Dissertations / Theses on the topic 'Panthea'

Ecology and conservation of tigers Panthera tigris and leopards Panthera pardus are studied in this thesis. The study was carried out between 2008 and 2011 in the Shuklaphanta Wildlife Reserve (SWR), a subtropical lowland area in Nepal. Both these large carnivores are sympatric in many parts of their distributional ranges in Asia. Due to poaching, habitat loss and prey depletion, the tiger is already considered an endangered species globally, whereas leopard is nearly threatened. The present study addresses the ecology and conservation of these sympatric carnivores in one densely settled area situated within the Terai Arc Landscape of Nepal, where the tiger population recently declined by about sixty percent within a decade long period. Because carnivore ecology is largely governed by their prey, understanding the feeding ecology and behavioural flexibility of felids in prey selection is essential to address their conservation requirements. The prey selection by the two carnivores were quantified by scat analysis and the distance sampling line transect method in an area of about 250 km2. Results obtained from camera trapping were used to quantify the activity patterns as well as the status and spatial behaviour of the tigers and leopards. In addition, non- invasive genetic analysis of their scats were made to identify the minimum number of tigers and leopards in SWR. For the genetics part, the Karnali floodplain area (ca. 100km2) of Bardia National Park (BNP) located 150 km further east was also included. On average, 131 and 175 individual prey animals per km2 were estimated during the dry seasons of 2010 and 2011, respectively. Of these, 62-63% was wild prey and 38% were domestic animals. Individually, swamp deer was the most abundant wild prey, followed by chital, rhesus, langur, hog deer, wild boar, nilgai and muntjac in 2010. However, in 2011 chital was the most abundant among wild prey, followed by swamp deer, rhesus, hog deer, langur, wild boar, muntjac and nilgai. The analysis of 194 tiger and 42 leopard scats showed the occurrence of 12 and 14 prey species, respectively. Tiger and leopard diets were composed of a large quantity of wild ungulates (77% for tigers and 51% for leopards). The relative occurrences of prey items (wild ungulates) in the diet differed significantly between tiger and leopard (G=11.12; df=1, p<0.001). Medium sized prey species, such as chital were most common in the tiger diet, whereas small species showed up most frequently in the leopard diet, followed by medium sized species. Tigers consumed more large prey than the leopards did. The niche overlap values indicated a great dietary overlap of tiger than leopard. Camera trapping data showed that both tigers and leopards were photo-captured more frequently at night than during the day thus indicating that both have a nocturnal activity, however, tigers were found to have more diurnal activity than leopards. Variances in time use, temporally or spatially, have been recognized as behavioural characteristics that may motivate coexistence. In general, between 11AM- 5PM leopards were less active than tigers, probably to avoid the hottest period of the day, and because of a preference for the small sized prey that are most active during dusk and dawn. Concentration within certain areas and limited diurnal activity of leopards indicated the existence of temporal niche segregation between these cats. Camera trapping identified 11 individual tigers (six males and five females) and 9 leopards (five males and four females) in SWR. The genetic analysis identified only 5 tigers and 4 leopards from SWR, and 6 tigers from the Karnali floodplain of BNP. Population density of tigers in SWR was estimated at between 1.8 and 2.9/100 km2, while that for leopards was estimated at between 1.8 and 2.6/100 km2 during the study period. From 9 tigers in SWR. I calculated an average home range (HR) of 36.6 km2, with male HR (43.3 km2) being 1.45 times larger on average than those of females (29.9 km2). Among leopards (n=7) an average HR of 17.9 km2, was recorded, with males HRs (26.6 km2) 2.86 times larger than those of females (9.3 km2). The HRs of all male tigers overlapped each other at least partially and almost completely in some cases. HRs of male tigers overlapped more than those of female tigers, and male HRs overlapped with more than one individual female. Leopard HRs tended to overlap less than those of tigers, with values ranging up to 7 km2 for females to 2-24 km2 for males (overall mean 8.83 km2). As displayed by the tiger, male leopard HRs tended to overlap with those of several females. The data suggested that even though there was 12 to 18 % median overlap between tiger and leopard HRs, there was a clear spatial separation between them. Leopards were more restricted to the periphery of the reserve, while tigers occupied the core or mostly undisturbed areas of the reserve. This research provides the first set of data on tigers, leopards and their prey in SWR, Nepal during the dry season. However, immediate needs for further research on wildlife disease, especially focused on large carnivores, and human-disturbance in the reserve including prey availability in the eastern selection of the reserve area, an issue which was not included in this study. Furthermore research is needed on predator-prey relation with the inclusion of trans-boundary wildlife corridor utilization and the link between the smaller protected areas in the trans-border level.

The Florida panther (Puma concolor coryi) is a relatively well studied species, but some aspects of its habitat requirements remain poorly understood. While it has been well established that the most important threat to panthers include limited habitat area and continued habitat loss and fragmentation, the importance of roads in this context has not been determined. The goal of this research is to determine the influence of roads on the movement patterns of the Florida panther. Panther telemetry data from 1981 until 2003 was used, as well as detailed road networks and vegetation maps. The influence of roads on individual panthers was determined through an analysis of: 1) vehicular mortality; 2) road crossing behavior; 3) road barrier effects; and 4) effectiveness of preventative measures. Results indicate that vehicle collisions continue to be a major threat to the Florida panther population, specifically adult males. Major roads form more of a barrier to movement than minor roads, but females are affected more than males. The combination of wildlife underpasses and high right-of-way fencing on I-75 has been extremely effective at vehicular mortality prevention, but the roadway remains a major barrier, particularly for female panthers. This has essentially segregated the movement of the sexes and has fragmented not only the limited habitat of the Florida panther, but also segments of the adult population critical to the propagation of the species.

As ecosystems become increasingly fragmented, there has been a proliferation of research into fields such as resource use, movement ecology and habitat connectivity. To understand how species may adapt to threats associated with habitat fragmentation it is necessary to study these processes in dispersing individuals. However, this is seldom done. Dispersal is one of the most important life-history traits involved in species persistence and evolution, but the consequences of dispersal are determined primarily by those that survive to reproduce. Although dispersal is most effectively studied as a three-stage process (departure, transience and settlement), empirical studies rarely do so and an investigation into the entire process has probably never been carried out on any one species. Here I investigate the survival, resource use, movement ecology and connectivity of African lions (Panthera leo) in all three dispersal phases in addition to adulthood. I make use of a longterm dataset incorporating radio-telemetry and observational data from lions in Hwange National Park, Zimbabwe. Dispersal is inherently risky and my results show that male lions that disperse while young suffer high mortality, young dispersal being brought about by high off-take of territorial males. Dispersing males may be aware of risks associated with territorial adults as they position themselves far from them and utilise habitats and resources differently. However, dispersers, compared to adult males and females, are far less averse of risky, anthropogenic landscapes, suggesting they are the demographic most prone to human-lion conflict. The ontogenetic movement behaviour of lions reflects a transition from directional movement during transience, suggestive of sequential search strategies, to random or periodic use of a fixed territory after settlement. In terms of habitat connectivity, I show that radically different conclusions emerge depending on which demographic is used to parameterise connectivity models. Understanding the shifting mechanisms that species adopt throughout ontogeny is critical to their conservation in an increasingly fragmented world.

Com o objetivo de realizar estratégias eficientes de manejo e conservação para a onça-pintada (Panthera onca), estudos ecológicos vêm sendo realizados em diferentes áreas ao longo de sua distribuição geográfica. No entanto, análises moleculares complementares a estas abordagens ecológicas são necessárias para garantir a viabilidade deste felídeo a longo prazo. Desta maneira, os estudos aqui apresentados tiveram por finalidade desenvolver metodologias para auxiliar estudos genéticos e ecológicos extremamente necessários para a conservação desta espécie, assim como embasar estudos populacionais com uma perspectiva genético-molecular. No primeiro capítulo, devido à enorme dificuldade de se obter amostras biológicas deste felídeo, foi desenvolvida uma abordagem baseada no sequenciamento de um segmento curto de um gene (ATP6) do DNA mitocondrial para identificar de maneira rigorosa amostras fecais de onça-pintada coletadas em campo. Os resultados indicaram a importância de se utilizar um método molecular para a identificação correta de amostras fecais coletadas em campo. No segundo capítulo foi demonstrado que é possível identificar a coloração de onças-pintadas a partir de DNA fecal, através da genotipagem molecular do polimorfismo envolvido no padrão de coloração desta espécie. Embora indivíduos melânicos de onça-pintada sejam relativamente comuns em algumas áreas da sua distribuição, até o momento, nenhum estudo científico envolvendo esta característica foi realizado com populações naturais desta espécie. O uso de amostragem não-invasiva possivelmente é uma das únicas maneiras para estudar diretamente populações de onça-pintada que apresentam esta característica. No terceiro capítulo foi realizado o primeiro estudo envolvendo estruturação e conectividade de populações naturais deste felídeo em uma escala regional. O estudo abrangeu as populações remanescentes de onça-pintada da Ecorregião do Alto Rio Paraná, contida na Mata Atlântica de Interior. Os resultados indicaram perda de variabilidade genética em populações recentemente isoladas e uma considerável diferenciação entre os fragmentos, sugerindo forte efeito da deriva genética, por sua vez induzida pelo pequeno tamanho efetivo em cada área e o crescente isolamento entre as mesmas. Ao mesmo tempo, análises genéticas identificaram evidência de conexão demográfica recente entre áreas, sugerindo que este processo natural de conectividade deve ser mantido para garantir a viabilidade destas populações em longo prazo. Os resultados serão integrados ao plano de manejo que vem sendo desenvolvido para este felídeo no Alto Rio Paraná, subsidiando a elaboração e efetivação de esforços urgentes para a conservação desta espécie nesta ecorregião.<br>Several ecological studies have been conducted aiming to aid in the design of effective management and conservation strategies for the jaguar (Panthera onca) in different areas throughout its geographic distribution. However, molecular analyses complementary to these ecological approaches are necessary to ensure that these strategies secure the long term viability of this felid. The studies presented here aimed to develop methodologies that aid in ecological and genetic studies focusing on the jaguar, which are essential to the conservation of this species, as well as to serve as a basis for in-depth populational analyses employing a molecular genetic perspective. In the first chapter, due to the enormous difficulty in obtaining biological samples of this felid, an approach based on the sequencing of a short segment of a mitochondrial DNA gene (ATP6) was developed to accurately identify jaguar faecal samples collected in the field. The results of this study indicated the importance of using a molecular method for the correct identification of faecal samples. In the second chapter, we demonstrated that it is possible to reliably identify the color of a jaguar from faecal DNA by genotyping the molecular polymorphism involved in this coloration variant. Although melanistic individuals are relatively common in some areas of their distribution, so far no scientific study has been conducted addressing this phenotype in the wild. The use of non-invasive sampling is likely one of the few approaches to study natural populations of jaguars exhibiting this characteristic. The third chapter contains the first study involving the structure and connectivity of natural jaguar populations on a regional scale. The study included remnant jaguar populations of the Upper Paraná Atlantic Forest Ecoregion. The results indicated loss of genetic variability in recently isolated populations and considerable genetic differentiation among fragments, suggesting strong effects of genetic drift induced by the small effective size in each area and increasing isolation among them. At the same time, genetic analyses identified clear evidence of recent demographic connectivity between areas, indicating that gene flow among them should be maintained to ensure the long term viability of these populations. The results will be integrated into the management plan that is being developed for this felid in the Upper Paraná Atlantic Forest, supplying data that is important for the development and implementation of urgent efforts to conserve this species in this ecoregion.

Made available in DSpace on 2015-04-14T13:09:48Z (GMT). No. of bitstreams: 1 459622.pdf: 7068084 bytes, checksum: 30b184abdf871f7ee7438f18072e7ddb (MD5) Previous issue date: 2014-03-06<br>Mitochondrial genomes (mitogenomes) are usually obtained through DNA sequencing produced by a set of conserved PCR primers that are designed to generate overlapping segments, thus completing the whole mitochondrial DNA. This may be a good strategy for some organisms. However, the translocation of cytoplasmic mitochondrial DNA (cymtDNA) into the nuclear genome (numt) is known to be a frequent phenomenon in many taxa, including the felid genus Panthera. Some strategies have been developed to avoid the unwanted amplification of numt, such as mitochondrial isolation followed by PCR or long-PCR. Recently, next-generation sequencing (NGS) approaches have begun to be extensively used in this field. Among these, RNA sequencing (RNAseq) seems to be extremely useful to generate mitogenomes and to avoid numts, as it allows the efficient capture at high coverage of mtDNA transcripts, avoiding pseudogenized nuclear copies. When we initiated this study, mitochondrial genomes of all species of the Panthera genus except the jaguar (P. onca) were available in public databases such as GenBank. Given the importance of this molecular marker for jaguar population studies and for phylogenetic analyses within the Panthera genus, the goals of this project were to (i) characterize the Panthera onca mitogenome, eliminating the possibility of erroneous amplification of numt; and (ii) to conduct the first mitogenomic analysis of the Panthera genus. We have characterized the mitochondrial genome of the jaguar employing RNA-seq data. The transcripts covered about 95% of the mitogenome, with the remaining gaps being complemented by PCR-based DNA sequencing, using specific primers designed for this purpose. All mitogenomic phylogenetic analyses (Maximum Likelihood, Maximum Parsimony, Neighbor-Joining and Bayesian Inference) supported a congruent topology (((N. nebulosa ((P. tigris (P. onca (P. uncia, (P. leo, P. pardus))))). This topology is unprecedented for the genus, but our results indicate that it correctly reflects the evolutionary history of mitochondrial DNA in this group. This study demonstrated that, with RNA-seq approach, almost the entire mitochondrial genome from an individual can be quickly characterized. Furthermore, this approach holds great promise especially in the case of groups plagued by the presence of large and recent numts, as is the case of Panthera species.<br>Genomas mitocondriais (mitogenomas) geralmente s?o obtidos atrav?s do sequenciamento de DNA realizado com uma s?rie de primers conservados desenhados de maneira a se sobreporem, completando assim todo o DNA mitocondrial. Esta estrat?gia ? bastante eficaz para alguns organismos. Entretanto, a transloca??o de segmentos do DNA mitocondrial citoplasm?tico (cymtDNA) para o genoma nuclear (numt) ? um fen?meno conhecido para muitos t?xons, incluindo os felinos pertencentes ao g?nero Panthera. Algumas estrat?gias foram desenvolvidas para evitar a amplifica??o indesejada do numt, como por exemplo o isolamento de DNA mitocondrial seguido de PCR ou de PCR longo. Recentemente, as t?cnicas de sequenciamento de alto desempenho v?m sendo amplamente utilizadas. Dentre estas, o sequenciamento de RNA (RNA-seq) parece ser extremamente ?til para gerar mitogenomas e evitar numts, uma vez que captura com alta cobertura apenas DNA mitocondrial transcrito, evitando as c?pias nucleares pseudogenizadas. Quando este estudo foi iniciado, genomas mitocondriais de todas as esp?cies do g?nero Panthera exceto P. onca estavam dispon?veis em bases de dados como o GenBank. Tendo em vista a import?ncia deste marcador molecular para estudos populacionais de on?a-pintada (Panthera onca) e para estudos filogen?ticos entre as esp?cies do g?nero Panthera, os objetivos deste trabalho foram (i) caracterizar o mitogenoma de Panthera onca de forma a eliminar a possibilidade de amplifica??o err?nea de numt e (ii) realizar a primeira an?lise mitogen?mica do g?nero Panthera. O genoma mitocondrial da on?a-pintada foi caracterizado utilizando dados de RNA-seq. Os transcritos cobriram cerca de 95% do mitogenoma, sendo os demais segmentos cobertos por sequenciamento de DNA baseado em PCR, atrav?s da utiliza??o de primers espec?ficos desenhados para esta finalidade. Todos os quatro tipos principais de an?lises filogen?ticas do mitogenoma (Maximum Likelihood, M?xima Parcim?nia, Neighbor- Joining e Infer?ncia Bayesiana) suportaram uma topologia congruente (((N. nebulosa ((P. tigris (P. onca (P. uncia, (P. leo, P. pardus))))). Esta topologia ? in?dita para o g?nero, por?m os resultados indicam ser esta a verdadeira hist?ria evolutiva do DNA mitocondrial dentro deste grupo. Neste trabalho, demonstrou-se que atrav?s de RNA-seq ? poss?vel obter-se praticamente todo o genoma mitocondrial de um indiv?duo. Al?m disso, esta abordagem parece ser bastante promissora especialmente em casos onde grandes e recentes numts ocorrem, como ? o caso das esp?cies pertencentes ao g?nero Panthera.

Pantoea ananatis causes disease symptoms in a wide range of economically important plants such as Eucalyptus, maize and onions. This study specifically focussed on the interactions of P. ananatis LMG20103 with onion seedlings where it causes symptoms that include water-soaked lesions, wilting and bleaching of the leaves, and maceration of the bulbs. The pathogenicity of P. ananatis is not well understood, however, motility plays an important role in many other well-known phytopathogens such as Ralstonia solanacearum and Pseudomonas syringae. It is therefore hypothesised that P. ananatis uses motility to colonise and infect its hosts. Chapter 1 reviews the literature on how motility aids phytopathogenic bacteria in locating their host, attaching and initiating infection, as well as dissemination. The two dominant forms of motility utilised are swimming and twitching motility. Swimming motility is essentially the rotation of flagella which propels the bacterial cell forward through a fluid environment in response to chemotactic signals. The motor that drives the flagella is made up of several proteins that include the MotAB proteins and its function is dependent on a proton motive force. While twitching motility is not as fast as swimming motility, it is a rapid means of surface colonisation. Bacteria twitch by extending their type IV pili, attaching to the surface, and then retracting, bringing the whole cell closer to the point of contact. This motion is powered by the ATPase PilT. In Chapter 2 the flagellum and type IV pilus biosynthetic gene clusters are compared between strains of P. ananatis and closely related enterobacterial strains. The four fully annotated and sequenced P. ananatis strains used in this study were isolated from various different sources and provided a greater understanding of how P. ananatis exploits its flagella and type IV pili to infect such a wide variety of hosts. While Chapter 3 focuses on the creation of four motility mutants and their respective complements in P. ananatis LMG20103, Chapter 4 consists of an array of tests and assays comparing the mutants to the wild-type strain to elucidate the role of swimming and twitching motility in the colonisation and infection of P. ananatis in onions. Chapter 5 is a published article titled, “Draft genome sequences of the onion centre rot pathogen Pantoea ananatis PA4 and maize brown stalk rot pathogen P. ananatis BD442.” Both strains are South African isolates and were sequenced using the Illumina HiSeq 2500 platform. A greater understanding of how P. ananatis uses motility to target tissues and infect its host plant increases the currently limited body of knowledge available to develop strategies to limit the damage caused by this pathogen to agronomic crops in plantations and nurseries.<br>Thesis (PhD)--University of Pretoria, 2015.<br>Microbiology and Plant pathology<br>PhD<br>Unrestricted

The delineation of bacterial species and genera has always been problematic as a clear definition of these concepts are lacking. In an attempt to classify bacteria into workable groups, operational criteria have been applied to delimitate boundaries for these taxonomic ranks. This approach has unfortunately led to artificial groupings that are often not comparable in terms of diversity in different groups of bacteria. A classification system needs to reflect natural groupings to depict the evolution of bacteria and predict the phenotypic and genetic diversity for these groups. In order to understand the forces that play a role in the evolution of a bacterial genus a review of the current literature was presented in Chapter 1. The major focus was on vertical inheritance and how this process can be used to depict the evolutionary path of members belonging to the same genus. The largest amount of genetic material in any one cell is thought to have been transferred from parent to progeny, supporting the idea that the vertical signal is recoverable and can in fact be the dominant signal present in the genome when looking at conserved genes. The effect of horizontal gene transfer (HGT) on the evolutionary picture obtained by vertical descent was also discussed. The core genome of a genus is defined as the genes conserved between all species of a genus and are thought to mostly include genes that are essential for the survival of members of that particular genus. In Chapter 2, the hypothesis was tested that the boundaries used to delineate genera could be based on an analysis of the shared core genome. For this purpose coherence within the core genome of the genus Pantoea was investigated. The core was characterised in terms of its functional diversity through Clusters of Orthologous Genes (COGs) and compared to the core genomes of other bacterial genera. It was seen that the core genome does give an indication of the coherence of a genus and that shared genome content can be used as a tool to delimitate genera. Previous taxonomic studies have shown that species in the genus Pantoea are well defined but that the phylogenetic relationships between these species are not well elucidated. Generally accepted approaches for phylogenetic inference, like 16S rRNA gene trees and multi-locus sequence analysis (MLSA), does not give sufficient resolution to determine the deeper evolutionary relationships between these species. In Chapter 3, phylogenomic analyses were performed to determine if a robust phylogeny, reflecting the evolutionary history of the genus, can be obtained using the core genome of the genus. The core genome as well as subsets thereof (based on COGs), was used for phylogenetic inference, to obtain a robust phylogeny for the genus.<br>Dissertation (MSc)--University of Pretoria, 2014.<br>Microbilogy and Plant pathology<br>MSc<br>Unrestricted

A building and its environment can work together to express unity and harmony. The concept behind my project stems from the specific nature of a public place and its needs. These elements, synthesized through a process of transformation and redefinition, bring the building as close as possible to its architectural reality. My thesis is that the awareness of order is achieved when an object has established a language that clarifies its existence.<br>Master of Architecture

Large carnivores in human care have been reported to engage in stereotypic behaviors. Such behavior is thought to be correlated with high stress levels, in part, due to captive environments limiting opportunities for functional consequences and environmental stimuli. Moreover, there are several arguments stating that stereotypic behaviors can be indicative of poor welfare, as they can often have severe negative emotional and physical effects on the animal. The first portion of this study included a five-phase treatment analysis which evaluated whether environmental manipulations decrease the frequency of stereotypic behaviors including pacing, over-grooming and tail-sucking exhibited by a single male jaguar housed at Jacksonville Zoo and Gardens. The aim of the present study was to evaluate possible environmental variables that were reported by staff as likely variables maintaining or promoting stereotypic behavior. Data collection occurred during a 10-week evaluation and followed an ABCAD reversal design. Both behavioral data and fecal glucocorticoid metabolite levels were analyzed. The second portion of this analysis included a multi-institutional survey to assess the prevalence of the stereotypic behaviors exhibited by zoo-housed jaguars in North American AZA-accredited institutions. Results from the behavioral assessment revealed a decrease in stereotypic behaviors with the implementation of treatment conditions. Hormone analyses revealed that stereotypic pacing is not presently correlated with higher stress levels for this animal. Finally, survey results revealed that a significant portion of the North American jaguar population engages in stereotypic behaviors. Further analyses are necessary to identify potential patterns or environmental predictors for the development of stereotypic behaviors.

Olfactory signals are an important means of social communication among felids. However, not much is known about how individual volatiles of body-borne odours influence behavioural responses. 2-acetyl-1pyrroline has recently been identified as a characteristic component of tiger marking fluid, while being absent from lion marking fluid. One pride each of captive Amur tigers (Panthera tigris altaica) and African lions (Panthera leo) were presented with wooden logs impregnated with four different odours and their behaviour was observed. The tigers displayed significantly more interactions towards the marking fluid component (2-acetyl-1-pyrroline), the conspecific urine odour, and the fruity odour (iso-pentyl acetate) than towards the near odourless control (diethyl phthalate). The lions displayed significantly more behaviours towards conspecific urine than towards any of the other odours.  In general all lions interacted more with the logs than tigers. Hence, these results support the notion that 2-acetyl-1-pyrroline is a species-specific odorant for tiger olfactory communication. Furthermore, the results show that a single compound (2-acetyl-1pyrroline) can elicit behavioural responses to the same degree as a complex chemical mixture (tiger urine). The high number of interactions performed by both species towards the wooden logs impregnated with conspecific urine suggests that conspecific odours are suitable to use as olfactory enrichment for captive felids.

Pantoea agglomerans strain Eh1087 produces the phenazine antibiotic Dalanylgriseoluteic acid (AGA). A cluster of 16 genes has previously been shown to be responsible for the production of, and resistance to, AGA. The present study has refined and tested a number of hypotheses arising from the preliminary characterisation of the AGA pathway. The products of the first five genes of the AGA cluster, Group 1, are similar to proteins responsible for phenazine-1-carboxy lie acid by fluorescent pseudomonads. However, Eh1087 appears to be missing a duplication of the ehpA gene, and it was hypothesised that EhpA was responsible for the ability of Eh1087 to produce both phenazine-1- carboxylic acid and phenazine-1,6-dicarboxylic. Comparison of EhpA to related proteins of known structure suggested a catalytic function, and EhpA was found to influence the relative amounts of phenazine-1-carboxylic acid and phenazine-1,6- dicarboxylic acid produced by Group 1. The final step in the AGA pathway is the addition of a D-alanyl residue to griseoluteic acid to form AGA, and is catalysed by the EhpMNO proteins. The previous model for AGA biosynthesis suggested that EhpM was an integral membrane protein and that EhpMNO operated in the periplasm. EhpM and EhpN are similar to components of nonribosomal peptide synthetases, while EhpO is similar to ketosynthases involved in fatty acid and polyketide biosynthesis. Comparison of EhpM with known structures, and preliminary analysis of the subcellular location of EhpMNO suggest that these proteins may be localised to the cytoplasmic side of the inner membrane, rather than the periplasm. An Eh1087 transposon-mutant with an insertion that affected the expression of glnA was isolated. This mutant lacked glutamine synthetase, and was, therefore, not able to incorporate labelled nitrogen from ammonium sulphate, via glutamine, into phenazines. It was concluded that glutamine is the source of the two nitrogen atoms of the phenazine nucleus. In addition, the function of the putative Eh1087 glnA locus was confirmed by complementation of an E.coli glnA mutant and the gene found to encode a type I glutamine synthetase typical of the Enterobacteriaceae.

Made available in DSpace on 2015-03-26T13:47:08Z (GMT). No. of bitstreams: 1 texto completo.pdf: 829087 bytes, checksum: 53a595f1be1470ef16a089fa9a53d992 (MD5) Previous issue date: 2004-03-31<br>The present work proposed evaluating the organization of the components of the testes, the seminiferous epithelium cycle, the intrinsic yield of each fase of spermatogenic process, the testicular sperm reserve, as well as the correlations of these items with corporal and testicular biometric parameters.The medium corporal weight of the jaguar in the present experiment was 78,5 kg, of which about 0,034% are located in the testicular mass, and 0,022% specifically in the seminiferous tubules, which represented about 77,7% of the testicular parenchyma. The average diameter of seminiferous tubules in jaguars was 257 µm, and the average thickness of the seminiferous epithelium was about 90m. Jaguars have about 12,2 meters of seminiferous tubules by testicle gram. The general spermatogenic yield of the jaguar was about 23,4 cells and each Sertoli cell was able to sustain and to keep about 19,2 germ cells, 11 of which were round spermatides. In each seminiferous epithelium cycle about 166 million of spermatozoids were produced by testicle gram. In the jaguar the Leydig cells occupy an average 0,0036% of the corporeal weight and its average number by testicle gram is within the scope for most mammals: between 20 and 40 million. The obtained data supplied pertinent information about the spermatogenic process of this feline of the brazilian fauna, for subsidy to projects of conservation and protection of the wild life that involve reproduction programs.<br>O presente trabalho propôs avaliar a organização dos componentes do testículo, o ciclo do epitélio seminífero, o rendimento intrínseco de cada fase do processo espermatogênico, a reserva espermática testicular, bem como as correlações destes itens com parâmetros biométricos corporais e testiculares. O peso corporal médio das onças-pintadas do presente experimento foi de 78,5 kg, dos quais cerca de 0,034% são alocados em massa testicular e 0,022% especificamente em túbulos seminíferos, que representaram cerca de 77,7% do parênquima testicular. O diâmetro médio dos túbulos seminíferos em onça-pintada foi de 257&#956;m, e a espessura média do epitélio seminífero foi de aproximadamente 90&#956;m. A onça-pintada apresenta cerca de 12,2 metros de túbulo seminífero por grama de testículo. O rendimento geral da espermatogênese da onça-pintada foi de aproximadamente 23,4 células, e cada célula de Sertoli foi capaz de sustentar e manter aproximadamente 19,2 células da linhagem germinativa, das quais cerca de 11 são espermátides arredondadas. A cada ciclo do epitélio seminífero, cerca de 166 milhões de espermatozóides são produzidos por grama de testículo. Em onças-pintadas as células de Leydig ocupam em média 0,0036% do peso corporal e seu número médio por grama de testículo apresentou-se dentro da amplitude descrita para a maioria dos mamíferos, entre 20 e 40 milhões. Os dados obtidos fornecem informações pertinentes sobre o processo espermatogênico deste felino da fauna brasileira, para subsídio a projetos de conservação e proteção da vida silvestre que envolvam programas de reprodução.

Pantoea ananatis, a plant pathogenic bacterium, inflicts significant economic losses to the agricultural and forestry industries. It is ubiquitous and capable of surviving in a diverse range of environmental conditions. The mechanism underlying host infection and colonization by this pathogen is poorly understood. The genome sequence of P. ananatis led to the discovery of putative pathogenicity determinants such as quorum sensing. In this study, a PCR-mediated protocol that makes use of the lambda () red genes was used to knockout the genes for the three quorum sensing systems in P. ananatis LMG 2665T. The mutant strain was named EanΔI/R,RhlΔI/R,ΔLuxS. Growth assays conducted using this mutant and the wild-type strain showed that the mutations did not affect its growth in liquid broth. This mutant was used to determine the role of quorum sensing in the virulence of P. ananatis. Virulence assays conducted showed that quorum sensing is required for virulence in P. ananatis. To elucidate the role of individual quorum sensing systems in the virulence of P. ananatis, mutants lacking one system were constructed following the  Red-mediated PCR protocol. The mutant strains were complemented by cloning the wild-type genes for the respective quorum sensing systems into the broad-host-range plasmid pBR1MCS-5. The mutant strains were named EanΔI/R, RhlΔI/R and ΔLuxS based on the quorum sensing genes that were mutated. The complemented strains were named EanΔI/R::EanI/R, RhlΔI/R::RhlI/R and ΔLuxS::LuxS, respectively. In vitro growth studies showed that the genetically modified P. ananatis strains were not impaired in their growth. The P. ananatis quorum sensing mutant strains and complemented mutant strains were used to determine the functional role of each quorum sensing system in P. ananatis. Characterization of the quorum sensing mutant strains revealed that the three quorum sensing systems are required for virulence of P. ananatis in onion seedlings. The virulence assays conducted showed that the LuxS quorum sensing system is the most crucial system for virulence in P. ananatis. Furthermore, in vitro studies of quorum sensing regulation of specific phenotypes of P. ananatis showed that quorum sensing governs biofilm formation and exopolysaccharide production. The phenotypes that were impaired in the quorum sensing mutant strains were restored to wild-type levels by genetic complementation. This study also showed that swarming and twitching motility, as well as rhamnolipid production are not influenced by quorum sensing in P. ananatis. The dependence of specific phenotypes on quorum sensing indicates the significance of the functional role of quorum sensing genes in the virulence of P. ananatis.<br>Dissertation (MSc)--University of Pretoria, 2012.<br>Microbiology and Plant Pathology<br>MSc<br>Unrestricted

Civil society has come to dominate the discourses of development and social change for the last few decades. This thesis is a critical engagement with the liberal ideas of civil society; it specifically explores the politics that surfaces in the civic sphere in the context of caste inequalities through the study of Dalit socio-political organisations that occupy the margins of civil society in India. This ethnography of Dalit politics interrogates the intersections of caste and civil society in current globalised times and spaces through exploration into post-Panther phase of Dalit politics in rural Maharashtra. The focus is on two socio-political movements; one is Manavi Hakk Abhiyan (MHA), a grassroots Dalit organisation with international networks and the other is Bahujan Samaj Party (BSP) a national Dalit political party. This study offers insights into the dynamic nature of caste and its vitality in constructing localised form/s of civil society in India. A common running theme in the thesis is Dalit politics of resistance and their struggle to access justice through the state despite the continued denial of justice to Dalits through fragmented institutions of the state. The study, thus, observes how the participation of Dalit movements in claiming democratic citizenship through party politics occurs alongside the marginalisation of Dalit assertion in electoral politics. Looking beyond the state, the thesis charts the relationships between Dalits and the external relational fields within which they operate: it details the vernacular modes of communication in the civic sphere where protests and violence are important modes; the innovative uses of caste and cultural repertoires by Dalit movements in challenging caste hierarchy and forming collective identities of protest; and finally, the context of global associational revolution and engagement of NGOs and INGOs as new associations in Dalit politics of resistance. This thesis contributes to the larger debates on the makings of caste and civil society in India and argues that caste and Dalit movements have a key role in constructing localised forms of civility and civil society that challenge the dynamic hierarchies and exclusions of caste.

Life-history patterns in lions Panthera leo living in savanna woodlands of the Kruger National Park, South Africa, were investigated and compared with those of the Tanzanian ‘plains-like’ ecosystems (e.g. Serengeti Plains and Ngorongoro Crater). First, lower levels of mortality in the juvenile age classes were found in Kruger lions, which in turn, extend the inter-birth period. A further difference was a prolonged period of association of sub-adult males with their natal pride, either directly or in a land tenure system that has not been described previously. Most (80%) of young male coalitions rather than becoming nomadic, remained close to their natal territory after leaving the pride, either as non-territorial sub-adults or adults and even as territorial adults. Only 20% of coalitions did not stay close to their natal range, one of which acquired a territory 20 km away from its natal pride. The pattern of territory acquisition, in fact, was one in which the majority of holders acquired territories close to their natal ranges. These behaviour patterns contrast markedly with those from ‘plains-like’ ecosystems where dispersing males usually move far away from their natal pride’s range (>200) km and often remain nomadic for extended periods of time. Dense bush and access to sufficient prey resources in the form of resident buffalo Syncerus caffer herds may be important factors allowing extended residence near the natal pride’s territory. Buffalo were more available in our study area habitat than in neighbouring habitats, and comprised the majority of male lion kills. Extended male residence contrasts markedly with current theory on dispersal in polygynous mammals, which holds that only one sex (females for lions) gain an advantage by staying close to the territory of their natal pride. In Kruger it seems that both sexes gain an advantage by not dispersing far, and use currently undocumented mechanisms to avoid inbreeding.

Life-history patterns in lions Panthera leo living in savanna woodlands of the Kruger National Park, South Africa, were investigated and compared with those of the Tanzanian ‘plains-like’ ecosystems (e.g. Serengeti Plains and Ngorongoro Crater). First, lower levels of mortality in the juvenile age classes were found in Kruger lions, which in turn, extend the inter-birth period. A further difference was a prolonged period of association of sub-adult males with their natal pride, either directly or in a land tenure system that has not been described previously. Most (80%) of young male coalitions rather than becoming nomadic, remained close to their natal territory after leaving the pride, either as non-territorial sub-adults or adults and even as territorial adults. Only 20% of coalitions did not stay close to their natal range, one of which acquired a territory 20 km away from its natal pride. The pattern of territory acquisition, in fact, was one in which the majority of holders acquired territories close to their natal ranges. These behaviour patterns contrast markedly with those from ‘plains-like’ ecosystems where dispersing males usually move far away from their natal pride’s range (>200) km and often remain nomadic for extended periods of time. Dense bush and access to sufficient prey resources in the form of resident buffalo Syncerus caffer herds may be important factors allowing extended residence near the natal pride’s territory. Buffalo were more available in our study area habitat than in neighbouring habitats, and comprised the majority of male lion kills. Extended male residence contrasts markedly with current theory on dispersal in polygynous mammals, which holds that only one sex (females for lions) gain an advantage by staying close to the territory of their natal pride. In Kruger it seems that both sexes gain an advantage by not dispersing far, and use currently undocumented mechanisms to avoid inbreeding.

Made available in DSpace on 2013-08-07T19:12:23Z (GMT). No. of bitstreams: 1 000426215-Texto+Completo-0.pdf: 1203023 bytes, checksum: a4c95024eb4a04a350ac7a3aeb621944 (MD5) Previous issue date: 2010<br>Population size reduction currently constitutes a real problem for several natural populations, and many studies have focused on the identification and management of adequate protected areas for threatened species. The conservation of natural areas aims to guarantee good-quality habitats to keep populations at a viable size, which includes an avoidance of potentially deleterious effects of inbreeding. Additionally, conservation plans aim to keep dispersal corridors and consequently to maintain gene flow among populations that were originally connected. Large carnivores, due to their need for large home ranges and frequent persecution by hunters, are extremely vulnerable to habitat fragmentation. Since they are top-predators, their local elimination may cause the alteration of the whole ecosystem, while their protection might impact the persistence and demography of several co-occurring species. Carnivores usually cause major challenges to conservation managers, since considerably large areas are necessary to encompass the home range of a single individual and even larger regions are required to comprise an entire population. The jaguar is the largest predator in the Americas, and currently persists in less than 50% of its original distribution. Also, many remnant areas do not contain sufficient habitat and prey base to hold viable populations in the long term. In Brazil, the Amazon Basin and the Pantanal are the largest areas of the current distribution of the species, and where populations with high probability of long-term survival are still found. However, little is known about the dynamics of jaguar populations in these biomes, and thus population-genetic analyses are extremely necessary. The present study aimed to analyze 52 individuals sampled in the southern Pantanal from 2001 and 2008 to make genetic inferences on jaguar populations, as well as to compare them to previously investigated fragments in the Atlantic Forest biome, where high levels of structuring had been found. We estimated genetic differentiation among populations using an AMOVA approach to generate Fst and Rst indices. Population structuring analyses were also performed with the Bayesian approach implemented in the software STRUCTURE. Variability indices were quite high, and comparable to those found for the species when analyzed under on a phylogeographic scale. When Pantanal populations were assessed separately, a single genetic cluster was inferred, supporting the expectation of demographic connectivity throughout this area. However, when Atlantic Forest jaguars were also included in the analysis, the Pantanal population was divided into two groups, probably due to relatedness among some of the sampled individuals, combined with complex historical admixture with respect to transitional areas between the two biomes. One such area was likely the region adjacent to Porto Primavera dam, on the bank of the upper Paraná river, whose population has already been extirpated due to human activities. Results obtained in the present study support the idea that, in the past, there was genetic connectivity between populations from the Pantanal and the Upper Paraná region, which helps provide baseline data to aid in the design of adequate management actions that may reconnect these biomes. Moreover, the data shown here represent the first jaguar sampling of a genetically healthy local population, and may be used as a comparative reference for the evaluation and monitoring of the observed variability in fragmented regions.<br>Atualmente, a redução do tamanho populacional constitui um problema real para muitas populações selvagens e cativas, e muitos estudos têm sido realizados nesse contexto com o intuito de identificar áreas de manejo e proteção de espécies ameaçadas. O manejo de populações naturais tem como objetivo assegurar hábitats adequados para manter populações em tamanhos viáveis evitando assim que os efeitos do endocruzamento se pronunciem, além de manter corredores para facilitar a dispersão dos organismos e consequentemente o fluxo gênico entre populações. Os grandes carnívoros, por necessitarem de grandes áreas de vida e serem usualmente perseguidos por caçadores, são bastante vulneráveis à fragmentação de hábitats Devido ao fato de serem predadores-topo, sua extinção local geralmente leva à alteração de todo o ecossistema. Desta forma, sua conservação afeta, de maneira direta e indireta, muitos outros organismos. Os carnívoros estão entre os organismos que causam maiores desafios e preocupações às autoridades referentes à conservação. Áreas consideravelmente grandes são necessárias para englobar a área de vida de um único individuo, e territórios ainda maiores são necessários para abranger uma comunidade inteira deste grupo. A onça-pintada, o maior felídeo das Américas, encontra-se atualmente em menos de 50% da sua distribuição original e muitas áreas remanescentes não apresentam tamanho e disponibilidade suficiente de presas para manter uma população saudável em longo prazo. No Brasil, a Bacia Amazônica e o Pantanal são as maiores áreas de distribuição da espécie onde ainda se encontra populações grandes o suficiente para uma viabilidade por um longo período de tempo. No entanto, pouco se sabe sobre a dinâmica das populações de onça-pintada nesses biomas, havendo assim uma extrema necessidade de análises em nível genético-populacional da espécie. O presente trabalho teve como objetivo analisar 52 indivíduos provenientes do Pantanal brasileiro amostrados no período de 2001 a 2008, e fazer inferências genéticas sobre esta população, bem como compará-la com uma área previamente estudada na Mata Atlântica, onde altos níveis de estruturação foram encontrados. Foram analisados índices de diversidade genética intra-populacional e calculados índices de estruturação (Fst e Rst) assim como análise Bayesiana de estruturação no programa STRUCTURE. Os níveis de variabilidade foram bastante altos e comparáveis com aqueles encontrados para a espécie quando analisada de uma forma mais ampla (em escala filogeográfica). Quando as amostras do Pantanal foram analisadas em relação à sua estruturação, os dados indicaram a presença de apenas uma população, sugerindo que a região amostrada (Pantanal sul) consiste de uma só unidade genética. No entanto, quando as populações da Mata Atlântica foram incluídas na análise, as amostras do Pantanal foram alocadas em duas unidades genéticas incompletamente diferenciadas, devido provavelmente à influência de parentesco entre alguns dos indivíduos desta região, em combinação à provável miscigenação histórica com áreas transicionais entre os dois biomas. Este parece ter sido o caso da população amostrada na área de influência da UHE Porto Primavera (MS/SP), situada no limite interior do bioma Mata Atlântica e que atualmente encontra-se extinta por ação humana. Os resultados obtidos apóiam a inferência de que, no passado, havia conectividade genética entre populações do Pantanal e da Mata Atlântica de Interior, embasando o delineamento de possíveis ações de manejo a fim de retomar a conexão entre estes dois biomas. Além disso, os dados do Pantanal representam a primeira amostragem de uma população geneticamente saudável de onças-pintadas, podendo servir como base para a avaliação e monitoramento da variabilidade observada nesta espécie em regiões fragmentadas.

Despite intense persecution over the last century, the jaguar (Panthera onca) has sustained a wide geographic distribution, perhaps due to its elusive nature and rather flexible ecology. This study investigated jaguar ecology under anthropogenic pressures in Belize, Central America. A suite of methods including camera-trap surveys, diet analysis, discussions with local stakeholders, and population simulations were used to study a population of jaguars spanning the boundary of a protected forest. Camera-trap data combined with capture-recapture population models are increasingly used to estimate the density of mammals such as jaguars with individually identifiable coat patterns. A review of current methods highlighted problems associated with estimating the sizes of lowdensity populations. Simulations to assess the robustness of the method found that camera failure can negatively or positively bias the abundance estimate, depending on the particular nature of capture histories. The most commonly used model estimator in the literature was nevertheless robust to failures of up to 10% of trap-occasions. Pooling trap-occasions reduced the effect of camera failure. Sub-sampling data from large-scale surveys indicated a threshold survey area of ~170 km2, below which estimates of density were inflated and unreliable. For surveys exceeding this threshold size, jaguar density varied across the landscape from the protected forest to the human-influenced lands such that <30% contiguous forest precipitated reduction. Reduced densities with distance from contiguous forest and proximity to human habitation may result principally from direct conflicts with people. The influence of anthropogenic factors on the coexistence of jaguars and pumas (Puma concolor) was investigated by comparing their habitat use and feeding ecology. Diet was analysed from the largest sample to date of scats from one area identified to species. Jaguars and pumas made similar use of the secondary rainforest, despite differences in diet. Although both cats relied heavily on one species of small prey (5-10 kg), for jaguars this was the nine-banded armadillo (Dasypus novemcinctus) while for pumas it was the paca (Agouti paca). Both cats took some larger prey, mainly white-lipped peccaries (Dictolyes pecari) by jaguars and red brocket deer (Mazama americana) by pumas. Energetics models indicated that reproduction may be limited for either species if large prey are unavailable for females with dependents. Outside the forest block, jaguars rarely ate large wild prey species; instead, a diet of smaller wild prey was supplemented with large domestic stock. Pumas were scarce outside the protected forest, possibly reflecting a reluctance to utilise domestic species near human developments and competition with humans for their preferred prey of paca and deer, which are also prized regionally as game species. Human-induced mortality of jaguars outside the protected forest was mainly associated with livestock predation. Both sexes were equally active on pastures and were persecuted at a similar rate. Many of those killed were young individuals in good body condition, suggesting high turnover rates augmented by immigration. Population simulations indicated that the observed levels of human-induced mortality could be maintained only with immigration from the protected forest. Without natal dispersers (2-4 year olds) immigrating in, the hunted population had zero probability of persisting beyond 20 years. Simulations indicated that the jaguar populations inhabiting the two main protected forest blocks in Belize could persist in isolation and maintain low levels of emigration to the unprotected population. However the probability of all three populations persisting for 100 years fell to ~50% if the migration of natal dispersers from the protected to unprotected population exceeded ~12% per year.

Providing captive animals with optimal welfare is a key aim of zoos and aquariums and has traditionally been evaluated through “input measures”. These measures are important but fail to capture the experience of the animal, a critical component of welfare. This project is a first step towards developing “output measures” - positive animal-based metrics – to be used as a benchmark to assess the welfare. This study provided a thorough account of captive lion behaviour in modern facilities and compared this behaviour to that of wild conspecifics. Nine adult African lions from three facilities were studied. Hair (unsuccessful) and faecal (successful) sample collection was attempted for measurement of corticosterone levels as a stress indicators. Behavioural data for each lion was also measured daily, collected through instantaneous scans and continuous focal follows. A comprehensive behavioural ethogram and activity budget was generated for captive lions and behaviour was aligned with corticosterone levels. The lions exhibited variation in daily faecal glucocorticoid metabolite (FGM) levels with few peaks, demonstrating that they were not chronically stressed. Mean baseline FGM levels in dry faeces was 128.96 ± 10.47 ng/g, with significant differences between sexes and facilities. There was no significant relationship between FGM and aggression or activity (p= 0.27). This suggests that prior validations are required to identify certain behaviours as indicators of stress or poor welfare. The results provide an account of captive lion behaviour and FGM levels, in addition to trialling multiple measurements of welfare to provide robust animal welfare assessment. This study is the first step in linking excreted hormones and observed behaviour for captive lions. The results presented provide opportunities for animal institutions to evaluate which aspects of their lion husbandry practices promote optimal lion welfare.

Lions, tigers and cheetahs are commonly held in zoos, experiencing greater longevity in captivity than the wild. As a result, they are more likely to develop age-related diseases, including degenerative joint disease (DJD). However, the prevalence, distribution, severity and clinical presentation of DJD in these species is currently unclear. To address these knowledge gaps, 14 institutions provided radiographic studies and matched clinical records for all cheetahs, lions and tigers that underwent imaging between 1979-2019. Radiographic arthropathies were identified and the correlation between arthropathy status and a range of predictors was examined. Radiographic DJD status was then matched with clinical entries to investigate the presenting signs of DJD in these three species. Arthropathies were found to be common and almost exclusively degenerative in nature. Increasing age was the strongest predictor for joint disease, and a significantly lower prevalence of disease was recorded for the cheetah. Whilst all species showed unique patterns of disease, similarities existed between the lion and tiger, with severe axial DJD a feature. There was a conspicuous absence of appendicular DJD detected in older cheetahs, however axial DJD is reported in this species for the first time, with both increased prevalence and severity found in cheetahs from urban compared with open-range zoos. The meniscal ossicle and supinator sesamoid bone were identified as normal structures that become radiographically evident with skeletal maturation, with the supinator sesamoid bone reported in the tiger, and the meniscal ossicle in the Sumatran tiger, for the first time. A spectrum of DJD-associated presenting clinical signs was established for the three species. Combined, these findings will facilitate radiographic diagnosis of DJD and enhance understanding of the clinical impact of this disease in captive nondomestic felids, whilst also providing impetus for further research in this area.

Genetic variation is crucial for the long-term survival of the species as it provides the potential for adaptive responses to environmental changes such as emerging diseases. The Major Histocompatibility Complex (MHC) is a gene family that plays a central role in the vertebrate’s immune system by triggering the adaptive immune response after exposure to pathogens. MHC genes have become highly suitable molecular markers of adaptive significance. They synthesize two primary cell surface molecules namely MHC class I and class II that recognize short fragments of proteins derived respectively from intracellular (e.g. viruses) and extracellular (e.g. bacteria, protozoa, arthropods) origins and present them to immune cells. High levels of MHC polymorphism frequently observed in natural populations are interpreted as an adaptation to detect and present a wide array of rapidly evolving pathogens. This variation appears to be largely maintained by positive selection driven mainly by pathogenic selective pressures. For my doctoral research I focused on MHC I and II variation in free-ranging cheetahs (Acinonyx jubatus) and leopards (Panthera pardus) on Namibian farmlands. Both felid species are sympatric thus subject to similar pathogenic pressures but differ in their evolutionary and demographic histories. The main aims were to investigate 1) the extent and patterns of MHC variation at the population level in both felids, 2) the association between levels of MHC variation and disease resistance in free-ranging cheetahs, and 3) the role of selection at different time scales in shaping MHC variation in both felids. Cheetahs and leopards represent the largest free-ranging carnivores in Namibia. They concentrate in unprotected areas on privately owned farmlands where domestic and other wild animals also occur and the risk of pathogen transmission is increased. Thus, knowledge on adaptive genetic variation involved in disease resistance may be pertinent to both felid species’ conservation. The cheetah has been used as a classic example in conservation genetics textbooks due to overall low levels of genetic variation. Reduced variation at MHC genes has been associated with high susceptibility to infectious diseases in cheetahs. However, increased disease susceptibility has only been observed in captive cheetahs whereas recent studies in free-ranging Namibian cheetahs revealed a good health status. This raised the question whether the diversity at MHC I and II genes in free-ranging cheetahs is higher than previously reported. In this study, a total of 10 MHC I alleles and four MHC II alleles were observed in 149 individuals throughout Namibia. All alleles but one likely belong to functional MHC genes as their expression was confirmed. The observed alleles belong to four MHC I and three MHC II genes in the species as revealed by phylogenetic analyses. Signatures of historical positive selection acting on specific sites that interact directly with pathogen-derived proteins were detected in both MHC classes. Furthermore, a high genetic differentiation at MHC I was observed between Namibian cheetahs from east-central and north-central regions known to differ substantially in exposure to feline-specific viral pathogens. This suggests that the patterns of MHC I variation in the current population mirrors different pathogenic selective pressure imposed by viruses. Cheetahs showed low levels of MHC diversity compared with other mammalian species including felids, but this does not seem to influence the current immunocompetence of free-ranging cheetahs in Namibia and contradicts the previous conclusion that the cheetah is a paradigm species of disease susceptibility. However, it cannot be ruled out that the low MHC variation might limit a prosperous immunocompetence in the case of an emerging disease scenario because none of the remaining alleles might be able to recognize a novel pathogen. In contrast to cheetahs, leopards occur in most parts of Africa being perhaps the most abundant big cat in the continent. Leopards seem to have escaped from large-scale declines due to epizootics in the past in contrast to some free-ranging large carnivore populations in Africa that have been afflicted by epizootics. Currently, no information about the MHC sequence variation and constitution in African leopards exists. In this study, I characterized genetic variation at MHC I and MHC II genes in free-ranging leopards from Namibia. A total of six MHC I and six MHC II sequences were detected in 25 individuals from the east-central region. The maximum number of sequences observed per individual suggests that they likely correspond to at least three MHC I and three MHC II genes. Hallmarks of MHC evolution were confirmed such as historical positive selection, recombination and trans-species polymorphism. The low MHC variation detected in Namibian leopards is not conclusive and further research is required to assess the extent of MHC variation in different areas of its geographic range. Results from this thesis will contribute to better understanding the evolutionary significance of MHC and conservation implications in free-ranging felids. Translocation of wildlife is an increasingly used management tool for conservation purposes that should be conducted carefully as it may affect the ability of the translocated animals to cope with different pathogenic selective pressures.<br>Genetische Variabilität ist entscheidend für das langfristige Überleben von Arten, denn es ermöglicht dem Organismus sich Umweltveränderungen, wie z.B. neu aufkommende Krankheiten, schneller anzupassen. Der Haupthistocompatibilitätskomplex (MHC) ist eine Familie von Genen, der eine zentrale Rolle im Immunsystem von Wirbeltieren zukommt, da sie nach Pathogenkontakt das adaptive Immunsystem aktivieren. Zudem sind MHC Gene geeignete molekulare Marker um Anpassungsfähigkeiten aufzuzeigen. MHC Gene kodieren primär für Zelloberflächenmoleküle, die kurze Peptidfragmente erkennen und den Immunzellen präsentieren, die im Falle der Klasse I Gene intrazellulären (z.B. von Viren) oder im Falle der Klasse II Gene extrazellulären (z.B. von Bakterien, Protozoen, Arthropoden) Ursprungs sein können. In der Regel wird in natürlich vorkommenden Populationen ein hoher Grad an Polymorphismus im MHC beobachtet, was als Anpassung an das Erkennen und Präsentieren einer großen Anzahl sich schnell entwickelnder Pathogene interpretiert wird. Das Bestehen vieler MHC Varianten über große Zeiträume hinweg wird hauptsächlich durch positive Selektion bewirkt, der ein pathogengetriebener Selektionsdruck zugrunde liegt. In meiner Doktorarbeit habe ich mich mit der Variation von MHC I and MHC II in freilebenden Geparden (Acinonyx jubatus) und Leoparden (Panthera pardus) in Farmgebieten innerhalb Namibias beschäftigt. Beide Felidenarten leben sympatrisch und sind so demselben Pathogendruck ausgesetzt, sie unterscheiden sich allerdings in ihrem evolutionären und demographischen Hintergrund. Mein Hauptziel war es 1) das Ausmaß und Muster der MHC Variation auf Populationsebene beider Feliden zu untersuchen; 2) einen möglichen Zusammenhang zwischen dem Grad der MHC Variation und der Krankheitsresistenz in frei lebenden Geparden aufzudecken und 3) zu untersuchen, welche Rolle der Selektion auf die MHC Variabilität beider Arten in der Vergangenheit wie auch gegenwärtig zukommt. Geparden und Leoparden repräsentieren die größten frei lebenden Carnivoren Namibias. Beide Arten kommen hauptsächlich in Farmgebieten vor, die sich in Privatbesitz befinden, und können dort mit anderen Wild- aber auch Haustieren zusammentreffen und potentiell Krankheitserreger austauschen. Die Kenntnis über die adaptive genetische Variation, die für Krankheitsresistenzen mitverantwortlich ist, kann für den Schutz beider Felidenarten von Bedeutung sein. Geparden werden häufig in Lehrbüchern als klassische Beispiele für eine Tierart mit einer generell geringen genetischen Diversität verwendet. Neben neutralen Markern ist bei Geparden auch eine geringe Variabilität der MHC Gene beschrieben worden, die als Ursache einer hohen Anfälligkeit für infektiöse Krankheiten gesehen wird. Bisher wurde allerdings eine erhöhte Krankheitsanfälligkeit nur bei Geparden aus Gefangenschaft beschrieben, wohingegen neuste Studien an frei lebenden Geparden diesen einen guten Gesundheitsstatus attestierten. Dadurch stellt sich die Frage, ob die MHC I und II Diversität in frei lebenden Geparden nicht höher sein könnte als bisher angenommen. In dieser Arbeit konnten insgesamt 10 MHC I und vier MHC II Allele in 149 frei lebenden Geparden aus ganz Namibia nachgewiesen werden. Die Zugehörigkeit zu funktionellen MHC Genen wurde durch Expressionsanalysen bei allen Allelen, außer einem, bestätigt. Durch phylogenetische Analysen konnten die Allele vier MHC I und drei MHC II Genen zu geordnet werden. Das Wirken von positiver Selektion in der Vergangenheit konnte an spezifischen Aminosäuren des Proteins, die in direktem Kontakt zu den pathogenen Antigenen stehen, festgestellt werden. Dies traf für beide MHC Klassen zu. Des Weiteren konnte eine starke genetische Differenzierung des MHC I zwischen Geparden aus einer nord-zentralen und einer ost-zentralen Region festgestellt werden, von denen auch bekannt ist, dass sie unterschiedlichen, felidenspezifischen, viralen Pathogenen ausgesetzt sind. Das lässt vermuten, dass die unterschiedlichen Muster der MHC I Variation in der gegenwärtigen Population den unterschiedlichen pathogengetriebenen Selektionsdruck durch Viren in den beiden Regionen widerspiegelt. Verglichen mit anderen Säugetierarten, insbesondere andere Feliden, zeigen Geparden einen geringen Grad an MHC Diversität, doch das scheint die derzeitige Immunkompetenz frei lebender Geparden in Namibia nicht einzuschränken und widerspricht der bisherigen Meinung dass Geparden ein typisches Beispiel für eine krankheitsanfällige Tierart sind. Es kann allerdings nicht ausgeschlossen werden, dass bei neu auftauchenden Krankheiten die geringe MHC Variation eine erfolgreiche Immunkompetenz verhindert, da möglicherweise keines der gegenwärtigen Allele die Fähigkeit besitzt neue Pathogene zu erkennen. Im Gegensatz zu Geparden kommen Leoparden in allen Teilen Afrikas vor und sind wahrscheinlich die am weitverbreiteste Großkatze des afrikanischen Kontinents. Es scheint, dass Leoparden, im Gegensatz zu anderen afrikanischen Großkatzen, einer ausgedehnten Dezimierung durch Tierseuchen in der Vergangenheit, der einige Populationen afrikanischer Großkatzen ausgesetzt waren, entkommen sind. Bisher fehlten Information über die MHC Variabilität in afrikanischen Leoparden. In dieser Studie konnte ich die genetische Variation der MHC I und MHC II Gene frei lebender namibischer Leoparden charakterisieren. In 25 Tieren aus einer Population der ost-zentralen Region konnten sechs MHC I sowie sechs MHC II Sequenzen nachgewiesen werden. Aus der maximalen Anzahl Allele pro Tier kann auf drei MHC I und auf drei MHC II Gene geschlossen werden. Außerdem konnten die typischen Kennzeichen einer variationserhaltenden MHC Evolution betätigt werden, wie positive Selektion in der Vergangenheit, Rekombination und über Artgrenzen hinaus bestehender Polymorphismus. Der geringe Grad an MHC Variation in namibischen Leoparden ist jedoch noch nicht endgültig und weitere Untersuchungen in unterschiedlichen Regionen aus der gesamten geographischen Verbreitung des Leoparden sind notwendig um die MHC Variation der Leoparden in Gänze einschätzen zu können. Die Ergebnisse dieser Arbeit werden zu einem besseren Verständnis des evolutionären Stellenwerts des MHC und in Folge zu einem besseren Schutz von frei lebenden Feliden beitragen. Die Umsiedelung von Wildtieren ist ein zunehmend angewendetes Hilfsmittel im Natur- und Artenschutz, welches jedoch mit Sorgfalt eingesetzt werden sollte, da die umgesiedelten Tiere möglicherweise einem anderen pathogenen Selektionsdruck ausgesetzt sind, dem sie nichts entgegenzusetzen haben.

Thesis (MSc (Botany and Zoology))--University of Stellenbosch, 2006.<br>Although the Bengal tiger, Panthera tigris tigris, appears on the IUCN Red Data List for endangered animals, very little information is available in the literature on the components of this animal's marking fluid. Scent marking is the main form of communication in all cat species. In some species, including the Bengal tiger, the liquid used for spraying is not pure urine, but is mixed with scent gland secretions. The objective of this study was to characterise the volatile components in the marking fluid of the Bengal tiger to achieve a better understanding of the semiochemical communication of this animal. The marking fluid of the tiger was characterised through the use of analytical techniques, such as gaschromatography, low resolution gas chromatography - mass spectrometry and retention time comparison. Homologous series of alkanes, alcohols, aldehydes, methyl ketones, carboxylic acids, γ- and δ-lactones, amides and lactams, as well as esters and nitrogen containing compounds, were identified. Of these identified compounds the unbranched alkanes, saturated alcohols, aldehydes, branched methyl ketones, saturated carboxylic acids and γ- and δ- lactones are commonly found in mammalian secretions. Compounds that aren't as common in their secretions are the methyl ketones, branched carboxylic acids, dimethyl esters of dicarboxylic acids and amides. The marking fluid contains a phthalic acid ester. Phthalic acid esters are used in the polymer industry and are nowadays found almost everywhere in nature. It is known that these pollutants have endocrine disrupting properties. The heat, humidity and wet conditions that are characteristic of the Bengal tiger's natural habitat makes it necessary for the tiger to make use of a fixative to prolong the life of the semiochemical message. The compounds and the concentrations in which these compounds are present in the urine and the lipid fraction of the marking fluid of the tiger was determined and compared to assess the fixative role of the lipids. This study has provided evidence that the lipid material has a greater affinity for the volatile organic constituents of the marking fluid and that it can therefore extend the lifetime of a semiochemical message left by the tiger.

Thesis (MSc)--Stellenbosch University, 2014.<br>ENGLISH ABSTRACT: Lion populations globally are on the decrease and their habitats are fragmenting. Despite their importance in the Zambezi Region in Namibia, very little research has yet been undertaken to understand their occurrence in this area. One of the primary motivations behind this study was the Kavango Zambezi Trans Frontier Conservation Area’s (KAZA TFCA) need to identify trans-boundary movement of carnivores. The collaborative approach with the Ministry of Environment and Tourism in Namibia facilitated the collaring of lions in three National Parks. A number of species were collared and this study focuses on the occurrence of lions in the Zambezi Region. From the lion home range analysis we could see that the home-range sizes of the collared lions varied greatly across the study area. The difference in home range size is largely due to human pressure surrounding the protected areas. Geographically weighted regression assisted in understanding which were the main drivers of lion occurrence, but further investigation was needed using the Maximum Entropy (MaxEnt) model for presence-only data. The factors that were investigated as possibly affecting the occurrence of lions included the following: rivers, land cover, land use, elevation and human activity. After pursuing various research models and manipulating data among all these factors, no single factor or combination of factors was found to be reliable predictors on lion occurrence in the study area. As is discussed in recommendations for further research in Chapter 6, it became clear that quantitative data cannot be used in isolation to predict where lions may occur.<br>AFRIKKANSE OPSOMMING: Leeu-bevolkings is wêreldwyd aan die afneem en hulle habitatte fragmenteer al hoe meer. Ten spyte van hulle intrinsieke belang vir die Zambezi streek in Namibië is daar ‘n gebrek aan navorsing om die voorkome van leeus in hierdie streek te verstaan. ‘n Belangrike motivering vir hierdie studie was die vereiste van die “Kavango Zambezi Trans Frontier Conservation Area” (KAZA TFCA) om grensoorstekende bewegings te verstaan, in onder andere karnivore. In samewerking met KAZA TFCA is GPS-halsbande aangebring aan leeus in drie wildsparke, asook aan individue van ander spesies; hierdie studie fokus spesifiek op leeus in die Zambezi streek. Analise van die leeus se loopgebied toon breë variasies oor die studiegebied, vir die individue met halsbande, hoofsaaklik te wyte aan menslike druk vanuit omliggende nedersettings. Hierdie studie gebruik geografies geweegde regressie om die belangrikste faktore in die teenwoordigheid van leeus te verstaan, terwyl Maximale Entropie modelle (MaxEnt) vir slegs teenwoordigheid data in verdere ondersoeke ingespan is. Die volgende faktore is ondersoek ten opsigte van hulle moontlike bydrae tot die voorkome van leeus: riviere, land bedek, grondgebruik, hoogte en menslike aktiwiteite. Verskeie statistiese navorsingsmodelle is ondersoek, met inagneming van data vir al die faktore, maar geen betroubare aanwyser of aanwysers vir leeu-teenwoordigheid is gevind nie. Dit is duidelik dat bloot kwantitatiewe data ontoereikend is om leeuteenwoordigheid te voorspel, soos uiteengesit in hoofstuk 6.

The Persian leopard is the largest cat in west Asia, and is considered to be endangered - poaching and habitat degradation are thought to be responsible. The rugged mountains and high altitudes it favours present considerable challenges for scientists, and it is consequently one of the least known subspecies. I have addressed this through exploring the subspecies' fundamental ecology across three national parks in northeastern Iran. I used satellite telemetry, camera trapping, genetic analysis and questionnaire surveys. The perceived role of leopards in livestock depredation was negligible compared to that of wolves. This was associated with relative tolerance of leopards compared with wolves; but the economic loss associated with predator damage did appear to influence peoples' attitudes. I also estimated a mean home range of 103.4 ± SE 51.8 km2 for resident males which is larger than what has been observed in other studies on Asian leopard. Five out of six of leopards spent 17.9% of their time outside the national park, among human communities. The kill rate was quantified as 3.7 ± SE 0.5 medium-sized prey/month per leopard, which is higher than reported by previous studies. Surprisingly, considering the subspecies' reported low density based on previous studies, I found relatively high population densities, varying between 4.01 ± SE 1.98 and 8.02 ± SE 2.67 individuals/100 km². The number of adult leopards detected in Tandoureh (30 individuals) was larger than identified during comparable surveys at any other site globally. Persian leopards exhibited moderately high genetic diversity at six microsatellites (A_N = 7.45, H_O = 0.69, H_E =0.75) and low haplotype diversity (Hd = 0.198) across three closely related haplotypes in NADH-5 gene. There was a weak evidence of spatial population partitioning. My research findings highlight the key role of mountainous ecosystems as refugia in supporting a high density of apex predators. Although land sharing is an inevitable solution for coexistence across Asian crowded montane landscapes, sparing mountains with improved law enforcement is encouraged for large cat conservation in Asian mountains. Finally, my thesis raises new hope for leopard viability as well as highlights the potential capacity of the Kopet Dag Ecoregion as a significant conservation unit for leopards.

Pantoea stewartii subsp. stewartii is a bacterium that causes Stewart’s wilt disease in corn plants. The bacteria are transmitted to the plants via an insect vector, the corn flea beetle Chaetocnema pulicaria. Once in the plant, the bacteria migrate to the xylem and grow to high cell densities, forming a biofilm by secreting excess capsular exopolysaccharide, which blocks water transport and causes wilting. The timing of virulence factor synthesis is regulated by the cell-density dependent quorum sensing (QS) system. Such temporal regulation is crucial in establishing infection and is orchestrated by the QS-dependent transcriptional regulator EsaR. EsaR represses expression of capsular exopolysaccharide at low cell densities. At high cell densities, an acylated homoserine lactone (AHL) molecule produced during growth by the cognate AHL-synthase EsaI accumulates. The AHL binds to and inactivates EsaR, causing derepression of capsule production. EsaR is a member of the LuxR family of QS-dependent transcriptional factors. Most LuxR homologs are unstable and/or insoluble in the absence of AHL which has hindered structural studies. Chapter Two describes the changes in the structure of EsaR due to binding of AHL ligand as determined through biochemical methods. EsaR was found to be stable and retain its multimeric state in the absence or presence of AHL, but intra- and inter-domain changes occurred that affect its DNA-binding capacity. Apart from repressing expression of capsule at low cell-densities, EsaR represses its own expression and activates production of a small RNA, EsaS, with unknown function. In Chapter Three a proteomic approach was used to identify an additional 30 QS-controlled proteins. Genes encoding three of these proteins are directly regulated by EsaR and the EsaR binding sites in the respective promoters were defined. In Chapter Four, a high-throughput RNA-Seq method identified even more genes in the QS regulon that the proteomic approach overlooked. RNA-Seq analysis of rRNA-depleted RNA from two strains of P. stewartii was used as a screen to help identify 11 promoters, subsequently shown to be directly regulated by EsaR in vitro. Most of the genes controlled by QS grouped into three major physiological responses, capsule & cell wall production, surface motility & adhesion and stress response. In Chapter Five, the role of two QS regulated genes, dkgA (encoding 2, 5-diketo-D-gluconate) and lrhA (encoding a repressor of chemotaxis, adhesion and motility), in plant virulence were examined. These studies have better characterized the QS regulator EsaR and its interaction with the AHL ligand, and shown that QS has a more global response in P. stewartii than previously recognized. Further characterization of the genes identified in this study could facilitate identification of factors crucial in plant pathogenesis or insect-vector symbiosis and aid in the development of molecular-based approaches for possible disease intervention.<br>Ph. D.

The pulp and paper industry is expanding world-wide to supply the needs and demands of the consumer. Due to this rapid expansion of commercial forests and our ever changing climate including the sporadic increase and decrease in rain and the increasing temperature caused by global warming, previously described and new pathogens are emerging which infect and cause diseases on commercial forest trees and agricultural crops. Research efforts are required to investigate mechanisms of disease control and eradication to prevent the propagation and rapid spread of these pathogens and ensure that there is limited economical loss of forestry and other agriculturally important plants and trees. Since both Xanthomonas and Pantoea species are becoming increasing important as emerging bacterial pathogens, their rapid and accurate identification is crucially important. Little is known about bacterial pathogens on forestry trees since the most prominent diseases of these hosts are caused by fungi. The focus of this study was to investigate and identify the bacterial pathogens associated with Eucalyptus. However, as has been seen in various studies including this one, the identification of these pathogens is not always straightforward and often time consuming. In this study the use of polyphasic identification approach was used which employs a combination of phenotypic and genotypic identification techniques. Both of the genera investigated in this study, namely Pantoea and Xanthomonas, have been found to infect a variety of agriculturally important plant hosts. Pantoea species have previously been isolated from Eucalyptus trees suffering from blight and dieback symptoms. The species isolated have included P. eucalypti from Uruguay, P. vagans isolated from Argentina, Colombia, Uganda and Uruguay and P. deleyi from Uganda. Since the first report of Pantoea on Eucalyptus trees from South Africa in 2002 it has spread locally causing sporadic outbreaks. This pathogen has also been isolated from Eucalyptus trees in other parts of the world including, Argentina, Colombia, Thailand, Uganda and Uruguay. Xanthomonas campestris pv. eucalypti was previously found to cause disease on Eucalyptus trees in Australia. Since then, three other Xanthomonas species have been isolated from Eucalyptus, namely, Xanthomonas spp. from Brazil (Goncalves et al., 2008), X. vasicola from South Africa and X. fuscans from Uruguay as seen in this study.<br>Dissertation (MSc)--University of Pretoria, 2010.<br>Microbiology and Plant Pathology<br>Unrestricted

The objectivie of this study was to describe the splanchnology and topography of the female reproductive organs of the African lion. The reproductive organs of three embalmed cadavers from three-year-old known aged nulliparous lionesses weighing between 120 kg and 140 kg were studied. Two fresh carcasses from another study were used for some of the topographical photos since these rendered better quality images. The project was approved by the Animal Use and Care Committee and Research Committee of the University of Pretoria (protocol number V038-09). The topography and splanchnology of the reproductive organs were studied and described in situ and after removal. The kidneys were located far caudally in relation to the thirteenth ribs with the left kidney further caudal. The suspensory ligament was very well developed. It originated in a fan-like manner from the dorso-lateral abdominal wall lateral to the kidney extending up to a few centimetres cranial to the kidney. The proper ligament of the ovary was well developed and consisted of several clearly distinguishable bands. The broad ligament resembled that of the cat with the exeption of the cranial part of the mesovarium being very well developed. The round ligament was well developed and inserted on the medial femoral fascia. It therefore did not extend to the vulva as in other canine and feline species. The left ovary was longer, wider and heavier than its right counterpart and the ovaries were relatively small in relation to body weight. The ovarian bursa had a short mesosalpinx that did not cover any part of the ovary and the fimbriae extended the entire length of the ovary. The urethral tuberculum as well as the urethral crest was very well developed. The left uterine horn was longer than the right and the tip of the uterine horn was located dorsal to the proper ligament. The uterine tube was prominently convoluted, situated entirely on the lateral aspect of the ovary and was found to open directly into the tip of the uterine horn and not onto a papilla. The female reproductive organs of the African lion resemble that of the domestic cat and dog with some major differences especially to the size and development of certain structures. The clinical relevance of these differences has to be debated and some thoughts might include the following: 1) does the suspensory and proper ligaments of the gravid uterus contract to suspend the entire uterus closer to the body wall during hunting since the lioness is the primary hunter in the pride? 2) does the lioness have to roll on her back and extend her back legs after mating to facilitate sperm entering the dorsally located tip of the uterine horn while the round ligament stabilises the terminal part of the uterine horn, and does this have a bearing on the fact that multiple copulations are required over a prolonged period for conception by lions? 3) do more ovulations take place from the bigger left ovary and? 4) are more conceptusses borne by the longer left uterine horn? The anatomical information obtained during this study was subsequently applied in a surgical study on sixteen lionesses using laparoscopy to perform laparoscopic ovariectomy and salpingectomy. The availability of these two laparoscopic procedures subsequently led to a wider interest to its application in population control of lions in the smaller national parks of South Africa.<br>Dissertation (MMedVet)--University of Pretoria, 2012.<br>gm2014<br>Companion Animal Clinical Studies<br>unrestricted

Thesis (MTech (Nature Conservation))--Cape Peninsula University of Technology, 2016.<br>Lions are threatened across their natural range. The Kgalagadi Transfrontier Park (KTP), comprising the Kalahari Gemsbok National Park (KGNP; South Africa) and Gemsbok National Park (GNP; Botswana), is a stronghold for the species. Population size and demography of lions in the KGNP has been addressed in four historic studies. Studies in mid-1970 and 1990 reported a female biased population whereas in 2010 the sex structure was skewed towards males (56%). The bias in sex ratios towards males was first observed in cubs and sub-adults in 2001 and later, in 2010, throughout the population. Furthermore, in the 2010 assessment of the lion population, a smaller proportion of cubs (< 2 yrs) were observed in comparisons to the preceding studies (10% vs. ≥ 23%). The skew in age and sex structures that were observed in the KGNP led to concerns over the long-term sustainability of the greater KTP lion population. The lion population carries further risks associated with the stochastic, arid environment, in which the KTP lion population persists. Human-lion conflict on the borders of the KTP and anthropogenic alterations of the environment further threaten lion demographic stability.

Thesis: S.M. in Building Technology, Massachusetts Institute of Technology, Department of Architecture, 2016.<br>Cataloged from PDF version of thesis.<br>Includes bibliographical references (pages 27-31).<br>The Roman Pantheon is among the largest unreinforced masonry dome ever built and is an unparalleled example of the construction capabilities of the ancient Romans. As one of the most well-known buildings in the world, its preservation remains important because of its cultural and societal significance, and the methods used to assess the safety of historic masonry structures continue to be developed, particularly for three-dimensional vaulted forms. Through a study of the Roman Pantheon, this thesis compares analytical and experimental results on a 1:100 scale model of the variable thickness, hemispherical dome. The model is created using additive manufacturing for accuracy. This thesis, using a physical scale model, quantifies the safety of the Roman Pantheon against the two most probable causes of collapse (i) deformation of the building geometry and (2) seismic activity. The structural behavior of the model is compared to analytical predictions of (1) spreading supports, simulating leaning walls that result from the dome thrust or settling of the foundations, and (2) tilting, a first-order approximation of horizontal ground acceleration. The experimental tests lead to the formation of a mechanism and collapse due to instability. High-speed imagery captures the observed collapse mechanisms and failure limits. Experimental results are compared to analytical predictions for hemispherical masonry domes. The results of the physical experiment demonstrate the potential for digitally fabricated scale models in approximating the behavior of three-dimensional structures with complex geometries. The low cost and rapid approach provides a useful method for validating analytical predictions of the limit states and collapse mechanisms of unreinforced masonry structures.<br>by J. William Plunkett.<br>S.M. in Building Technology

Poucos são os estudos acerca da saúde de onças-pintadas em vida livre. Visando obter melhores parâmetros para avaliação clínica desta espécie ameaçada de extinção, foram realizados exame clínico, hemograma, perfil bioquímico e acompanhamento de 10 onças-pintadas da região de Corumbá, no Pantanal do Mato Grosso do Sul. Além disso, buscando obter informações sobre o possível papel da espécie como suscetível, hospedeira ou sentinela de patógenos de importância em saúde pública e animal, amostras destas 10 onças foram testadas através de métodos sorológicos para verificar contato com vírus rábico, Rickettsia spp. e Ehrlichia canis. As amostras das onças e os carrapatos que as parasitavam no momento das capturas foram testados por reação em cadeia pela polimerase para a família Anaplasmataceae e os gêneros Rickettsia, Borrelia, Coxiella, Hepatozoon e Babesia. Este é o primeiro estudo a relatar os valores de hemograma e perfil bioquímico de uma população de onças-pintadas de vida livre. Dois animais, assintomáticos, apresentaram baixo título sorológico para o vírus da raiva, sugerindo contato da espécie com este patógeno. Todas as onças capturadas foram consideradas soropositivas para Rickettsia spp., e Rickettsia parkeri foi sequenciada a partir de um Amblyomma triste que estava parasitando um dos animais. Foi descoberta uma possível nova espécie do gênero Ehrlichia através do sequenciamento de DNA obtido de um Amblyomma triste e um Amblyomma cajenense que estavam parasitando onças. Quatro onças-pintadas foram consideradas soropositivas para Ehrlichia canis, possivelmente uma reação cruzada com esta outra espécie. Todas as onças-pintadas avaliadas neste estudo apresentaram DNA de Cytauxzoon sp., com 98% de similaridade a C. felis, em amostras sanguíneas. Todas as onças avaliadas neste estudo apresentaram DNA de Hepatozoon sp., com 98% de similaridade a H. felis, em amostras sanguíneas. As onças apresentavam boas condições de saúde geral.<br>Few studies have been conducted to investigate the health of free-ranging jaguars. In order to obtain better parameters for clinical evaluation of this endangered species, clinical exams, hemogram, biochemical tests and ecological monitoring were done for 10 jaguars in the Pantanal region - Corumbá City, Mato Grosso do Sul State. This project also evaluated the possible role of this species as susceptible, host or sentinel for pathogens of public and/or animal health importance, testing samples from these animals by serological methods to rabies virus, Rickettsia spp. and Ehrlichia canis. All samples and all ticks collected from the jaguars were also tested by polymerase chain reaction to the Anaplasmataceae family and the genera Rickettsia, Borrelia, Coxiella, Hepatozoon and Babesia. This is the first report of hemograms and biochemical profile of a free-ranging jaguar population. Two asymptomatic animals presented low seropositivity for rabies virus, suggesting contact with this pathogen. All jaguars were considered seropositive for Rickettsia spp., and Rickettsia parkeri was sequenced from an Amblyomma triste that was parasitizing one of the animals. A possible new species of the genus Ehrlichia has been identified by DNA sequencing obtained from an Amblyomma triste and an Amblyomma cajenense that were parasitizing jaguars. Four jaguars were considered seropositive for Ehrlichia canis, possibly a cross-reaction with this other species. All jaguars evaluated in this study presented DNA fragments of Cytauxzoon sp., 98% similarity to C. felis in blood samples. In addition, all jaguars presented DNA fragments of Hepatozoon sp., 98% similarity to H. felis in blood samples. In general, these jaguars presented good health.

Neisseria gonorrhoeae (NG) har successivt utvecklat resistens mot många antimikrobiella medel och betraktas som ett av de tre reella hoten bland antibiotikaresistenta bakterier. Ciprofloxacin är ett bredspektrum-antibiotikum tillhörande gruppen kinoloner som, förutom att behandla urinvägsinfektioner, används mot NG och infektioner i mage och tarm. Dock har det rapporterats att ca 30 % av NG-isolat som samlats in genom gonokock-isolatövervakningsprojekt (GISP) under 2017 var resistenta mot ciprofloxacin. På molekylnivå är resistens mot ciprofloxacin starkt associerad med en enda mutation i kodon 91 i gyras-genen (gyrA). Detta projekt har undersökt om det går att använda molekylärbiologiska metoder för att detektera NG-isolat med gyrA mutationen. Analysen gjordes med två olika PCR-system, ”7500 Fast Real-Time PCR System” från Applied Biosystems (ABI) och Panther Fusion från Hologic. Proberna som användes designades för påvisning av vildtyp gyrA (ciprofloxacin-känslig) och mutant gyrA (ciprofloxacin-resistent) hos NG. I projektet analyserades 50 NG-positiva prov (analyserade med screeningtest APTIMA COMBO2 från Hologic), från 43 patienter som provtagits under januari-februari 2020 i Region Skåne. Några patienter testades flera gånger vid olika tillfällen. NG-odling hade utförts parallellt från motsvarande tagna prov från patienterna. ABI-metoden påvisade genen hos 90 % (45/50) av NG-positiva prover (APTIMA COMBO2) medan endast 24 av de 49 proven (49 %) kunde odlas med traditionell metodik för att därefter resistensbestämmas. Av de 45 prov där gyras-genen kunde detekteras med ABI-metoden, uppvisade 28 (62 %) av proven en muterad gen och därmed en potentiell resistens för ciprofloxacin. Panther Fusion-metoden påvisade genen hos 80 % (40/50) av NG-positiva prover (APTIMA COMBO2), och såsom tidigare nämnts, kunde endast 24 av de 49 proven (49 %) odlas med traditionell metodik för att därefter resistensbestämmas. Av de 40 prov där gyras-genen kunde detekteras med Panther Fusion-metoden, uppvisade 26 av proven (65 %) en muterad gen och därmed en potentiell resistens för ciprofloxacin. En jämförelse mellan resultaten från PCR-metoderna och odlingarna visar att av de 24 odlingarna som kunde resistensbestämmas fick ABI-metoden resultat för 23 och Panther Fusion för 22. PCR-metodernas resultat överensstämde perfekt med resultaten från odling med samma 8 känsliga och 15 respektive 14 resistenta NG-isolat som odling. De båda PCR-metoderna och traditionell odling uppvisade jämförbara resultat. Av de 24 prov som kunde odlas och därmed resistensbestämmas, detekterades med ABI-metoden gyras-genen i 23 av dessa prov och i 22 av proven med Panther Fusion-metoden. Resistens mot ciprofloxacin uppvisades genom odling i 16 av de 24 odlingsbara prov, och av dessa 24 odlingsbara prov uppvisade ABI-metoden en muterad gen i 15 av proven och Panther Fusion-metoden en muterad gen i 14 av proven. Traditionell odling kunde bara genomföras på 24 av proven och PCR-metoderna identifierade signifikant fler prov innehållande vildtyp eller muterad gyras-gen, 45 respektive 40 prov. Projektet visade tydligt att PCR-metoderna kan identifiera fler prov än genom traditionell odling och kan därmed upptäcka fler prov med förväntad ciprofloxacin-resistens än vad som kan bestämmas genom traditionell odling.<br>Neisseria gonorrhoeae (NG) has been developing a resistance towards several different antibiotics and is viewed as one of the three real threats among resistant bacteria. Ciprofloxacin is a broad-spectrum-antibiotic belonging to the group quinolone antibiotics which, in addition to being used to treat urinal infections, is used to treat NG and infections in the stomach and intestines. However, it has been reported that 30 % of NG-isolates that have been gathered through the Gonococcal Isolate Surveillance Project (GISP) throughout 2017 were resistant to ciprofloxacin. On a molecular level, resistance to ciprofloxacin is strongly associated with a single mutation in kodon 91 in the gyras-gene (gyrA). This project sought to examine if it is possible to use methods from molecular biology to detect which NG that have the gyrA-mutation. The test was done using two different PCR-systems, ”7500 Fast Real-Time PCR System” from Applied Biosystems (ABI) and Panther Fusion from Hologic. The probes used were designed to show wild type gyrA (ciprofloxacin sensitive), and mutated gyrA (ciprofloxacin resistant) in NG. In this project 50 NG-positive samples (analysed with screentest APTIMA COMBO2 from Hologic), from 43 patients that had been tested during January-February 2020 in Region Skåne, were analysed. Some patients were tested several times, within the time period. NG-cultivation had been done in parallel from corresponding samples taken from the patients. The ABI-method showed the gene in 90 % (45/50) of NG-positive samples (APTIMA COMBO2) while only 24 of the 49 samples (49 %) could be cultivated by traditional methodology, and then tested for resistance. Of the 45 samples where the gyras-gene could be detected with the ABI-method, 28 samples (62 %) exhibited a mutated gene and thus a potential resistance to ciprofloxacin. The Panther fusion-method showed the gene in 80 % (40/50) of NG-positive samples (APTIMA COMBO2), and as mentioned earlier, only 24 of the 49 samples (49 %) could be cultivated by traditional methodology to then be tested for resistance. Of the 40 samples where the gyras-gene could be detected with the Panther Fusion-method, 26 samples (65 %) exhibited a mutated gene and thus a potential resistance to ciprofloxacin. The two PCR-methods and traditional cultivation exhibited comparable results. Of the 24 samples that could be cultivated and thus tested for resistance, the ABI-method detected the gyras-gene in 23 of these samples and the Panther Fusion-method detected the gene in 22 of the samples. Cultivation exhibited resistance to ciprofloxacin in 16 of the 24 samples that could be cultivated, and of these 24 cultivatable samples the ABI method exhibited a mutated gene in 15 of the samples and the Panther Fusion-method exhibited a mutated gene in 14 of the samples. Traditional cultivation could only be done on 24 of the samples and the PCR-methods could identify significantly more samples containing either wild type or mutated gyras-gene, 45 and 40 samples, respectively. The project clearly showed that more samples can be identified with the PCR-methods than through traditional cultivation, and thereby discover more samples with expected ciprofloxacin-resistance, than can be determined through traditional cultivation.