Seawater carbonate chemistry and processes during experiments with amphipod Gammarus locusta, 2009

We report an investigation of the effects of increases in pCO2 on the survival, growth and molecular physiology of the neritic amphipod Gammarus locusta which has a cosmopolitan distribution in estuaries. Amphipods were reared from juvenile to mature adult in laboratory microcosms at three different levels of pH in nominal range 8.1-7.6. Growth rate was estimated from weekly measures of body length. At sexual maturity the amphipods were sacrificed and assayed for changes in the expression of genes coding for a heat shock protein (hsp70 gene) and the metabolic enzyme glyceraldehyde-3-phosphate dehydrogenase (gapdh gene). The data show that the growth and survival of this species is not significantly impacted by a decrease in sea water pH of up to 0.5 units. Quantitative real-time PCR analysis indicated that there was no significant effect of growth in acidified sea water on the sustained expression of the hsp70 gene. There was a consistent and significant increase in the expression of the gapdh gene at a pH of ~7.5 which, when combined with observations from other workers, suggests that metabolic changes may occur in response to acidification. It is concluded that sensitive assays of tissue physiology and molecular biology should be routinely employed in future studies of the impacts of sea water acidification as subtle effects on the physiology and metabolism of coastal marine species may be overlooked in conventional gross "end-point" studies of organism growth or mortality.

Seawater carbonate chemistry and processes during experiments with cyanobacterium Trichodesmium (IMS101), 2009

We investigated carbon acquisition by the N2-fixing cyanobacterium Trichodesmium IMS101 in response to CO2 levels of 15.1, 37.5, and 101.3 Pa (equivalent to 150, 370, and 1000 ppm). In these acclimations, growth rates as well as cellular C and N contents were measured. In vivo activities of carbonic anhydrase (CA), photosynthetic O2 evolution, and CO2 and HCO3- fluxes were measured using membrane inlet mass spectrometry and the 14C disequilibrium technique. While no differences in growth rates were observed, elevated CO2 levels caused higher C and N quotas and stimulated photosynthesis and N2 fixation. Minimal extracellular CA (eCA) activity was observed, indicating a minor role in carbon acquisition. Rates of CO2 uptake were small relative to total inorganic carbon (Ci) fixation, whereas HCO{3 contributed more than 90% and varied only slightly over the light period and between CO2 treatments. The low eCA activity and preference for HCO3- were verified by the 14C disequilibrium technique. Regarding apparent affinities, half-saturation concentrations (K1/2) for photosynthetic O2 evolution and HCO3- uptake changed markedly over the day and with CO2 concentration. Leakage (CO2 efflux : Ci uptake) showed pronounced diurnal changes. Our findings do not support a direct CO2 effect on the carboxylation efficiency of ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) but point to a shift in resource allocation among photosynthesis, carbon acquisition, and N2 fixation under elevated CO2 levels. The observed increase in photosynthesis and N2fixation could have potential biogeochemical implications, as it may stimulate productivity in N-limited oligotrophic regions and thus provide a negative feedback in rising atmospheric CO2 levels.

Policy processes and collective action in water reforms: the cases of Nicaragua and Suriname

Las reformas de agua en países en desarrollo suelen llevarse a cabo junto con cambios institucionales más profundos o, incluso, acompañadas de cambios constitucionales o de régimen político. Por lo tanto, los marcos institucionales adaptados a países gobernados sujetos al estado de derecho pueden no ser apropiados para contextos gobernados fundamentalmente, al menos en sus inicios, por instituciones informales o poco maduras. Esta tesis toma las reformas de agua como punto de partida y pretende contribuir a la literatura mediante una serie de análisis empíricos tanto del ámbito general como del plano individual o sujeto personal de la política del agua. En el ámbito general, el foco se pone en los factores que explican el fallo de la acción colectiva en dos contextos diferentes: 1) en la implementación de la nueva Ley de Aguas de Nicaragua y 2) en el mantenimiento y revitalización de las instituciones de riego en Surinam. En el plano del individuo, la investigación se centra en las decisiones de los usuarios de los recursos y analiza el papel crítico de las variables sociales para la gestión de los recursos comunes. Para ello, el método de investigación utilizado es mixto, combinando el análisis de entrevistas, encuestas y experimentos. En el ámbito general, los resultados muestran que las principales barreras para la implementación de la nueva Ley de Aguas de Nicaragua podrían tener su reflejo en el lenguaje de la Ley y, por tanto, en la forma en la que se definen y configuran las instituciones incluidas en dicha Ley. Así, la investigación demuestra que la implementación de políticas no puede ser estudiada o entendida sin tener en cuenta tanto el diseño de la propia política como el marco socio-ecológico en el que se enmarca. El contexto específico de Nicaragua remarca la importancia de considerar tanto las instituciones formales como informales en los procesos de transición política. A pesar de que las reformas de agua requieren plazos largos para su implementación, el hecho de que exista una diferencia entre las reglas tal cual se definen formalmente y las reglas que operan en la realidad merece una mayor consideración en el diseño de políticas basadas fundamentalmente en instituciones formales. En el ámbito de la conducta individual, el análisis de la acción colectiva ofrece una serie de observaciones empíricas interesantes. En el caso de Nicaragua, los resultados indican que la intensidad de las relaciones sociales, el tipo de agentes dispuestos a proporcionar apoyo social y el nivel de confianza en la comunidad son factores que explican de manera significativa la participación en la comunidad. Sin embargo, el hecho de que la gestión colectiva de riego se produzca, en la mayoría de casos, en torno a lazos familiares sugiere que las variables de capital social críticas se definen en gran medida en la esfera familiar, siendo difícil que se extiendan fuera de estos nexos. El análisis experimental de los resultados de un juego de uso de recurso común y contribución al bien público muestra que las preferencias pro-sociales de los individuos y la heterogeneidad del grupo en términos de composición por sexo son factores que explican significativamente los resultados y las decisiones de apropiación a lo largo del juego. En términos del diseño de las políticas, es fundamental tener en cuenta las dinámicas de participación y uso de los recursos comunes de manera que los niveles de cooperación puedan mantenerse en el largo plazo, lo cual, como se observa en el caso de Surinam, no es siempre posible. Finalmente, el caso de Surinam es un ejemplo ilustrativo de los procesos de acción colectiva en economías en transición. El análisis del fallo de la acción colectiva en Surinam muestra que los procesos políticos vinculados al período colonial y de independencia explican en gran medida la falta de claridad en las reglas operacionales y colectivas que gobiernan la gestión de los sistemas de riego y drenaje. Los resultados empíricos sugieren que a pesar de que la acción colectiva para la provisión de los servicios de riego y drenaje estaba bien establecida bajo el régimen colonial, la auto-organización no prosperó en un contexto dependiente del apoyo externo y regido fundamentalmente por reglas diseñadas al nivel competencial del gobierno central. El sistema socio-ecológico que se desarrolló durante la transición post-colonial favoreció, así, la emergencia de comportamientos oportunistas, y posteriormente la inoperancia de los Water Boards (WBs) creados en la época colonial. En este sentido, cualquier intento por revitalizar los WBs y fomentar el desarrollo de la auto-organización de los usuarios necesitará abordar los problemas relacionados con los patrones demográficos, incluyendo la distribución de la tierra, el diseño de instituciones y la falta de confianza en el gobierno, además de las inversiones típicas en infraestructura y sistemas de información hidrológicos. El liderazgo del gobierno, aportando empuje de arriba-abajo, es, además, otro elemento imprescindible en Surinam. ABSTRACT Water reforms in developing countries take place along deeper institutional and even constitutional. Therefore, institutional frameworks that might result in positive outcomes in countries governed by the rule of law might not fit in contexts governed mainly by informal or immature institutions. This thesis takes water reforms as the starting point and aims to contribute to the literature by presenting several conceptual and empirical analyses at both general and individual levels. At the general national level, the focus is on the factors explaining failure of collective action in two different settings: 1) in the implementation of the new Nicaraguan Water Law and 2) in sustaining and revitalizing irrigation institutions in Suriname. At the individual level, the research focuses on the actions of resource users and analyzes the critical role of social variables for common pool resources management. For this purpose, the research presented in this thesis makes use of a mixed-method approach, combining interviews, surveys and experimental methods. Overall, the results show that major barriers for the implementation of the new Nicaraguan Water Law have its reflection on the language of the Law and, therefore, on the way institutions are defined and configured. In this sense, our study shows that implementation cannot fruitfully be studied and understood without taking into account both the policy design and the social-ecological context in which it is framed. The specific setting of Nicaragua highlights the relevance of considering both formal and informal institutions when promoting policy transitions. Despite the unquestionable fact that water reforms implementation needs long periods of time, there is still a gap between the rules on paper and the rules on the ground that deserves further attention when proposing policy changes on the basis of formal institutions. At the level of the individual agent, the analysis of collective action provides a number of interesting empirical insights. In the case of Nicaragua, I found that the intensity of social networks, the type of agents willing to provide social support and the level of trust in the community are all significant factors in explaining collective action at community level. However, the fact that most collective irrigation relies on family ties suggests that critical social capital variables might be defined within the family sphere and making it difficult to go beyond it. Experimental research combining a common pool resource and a public good game in Nicaragua shows that individuals’ pro-social traits and group heterogeneity in terms of sex composition are significant variables in explaining efficiency outcomes and effort decisions along the game. Thus, with regard to policy design, it is fundamental to consider carefully the dynamics of agents' participation and use of common pool resources, for sustaining cooperation in the long term, which, as seen in the case and Surinam, is not always possible. The case of Suriname provides a rich setting for the analysis of collective action in transition economies. The analysis of decay of collective irrigation in Suriname shows that the lack of clear operational and collective choice rules appear to be rooted in deeper political processes that date back to the colonial period. The empirical findings suggest that despite collective action for the provision of irrigation and drainage services was well established during the colonial period, self-organization did not flourish in a context governed by colonial state-crafted rules and mostly dependent on external support. The social-ecological system developed during the post-colonial transition process favored the emergence of opportunistic behavior. In this respect, any attempt to revitalize WBs and support self-organization will need to tackle the problems derived from demographic patterns, including land allocation, institutions design and government distrust, in addition to the typical investments in both physical infrastructure and hydrological information systems. The leadership role of the government, acting as a top-down trigger, is another essential element in Suriname.

Changes in spatial point patterns of pioneer woody plants across a large tropical landslide

We assessed whether the relative importance of positive and negative interactions in early successional communities varied across a large landslide on Casita Volcano (Nicaragua). We tested several hypotheses concerning the signatures of these processes in the spatial patterns of woody pioneer plants, as well as those of mortality and recruitment events, in several zones of the landslide differing in substrate stability and fertility, over a period of two years (2001 and 2002). We identified all woody individuals with a diameter >1 cm and mapped them in 28 plots measuring 10 × 10-m. On these maps, we performed a spatial point pattern analysis using univariate and bivariate pair-correlation functions; g (r) and g12 (r), and pairwise differences of univariate and bivariate functions. Spatial signatures of positive and negative interactions among woody plants were more prevalent in the most and least stressful zones of the landslide, respectively. Natural and human-induced disturbances such as the occurrence of fire, removal of newly colonizing plants through erosion and clearcutting of pioneer trees were also identified as potentially important pattern-creating processes. These results are in agreement with the stress-gradient hypothesis, which states that the relative importance of facilitation and competition varies inversely across gradients of abiotic stress. Our findings also indicate that the assembly of early successional plant communities in large heterogeneous landslides might be driven by a much larger array of processes than previously thought.

Feo, inútil, inestable: pensamiento crítico contemporáneo y procesos proyectivos en arquitectura = Ugly, useless, unstable: contemporary critical thought and projective processes in architecture

La presente tesis doctoral persigue dos objetivos simultáneos: Determinar el alcance de los criterios clásicos para la evaluación de arquitectura y poner en crisis la prevalencia de esos mismos criterios dentro del marco crítico y productivo actual. En concreto, esta tesis se interroga sobre la posible contribución de determinadas corrientes del pensamiento post-estructuralista y neo-materialista a las tareas de expansión y transformación de los criterios clásicos antes mencionados. Asimismo, se plantea la oportunidad de formalizar estas incorporaciones conceptuales como metodologías para el proyectar arquitectónico. La tesis emplea un análisis pormenorizado de las cualidades implícitas en la triada Firmitas, Utilitas, Venustas elaborada por Vitruvio como vehículo para calibrar la influencia de los paradigmas de pensamiento clásico en nuestras posiciones críticas contemporáneas. Como reacción al carácter dominante de dichos paradigmas, y con la ayuda de una compilación selectiva de ejemplos procedentes de los campos artístico y arquitectónico, la presente tesis procede a examinar y clasificar diversas estrategias arquitectónicas basadas en la no conformidad con los criterios clásicos de evaluación de la disciplina. A la hora de realizar esta tarea, y con el objetivo de superar el dualismo trascendental que caracteriza la gran mayoría de dichos criterios clásicos, se propone un modelo analítico y multidimensional que formula las instancias arquitectónicas como posibles posiciones dentro de un extenso continuo combinatorio de cualidades formales, estructurales y organizativas. Este modelo conceptual permite replantear el aparente antagonismo entre los principios de Vitruvio y sus opuestos, estableciendo en su lugar un dominio operativo continuo de producción arquitectónica. Esta operación abre una ventana de oportunidad para expandir los límites del marco crítico actual más allá de las fronteras establecidas por nuestra herencia clásica. En consecuencia con esta voluntad, la presente tesis pretende habilitar un ámbito para el análisis crítico de las estrategias que caracterizan ciertas corrientes del proyectar contemporáneo, pero también contribuir a informar nuevas aproximaciones metodológicas al proceso de proyecto, desplazando progresivamente su foco desde lo descriptivo hacia lo proyectivo. ABSTRACT This doctoral thesis attempts to simultaneously determine the scope of the classical criteria for the evaluation of architecture and challenge their prevalence within the current framework of architectural production and criticism. It examines how specific strands of post-structuralism and neo-materialism may contribute to both the expansion and the transformation of these criteria and, in doing so, sets itself the goal of mobilising these conceptual incorporations as explicit design methodologies. A detailed analysis of the formal, structural and organisational qualities implicit in Vitruvius’ triad Firmitas, Utilitas, Venustas is used as a starting point to determine the influence of classical paradigms in our current critical positions. As a reaction to this critical pervasiveness, and supported by a curated collection of artistic and architectural works, diverse approaches to non-compliance with the classical criteria of assessment are examined and classified. In order to facilitate this endeavour -and to overcome the transcendental dualism of most classical critical approaches in architecture- this thesis puts forward an analytical, multidimensional model that formulates architectural instances as possible positions within a larger combinatory continuum of formal, structural and organisational qualities. Using this conceptual model, the apparent antagonism between Vitruvius’ principles and its non-compliant opposites is reframed as a continuous operative domain of architectural production, which in turn opens up a window of opportunity to expand the limits of our critical framework beyond the boundaries of classical paradigms. In doing so, this thesis attempts not only to foster a better understanding of some of the strategic approaches that characterise contemporary systems of architectural production, but also to inform future methodological approaches to architectural design, hence situating itself beyond the domain of the descriptive and moving towards the projective.

3D Maize Plant Reconstruction Based on Georeferenced Overlapping LiDAR Point Clouds

3D crop reconstruction with a high temporal resolution and by the use of non-destructive measuring technologies can support the automation of plant phenotyping processes. Thereby, the availability of such 3D data can give valuable information about the plant development and the interaction of the plant genotype with the environment. This article presents a new methodology for georeferenced 3D reconstruction of maize plant structure. For this purpose a total station, an IMU, and several 2D LiDARs with different orientations were mounted on an autonomous vehicle. By the multistep methodology presented, based on the application of the ICP algorithm for point cloud fusion, it was possible to perform the georeferenced point clouds overlapping. The overlapping point cloud algorithm showed that the aerial points (corresponding mainly to plant parts) were reduced to 1.5%–9% of the total registered data. The remaining were redundant or ground points. Through the inclusion of different LiDAR point of views of the scene, a more realistic representation of the surrounding is obtained by the incorporation of new useful information but also of noise. The use of georeferenced 3D maize plant reconstruction at different growth stages, combined with the total station accuracy could be highly useful when performing precision agriculture at the crop plant level.

The Development of Cell Processes Induced by tau Protein Requires Phosphorylation of Serine 262 and 356 in the Repeat Domain and Is Inhibited by Phosphorylation in the Proline-rich Domains

The differentiation of neurons and the outgrowth of neurites depends on microtubule-associated proteins such as tau protein. To study this process, we have used the model of Sf9 cells, which allows efficient transfection with microtubule-associated proteins (via baculovirus vectors) and observation of the resulting neurite-like extensions. We compared the phosphorylation of tau23 (the embryonic form of human tau) with mutants in which critical phosphorylation sites were deleted by mutating Ser or Thr residues into Ala. One can broadly distinguish two types of sites, the KXGS motifs in the repeats (which regulate the affinity of tau to microtubules) and the SP or TP motifs in the domains flanking the repeats (which contain epitopes for antibodies diagnostic of Alzheimer’s disease). Here we report that both types of sites can be phosphorylated by endogenous kinases of Sf9 cells, and that the phosphorylation pattern of the transfected tau is very similar to that of neurons, showing that Sf9 cells can be regarded as an approximate model for the neuronal balance between kinases and phosphatases. We show that mutations in the repeat domain and in the flanking domains have opposite effects. Mutations of KXGS motifs in the repeats (Ser262, 324, and 356) strongly inhibit the outgrowth of cell extensions induced by tau, even though this type of phosphorylation accounts for only a minor fraction of the total phosphate. This argues that the temporary detachment of tau from microtubules (by phosphorylation at KXGS motifs) is a necessary condition for establishing cell polarity at a critical point in space or time. Conversely, the phosphorylation at SP or TP motifs represents the majority of phosphate (>80%); mutations in these motifs cause an increase in cell extensions, indicating that this type of phosphorylation retards the differentiation of the cells.

Identification of the proton pathway in bacterial reaction centers: Both protons associated with reduction of QB to QBH2 share a common entry point

The reaction center from Rhodobacter sphaeroides uses light energy for the reduction and protonation of a quinone molecule, QB. This process involves the transfer of two protons from the aqueous solution to the protein-bound QB molecule. The second proton, H+(2), is supplied to QB by Glu-L212, an internal residue protonated in response to formation of QA− and QB−. In this work, the pathway for H+(2) to Glu-L212 was studied by measuring the effects of divalent metal ion binding on the protonation of Glu-L212, which was assayed by two types of processes. One was proton uptake from solution after the one-electron reduction of QA (DQA→D+QA−) and QB (DQB→D+QB−), studied by using pH-sensitive dyes. The other was the electron transfer kAB(1) (QA−QB→QAQB−). At pH 8.5, binding of Zn2+, Cd2+, or Ni2+ reduced the rates of proton uptake upon QA− and QB− formation as well as kAB(1) by ≈an order of magnitude, resulting in similar final values, indicating that there is a common rate-limiting step. Because D+QA− is formed 105-fold faster than the induced proton uptake, the observed rate decrease must be caused by an inhibition of the proton transfer. The Glu-L212→Gln mutant reaction centers displayed greatly reduced amplitudes of proton uptake and exhibited no changes in rates of proton uptake or electron transfer upon Zn2+ binding. Therefore, metal binding specifically decreased the rate of proton transfer to Glu-L212, because the observed rates were decreased only when proton uptake by Glu-L212 was required. The entry point for the second proton H+(2) was thus identified to be the same as for the first proton H+(1), close to the metal binding region Asp-H124, His-H126, and His-H128.

Characterization of rock slopes through slope mass rating using 3D point clouds

Rock mass classification systems are widely used tools for assessing the stability of rock slopes. Their calculation requires the prior quantification of several parameters during conventional fieldwork campaigns, such as the orientation of the discontinuity sets, the main properties of the existing discontinuities and the geo-mechanical characterization of the intact rock mass, which can be time-consuming and an often risky task. Conversely, the use of relatively new remote sensing data for modelling the rock mass surface by means of 3D point clouds is changing the current investigation strategies in different rock slope engineering applications. In this paper, the main practical issues affecting the application of Slope Mass Rating (SMR) for the characterization of rock slopes from 3D point clouds are reviewed, using three case studies from an end-user point of view. To this end, the SMR adjustment factors, which were calculated from different sources of information and processes, using the different softwares, are compared with those calculated using conventional fieldwork data. In the presented analysis, special attention is paid to the differences between the SMR indexes derived from the 3D point cloud and conventional field work approaches, the main factors that determine the quality of the data and some recognized practical issues. Finally, the reliability of Slope Mass Rating for the characterization of rocky slopes is highlighted.

Making the impossible possible: the prospects for visa-free movement between the EU and its eastern partners. OSW Point of View Number 27, May 2012

To make the abolition of visas in relations between the EU and the Eastern European countries possible, the ”spell cast” must be broken on this issue. With the present levels of mobility and people-to-people, business and political contacts the introduction of a visa-free regime will be a natural consequence of the liberalisation processes which have been at work for years.Moreover, the decision to lift the visa requirement is unlikely to significantly stimulate an increase in migration pressure from Eastern European countries but could reduce the operating costs of expanded Schengen consular network. Lifting the visa requirement for Eastern European citizens can be temporary and conditional and allow for actual implementation of an increased conditionality rule. In political terms, making visa liberalisation a key issue would fundamentally change the partners’ approach to the Eastern Partnership and would provide a link to the Partnership for Modernisation targeted at Russia.

Partnership in times of crisis: challenges for the Eastern European countries' integration with Europe. OSW Point of View Number 36, July 2013

Over the four years since its launch, the Eastern Partnership initiative has created frameworks and mechanisms for the integration of Eastern Partnership countries with the European Union. Despite this, the partner countries have so far made little meaningful progress in modernisation, implementation of reforms or integration with the EU.Since the European Neighbourhood Policy was launched in 2004, the situation in areas of key importance for the EU, such as democratisation, free-market transformations, European integration, political stability and regional security, has not improved significantly. In this context, it is legitimate to ask questions about the extent to which the European Neighbourhood Policy and the Eastern Partnership have brought the Union closer to achieving its declared objectives in the relations with eastern neighbours. What is the underlying cause of the dwindling involvement and declining interest in achieving real progress in integration? How may the events that have been dominating the political agenda – i.e. the EU’s financial crisis, the debate on the future of the Union, but also the political processes taking place within the partner countries – affect the future of mutual relations?

Unity stronger than divisions. Ukraine's internal diversity. OSW Point of View Number 40, March 2014

Ukraine is deeply divided internally, although as a result of the changes that have taken place since its independence, the country’s internal divisions now have less and less to do with territorial divides, and the split into historical ‘sub-Ukraines’ has become less pronounced, especially for the younger generation. Ukraine is not a country of two competing regional identities, one in the west, the other in the east. The western identity, in which the unity of Ukraine is a key value, coexists with the multiple and diverse local patriotisms of the different regions in the east and the south of the country. The present protest movement has consolidated the country’s sense of unity. Its opponents have also been championing the indivisibility of Ukraine, even while they demanded a thorough decentralisation of the country, which was often mistaken for separatism. Russia has been stirring up separatist tendencies in Ukraine, but with little success. Crimea is an exception here, because in most respects it has remained unaffected by the dynamics of the social processes transforming mainland Ukraine – separatist tendencies are indeed deeply rooted in the peninsula.

The invisible hand... of the Kremlin. Capitalism 'a la russe'. OSW Point of View, February 2007

This study describes the two main economic processes observed in Russia during President Vladimir Putin's second term; renationalisation, and the concentration of economic assets. As a result of these processes, the share of state-owned property has increased and the position of the state in the economy has strengthened. According to the authorities, the wide-range renationalisation of the assets and the construction of superholdings based on the state enterprises are intended to boost Russia's potential and stimulate the development of the whole economy. However, in practice the current ruling elite are using these superholdings to strengthen Russia's position on the international arena and to promote their vested interests.