Limitations of spoligotyping and variable-number tandem-repeat typing for molecular tracing of Mycobacterium bovis in a high-diversity setting

This study describes the attempt to trace the first Mycobacterium bovis outbreak in alpacas (Lama pacos) in Spain by spoligotyping and variable-number tandem-repeat (VNTR) analysis. Due to high genotype diversity, no matching source was identified, but local expansion of a clonal group was found and its significance for molecular tracing is discussed.

FROM GENES TO GENOMES: LOCAL ADAPTATION AND ADAPTIVE POTENTIAL IN TWO ARCTIC SEABIRDS

By investigating the mechanisms underlying the evolution and the maintenance of local adaptations we can help predict how species will adapt to future environmental change. In this thesis I investigate local adaptation and adaptive potential in thick-billed and common murres (Uria lomvia and U. aalge), two arctic seabirds of international conservation concern. Thanks to the recent development of new genomic methods, I address three major themes that are relevant for both the development of evolutionary theory and conservation: 1) the role of gene flow in the origin and maintenance of adaptation; 2) levels and distribution of standing genetic variation, and their contribution to adaptive potential; and 3) the genomic mechanisms maintaining an adaptive dimorphism within a single interbreeding population. First, I review the literature on genomics of local adaptation with gene flow and find that adaptation can be maintained despite gene flow, that gene flow itself can promote adaptation, and that genetic architecture is important in the origin and maintenance of local adaptations. Second, I genotype genome-wide markers and toll-like receptor genes (TLRs) to investigate local adaptation and adaptive potential in thick-billed murres. Thick-billed murres do not show signatures of local adaptation to their breeding grounds, but outlier loci group birds according to their non-breeding distributions, suggesting that selection and/or demographic connectivity in the winter may explain patterns of differentiation in this species. Genetic variation at TLRs does not decrease with increasing latitude as predicted, but tests of selection and measures of genetic diversity suggest differences in local selective regimes at most genes. Thick-billed murres show high levels of standing genetic variation and their adaptive potential will mostly depend on rate and magnitude of environmental change. Finally, I improve and annotate the assembly of the highly heterozygous genome of the thick-billed murre. Using this assembly as a reference, I perform whole genome analyses to investigate the genomic basis of an adaptive dimorphism in Atlantic common murres. I show for the first time that a 60 kb complex copy number variant in a non-coding region maintains differences in plumage and cold adaptation despite high gene flow.

A finite-strain solid–shell using local Löwdin frames and least-squares strains

A finite-strain solid–shell element is proposed. It is based on least-squares in-plane assumed strains, assumed natural transverse shear and normal strains. The singular value decomposition (SVD) is used to define local (integration-point) orthogonal frames-of-reference solely from the Jacobian matrix. The complete finite-strain formulation is derived and tested. Assumed strains obtained from least-squares fitting are an alternative to the enhanced-assumed-strain (EAS) formulations and, in contrast with these, the result is an element satisfying the Patch test. There are no additional degrees-of-freedom, as it is the case with the enhanced-assumed-strain case, even by means of static condensation. Least-squares fitting produces invariant finite strain elements which are shear-locking free and amenable to be incorporated in large-scale codes. With that goal, we use automatically generated code produced by AceGen and Mathematica. All benchmarks show excellent results, similar to the best available shell and hybrid solid elements with significantly lower computational cost.

Survey of demographic and phenotypic data of local pig breeds of Treasure Project

Local genetic resources represent an important reservoir of biodiversity in the animal sector. Sustainable use of these resources can be an important source of income for farmers taking advantage of the peculiar characteristics of their products. The different European local pig breeds have a different level of knowledge of their characteristics both at demographic and phenotypic level. This information, however, is fundamental to the management of the breeds and represent one of the first steps in a project for the enhancement of production. This paper reports the results of a survey on the demographic and phenotypic characterization of the 20 European local pig breeds involved in the TREASURE* project. The first part of the survey shows, for all populations involved, the available demographic parameters, the structure of the breed (i.e. number of males, females and replacements), the main morphological features, the reproductive information as well as some additional information collected at herd-level (i.e. temperament, holding, mating practices). A second module reports the results related to the origins and development of the breeds, to market characteristics and the presence and distribution of niche products. The survey concludes with a module related to the specific characteristics of each breed and the management of the same in relation to food and the environment. The survey is the starting point of the genetic and productive characterization of the breeds involved that are future actions of the TREASURE project.

Valuing landscape identity of local inhabitants through a tourism discourse

Landscape, people and identity Landscape is about the interaction of a place or an area with people, which is reflected in the material interaction of people creating or shaping the landscape as well as in their mental perception, valuation and symbolic meaning of that landscape (Cosgrove 1998). This mutual and dynamic interaction forms the fundamental principle of the concept of landscape identity. Landscape identity has been described in scientific literature as a concept to bridge the physical, social and cultural aspects of landscapes. Also policy documents related with landscape and heritage (for example the UNESCO World Heritage Convention, the European Landscape Convention, the Faro Convention) are mentioning identity and landscape as key concepts. In those examples, landscape identity can refer to either the landscape itself - its features that makes the landscape unique (thus the landscape character), or to the social and personal construction. However, there is an interdependency between those two perspectives that needs to be conceptualised. Landscape identity is therefore defined as the multiple ways and dynamic relation between landscape and people (Loupa Ramos et al 2016).

Training and Updating of Education Boards in Indigenous Schools of Rural Areas: Strengthening Local Education Management

Education management in the schools of indigenous rural areas faces a number of difficulties to implement and comply with the guidelines and requirements of the laws related to budgetary management of resources allocated to Education or Administrative Boards. In addition to being located in scattered rural areas, far from the municipal heads and regional offices of the Ministry of Public Education, one of the main obstacles is that all regulations, laws and guidelines are written in Spanish, and there is people, in this indigenous rural communities, who do not speak, write, read or understand this language. This puts them at an enormous disadvantage, which has a direct impact on the indigenous children’s right to education.

Determination of α-Amylase Enzyme Activity and Blood Glucose Level in Local Duck

A α-amylase is included in hydrolase’s enzyme (E.C. 3.2.1.3), which catalyzed the breaking down of α-1,3-glycosidic bound on amylase chain and produced glucose as end product. In mammalian and poultry, α-amylase enzyme has a function as starch breaking down or changed glycogen to glucose. It was used as energy resource in the body. A α-amylase enzyme is protein that resulted in expression from one or several genes, so that has various characteristics among individual. To study the existence and the characteristic of α-amylase enzyme, therefore it has been conducted a research about the connection of α-amylase enzyme unit number  with glucose content in Tegal, Magelang and Mojosari duck blood (each of them consisted of 28 birds). This research used Completely Randomized Design (CRD) with seven replicates for each treatment. The result research showed that either the unit number of α-amylase enzyme activity or glucose content in these local breed of duck has a highly significant different (P<0.01). This result showed that genetic factor (breed of duck) has influenced either enzyme unit number or their catalytic activity on substrate, so the capability to form blood glucose inter breed of duck also different. It was suggested that their enzyme characteristics have strong connection with the sequence of amino acid as α-amylase enzyme protein composer, which was the result of gene expression. From the result, it was concluded that the unit number and catalytic activity of α-amylase enzyme and blood glucose content in the breed of local duck was affected by genetic factor (breed of duck). (Animal Production 5(1): 50-56 (2003) Key words: Enzyme, K-Amylase, Blood, Glucose, Duck

Texture for Script identification

The problem of determining the script and language of a document image has a number of important applications in the field of document analysis, such as indexing and sorting of large collections of such images, or as a precursor to optical character recognition (OCR). In this paper, we investigate the use of texture as a tool for determining the script of a document image, based on the observation that text has a distinct visual texture. An experimental evaluation of a number of commonly used texture features is conducted on a newly created script database, providing a qualitative measure of which features are most appropriate for this task. Strategies for improving classification results in situations with limited training data and multiple font types are also proposed.

Smoothing a Discrete Hazard Function for the Number of Patients Colonized with Methicillin-Resistance Staphylococcus Aureus in an Intensive Care Unit

A new method for estimating the time to colonization of Methicillin-resistant Staphylococcus Aureus (MRSA) patients is developed in this paper. The time to colonization of MRSA is modelled using a Bayesian smoothing approach for the hazard function. There are two prior models discussed in this paper: the first difference prior and the second difference prior. The second difference prior model gives smoother estimates of the hazard functions and, when applied to data from an intensive care unit (ICU), clearly shows increasing hazard up to day 13, then a decreasing hazard. The results clearly demonstrate that the hazard is not constant and provide a useful quantification of the effect of length of stay on the risk of MRSA colonization which provides useful insight.