Structure of the N intermediate of bacteriorhodopsin revealed by x-ray diffraction.

X-ray diffraction experiments revealed the structure of the N photointermediate of bacteriorhodopsin. Since the retinal Schiff base is reprotonated from Asp-96 during the M to N transition in the photocycle, and Asp-96 is reprotonated during the lifetime of the N intermediate, or immediately after, N is a key intermediate for understanding the light-driven proton pump. The N intermediate accumulates in large amounts during continuous illumination of the F171C mutant at pH 7 and 5 degrees Celsius. Small but significant changes of the structure were detected in the x-ray diffraction profile under these conditions. The changes were reversible and reproducible. The difference Fourier map indicates that the major change occurs near helix F. The observed diffraction changes between N and the original state were essentially identical to the diffraction changes reported for the M intermediate of the D96N mutant of bacteriorhodopsin. Thus, we find that the protein conformations of the M and N intermediates of the photocycle are essentially the same, in spite of the fact that in M the Schiff base is unprotonated and in N it is protonated. The observed structural change near helix F will increase access of the Schiff base and Asp-96 to the cytoplasmic surface and facilitate the proton transfer events that begin with the decay of the M state.

An RNA structure involved in feedback regulation of splicing and of translation is critical for biological fitness.

While studies of the regulation of gene expression have generally concerned qualitative changes in the selection or the level of expression of a gene, much of the regulation that occurs within a cell involves the continuous subtle optimization of the levels of proteins used in macromolecular complexes. An example is the biosynthesis of the ribosome, in which equimolar amounts of nearly 80 ribosomal proteins must be supplied by the cytoplasm to the nucleolus. We have found that the transcript of one of the ribosomal protein genes of Saccharomyces cerevisiae, RPL32, participates in such fine tuning. Sequences from exon I of the RPL32 transcript interact with nucleotides from the intron to form a structure that binds L32 to regulate splicing. In the spliced transcript, the same sequences interact with nucleotides from exon II to form a structure that binds L32 to regulate translation, thus providing two levels of autoregulation. We now show, by using a sensitive cocultivation assay, that these RNA structures and their interaction with L32 play a role in the fitness of the cell. The change of a single nucleotide within the 5' leader of the RPL32 transcript, which abolishes the site for L32 binding, leads to detectably slower growth and to eventual loss of the mutant strain from the culture. Experiments designed to assess independently the regulation of splicing and the regulation of translation are presented. These observations demonstrate that, in evolutionary terms, subtle regulatory compensations can be critical. The change in structure of an RNA, due to alteration of just one noncoding nucleotide, can spell the difference between biological success and failure.

Receptive field structure in the visual cortex: does selective stimulation induce plasticity?

Sensory areas of adult cerebral cortex can reorganize in response to long-term alterations in patterns of afferent signals. This long-term plasticity is thought to play a crucial role in recovery from injury and in some forms of learning. However, the degree to which sensory representations in primary cortical areas depend on short-term (i.e., minute to minute) stimulus variations remains unclear. A traditional view is that each neuron in the mature cortex has a fixed receptive field structure. An alternative view, with fundamentally different implications for understanding cortical function, is that each cell's receptive field is highly malleable, changing according to the recent history of the sensory environment. Consistent with the latter view, it has been reported that selective stimulation of regions surrounding the receptive field induces a dramatic short-term increase in receptive field size for neurons in the visual cortex [Pettet, M. W. & Gilbert, C. D. (1992) Proc. Natl. Acad. Sci. USA 89, 8366-8370]. In contrast, we report here that there is no change in either the size or the internal structure of the receptive field following several minutes of surround stimulation. However, for some cells, overall responsiveness increases. These results suggest that dynamic alterations of receptive field structure do not underlie short-term plasticity in the mature primary visual cortex. However, some degree of short-term adaptability could be mediated by changes in responsiveness.

Three-dimensional structure of a cysteine-rich repeat from the low-density lipoprotein receptor.

The low-density lipoprotein (LDL) receptor plays a central role in mammalian cholesterol metabolism, clearing lipoproteins which bear apolipoproteins E and B-100 from plasma. Mutations in this molecule are associated with familial hypercholesterolemia, a condition which leads to an elevated plasma cholesterol concentration and accelerated atherosclerosis. The N-terminal segment of the LDL receptor contains a heptad of cysteine-rich repeats that bind the lipoproteins. Similar repeats are present in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement. The first repeat of the human LDL receptor has been expressed in Escherichia coli as a glutathione S-transferase fusion protein, and the cleaved and purified receptor module has been shown to fold to a single, fully oxidized form that is recognized by the monoclonal antibody IgG-C7 in the presence of calcium ions. The three-dimensional structure of this module has been determined by two-dimensional NMR spectroscopy and shown to consist of a beta-hairpin structure, followed by a series of beta turns. Many of the side chains of the acidic residues, including the highly conserved Ser-Asp-Glu triad, are clustered on one face of the module. To our knowledge, this structure has not previously been described in any other protein and may represent a structural paradigm both for the other modules in the LDL receptor and for the homologous domains of several other proteins. Calcium ions had only minor effects on the CD spectrum and no effect on the 1H NMR spectrum of the repeat, suggesting that they induce no significant conformational change.

On the possibility of coherently stimulated recombination and cosmological structure generation: recombination instability.

Possible instabilities during cosmological recombination may produce an epoch of nonlinear density growth and fractal-like structural patterns out to the horizon scale at that epoch (approximately 200 Mpc today). With this motivation, we examine the consequences of the change in effective radiative recombination reaction rate coefficients produced by intense stimulated emission. The proton-electron recombination is considered as a natural laser, leading to the formation of spatially nonuniform distributions of neutral matter earlier than the recombination epoch.

Rethinking cell structure.

Cell structure, emerging from behind the veil of conventional electron microscopy, appears far more complex than formerly realized. The standard plastic-embedded, ultrathin section can image only what is on the section surface and masks the elaborate networks of the cytoplasm and nucleus. Embedment-free electron microscopy gives clear, high-contrast micrographs of cell structure when combined with removal of obscuring material such as soluble proteins. The resinless ultrathin section is the technique of choice; it is simple and inexpensive, and it uses ordinary electron microscopes. The resulting pictures reveal a world of complex cell structure and function. These images necessarily change our conception of the cytoskeleton, nuclear matrix, mitosis, and the relation of membranes to cytostructure.

Soil quality response to land-use change for sugarcane expansion in Brazil

Globally, increasing demands for biofuels have intensified the rate of land-use change (LUC) for expansion of bioenergy crops. In Brazil, the world\'s largest sugarcane-ethanol producer, sugarcane area has expanded by 35% (3.2 Mha) in the last decade. Sugarcane expansion has resulted in extensive pastures being subjected to intensive mechanization and large inputs of agrochemicals, which have direct implications on soil quality (SQ). We hypothesized that LUC to support sugarcane expansion leads to overall SQ degradation. To test this hypothesis we conducted a field-study at three sites in the central-southern region, to assess the SQ response to the primary LUC sequence (i.e., native vegetation to pasture to sugarcane) associated to sugarcane expansion in Brazil. At each land use site undisturbed and disturbed soil samples were collected from the 0-10, 10-20 and 20-30 cm depths. Soil chemical and physical attributes were measured through on-farm and laboratory analyses. A dataset of soil biological attributes was also included in this study. Initially, the LUC effects on each individual soil indicator were quantified. Afterward, the LUC effects on overall SQ were assessed using the Soil Management Assessment Framework (SMAF). Furthermore, six SQ indexes (SQI) were developed using approaches with increasing complexity. Our results showed that long-term conversion from native vegetation to extensive pasture led to soil acidification, significant depletion of soil organic carbon (SOC) and macronutrients [especially phosphorus (P)] and severe soil compaction, which creates an unbalanced ratio between water- and air-filled pore space within the soil and increases mechanical resistance to root growth. Conversion from pasture to sugarcane improved soil chemical quality by correcting for acidity and increasing macronutrient levels. Despite those improvements, most of the P added by fertilizer accumulated in less plant-available P forms, confirming the key role of organic P has in providing available P to plants in Brazilian soils. Long-term sugarcane production subsequently led to further SOC depletions. Sugarcane production had slight negative impacts on soil physical attributes compared to pasture land. Although tillage performed for sugarcane planting and replanting alleviates soil compaction, our data suggested that the effects are short-term with persistent, reoccurring soil consolidation that increases erosion risk over time. These soil physical changes, induced by LUC, were detected by quantitative soil physical properties as well as by visual evaluation of soil structure (VESS), an on-farm and user-friendly method for evaluating SQ. The SMAF efficiently detected overall SQ response to LUC and it could be reliably used under Brazilian soil conditions. Furthermore, since all of the SQI values developed in this study were able to rank SQ among land uses. We recommend that simpler and more cost-effective SQI strategies using a small number of carefully chosen soil indicators, such as: pH, P, K, VESS and SOC, and proportional weighting within of each soil sectors (chemical, physical and biological) be used as a protocol for SQ assessments in Brazilian sugarcane areas. The SMAF and SQI scores suggested that long-term conversion from native vegetation to extensive pasture depleted overall SQ, driven by decreases in chemical, physical and biological indicators. In contrast, conversion from pasture to sugarcane had no negative impacts on overall SQ, mainly because chemical improvements offset negative impacts on biological and physical indicators. Therefore, our findings can be used as scientific base by farmers, extension agents and public policy makers to adopt and develop management strategies that sustain and/or improving SQ and the sustainability of sugarcane production in Brazil.

A Discursive Perspective on China's Global Politics of Climate Change, 1992-2013

This dissertation investigates China’s recent shift in its climate change policy with a refined discourse approach. Methodologically, by adopting a neo-Gramscian notion of hegemony, a generative definition of discourse and an ontological pluralist position, the study constructs a theoretical framework named “discursive hegemony” that identifies the “social forces” for enabling social change and focuses on the role of discursive mechanisms via which the forces operate and produce effects. The key empirical finding of this study was that it was a co-evolution of conditions that shaped the outcome as China’s climate policy shift. In examining the case, a before-after within-case comparison was designed to analyze the variations in the material, institutional, and ideational conditions, with methods including interviews, conventional narrative/text analysis and descriptive statistics. Specifically, changes in energy use, the structure of decision-making body, and the narratives about sustainable development reflected how the above three types of social force processed in China in the first few years of the 21st century, causing the economic development agenda to absorb the climate issue, and turning the policy frame for the latter from mainly a diplomatic matter to a potential opportunity for better-quality growth. With the discursive operation of the “Science-based development”, China’s energy policy has been a good example of the Chinese understanding of sustainability characterized by economic primacy, ecological viability and social green-engineering. This way of discursive evolution, however, is a double-edged sword that has pushed forward some fast, top-down mitigation measures on the one hand, but has also created and will likely continue creating social and ecological havoc on the other hand. The study makes two major contributions. First and on the empirical level, because China is an international actor that was not expected to cooperate on the climate issue according to major IR theories, this study would add one critical case to the studies on global (environmental) governance and the ideational approach in the IR discipline. Second and on the theory-building level, the model of discursive hegemony can be a causally deeper mode of explanation because it traces the process of co-evolution of social forces.

Ethnogenesis and Craniofacial Change in Japan from the Perspective of Nonmetric Traits

To examine population affinities in light of the ‘dual structure model’, frequencies of 21 nonmetric cranial traits were analyzed in 17 prehistoric to recent samples from Japan and five from continental northeast Asia. Eight bivariate plots, each representing a different bone or region of the skull, as well as cluster analysis of 21-trait mean measures of divergence using multidimensional scaling and additive tree techniques, revealed good discrimination between the Jomon-Ainu indigenous lineage and that of the immigrants who arrived from continental Asia after 300 BC. In Hokkaido, in agreement with historical records, Ainu villages of Hidaka province were least, and those close to the Japan Sea coast were most, hybridized with Wajin. In the central islands, clines were identified among Wajin skeletal samples whereby those from Kyushu most resembled continental northeast Asians, while those from the northernmost prefectures of Tohoku apparently retained the strongest indigenous heritage. In the more southerly prefectures of Tohoku, stronger traces of Jomon ancestry prevailed in the cohort born during the latest Edo period than in the one born after 1870. Thus, it seems that increased inter-regional mobility and gene flow following the Meiji Restoration initiated the most recent episode in the long process of demic diffusion that has helped to shape craniofacial change in Japan.

Les effets du dalcetrapib, un inhibiteur de la protéine de transfert des esters de cholestérol (CETP), sur la structure et la fonction des lipoprotéines de haute densité (HDL) dans l’étude dal-PLAQUE2

Introduction : Le dalcetrapib, inhibiteur de la glycoprotéine hydrophobe de transfert des esters de cholestérol (CETP), a été étudié dans le cadre de l’essai clinique de phase II dal-PLAQUE2 (DP2). L’objectif principal est d’étudier l’effet du dalcetrapib après 1 an de traitement sur la structure et la fonction des HDL dans une sous-population de la cohorte DP2. Méthode : Les sujets de la cohorte DP2 ayant une série de mesures de cIMT et des échantillons de plasma et sérum au baseline et à 1 an de traitement furent sélectionnés (379 sujets: 193 du groupe placebo (PCB) et 186 du groupe dalcetrapib (DAL)). Des données biochimiques prédéterminées, le profil des concentrations et tailles des sous-classes de HDL et LDL en résonance magnétique nucléaire (RMN) et 2 mesures de capacité d’efflux de cholestérol (CEC) du sérum ont été explorées. Les données statistiques furent obtenues en comparant les changements à un an à partir du « baseline » avec un ANOVA ou ANCOVA. La procédure normalisée de fonctionnement d’essai d’efflux de cholestérol permet de calculer l’efflux fractionnel (en %) de 3H-cholestérol des lignées cellulaires BHK-ABCA1 (fibroblastes) et J774 (macrophages, voie ABCA1) et HepG2 (hépatocytes, voie SR-BI), vers les échantillons sériques de la cohorte DP2. Résultats : Pour la biochimie plasmatique, un effet combiné des changements d’activité de CETP dans les 2 groupes a causé une réduction de 30% dans le groupe DAL. Après 1 an de traitement dans le groupe DAL, la valeur de HDL-C a augmenté de 35,5% (p < 0,001) et l’apoA-I a augmenté de 14,0% (p < 0,001). Au profil RMN, dans le groupe DAL après 1 an de traitement, il y a augmentation de la taille des HDL-P (5,2%; p < 0,001), des grosses particules HDL (68,7%; p < 0,001) et des grosses particules LDL (37,5%; p < 0,01). Les petites particules HDL sont diminuées (-9,1%; p < 0,001). Il n’y a aucune différence significative de mesure de cIMT entre les deux groupes après 1 an de traitement. Pour la CEC, il y a augmentation significative par la voie du SR-BI et une augmentation via la voie ABCA1 dans le groupe DAL après 1 an de traitement. Conclusion : Après un an de traitement au dalcetrapib, on note une hausse de HDL-C, des résultats plutôt neutres au niveau du profil lipidique par RMN et une CEC augmentée mais trop faible pour affecter la valeur de cIMT chez les échantillons testés.

EU actorness and effectiveness under political pressure at the Copenhagen climate change negotiations

This paper analyses the extent of European Union (EU) actorness and effectiveness at the fifteenth United Nations Framework Convention on Climate Change (UNFCCC) Conference of the Parties (COP) meeting in Copenhagen in December 2009. For over a decade the European Union has been characterised as a leader in international climate policy-making and as an important actor in international climate change negotiations. The COP15 meeting in Copenhagen has overall brought about disappointing outcomes, especially from the perspective of the European Union. This casts doubts on EU leadership and begs the question of what has happened to EU actorness and effectiveness in this field. In terms of actorness we take Jupille and Caporaso (1998) as a point of departure and then specify a more parsimonious actorness framework that consists of cohesion and autonomy. Effectiveness (i.e. goal attainment) is seen as conceptually separate from actorness. Effectiveness is conceptualised as the result of actorness conditioned by the ‘opportunity structure’, i.e. the external context (of other actors, events and ideas) that enables or constrains EU actions. We hold that the EU’s actorness has been only moderate, especially given somewhat limited preference cohesion. In terms of the opportunity structure in Copenhagen we argue that the high degree of politicisation constrained the EU’s ability to negotiate and thus to attain its goals. Another external factor that had a substantial adverse impact on the EU’s effectiveness at the Copenhagen negotiations was the strong involvement of other actors with rather different positions, namely the United States (US) and the BASIC countries (Brazil, South Africa, India, and China).

Climate change in mountain regions: how local communities adapt to extreme events

This paper examines how local communities adapt to climate change and how governance structures can foster or undermine adaptive capacity. Climate change policies, in general, and disaster risk management in mountain regions, in particular, are characterised by their multi-level and multi-sectoral nature during formulation and implementation. The involvement of numerous state and non-state actors at local to national levels produces a variety of networks of interaction and communication. The paper argues that the structure of these relational patterns is critical for understanding adaptive capacity. It thus proposes an expanded concept of adaptive capacity that incorporates (horizontal and vertical) actor integration and communication flow between these actors. The paper further advocates the use of formal social network analysis to assess these relational patterns. Preliminary results from research on adaptation to climate change in a Swiss mountain region vulnerable to floods and other natural hazards illustrate the conceptual and empirical significance of the main arguments.

Education and Development : A spatial-econometric approach on spatial change and permanence in southern Brazil

The Brazilian state of Paraná exhibits a violent geography of inequality and duality, hosting both the most developed city in the country, internationally recognized by its urban and environmental innovations, and southern Brazil’s most concentrated cluster of poverty and underdevelopment. Over the course of the past decades, the state underwent a major economic transformation, modernizing and increasing its industrial structure and shifting to the service sector with a larger participation of the knowledge economy. This study is concerned on the interplay between formal education and socioeconomic development during this process, and above all its spatial character. It attempts make sense of the rich literature on education and growth and/or development, discussing it through the lenses of human geography and planning. In order for the analysis to be possible, this study created a consistent database of municipal scores of education over the course of 40 years, dealing with changing census methodologies and municipal boundaries. Making use of modern exploratory spatial data analysis combined with spatial regressions, the study identifies a clustered, time-persistent interplay between education and development that is stronger for low and basic levels of education. Moreover, it provides evidence that not only education is a predictor of future development, but also that analyses of this kind must take into consideration spatial autocorrelation in order to be accurate.

Mapping hippocampal and ventricular change in Alzheimer disease

We developed an anatomical mapping technique to detect hippocampal and ventricular changes in Alzheimer disease (AD). The resulting maps are sensitive to longitudinal changes in brain structure as the disease progresses. An anatomical surface modeling approach was combined with surface-based statistics to visualize the region and rate of atrophy in serial MRI scans and isolate where these changes link with cognitive decline. Fifty-two high-resolution MRI scans were acquired from 12 AD patients (age: 68.4 +/- 1.9 years) and 14 matched controls (age: 71.4 +/- 0.9 years), each scanned twice (2.1 +/- 0.4 years apart). 3D parametric mesh models of the hippocampus and temporal horns were created in sequential scans and averaged across subjects to identify systematic patterns of atrophy. As an index of radial atrophy, 3D distance fields were generated relating each anatomical surface point to a medial curve threading down the medial axis of each structure. Hippocampal atrophic rates and ventricular expansion were assessed statistically using surface-based permutation testing and were faster in AD than in controls. Using color-coded maps and video sequences, these changes were visualized as they progressed anatomically over time. Additional maps localized regions where atrophic changes linked with cognitive decline. Temporal horn expansion maps were more sensitive to AD progression than maps of hippocampal atrophy, but both maps correlated with clinical deterioration. These quantitative, dynamic visualizations of hippocampal atrophy and ventricular expansion rates in aging and AD may provide a promising measure to track AD progression in drug trials. (C) 2004 Elsevier Inc. All rights reserved.