Characterization of DnmA, the Dnmt2 homolog in Dictyostelium discoideum

Eukaryotic DNA m5C methyltransferases (MTases) play a major role in many epigenetic regulatory processes like genomic imprinting, X-chromosome inactivation, silencing of transposons and gene expression. Members of the two DNA m5C MTase families, Dnmt1 and Dnmt3, are relatively well studied and many details of their biological functions, biochemical properties as well as interaction partners are known. In contrast, the biological functions of the highly conserved Dnmt2 family, which appear to have non-canonical dual substrate specificity, remain enigmatic despite the efforts of many researchers. The genome of the social amoeba Dictyostelium encodes Dnmt2-homolog, the DnmA, as the only DNA m5C MTase which allowed us to study Dnmt2 function in this organism without interference by the other enzymes. The dnmA gene can be easily disrupted but the knock-out clones did not show obvious phenotypes under normal lab conditions, suggesting that the function of DnmA is not vital for the organism. It appears that the dnmA gene has a low expression profile during vegetative growth and is only 5-fold upregulated during development. Fluorescence microscopy indicated that DnmA-GFP fusions were distributed between both the nucleus and cytoplasm with some enrichment in nuclei. Interestingly, the experiments showed specific dynamics of DnmA-GFP distribution during the cell cycle. The proteins colocalized with DNA in the interphase and were mainly removed from nuclei during mitosis. DnmA functions as an active DNA m5C MTase in vivo and is responsible for weak but detectable DNA methylation of several regions in the Dictyostelium genome. Nevertheless, gel retardation assays showed only slightly higher affinity of the enzyme to dsDNA compared to ssDNA and no specificity towards various sequence contexts, although weak but detectable specificity towards AT-rich sequences was observed. This could be due to intrinsic curvature of such sequences. Furthermore, DnmA did not show denaturant-resistant covalent complexes with dsDNA in vitro, although it could form covalent adducts with ssDNA. Low binding and methyltransfer activity in vitro suggest the necessity of additional factor in DnmA function. Nevertheless, no candidates could be identified in affinity purification experiments with different tagged DnmA fusions. In this respect, it should be noted that tagged DnmA fusion preparations from Dictyostelium showed somewhat higher activity in both covalent adduct formation and methylation assays than DnmA expressed in E.coli. Thus, the presence of co-purified factors cannot be excluded. The low efficiency of complex formation by the recombinant enzyme and the failure to define interacting proteins that could be required for DNA methylation in vivo, brought up the assumption that post-translational modifications could influence target recognition and enzymatic activity. Indeed, sites of phosphorylation, methylation and acetylation were identified within the target recognition domain (TRD) of DnmA by mass spectrometry. For phosphorylation, the combination of MS data and bioinformatic analysis revealed that some of the sites could well be targets for specific kinases in vivo. Preliminary 3D modeling of DnmA protein based on homology with hDNMT2 allowed us to show that several identified phosphorylation sites located on the surface of the molecule, where they would be available for kinases. The presence of modifications almost solely within the TRD domain of DnmA could potentially modulate the mode of its interaction with the target nucleic acids. DnmA was able to form denaturant-resistant covalent intermediates with several Dictyostelium tRNAs, using as a target C38 in the anticodon loop. The formation of complexes not always correlated with the data from methylation assays, and seemed to be dependent on both sequence and structure of the tRNA substrate. The pattern, previously suggested by the Helm group for optimal methyltransferase activity of hDNMT2, appeared to contribute significantly in the formation of covalent adducts but was not the only feature of the substrate required for DnmA and hDNMT2 functions. Both enzymes required Mg2+ to form covalent complexes, which indicated that the specific structure of the target tRNA was indispensable. The dynamics of covalent adduct accumulation was different for DnmA and different tRNAs. Interestingly, the profiles of covalent adduct accumulation for different tRNAs were somewhat similar for DnmA and hDNMT2 enzymes. According to the proposed catalytic mechanism for DNA m5C MTases, the observed denaturant-resistant complexes corresponded to covalent enamine intermediates. The apparent discrepancies in the data from covalent complex formation and methylation assays may be interpreted by the possibility of alternative pathways of the catalytic mechanism, leading not to methylation but to exchange or demethylation reactions. The reversibility of enamine intermediate formation should also be considered. Curiously, native gel retardation assays showed no or little difference in binding affinities of DnmA to different RNA substrates and thus the absence of specificity in the initial enzyme binding. The meaning of the tRNA methylation as well as identification of novel RNA substrates in vivo should be the aim of further experiments.

Right to Food, Food Security and Food Aid Under International Law, or the Limits of a right-based approach

The right to food has become a pillar of international humanitarian and human rights law. The increasing number of food-related emergencies and the evolution of the international order brought the more precise notion of food security and made a potential right to receive food aid emerge. Despite this apparent centrality, recent statistics show that a life free from hunger is for many people all over the world still a utopian idea. The paper will explore nature and content of the right to food, food security and food aid under international law in order to understand the reasons behind the substantial failure of this right-centred approach, emphasising the lack of legal effects of many food-related provisions because of excessive moral connotations of the right to be free from hunger. Bearing in mind the three-dimensional nature of food security, the paper will also suggest that all attention has been focused on the availability of food, while real difficulties arise in terms of accessibility and adequacy. Emergency situations provide an excellent example of this unbalance, as the emerging right to receive food aid focus itself on the availability of food, without improving local production and adequacy. Looking at other evolving sectors of international law, such as the protection of the environment, and particularly the safeguard of biological diversity, alternative solutions will be envisaged in order to “feed” the right to food.

Cooperative Physics of Fly Swarms: An Emergent Behavior

We have simulated the behavior of several artificial flies, interacting visually with each other. Each fly is described by a simple tracking system (Poggio and Reichardt, 1973; Land and Collett, 1974) which summarizes behavioral experiments in which individual flies fixate a target. Our main finding is that the interaction of theses implemodules gives rise to a variety of relatively complex behaviors. In particular, we observe a swarm-like behavior of a group of many artificial flies for certain reasonable ranges of our tracking system parameters.

Perceptually-based Comparison of Image Similarity Metrics

The image comparison operation ??sessing how well one image matches another ??rms a critical component of many image analysis systems and models of human visual processing. Two norms used commonly for this purpose are L1 and L2, which are specific instances of the Minkowski metric. However, there is often not a principled reason for selecting one norm over the other. One way to address this problem is by examining whether one metric better captures the perceptual notion of image similarity than the other. With this goal, we examined perceptual preferences for images retrieved on the basis of the L1 versus the L2 norm. These images were either small fragments without recognizable content, or larger patterns with recognizable content created via vector quantization. In both conditions the subjects showed a consistent preference for images matched using the L1 metric. These results suggest that, in the domain of natural images of the kind we have used, the L1 metric may better capture human notions of image similarity.

Role of phosphatidylinositol 3-kinase pathway (PI3K/Akt) in humans

The signaling pathway of phosphatidylinositol 3-kinase (PI3K) is critical in many aspects of growth and cell survival. The path of PI3K is stimulated physiologically as a result of many growth factors and regulatory factors. Several genetic alterations such as amplification, mutation and chromosomal arrangements may compromise the PI3K pathway, generating permanent activation in different cancer types have found evidence of these deleterious genetic modifications. Abnormal activation of the PI3K pathway results in alteration of the control mechanisms of growth and cell survival, which favors the competitive growth, and frequently metastatic capacity, greater resistance to treatment. The aim of this paper is to review matters relating to the operation of the PI3K/Akt signaling pathway and its role in the process of carcinogenesis in humans.

Advances and limitations in the attention to the problems of housing and urban land in Mexico. An approach from the legal-institutional frame

In this work we analyze the reforms carried out by the Mexican state in the nineties of the 20th century, in the items concerning the policies of housing and urban land, based on an exhaustive review of the main actions, programs and changes in the legal and institutional frame that applies for each of these fields. The nineties represent a "breaking point" in the way the State considers the satisfaction of the right to the housing and attends the offer of urbanized land for a tidy and sustainable urban development. In this period of time, the approach of direct intervention in developing and financing housing and creation of land reserves has changed into another one, ruled by the logic of the market. The balance to the first decade of the 21st century is ambiguous, as neither the housing policy has solved the housing shortage for low-income population, nor the land policy has eliminated the illegal urban growth.

The Construction of a State Peace Policy and the Process of Conflict Resolution

The academic literature specialized on processes of conflict resolution has focused on how third party intervention and mediation can contribute to end violent conflict, however it has also ignored the potential role of the state in countries affected by internal war. This article calls for a better understanding of the state, not only as a source of contemporary conflict but as a potential advocate of conflict resolution processes. It suggests that it is necessary and possible to involve the state in more effective processes of conflict resolution through the implementation of a State Peace Policy. The central argument is that some of the critical elements that should guide the state action when confronting the destructive logic of war and violence can be effectively undertaken through a public policy focused on building peace. After suggesting a general definition of State Peace Policy and highlighting some of its main attributes, the article recognizes that this sort of policy can also orientate the unfinished process of state consolidation in Colombia and other countries affected by internal conflict. The role of the state in the process of conflict resolution is crucial; however there are some issues normally ignored within the policy-making process, they must be seriously taken into account in order to eliminate the underlying structures that perpetuate conflict and delay the consolidation of sustainable peace.-----La literatura académica especializada en procesos de resolución de conflictos se ha centrado en el estudio de cómo la intervención de terceras partes y la labor de mediación pueden contribuir a poner fin a los conflictos violentos, sin embargo, también ha ignorado el rol potencial del estado en aquellos países afectados por la guerra interna. Este artículo llama la atención sobre la necesidad de estudiar al estado no sólo como la fuente de los conflictos contemporáneos, sino como un colaborador potencial en procesos de resolución de conflictos. Se sugiere que es necesario y también posible involucrar al estado en este tipo de procesos de una manera más efectiva a través de la implementación de una Política de Estado centrada en la Paz. El argumento central es que algunos de los elementos claves que deben guiar la acción del estado cuando éste se enfrenta a la lógica destructiva de la guerra y la violencia, pueden ser efectivamente tratados a través de una política pública que de prioridad a la construcción de la paz. Luego de sugerir una definición general y destacar algunos de los principales atributos de ésta clase de Política de Estado, el artículo reconoce que ésta podría también orientar el proceso inacabado de consolidación del estado en Colombia y en otros países afectados por conflictos internos. El rol del estado en el proceso para resolver los conflictos es crucial, sin embargo hay algunos aspectos normalmente ignorados durante el proceso de formulación de políticas que deben ser tomados en cuenta seriamente para eliminar las estructuras que perpetúan el conflicto y que retrasan la consolidación de la paz sostenible.

Publicness of goods and violent conflict : evidence from Colombia

How the degree of publicness of goods affect violent conflict? Based on the theoretical model in Esteban and Ray (2001) we find that the effect of the degree of publicness depends on the group size. When the group is small (large), the degree of publicness increases (decreases) the likelihood of conflict. This opens an empirical question that we tackle using microdata from the Colombian conflict at the municipality level. We use three goods with different publicness degree to identify the sign of the effect of publicness on conflict. These goods are coca crops (private good), road density (public good subject to congestion) and average education quality (a purer public good). After dealing with endogeneity issues using an IV approach, we find that the degree of publicness reduces the likelihood of both paramilitary and guerrilla attacks. Moreover, coca production exacerbates conflict and the provision of both public goods mitigates conflict. These results are robust to size, geographical, and welfare controls. Policies that improve public goods provision will help to fight the onset of conflict.

Sector agrícola y política de competencia

Los procesos de integración económica han puesto en evidencia que la separación tradicionalmente hecha entre las políticas comercial y de competencia no sólo es ficticia, sino que mantenerla es simplemente contradictorio con la realidad de la economía internacional. En la medida en que los mercados domésticos se han abierto al comercio internacional, se ha considerado que las políticas de competencia pueden hacerse redundantes, ya que la competencia extranjera tiende a garantizar que dichos mercados tienen un nivel adecuado de contestabilidad. Sin embargo, como se muestra en este documento para el caso del sector agrícola, en estas circunstancias, la política de competencia adquiere un nuevo e importante papel que cumplir. Acá se discute la relación general entre el sector agrícola y la política de competencia, en un contexto de relativa liberalización comercial. Se sostiene que es necesario aplicar la política de competencia al sector, ya que esto garantiza las mejores condiciones posibles para incentivar los procesos de cambio tecnológico, indispensables para desarrollar una agricultura dinámica. Igualmente, se afirma que es indispensable una aplicación rigurosa de la política de competencia que, teniendo en cuenta las particularidades de la estructura de mercado de los sectores vinculados a la agricultura hacia adelante y hacia atrás, garantice que el más competitivo sector agrícola no sea sujeto de prácticas anticompetitivas por otros agentes. Esto puede incluir la instauración de algunas excepciones puntuales para el sector, con relación a la política de competencia,

Effects of priority and emerging pollutants on river biofilms

L'activitat humana representa una de les majors causes d'entrada d'una gran varietat de substàncies en els ecosistemes fluvials. L'objectiu principal d'aquest treball es investigar els efectes que els tòxics orgànics poden exercir en els biofilms fluvials. El riu Llobregat ha estat sotmès a fortes pressions, fet que l'ha portat a uns nivells molt elevats de contaminació. En aquest estudi s'ha observat una influència dels plaguicides presents al riu en la distribució de la comunitat de diatomees, així com efectes en el biofilm a nivell funcional i estructural. Experiments amb canals experimentals han mostrat que l'herbicida diuron i el bactericida triclosan poden ocasionar una cadena d'efectes en els biofilms, incloent efectes directes i també efectes indirectes en les relacions entre els components del biofilm. Experiments amb cultius algals han mostrat que aquests tòxics, aplicats en barreja, poden tenir una major toxicitat de la prevista pels models, resultant en efectes sinèrgics.

O empreendedorismo e a inovação na saúde, factores potenciadores de novos projetos

O objetivo geral deste trabalho é investigar o empreendedorismo e a inovação, assim como a forma como estes instrumentos se têm ligado, ou podem vir a ligar-se, à atividade da saúde potenciando novos projetos empresariais inovadores com elevados níveis de competitividade e rentabilidade, numa lógica de criação de um modelo que sintetize estes instrumentos e os potencie para resultados noutros projetos empresariais. No seu desenvolvimento, pretende-se compreender e melhorar a influência positiva que o empreendedorismo e a inovação têm na área da saúde e compreender a influência destes instrumentos como fatores potenciadores de novos projetos contribuindo para a regeneração dos tecidos empresariais, quer ao nível da criação de novas empresas inovadoras, quer ao nível da modernização, reposicionamento ou reorientação de empresas existentes. O objetivo específico desta investigação sobre empreendedorismo e inovação na saúde, como fatores potenciadores de novos projetos, pode evidenciar sinais de êxito mais evidentes, que permita tirar ilações da importância das sinergias entre empreendedorismo e inovação, nas suas várias vertentes da saúde, que alavanquem novas oportunidades para projetos empresariais, sustentáveis e com forte probabilidade de sucesso, muitos deles já identificados, mas ainda não desenvolvidos quer por potenciais empreendedores ou investidores.

The postoccidental deconstruction and resignification of "Modernity'': a critical analysis

The thesis which follows, entitled ''The Postoccidental Deconstruction and Resignification of 'Modemity': A Critical Analysis", is an exposition and criticism of the critique of occidental modemity found in a group of writings which identify their critique with a "postoccidental" point of view with respect to postcolonial studies. The general problem ofthe investigation concems the significance and reach ofthis critique of modemity in relation to the ongoing debate, in Latín American studies, about the historical relationship between Latín America, as a mu1ticultural/ structurally heterogeneous region, and the industrial societies of Euro pe and North America. A brief Preface explains the genealogy of the author's ideas on this subject Following this preface, the thesis proceeds to analyze the writings in this corpus through an intertextual, schematic approach which singles out two rnajor elements of the postoccidental critique: "coloniality" and "eurocentrism". These two main elements are investigated in the Introduction and Chapters One and Two, in terms of how they distinguish postoccidental analysis from other theoretical tendencias with which it has affinities but whose key concepts it reformu1ates in ways that are key to the unique approach which postoccidental analysis takes to modemity, the nature of the capitalist world system, colonialism, subaltemization, center/periphery and development . Chapter Three attempts a critical analysis of the foregoing postoccidentalist deconstruction according to the following question: to what extent does it succeed in deconstructing "modernity" as a term which refers to a historically articulated set of discourses whose underlying purpose has been to justify European and North American hegemony and structural asymmetries vis-a-vis the peripheries of the capitalist world system, based on an ethnocentric, racialist logic of exploitation and subalternization of non-European peoples? A Conclusion follows Chapter Three.

Agricultural Policy and Nest Success of Prairie Ducks in Canada and the United States

The Prairie Pothole Region of North America has been modified by agriculture during the past 100 yr, resulting in habitat loss, fragmentation, and degradation that have reduced the abundance and productivity of many wildlife species. The 1985 U.S. Farm Bill provided economic incentives to agriculture that are considered by many to be beneficial to nesting waterfowl and other wildlife. Canada has not experienced an equally comprehensive legislative initiative, which would seem to indicate that benefits to waterfowl in Canada should lag behind those in the United States. However, with the removal of some agricultural subsidies in Canada during the 1990s, the amount of perennial cover in the Canadian prairies increased to levels similar to those of the 1970s. Therefore, it is unclear whether and how the U.S. and Canadian prairies might differ with regard to habitat quality for nesting waterfowl. We used historical and contemporary data to compare temporal trends in duck nest success between the United States and Canada and to assess how mean nest success varied with proportion of cropland and wetland density. The data best supported models with nonlinear temporal trends that varied between the two countries and suggested that mean nest success in Canada declined from its high point in 1930s and remained below the long-term value of 0.16 until the end of the time series in 2005. Mean nest success in the United States also declined from its high point in the 1930s, but increased to above the long-term value of 0.25 during the early 2000s. Mean nest success varied negatively with proportion of cropland in both the United States and Canada. Mean nest success was positively correlated with pond density at Canadian sites, but showed only a weak association with pond density at U.S. sites. All models explained the low proportions of the variation in nest success, suggesting that unmeasured factors such as the abundance and identity of nest predators may have strong effects on nest success. Nonetheless, these results support earlier suggestions that agricultural policy that encourages permanent cover positively influences duck reproductive success. We also found that, for reasons that are not entirely clear, nest success for the same intensity of row cropping was generally higher in the United States than in Canada. Further research is required to elucidate the exact nature of the composition, size, and distribution of permanent cover that coincides with greater average nest success by dabbling ducks in the United States. In addition, the data suggest that the benefits that might accrue from increases in the amount of perennial cover in Canada would be better realized if these efforts are accompanied by strong measures to conserve wetlands.

Understanding Demographic and Behavioral Mechanisms that Guide Responses of Neotropical Migratory Birds to Urbanization: a Simulation Approach

Although studies often report that densities of many forest birds are negatively related to urbanization, the mechanisms guiding this pattern are poorly understood. Our objective was to use a population simulation to examine the relative influence of six demographic and behavioral processes on patterns of avian abundance in urbanizing landscapes. We constructed an individual-based population simulation model representing the annual cycle of a Neotropical migratory songbird. Each simulation was performed under two landscape scenarios. The first scenario had similar proportions of high- and low-quality habitat across the urban to rural gradient. Under the first scenario, avian density was negatively related to urbanization only when rural habitats were perceived to be of higher quality than they actually were. The second landscape scenario had declining proportions of high-quality habitat as urbanization increased. Under the second scenario, each mechanism generated a negative relationship between density and urbanization. The strongest effect on density resulted when birds preferentially selected habitats in landscapes from which they fledged or were constrained from dispersing. The next strongest patterns occurred when birds directly evaluated habitat quality and accurately selected the highest-quality available territories. When birds selected habitats based on the presence of conspecifics, the density–urbanization relationship was only one-third the strength of other habitat selection mechanisms and only occurred under certain levels of population survival. Although differences in adult or nest survival in the face of random habitat selection still elicited reduced densities in urban landscapes, the relationships between urbanization and density were weaker than those produced by the conspecific attraction mechanism. Results from our study identify key predictions and areas for future research, including assessing habitat quality in urban and rural areas in order to determine if habitats in urban areas are underutilized.

Nonbreeding-Season Drivers of Population Dynamics in Seasonal Migrants: Conservation Parallels Across Taxa

For seasonal migrants, logistical constraints have often limited conservation efforts to improving survival and reproduction during the breeding season only. Yet, mounting empirical evidence suggests that events occurring throughout the migratory life cycle can critically alter the demography of many migrant species. Herein, we build upon recent syntheses of avian migration research to review the role of non-breeding seasons in determining the population dynamics and fitness of diverse migratory taxa, including salmonid fishes, marine mammals, ungulates, sea turtles, butterflies, and numerous bird groups. We discuss several similarities across these varied migrants: (i) non-breeding survivorship tends to be a strong driver of population growth; (ii) non-breeding events can affect fitness in subsequent seasons through seasonal interactions at individual- and population-levels; (iii) broad-scale climatic influences often alter non-breeding resources and migration timing, and may amplify population impacts through covariation among seasonal vital rates; and (iv) changes to both stationary and migratory non-breeding habitats can have important consequences for abundance and population trends. Finally, we draw on these patterns to recommend that future conservation research for seasonal migrants will benefit from: (1) more explicit recognition of the important parallels among taxonomically diverse migratory animals; (2) an expanded research perspective focused on quantification of all seasonal vital rates and their interactions; and (3) the development of detailed population projection models that account for complexity and uncertainty in migrant population dynamics.