Ligand-independent assembly of recombinant human CD1 by using oxidative refolding chromatography

CD1 is an MHC class I-like antigen-presenting molecule consisting of a heavy chain and β2-microglobulin light chain. The in vitro refolding of synthetic MHC class I molecules has always required the presence of ligand. We report here the use of a folding method using an immobilized chaperone fragment, a protein disulphide isomerase, and a peptidyl-prolyl cis-trans isomerase (oxidative refolding chromatography) for the fast and efficient assembly of ligand-free and ligand-associated CD1a and CD1b, starting with material synthesized in Escherichia coli. The results suggest that “empty” MHC class I-like molecules can assemble and remain stable at physiological temperatures in the absence of ligand. The use of oxidative refolding chromatography thus is extended to encompass complex multisubunit proteins and specifically to members of the extensive, functionally diverse and important immunoglobulin supergene family of proteins, including those for which a ligand has yet to be identified.

The structure of bovine F1-ATPase complexed with the antibiotic inhibitor aurovertin B.

In the structure of bovine mitochondrial F1-ATPase that was previously determined with crystals grown in the presence of adenylyl-imidodiphosphate (AMP-PNP) and ADP, the three catalytic beta-subunits have different conformations and nucleotide occupancies. Adenylyl-imidodiphosphate is bound to one beta-subunit (betaTP), ADP is bound to the second (betaDP), and no nucleotide is bound to the third (betaE). Here we show that the uncompetitive inhibitor aurovertin B binds to bovine F1 at two equivalent sites in betaTP and betaE, in a cleft between the nucleotide binding and C-terminal domains. In betaDP, the aurovertin B pocket is incomplete and is inaccessible to the inhibitor. The aurovertin B bound to betaTP interacts with alpha-Glu399 in the adjacent alphaTP subunit, whereas the aurovertin B bound to betaE is too distant from alphaE to make an equivalent interaction. Both sites encompass betaArg-412, which was shown by mutational studies to be involved in binding aurovertin. Except for minor changes around the aurovertin pockets, the structure of bovine F1-ATPase is the same as determined previously. Aurovertin B appears to act by preventing closure of the catalytic interfaces, which is essential for a catalytic mechanism involving cyclic interconversion of catalytic sites.

The viruses in all of us: characteristics and biological significance of human endogenous retrovirus sequences.

Human endogenous retroviruses (HERVs) are very likely footprints of ancient germ-cell infections. HERV sequences encompass about 1% of the human genome. HERVs have retained the potential of other retroelements to retrotranspose and thus to change genomic structure and function. The genomes of almost all HERV families are highly defective. Recent progress has allowed the identification of the biologically most active family, HTDV/HERV-K, which codes for viral proteins and particles and is highly expressed in germ-cell tumors. The demonstrable and potential roles of HTDV/HERV-K as well as of other human elements in disease and in maintaining genome plasticity are illustrated.

Método multigrid algébrico: reutilização das estruturas multigrid no transporte de contaminantes

A necessidade de obter solução de grandes sistemas lineares resultantes de processos de discretização de equações diferenciais parciais provenientes da modelagem de diferentes fenômenos físicos conduz à busca de técnicas numéricas escaláveis. Métodos multigrid são classificados como algoritmos escaláveis.Um estimador de erros deve estar associado à solução numérica do problema discreto de modo a propiciar a adequada avaliação da solução obtida pelo processo de aproximação. Nesse contexto, a presente tese caracteriza-se pela proposta de reutilização das estruturas matriciais hierárquicas de operadores de transferência e restrição dos métodos multigrid algébricos para acelerar o tempo de solução dos sistemas lineares associados à equação do transporte de contaminantes em meio poroso saturado. Adicionalmente, caracteriza-se pela implementação das estimativas residuais para os problemas que envolvem dados constantes ou não constantes, os regimes de pequena ou grande advecção e pela proposta de utilização das estimativas residuais associadas ao termo de fonte e à condição inicial para construir procedimentos adaptativos para os dados do problema. O desenvolvimento dos códigos do método de elementos finitos, do estimador residual e dos procedimentos adaptativos foram baseados no projeto FEniCS, utilizando a linguagem de programação PYTHONR e desenvolvidos na plataforma Eclipse. A implementação dos métodos multigrid algébricos com reutilização considera a biblioteca PyAMG. Baseado na reutilização das estruturas hierárquicas, os métodos multigrid com reutilização com parâmetro fixo e automática são propostos, e esses conceitos são estendidos para os métodos iterativos não-estacionários tais como GMRES e BICGSTAB. Os resultados numéricos mostraram que o estimador residual captura o comportamento do erro real da solução numérica, e fornece algoritmos adaptativos para os dados cuja malha retornada produz uma solução numérica similar à uma malha uniforme com mais elementos. Adicionalmente, os métodos com reutilização são mais rápidos que os métodos que não empregam o processo de reutilização de estruturas. Além disso, a eficiência dos métodos com reutilização também pode ser observada na solução do problema auxiliar, o qual é necessário para obtenção das estimativas residuais para o regime de grande advecção. Esses resultados englobam tanto os métodos multigrid algébricos do tipo SA quanto os métodos pré-condicionados por métodos multigrid algébrico SA, e envolvem o transporte de contaminantes em regime de pequena e grande advecção, malhas estruturadas e não estruturadas, problemas bidimensionais, problemas tridimensionais e domínios com diferentes escalas.

Fragmentação florestal e prioridades para a conservação da biodiversidade

Um modelo dedicado ao planejamento da conservação e restauração de habitats deve incluir informações estratégicas para assegurar a eficácia e de fácil obtenção, para assegurar a agilidade necessária. Planos e estratégias para conservação usualmente são complexos e demandam informações detalhadas, difíceis de se obter, como inventários biológicos e certos tipos de mapeamento, o que traz limitações em termos de disponibilidade, qualidade e custo das informações. Assim, procurou-se testar a eficiência de métodos simples para a seleção, em escala local, de áreas prioritárias para conservação de habitats fortemente fragmentados e reduzidos, uma situação comum no sul do Brasil, usando dados de imagens LANDSAT e planos de informações disponíveis em mapeamentos comuns, e trabalho de campo. Inicialmente analisou-se a estrutura da paisagem e o padrão de fragmentação em parte da região norte do estado do Paraná, e testar se tamanho e forma são adequados para selecionar os fragmentos florestais mais importantes para a conservação, ou seja, as que contribuem para manter maior quantidade e melhor qualidade de habitats, bem como tenham maior impacto (positivo) na conectividade e em outras variáveis da paisagem. Os resultados mostram que a floresta madura cobre cerca de 3% da paisagem, e a cobertura florestal total atinge perto de 8%, consistindo principalmente de pequenos fragmentos (82% tem entre 1 e 10 ha). Fragmentos grandes (>100 ha) são apenas 1,4% dos remanescentes, mas somam 34% da área de floresta. Apesar de estarem sujeitos a efeitos de borda em toda ou quase toda a sua área, fragmentos pequenos mostraram ter um papel importante na conectividade da paisagem. Numa área maior, foi feita uma pré-seleção de áreas com potencial para estabelecimento de redes de conservação. A pré-seleção procurou responder às seguintes perguntas: 1-Quais são os sítios com maior potencial para a conservação da biodiversidade? 2-Quais são os sítios sob maior risco para objetivos de conservação? e 3-Quais sítios têm melhores oportunidades para o estabelecimento de zonas de conservação de uso múltiplo? Foi identificado um conjunto de 11 fragmentos pertencendo a 5 sub-regiões, sofrendo variados graus de pressão antrópica. Adicionalmente, usando medidas simples de estrutura da paisagem, relacionadas com tamanho, forma e conectividade dos fragmentos, procurou-se identificar tipos estruturais de fragmentos, como uma forma alternativa para auxiliar o estabelecimento de prioridades para conservação a partir do seu papel, efetivo ou potencial, na paisagem. Foram identificados 5 tipos de fragmentos, pequenos (ilhotas isoladas, trampolins), médios (núcleos auxiliares e corredores) e grandes (núcleos principais), que podem ser usados para subsidiar estratégias de conservação. Utilizando informações sobre a estrutura da paisagem, hidrografia e legislação ambiental, propõe-se aqui uma estratégia de conservação para o complexo das bacias dos ribeirões Apertados-Três Bocas (CATB), ordenando atividades de restauração e conservação de fragmentos florestais, criação e expansão de unidades de conservação, além da proposição de formas de uso do solo compatíveis com o entorno de unidades de conservação.

Evaluación del bienestar espiritual en pacientes en hemodiálisis

Introducción: Se define la espiritualidad como la búsqueda personal de propósito y significado en la vida, pudiendo incorporar o no la religión. En este artículo se presenta el desarrollo y la aplicación de una medida de bienestar espiritual a una muestra de pacientes en hemodiálisis. Material y métodos: El instrumento básico empleado se denomina Cuestionario del Sentido de la Vida (Meaning in Life Scale, MiLS), con 21 ítems y cuatro escalas: Propósito, Falta de significado, Paz y Beneficios de la espiritualidad. También se proporciona una puntuación global de espiritualidad. Además, se registraron variables de tipo clínico (tiempo en hemodiálisis, índice de comorbilidad de Charlson) y sociodemográfico (edad, género), así como estimaciones del estado de salud, calidad de vida (general y actual), felicidad personal, el grado de religiosidad y la creencia en la existencia de vida ultraterrena. Se ha utilizado un diseño transversal con 94 pacientes en hemodiálisis. Resultados: Los resultados muestran que la versión española de este instrumento (MiLS-Sp) es una medida de bienestar espiritual con garantías psicométricas de calidad (fiabilidad, validez), adecuada para evaluar las complejas exigencias generadas por la problemática de salud del paciente en hemodiálisis. El bienestar espiritual se relaciona significativamente con diversas variables de calidad de vida, percepción de salud, felicidad personal o religiosidad. No existe una relación significativa entre las puntuaciones de espiritualidad y la edad, el sexo, el tiempo en diálisis o el índice de comorbilidad. El grado de bienestar espiritual de estos pacientes es relativamente bajo. Conclusión: La espiritualidad parece desempeñar un papel importante en el bienestar psicológico, el estado de salud y la calidad de vida percibidos por el paciente en hemodiálisis. El grado de bienestar espiritual de estos pacientes es relativamente bajo. Estos resultados sugieren que considerar y evaluar el grado de bienestar espiritual en los pacientes en hemodiálisis puede ser de utilidad para la práctica clínica.

Importancia de los procesos de validación topológica en la gestión de alteraciones catastrales

Las tecnologías de la información y la comunicación están consiguiendo que la información geográfica sea asequible a un mayor número de profesionales a través de las Tecnologías de la Información Geográfica. La intervención multidisciplinar en el territorio enriquece la investigación y las formas de aplicación de este tipo de recursos tecnológicos. Pero esta facilidad tecnológica puede suponer el riesgo de un uso inadecuado, por falta de conocimientos técnicos adecuados a la complejidad de la información geográfica o por el mal uso de las aplicaciones informáticas. El trabajo catastral puede beneficiarse mucho del empleo de estas tecnologías de información geográfica, al facilitar el uso, la comunicación y su administración electrónica, pero el desconocimiento de las propiedades geométricas y topológicas de la información geográfica puede llevar a cometer errores de graves consecuencias a profesionales no especializados. En este artículo ofrecemos el resultado de la investigación del trabajo de diversos juristas y técnicos, con el objetivo de desarrollar métodos automatizados y aplicaciones informáticas que permitan a los especialistas no expertos en Cartografía usar este tipo de información con garantías de exactitud al más alto nivel, como una solución eficaz para que la información geográfica con calidad topológica enriquezca la seguridad jurídica en el tráfico inmobiliario.

A GIS-based methodology to quantitatively define an Adjacent Protected Area in a shallow karst cavity: The case of Altamira cave

Different types of land use are usually present in the areas adjacent to many shallow karst cavities. Over time, the increasing amount of potentially harmful matter and energy, of mainly anthropic origin or influence, that reaches the interior of a shallow karst cavity can modify the hypogeal ecosystem and increase the risk of damage to the Palaeolithic rock art often preserved within the cavity. This study proposes a new Protected Area status based on the geological processes that control these matter and energy fluxes into the Altamira cave karst system. Analysis of the geological characteristics of the shallow karst system shows that direct and lateral infiltration, internal water circulation, ventilation, gas exchange and transmission of vibrations are the processes that control these matter and energy fluxes into the cave. This study applies a comprehensive methodological approach based on Geographic Information Systems (GIS) to establish the area of influence of each transfer process. The stratigraphic and structural characteristics of the interior of the cave were determined using 3D Laser Scanning topography combined with classical field work, data gathering, cartography and a porosity–permeability analysis of host rock samples. As a result, it was possible to determine the hydrogeological behavior of the cave. In addition, by mapping and modeling the surface parameters it was possible to identify the main features restricting hydrological behavior and hence direct and lateral infiltration into the cave. These surface parameters included the shape of the drainage network and a geomorphological and structural characterization via digital terrain models. Geological and geomorphological maps and models integrated into the GIS environment defined the areas involved in gas exchange and ventilation processes. Likewise, areas that could potentially transmit vibrations directly into the cave were identified. This study shows that it is possible to define a Protected Area by quantifying the area of influence related to each transfer process. The combined maximum area of influence of all the processes will result in the new Protected Area. This area will thus encompass all the processes that account for most of the matter and energy carried into the cave and will fulfill the criteria used to define the Protected Area. This methodology is based on the spatial quantification of processes and entities of geological origin and can therefore be applied to any shallow karst system that requires protection.

Iniciativas de participação cidadã de idosos em Portugal: um estudo exploratório

A perspetiva participativa tem ganho destaque na área do envelhecimento, impulsionada em parte pela divulgação da noção de envelhecimento ativo. Tal ênfase não foi contudo acompanhado por equivalente aprofundamento do conceito e das práticas, assistindo-se à perda de especificidade do termo, em particular na aceção de envolvimento cívico e político dos cidadãos idosos. Como se pode afinal definir participação cidadã sénior? Que tipo de atividades inclui? E o que se está concretamente a fazer em Portugal neste âmbito? Estas são questões a que o artigo procura responder, com base num estudo exploratório de levantamento de iniciativas locais de “participação sénior”.

Descent from banking union to political chaos. CEPS Commentary, 24 January 2014

To counteract the powerful anti-Europe sentiments swirling throughout the EU today and to motivate EU citizens to vote in a constructive spirit in the upcoming European elections, Karel Lannoo argues in this commentary that the functioning of the EU institutions needs to be openly discussed and proposals need to be aired for improving the decision-making process to render it more transparent and democratic. This process would encompass, in his view, the proper role and functioning of the European Commission, the European Parliament and the member states in the EU Council and the interrelationships between these institutions.

Strategic Insurance: The Future of the Belgian Armed Forces. IES Policy Brief Issue 2014/04/May 2014

Summary. Belgium is on the cusp of its next defence reform. While the security landscape throughout Europe’s neighbourhood and beyond deteriorates, the armed forces face numerous challenges. Most importantly, the next defence plan needs to recalibrate the force structure in function of political ambitions and budgetary realities. This Policy Brief argues that Belgium must embrace a nimble but broad-spectrum force. Any future structure must encompass agile land forces as well as a modern combat air force, without neglecting the need to safeguard a sizeable navy and invest in cyber capabilities. European cooperation should be pursued wherever possible while recognising that this necessitates budgetary convergence. For Belgium this means the investment budget needs to grow significantly in order to acquire interoperable but self-owned assets. Such a choice can be justified on the recognition that defence is not just about expeditionary operations, but also economic stimulus, intergenerational solidarity and strategic insurance: maintaining the ability to respond to whatever the future may bring.

A ship run aground Deepening problems in the Ukrainian economy. OSW Commentary Number 173, 16 June 2015

The drop in Ukraine’s GDP by nearly 18% in the first three months of 2015 (versus the corresponding period in 2014) has confirmed the decline of the country’s economy. Over the last 14 months, the Ukrainian currency was subject to an almost threefold devaluation against the US dollar, and in April 2015 the inflation rate was 61% (year-on-year), which exacerbated the impoverishment of the general public and weakened domestic demand. The main reason behind the crisis has been the destruction of heavy industry and infrastructure in the war-torn Donbas region, over which Kyiv no longer has control, as well as a sharp decline in foreign trade (by 24% in 2014 and by 34% in the first quarter of 2015), recorded primarily in trading volume with Ukraine’s major trade partner, i.e. Russia (a drop of 43%). The conflict has also had a negative impact on the production figures for the two key sectors of the Ukrainian economy: agriculture and metallurgy, which account for approximately 50% of Ukrainian exports. The government’s response to the crisis has primarily been a reduction in the costs of financing the Donbas and an increase in the financial burden placed on the citizens and companies of Ukraine. No radical reforms which would encompass the entire system, including anti-corruption reforms, have been carried out to stop the embezzlement of state funds and to facilitate business activity. The reasons for not initiating reforms have included the lack of will to launch them, Ukraine’s traditionally slow pace of bureaucratic action and growing dissonance among the parties making up the parliamentary coalition. The few positive changes, including marketisation of energy prices and sustaining budgetary discipline (in the first quarter of 2015, budgetary revenues grew by 25%, though partly as a result of currency devaluation), are being carried out under pressure from the International Monetary Fund, which is making the payment of further loan instalments to the tune of US$ 17.5 billion conditional upon reforms. Despite assistance granted by Western institutional donors and by individual states, the risk of Ukraine going bankrupt remains real. The issue of restructuring foreign debt worth US$ 15 billion has not been resolved, as foreign creditors who hold Ukrainian bonds have not consented to any partial cancellation of the debt. Whether Ukraine’s public finances can be stabilised will depend mainly on the situation in the east of the country and on the possible renewal of military action. It seems that the only way to rescue Ukraine’s public finances from deteriorating further is to continue to ‘freeze’ the conflict, to gradually implement wide-ranging reforms and to reach a consensus in negotiations with lenders.

Accelerator and detector physics at the Bern medical cyclotron and its beam transport line.

The cyclotron laboratory for radioisotope production and multi-disciplinary research at the Bern University Hospital (Inselspital) is based on an 18-MeV proton accelerator, equipped with a specifically conceived 6-m long external beam line, ending in a separate bunker. This facility allows performing daily positron emission tomography (PET) radioisotope production and research activities running in parallel. Some of the latest developments on accelerator and detector physics are reported. They encompass novel detectors for beam monitoring and studies of low current beams.

Granular computing as a basis of human–data interaction: a cognitive cities use case

The article proposes granular computing as a theoretical, formal and methodological basis for the newly emerging research field of human–data interaction (HDI). We argue that the ability to represent and reason with information granules is a prerequisite for data legibility. As such, it allows for extending the research agenda of HDI to encompass the topic of collective intelligence amplification, which is seen as an opportunity of today’s increasingly pervasive computing environments. As an example of collective intelligence amplification in HDI, we introduce a collaborative urban planning use case in a cognitive city environment and show how an iterative process of user input and human-oriented automated data processing can support collective decision making. As a basis for automated human-oriented data processing, we use the spatial granular calculus of granular geometry.

Uppermost Limit, Extent, and Fluctuations of the Timberline and Treeline Ecocline in the Swiss Central Alps during the past 11,500 Years

Pollen and macrofossils were analyzed at two sites above today's treeline (or tree limit) in the Swiss Central Alps (Gouillé Loéré, 2503 m a.s.l., and Lengi Egga, 2557 m a.s.l.) to test two contrasting hypotheses about the natural formation of timberline (the upper limit of closed forest) in the Alps. Our results revealed that Pinus cembra--Larix decidua forests near timberline were rather closed between 9000 and 2500 B.C. (9600-4000 ¹⁴C yr BP), when timberline fluctuations occurred within a belt 100-150 m above today's tree limit. The treeline ecocline above timberline was characterized by the mixed occurrence of tree, shrub, dwarf-shrub, and herbaceous species, but it did not encompass more than 100-150 altitudinal meters. The uppermost limit reached by timberline and treeline during the Holocene was ca. 2420 and 2530 m, respectively, i.e., about 120 to 180 m higher than today. Between 3500 and 2500 B.C. (4700-4000 ¹⁴C yr BP) timberline progressively sank by about 300 m, while treeline was lowered only ca. 100 m. This change led to an enlargement of the treeline-ecocline belt (by ca. 300 m) after 2500 B.C. (4000 ¹⁴C yr BP). Above the treeline ecocline, natural meadows dominated by dwarf shrubs (e.g., Salix herbacea) and herbaceous species (e.g., Helianthemum, Taraxacum, Potentialla, Leontodon t., Cerastium alpinum t., Cirsium spinosissimum, Silene exscapa t., and Saxifraga stellaris) have been present since at least 11,000 cal yr ago. In these meadows tree and tall shrub species (>0.5 m) never played a major role. These results support the conventional hypothesis of a narrow ecocline with rather sharp upper timberline and treeline boundaries and imply that today's treeless alpine communities in the Alps are close to a natural stage. Pollen (percentages and influx), stomata, and charcoal data may be useful for determining whether or not a site was treeless. Nevertheless, a reliable and detailed record of past local vegetation near and above timberline is best achieved through the inclusion of macrofossil analysis.