Ataxia-telangiectasia-mutated (ATM) and NBS1-dependent phosphorylation of Chk1 on Ser-317 in response to ionizing radiation

In mammals, the ATM (ataxia-telangiectasia-mutated) and ATR (ATM and Rad3-related) protein kinases function as critical regulators of the cellular DNA damage response. The checkpoint functions of ATR and ATM are mediated, in part, by a pair of checkpoint effector kinases termed Chk1 and Chk2. In mammalian cells, evidence has been presented that Chk1 is devoted to the ATR signaling pathway and is modified by ATR in response to replication inhibition and UV-induced damage, whereas Chk2 functions primarily through ATM in response to ionizing radiation (IR), suggesting that Chk2 and Chk1 might have evolved to channel the DNA damage signal from ATM and ATR, respectively. We demonstrate here that the ATR-Chk1 and ATM-Chk2 pathways are not parallel branches of the DNA damage response pathway but instead show a high degree of cross-talk and connectivity. ATM does in fact signal to Chk1 in response to IR. Phosphorylation of Chk1 on Ser-317 in response to IR is ATM-dependent. We also show that functional NBS1 is required for phosphorylation of Chk1, indicating that NBS1 might facilitate the access of Chk1 to ATM at the sites of DNA damage. Abrogation of Chk1 expression by RNA interference resulted in defects in IR-induced S and G(2)/M phase checkpoints; however, the overexpression of phosphorylation site mutant (S317A, S345A or S317A/S345A double mutant) Chk1 failed to interfere with these checkpoints. Surprisingly, the kinase-dead Chk1 (D130A) also failed to abrogate the S and G(2) checkpoint through any obvious dominant negative effect toward endogenous Chk1. Therefore, further studies will be required to assess the contribution made by phosphorylation events to Chk1 regulation. Overall, the data presented in the study challenge the model in which Chk1 only functions downstream from ATR and indicate that ATM does signal to Chk1. In addition, this study also demonstrates that Chk1 is essential for IR-induced inhibition of DNA synthesis and the G(2)/M checkpoint.

Measuring the significance of inconsistency in the Viewpoints framework

Measuring inconsistency is crucial to effective inconsistency management in software development. A complete measurement of inconsistency should focus on not only the degree but also the significance of inconsistency. However, most of the approaches available only take the degree of inconsistency into account. The significance of inconsistency has not yet been given much needed consideration. This paper presents an approach for measuring the significance of inconsistency arising from different viewpoints in the Viewpoints framework. We call an individual set of requirements belonging to different viewpoints a combined requirements collection in this paper. We argue that the
significance of inconsistency arising in a combined requirements collection is closely associated with global priority levels of requirements involved in the inconsistency. Here we assume that the global priority level of an individual requirement captures the relative importance of every viewpoint including this requirement as well as the local priority level of the requirement within the viewpoint. Then we use the synthesis of global priority levels of all the requirements in a combined collection to measure the significance of the
collection. Following this, we present a scoring matrix function to measure the significance of inconsistency in an inconsistent combined requirements collection, which describes the contribution made by each subset of the requirements collection to the significance of the set of requirements involved in the inconsistency. An ordering relationship between inconsistencies of two combined requirements collections, termed more significant than, is also presented by comparing their significance scoring matrix functions. Finally, these techniques were implemented in a prototype tool called IncMeasurer, which we developed as a proof of concept.

PCR amplification of short tandem repeat sequences allows serial studies of chimaerism/engraftment following BMT in rodents

Animal models of bone marrow transplantation (BMT) allow evaluation of new experimental treatment strategies. One potential strategy involves the treatment of donor marrow with ultra-violet B light to allow transplantation across histocompatibility boundaries without an increase in graft rejection or graft-versus-host disease. A major requirement for a new experimental protocol, particularly if it involves manipulation of the donor marrow, is that the manipulated marrow gives rise to long-term multilineage engraftment. DNA based methodologies are now routinely used by many centres to evaluate engraftment and degree of chimaerism post-BMT in humans. We report the adaptation of this methodology to the serial study of engraftment in rodents. Conditions have been defined which allow analysis of serial tail vein samples using PCR of short tandem repeat sequences (STR-PCR). These markers have been used to evaluate the contribution of ultraviolet B treated marrow to engraftment following BMT in rodents without compromising the health of the animals under study. Chimaerism data from sequential tail vein samples and bone marrow from selected sacrificed animals showed excellent correlation, thus confirming the validity of this approach in analysing haemopoietic tissue. Thus the use of this assay may facilitate experimental studies in animal BMT.

Microstructure design of Titanate-based electroceramics

Electrocerâmicos são uma classe de materiais avançados com propriedades eléctricas valiosas para aplicações. Estas propriedades são geralmente muito dependentes da microestrutura dos materiais. Portanto, o objectivo geral deste trabalho é investigar o desenho da resposta dieléctrica de filmes espessos obtidos por Deposição Electroforética (EPD) e cerâmicos monolíticos, através do controlo da evolução da microestrutura durante a sinterização de electrocerâmicos à base de titanatos. Aplicações sem fios na indústria microelectrónica e de comunicações, em rápido crescimento, tornaram-se um importante mercado para os fabricantes de semicondutores. Devido à constante necessidade de miniaturização, redução de custos e maior funcionalidade e integração, a tecnologia de filmes espessos está a tornar-se uma abordagem de processamento de materiais funcionais cada vez mais importante. Uma técnica adequada neste contexto é EPD. Os filmes espessos resultantes necessitam de um passo subsequente de sinterização que é afectada pelo substrato subjacente, tendo este um forte efeito sobre a evolução da microestrutura. Relacionado com a miniaturização e a discriminação do sinal, materiais dieléctricos usados como componentes operando a frequências das microondas em aplicações na industria microelectrónica de comunicações devem apresentar baixas perdas dieléctricas e elevadas permitividade dieléctrica e estabilidade com a temperatura. Materiais do sistema BaO-Ln2O3- TiO2 (BLnT: Ln = La ou Nd), como BaLa4Ti4O15 (BLT) e Ba4.5Nd9Ti18O54 (BNT), cumprem esses requisitos e são interessantes para aplicações, por exemplo, em estações de base para comunicações móveis ou em ressonadores para telefones móveis, onde a miniaturização dos dispositivos é muito importante. Por sua vez, o titanato de estrôncio (SrTiO3, STO) é um ferroeléctrico incipiente com constante dieléctrica elevada e baixas perdas, que encontra aplicação em, por exemplo, condensadores de camada interna, tirando partido de fronteiras de grão altamente resistivas. A dependência da permitividade dieléctrica do campo eléctrico aplicado torna este material muito interessante para aplicações em dispositivos de microondas sintonizáveis. Materiais à base de STO são também interessantes para aplicações termoeléctricas, que podem contribuir para a redução da actual dependência de combustíveis fósseis por meio da geração de energia a partir de calor desaproveitado. No entanto, as mesmas fronteiras de grão resistivas são um obstáculo relativamente à eficiência do STO para aplicações termoeléctricas. Para além do efeito do substrato durante a sinterização constrangida, outros factores, como a presença de fase líquida, a não-estequiometria ou a temperatura de sinterização, afectam significativamente não apenas a microestrutura dos materiais funcionais, mas também a sua resposta dieléctrica. Se adequadamente compreendidos, estes factores podem ser intencionalmente usados para desenhar a microestrutura dos electrocerâmicos e, desta forma, as suas propriedades dieléctricas. O efeito da não-estequiometria (razão Sr/Ti 0.995-1.02) no crescimento de grão e resposta dieléctrica de cerâmicos de STO foi investigado neste trabalho. A mobilidade das fronteiras de grão aumenta com a diminuição da razão Sr/Ti. A resistividade do interior dos grãos e das fronteiras de grão é sistematicamente diminuída em amostras não-estequiométricas de STO, em comparação com o material estequiométrico. O efeito é muito mais forte para as fronteiras de grão do que para o seu interior. Dependências sistemáticas da não-estequiometria foram também observadas relativamente à dependência da condutividade da temperatura (muito mais afectada no caso da contribuição das fronteiras de grão), à capacitância do interior e fronteiras de grão e à espessura das fronteiras de grão. Uma anomalia no crescimento de grão em cerâmicos de STO ricos em Ti foi também observada e sistematicamente analisada. Foram detectadas três descontinuidades na dependência do tipo Arrhenius do crescimento de grão relativamente à temperatura com diminuições no tamanho de grão a temperaturas em torno de 1500, 1550 e 1605 °C. Além disso, descontinuidades semelhantes foram também observadas na dependência da energia de activação relativamente à condutividade das fronteiras de grão e na espessura das fronteiras de grão, avaliadas por Espectroscopia de Impedância. Estas notáveis coincidências suportam fortemente a formação de diferentes complexos de fronteira de grão com transições entre os regimes de crescimento de grão observados, que podem ser correlacionados com diferentes mobilidades de fronteira de grão e propriedades dieléctricas. Um modelo é sugerido, que se baseia na diminuição da fase líquida localizada nas fronteiras de grão, como o aumento da temperatura de sinterização, um cenário compatível com um fenómeno de solubilidade retrógrada, observado anteriormente em metais e semicondutores, mas não em cerâmicos. A EPD de filmes espessos de STO em substratos de folha de Pt e a sinterização constrangida dos filmes fabricados foram também preliminarmente tratadas. Filmes espessos de STO foram depositados com êxito por EPD sobre substratos de Pt e, depois de sinterizados, atingiram densidades elevadas. Um aumento da densificação e do tamanho de grão assim como o alargamento da distribuição de tamanho do grão foram observados com a diminuição da razão Sr/Ti, tal como anteriormente observado em amostras cerâmicas. Grãos equiaxiados foram observados para todas as composições, mas um certo grau de anisotropia na orientação dos poros foi detectado: os poros revelaram uma orientação vertical preferencial. Este trabalho focou-se também na sinterização constrangida do sistema BLnT (Ln = La ou Nd), nomeadamente de filmes espessos de BLT e BNT sobre substratos de folha de platina, e na relação do desenvolvimento de anisotropia microestrutural com as propriedades dieléctricas. As observações durante a sinterização constrangida foram comparadas com cerâmicos monolíticos equivalentes sinterizados livremente. Filmes espessos de BLnT (Ln = La ou Nd) com elevada densidade foram obtidos por EPD e subsequente sinterização constrangida. A anisometria cristalográfica do material em conjunto com um passo de sinterização constrangida resultou em grãos alongados e microestruturas anisotrópicas. O efeito do stress do substrato durante a sinterização constrangida originou graus mais elevados de anisotropia (grãos e poros alongados e orientação preferencial, bem como textura cristalográfica) nos filmes sinterizados relativamente aos cerâmicos equivalentes sinterizados livremente, não obstante o estado equivalente das amostras em verde. A densificação dos filmes de BLnT (Ln = La ou Nd) é retardada em comparação com os cerâmicos, mas depois de longos tempos de sinterização densidades semelhantes são obtidas. No entanto, em oposição a observações na sinterização constrangida de outros sistemas, o crescimento do grão em filmes de BLnT (Ln = La ou Nd) é favorecido pelo constrangimento causado pelo substrato. Além disso, grãos e poros alongados orientados paralelamente ao substrato foram desenvolvidos durante a sinterização constrangida de filmes espessos. Verificou-se uma forte correlação entre a evolução de grãos e poros, que começou assim que o crescimento do grão se iniciou. Um efeito da tensão do substrato no aumento do crescimento de grão, bem como um forte “Zener pinning”, origina microestruturas altamente texturizadas, o que também é observado a nível cristalográfico. Efeitos marcantes da anisotropia microestrutural foram também detectados nas propriedades dieléctricas dos filmes de BLnT (Ln = La ou Nd). Juntamente com o aumento da razão de aspecto dos grãos, do factor de orientação e do grau de textura cristalográfica, a permitividade relativa é ligeiramente diminuída e o coeficiente de temperatura da permitividade evolui de negativo para positivo com o aumento do tempo isotérmico de sinterização. Este trabalho mostra que a não-estequiometria pode ser usada para controlar a mobilidade das fronteiras de grão e, portanto, desenhar a microestrutura e as propriedades dieléctricas de electrocerâmicos à base de STO, com ênfase nas propriedades das fronteiras de grão. O papel da não-estequiometria no STO e dos complexos de fronteira de grão no desenvolvimento microestrutural é discutido e novas oportunidades para desenhar as propriedades de materiais funcionais são abertas. As observações relativamente à sinterização constrangida apontam para o efeito de tensões mecânicas desenvolvidas devido ao substrato subjacente no desenvolvimento da microestrutura de materiais funcionais. É assim esperado que a escolha adequada de substrato permitia desenhar a microestrutura de filmes espessos funcionais com desempenho optimizado. “Stress Assisted Grain Growth” (SAGG) é então proposto como uma técnica potencial para desenhar a microestrutura de materiais funcionais, originando microestruturas anisotrópicas texturizadas com propriedades desejadas.

The rise and demise of a book-review magazine interpreting the cultural work of Books in Canada (1971-2008)

This interdisciplinary study examines the contribution that a book-review magazine makes to the cultural identity of its readers. It is the result of reflections on the cultural work of Books in Canada , on whether or not this periodical was a cultural worksite and if that is the case how it performed that cultural work. In addition, it interrogates factors that may have contributed to the magazine's demise. The study affirms that Books in Canada, a cultural enterprise from 1971 to 2008, mirrored and helped to shape book and literary culture in Canada through its circulation, through the personalities of its editors, through its front covers and through its reviewers and their reviews. Furthermore, it proposes that the demise of the enterprise was due to a combination of factors. The study begins with an introduction to book reviewing and special-interest magazines. Chapter I examines the interplay between selected visual and textual contents published in Books in Canada in its founding years. These components reflected and helped to fuel the cultural nationalism that was sweeping Canada subsequent to the 1967 World's Fair in Montreal. There were also persistent rumours and comments about the magazine that caused certain"cracks in the foundation" to appear. Chapter II compares the aims and editorial challenges of Val Clery, founder of Books in Canada , with those of Adrien Thério, founder of Lettres québécoises, and of the editors of the magazines' twentieth-anniversary issues, Paul Stuewe in the case of the former and André Vanasse in the case of the latter. Evidence in the content of the magazine, editorial and otherwise, indicated that the"contracts" that the editors made with their readers over the years were similar, to reflect and shape a cultural identity, but the result of their"projects," that is, the nature of those identities, was distinctly different. Evidently then, personal aims, preferences and political leanings of editors can have a major impact on the content of a book-review magazine and thus on the cultural work that it does. Therefore, in Chapter III, I focus on selected contents published during the tenures of two of Books in Canada 's key editors, Paul Stuewe and Olga Stein, in order to understand ways that their choices constituted a form of cultural work. The second part of this chapter moves from an analysis of the cultural work of editors to an examination of the cultural work of reviewers. Here, through a close-reading of a selection of reviews published in Books in Canada, and in other periodicals, I argue that reviewers do cultural work in the way that they negotiate their presence in a review, and in how they signal that presence through lexical choices and through the degree of intellectual interaction that they invite. Intellectual interaction is at the core of Chapter IV.This chapter consists of close readings of some of the"billboards" of the enterprise, that is, the front covers of Books in Canada , in order to show how these important components do cultural work by requiring readers to make an intellectual leap from image to text. Chapter V suggests that book reviews, the company's"bills of goods," do cultural work in much the same way as the paratexts of a book. One of my own reviews is offered as a case-study along with a number of other reviews of how central components of a book-review magazine do cultural work through the illocutionary force of their sentences. The first part of Chapter VI, the final chapter, measures the legacy of the magazine, in particular, the annual Books in Canada First Novel Award. Created in 1976, this prize is awarded to the author of the novel judged by a Books in Canada prize committee to be the best first novel in English of the year. The second part of Chapter VI sheds light on factors that may have contributed to the closure of the enterprise, including the copyright uproar that accompanied the agreement that Adrian Stein, publisher of Books in Canada and Olga Stein's husband, made in 2001 with the online book merchant, Amazon.com. Furthermore, this penultimate section of the study suggests that one of the most important factors in the magazine's demise was the decision by the Steins to exploit their position as owners, publisher, and editor of a book-review periodical, a government-subsidized one at that, to publish their own lengthy pre-trial defense of Conrad Black. The chapter then zooms back from the particular to the general with a broader consideration of the impact of technology and globalization on the book industry and on the ability of Books in Canada to survive in any form, print or digital.

Development and standardization of a protocol for sperm cryopreservation of two important commercial oyster species

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

Three-level energy decoupling : energy decoupling at the primary, final and useful levels of energy use

Tese de doutoramento, Sistemas Sustentáveis de Energia, Universidade de Lisboa, Faculdade de Ciências, 2015

Trophic ecology of jumbo squid and predatory fishes in the Northern Humboldt Current System

This work provides a contribution to a better understanding of the trophic ecology of important predators in the Northern Humboldt Current System, the jack mackerel (Trachurus murphyi), the chub mackerel (Scomber japonicus) and the jumbo squid (Dosidicus gigas) by the characterization of the highly variable feeding patterns of these species at different spatiotemporal scales. We provided new knowledge on the comparative trophic behaviour of these species, defined as opportunistic in previous investigations. For that purpose we applied a variety of statistical methods to an extensive dataset of 27,188 non-empty stomachs. We defined the spatial organization of the forage fauna of these predators and documented changes in prey composition according to predators’ size and spatiotemporal features of environment. Our results highligh the key role played by the dissolved oxygen. We also deciphered an important paradox on the jumbo squid diet: why do they hardly forage on the huge anchovy (Engraulis ringens) biomass distributed of coastal Peru? We showed that the shallow oxygen minimum zone present off coastal Peru could hamper the co-occurrence of jumbo squids and anchovies. In addition, we proposed a conceptual model on jumbo squid trophic ecology including the ontogenetic cycle, oxygen and prey availability. Moreover we showed that the trophic behaviour of jack mackerel and chub mackerel is adapted to forage on more accessible species such as for example the squat lobster Pleurocondes monodon and Zoea larvae. Besides, both predators present a trophic overlap. But jack mackerel was not as oracious as chub mackerel, contradictorily to what was observed by others authors. Fish diet presented a high spatiotemporal variability, and the shelf break appeared as a strong biogeographical frontier. Diet composition of our fish predators was not necessarily a consistent indicator of changes in prey biomass. El Niño events had a weak effect on the stomach fullness and diet composition of chub mackerel and jack mackerel. Moreover, decadal changes in diet diversity challenged the classic paradigm of positive correlation between species richness and temperature. Finally, the global patterns that we described in this work, illustrated the opportunistic foraging behaviour, life strategies and the high degree of plasticity of these species. Such behaviour allows adaptation to changes in the environment.

Interactions of diploid embryonal carcinoma cells and normal cell mass cells with 2.5 day mouse embryos following aggregation

Spontaneous teratocarcinomas are ovarian or testicular tumors which have their origins in germ cells. The tumors contain a disorganized array of benign differentiated cells as well as an undifferentiated population of malignant stem cells, the embryonal carcinoma or EC cells. These pluripotent stem cells in tissue culture share many properties with the transient pluripotent cells of the early embryo, and might therefore serve as models for the investigation of developmental events ill vitro. The property of EC cells of prime interest in this study is an in vivo phenomenon. Certain EC cell lines are known to be regulated ill vivo and to differentiate normally in association with normal embryonic cells, resulting in chimeric mice. These mice have two genetically distinct cell populations, one of which is derived from the originally malignant EC cells. This has usually been accomplished by injection of the EC cells into the Day 3 blastocyst. In this study, the interactions between earlier stage embryos and EC cells have been tested by aggregating clumps of EC cells with Day 2 embryos. The few previous aggregation studies produced a high degree of abnormality in chimeric embryos, but the EC cells employed had known chromosomal abnormalities. In this study, two diploid EC cell lines (P19 and Pi0) were aggregated with 2.5 day mouse embryos, and were found to behave quite differently in the embryonic environment. P19 containing aggregates generally resorbed early, and the few embryos recovered at midgestation were normal and non-chimeric. Pi0 containing aggregates survived in high numbers to midgestation, and the Pi0 cells were very successful in colonizing the embryo. All these embryos were chimeric, and the contribution by the EC cells to each chimera was very high. However, these heavily chimeric embryos were all abnormal. Blastocyst injection had previously produced some abnormal embryos with high Pl0 contributions in addition to the live born mice, which had lower EC contributions. This study now adds more support to the hypothesis that high EC contributions may be incompatible with normal development. The possibility that the abnormalities were due to the mixing of temporally asynchronous embryonic cell types in the aggregates was tested by aggregating normal pluripotent cells taken from 3.5 day embryos with 2.5 day embryos. Early embryo loss was very high, and histological studies showed that the majority of these embryos died by 6.5 days development. Some embryos escaped this early death such that some healthy chimeras were recovered, in contrast to recovery of abnormal chimeric embryos following Pl0-morula aggregations, and non-chimeric embryos following P19-morula aggregations. This somewhat surprising adverse effect on development following aggregation of normal cell types suggests that there are developmental difficulties associated with the mixing of asynchronous cell types in aggregates. However, the greater magnitude of the adverse effects when the aggregates contained tumor derived cells suggests that EC cells should not be considered the complete equivalent of the pluripotent cells of the early embryo.

Localization of the mechanism of pH-dependent non- photochemical fluorescence quenching in thylakoid membranes

Higher plants have evolved a well-conserved set of photoprotective mechanisms, collectively designated Non-Photochemical Quenching of chlorophyll fluorescence (qN), to deal with the inhibitory absorption of excess light energy by the photosystems. Their main contribution originates from safe thermal deactivation of excited states promoted by a highly-energized thylakoid membrane, detected via lumen acidification. The precise origins of this energy- or LlpH-dependent quenching (qE), arising from either decreased energy transfer efficiency in PSII antennae (~ Young & Frank, 1996; Gilmore & Yamamoto, 1992; Ruban et aI., 1992), from alternative electron transfer pathways in PSII reaction centres (~ Schreiber & Neubauer, 1990; Thompson &Brudvig, 1988; Klimov et aI., 1977), or from both (Wagner et aI., 1996; Walters & Horton, 1993), are a source of considerable controversy. In this study, the origins of qE were investigated in spinach thylakoids using a combination of fluorescence spectroscopic techniques: Pulse Amplitude Modulated (PAM) fluorimetry, pump-probe fluorimetry for the measurement of PSII absorption crosssections, and picosecond fluorescence decay curves fit to a kinetic model for PSII. Quenching by qE (,..,600/0 of maximal fluorescence, Fm) was light-induced in circulating samples and the resulting pH gradient maintained during a dark delay by the lumenacidifying capabilities of thylakoid membrane H+ ATPases. Results for qE were compared to those for the addition of a known antenna quencher, 5-hydroxy-1,4naphthoquinone (5-0H-NQ), titrated to achieve the same degree of Fm quenching as for qE. Quenching of the minimal fluorescence yield, F0' was clear (8 to 130/0) during formation of qE, indicative of classical antenna quenching (Butler, 1984), although the degree was significantly less than that achieved by addition of 5-0H-NQ. Although qE induction resulted in an overall increase in absorption cross-section, unlike the decrease expected for antenna quenchers like the quinone, a larger increase in crosssection was observed when qE induction was attempted in thylakoids with collapsed pH gradients (uncoupled by nigericin), in the absence of xanthophyll cycle operation (inhibited by DTT), or in the absence of quenching (LlpH not maintained in the dark due to omission of ATP). Fluorescence decay curves exhibited a similar disparity between qE-quenched and 5-0H-NQ-quenched thylakoids, although both sets showed accelerated kinetics in the fastest decay components at both F0 and Fm. In addition, the kinetics of dark-adapted thylakoids were nearly identical to those in qEquenched samples at F0' both accelerated in comparison with thylakoids in which the redox poise of the Oxygen-Evolving Complex was randomized by exposure to low levels of background light (which allowed appropriate comparison with F0 yields from quenched samples). When modelled with the Reversible Radical Pair model for PSII (Schatz et aI., 1988), quinone quenching could be sufficiently described by increasing only the rate constant for decay in the antenna (as in Vasil'ev et aI., 1998), whereas modelling of data from qE-quenched thylakoids required changes in both the antenna rate constant and in rate constants for the reaction centre. The clear differences between qE and 5-0H-NQ quenching demonstrated that qE could not have its origins in the antenna alone, but is rather accompanied by reaction centre quenching. Defined mechanisms of reaction centre quenching are discussed, also in relation to the observed post-quenching depression in Fm associated with photoinhibition.

Réintroduire la multifonctionnalité des paysages en zone d’intensification agricole : contribution des approches intégrées en écologie du paysage

Depuis l’avènement de l’agriculture productiviste, les paysages des zones d’intensification agricole des pays industrialisés ont été marqués par la perte sévère de leur diversité et la dégradation de leurs fonctions environnementales, récréatives, esthétiques et sociales. Au moment où la qualité des paysages constitue un facteur clé du dynamisme des collectivités rurales, il devient urgent de développer des stratégies d’aménagement aptes à réintroduire le caractère multifonctionnel de ces paysages. Dans ce contexte, cette thèse propose un éclairage sur les enjeux d’aménagement de ces paysages sous l’angle des approches dialectiques en paysage issues de la Holistic Landscape Ecology. En développant un modèle conceptuel des trajectoires des paysages s’inscrivant dans les approches intégrées en paysage, elle établit une double lecture des dynamiques physico-spatiale et socioculturelle des paysages des zones d’intensification agricole afin d’en arriver à qualifier les écarts entre celles-ci. Pour y parvenir, elle prend appui sur une étude de cas d’un bassin versant agricole du sud du Québec. En puisant tantôt dans l’écologie du paysage, tantôt dans la sociologie du paysage, les résultats de cette thèse soulignent d’une part le poids des forces politiques et économiques dans le façonnement de ces paysages. Mais ils révèlent également le rôle des valorisations paysagères des agriculteurs dans la modulation de ces forces. Plus encore, l’étude des dynamiques socioculturelles révèle une diversité au sein des populations locales au plan des valorisations de ces paysages et des pratiques qui les façonnent qui vient renouveler l’image d’uniformité de ces territoires. Le maintien et l’accentuation de cette diversité apparaissent susceptibles de contribuer significativement à la réintroduction du caractère multifonctionnel des paysages au sein des zones d’intensification agricole. Des pistes concrètes pour l’aménagement concluent cette thèse.

Contribution du globus pallidus lors de la locomotion sous guidage visuel.

Les nombreuses études cliniques sur les maladies affectant les noyaux gris centraux (NGC) ont montré l’importance des déficits moteurs engendrés par un dysfonctionnement de ces structures. La locomotion est particulièrement affectée chez ces patients, ce qui suggère un rôle important des NGC dans le contrôle de celle-ci. En revanche, très peu d’études fondamentales ont enregistré l’activité des neurones des NGC durant la locomotion chez des modèles intacts. Le globus pallidus, en tant qu’une des principales structures de sortie des NGC, constitue une cible idéale pour étudier le signal transmis par les NGC au thalamus et au tronc cérébral. L’objectif de notre étude est de mieux comprendre la contribution que joue le segment externe du globus pallidus (GPe) dans le contrôle de la locomotion sous guidage visuel. Cette étude constitue le premier rapport d’enregistrements de l’activité des neurones du GPe lors de modifications volontaires de la marche sous guidage visuel. Notre hypothèse générale est que le GPe contribue au contrôle de la locomotion, et particulièrement lors des modifications de la marche. Nous avons enregistré l’activité des neurones du GPe de chats au repos, puis marchant sur un tapis et enjambant des obstacles. Nos résultats ont révélé que la plupart des cellules montraient peu de changements lors de la locomotion non-obstruée par rapport au repos. En revanche, la moitié des neurones enregistrés présentaient une modulation significative de leur décharge durant l’enjambement de l’obstacle. Nous avons observé une majorité de ces cellules qui diminuaient leur fréquence et un tiers de neurones qui l’augmentaient pendant le pas modifié, suggérant que le GPe exerce sur le mouvement un contrôle dépendant du contexte, permettant sélectivement l’augmentation ou la diminution de l’activité motrice. De plus, presque toutes les cellules déchargeaient durant la totalité de la phase de balancement du membre antérieur controlatéral, ce qui semble indiquer une contribution du GPe dans le timing et la durée de cette phase. Finalement, la moitié des neurones présentaient un changement réciproque entre la condition de lead et la condition de trail. Ce résultat suggère que le GPe participerait à la sélection d’action du membre lors des modifications de la marche. Nos résultats illustrent la complexité de l’activité du GPe lors de la locomotion sous guidage visuel et ils sont compatibles avec une contribution plus générale au mouvement que celle exercée par le cortex moteur.

Quantitative functional MRI of the Cerebrovascular Reactivity to CO2

Le dioxyde de carbone (CO2) est un résidu naturel du métabolisme cellulaire, la troisième substance la plus abondante du sang, et un important agent vasoactif. À la moindre variation de la teneur en CO2 du sang, la résistance du système vasculaire cérébral et la perfusion tissulaire cérébrale subissent des changements globaux. Bien que les mécanismes exacts qui sous-tendent cet effet restent à être élucidés, le phénomène a été largement exploité dans les études de réactivité vasculaire cérébrale (RVC). Une voie prometteuse pour l’évaluation de la fonction vasculaire cérébrale est la cartographie de la RVC de manière non-invasive grâce à l’utilisation de l’Imagerie par Résonance Magnétique fonctionnelle (IRMf). Des mesures quantitatives et non-invasives de de la RVC peuvent être obtenus avec l’utilisation de différentes techniques telles que la manipu- lation du contenu artériel en CO2 (PaCO2) combinée à la technique de marquage de spin artériel (Arterial Spin Labeling, ASL), qui permet de mesurer les changements de la perfusion cérébrale provoqués par les stimuli vasculaires. Toutefois, les préoccupations liées à la sensibilité et la fiabilité des mesures de la RVC limitent de nos jours l’adoption plus large de ces méthodes modernes de IRMf. J’ai considéré qu’une analyse approfondie ainsi que l’amélioration des méthodes disponibles pourraient apporter une contribution précieuse dans le domaine du génie biomédical, de même qu’aider à faire progresser le développement de nouveaux outils d’imagerie de diagnostique. Dans cette thèse je présente une série d’études où j’examine l’impact des méthodes alternatives de stimulation/imagerie vasculaire sur les mesures de la RVC et les moyens d’améliorer la sensibilité et la fiabilité de telles méthodes. J’ai aussi inclus dans cette thèse un manuscrit théorique où j’examine la possible contribution d’un facteur méconnu dans le phénomène de la RVC : les variations de la pression osmotique du sang induites par les produits de la dissolution du CO2. Outre l’introduction générale (Chapitre 1) et les conclusions (Chapitre 6), cette thèse comporte 4 autres chapitres, au long des quels cinq différentes études sont présentées sous forme d’articles scientifiques qui ont été acceptés à des fins de publication dans différentes revues scientifiques. Chaque chapitre débute par sa propre introduction, qui consiste en une description plus détaillée du contexte motivant le(s) manuscrit(s) associé(s) et un bref résumé des résultats transmis. Un compte rendu détaillé des méthodes et des résultats peut être trouvé dans le(s) dit(s) manuscrit(s). Dans l’étude qui compose le Chapitre 2, je compare la sensibilité des deux techniques ASL de pointe et je démontre que la dernière implémentation de l’ASL continue, la pCASL, offre des mesures plus robustes de la RVC en comparaison à d’autres méthodes pulsés plus âgées. Dans le Chapitre 3, je compare les mesures de la RVC obtenues par pCASL avec l’utilisation de quatre méthodes respiratoires différentes pour manipuler le CO2 artérielle (PaCO2) et je démontre que les résultats peuvent varier de manière significative lorsque les manipulations ne sont pas conçues pour fonctionner dans l’intervalle linéaire de la courbe dose-réponse du CO2. Le Chapitre 4 comprend deux études complémentaires visant à déterminer le niveau de reproductibilité qui peut être obtenu en utilisant des méthodes plus récentes pour la mesure de la RVC. La première étude a abouti à la mise au point technique d’un appareil qui permet des manipulations respiratoires du CO2 de manière simple, sécuritaire et robuste. La méthode respiratoire améliorée a été utilisée dans la seconde étude – de neuro-imagerie – où la sensibilité et la reproductibilité de la RVC, mesurée par pCASL, ont été examinées. La technique d’imagerie pCASL a pu détecter des réponses de perfusion induites par la variation du CO2 dans environ 90% du cortex cérébral humain et la reproductibilité de ces mesures était comparable à celle d’autres mesures hémodynamiques déjà adoptées dans la pratique clinique. Enfin, dans le Chapitre 5, je présente un modèle mathématique qui décrit la RVC en termes de changements du PaCO2 liés à l’osmolarité du sang. Les réponses prédites par ce modèle correspondent étroitement aux changements hémodynamiques mesurés avec pCASL ; suggérant une contribution supplémentaire à la réactivité du système vasculaire cérébral en lien avec le CO2.

ToxicMetals Enrichment in the Surficial Sediments of a Eutrophic Tropical Estuary (Cochin Backwaters, Southwest Coast of India)

Concentrations and distributions of trace metals (Cd, Co, Cr, Cu, Fe, Mn, Ni, Pb, and Zn) in surficial sediments of the Cochin backwaters were studied during both monsoon and pre-monsoon periods. Spatial variations were in accordance with textural charaterstics and organic matter content. A principal component analysis distinguished three zones with different metal accumulation capacity: (i) highest levels in north estuary, (ii) moderate levels in central zone, and (iii) lowest levels in southern part. Trace metal enrichments are mainly due to anthropogenic contribution of industrial, domestic, and agricultural effluents, whose effect is enhanced by settling of metals due to organic flocculation and inorganic precipitation associated with salinity changes. Enrichments factors using Fe as a normalizer showed that metal contamination was the product of anthropogenic activities. An assessment of degree of pollution-categorized sediments as moderately polluted with Cu and Pb, moderately-to-heavily polluted with Zn, and heavily-to-extremely polluted with Cd. Concentrations at many sites largely exceed NOAA ERL (e.g., Cu, Cr, and Pb) or ERM (e.g., Cd, Ni, and Zn). This means that adverse effects for benthic organisms are possible or even highly probable.

Influence of the buffer environment on the Relative Biological Effectiveness of carbon ion radiation, investigated by Scanning Force Microscopy and gel electrophoresis

This work focuses on the analysis of the influence of environment on the relative biological effectiveness (RBE) of carbon ions on molecular level. Due to the high relevance of RBE for medical applications, such as tumor therapy, and radiation protection in space, DNA damages have been investigated in order to understand the biological efficiency of heavy ion radiation. The contribution of this study to the radiobiology research consists in the analysis of plasmid DNA damages induced by carbon ion radiation in biochemical buffer environments, as well as in the calculation of the RBE of carbon ions on DNA level by mean of scanning force microscopy (SFM). In order to study the DNA damages, besides the common electrophoresis method, a new approach has been developed by using SFM. The latter method allows direct visualisation and measurement of individual DNA fragments with an accuracy of several nanometres. In addition, comparison of the results obtained by SFM and agarose gel electrophoresis methods has been performed in the present study. Sparsely ionising radiation, such as X-rays, and densely ionising radiation, such as carbon ions, have been used to irradiate plasmid DNA in trishydroxymethylaminomethane (Tris buffer) and 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES buffer) environments. These buffer environments exhibit different scavenging capacities for hydroxyl radical (HO0), which is produced by ionisation of water and plays the major role in the indirect DNA damage processes. Fragment distributions have been measured by SFM over a large length range, and as expected, a significantly higher degree of DNA damages was observed for increasing dose. Also a higher amount of double-strand breaks (DSBs) was observed after irradiation with carbon ions compared to X-ray irradiation. The results obtained from SFM measurements show that both types of radiation induce multiple fragmentation of the plasmid DNA in the dose range from D = 250 Gy to D = 1500 Gy. Using Tris environments at two different concentrations, a decrease of the relative biological effectiveness with the rise of Tris concentration was observed. This demonstrates the radioprotective behavior of the Tris buffer solution. In contrast, a lower scavenging capacity for all other free radicals and ions, produced by the ionisation of water, was registered in the case of HEPES buffer compared to Tris solution. This is reflected in the higher RBE values deduced from SFM and gel electrophoresis measurements after irradiation of the plasmid DNA in 20 mM HEPES environment compared to 92 mM Tris solution. These results show that HEPES and Tris environments play a major role on preventing the indirect DNA damages induced by ionising radiation and on the relative biological effectiveness of heavy ion radiation. In general, the RBE calculated from the SFM measurements presents higher values compared to gel electrophoresis data, for plasmids irradiated in all environments. Using a large set of data, obtained from the SFM measurements, it was possible to calculate the survive rate over a larger range, from 88% to 98%, while for gel electrophoresis measurements the survive rates have been calculated only for values between 96% and 99%. While the gel electrophoresis measurements provide information only about the percentage of plasmids DNA that suffered a single DSB, SFM can count the small plasmid fragments produced by multiple DSBs induced in a single plasmid. Consequently, SFM generates more detailed information regarding the amount of the induced DSBs compared to gel electrophoresis, and therefore, RBE can be calculated with more accuracy. Thus, SFM has been proven to be a more precise method to characterize on molecular level the DNA damage induced by ionizing radiations.