The thesis is devoted to the issue of vaccination problematics and awareness of tick-borne encephalitis in a selected population group in South Bohemia. For the needs of research, the selected group was composed of students of secondary schools and grammar schools in the South Bohemian Region in the age group from 13 to 19 years old. The objectives of this work was to analyze the incidence of tick-borne encephalitis in the Czech Republic and the South Bohemian Region between 2000 and 2015, to compare the vaccination in the Czech Republic with the other European countries, to find the vaccination of a selected age group in the South Bohemian Region and to analyze the level of awareness of the risks of tick-borne encephalitis by the polling method and the attitude of the age group to vaccination against this disease. To achieve the objectives was used a secondary analysis of the data from the EpiDat system, where the incidence of the disease was detected in the period in the South Bohemian Region and the Czech Republic. The questionnaire survey was used to obtain awareness on observed disease and attitude of the study group towards vaccination against tick-borne encephalitis. The conclusions of the questionnaire survey were obtained on the basis of statistical processing in the MS Excel spreadsheet. For my significant findings from my research, I consider 80% of the vaccination in the monitored group. Information on tick-borne encephalitis in most cases did not get the respondents from a doctor, but from family members, from the internet or from television. However, information on vaccination is given to respondents to a greater extent. Contributions by insurance companies do not motivate more than half of respondents to inoculation. Research has also shown, that respondents have insufficient information about the amount of the contribution and whether their insurance company provide the contribution at all. In view of these circumstances, I consider the increased promotion of this vaccination by insurance companies to be very desirable.

En utilisant des données haute-fréquence inédites, cette thèse étudie trois types de regroupements (“clusters”) présents dans le marché des changes: la concentration d'ordres sur certains prix, la concentration des transactions dans le temps et l'existence de groupes d'investisseurs prenant les mêmes décisions. Nous commençons par étudier les propriétés statistiques du carnet d'ordres EBS pour les paires de devises EUR/USD et USD/JPY et l'impact d'une réduction de la taille du tick sur sa dynamique. Une grande part des ordres limites est encore placée sur les anciens prix autorisés, entraînant l'apparition de prix-barrières, où figurent les meilleures limites la plupart du temps. Cet effet de congestion se retrouve dans la forme moyenne du carnet où des pics sont présents aux distances entières. Nous montrons que cette concentration des prix est causée par les traders manuels qui se refusent d’utiliser la nouvelle résolution de prix. Les traders automatiques prennent facilement la priorité, en postant des ordres limites un tick devant les pics de volume.Nous soulevons ensuite la question de l'aptitude des processus de Hawkes à rendre compte de la dynamique du marché. Nous analysons la précision de tels processus à mesure que l'intervalle de calibration est augmenté. Différent noyaux construits à partir de sommes d'exponentielles sont systématiquement comparés. Le marché FX qui ne ferme jamais est particulièrement adapté pour notre but, car il permet d’éviter les complications dues à la fermeture nocturne des marchés actions. Nous trouvons que la modélisation est valide selon les trois tests statistiques, si un noyau à deux exponentielles est utilisé pour fitter une heure, et deux ou trois pour une journée complète. Sur de plus longues périodes la modélisation est systématiquement rejetée par les tests à cause de la non-stationnarité du processus endogène. Les échelles de temps d'auto-excitation estimées sont relativement courtes et le facteur d'endogénéité est élevé mais sous-critique autour de 0.8. La majorité des modèles à agents suppose implicitement que les agents interagissent à travers du prix des actifs et des volumes échangés. Certains utilisent explicitement un réseau d'interaction entre traders, sur lequel des rumeurs se propagent, d'autres, un réseau qui représente des groupes prenant des décisions communes. Contrairement à d'autres types de données, de tels réseaux, s'ils existent, sont nécessairement implicites, ce qui rend leur détection compliquée. Nous étudions les transactions des clients de deux fournisseur de liquidités sur plusieurs années. En supposant que les liens entre agents sont déterminés par la synchronisation de leur activité ou inactivité, nous montrons que des réseaux d'interactions existent. De plus, nous trouvons que l'activité de certains agents entraîne systématiquement l’activité d'autres agents, définissant ainsi des relations de type “lead-lag” entre les agents. Cela implique que le flux des clients est prévisible, ce que nous vérifions à l'aide d'une méthode sophistiquée d'apprentissage statistique. / The aim of this thesis is to study three types of clustering in foreign exchange markets, namely in price, trades arrivals and investors decisions. We investigate the statistical properties of the EBS order book for the EUR/USD and USD/JPY currency pairs and the impact of a ten-fold tick size reduction on its dynamics. A large fraction of limit orders are still placed right at or halfway between the old allowed prices. This generates price barriers where the best quotes lie for much of the time, which causes the emergence of distinct peaks in the average shape of the book at round distances. Furthermore, we argue that this clustering is mainly due to manual traders who remained set to the old price resolution. Automatic traders easily take price priority by submitting limit orders one tick ahead of clusters, as shown by the prominence of buy (sell) limit orders posted with rightmost digit one (nine).The clustering of trades arrivals is well-known in financial markets and Hawkes processes are particularly suited to describe this phenomenon. We raise the question of what part of market dynamics Hawkes processes are able to account for exactly. We document the accuracy of such processes as one varies the time interval of calibration and compare the performance of various types of kernels made up of sums of exponentials. Because of their around-the-clock opening times, FX markets are ideally suited to our aim as they allow us to avoid the complications of the long daily overnight closures of equity markets. One can achieve statistical significance according to three simultaneous tests provided that one uses kernels with two exponentials for fitting an hour at a time, and two or three exponentials for full days, while longer periods could not be fitted within statistical satisfaction because of the non-stationarity of the endogenous process. Fitted timescales are relatively short and endogeneity factor is high but sub-critical at about 0.8.Most agent-based models of financial markets implicitly assume that the agents interact through asset prices and exchanged volumes. Some of them add an explicit trader-trader interaction network on which rumors propagate or that encode groups that take common decisions. Contrarily to other types of data, such networks, if they exist, are necessarily implicit, which makes their determination a more challenging task. We analyze transaction data of all the clients of two liquidity providers, encompassing several years of trading. By assuming that the links between agents are determined by systematic simultaneous activity or inactivity, we show that interaction networks do exist. In addition, we find that the (in)activity of some agents systematically triggers the (in)activity of other traders, defining lead-lag relationships between the agents. This implies that the global investment flux is predictable, which we check by using sophisticated machine learning methods.

Infestações com Rhipicephalus microplus, o carrapato dos bovinos, causam enormes prejuízos econômicos para a pecuária. Os carrapatos estão desenvolvendo resistência aos carrapaticidas que, além dessa desvantagem, deixam resíduos em carne e leite. Vacinas anticarrapato representam uma alternativa sustentável de controle de infestações, mas as atualmente disponíveis têm efeitos parciais e transitórios. Surge, assim, a necessidade de identificar novos antígenos vacinais. Para alcançar esse objetivo este trabalho explora o fato de que bovinos apresentam fenótipos contrastantes e herdáveis de infestações que são específicos de certas raças. Além disso, o nível de imunidade do hospedeiro afeta a transcrição de genes de glândulas salivares do carrapato, órgão que produz proteínas que medeiam o parasitismo. A hipótese de trabalho é a que os diferentes níveis da imunidade anticarrapato do hospedeiro afetam, também, a composição salivar do parasita. Assim, em carrapatos alimentando-se em hospedeiros resistentes as proteínas que são cruciais ao parasitismo poderão estar ausentes ou deficientes na sua saliva e por isso os carrapatos não terminam sua refeição de sangue. A neutralização dessas mesmas proteínas pela imunidade humoral pode ter o mesmo efeito e por isso, essas proteínas constituem bons antígenos vacinais. Assim, o objetivo do trabalho foi identificar novos antígenos vacinais em saliva de fêmeas e glândulas salivares de ninfas, machos e fêmeas de carrapatos alimentados em hospedeiros resistentes e suscetíveis, bem como em larvas não alimentadas oriundas de ovos de fêmeas alimentadas nestes mesmos hospedeiros. Para isso, foram empregadas abordagens de sequenciamento de nova geração \"RNA-Seq\" (454) e abordagens proteômicas, como análise diferencial em gel (DIGE) e Western Blots (imunoproteoma) seguido de sequenciamento de massa, além da tecnologia de identificação de proteínas multidimensionais (ou Multidimensional Protein Identification Technology, MudPIT) para descrever o proteoma das glândulas salivares e da saliva de fêmeas. A análise transcriptômica resultou no sequencimanto de 1.999.086 reads que permitiu identificar e classificar 11.676 sequências codificadoras (CDS), muitas das quais (3.600 CDS) contêm peptídeo sinal que é indicativo de secreção, portanto podendo estar presente na saliva e Resumo Gustavo Rocha Garcia apresentar função importante na hematofagia. Por meio de MudPIT, identificamos 321 proteínas salivares diferentes, além de 126 proteínas no DIGE e 266 proteínas nos imunoproteomas. Muitas dessas proteínas podem ser consideradas antígenos potenciais por estarem associadas com a hematofagia/parasitismo, tais como proteases, nucleases, inibidores de proteases, peptídeos antimicrobianos, proteínas de fixação, entre outros, inclusive proteínas ainda não caracterizadas. A maioria dos genes codificantes dessas proteínas está mais expressa em carrapatos alimentados em hospedeiros suscetíveis, principalmente em carrapatos machos. Além disso, muitas dessas proteínas não são reconhecidas por soros bovinos, inclusive soros de bovinos infestados, embora soros de bovinos infestados e resistentes ao carrapato apresente a maioria das reatividades. O conjunto dos resultados sugere que em nível de proteína a composição da saliva também é afetada pelos diferentes níveis de imunidade dos hospedeiros, além de variar com o ciclo de vida do carrapato. Desse modo, concluímos que as estratégias de investigação empregadas foram satisfatórias para identificar um conjunto de antígenos salivares do carrapato R. microplus que representam proteínas alvos para compor vacinas multicomponentes anticarrapato. / Infestation with Rhipicephalus microplus, the cattle tick, causes huge economic losses to livestock. Ticks are developing resistance to acaricides that, besides this disadvantage, leave residues in meat and milk. The anti tick vaccines represent a sustainable alternative of the infestations control, but the currently available has partial and transient effects. Thus arises the need to identify new vaccine antigens. To achieve this goal, this work explores the fact that cattle exhibit contrasting phenotypes and inheritable of infestations that are specific to certain breeds. Furthermore, the level of immunity of the host affects gene transcription tick salivary gland, organ that produces proteins that mediate the parasitism. The working hypothesis is that different levels of anti tick immunity of host affect also the salivary composition of the parasite. So in ticks feeding on resistant hosts the proteins that are crucial to parasitism may be absent or deficient in their saliva, and by this the ticks do not finish your meal blood. The neutralization of these same proteins by humoral immunity can have the same effect and by this, these proteins are good vaccine antigens. So, the aim of the study was to identify new vaccine antigens in saliva from females and salivary glands of nymphs, males and females of ticks fed on resistant and susceptible hosts as well as in unfed larvae originating from eggs of females fed on these same hosts. To this, were employed sequencing approaches of new generation \"RNA-Seq\" (454) and proteomic approaches, such as differential analysis in gel (DIGE) and Western Blots (immunoproteomics) followed by sequencing mass, besides the Multidimensional Protein Identification Technology (MudPIT) to describe the proteome of the salivary glands and saliva of females. The transcriptomics analysis identified 11,676 coding sequences (CDS), many of which (3,600 CDS) contain predicted signal peptide indicative of secretion, therefore may be present in saliva and provide an important function in blood feeding. Through MudPIT, we identify 321 different salivary proteins, besides 126 proteins in DIGE and 266 proteins in immunoproteomics. Many of these proteins may be considered as potential antigens to be associated with the blood meal/ parasitism, such as proteases, nucleases, protease inhibitors, antimicrobial peptides, proteins of attachment, among Abstract Gustavo Rocha Garcia others, including proteins not yet characterized. Most of the genes encoding of these proteins are more expressed in ticks fed on susceptible hosts, especially in male ticks. Moreover, many of these proteins are not recognized by bovine sera, including sera from infested hosts, although sera from infested and resistant host to tick present the most reactivities. The overall results suggest that in protein level, the composition of saliva is also affected by the different levels of immunity of the host, besides vary with the tick life cycle. Thus, we conclude that the research strategies employed were satisfactory to identify a set of tick salivary antigens from R. microplus that represent target proteins for composing anti tick multicomponent vaccines.

Submitted by Renata Lopes (renatasil82@gmail.com) on 2016-05-20T13:32:38Z No. of bitstreams: 1 janedaisydesousaalmadaresende.pdf: 213211 bytes, checksum: 7f0d7ee1b43dfa3fc109755fd5562c3c (MD5) / Approved for entry into archive by Adriana Oliveira (adriana.oliveira@ufjf.edu.br) on 2016-07-02T11:22:02Z (GMT) No. of bitstreams: 1 janedaisydesousaalmadaresende.pdf: 213211 bytes, checksum: 7f0d7ee1b43dfa3fc109755fd5562c3c (MD5) / Made available in DSpace on 2016-07-02T11:22:02Z (GMT). No. of bitstreams: 1 janedaisydesousaalmadaresende.pdf: 213211 bytes, checksum: 7f0d7ee1b43dfa3fc109755fd5562c3c (MD5) Previous issue date: 2012-01-26 / O presente trabalho teve o objetivo de verificar a sensibilidade de larvas de Amblyomma cajennense e Dermacentor nitens frente os solventes etanol, metanol, acetona, xilol e dimetilsulfóxido (DMSO) e o agente tensoativo Tween 80. Os solventes etanol, metanol, acetona e xilol foram testados em pureza analítica, enquanto o DMSO e o agente tensoativo Tween 80 foram testados na concentração de 1%, sendo estabelecido que as substâncias testadas em pureza analítica que causassem alta mortalidade seriam testadas também nas concentrações de 50, 25 e 1%. Foi utilizado o teste de pacote de larvas, sendo feitas dez repetições para cada tratamento. Também foi formado um grupo controle com o mesmo número de repetições, em que as larvas foram tratadas com água destilada. No primeiro experimento, nas concentrações testadas, apenas o xilol se mostrou como substância de alta toxicidade, uma vez que a mortalidade observada foi superior a 90% para larvas de A. cajennense e D. nitens. No segundo experimento, o xilol a 1 e a 25% apresentou baixa toxicidade para larvas de A. cajennense e D. nitens, respectivamente, uma vez que o percentual de mortalidade foi estatisticamente semelhante (p>0,05) ao do controle. / The objective of this work was to verify the sensitivity of Amblyomma cajennense and Dermacentor nitens larvae to the solvents ethanol, methanol, acetone, xylol and dimethyl sulfoxide (DMSO) and the surfactant Tween 80. The first four solvents were tested at analytical purity while the DMSO and surfactant Tween 80 were tested at a concentration of 1%. The substances tested at analytical purity that caused high mortality were also tested at concentrations of 50, 25 and 1%. The larval packet test was used, with ten repetitions for each treatment. A control group was also formed with the same number of repetitions, in which the larvae were only exposed to distilled water. In the first experiment, only xylol was highly toxic at the concentrations tested, causing mortality above 90% for larvae of both species. In the second experiment, xylol at 1 and 25% showed low toxicity to the A. cajennense and D. nitens larvae, respectively, since the mortality percentage was statistically similar to that of the control group (p>0.05).

Submitted by Renata Lopes (renatasil82@gmail.com) on 2017-04-20T19:47:06Z No. of bitstreams: 1 paulabarrosocruz.pdf: 1781659 bytes, checksum: 62d0ee084bc070be10b7ca48781a98c6 (MD5) / Approved for entry into archive by Adriana Oliveira (adriana.oliveira@ufjf.edu.br) on 2017-04-24T16:51:51Z (GMT) No. of bitstreams: 1 paulabarrosocruz.pdf: 1781659 bytes, checksum: 62d0ee084bc070be10b7ca48781a98c6 (MD5) / Made available in DSpace on 2017-04-24T16:51:51Z (GMT). No. of bitstreams: 1 paulabarrosocruz.pdf: 1781659 bytes, checksum: 62d0ee084bc070be10b7ca48781a98c6 (MD5) Previous issue date: 2016-07-29 / CAPES - Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / O objetivo do presente trabalho foi avaliar a atividade carrapaticida do extrato metanólico de Acmella oleracea e do espilantol sobre Rhipicephalus microplus e Dermacentor nitens. O extrato metanólico foi obtido através de maceração com metanol. Desse extrato, foi obtida uma fração diclorometano com 99% de espilantol (que pode ser considerado um composto puro), que também foi testada sobre larvas e fêmeas ingurgitadas de R. microplus e larvas de D. nitens. Para a avaliação da atividade sobre larvas, foi utilizado o teste de pacote de larvas modificados e o extrato metanólico e a fração diclorometano (99% de espilantol) foram testadas em concentrações de 0,2 a 50,0 mg/mL. No teste de tempo letal, também foi utilizado a técnica de pacote de larvas, o extrato metanólico foi usado na concentração de 12,5 mg/mL e a avaliação do percentual de mortalidade foi feita após 15, 30, 45, 60, 75, 90, 120 minutos e 24 horas. Nesse teste foi feito o cálculo de tempo letal 50% (TL50). O teste com fêmeas ingurgitadas foi feito apenas com R. microplus, sendo testadas concentrações de 25 a 200 mg/mL do extrato metanólico e concentrações entre 2,5 a 20,0 mg/mL para o espilantol. O extrato metanólico ocasionou mortalidade de 100% das larvas de R. microplus e D. nitens a partir de concentrações de 3,1 e 12,5 mg/mL, respectivamente. O espilantol resultou em mortalidade de 100% para larvas de R. microplus a partir da concentração 1,6 mg/mL e de 12,5 mg/mL para D. nitens. No experimento de tempo letal, a mortalidade foi de 100% para larvas de R. microplus e D. nitens após 120 minutos e 24 horas, com TL50 de 38 e 57 minutos. No teste com fêmeas, o peso da massa de ovos e percentagem de eclosão dos grupos tratados com concentrações iguais e/ou superiores a 50,0 mg/mL do extrato metanólico apresentaram redução significativa (p> 0,05) em relação ao controle, enquanto o espilantol provocou redução significativa do peso da massa de ovos e percentagem de eclosão em concentrações de 10,0 mg/mL e 2,5 mg/mL, respectivamente. As fêmeas tratadas com 200,0 mg/mL do extrato morreram antes de iniciar o processo de oviposição, resultando em eficácia de 100%, enquanto a melhor eficácia para espilantol foi de 92,9% na concentração de 20,0 mg/mL. Portanto, é possível concluir que o extrato metanólico da A. oleracea e o espilantol apresentam atividade acaricida sobre R. microplus e D. nitens. / We evaluate the acaricidal activity of Acmella oleracea methanol extract and spilanthol on Rhipicephalus microplus and Dermacentor nitens. The methanol extract was made through maceration with methanol. From this extract, a dichloromethane fraction with approximately 100% spilanthol was obtained and tested on R. microplus larvae and engorged females and D. nitens larvae. For evaluation against larvae, modified larvae test packages were used, and both methanol extract and the dichloromethane fraction were tested at concentrations of 0.2 to 50.0 mg/mL. The larvae package technique was also used in the lethal time (LT) test, with methanol extract at a concentration of 12.5 mg/mL and the mortality percentage assessment was made after 15, 30, 45, 60, 75, 90, 120 minutes and 24 hours. The lethal time calculation 50% (LT50) was performed in this test. The engorged female test was done with R. microplus only, at concentrations of 25 to 200 mg/mL for methanol extract and 2.5 to 20.0 mg/mL for spilanthol. The methanol extract caused 100% mortality of the R. microplus and D. nitens larvae at concentrations from 3.1 and 12.5 mg/mL, respectively. Spilanthol resulted in 100% mortality for R. microplus larvae at concentration from 1.6 mg/mL and 12.5 for D. nitens. In the lethal time essay using the methanol extract, the mortality rate was 100% for R. microplus and D. nitens larvae after 120 minutes and 24 hours with LT50 of 38 and 57 minutes. In the test of females, the egg mass weight and the hatching percentage of the groups treated with concentrations equal to and/or higher than 100.0 mg/mL of methanol extract showed significant differences (p> 0.05) while spilanthol causes significant reduction of the egg mass weight and hatching percentage at concentrations of 10.0 mg/mL and 2.5 mg/mL, respectively. Females treated with 200.0 mg/mL of extract died before starting the oviposition process, resulting in 100% effectiveness, while the best efficacy for spilanthol was 92.9% at concentration of 20.0 mg/mL. Thus we conclude that the methanol extract of A. oleracea and spilanthol present acaricide activity against R. microplus and D. nitens.

Cette thèse est composée de deux parties reliées, le premier sur le carnet d'ordre et le deuxième sur les effets de valeur de tick. Dans la première partie, nous présentons notre cadre de modélisation de carnet. Le modèle queue-réactive est d'abord introduit, dans laquelle nous révisons l'approche zéro intelligence traditionnelle en ajoutant dépendance envers l'État de carnet. Une étude empirique montre que ce modèle est très réaliste et reproduit de nombreuses fonctionnalités intéressantes microscopiques de l'actif sous-jacent comme la distribution du carnet de commandes. Nous démontrons également qu'il peut être utilisé comme un simulateur de marché efficace, ce qui permet l'évaluation de la tactique de placement complexes. Nous étendons ensuite le modèle de queue-réactive à un cadre markovien général. Conditions de Ergodicité sont discutés en détail dans ce paramètre. Dans la deuxième partie de cette thèse, nous sommes intéressés à étudier le rôle joué par la valeur de la tique à deux échelles microscopiques et macroscopiques. Tout d'abord, une étude empirique sur les conséquences d'un changement de la valeur de tick est effectuée à l'aide des données du programme pilote de réduction de la taille 2014 tick japonais. Une formule de prédiction pour les effets d'un changement de valeur de tique sur les coûts de transactions est dérivé. Ensuite, un modèle multi-agent est introduit afin d'expliquer les relations entre le volume du marché, la dynamique des prix, spread bid-ask, la valeur de la tique et de l'état du carnet d'ordres d'équilibre. / This thesis is made of two connected parts, the first one about limit order book modeling and the second one about tick value effects. In the first part, we present our framework for Markovian order book modeling. The queue-reactive model is first introduced, in which we revise the traditional zero-intelligence approach by adding state dependency in the order arrival processes. An empirical study shows that this model is very realistic and reproduces many interesting microscopic features of the underlying asset such as the distribution of the order book. We also demonstrate that it can be used as an efficient market simulator, allowing for the assessment of complex placement tactics. We then extend the queue-reactive model to a general Markovian framework for order book modeling. Ergodicity conditions are discussed in details in this setting. Under some rather weak assumptions, we prove the convergence of the order book state towards an invariant distribution and that of the rescaled price process to a standard Brownian motion. In the second part of this thesis, we are interested in studying the role played by the tick value at both microscopic and macroscopic scales. First, an empirical study of the consequences of a tick value change is conducted using data from the 2014 Japanese tick size reduction pilot program. A prediction formula for the effects of a tick value change on the trading costs is derived and successfully tested. Then, an agent-based model is introduced in order to explain the relationships between market volume, price dynamics, bid-ask spread, tick value and the equilibrium order book state.

The field of vector-borne disease research uses multidisciplinary approaches to help understand complicated interactions. This dissertation, covers three different aspects of tick-borne disease research which all focus on exploring tick-borne diseases in the non-endemic areas of Denton, County Texas and the state of Texas with a focus on Rickettsia spp. These aspects include tick sampling, testing ticks for the presence of Rickettsia spp., and creating species distribution maps of the Rickettsia spp. Rickettsia amblyommatis and tick species Amblyomma americanum.

Thesis (PhD)--Stellenbosch University, 2015. / ENGLISH ABSTRACT: The broad objective of this study was to identify single nucleotide polymorphisms (SNP) markers associated with tick resistance in South African Nguni cattle and it was addressed by three specific objectives. The first objective was to assess tick load and prevalence in Nguni cattle in different agro-climatic regions of South Africa using tick count data collected monthly from 586 Nguni cattle reared under natural grazing conditions, over two years. Tick counts were assessed under natural challenge at ARC Roodeplaat and Loskop farms (warm climate), and Mukhuthali Nguni Community and University of Fort Hare farms (cool climate). The second objective was to estimate genetic parameters for tick counts in Nguni cattle. The third objective was to identify SNPs associated with tick resistance in Nguni cattle. Counts for each tick species were conducted on each animal in the herd once a month on different body locations, including the head, ears, neck, back, legs, belly, perineum and tail. Distribution of counts was determined using the PROC FREQ (SAS, 2002 - 2010). The tick counts were then analysed with the PROC GLM procedure using the two fixed effect models. Genetic parameters for log-transformed counts were estimated from univariate animal and sire models and bivariate sire models using the ASREML program. Animals were genotyped using Illumina BovineSNP50K assay. After Quality Control (call rate >90%, minor allele frequency > 0.02), 40 436 SNPs were retained for analysis. Association analysis for tick resistance was carried out using two approaches: genome-wide association (GWA) analysis using the GenABEL package and a Regional Heritability Mapping (RHM) analysis. Six tick species were identified: Amblyomma hebraeum (42%), Rhipicephalus evertsi evertsi (22%), Rhipicephalus (Boophilus) spp. (16%), Rhipicephalus appendiculatus (11%), Hyalomma marginatum (5%) and Rhipicephalus simus (4%). Tick infestation was significantly affected by location, season, year, month of counting and age of the animal. Loskop farm, as the warmest location, had the highest tick counts and also showed the largest variation in tick loads. Higher tick counts were also observed in the hot-dry (September to November) and hot-wet (December to February) seasons compared to the other seasons. Amblyomma hebraeum was the dominant tick species across all four locations. Heritability estimates for tick count varied according to season and trait (body part or tick species) and ranged from 0.01±0.01 to 0.26±0.01. Genetic correlations ranged from -0.79±0.33 to 1.00±0.00 among counts for different body parts and 0.00±0.00 to 0.99±0.00 among tick species. Phenotypic correlations ranged from 0.06±0.01 to 0.72±0.01 among body parts and 0.01±0.02 to 0.44±0.01 for tick species. Whole body count was highly correlated to the perineum and the belly. These two traits appear to be the most suitable surrogates for whole body count. Several genomic regions of interest were identified for different traits by both the GWA and RHM approaches. Three genome-wide significant regions on chromosomes 7, 10 and 19 were identified for total tick count on the head, total A. hebraeum ticks and for total number of A. hebraeum in the perineum region. Suggestive significant regions were identified on chromosomes 1, 3, 6, 7, 8, 10, 11, 12, 14, 15, 17, 19 and 26 for several of the tick traits analysed. The GWA approach identified more genomic regions than did the RHM approach. These findings provide information that would be useful in developing strategies for genetic improvement of tick resistance through selection. The chromosome regions identified as harbouring quantitative trait loci (QTL) underlying variation in tick burden form the basis for further analyses to identify specific candidate genes related to cattle tick resistance and provide the potential for marker-assisted selection in Nguni. / AFRIKAANSE OPSOMMING: Die doel van hierdie studie was om enkel nukleotied polimorfismes (ENPs) merkers te identifiseer wat verwant is aan bosluisweerstand in Suid-Afrikaanse Nguni beeste; dit is aangespreek deur drie doelwitte. Die eerste doelwit was om bosluislading en -voorkoms van bosluise in Nguni beeste in verskillende landbou-klimaatstreke van Suid-Afrika te bepaal deur die gebruik van bosluistelling data wat maandeliks van 586 Nguni beeste, grootgemaak op natuurlike weiding, oor 'n tydperk van twee jaar versamel was. Die tweede doelwit van die studie, was om die genetiese parameters te bepaal vir die bosluistellings in die Nguni beesras. Om hierdie doelwit aan te spreek, is vier verskillende datastelle onderskei in die bosluistelling data wat oor die twee jaar periode versamel was. Genetiese parameters is derhalwe beraam vir die telling van bosluise om sodoende die beste seisoen te identifiseer vir die insameling van bosluistelling data om ten einde strategieë te ontwikkel vir die genetiese seleksie vir vehoogde weerstand teen bosluise. Die derde doelwit was om ENP streke te identifiseer wat verband hou met bosluisweerstand in Nguni beeste. Verskillende bosluisspesies was getel op elke dier in die kudde een keer per maand op verskillende plekke op die liggaam, insluitend die kop, ore, nek, rug, bene, maag, perineum en stert. Bosluistelling data is ontleed met behulp van die SAS program om bosluislading variasie te bepaal. Genetiese parameter skattings vir log getransformeerde bosluistellings data was bereken vanaf twee-veranderlike vaar modelle en een-veranderlike dier- en vaar modelle met behulp van die ASREML program. Om ‘n genomiese wye assosiasie studie (GWAS) uit te voer, is DNS geïsoleer en genotipering gedoen met behulp van die Illumina BovineSNP50K toets. Na kwaliteit kontrole (oproep frekwensie>90%, klein alleelfrekwensie>0.02) is 40.436 ENPs behou vir ontleding. Assosiasie analise vir bosluisweerstand is uitgevoer met behulp twee benaderings, d.i. 'n genoom-wye assosiasie (GWA) analise met behulp van die GenABEL pakket en 'n plaaslike oorerflikheid karterings (POK) analise. Ses bosluisspesies is geïdentifiseer, d.i. Amblyomma hebraeum (42%), Rhipicephalus evertsi evertsi (22%), Rhipicephalus (Boophilus) spp. (16%), Rhipicephalus appendiculatus (11%), Hyalomma marginatum (5%) en Rhipicephalus simus (4%). Bosluis besmetting was beduidend beïnvloed deur die plek, seisoen, jaar, maand tel en ouderdom van die dier. Loskop plaas het die warmste weer ervaar en het die hoogste bosluis tellings en ook die grootste variasie in bosluislading gehad. Hoër bosluistellings is ook waargeneem in die warm droë (September tot November) en warm nat (Desember-Februarie) seisoene in vergelyking met die ander seisoene. Amblyomma hebraeum is geïdentifiseer as die mees dominante bosluisspesies oor al vier lokaliteite. Die voorkeur aanhegtingsarea vir die bosluise was onder die stert, perineum en maag areas op die liggaam. Die oorerflikheid beraming vir bosluistelling, soos beïnvloed deur die seisoen en eienskap (d.i. deel van die liggaam of bosluisspesies), het gewissel van 0.01±0.01 tot 0.26±0.01. Genetiese korrelasies het gewissel van -0.79±0.33 tot 1.04±0.01 vir bosluistellings op verskillende liggaamsdele en tussen 0.00±0.00 en 0.99±0.19 vir bosluisspesies. Fenotipiese korrelasies was laag tot matig en het gewissel van 0.06±0.01 tot 0.72±0.01 vir liggaamsdele en 0.01±0.02 to 0.44±0.01 vir bosluisspesies. Die datastel D wat September-Januarie bosluistellings bevat het die hoogste genetiese variasie aangedui. Heel liggaam bosluistellings was hoogs gekorreleerd met bosluistellings rondom die perineum en maag. Hierdie twee lokaliteite blyk die mees geskikte plaasvervanger vir die heel liggaam bosluistelling te wees. Verskeie genoom gebiede van belang is geïdentifiseer vir die verskillende eienskappe van beide die GWA en RHM benaderings. Drie genoom-wye beduidende streke (op chromosome 7, 10 en 19) is geïdentifiseer vir die totale bosluistelling op die kop, totale A. hebraeum bosluise en vir die totale aantal A. hebraeum in die perineum streek. Aanbevelende beduidende streke is geïdentifiseer op chromosome 1, 3, 6, 7, 8, 10, 11, 12, 14, 15, 17, 19 en 26 vir 'n paar van die bosluis eienskappe wat ontleed was. Die GWA benadering identifiseer meer genoom gebiede as die POK benadering. Hierdie bevindinge bied nuttige inligting vir die ontwikkeling van strategieë vir die genetiese verbetering van bosluisweerstand deur seleksie. Die chromosome streke hier geïdentifiseer is skuiling kwantitatiewe eienskap loki (KEL) vir die onderliggende variasie in bosluislading en vorm die basis vir verdere ontledings vir spesifieke kandidaat gene te identifiseer wat verband hou met die vee bosluisweerstand en bied die potensiaal vir merkerbemiddelde seleksie in Nguni.

This study examines, from a modelling point of view, the dynamics of infectious diseases in wildlife caused by macroparasites and by tick-borne infections. The overall aim was to investigate the important role played by parasite aggregation in the dynamics of both systems. For macroparasites we first developed some deterministic models that incorporate explicit mechanisms for generating aggregation in parasite distribution, specifically multiple infections and host heterogeneity. We explored the role of aggregation in host regulation and in determining a threshold value for parasite establishment. A large aggregation makes it more difficult for parasites both to regulate hosts, and to get established in a population at carrying capacity. Furthermore, the stabilization yielded by aggregation strongly depends on the mechanism that produces the aggregation. We then introduced some uncertainties into the host-macroparasite system, presenting an individual-based stochastic model that incorporated the same assumptions as the deterministic model. Stochastic simulations, using parameter values based on some real case studies, preserved many features of the deterministic model, like the average value of the variables and the approximate length of the cycles. An important difference is that, even when deterministic models yield damped oscillations, stochastic simulations yield apparently sustained oscillations. The amplitude of such oscillations may be so large as to threaten the parasites’ persistence. With respect to tick-borne diseases we presented a general model framework that incorporated both viraemic and non-viraemic routes of infections. We compute the threshold for disease persistence and study its dependence on the parameters and on host densities. The effects of tick aggregation and correlation between different tick stages on the host have both an important effect on infection persistence, if non-viraemic transmission occurred. In the case of Lyme Disease and Tick-borne Encephalitis (TBE) in Trentino (northern Italy) we showed some numerical results, using parameter estimates based on a detailed field study, and explored the effects of uncertainty on the endemic equilibrium of both diseases assuming only viraemic transmission for Lyme Disease while for TBE we permitted only non-viraemic transmission through co-feeding ticks. In conclusion we have examined the patterns and changes of aggregation in a number of contrasting systems and believe that these studies highlight both the importance of considering heterogeneities in modelling host-parasite interactions and, more specifically, modelling the biological mechanisms that produce aggregation in parasite distributions.

Kyasanur Forest disease virus (KFDV) of the Flaviviridae virus family has caused seasonal infections and periodic outbreaks in Karnataka, India. First identified in 1957, KFDV annually infects 400-500 people and has a fatality rate of 3-5%; there are no approved antivirals and the existing licensed vaccine’s effectiveness appears to be questionable. Many tools for KFDV research are limited and this work sought to develop methods for analysing antivirals, including interferon (IFN)-α/β species. The BHK-21 (ATCC) cell line allowed for high virus propagation and distinguishable cytopathic effects (CPE) for determining antiviral effectiveness. The additional tool of a reverse genetics system expressing a full-length cDNA KFDV genome with a GFP reporter failed to propagate, despite numerous GFP genome-insertion strategies. The clinically approved IFN-α2a or IFN-α2b has had variable success at combatting flavivirus diseases in people, especially in the immuno-compromised. The continued passaging of KFDV-infected cells with repeated IFN-α2a treatment did not eliminate KFDV and had little effect on infectious particle production. IFN-αspecies, αWA and α were more effective than IFN-α2a and α2b at reducing KFDV; however dose ranges indicated that while low concentrations could limit CPE, higher concentrations were needed to inhibit virion release. Avoidance of IFN-α/β through Jak/STAT signalling repression was attributed to the NS5 protein, specifically the RdRp domain based on data obtained with luciferase and vesicular stomatitis virus (VSV) recovery assays. However, the mechanism appears to act subsequently to STAT1/2 activation without NS5 binding to any Jak/STAT components. A non-infectious, replicative system serving as a platform for antiviral drug testing against KFDV in a high throughput manner could only provide luciferase signals when the NS proteins capable of driving replication, were supplied in cis (subgenomic) but not in trans (antigenome). To conclude, IFN-α species such as IFN-αWA may be better suited than the licensed IFN-α2a for treatment of KFDV infections; however, IFN effects appear to be subdued in vitro due to the actions of the NS5 protein. While IFN may not be a successful antiviral against KFDV, the work in this thesis provides a foundation for evaluating other potential anti-KFDV therapeutics. / February 2016