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Prolifererande verrukös leukoplaki, PVL, är en ovanlig sjukdom som yttrar sig genom multipla, vita förändringar i munslemhinnan som recidiverar och med tiden riskerar att utvecklas till cancer. Diagnosen kan endast ställas kliniskt när sjukdomsförloppet pågått under lång tid och det finns heller inga effektiva behandlingsmetoder. Etiologin till sjukdomen är okänd, men idag vet man att det finns ett samband mellan cancerutveckling och vissa virustyper.Syftet med studien är att undersöka om det går att påvisa humant papillom virus, HPV, i vävnadsprover från patienter som kan misstänkas ha PVL. Urvalet bestod av 11 patientfall, där vävnadsprover från biobanken vid avdelningen för oral patologi, Malmö högskola, samlats in och studerats med kromogen in situ hybridisering. Resultaten visade en högre förekomst av HPV i biopsier tagna i det senare skedet av sjukdomen jämfört med tidigare biopsier. En specifik HPV-genotyp kunde dock inte identifieras. I denna studie har det inte varit möjligt att påvisa HPV med in situ hybridisering, i ett tidigt staddium av PVL, som en möjlig indikator på sjukdomsutveckling. / Proliferative verrucous leukoplakia, PVL, is a rare disease that is characterized by multiple and recurrent white lesions in the oral epithelium which over time may develop into cancer. The diagnosis can only be made by the clinician when the disease has progressed for a long time. There is no effective treatment. The etiology of the disease is unknown but today it is known that there is a link between cancer and certain viruses.The purpose of this study is to investigate whether it is possible to detect human papilloma virus, HPV, in tissue samples from patients who possibly are affected by PVL.The selected samples consisted of 11 cases in which tissue samples from the biobank at the Department of Oral Pathology at Malmö University, were collected and HPV was detected by chromogenic in situ hybridization. The results showed a higher incidence of HPV in biopsies taken at a later stage of the disease compared with previous biopsies. However, a specific HPV genotype could not be identified.In this study, it has not been possible to demonstrate HPV with in situ hybridization at an early state of PVL as a putative indicator of disease development

United Nations (UN) peacekeeping operations are regularly evaluated and critiqued by both scholars and policy-makers, however this scrutiny is commonly restricted to program- and project-level effects. This neglects the unique impacts that emerge from the individuals who populate interventions and those they encounter in conflict-affected communities. The objective of this research is to place these individuals, and their actions and relationships, at the centre of analysis and investigate their impacts independent of, or distinct from, program-level effects. Through the case study of south Lebanon and the United Nations Interim Force in Lebanon (UNIFIL), this dissertation explores the social and physical spaces that connect peacekeepers and Lebanese individuals in the course of their everyday lives and actions. Through the theoretical lenses of cultural peacebuilding and hybridity, I conceptualize the meaning of these relationships to the individuals involved, to the UNIFIL mission, and to peace at a broader level. This political ethnography undertakes a complex, relational approach to understanding intervention impacts and effectiveness, thereby 'peopling' a UN peacekeeping operation. Based on original empirical data consisting of 82 ethno-biographical interviews with Lebanese individuals and UNIFIL veterans, alongside 14 months of participant and field observation, I argue that Lebanese people agentially transform superficial, formal encounters with peacekeepers into substantial, impactful relationships through the Lebanese culture of hospitality. In informal, private and local spaces and contexts, 'thick' identities are enacted and cultural exchange occurs, which transforms and hybridizes the knowledges and identities of both peacekeepers and Lebanese people. Through this process of hybridization, interlocutors emerge who facilitate the connections of others in their social networks and function as bridges across the international-local divide. This hybridization augments UNIFIL's access to local knowledge, which improves local support and operational effectiveness. Further, the relationships and connections between peacekeepers and Lebanese people contribute to the restoration or amelioration of Lebanese human identity needs, which are threatened by the conflict with Israel and the ways in which it intersects with intrastate tensions. This constitutes incremental change productive to complex pathways toward peace in south Lebanon.

The Malacothamnus alliance consists of three genera, Iliamna, Malacothamnus, and Phymosia. The genera are considered taxonomically complex since hybridization freely occurs, polyploidy levels vary, and there is a lack of distinct morphological characters to delineate taxa. Several taxonomic treatments have been prepared for each genus, but relationships within the genera and the relationship of the Malacothamnus alliance to others in the Malvaceae remains unknown. This multifaceted study aimed to (a) examine the monophyly of the Malacothamnus alliance and its position in the Malvaceae, (b) determine the relationships between genera in the alliance, (c) compare variation of nuclear and chloroplast genes in the alliance, (d) prepare revised taxonomic treatments for Iliamna and Malacothamnus, and (e) examine the probability of successful hybridization in Iliamna. The monophyly of the Malacothamnus alliance was not confirmed using DNA sequences of both nuclear and chloroplast regions. In Iliamna, little sequence variation was detected among taxa in the Rocky Mountains; however, the nuclear and chloroplast regions conflicted with regard to the relationships of the western and eastern taxa. An ancestral copy of the chloroplast genome is shared between the two eastern U.S. Iliamna species and Phymosia (Bahamas and Mexico). The nuclear ITS sequences indicated the western U.S. Iliamna species were more closely related to Phymosia and Malacothamnus than to other species in Iliamna. Neither data set provided sufficient variation to resolve relationships of species in Malacothamnus. Genetic variation and the feasibility of hybridization in Iliamna supported the results of the broader phylogenetic studies. Iliamna corei and I. remota are recently derived from I. rivularis. Hybrid offspring of I. corei and I. remota had higher viability and fecundity than did hybrids between crosses of either species and I. rivularis. The Virginia populations of I. corei and I. remota are more genetically similar than either is to Illinois populations of I. remota. However, the species are morphologically distinct and can easily be distinguished from others in the genus. Revised taxonomic treatments for Iliamna and Malacothamnus based on surveys of herbarium material are presented. Taxonomic revisions include the new combinations of Iliamna grandiflora subsp. grandiflora and I. grandiflora supsp. crandallii and the resurrection of Malacothamnus hallii and M. orbiculatus. / Ph. D.

The Culicinae is the most extensive subfamily among the Culicidae family of mosquitoes. Two genera, Culex and Aedes, from this subfamily have world-wide distribution and are responsible for transmitting of several deadly diseases including Zika, West Nile fevers, chikungunya, dengue, and Rift Valley fevers. Developing high-quality genome assembly for mosquitoes, studying their population structure, and evolution can help to facilitate the development of new strategies for vector control. Studies on Aedes albopitcus as well as on species from the Culex pipiens complex, which are widely spread in the United States, provide excellent models on these topics. Ae. albopictus is one of the most dangerous invasive mosquito species in the world that transmits more than 20 arboviruses. This species has highly repetitive genome that is the largest among mosquito genomes sequenced so far. Thus, sequencing and assembling of such genome is extremally challenging. As a result, the lack of high-quality Ae. albopictus genome assembly has delayed the progress in understanding its biology. To produce a high-quality genome assembly, it was important to anchor genomic scaffolds to the cytogenetic map creating a physical map of the genome assembly. We first developed a new gene-based approach for the physical mapping of repeat-rich mosquito genomes. The approach utilized PCR amplification of the DNA probes based on complementary DNA (cDNA) that does not include repetitive DNA sequences. This method was then used for the development of a physical map for Ae. albopictus based on the in situ hybridization of fifty cDNA fragments or gene exons from twenty-four scaffolds to the mitotic chromosomes from imaginal discs. This study resulted in the construction of a first physical map of the Ae. albopictus genome as well as mapping viral integration and polyphenol oxidase genes. Moreover, comparing our present Ae. albopictus physical map to the current Ae. aegypti assembly indicated the presence of multiple chromosomal inversions between them. To better understand population structure and chromosome evolution in Culicinae mosquitoes, especially in the Culex pipiens complex, we studied genomic and chromosomal differentiation between two subspecies Cx. pipiens pipiens and Cx. pipiens molestus. For the species responsible for the spread of human diseases, understanding the population dynamics and processes of taxa diversification is important for an effective mosquito control . Two vectors of West Nile virus, Cx. p. pipiens and Cx. p. molestus, exhibit epidemiologically important behavioral and physiological differences, but the whole-genome divergence between them was unexplored. The first goal of this study was to better understand the level of genomic differentiation and population structures of Cx. p. pipiens and Cx. p. molestus from different continents. We sequenced and compared whole genomes of 40 individual mosquitoes from two locations in Eurasia and two in North America. Principal Component, ADMIXTURE, and neighbor joining analyses of the nuclear genomes identified two major intercontinental, monophyletic clusters of Cx. p. pipiens and Cx. p. molestus. The level of genomic differentiation between the subspecies was uniform along chromosomes. The ADMIXTURE analysis determined signatures of admixture in Cx. p. pipens populations, but not in Cx. p. molestus populations. Thus, our study identified that Cx. p. molestus and Cx. p. pipiens represent different evolutionary units with monophyletic origin that have undergone incipient ecological speciation. The second goal was to study differences at the chromosome level between these two organisms. We first measured whole chromosome and chromosome arm length differences between Cx. p. molestus and Cx. p. pipiens as a basic cytogenetic approach. In addition, we used the novel Hi-C approach to detect chromosomal rearrangements between them since Hi-C was successful in detecting a known inversion in Cx. quinquefasciatus. Cx. p. molestus and Cx. p. pipiens embryos were used to perform the Hi-C technique. Analysis of the Hi-C data showed the presence of two different inversions in Cx. p. pipiens and Cx. p. molestus heatmap, which could explain their different physiology and adaptation in nature. Developing modern genomic and cytogenetic tools is important to enhance the quality of genome assemblies, improve gene annotation, and provide a better framework for comparative and population genomics of mosquitoes; also it is the foundation for the development of novel genome-based approaches for vector control. / Doctor of Philosophy / Mosquitoes are medically important insects because they vector a range of diseases that infect humans. The subfamily Culicinae is responsible for transmitting such diseases as Zika, dengue, and West Nile fevers, which have triggered fatal infections and epidemics in multiple parts of the world. Since 2010-2016, studies have reported exceeding levels of insecticide resistance that slows the disease elimination process. Novel transgenic techniques have a tremendous potential for more efficiently minimizing mosquito-borne diseases and transmission. Availability of high-quality genome assemblies for mosquitoes may help to better understand their population structure and to develop effective and safe vector-control approaches that we urgently need. For the development of high-quality genome assemblies, we need to construct a physical genome map, that shows the physical locations of genes or other DNA sequences of interest along the chromosomes. For this reason, we developed a new gene-based approach for the physical mapping of the mosquito genomes. This method was then used for the development of a physical map for Ae. albopictus. This study resulted in the generation of the first physical map of the Ae. albopictus genome. To understand population structure in Culicinae mosquitoes, we used mosquitoes from the Culex pipiens complex. Species in this complex transmit different arthropod-borne viruses or arboviruses. Notable is the West Nile Virus, which has triggered fatal infections and epidemics in Eastern and Central Europe, North America and is also known in Asia, Australia, Africa, and the Caribbean. We specifically focused on two subspecies in this complex, Cx. pipiens pipiens and Cx. pipiens molestus that are morphologically identical, but are different physiologically and behaviorally. Although they are spread globally in temperate regions, their population structure and taxonomic status remains unclear. The first goal of this study was to better understand the level of genomic differentiation of Cx. p. pipiens and Cx. p. molestus from different continents. We sequenced and compared the whole genomes of 40 individual mosquitoes from two locations in Eurasia and two in North America. Our study identified that Cx. p. molestus and Cx. p. pipiens represent different evolutionary units that are currently undergoing ecological speciation. The second goal was to study differences at the chromosome level between them. Using the Hi-C approach we detected presence of two different inversions in Cx. p. pipiens and Cx. p. molestus, which could potentially explain their different physiology and adaptation.

The incubation period is crucial for development and overall quality of a chick. The selection for fast growing broilers has allowed the birds to reach market weight at a faster rate making the incubation period a larger portion of a broiler's life. A faster growth rate can lead to the release of more metabolic heat inside of the egg toward the second half of incubation because the embryo shifts to a homeothermic state. More heat being released into the incubator can cause the incubation temperature to rise if the incubator is not electronically regulated or cannot be ventilated properly due to malfunction. A high incubation temperature can impact the hatchability, growth, and development of the chick. This thesis provides a more in-depth analysis of the effects of high incubation temperature (37.5°C versus 39.5°C) on the developing small intestine and yolk sac, which provide the chick with nutrients posthatch and during embryogenesis. Studying these organs and mechanisms occurring during this time could potentially indicate why chicks from eggs subjected to a higher incubation temperature are not developing and growing properly. Chicks from eggs incubated at a higher temperature had lower body weights, lower hatchability and lower villus height in the duodenum, jejunum, and ileum. There were also differences seen in the depth of the crypt, which is the site for stem cells. Chicks from eggs incubated at a higher temperature had a lower crypt depth in the duodenum and jejunum. There was no difference in the expression of the intestinal stem cell marker olfactomedin 4 (Olfm4) and mucin 2, which is secreted by goblet cells and forms mucus. In the yolk sac, heat shock proteins (HSP) 70 and 90 were elevated at embryonic day 15, and HSP90 still remained elevated at embryonic day 17. Chicks from eggs incubated at a higher temperature showed greater expression of peptide transporter 1 and avian beta-defensin 10 mRNA at embryonic day 13. Even though small intestinal morphology was impacted early posthatch and expression of genes in the yolk sac were elevated at embryonic day 13, there does not seem to be a long-lasting effect on the development of the small intestine or the yolk sac. It is still important to study the impact of the incubation environment to understand the development and growth of the chicks and how different incubation factors can impact the overall hatchability and health of the chick. / Master of Science / The incubation period is crucial for development and overall quality of a chick. The selection for fast growing broilers has allowed the birds to reach market weight at a faster rate making the incubation period a larger portion of a broiler’s life. A faster growth rate can lead to the release of more metabolic heat inside of the egg toward the second half of incubation because the embryo shifts to a homeothermic state. More heat being released into the incubator can cause the incubation temperature to rise if the incubator is not electronically regulated or cannot be ventilated properly due to malfunction. A high incubation temperature can impact the hatchability, growth, and development of the chick. This thesis provides a more in-depth analysis of the effects of high incubation temperature (37.5°C versus 39.5°C) on the developing small intestine and yolk sac, which provide the chick with nutrients posthatch and during embryogenesis. Studying these organs and mechanisms occurring during this time could potentially indicate why chicks from eggs subjected to a higher incubation temperature are not developing and growing properly. Chicks from eggs incubated at a higher temperature had lower body weights, lower hatchability and lower villus height in the duodenum, jejunum, and ileum. There were also differences seen in the depth of the crypt, which is the site for stem cells. Chicks from eggs incubated at a higher temperature had a lower crypt depth in the duodenum and jejunum. There was no difference in the expression of the intestinal stem cell marker olfactomedin 4 (Olfm4) and mucin 2, which is secreted by goblet cells and forms mucus. In the yolk sac, heat shock proteins (HSP) 70 and 90 were elevated at embryonic day 15, and HSP90 still remained elevated at embryonic day 17. Chicks from eggs incubated at a higher temperature showed greater expression of peptide transporter 1 and avian beta-defensin 10 mRNA at embryonic day 13. Even though small intestinal morphology was impacted early posthatch and expression of genes in the yolk sac were elevated at embryonic day 13, there does not seem to be a long-lasting effect on the development of the small intestine or the yolk sac. It is still important to study the impact of the incubation environment to understand the development and growth of the chicks and how different incubation factors can impact the overall hatchability and health of the chick.

Nitrification is the biological process whereby ammonia is converted first to nitrite by ammonia-oxidizing bacteria, and then the nitrite is subsequently converted to nitrate by nitrite-oxidizing bacteria. Ammonia and nitrite levels are closely monitored during treatment of wastewater due to their toxicity to other biological processes. Sybron Chemicals, Inc., is a company that manufactures a nitrifying bioaugmentation culture (1010N) that is used to enhance the naturally occurring levels of biological nitrification. The microbial population of the 1010N product has been examined using a combination of conventional bacteriological methods and modern molecular techniques, with the goal of developing nucleic acid probes that can be used to detect the product in an environmental sample. Small regions of the 16S rRNA genes of the bacteria in 1010N (and two new nitrifying enrichment cultures) were amplified via the polymerase chain reaction (PCR) and analyzed via temperature gradient gel electrophoresis (TGGE). TGGE is a procedure that allows for separation and visualization of individual PCR products that are the same size, based on differences in their sequence. Two of the predominant PCR products in 1010N were purified from the TGGE gel matrix, reamplified via PCR, and sequenced to allow for phylogenetic analysis and nucleic acid probe design. Coincidentally, two strains (NS500-9 and MPN2) that had been isolated from the 1010N mixed consortium and grown in pure culture were found, via TGGE, to have identical 16S rRNA sequences to the PCR products under investigation. Nearly the full-length 16S rRNA genes from these two organisms were PCR amplified, cloned, and sequenced in order to provide a basis for more accurate phylogenetic analysis. The two dominant organisms in the 1010N product, NS500-9 and MPN2, were thereby found to be most closely related to Nitrosomonas and Nitrobacter, respectively, in the existing database. Using the nucleic acid sequences of the cloned DNA, organism-specific DNA probes were designed for both NS500-9 and MPN2. Unfortunately, difficulties were encountered in using the probes to monitor 1010N activity levels via quantitative dot blot hybridizations (rRNA-DNA). Therefore, efforts were redirected to using the TGGE semi-quantitatively with an internal PCR standard (Brüggeman, et al., 2000) to estimate original cell numbers of 1010N within a mixed consortium. This method was not applicable to our system due to substantial preferential binding of the primers to template other than the standard. Samples from a laboratory-scale bioreactor, bioaugmented with 1010N, were used in an attempt to correlate an increase in activity with a detectable shift in population via TGGE. No detectable shift in population was detected in these samples even though the system exhibited increased levels of nitrification. Therefore, the sensitivity of the TGGE system was also examined by determining the limits of detection when 1010N was present in activated sludge. In both whole cell spiking experiments and genomic DNA spiking experiments, it was found that 1010N must be present at a level of at least 5% of the total population in order to be detected. While this provides some information about microbial populations, in order to evaluate the biological activity of a system, nucleic acid probes should be used in a rRNA based study. / Master of Science