Linking the population genetics and ecology of arbuscular mycorrhizal fungi

Résumé Les champignons endomycorhiziens arbusculaires (CEA) ont co-évolué avec les plantes terrestres depuis plus de 400 millions d'années. De nos jours, les CEA forment une symbiose avec les racines de la majorité des plantes terrestres. Les CEA sont écologiquement importants parce qu'ils influencent non seulement la croissance des plantes, mais aussi leur diversité. Les CEA sont des biotrophes obligatoires qui reçoivent leur énergie sous forme de glucides issus de la photosynthèse des plantes. En contrepartie, les CEA apportent à leurs hôtes du phospore. Les CEA croissent et se reproduisent clonalement en formant des hyphes et des spores. De plus, les CEA sont coenocytiques et multigénomiques; le cytoplasme d'un CEA contient des noyeaux génétiquement différents. De nombreuses études ont démontré que différentes espèces de CEA agissent différentiellement sur la croissance des plantes. Malgré une conscience de plus en plus forte de l'existence d'une variabilité intraspécifique, la question de savoir si les populations de CEA sont génétiquement variables a été largement négligée. Dans le Chapitre 2, j'ai cherché à savoir si une population de CEA provenant d'un seul champ possède une diversité génétique. Cette étude a mis en évidence une importante variation génétique et phénotypique au sein d'individus de la même population. Des différences au niveau de traits de croissance, héritables et liés à la valeur sélective, indiquent que la variation génétique observée entre isolats n'est pas entièrement neutre. Dans le Chapitre 3, je montre que les différences génétiques entre isolats de CEA d'une population provoquent de la variation dans la croissance des plantes. L'effet des isolats dépend des conditions environnementales et varie de bénéfique à parasitique. Dans le Chapitre 4, je montre que des traits de croissance de CEA varient significativement dans des environnements contrastés. J'ai détecté de fortes interactions entre différents génotypes de CEA et différentes espèces de plantes. Ceci suggère que dans un environnement hétérogène, la sélection pourrait localement favoriser différents génotypes de CEA, maintenant ainsi la diversité génétique dans la population. Les résultats de ce travail aident à mieux comprendre l'importance écologique de la variation intraspécifique des CEA. La possibilité de pouvoir cultiver des individus d'une population de CEA au laboratoire nous a permis une meilleure compréhension de la génétique de ces champignons. De plus, ce travail est une base pour de futures expériences visant à comprendre l'importance évolutive de la diversité intraspécifique des CEA. Abstract Arbuscular mycorrhizal fungi (A1VIF) have co-evolved with land plants -for over 400 million years. Today, AMF form symbioses with roots of most land plants and are ecologically important because they alter plant growth and affect plant diversity. AMF are obligate biotrophs, obtaining their energy in form of plant-derived photosynthates. In return,- they supply their host plants with phosphorous. These fungi grow and reproduce clonally by hyphae and spores. They are coenocytic and multigenomic, harbouring genetically different nuclei in a common cytoplasm. Many studies have shown different AMF species differentially alter plant growth. Despite the increasing awareness of intraspecific variability the question whether there is any genetic variation among different individuals of the same population has been largely neglected. In Chapter 2, we investigated whether there is genetic diversity in a field population of the AMF G. intraradices. This work revealed that large genetic and heritable phenotypic variation exists in this AMF population. Differences in fitness-related growth traits among isolates suggest that some of the observed genetic variation is not selectively neutral. In Chapter 3, we show that genetic differences among isolates from the same population also cause variation in plant growth. The isolate effects on plant growth depended on the environmental conditions and varied from beneficial to detrimental. In Chapter 4, fitnessrelated growth traits of genetically different isolates were significantly altered in contrasting environments. we detected strong AMF isolate by host species interacfions which suggests that in a heterogeneous environment selection could locally favour different AMF genotypes, thereby maintaining high genetic diversity in the population. The results of this work contribute to the understanding of the ecological importance of intraspecific diversity in AMF. The possibility of culturing individuals of an AMF field population under laboratory condition gave new insights into AMF genetics and lays a foundation for future studies to analyse the evolutionary significance of intraspecific genetic diversity in AMF.

Three essays on the determinants of output, inflation and interest rates

Résumé: Output, inflation and interest rates are key macroeconomic variables, in particular for monetary policy. In modern macroeconomic models they are driven by random shocks which feed through the economy in various ways. Models differ in the nature of shocks and their transmission mechanisms. This is the common theme underlying the three essays of this thesis. Each essay takes a different perspective on the subject: First, the thesis shows empirically how different shocks lead to different behavior of interest rates over the business cycle. For commonly analyzed shocks (technology and monetary policy errors), the patterns square with standard models. The big unknown are sources of inflation persistence. Then the thesis presents a theory of monetary policy, when the central bank can better observe structural shocks than the public. The public will then seek to infer the bank's extra knowledge from its policy actions and expectation management becomes a key factor of optimal policy. In a simple New Keynesian model, monetary policy becomes more concerned with inflation persistence than otherwise. Finally, the thesis points to the huge uncertainties involved in estimating the responses to structural shocks with permanent effects.

Information System ProcessInnovation Adoption, Adaptation, Learning, and Unlearning: A Longitudinal Case Study

This thesis examines the history and evolution of information system process innovation (ISPI) processes (adoption, adaptation, and unlearning) within the information system development (ISD) work in an internal information system (IS) department and in two IS software house organisations in Finland over a 43-year time-period. The study offers insights into influential actors and their dependencies in deciding over ISPIs. The research usesa qualitative research approach, and the research methodology involves the description of the ISPI processes, how the actors searched for ISPIs, and how the relationships between the actors changed over time. The existing theories were evaluated using the conceptual models of the ISPI processes based on the innovationliterature in the IS area. The main focus of the study was to observe changes in the main ISPI processes over time. The main contribution of the thesis is a new theory. The term theory should be understood as 1) a new conceptual framework of the ISPI processes, 2) new ISPI concepts and categories, and the relationships between the ISPI concepts inside the ISPI processes. The study gives a comprehensive and systematic study on the history and evolution of the ISPI processes; reveals the factors that affected ISPI adoption; studies ISPI knowledge acquisition, information transfer, and adaptation mechanisms; and reveals the mechanismsaffecting ISPI unlearning; changes in the ISPI processes; and diverse actors involved in the processes. The results show that both the internal IS department and the two IS software houses sought opportunities to improve their technical skills and career paths and this created an innovative culture. When new technology generations come to the market the platform systems need to be renewed, and therefore the organisations invest in ISPIs in cycles. The extent of internal learning and experiments was higher than the external knowledge acquisition. Until the outsourcing event (1984) the decision-making was centralised and the internalIS department was very influential over ISPIs. After outsourcing, decision-making became distributed between the two IS software houses, the IS client, and itsinternal IT department. The IS client wanted to assure that information systemswould serve the business of the company and thus wanted to co-operate closely with the software organisations.

Fouling, prevention of fouling, and clearing in filtration

In this thesis fouling of conventional filter fabrics and membranes was studied. In the beginning of the thesis fouling and how it can be measured and predicted is reviewed. Information on different methods on how fouling canbe decreased or cleaned away is also given. The experimental part is divided into two sections; fabric filtration and membrane filtration. Fouling of the filter fabrics was studied with silica or cupper slurries and fouling of the membranes was studied with pulp and paper mill waters. The fouled filter materials were characterised according to many different methods. The most useful way to observe fouling is to measure the changes in the permeate flux. Fouling can also be seen visually e.g. with scanning electron microscopy. Consequently, also the reason for the fouling in question might be found. Different filtration characteristics affect fouling e.g. as the filtration pressure was increased it did not have much influence on the permeate flux, but the pressure caused the membrane to get fouled faster. Also, an increase of shear rate on the membrane surface decreased fouling. Different pretreatment methods for the effluent were tested in membrane filtration to decrease fouling. The tested methods; biological treatment, ozonation, enzymatic treatment and flocculation, did not have a clear influence on the fouling of the membrane, but e.g. a biological treatment combined with ultrafiltration made the tested groundwood mill circulation water purer than ultrafiltration alone.

Establishing intercompany relationships: Motives and methods for successful collaborative engagement

This study explores the early phases of intercompany relationship building, which is a very important topic for purchasing and business development practitioners as well as for companies' upper management. There is a lot ofevidence that a proper engagement with markets increases a company's potential for achieving business success. Taking full advantage of the market possibilities requires, however, a holistic view of managing related decision-making chain. Most literature as well as the business processes of companies are lacking this holism. Typically they observe the process from the perspective of individual stages and thus lead to discontinuity and sub-optimization. This study contains a comprehensive introduction to and evaluation of literature related to various steps of the decision-making process. It is studied from a holistic perspective ofdetermining a company's vertical integration position within its demand/ supplynetwork context; translating the vertical integration objectives to feasible strategies and objectives; and operationalizing the decisions made through engagement with collaborative intercompany relationships. The empirical part of the research has been conducted in two sections. First the phenomenon of intercompany engagement is studied using two complementary case studies. Secondly a survey hasbeen conducted among the purchasing and business development managers of several electronics manufacturing companies, to analyze the processes, decision-makingcriteria and success factors of engagement for collaboration. The aim has been to identify the reasons why companies and their management act the way they do. As a combination of theoretical and empirical research an analysis has been produced of what would be an ideal way of engaging with markets. Based on the respective findings the study concludes by proposing a holistic framework for successful engagement. The evidence presented throughout the study demonstrates clear gaps, discontinuities and limitations in both current research and in practical purchasing decision-making chains. The most significant discontinuity is the identified disconnection between the supplier selection process and related criteria and the relationship success factors.

Effects of crop and weed densities on the interactions between barley and Lolium rigidum in several Mediterranean locations

The effects of both barley and Lolium rigidum densities on weed growth and spike production and on crop yield were examined in five field experiments carried out in the Mediterranean drylands of Spain and Western Australia. The aim was to check the consistency of the competitiveness of the crop in different environmental and management conditions. L. rigidum reduced barley yields in most of the experiments (between 0 and 85%), the number of ears per m2 being the most affected. It was found that increasing the barley seeding rate did not reduce the crop losses but did limit weed biomass (between 5 and 61%) and spike production (between 24 and 85%). The variability observed in crop yield losses between sites and seasons was related to rainfall at the beginning of the season. The most sensitive component of yield to weed competition was the number of ears per plant.

Between Immunology And Tolerance: Controlling Immune Responses Employing Tolerogenic Dendritic Cells

Dendritic cells (DCs) are the most efficient antigen presenting cells, they provide co-stimulation, are able to secrete various proinflammatory cytokines and therefore play a pivotal role in shaping adaptive immune responses. Moreover, they are important for the promotion and maintenance of central and peripheral tolerance through several mechanisms like the induction of anergy or apoptosis in effector T cells or by promoting regulatory T cells. The murine CD8α+ (MuTu) dendritic cell line was previously derived and described in our laboratory. The MuTu cell line has been shown to maintain phenotypical and functional characteristics of endogenous CD8α+ DCs. They are able to cross-present exogenous antigens to CD8+ T cells and produce interleukin (IL-) 12 upon engagement of Toll like receptors. The cell line constitutes an infinite source of homogenous, phenotypically well-defined dendritic cells. This allows us to investigate the role and potential of specific molecules in the induction as well as regulation of immune responses by DCs in a rational and standardized way. In a first project the MuTu dendritic cell line was transduced in order to stably express the immunosuppressive molecules IL-10, IL-35 or the active form of TGF-β (termed IL-10+DC, IL-35+DC or actTGFβ+DC). We investigated the capability of these potentially suppressive or tolerogenic dendritic cell lines to induce immune tolerance and explore the mechanisms behind tolerance induction. The expression of TGF-β by the DC line did not affect the phenotype of the DCs itself. In contrast, IL-10+ and IL-35+DCs were found to exhibit lower expression of co-stimulatory molecules and MHC class I and II, as well as reduced secretion of pro-inflammatory cytokines upon activation. In vitro co-culture with IL-35+, IL10+ or active TGFβ+ DCs interfered with function and proliferation of CD4+ and CD8+ T cells. Furthermore, IL-35 and active TGF-β expressing DC lines induced regulatory phenotype on CD4+ T cells in vitro without or with expression of Foxp3, respectively. In different murine cancer models, vaccination with IL-35 or active TGF-β expressing DCs resulted in faster tumor growth. Interestingly, accelerated tumor growth could be observed when IL-35-expressing DCs were injected into T cell-deficient RAG-/- mice. IL-10expressing DCs however, were found to rather delay tumor growth. Besides the mentioned autocrine effects of IL-35 expression on the DC line itself, we surprisingly observed that the expression of IL-35 or the addition of IL-35 containing medium enhances neutrophil survival and induces proliferation of endothelial cells. Our findings indicate that the cytokine IL-35 might not only be a potent regulator of adaptive immune responses, but it also implies IL-35 to mediate diverse effects on an array of cellular targets. This abilities make IL-35 a promising target molecule not only for the treatment of auto-inflammatory disease but also to improve anti-cancer immunotherapies. Indeed, by applying active TGFβ+ in murine autoimmune encephalitis we were able to completely inhibit the development of the disease, whereas IL-35+DCs reduced disease incidence and severity. Furthermore, the preventive transfer of IL-35+DCs delayed rejection of transplanted skin to the same extend as the combination of IL-10/actTGF-β expressing DCs. Thus, the expression of a single tolerogenic molecule can be sufficient to interfere with the adequate activation and function of dendritic cells and of co-cultured T lymphocytes. The respective mechanisms of tolerance induction seem to be different for each of the investigated molecule. The application of a combination of multiple tolerogenic molecules might therefore evoke synergistic effects in order to overcome (auto-) immunity. In a second project we tried to improve the immunogenicity of dendritic cell-based cancer vaccines using two different approaches. First, the C57BL/6 derived MuTu dendritic cell line was genetically modified in order to express the MHC class I molecule H-2Kd. We hypothesized that the expression of BALB/c specific MHC class I haplotype (H-2Kd) should allow the priming of tumor-specific CD8+ T cells by the otherwise allogeneic dendritic cells. At the same time, the transfer of these H-2Kd+ DCs into BALB/c mice was thought to evoke a strong inflammatory environment that might act as an "adjuvant", helping to overcome tumor induced immune suppression. Using this so called "semi-allogeneic" vaccination approach, we could demonstrate that the delivery of tumor lysate pulsed H-2Kd+ DCs significantly delayed tumor growth when compared to autologous or allogeneic vaccination. However, we were not able to coherently elucidate the cellular mechanisms underlying the observed effect. Second, we generated MuTu DC lines which stably express the pro-inflammatory cytokines IL-2, IL-12 or IL-15. We investigated whether the combination of DC vaccination and local delivery of pro-inflammatory cytokines might enhance tumor specific T cell responses. Indeed, we observed an enhanced T cell proliferation and activation when they were cocultured in vitro with IL-12 or IL-2-expressing DCs. But unfortunately we could not observe a beneficial or even synergistic impact on tumor development when cytokine delivery was combined with semi-allogeneic DC vaccination.

The Impact of ICTs on Lecturer and Student Interaction in University Education Processes

Interaction is a basic element in any educational process, and it is something that needs to be reconsidered in the light of technology. In order to examine the methodological changes that ICTs bring to teaching from an interaction perspective, a study was carried out at the University of Lleida to observe interaction processes in various face-to-face, blended learning and e-learning subjects. The methodological design was based on three data collection techniques: documentary analysis of subject curricula, lecturer and student questionnaires, and lecturer interviews. The data showed that, as the online component of subjects increased, the lecturers and students used more technological tools to communicate (e-mail, forums, chats, social networks, etc.). Furthermore, we found that the lecturers and students basically communicated for academic purposes. While they hardly ever communicated for personal reasons (guidance, support, etc.), they claimed that closer contact with a non-academic focus would be preferable. We also observed that the students’ work was more individual in e-learning subjects. Although there is still a considerable way to go in ICT-mediated lecturer-student interaction, both the lecturers and students recognise the potential of such technologies, even though they still do not use them as they feel they should.

Chromosome 7 gain and DNA hypermethylation at the HOXA10 locus are associated with expression of a stem cell related HOX-signature in glioblastoma.

BACKGROUND: HOX genes are a family of developmental genes that are expressed neither in the developing forebrain nor in the normal brain. Aberrant expression of a HOX-gene dominated stem-cell signature in glioblastoma has been linked with increased resistance to chemo-radiotherapy and sustained proliferation of glioma initiating cells. Here we describe the epigenetic and genetic alterations and their interactions associated with the expression of this signature in glioblastoma. RESULTS: We observe prominent hypermethylation of the HOXA locus 7p15.2 in glioblastoma in contrast to non-tumoral brain. Hypermethylation is associated with a gain of chromosome 7, a hallmark of glioblastoma, and may compensate for tumor-driven enhanced gene dosage as a rescue mechanism by preventing undue gene expression. We identify the CpG island of the HOXA10 alternative promoter that appears to escape hypermethylation in the HOX-high glioblastoma. An additive effect of gene copy gain at 7p15.2 and DNA methylation at key regulatory CpGs in HOXA10 is significantly associated with HOX-signature expression. Additionally, we show concordance between methylation status and presence of active or inactive chromatin marks in glioblastoma-derived spheres that are HOX-high or HOX-low, respectively. CONCLUSIONS: Based on these findings, we propose co-evolution and interaction between gene copy gain, associated with a gain of chromosome 7, and additional epigenetic alterations as key mechanisms triggering a coordinated, but inappropriate, HOX transcriptional program in glioblastoma.

Blueberry pollination in southern Brazil and their influence on fruit quality

Blueberry (Vaccinium ashei) is a relatively new crop in cultivation under Southern Brazil conditions. The first collection introduced in the area was formed by rabbiteye cultivars which need insect pollinators and also pollinizers. The aim of this work was to observe if there were differences between pollinizers on fruit quality of the commercial cultivar and also to observe the most effective and frequent insect pollinators, under natural conditions. It was concluded that pollen source has an effect on quality of blueberry fruits. Bumblebees are the most efficient pollinators; however the species found in southern Brazil are different from the ones mentioned in the U.S. literature.

Current transport and electroluminescence mechanisms in thin SiO2 films containing Si nanocluster-sensitized erbium ions.

We have studied the current transport and electroluminescence properties of metal oxide semiconductor MOS devices in which the oxide layer, which is codoped with silicon nanoclusters and erbium ions, is made by magnetron sputtering. Electrical measurements have allowed us to identify a Poole-Frenkel conduction mechanism. We observe an important contribution of the Si nanoclusters to the conduction in silicon oxide films, and no evidence of Fowler-Nordheim tunneling. The results suggest that the electroluminescence of the erbium ions in these layers is generated by energy transfer from the Si nanoparticles. Finally, we report an electroluminescence power efficiency above 10−3%. © 2009 American Institute of Physics. doi:10.1063/1.3213386

A parameterization method for the computation of invariant tori and their whiskers in quasi-periodic maps: explorations and mechanisms for the breakdown of hyperbolicity

In two previous papers [J. Differential Equations, 228 (2006), pp. 530 579; Discrete Contin. Dyn. Syst. Ser. B, 6 (2006), pp. 1261 1300] we have developed fast algorithms for the computations of invariant tori in quasi‐periodic systems and developed theorems that assess their accuracy. In this paper, we study the results of implementing these algorithms and study their performance in actual implementations. More importantly, we note that, due to the speed of the algorithms and the theoretical developments about their reliability, we can compute with confidence invariant objects close to the breakdown of their hyperbolicity properties. This allows us to identify a mechanism of loss of hyperbolicity and measure some of its quantitative regularities. We find that some systems lose hyperbolicity because the stable and unstable bundles approach each other but the Lyapunov multipliers remain away from 1. We find empirically that, close to the breakdown, the distances between the invariant bundles and the Lyapunov multipliers which are natural measures of hyperbolicity depend on the parameters, with power laws with universal exponents. We also observe that, even if the rigorous justifications in [J. Differential Equations, 228 (2006), pp. 530-579] are developed only for hyperbolic tori, the algorithms work also for elliptic tori in Hamiltonian systems. We can continue these tori and also compute some bifurcations at resonance which may lead to the existence of hyperbolic tori with nonorientable bundles. We compute manifolds tangent to nonorientable bundles.

Action Dominates Valence in Anticipatory Representations in the Human Striatum and Dopaminergic Midbrain

The acquisition of reward and the avoidance of punishment could logically be contingent on either emitting or withholding particular actions. However,the separate pathways inthe striatumfor go and no-go appearto violatethis independence, instead coupling affect and effect. Respect for this interdependence has biased many studies of reward and punishment, so potential action- outcome valence interactions during anticipatory phases remain unexplored. In a functional magnetic resonance imaging study with healthy human volunteers, we manipulated subjects" requirement to emit or withhold an action independent from subsequent receipt of reward or avoidance of punishment. During anticipation, in the striatum and a lateral region within the substantia nigra/ventral tegmental area (SN/VTA), action representations dominated over valence representations. Moreover, we did not observe any representation associated with different state values through accumulation of outcomes, challenging a conventional and dominant association between these areas and state value representations. In contrast, a more medial sector of the SN/VTA responded preferentially to valence, with opposite signs depending on whether action was anticipatedto be emitted or withheld. This dominant influence of action requires an enriched notion of opponency between reward and punishment.

Tissue-Specific Evolution of Protein Coding Genes in Human and Mouse.

Protein-coding genes evolve at different rates, and the influence of different parameters, from gene size to expression level, has been extensively studied. While in yeast gene expression level is the major causal factor of gene evolutionary rate, the situation is more complex in animals. Here we investigate these relations further, especially taking in account gene expression in different organs as well as indirect correlations between parameters. We used RNA-seq data from two large datasets, covering 22 mouse tissues and 27 human tissues. Over all tissues, evolutionary rate only correlates weakly with levels and breadth of expression. The strongest explanatory factors of purifying selection are GC content, expression in many developmental stages, and expression in brain tissues. While the main component of evolutionary rate is purifying selection, we also find tissue-specific patterns for sites under neutral evolution and for positive selection. We observe fast evolution of genes expressed in testis, but also in other tissues, notably liver, which are explained by weak purifying selection rather than by positive selection.

NLRP3 Inflammasome Is Expressed and Functional in Mouse Brain Microglia but Not in Astrocytes.

Neuroinflammation is the local reaction of the brain to infection, trauma, toxic molecules or protein aggregates. The brain resident macrophages, microglia, are able to trigger an appropriate response involving secretion of cytokines and chemokines, resulting in the activation of astrocytes and recruitment of peripheral immune cells. IL-1β plays an important role in this response; yet its production and mode of action in the brain are not fully understood and its precise implication in neurodegenerative diseases needs further characterization. Our results indicate that the capacity to form a functional NLRP3 inflammasome and secretion of IL-1β is limited to the microglial compartment in the mouse brain. We were not able to observe IL-1β secretion from astrocytes, nor do they express all NLRP3 inflammasome components. Microglia were able to produce IL-1β in response to different classical inflammasome activators, such as ATP, Nigericin or Alum. Similarly, microglia secreted IL-18 and IL-1α, two other inflammasome-linked pro-inflammatory factors. Cell stimulation with α-synuclein, a neurodegenerative disease-related peptide, did not result in the release of active IL-1β by microglia, despite a weak pro-inflammatory effect. Amyloid-β peptides were able to activate the NLRP3 inflammasome in microglia and IL-1β secretion occurred in a P2X7 receptor-independent manner. Thus microglia-dependent inflammasome activation can play an important role in the brain and especially in neuroinflammatory conditions.