Use of bacterial whole-genome sequencing to investigate local persistence and spread in bovine tuberculosis

Mycobacterium bovis is the causal agent of bovine tuberculosis, one of the most important diseases currently facing the UK cattle industry. Here, we use high-density whole genome sequencing (WGS) in a defined sub-population of M. bovis in 145 cattle across 66 herd breakdowns to gain insights into local spread and persistence. We show that despite low divergence among isolates, WGS can in principle expose contributions of under-sampled host populations to M. bovis transmission. However, we demonstrate that in our data such a signal is due to molecular type switching, which had been previously undocumented for M. bovis. Isolates from farms with a known history of direct cattle movement between them did not show a statistical signal of higher genetic similarity. Despite an overall signal of genetic isolation by distance, genetic distances also showed no apparent relationship with spatial distance among affected farms over distances <5 km. Using simulations, we find that even over the brief evolutionary timescale covered by our data, Bayesian phylogeographic approaches are feasible. Applying such approaches showed that M. bovis dispersal in this system is heterogeneous but slow overall, averaging 2 km/year. These results confirm that widespread application of WGS to M. bovis will bring novel and important insights into the dynamics of M. bovis spread and persistence, but that the current questions most pertinent to control will be best addressed using approaches that more directly integrate WGS with additional epidemiological data.

Kernelized structural classification for 3D dogs body parts detection

Despite pattern recognition methods for human behavioral analysis has flourished in the last decade, animal behavioral analysis has been almost neglected. Those few approaches are mostly focused on preserving livestock economic value while attention on the welfare of companion animals, like dogs, is now emerging as a social need. In this work, following the analogy with human behavior recognition, we propose a system for recognizing body parts of dogs kept in pens. We decide to adopt both 2D and 3D features in order to obtain a rich description of the dog model. Images are acquired using the Microsoft Kinect to capture the depth map images of the dog. Upon depth maps a Structural Support Vector Machine (SSVM) is employed to identify the body parts using both 3D features and 2D images. The proposal relies on a kernelized discriminative structural classificator specifically tailored for dogs independently from the size and breed. The classification is performed in an online fashion using the LaRank optimization technique to obtaining real time performances. Promising results have emerged during the experimental evaluation carried out at a dog shelter, managed by IZSAM, in Teramo, Italy.

A pilot study to develop an assessment tool for sheep welfare after long journey transport

Sheep transport within Europe involves 9.5 million animals yearly, 63% of which travel over longjourneys (> 8 h). Livestock transport, particularly over long journeys, gives rise to concern about the welfare of transported animals. The European Commission stimulates the development of market-oriented animal welfare standards for all phases of livestock production, providing an alternative to the 'regulatory approach'. This study aimed to develop and test a new sheep welfare assessment protocol to be used following transport, irrespective of the journey purpose. The protocol included outcome (animal-based measures) and input variables (resource-based and management-based measures), being welfare-relevant aspects of both transport and unloading procedures. Weighted Cohen's Kappa and Heiss' Kappa index of agreement were calculated to evaluate the raters accuracy and the inter-observer reliability.Overall, good agreement levels were found. The protocol was tested on 40 commercial transports arriving at previously selected assembly centres and slaughterhouses in Italy and Greece. The protocol was found to be feasible when applied to commercial transports, allowing for a comprehensive and quick sheep welfare assessment during unloading, without impairing stockman work. Univariate analysis was carried out to evaluate associations between outcome and input variables. In this study, significant association between outcome measures and risk factors were identified when associated to unloading procedures but not to travel conditions. In collaboration with the relevant stakeholders, this protocol might be developed into a tool for routine checks for certification purposes and could provide direct feedback to all professionals involved in animal transportation on the weaknesses and strengths of their work.

SnaPshot based genotyping of the RYR1 mutation in Portuguese breeds of pigs

The porcine stress syndrome or malignant hyperthermia is an inherited autosomic recessive disease, which results in neuromuscular disorders leading to death in homozygous individuals and is associated with deterioration of meat quality. The defect in susceptible animals results from modifications in the calcium release channel or Ryanodine Receptor (RYR1), with a mutation leading to a C to T transition in nucleotide 1843 of the gene. The objective of this work was to develop a method based on analysis of SNPs to detect the mutation described in the RYR1 locus in pigs, and study polymorphisms of the gene in four exotic (Large White, Landrace, Duroc and Pietrain) and three native (Bísaro, Alentejano and Malhado de Alcobaça) breeds of pigs in Portugal. The method was successful in identifying the mutation by analysis of SNPs, and results indicate a high incidence of the mutant allele in Pietrain (0.75) and, to a lesser degree, in Malhado de Alcobaça (0.34) and Landrace (0.28); frequencies in Alentejano, Bísaro and Large White ranged between 0.04 and 0.09. These results suggest the need to establish breeding programs aimed at eliminating the susceptibility allele from those populations.

A influência dos factores humanos, ambientais e do pastoreio na ocorrência de geneta (Genetta genetta) no Sítio Monfurado

O presente estudo determina e analisa a importância relativa de diversos descritores ambientais, de pastoreio e de influência humana directa na distribuição da geneta (Genetta genetta L., 1758). O estudo decorreu em Monfurado, Sítio de Importância Comunitária, no Sul de Portugal. A área de estudo é predominantemente agrícola, maioritariamente ocupada por montado. A análise do padrão de distribuição deste carnívoro através de partição da variância e de ITMC (lnformation Theoretic Model Comparison) teve como objectivo orientar as prioridades na gestão das actividades humanas, compatíveis com a presença da espécie. Os resultados mostram que a distribuição da geneta é maioritariamente influenciada pelos descritores ambientais, apresentando uma relação positiva com densidade de montado com matos, conteúdo de matéria orgânica do solo e índice de Shannon de diversidade vertical da vegetação. A sua presença parece também ser promovida por níveis intermédios de pastoreio e fora das zonas de caça do regime cinegético especial. ABSTRACT; This study determines and analyses the relative importance of several environmental, livestock and human descriptors in the distribution of the common genet (Genetta genetta L., 1758). The study was conducted in Monfurado, a Site of Communitary lmportance, in South Portugal. The study area is Mediterranean farmland and is dominated by evergreen oak tree stands, named "montado". Modeling the distribution of this carnivore species was evaluated on the basis of ITMC (lnformation Theoretic Model Comparison) and variation partitioning techniques aiming to define human management activities compatible with the species conservation. The results show that the species distribution is mainly influenced by the environmental descriptors, and is positively related with montado and shrubs density, soil organic matter and Shannon's index of vertical vegetation diversity. Genet presence is favoured by intermediate levels of grazing and outside of game estates areas.

A desagregação espacial de dados agrícolas: aplicação de uma abordagem baseada na máxima entropia ao concelho de Castelo de Vide

Dissertação mest., Gestão Sustentável de Espaços Rurais, Universidade do Algarve, 2009

Catchment influences on the hydrological flows to lake terra alta (Linhares, ES, Brazil) and ecohydrology perspectives

Dissertação de mestrado, Ecohidrologia, Faculdade de Ciências e Tecnologia, Universidade do Algarve, 2015

Influence of environmental variables on the predatory sucess of the iberian wolf in the north of Portugal

Tese de mestrado em Biologia da Conservação, apresentada à Universidade de Lisboa, através da Faculdade de Ciências, 2016

Role Ambiguity and Perceived Organizational Politics in Wolf Recovery: Washington State Wildlife Agency Personnel Perspectives

Thesis (Master's)--University of Washington, 2015-12

Avaliação do efeito de um probiótico na performance zootécnica e microbiota entérica em coelhos (Oryctolagus cuniculus) de produção

A cunicultura é uma atividade pecuária em crescente desenvolvimento e isso traduz-se em novos desafios. Durante muitos anos a criação de coelhos recorreu em demasia ao uso de antimicrobianos com o objetivo de tratar e prevenir o aparecimento de diversas doenças. Paralelamente, estes compostos foram também usados como “promotores de crescimento”, visando essencialmente uma melhoria da eficiência digestiva. Porém, o uso indiscriminado destas substâncias levantou questões de saúde pública, como a emergência de estirpes bacterianas multirresistentes e a inerente disseminação de genes de resistência, possivelmente transferíveis ao Homem através da cadeia alimentar. No presente, existe uma enorme pressão para a adoção de estratégias que possibilitem uma redução massiva na quantidade de antimicrobianos administrados a espécies pecuárias. Este trabalho visou contribuir para o estudo de uma alternativa ao uso de antimicrobianos - os probióticos – enquanto suplementos alimentares constituídos por microrganismos vivos capazes de equilibrar a microbiota intestinal do hospedeiro. Para tal, foram constituídos dois grupos de coelhos com base na alimentação: i) grupo antibiótico, com acesso a um alimento composto suplementado com antibióticos e ii) o grupo probiótico alimentado com a mesma dieta, mas sem antibióticos e inoculado com um probiótico constituído por Escherichia coli e Enterococcus spp.. Ao longo de 22 dias de estudo foram monitorizados alguns indicadores produtivos e efetuadas recolhas periódicas de fezes para estudo microbiológico. A análise dos resultados zootécnicos permitiram verificar que o uso de probióticos em detrimento de antibióticos parece promover o crescimento de coelhos, tornando-se um método mais rentável na produção cunícula. Através de genotipagem por ERIC-PCR e PFGE, pretendeu-se verificar se as estirpes estranhas ao trato gastrointestinal dos coelhos seriam capazes de coloniza-lo, permanecendo ao longo do tempo de estudo. O facto de as estirpes inoculadas no probiótico terem sido encontradas ao longo dos dias de estudo nos coelhos aos quais foram administradas, sugere que os efeitos observados na performance zootécnica estejam relacionados com as estirpes administradas no probiótico, pelo que este poderá ser um sistema viável na substituição de antibióticos na alimentação de coelhos de produção.

Assessment of groundwater contamination in an agricultural peri-urban area (NW Portugal): an integrated approach

The excessive use of pesticides and fertilisers in agriculture has generated a decrease in groundwater and surface water quality in many regions of the EU, constituting a hazard for human health and the environment. Besides, on-site sewage disposal is an important source of groundwater contamination in urban and peri-urban areas. The assessment of groundwater vulnerability to contamination is an important tool to fulfil the demands of EU Directives. The purpose of this study is to assess the groundwater vulnerability to contamination related mainly to agricultural activities in a peri-urban area (Vila do Conde, NW Portugal). The hydrogeological framework is characterised mainly by fissured granitic basement and sedimentary cover. Water samples were collected and analysed for temperature, pH, electrical conductivity, chloride, phosphate, nitrate and nitrite. An evaluation of groundwater vulnerability to contamination was applied (GOD-S, Pesticide DRASTIC-Fm, SINTACS and SI) and the potential nitrate contamination risk was assessed, both on a hydrogeological GIS-based mapping. A principal component analysis was performed to characterised patterns of relationship among groundwater contamination, vulnerability, and the hydrogeological setting assessed. Levels of nitrate above legislation limits were detected in 75 % of the samples analysed. Alluvia units showed the highest nitrate concentrations and also the highest vulnerability and risk. Nitrate contamination is a serious problem affecting groundwater, particularly shallow aquifers, especially due to agriculture activities, livestock and cesspools. GIS-based cartography provided an accurate way to improve knowledge on water circulation models and global functioning of local aquifer systems. Finally, this study highlights the adequacy of an integrated approach, combining hydrogeochemical data, vulnerability assessments and multivariate analysis, to understand groundwater processes in peri-urban areas.

Gastrointestinal symbionts of chimpanzees in Cantanhez National Park, Guinea-Bissau with respect to habitat fragmentation

One of the major factors threatening chimpanzees (Pan troglodytes verus) in Guinea-Bissau is habitat fragmentation. Such fragmentation may cause changes in symbiont dynamics resulting in increased susceptibility to infection, changes in host specificity and virulence. We monitored gastrointestinal symbiotic fauna of three chimpanzee subpopulations living within Cantanhez National Park (CNP) in Guinea Bissau in the areas with different levels of anthropogenic fragmentation. Using standard coproscopical methods (merthiolate-iodine formalin concentration and Sheather's flotation) we examined 102 fecal samples and identified at least 13 different symbiotic genera (Troglodytella abrassarti, Troglocorys cava, Blastocystis spp., Entamoeba spp., Iodamoeba butschlii, Giardia intestinalis, Chilomastix mesnili, Bertiella sp., Probstmayria gombensis, unidentified strongylids, Strongyloides stercoralis, Strongyloides fuelleborni, and Trichuris sp.). The symbiotic fauna of the CNP chimpanzees is comparable to that reported for other wild chimpanzee populations, although CNP chimpanzees have a higher prevalence of Trichuris sp. Symbiont richness was higher in chimpanzee subpopulations living in fragmented forests compared to the community inhabiting continuous forest area. We reported significantly higher prevalence of G. intestinalis in chimpanzees from fragmented areas, which could be attributed to increased contact with humans and livestock.

Mapping the Pasture Steppe in Bayankhongor, Mongolia: comparison of classification methods, using Landsat-8 and geophysical data

Grasslands in semi-arid regions, like Mongolian steppes, are facing desertification and degradation processes, due to climate change. Mongolia’s main economic activity consists on an extensive livestock production and, therefore, it is a concerning matter for the decision makers. Remote sensing and Geographic Information Systems provide the tools for advanced ecosystem management and have been widely used for monitoring and management of pasture resources. This study investigates which is the higher thematic detail that is possible to achieve through remote sensing, to map the steppe vegetation, using medium resolution earth observation imagery in three districts (soums) of Mongolia: Dzag, Buutsagaan and Khureemaral. After considering different thematic levels of detail for classifying the steppe vegetation, the existent pasture types within the steppe were chosen to be mapped. In order to investigate which combination of data sets yields the best results and which classification algorithm is more suitable for incorporating these data sets, a comparison between different classification methods were tested for the study area. Sixteen classifications were performed using different combinations of estimators, Landsat-8 (spectral bands and Landsat-8 NDVI-derived) and geophysical data (elevation, mean annual precipitation and mean annual temperature) using two classification algorithms, maximum likelihood and decision tree. Results showed that the best performing model was the one that incorporated Landsat-8 bands with mean annual precipitation and mean annual temperature (Model 13), using the decision tree. For maximum likelihood, the model that incorporated Landsat-8 bands with mean annual precipitation (Model 5) and the one that incorporated Landsat-8 bands with mean annual precipitation and mean annual temperature (Model 13), achieved the higher accuracies for this algorithm. The decision tree models consistently outperformed the maximum likelihood ones.

Grantham Township Records Collection

Item one is a minute book for Grantham Township, Ontario. It records the proceedings of meetings from 1818-1854 and the names of parish and town officers from 1818 to 1842. Names include: Chisholm, Ball, Steele, TenBroeck, Shipman, Laraway, McKerney, Adams, Pawling, Merritt, Rolls, Robertson, Lampman, Phelps, Darling. Also notes the laws agreed upon for the period - mainly dealing with livestock. Item two is a report and evidence of boundary line disputes in the Township of Grantham. Includes affidavits from witnesses to the boundary dispute and a report to the Honourable the Commissioner of Crown Lands Quebec. The affadavits were recorded in 1844, and transcribed into the folio in 1852. Lewis A. Ball was the commissioner before whom the affadavits were sworn and duly recorded. Includes field notes by Frederic F. Passmore, Provincial land surveyor. The boundary lines in dispute were 1. between the 2nd and 3rd Concessions, from Lot no. 1 to Lot no. 5, 2. between the 4th and 5th concessions, from lot no. 4 to lot no. 5 and 3. between lots 14 in the 9th and 10th concession of the Township of Grantham.