgement. The majority of the school nurses reported that the governmental financial support given because of the vaccination programme had not been used for the intended purpose. Three out of four nurses had been contacted by parents who raised questions regarding the vaccine; most were related to side effects. The educational intervention had favourable effects on the adolescents’ beliefs regarding HPV prevention, especially among those with an immigrant background. Furthermore, the intention to use condom as well as actual vaccination rates among girls was slightly increased by the intervention. Trust in the governmental recommendations and the amounts of information given are important factors in the complex decision about HPV vaccination. Attention given to specific needs and cultural norms, as well as the possibility to discuss HPV vaccination with the school nurse and provision of extra vaccination opportunities at a later time are all strategies that might facilitate participation in the school-based HPV vaccination programme. School nurses need sufficient resources, knowledge and time to meet parents’ questions and concerns. The vaccinations are time-consuming and the governmental financial support needs to be used as intended, for managing the vaccination programme. A school-based intervention can have favourable effects on the beliefs and actual actions of young people and may possibly thus, in the long term, decrease the risk for HPV-related cancer.

Le VPH-16 de même que certains VPH, dont le VPH-18, causent le cancer du col utérin. Son intégration dans le génome humain pourrait être un marqueur de progression de l’infection. Les charges virales totale et intégrée sont présentement mesurées en quantifiant par PCR en temps réel les gènes E6 (RT-E6) et E2 (RT-E2-1) du VPH-16. Nous avons évalué l’impact du polymorphisme du gène E2 sur la quantification de l’ADN du VPH-16 dans des spécimens cliniques. Dans un premier temps, le gène E2 de 135 isolats de VPH-16 (123 appartenaient au clade Européen et 12 à des clades non- Européens) fut séquencé. Ensuite, un test de PCR en temps réel ciblant les séquences conservées dans E2 (RT-E2-2) fut développé et optimisé. Cent trente-neuf spécimens (lavages cervicaux et vaginaux) provenant de 74 participantes (58 séropositives pour le VIH, 16 séronégatives pour le VIH) ont été étudiés avec les trois tests E2 (RT-E2-2), E6 (RT-E6) et E2 (RT-E2-1). Les ratios de la quantité d’ADN de VPH-16 mesuré avec RT-E2-2 et RT-E2-1 dans les isolats Européens (médiane, 1.02; intervalle, 0.64-1.80) et Africains 1 (médiane, 0.80; intervalle, 0.53-1.09) sont similaires (P=0.08). Par contre, les ratios mesurés avec les isolats Africains 2 (médiane, 3.23; intervalle, 1.92-3.49) ou Asiatique- Américains (médiane, 3.78; intervalle, 1.47-37) sont nettement supérieurs à ceux obtenus avec les isolats Européens (P<0.02 pour chaque comparaison). Les distributions des quantités de E2 contenues dans les 139 échantillons mesurées avec RT-E2-2 (médiane, 6150) et RT-E2-1 (médiane, 8960) étaient statistiquement différentes (P<0.0001). Nous avons observé que les charges virales totale (odds ratio (OR) OR, 2.16 95% intervalle de confiance (IC) 1.11-4.19), et épisomale du VPH-16 (OR, 2.14 95% IC 1.09-4.19), mais pas la présence de formes intégrées (OR, 3.72 95% IC 1.03-13.4), sont associées aux néoplasies intraepitheliales cervicales de haut grade (CIN-2,3), et ce, en contrôlant pour des facteurs confondants tels que l’âge, le taux de CD4 sanguin, l’infection au VIH, et le polymorphisme de VPH-16. La proportion des échantillons ayant un ratio E6/E2 > 2 pour les femmes sans lésion intraépithéliale (7 de 35) est similaire à celle des femmes avec CIN-2,3 (5 de 11, p=0.24) ou avec CIN- 1 (4 de14, P=0.65). Le polymorphisme du gène E2 est un facteur qui influence la quantification des charges intégrées de VPH-16. / Episomal and integrated HPV-16 loads are currently estimated by quantitation with real-time PCR of HPV-16 E6 (RT-E6) and E2 (RT-E2-1) DNA. We assessed the impact of HPV-16 E2 polymorphism on quantitation of integrated HPV-16 DNA in clinical specimens. First, HPV-16 E2 was sequenced from 135 isolates (123 from European and 12 from non-European lineages). A novel assay targeting conserved HPV-16 E2 sequences (RT-E2-2) was optimized and applied with RT-E6 and RTE2- 1 on 139 HPV-16-positive cervicovaginal lavages collected from 74 women (58 HIV-seropositive, 16 HIV-seronegative). Ratios of HPV-16 DNA copies measured with RT-E2-2 and RT-E2-1 with European (median, 1.02; range, 0.64-1.80) and African 1 (median, 0.80; range, 0.53-1.09) isolates were similar (P=0.08). Ratios obtained with African 2 (median, 3.23; range, 1.92-3.49) or Asian-American (median, 3.78; range, 1.47-37) isolates were greater than those with European isolates (P<0.02 for each comparison). Distributions of HPV-16 E2 copies measured in 139 samples with RT-E2-2 (median, 6150) and RT-E2-1 (median, 8960) were different (P<0.0001). HPV-16 total (odds ratio (OR) OR, 2.16 95% confidence interval (CI) 1.11-4.19), episomal (OR, 2.14 95% CI 1.09-4.19) but not integrated (OR, 3.72 95% CI 1.03-13.4) load, were associated with high-grade cervical intraepithelial neoplasia (CIN-2,3) after controlling for age, CD4 count and HIV, and HPV-16 polymorphism. The proportion of samples with an E6/E2 ratio >2 in women without SIL (7 of 35) was similar to that of women with CIN-2,3 (5 of 11, P=0.24) or CIN-1 (4 of 14, P=0.65). E2 polymorphism was a factor that influenced measures of HPV-16 integrated load.

OBJECTIVES To determine if health care workers are aware of the HPV vaccine and its availability, uptake of the vaccine and prescribing practices and reasons for non – uptake of the vaccine . METHODS Health care providers working in the private sector, in the Ethekweni health district in Kwazulu Natal, were interviewed. Health care workers included: 100 general practitioners, 50 gynaecologists, 50 paediatricians, 50 medical staff and 50 nursing staff. A questionnaire was designed for purpose of this study. Visits were be made to health care providers. All heath care providers who were willing to participate were interviewed. STATISTICS Comparisons of awareness among subgroups of health care providers was analysed using Chi-square tests. If significant, pairwise comparisons were made using a Bonferroni adjustment for multiple comparisons. Associations between awareness and other factors, such as demographic, uptake and beliefs were tested using a chi square test. Analysis was done by Stata v11 (StataCorp, 2009) i RESULTS Three hundred health care workers were interviewed - 50 gynecologists (16.7%), 52 pediatricians (17.3%), 99 general practitioners (33%), 49 other medical doctors (16.3%) and 50 (16.7%) nurses. Two hundred and sixty seven health care workers (89%) were aware of the HPV vaccine and one hundred and eighty eight health care workers (70.4%) informed patients of the availability of the HPV vaccine. Most (77.9%) practitioners have only prescribed the vaccine less than ten times. Gardasil® was prescribed by 46%, Cervarix® by 6.5% and prescription of either vaccine of health care workers was 50.2%. Practitioners were generally unaware that Gardasil® could be prescribed to males (62.9%). CONCLUSION Health care workers were aware of the HPV vaccine and prescribed the vaccine on request. However even though practitioners were aware of the vaccine, most have prescribed the vaccine less than ten times since licensing in 2008. Knowledge with regards to the licensed use of the HPV vaccines is deficient. / Thesis (M.Med.)-University of KwaZulu-Natal, Durban, 2012.