Structure, dynamics, and interactions of jacalin. Insights from molecular dynamics simulations examined in conjunction with results of X-ray studies

Molecular dynamics simulations have been carried out on all the jacalin-carbohydrate complexes of known structure, models of unliganded molecules derived from the complexes and also models of relevant complexes where X-ray structures are not available. Results of the simulations and the available crystal structures involving jacalin permit delineation of the relatively rigid and flexible regions of the molecule and the dynamical variability of the hydrogen bonds involved in stabilizing the structure. Local flexibility appears to be related to solvent accessibility. Hydrogen bonds involving side chains and water bridges involving buried water molecules appear to be important in the stabilization of loop structures. The lectin-carbohydrate interactions observed in crystal structures, the average parameters pertaining to them derived from simulations, energetic contribution of the stacking residue estimated from quantum mechanical calculations, and the scatter of the locations of carbohydrate and carbohydrate-binding residues are consistent with the known thermodynamic parameters of jacalin-carbohydrate interactions. The simulations, along with X-ray results, provide a fuller picture of carbohydrate binding by jacalin than provided by crystallographic analysis alone. The simulations confirm that in the unliganded structures water molecules tend to occupy the positions occupied by carbohydrate oxygens in the lectin-carbohydrate complexes. Population distributions in simulations of the free lectin, the ligands, and the complexes indicate a combination of conformational selection and induced fit. Proteins 2009; 77:760-777.

Modelling heterogeneity of concrete using 2D lattice network for concrete fracture and comparison with AE study

In this paper, numerical modelling of fracture in concrete using two-dimensional lattice model is presented and also a few issues related to lattice modelling technique applicable to concrete fracture are reviewed. A comparison is made with acoustic emission (AE) events with the number of fractured elements. To implement the heterogeneity of the plain concrete, two methods namely, by generating grain structure of the concrete using Fuller's distribution and the concrete material properties are randomly distributed following Gaussian distribution are used. In the first method, the modelling of the concrete at meso level is carried out following the existing methods available in literature. The shape of the aggregates present in the concrete are assumed as perfect spheres and shape of the same in two-dimensional lattice network is circular. A three-point bend (TPB) specimen is tested in the experiment under crack mouth opening displacement (CMOD) control at a rate of 0.0004 mm/sec and the fracture process in the same TPB specimen is modelled using regular triangular 2D lattice network. Load versus crack mouth opening isplacement (CMOD) plots thus obtained by using both the methods are compared with experimental results. It was observed that the number of fractured elements increases near the peak load and beyond the peak load. That is once the crack starts to propagate. AE hits also increase rapidly beyond the peak load. It is compulsory here to mention that although the lattice modelling of concrete fracture used in this present study is very similar to those already available in literature, the present work brings out certain finer details which are not available explicitly in the earlier works.

Global processes, local strategies : migration of educated Dominicans.

The aim of this thesis is to examine migration of educated Dominicans in light of global processes. Current global developments have resulted in increasingly global movements of people, yet people tend to come from certain places in large numbers rather than others. At the same time, international migration is increasingly selective, which shows in the disproportional number of educated migrants. This study discovers individual and societal motivations that explain why young educated Dominicans decide to migrate and return. The theoretical framework of this thesis underlines that migration is a dynamic process rooted in other global developments. Migratory movements should be seen as a result of interacting macro- and microstructures, which are linked by a number of intermediate mechanisms, meso-structures. The way individuals perceive opportunity structures concretises the way global developments mediate to the micro-level. The case of the Dominican Republic shows that there is a diversity of local responses to the world system, as Dominicans have produced their own unique historical responses to global changes. The thesis explains that Dominican migration is importantly conditioned by socioeconomic and educational background. Migration is more accessible for the educated middle class, because of the availability of better resources. Educated migrants also seem less likely to rely on networks to organize their migrations. The role of networks in migration differs by socioeconomic background on the one hand, and by the specific connections each individual has to current and previous migrants on the other hand. The personal and cultural values of the migrant are also pivotal. The central argument of this thesis is that a veritable culture of migration has evolved in the Dominican Republic. The actual economic, political and social circumstances have led many Dominicans to believe that there are better opportunities elsewhere. The globalisation of certain expectations on the one hand, and the development of the specifically Dominican feeling of ‘externalism’ on the other, have for their part given rise to the Dominican culture of migration. The study also suggests that the current Dominican development model encourages migration. Besides global structures, local structures are found to ve pivotal in determining how global processes are materialised in a specific place. The research for this thesis was conducted by using qualitative methodology. The focus of this thesis was on thematic interviews that reveal the subject’s point of view and give a fuller understanding of migration and mobility of the educated. The data was mainly collected during a field research phase in Santo Domingo, the Dominican Republic in December 2009 and January 2010. The principal material consists of ten thematic interviews held with educated Dominican current or former migrants. Four expert interviews, relevant empirical data, theoretical literature and newspaper articles were also comprehensively used.

Novel Approaches to the Sampling of Atmospheric Aerosols and Determination of Chemical Composition

The Earth s climate is a highly dynamic and complex system in which atmospheric aerosols have been increasingly recognized to play a key role. Aerosol particles affect the climate through a multitude of processes, directly by absorbing and reflecting radiation and indirectly by changing the properties of clouds. Because of the complexity, quantification of the effects of aerosols continues to be a highly uncertain science. Better understanding of the effects of aerosols requires more information on aerosol chemistry. Before the determination of aerosol chemical composition by the various available analytical techniques, aerosol particles must be reliably sampled and prepared. Indeed, sampling is one of the most challenging steps in aerosol studies, since all available sampling techniques harbor drawbacks. In this study, novel methodologies were developed for sampling and determination of the chemical composition of atmospheric aerosols. In the particle-into-liquid sampler (PILS), aerosol particles grow in saturated water vapor with further impaction and dissolution in liquid water. Once in water, the aerosol sample can then be transported and analyzed by various off-line or on-line techniques. In this study, PILS was modified and the sampling procedure was optimized to obtain less altered aerosol samples with good time resolution. A combination of denuders with different coatings was tested to adsorb gas phase compounds before PILS. Mixtures of water with alcohols were introduced to increase the solubility of aerosols. Minimum sampling time required was determined by collecting samples off-line every hour and proceeding with liquid-liquid extraction (LLE) and analysis by gas chromatography-mass spectrometry (GC-MS). The laboriousness of LLE followed by GC-MS analysis next prompted an evaluation of solid-phase extraction (SPE) for the extraction of aldehydes and acids in aerosol samples. These two compound groups are thought to be key for aerosol growth. Octadecylsilica, hydrophilic-lipophilic balance (HLB), and mixed phase anion exchange (MAX) were tested as extraction materials. MAX proved to be efficient for acids, but no tested material offered sufficient adsorption for aldehydes. Thus, PILS samples were extracted only with MAX to guarantee good results for organic acids determined by liquid chromatography-mass spectrometry (HPLC-MS). On-line coupling of SPE with HPLC-MS is relatively easy, and here on-line coupling of PILS with HPLC-MS through the SPE trap produced some interesting data on relevant acids in atmospheric aerosol samples. A completely different approach to aerosol sampling, namely, differential mobility analyzer (DMA)-assisted filter sampling, was employed in this study to provide information about the size dependent chemical composition of aerosols and understanding of the processes driving aerosol growth from nano-size clusters to climatically relevant particles (>40 nm). The DMA was set to sample particles with diameters of 50, 40, and 30 nm and aerosols were collected on teflon or quartz fiber filters. To clarify the gas-phase contribution, zero gas-phase samples were collected by switching off the DMA every other 15 minutes. Gas-phase compounds were adsorbed equally well on both types of filter, and were found to contribute significantly to the total compound mass. Gas-phase adsorption is especially significant during the collection of nanometer-size aerosols and needs always to be taken into account. Other aims of this study were to determine the oxidation products of β-caryophyllene (the major sesquiterpene in boreal forest) in aerosol particles. Since reference compounds are needed for verification of the accuracy of analytical measurements, three oxidation products of β-caryophyllene were synthesized: β-caryophyllene aldehyde, β-nocaryophyllene aldehyde, and β-caryophyllinic acid. All three were identified for the first time in ambient aerosol samples, at relatively high concentrations, and their contribution to the aerosol mass (and probably growth) was concluded to be significant. Methodological and instrumental developments presented in this work enable fuller understanding of the processes behind biogenic aerosol formation and provide new tools for more precise determination of biosphere-atmosphere interactions.

Global Processes, Local Strategies : migration of educated Dominicans.

The aim of this thesis is to examine migration of educated Dominicans in light of global processes. Current global developments have resulted in increasingly global movements of people, yet people tend to come from certain places in large numbers rather than others. At the same time, international migration is increasingly selective, which shows in the disproportional number of educated migrants. This study discovers individual and societal motivations that explain why young educated Dominicans decide to migrate and return. The theoretical framework of this thesis underlines that migration is a dynamic process rooted in other global developments. Migratory movements should be seen as a result of interacting macro- and microstructures, which are linked by a number of intermediate mechanisms, meso-structures. The way individuals perceive opportunity structures concretises the way global developments mediate to the micro-level. The case of the Dominican Republic shows that there is a diversity of local responses to the world system, as Dominicans have produced their own unique historical responses to global changes. The thesis explains that Dominican migration is importantly conditioned by socioeconomic and educational background. Migration is more accessible for the educated middle class, because of the availability of better resources. Educated migrants also seem less likely to rely on networks to organize their migrations. The role of networks in migration differs by socioeconomic background on the one hand, and by the specific connections each individual has to current and previous migrants on the other hand. The personal and cultural values of the migrant are also pivotal. The central argument of this thesis is that a veritable culture of migration has evolved in the Dominican Republic. The actual economic, political and social circumstances have led many Dominicans to believe that there are better opportunities elsewhere. The globalisation of certain expectations on the one hand, and the development of the specifically Dominican feeling of ‘externalism’ on the other, have for their part given rise to the Dominican culture of migration. The study also suggests that the current Dominican development model encourages migration. Besides global structures, local structures are found to ve pivotal in determining how global processes are materialised in a specific place. The research for this thesis was conducted by using qualitative methodology. The focus of this thesis was on thematic interviews that reveal the subject’s point of view and give a fuller understanding of migration and mobility of the educated. The data was mainly collected during a field research phase in Santo Domingo, the Dominican Republic in December 2009 and January 2010. The principal material consists of ten thematic interviews held with educated Dominican current or former migrants. Four expert interviews, relevant empirical data, theoretical literature and newspaper articles were also comprehensively used.

Interfacial shear rheology of highly confined glassy polymers

We present results on interfacial shear rheology measurements on Langmuir monolayers of two different polymers, poly(vinyl acetate) and poly(methyl methacrylate) as a function of surface concentration and temperature. While for the high glass transition poly(methyl methacrylate) polymer we find a systematic transition from a viscous dominated regime to an elastic dominated regime as surface concentration is increased, monolayers of the low glass transition polymer, poly(vinyl acetate), remain viscous even at very high surface concentrations. We further interpret the results in terms of the soft glassy rheology model of Sollich et al. P. Sollich, F. C. Lequeux, P. Hebraud and M. E. Cates, Phys. Rev. Lett., 1997, 78, 2020-2023] and provide evidence of possible reduction in glass transition temperatures in both poly(methyl methacrylate) and poly(vinyl acetate) monolayers due to finite size effects.

Legalidad y derecho natural institucional

Resumen: En su obra The morality of law, Lon Fuller pretende indicar ocho principios de la legalidad (principles of legality) que orientan la actividad de la legislación. La legalidad se presenta como un ejemplo de una concepción procedimental o institucional del derecho natural (procedure natural law o institutional natural law). El objeto del “iusnaturalismo institucional” de Fuller no es el contenido ético universal del derecho (derecho natural sustantivo), sino su modo formal-procedimental de existencia (derecho natural institucional). Este artículo tiene cuatro partes. Primero, el proyecto del iusnaturalismo institucional; segundo, los ocho principios de la legalidad de Fuller señalando su presencia también en las obras de Tomás de Aquino, Hobbes y Von Hayek; tercero, algunos conceptos de Wittgenstein y de John Searle que iluminan el aspecto metodológico del iusnaturalismo institucional y cuarto, se apuntará que el proyecto de un iusnaturalismo institucional ya está presente en la reflexión tomista sobre el ius gentium. En la conclusión, se recurrirá a las contribuciones de Jeremy Waldron para establecer el locus del iusnaturalismo institucional en el interior de la tradición iusnaturalista.

Field Guide to Nonindigenous Marine Fishes of Florida

The purpose of this field guide is to provide information on nonindigenous (i.e., non-native) fishes that have been observed in Florida’s marine waters. Introductions of non-native marine fishes into Florida’s waters could be intentional or unintentional, and are likely from a variety of sources, including aquarium releases, escape from aquaculture, loss due to extreme weather events (e.g., flooding from hurricanes), and possibly transfer with ballast water or hull-fouling. Presently the lionfishes (Pterois volitans and P. miles) are the only non-native marine fish species known to be established along the coast of Florida. All other marine fishes in this guide (except the euryhaline species, see below) have infrequent occurrences, occur singly or in small groups, and have not yet become self-sustaining populations. Aquarium releases are one of the major pathways whereby nonindigenous fishes gain access to new environments (Ruiz et al. 1997; Fuller et al. 1999). Most of the nonindigenous marine fishes found in Florida’s waters are thought to be aquarium fishes that either were illegally released into the ocean or escaped captivity (e.g., during severe storm/flooding events). Indeed, south Florida is a hotspot for nonindigenous marine aquarium fishes (Semmens et al. 2004). Increased public awareness of the problems caused by released or escaped aquarium fishes may aid in stemming the frequency of releases. For example, HabitattitudeTM (www.habitattitude.net) is a national public awareness and partnership campaign that encourages aquarists and water gardeners to prevent the release of unwanted aquarium plants, fish and other animals. It prompts hobbyists to adopt alternative actions when dealing with these aquatic plants and animals. (PDF file contains 133 pages.)

Predicting the effects of climate change on sea turtle nesting habitat in Florida

Rising global temperatures threaten the survival of many plant and animal species. Having already risen at an unprecedented rate in the past century, temperatures are predicted to rise between 0.3 and 7.5C in North America over the next 100 years (Hawkes et al. 2007). Studies have documented the effects of climate warming on phenology (timing of seasonal activities), with observations of early arrival at breeding grounds, earlier ends to the reproductive season, and delayed autumnal migrations (Pike et al. 2006). In addition, for species not suited to the physiological demands of cold winter temperatures, increasing temperatures could shift tolerable habitats to higher latitudes (Hawkes et al. 2007). More directly, climate warming will impact thermally sensitive species like sea turtles, who exhibit temperature-dependent sexual determination. Temperatures in the middle third of the incubation period determine the sex of sea turtle offspring, with higher temperatures resulting in a greater abundance of female offspring. Consequently, increasing temperatures from climate warming would drastically change the offspring sex ratio (Hawkes et al. 2007). Of the seven extant species of sea turtles, three (leatherback, Kemp’s ridley, and hawksbill) are critically endangered, two (olive ridley and green) are endangered, and one (loggerhead) is threatened. Considering the predicted scenarios of climate warming and the already tenuous status of sea turtle populations, it is essential that efforts are made to understand how increasing temperatures may affect sea turtle populations and how these species might adapt in the face of such changes. In this analysis, I seek to identify the impact of changing climate conditions over the next 50 years on the availability of sea turtle nesting habitat in Florida given predicted changes in temperature and precipitation. I predict that future conditions in Florida will be less suitable for sea turtle nesting during the historic nesting season. This may imply that sea turtles will nest at a different time of year, in more northern latitudes, to a lesser extent, or possibly not at all. It seems likely that changes in temperature and precipitation patterns will alter the distribution of sea turtle nesting locations worldwide, provided that beaches where the conditions are suitable for nesting still exist. Hijmans and Graham (2006) evaluate a range of climate envelope models in terms of their ability to predict species distributions under climate change scenarios. Their results suggested that the choice of species distribution model is dependent on the specifics of each individual study. Fuller et al. (2008) used a maximum entropy approach to model the potential distribution of 11 species in the Arctic Coastal Plain of Alaska under a series of projected climate scenarios. Recently, Pike (in press) developed Maxent models to investigate the impacts of climate change on green sea turtle nest distribution and timing. In each of these studies, a set of environmental predictor variables (including climate variables), for which ‘current’ conditions are available and ‘future’ conditions have been projected, is used in conjunction with species occurrence data to map potential species distribution under the projected conditions. In this study, I will take a similar approach in mapping the potential sea turtle nesting habitat in Florida by developing a Maxent model based on environmental and climate data and projecting the model for future climate data. (PDF contains 5 pages)

Nuclear weak interaction rates during stellar evolution and collapse

Nuclear weak interaction rates, including electron and positron emission rates, and continuum electron and positron capture rates , as well as the associated v and –/v energy loss rates are calculated on a detailed grid of temperature and density for the free nucleons and 226 nuclei with masses between A = 21 and 60. Gamow-Teller and Fermi discrete-state transition matrix element systematics and the Gamow-Teller T^< →/← T^> resonance transitions are discussed in depth and are implemented in the stellar rate calculations. Results of the calculations are presented on an abbreviated grid of temperature and density and comparison is made to terrestrial weak transition rates where possible. Neutron shell blocking of allowed electron capture on heavy nuclei during stellar core collapse is discussed along with several unblocking mechanisms operative at high temperature and density. The results of one-zone collapse calculations are presented which suggest that the effect of neutron shell blocking is to produce a larger core lepton fraction at neutrino trapping which leads to a larger inner-core mass and hence a stronger post-bounce shock.

Designing conformational control of human tissue transglutaminase

Understanding the mechanisms of enzymes is crucial for our understanding of their role in biology and for designing methods to perturb or harness their activities for medical treatments, industrial processes, or biological engineering. One aspect of enzymes that makes them difficult to fully understand is that they are in constant motion, and these motions and the conformations adopted throughout these transitions often play a role in their function.

Traditionally, it has been difficult to isolate a protein in a particular conformation to determine what role each form plays in the reaction or biology of that enzyme. A new technology, computational protein design, makes the isolation of various conformations possible, and therefore is an extremely powerful tool in enabling a fuller understanding of the role a protein conformation plays in various biological processes.

One such protein that undergoes large structural shifts during different activities is human type II transglutaminase (TG2). TG2 is an enzyme that exists in two dramatically different conformational states: (1) an open, extended form, which is adopted upon the binding of calcium, and (2) a closed, compact form, which is adopted upon the binding of GTP or GDP. TG2 possess two separate active sites, each with a radically different activity. This open, calcium-bound form of TG2 is believed to act as a transglutaminse, where it catalyzes the formation of an isopeptide bond between the sidechain of a peptide-bound glutamine and a primary amine. The closed, GTP-bound conformation is believed to act as a GTPase. TG2 is also implicated in a variety of biological and pathological processes.

To better understand the effects of TG2’s conformations on its activities and pathological processes, we set out to design variants of TG2 isolated in either the closed or open conformations. We were able to design open-locked and closed-biased TG2 variants, and use these designs to unseat the current understanding of the activities and their concurrent conformations of TG2 and explore each conformation’s role in celiac disease models. This work also enabled us to help explain older confusing results in regards to this enzyme and its activities. The new model for TG2 activity has immense implications for our understanding of its functional capabilities in various environments, and for our ability to understand which conformations need to be inhibited in the design of new drugs for diseases in which TG2’s activities are believed to elicit pathological effects.

Descripción de la morfología externa e interna del langostino con algunas aplicaciones de indole taxonómica y biológica

In the present paper the external and internal morphology of the shrimp Pleoticus muelleri (Bate), is described in detail. Special attention is given to those features which are of diagnostic value or which are significant for a fuller understanding of the biology of this species. The major portion of the paper deals with the description of the cephalopereion, pleon and telson and its appendages, as well as the nervous, respiratory, circulatory, digestive, excretory and reproductive systems. Special attention is given to the digestive system, the stomodaeal apparatus and sexual dimorphism. The relations between form and function of several organs and systems are pointed out. A study is made of the development of the gonads, the sexual cycle in males and females; the variations found in relative weight and size are described. The phylogenetical jposition of the Penaeidae, the genera of the subfamily Solenoceridae and of P. muelleri are discussed. (PDF contains 72 pages)

Autonomia docente do conhecimento científico ao senso comum: uma representação social dos professores de Duque de Caxias

O presente texto vem apresentar a pesquisa Autonomia Docente do conhecimento científico ao senso comum: uma representação social dos professores de Duque de Caxias, cujo objetivo é investigar a autonomia, procurando caracterizar, descrever e comparar as representações sociais que os professores da rede municipal de Duque de Caxias constroem em relação à autonomia docente a partir dos discursos oficiais e extra-oficiais. Teve como espaços de estudo escolas públicas pertencentes ao município de Duque de Caxias - Rio de Janeiro. Pesquisou-se 200 professores da educação infantil ao segundo segmento do ensino fundamental da rede municipal de Duque de Caxias, separados em dois grupos: professores regentes de turma e professores que desempenham funções técnico-pedagógica (orientadores educacionais, orientadores pedagógicos). Como técnicas de coleta de dados foram utilizadas um teste de associação livre de palavras com todos os sujeitos e entrevista semi-estruturada com 10% da população pesquisada, ou seja, 20 sujeitos. Para análise de dados foram utilizados o software EVOC (para evocações) e análise de conteúdo (para as entrevistas). Como resultado encontrou-se a centralidade da representação social da autonomia docente nos elementos liberdade, compromisso e responsabilidade. Na comparação entre os dois subgrupos constatou-se que para ambos a representação social é a mesma, pois os elementos centrais permanecem os mesmos já citados, significando que a autonomia não é apenas uma conquista individual, mas também coletiva. Dos resultados apresentados pode-se concluir que para os sujeitos pesquisados a representação social da autonomia docente encerra uma forte dimensão valorativa, em que o professor considera tanto a liberdade, compreendida como condição indispensável para a profissão, a responsabilidade e o compromisso social.