This research seeks to explore the complexity of human-land relations in the Aspre, with respect to land degradation. It is argued that in human modified environments, such as this Mediterranean-Pyrenean borderland, nature and culture cannot be meaningfully studied apart. Consequently issues of land degradation must be situated within the broader context of socio-natural interaction. Such a study cannot be approached solely from a natural or social science perspective; what is required, and what has been developed in this research, is a transdisciplinary methodology whereby natural phenomena are situated within their historical and socio-cultural context. Central to that context is the need to position the system within a long term evolutionary dynamic, thus allowing us to view the system in process, rather than as a synchronic present day snapshot. Within this 'longue duree' temporal and spatial scales are seen to be critical. It is argued that land degradation is at root a perceptual issue, thus perception and cognition are seen as critically important in this study. The core field work acts to expose both the physical and social identities of the Aspre, and the multiple perceptions of land degradation held by its inhabitants. The research identifies a series of 'perceptual filters' through which the environment of the Aspre is experienced, and by means of which meaning is negotiated. The recognition of the multiple environmental perceptions and plural rationalities is of crucial importance when contemplating the possible future pathways open to the Aspre, with respect to sustainable futures. What emerges from this research is a redefinition of land degradation in the Aspre, from that of a purely physical issue, to the realization that what we are dealing with are changing social identities within changing landscapes.

No description available.

Many drug-resistant mechanisms in Candida albicans (C. albicans), a clinical important fungal pathogen, have been well characterized. However, few studies investigated the emergence of drug resistance from the evolutionary perspective and little is known about the evolutionary trajectories during the adaptation to the drug. Here, we examined the evolutionary dynamics of C. albicans both in the presence and absence of fluconazole, a first line drug, using the visualizing evolution in real-time (VERT) method. Evolutionary dynamics of replicate C. albicans populations, either in the presence or absence of fluconazole, were determined and adaptive mutants arose in the populations were systematically isolated using the VERT method. Drug susceptibility assays were performed to measure the fluconazole minimum inhibitory concentration (MIC) for the adaptive isolates from drug-exposed populations. Analysis of the evolutionary dynamics revealed that mutations arose more frequently in the presence of the drug compared to the absence of the drug and the drug-resistant mutations occurred in independent lineages, suggesting a heterogeneous nature of the populations during the adaptation. In addition, fitness effects were evaluated for each adaptive mutant both in the presence and absence of drug and we found most of them gained significant increase in the drug resistance without a fitness cost in the absence of the drug. Interestingly, the aneuploidy and gross chromosomal rearrangements, common drug-resistant mechanisms, were not responsible for the increased resistance to fluconazole of most adaptive isolates, suggesting single-nucleotide polymorphisms (SNPs) or other stable unknown chromosomal rearrangements may contribute to the increased drug resistance.

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Moral contractarianism, as demonstrated in the work of David Gauthier, is an attempt to derive moral principles from the non-moral premises of rational choice. However, this contractarian enterprise runs aground because it is unable to show that agents would commit to norms in a fairly realistic world where knowledge is limited in space and time, where random shocks are likely, and where agents can be arbitrarily differentiated from one another. In a world like this, agents will find that the most "rational" strategy is to behave "non-rationally," imitating the behavior of others in their vicinity and preserving a limited sort of ignorance.

Orientador: Claudia Marcia Aparecida Carareto / Banca: Cristina Vieira / Banca: Ricardo de Marco / Banca: Vera Lúcia da Silva Valente Gaiesky / Banca: Fátima Pereira de Souza / Resumo: Os elementos de transposição (TEs) são sequências de DNA com a capacidade de catalisar seu próprio movimento e de se inserir em novas regiões do genoma. Desde que TEs são fonte de variação genética, os estudos da dinâmica dessas sequências permitem a compreensão da evolução do genoma do hospedeiro. Na presente Tese foi estudado o retroposon Helena, um LINE que se encontra em diferentes estágios do seu ciclo evolutivo e, portanto, um bom modelo para estudos da dinâmica evolutiva de TEs. Por meio de análises de Bioinformática de 12 espécies de Drosophila que têm o genoma sequenciado, verificou-se que Helena varia de estágios em que se encontra ao menos uma cópia completa e ativa (D. mojavensis), ou putativamente completas, mas inativas (D. simulans), a estados em que as cópias são altamente degeneradas (D. yakuba, D. erecta, D. ananassae e D. virilis) ou ausentes (D. pseudoobscura, D. persimilis, D. willistoni e D. grimshawi). As análises filogenéticas mostram que esse TE estava presente no ancestral comum do gênero Drosophila e tem sido transmitido verticalmente nas linhagens derivadas, e perdido em algumas. Desde que uma cópia completa, e altamente ativa, foi observada apenas no genoma de D. mojavensis, estudamos em detalhe a região 5' dessa cópia e verificamos, por meio de análises in vitro com o uso de um gene reporter, a presença de promotor interno para a Pol II que se encontra associado com modificações epigenéticas de histonas tanto permissivas, típicas de eucromatina, onde a transcrição pode ocorrer (H3K4me2), como repressivas, típicas de heterocromatina facultativa (H3K27me3). Esses "domínios bivalentes", juntamente com a baixa associação de H3K9me2 (típica de heterocromatina constitutiva) indicam que Helena pode ser expresso em resposta a estímulos adequados. Análises preliminares do estudo da atividade transposicional... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: The transposable elements (TEs) are DNA sequences capable of catalyze its own movement and to enter into new regions of the genome. Since TEs are source of genetic variation, studies on their dynamics allow the understanding of the genome evolution. In the present study we studied Helena, a LINE element that is at different stages of its evolutionary cycle and therefore, it is a good model for studies of TEs evolutionary dynamics. Through bioinformatics analysis of 12 Drosophila species which have their genomes sequenced, we found Helena in different stages of its evolutionary cycle, that varies of at least one full active copy (D. mojavensis) an putatively complete copy, but inactive (D. simulans) to highly degenerate (D. yakuba, D. erecta, D. ananassae and D. virilis) or absent (D. pseudoobscura, D. persimilis, D. willistoni and D. grimshawi) sequences. Phylogenetic analysis showed that Helena was present in the common ancestor of the Drosophila genus and has been vertically transmitted in derived lineages, but lost on some of them. Since a complete highly active copy was observed only in D. mojavensis, we studied in more detail its 5' end region. Through in vitro assays using a reporter gene we verified the presence of internal promoter for Pol II that is associated with epigenetic histone modifications for permissive (could induce transcription (H3K4me2)) and repressive heterochromatin (facultative heterochromatin (H3K27me3)). These "bivalent marks" and poor association to H3K9me2 (constitutive heterochromatin) indicate that Helena can be expressed in response to specific stimulus. The preliminary analysis of Helena transposicional activity in vivo (by injection of complete copy in D. melanogaster) showed integration and activity of this TE in the transgenic lines. A study of BS element, a TE closely related to Helena, showed that the evolutionary dynamics of both... (Complete abstract click electronic access below) / Doutor

Moral contractarianism, as demonstrated in the work of David Gauthier, is an attempt to derive moral principles from the non-moral premises of rational choice. However, this contractarian enterprise runs aground because it is unable to show that agents would commit to norms in a fairly realistic world where knowledge is limited in space and time, where random shocks are likely, and where agents can be arbitrarily differentiated from one another. In a world like this, agents will find that the most "rational" strategy is to behave "non-rationally," imitating the behavior of others in their vicinity and preserving a limited sort of ignorance.

Made available in DSpace on 2014-06-11T19:32:15Z (GMT). No. of bitstreams: 0 Previous issue date: 2011-02-16Bitstream added on 2014-06-13T19:21:45Z : No. of bitstreams: 1 granzotto_a_dr_sjrp.pdf: 1610042 bytes, checksum: 27692bc1e2301a5aee3ec1445fded2d8 (MD5) / Os elementos de transposição (TEs) são sequências de DNA com a capacidade de catalisar seu próprio movimento e de se inserir em novas regiões do genoma. Desde que TEs são fonte de variação genética, os estudos da dinâmica dessas sequências permitem a compreensão da evolução do genoma do hospedeiro. Na presente Tese foi estudado o retroposon Helena, um LINE que se encontra em diferentes estágios do seu ciclo evolutivo e, portanto, um bom modelo para estudos da dinâmica evolutiva de TEs. Por meio de análises de Bioinformática de 12 espécies de Drosophila que têm o genoma sequenciado, verificou-se que Helena varia de estágios em que se encontra ao menos uma cópia completa e ativa (D. mojavensis), ou putativamente completas, mas inativas (D. simulans), a estados em que as cópias são altamente degeneradas (D. yakuba, D. erecta, D. ananassae e D. virilis) ou ausentes (D. pseudoobscura, D. persimilis, D. willistoni e D. grimshawi). As análises filogenéticas mostram que esse TE estava presente no ancestral comum do gênero Drosophila e tem sido transmitido verticalmente nas linhagens derivadas, e perdido em algumas. Desde que uma cópia completa, e altamente ativa, foi observada apenas no genoma de D. mojavensis, estudamos em detalhe a região 5’ dessa cópia e verificamos, por meio de análises in vitro com o uso de um gene reporter, a presença de promotor interno para a Pol II que se encontra associado com modificações epigenéticas de histonas tanto permissivas, típicas de eucromatina, onde a transcrição pode ocorrer (H3K4me2), como repressivas, típicas de heterocromatina facultativa (H3K27me3). Esses “domínios bivalentes”, juntamente com a baixa associação de H3K9me2 (típica de heterocromatina constitutiva) indicam que Helena pode ser expresso em resposta a estímulos adequados. Análises preliminares do estudo da atividade transposicional... / The transposable elements (TEs) are DNA sequences capable of catalyze its own movement and to enter into new regions of the genome. Since TEs are source of genetic variation, studies on their dynamics allow the understanding of the genome evolution. In the present study we studied Helena, a LINE element that is at different stages of its evolutionary cycle and therefore, it is a good model for studies of TEs evolutionary dynamics. Through bioinformatics analysis of 12 Drosophila species which have their genomes sequenced, we found Helena in different stages of its evolutionary cycle, that varies of at least one full active copy (D. mojavensis) an putatively complete copy, but inactive (D. simulans) to highly degenerate (D. yakuba, D. erecta, D. ananassae and D. virilis) or absent (D. pseudoobscura, D. persimilis, D. willistoni and D. grimshawi) sequences. Phylogenetic analysis showed that Helena was present in the common ancestor of the Drosophila genus and has been vertically transmitted in derived lineages, but lost on some of them. Since a complete highly active copy was observed only in D. mojavensis, we studied in more detail its 5' end region. Through in vitro assays using a reporter gene we verified the presence of internal promoter for Pol II that is associated with epigenetic histone modifications for permissive (could induce transcription (H3K4me2)) and repressive heterochromatin (facultative heterochromatin (H3K27me3)). These “bivalent marks” and poor association to H3K9me2 (constitutive heterochromatin) indicate that Helena can be expressed in response to specific stimulus. The preliminary analysis of Helena transposicional activity in vivo (by injection of complete copy in D. melanogaster) showed integration and activity of this TE in the transgenic lines. A study of BS element, a TE closely related to Helena, showed that the evolutionary dynamics of both... (Complete abstract click electronic access below)

Evolutionary dynamics arise from the interplay of mutation and selection. Fundamentally, these two processes operate at different levels: Mutations modify genetic information (the genotype), which is passed from parent to offspring. Selection is triggered by variation in reproductive success, which depends on the physical properties (the phenotype) of an organism and its environment. Thus the genotype-phenotype map determines if and how mutations can lead to selection. The aim of this dissertation is to incorporate this map explicitly into a theoretical description of evolutionary dynamics. The first part of the analysis presented here is concerned with the static properties of simple models of these maps, which are studied using exhaustive enumeration. The two most important observations are phenotypic bias – some phenotypes are realized by many more genotypes than most other phenotypes – and the existence of neutral spaces – genotypes with the same phenotype can often be reached from each other by single mutational steps. The remainder of the dissertation provides a theoretical description of evolutionary dynamics on and across neutral spaces. Two different mean-field approximations lead to simple analytic results for the first discovery of alternative phenotypes, highlighting the importance of phenotypic bias: Rare phenotypes are hard to find by evolutionary search. These results are used to discuss the relationship of robustness, the ability to withstand mutational change, and evolvability, the ability to create variation through mutation. Several types of fluctuations beyond the mean-field limit are studied, both theoretically and in simulations. The discrete structure of genotype spaces can lead to strong correlations in the spectra of phenotypes produced, increasing the probability that a particular phenotype is fixed in the population quickly after its discovery. Structural correlations between genotypes can increase the effect of phenotypic bias, while the qualitative features of the mean-field description remain valid. All these results highlight that neutral spaces impact evolutionary dynamics in many non-trivial ways, in particular by favouring phenotypes of high accessibly, but comparably low fitness over those phenotypes that are highly fit, but very hard to discover.

Self-assembly --- by which ordered structures spontaneously emerge from disordered components --- and biological evolution --- by which Charles Darwin's "endless forms most beautiful" have emerged from the simple chemistry of prehistoric Earth --- may both be pictured as search processes on high-dimensional landscapes, defined respectively by the concepts of energy and fitness. The rich dynamics of these search processes will be studied in order to explain biologically observed features of self-assembly and evolution. This study will introduce and analyse the behaviour of a model for a paradigmatic example of self-assembly, the icosahedral virus capsid, a symmetric structure formed from interacting protein subunits. Results for the thermodynamics and kinetics of model virus assembly will be presented, and the model will be extended to include complicating effects such as different subunit types and cellular crowding. A more general formalism for analysing self-assembling systems will then be introduced and used to suggest a well-defined complexity measure of universal applicability to self-assembled structures. The biological evolution of simple self-assembling structures will be studied using genetic algorithms. The suitability of this modelling approach and its dependence on the many parameters involved will be investigated. Several active areas of enquiry in the field of evolution, including the evolution of complexity, the presence and effect of neutral networks, fluctuations in evolutionary time series and the emergence of symmetry will be investigated within this framework. Throughout this study, we will use the picture of "exploration and exploitation": different approaches to performing optimisation on an unknown landscape, essentially corresponding to a random search and a hill-climbing approach respectively . We will show that, both in self-assembly and evolution, finding an optimal combination of these two approaches gives rise to many of the observed features in this study.