The thesis traces the successive urban responses made by the Hong Kong government from 1997 to 2014, in an attempt to achieve “imagined immunity” for the city. The urban responses being analysed are efforts to regulate the ways in which “live poultry” (especially live chickens) is metabolized and circulating in the city. The efforts are made to re-order the human-birds-microbes relationships in Hong Kong - a process conceptualized as “re-urbanization of nature.” The consequence of these re-urbanization of nature processes, led to changes in the specific practice of consuming “live poultry” in the city. Four periods of re-urbanization of nature are identified in the analysis, and it is argued that in each wave of restructuring there were markedly different frames constructed to generate distinctive meanings of the “contagion condition,” imagined urban immunity, and practices of re-urbanization of nature. Their meanings and resultant practices were products of negotiations, within an entangled web of human and nonhuman features in particular periods. The context of these interventions and the biopolitical contestations are analyzed in the thesis. It is then argued that such contingencies and context-sensitive processes, call for further studies of post-epidemic urban changes. The thesis also explores the possibility of developing a theoretical framework of “urban biopolitical immunology” to accomplish the inquiry. By so doing, it seeks to contribute to studies of the politics of contemporary epidemics, and to research on the production of urban nature.

Fujinami sarcoma virus encodes a 140/000 m.w. polypeptide (P140) which has been correlated as the agent of transformation in host chicken fibroblasts and mammalian fibroblasts. To conclusively identify the role of P140 in the transformation process it will be necessary to obtain intact/ purified P140. The availability of an antibody monoclonally specific to the N-terminal gag encoded portion of P140 suggested a one-step immunoaffinity purification of P140. After purification of the antibody out of mouse ascites fluid, by 50% ammonium sulfate fractionation and ion exchange chromatography, antibody was linked to a Sepharose 4-B matrix activated with cyanogen bromide. The anti-pl9 affinity matrix bound intact P140 as a doublet relative to a polyclonal anti-pl9. Chaotropic agents, high pH and low pH treatments all failed to elute the bound P140 from the affinity matrix. Failing the purification of intact P140 a method of partial proteolysis was used to produce varying sized fragments of P140/ with the goal of purifying these fragments for further work on the role of P140. Trypsin alone in a limited proteolysis produced small, unstable peptides too close in size distribution to be effectively purified. Chymotrypsin alone produced a broad range of more stable peptides, with a predominance of a 45,000 m.w. peptide. Chymotrypsin-trypsin consecutive proteolysis produced a very stable 35,000 m.w. peptide. Gel filtration of the chymotryptic peptides was ineffective as the peptides coraplexed and were not fractionated. Ion exchange chromatography fractionated the complexing chymotryptic peptides, making possible the purification of these peptides. The stable 45,000 m.w. peptide retained some kinase activity, as it phosphorylated the substrate enolase, similar to but less intense than intact P140. A 30,000 m.w. peptide only phosphorylating after ion exchange did not phosphorylate enolase. / Science, Faculty of / Microbiology and Immunology, Department of / Graduate

Os vírus da influenza aviária têm provocado epidemias e pandemias através dos tempos, a pandemia mais devastadora que se tem notícia, a gripe espanhola em 1918, teve sua origem no vírus aviário do tipo A subtipo H1N1. Desde 2003 o vírus aviário do subtipo H5N1 infectou 442 pessoas e levou a morte 262. Além do aspecto de saúde os vírus da gripe aviária causam grande impacto econômico. O Brasil como maior exportador de frango do mundo tem muito a perder caso a gripe aviária chegue ao país. Devido às aves selvagens serem o reservatório natural influenza A, é que se faz necessário a execução do monitoramento. Apesar de existir programas de monitoramento contínuo de aves selvagens na Europa, EUA, Canadá, Japão entre outros, pouco foi feito no Brasil. Amostras coletadas de 671 aves foram testadas por meio das técnicas de GeneScan, PCR em tempo real e RT-PCR e Duplex Nested-PCR. / The avian influenza virus has caused epidemics and pandemics through the ages, the most devastating pandemic that we know, the Spanish flu in 1918, had its origin in the avian virus type A subtype H1N1. Since 2003 the avian virus subtype H5N1 has infected 442 people and led to death 262. Besides the health aspect of the avian influenza viruses cause major economic impact. Brazil as the largest exporter of chicken in the world has much to lose if bird flu reaches the country. Because wild birds are the natural reservoir of influenza A, is that it is necessary to implement the monitoring. Although programs exist for continuous monitoring of wild birds in Europe, USA, Canada, Japan and others, little has been done in Brazil. Samples collected from 671 birds were tested by GeneScan techniques, real-time PCR and RT-PCR and nested-PCR Duplex.

Leg problems and disorders are of major concern for the poultry industry and animal welfare. Previous studies suggest that it may be possible to improve skeletal characteristics through nutrition. Omega-3 fatty acids, including Docosahexaenoic acid (DHA), are essential nutrients and are known to play an important role in bone tissue development. FORPLUS™ (Alltech, Inc.) is an unextracted, whole-cell microalgae (Aurantiochytrium limacinum CCAP 4087/2) that contains 64% fat and 16% DHA. Zinc (Zn) is a trace element and essential nutrient for growth and skeletal development. Bioplex® Zn (Alltech, Inc.) is a Zn proteinate that has been shown to be more bioavailable to broiler chickens compared to inorganic sources of Zn. One objective of this research was to investigate the effects of 2 dietary levels of FORPLUS™ (0% vs. 2%) and 2 dietary Zn sources (ZnO vs. Bioplex® Zn) on skeletal characteristics and reproduction of broiler breeders. Breeders were maintained on these diets throughout the entire pullet and layer phases. Subsequent studies were conducted to evaluate the effect of breeder diet and offspring dietary Zn sources (ZnO vs. Bioplex® Zn) and microalgae supplementation (0% vs. 1%) on offspring performance and skeletal characteristics. During the broiler breeder pullet phase, dietary supplementation of 2% FORPLUS™ increased (P < 0.05) femur ash content and length. Pullet uniformity was in increased (P < 0.05) by Bioplex® Zn vs ZnO when microalgae was not included in the diet. Hen day production (HDP) was increased (P < 0.05) by ZnO vs. Bioplex® Zn supplementation during post-peak lay. During post-peak lay, hatchability and hatch of fertile eggs were improved (P < 0.05) by dietary supplementation of 2% FORPLUS™ or Bioplex® Zn in breeder diets, however egg weight, egg yolk weight, offspring hatch weight, and offspring body weight gain (BWG) significantly were decreased (P < 0.05) by 2% FORPLUS™. Bioplex® Zn in breeder diets increased (P < 0.05) growth plate zone heights, bone-specific alkaline phosphatase enzyme activity, and dimensions of offspring bones at hatch. At 3 weeks of age, offspring from breeders fed Bioplex® Zn during peak-lay had greater (P < 0.05) Zn content in tibia ash and bone dimensions, while offspring from breeders fed 2% FORPLUS™ vs. 0% FORPLUS™ had longer (P < 0.05) femurs. No interaction effect of breeder diet and offspring diet on early performance was observed. Offspring fed diets containing Bioplex® Zn vs. ZnO had greater (P < 0.05) body weight (BW) and tibia dimensions at 3 wk of age. Offspring fed diets containing 1% FORPLUS™ had decreased feed conversion (feed intake: BWG), but no main effects were observed on skeletal characteristics. Overall, dietary microalgae supplementation in broiler breeder diets improved early bone development in broiler breeders, early bone development in broiler breeder offspring, and hatchability of offspring during post-peak lay, while Bioplex® Zn supplementation in broiler breeder diets improved broiler breeder pullet uniformity, offspring hatchability during post-peak lay, embryonic skeletal development of offspring, and offspring bone quality. Bioplex® Zn in offspring diets also improved offspring early growth performance and leg bone morphology.

Three main research products are reported in this dissertation. This research focused on estimation of the seroprevalence rates in agricultural workers with exposure to pigs and poultry, and determination of risk factors for infection. Chapter 2, "Are swine workers in the United States at increased risk of infection with zoonotic influenza virus?", reports controlled, cross-sectional seroprevalence studies among farmers, meat processing workers, veterinarians, and control subjects. Using a hemagglutination inhibition assay against six influenza A virus isolates, all 3 exposed study groups demonstrated markedly elevated titers against the H1N1 and H1N2 swine influenza virus isolates, compared with control subjects. Chapter 3, "Infection due to 3 avian influenza subtypes in United States veterinarians", describes a controlled, cross-sectional seroprevalence study that examined veterinarians in the United States for evidence of previous avian influenza virus infection. Using a microneutralization assay against 9 influenza A virus strains, veterinarians exposed to birds demonstrated statistically significant elevated titers against the H5, H6, and H7 avian influenza virus isolates compared with control subjects. In chapter 4, "Cases of swine influenza in humans: a review of the literature", all known human cases of swine influenza are compiled and analyzed. Fifty cases of apparent zoonotic swine influenza virus infection, including 37 civilians and 13 military personnel, were identified, with a case-fatality rate of 14% (7 of 50 persons). Most civilian subjects (61%) reported exposure to swine. These studies provide strong evidence that transmission of zoonotic influenza likely occurs much more frequently than previously thought, and that individuals with occupational exposure to pigs and birds are at elevated risk for acquiring zoonotic influenza infections. Agricultural workers should be included in pandemic influenza planning, should receive information and training on how to use personal protective equipment, and should be offered human influenza vaccine to reduce the risk of creating viral reassortants. In the event of a pandemic, workers should be considered for antiviral medications and pandemic strain vaccines.

Birds uniquely produce sound through a vocal organ known as a syrinx. The presence of wall shear stress acting on the airway cells of any organism will affect how airway cells develop and multiply. Unique features of avian airway geometry and breathing pattern might have contributed to the development of the syrinx. This thesis examines wall shear stress in the trachea and first bronchi of avian geometries using computational fluid dynamics. The computational fluid dynamic simulations underwent grid- and time-independence studies and were validated using particle image velocimetry. Parameters such as bird size, bronchial branching angle, and breathing waveform were examined to determine conditions that contributed to higher wall shear stress. Both simplified and CT scan-derived respiratory geometries were examined. Maximum wall shear stress for the simplified geometries was found to be highest during the inspiratory phase of breathing and was highest near the pessulus. Maximum wall shear stress in the CT scan-derived geometries was less phase-dependent and was highest near constrictions in the airway. Comparison between scanned and simplified geometry simulations revealed significant differences in wall shear stress magnitudes and flow features. If wall shear stress is found to be important in the development of the syrinx or the advantage of a syrinx, the thesis results are anticipated to aid in characterizing conditions that would have contributed to the development of the syrinx or advantages of syringeal vocal fold position over tracheal vocal fold position.

Orientador: Renata Cristina Batista Fonseca / Resumo: A fragmentação é uma das principais causas da perda de biodiversidade. Conciliar as atividades produtivas e a conservação dos recursos naturais é um dos principais desafios das empresas do setor florestal. Poucos estudos avaliam a composição e estrutura das comunidades em longo prazo, sendo o monitoramento de aves uma ferramenta eficaz para tal finalidade. Este estudo foi conduzido num fragmento de vegetação natural em unidade de manejo florestal no município de Agudos, interior de São Paulo, Brasil. Tem como objetivo verificar se houve alteração na comunidade de aves de um fragmento de no intervalo de 35 anos. Nesse intervalo o fragmento que no estudo inicial era isolado foi conectado a outras áreas de vegetação natural por meio de corredores ecológicos. A captura das aves foi realizada com o auxílio de redes de neblina, dispostas em cinco pontos, com quatro redes por ponto. As amostras foram realizadas por dois dias consecutivos/mês/ponto sendo o estudo inicial, realizado de março de 1982 a janeiro de 1983 e o atual, de novembro de 2017 a dezembro de 2018. No estudo inicial foram capturados 368 indivíduos, distribuídos em 16 famílias e 32 espécies. A diversidade foi de H’ = 2,7. Não houve dominância significativa entre as espécies (J = 0,77). No atual foi constatada diminuição significativa na riqueza e diversidade, sendo capturados 142 indivíduos, de 12 famílias e 18 espécies. A diversidade foi de H’ = 2,2. Não houve dominância significativa entre as espécies (J = 0,78). A... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Fragmentation is a major cause of biodiversity loss. Reconciling how productive activities and conservation of natural resources is one of the main challenges for companies in the forest sector. Few studies assess long-term community composition and structure, and bird monitoring is an effective tool for such use. This study was conducted on a fragment of natural vegetation in the forest unit in Agudos, São Paulo State, Brazil. It aims to verify if there was alteration in the bird community of a 35 years interval fragment. In this interval the fragment that in the initial study, was connected to other areas of natural vegetation through ecological corridors. The birds were captured with the aid of five point mist nets with four nets per point. Samples were taken for two consecutives days/month/point with the initial study conducted from March 1982 to January 1983 and the current study from November 2017 to December 2018. No initial study captured 368 individuals, distributed in 16 families and 32 species. The diversity was H '= 2.7. There was no significant dominance between species (J = 0.77). At the moment, there was a significant reduction in richness and diversity, and 142 individuals from 12 families and 18 species were captured. The diversity was H '= 2.2. There was no significant dominance between species (J = 0.78). A collector curve in the current study is not stabilized and an estimated 26 species (Jackknife1). The results show that despite the strategies adopted by... (Complete abstract click electronic access below) / Mestre

In addition to proving an excellent source of nutrients, eggs are used in the food, cosmetic, and biotechnology industries for their rheological and bioactive properties. Much of the potential for the added value is in individual components of the egg, rather than the whole egg. At low speed centrifugation, yolk separates into two distinct fractions—granules and plasma. It is becoming increasingly popular in the industry to remove the plasma fraction of the egg yolk to use for its livetins, particularly immunoglobulin Y, leaving behind a granule by-product (“yellow cake”). Previous research has shown potential added-value from the granule fraction, especially from its phosvitin and phospholipids. Granules are protein aggregates with complexes of phosvitin and high density lipoproteins linked by phosphocalcic bridges. In their native form, the proteins are mostly insoluble, however previous studies have shown the links can be broken by alterations in pH, ionic strength, and mechanical treatments. This thesis project seeks to find potential uses for the egg yolk by product after the removal of the livetin fraction by means of further fractionation with mechanical treatment (filtration). Two variables were tested to extract more proteins from the yellow cake. Salt was added to 10% solids solution of yellow cake in water before filtration at four different NaCl levels: 0%, .05%, 1%, and 2.5%. Additionally pH was tested at four different levels: 4.6, 4.8, 5.0, 5.2. The samples were also tested for antibacterial properties against Escherichia v coli with a minimum inhibitory concentration assay (MIC). Analysis with BCA showed salt concentration had a significant effect on the yield of protein. The highest concentration of salt tested, 2.5%, had the highest protein yield. Additionally, SDS PAGE showed 2.5% salt had the most unique protein bands. This could be to the disruption of the phosphocalcic links between the phosvitin and HDL by NaCl, allowing the protein to solubilize. pH did not have a significant effect on the yield or types of proteins in the range tested in this experiment. There is no conclusive evidence of antibacterial properties against E. coli from the protein extract. The MIC assay had growth show up in all wells with the protein extract, however there was a visible decrease in turbidity with higher concentration of the protein extract. This could mean that the protein extract does have some antibacterial properties, but needs testing at higher concentrations or with isolated proteins/peptides. The SDS-PAGE revealed bands showing phosvitin present, which has known antibacterial properties. Overall, improvements to the methods for further protein extraction from egg yolk by-products will help lead the industry to finding novel uses and product applications.

In this thesis, I investigated the relationship between host and pathogen in multi-host and multi-pathogen systems at the interface between wildlife and domestic species. The term “epidemiological interaction” was central to my thesis, and was defined as “any ecological interaction between two host populations resulting in the transmission of one or more pathogen”. Epidemiological interactions are related to the processes of transmission between hosts and I investigated how these epidemiological interactions between different host populations could be investigated in a given ecosystem. I developed two research frameworks to estimate these epidemiological interactions: 1) an a priori approach based on the host data and assuming that the mobility of hosts and the resulting contacts between host populations would be crucial factors influencing the epidemiological interactions; 2) an a posteriori approach based on the pathogen data, assuming that epidemiological pathways previously used by some pathogen species can be used in the future by other pathogens. The animalpathogen model used to test the first approach was the bird-avian influenza viruses’ model. Longitudinal counting and sampling protocols of domestic and wild birds over two years were used to analyse community composition and abundance of hosts to compare with the prevalence of avian influenza viruses. I could, for the first time, show a persistence of low pathogenic avian influenza strains in an African ecosystem, and investigate the relationships with both the potential maintenance hosts (Afro-tropical ducks and resident species) and hosts that introduced the virus into the system from Europe or Asia (paleartic migrants). With the estimation of epidemiological interaction using host community data, I estimated the contact rate between wild and domestic avian compartments (intensive poultry, backyard and farmed ostrich compartments) and assigned a risk to this interaction based on dynamic and non dynamic factors for each bird species. This approach highlights the species or seasons at risk for the domestic compartments (or for the wild bird compartments depending on the perspective) in order to orientate surveillance or control options. This type of data and framework can also be used in mechanistic modelling to predict the spread of a pathogen after its introduction in one compartment. I tested the host approach in a broader dataset at the Southern African region level with similar counting and sampling database in multiple study sites, showing that the variability of host communities across the region could explain the variability of pathogen detection (however, finding a causal relationship was impossible). Finally, I theoretically developed the pathogen approach by combining tools used in parasite community ecology, molecular epidemiology and social network analysis and gave a theoretical example using a rodent and human macro and microparasite dataset. This thesis has explored the field of transmission ecology and offered ways to quantify the processes of transmission between host populations. Theoretically, I have developed a fundamental reflexion around epidemiological interactions and formulated hypotheses on their potential for being independent of the parasite species. Practically, I have developed tools to provide information for decision-making in order to improve efficiency of surveillance and control programmes at the wildlife/domestic interface particularly adapted to detect emerging infectious disease spill-over process. / Thesis (PhD)--University of Pretoria, 2011. / Zoology and Entomology / unrestricted

Aposematic species of true bugs (Heteroptera) have multimodal signalization, which warns potential predators. This signalization consists of optical (coloration), chemical (unpalatable or repugnant substance) and acoustic (stridulation) warning signals. The aim of this thesis was to test whether the selected chemical substances have antipredatory function towards avian predators. Antipredatory function is anticipated in the chemical substances that form the majority in secretion in many taxa of true bugs (aldehydes and tridecane). In experiments with wild-caught great tits (Parus major) and blue tits (Cyanistes caeruleus) we tested if chemical substances and age of birds have influence on the latency related to the first manipulation with the prey. It was found that both species of tits reacted aversively to the mixture of aldehydes (2-decenal, 2-octenal, 2-hexenal) and to the total secretion of metathoracic glands of Graphosoma lineatum, whereas the mixture of the aldehydes with tridecane did not have any effect. The effect of age was not significant. We also tested the influence of immediate experience with striated shieldbug Graphosoma lineatum on naive great tits and their reactions to the prey with olfactoric signal of the shieldbug. Additionally, we investigated whether tested chemicals cause...