Secondary Ion Mass Spectrometry (SIMS): principles and applications

This article outlines the basis of the technique and shows some examples of applications in order to exhibit the expectations of this technique invaried scientific fields.

Analyzing peptides and proteins by mass spectrometry: principles and applications in proteomics

The study of proteins has been a key element in biomedicine and biotechnology because of their important role in cell functions or enzymatic activity. Cells are the basic unit of living organisms, which are governed by a vast range of chemical reactions. These chemical reactions must be highly regulatedin order to achieve homeostasis. Proteins are polymeric molecules that havetaken on the evolutionary process the role, along with other factors, of controlthese chemical reactions. Learning how proteins interact and control their up anddown regulations can teach us how living cells regulate their functions, as well asthe cause of certain anomalies that occur in different diseases where proteins areinvolved. Mass spectrometry (MS) is an analytical widely used technique to studythe protein content inside the cells as a biomarker point, which describesdysfunctions in diseases and increases knowledge of how proteins are working.All the methodologies involved in these descriptions are integrated in the fieldcalled Proteomics.

External forcings, oceanographic processes and particle flux dynamics in Cap de Creus submarine canyon, NW Mediterranean Sea

Particle fluxes (including major components and grain size), and oceanographic parameters (near-bottom water temperature, current speed and suspended sediment concentration) were measured along the Cap de Creus submarine canyon in the Gulf of Lions (GoL; NW Mediterranean Sea) during two consecutive winter-spring periods (2009 2010 and 2010 2011). The comparison of data obtained with the measurements of meteorological and hydrological parameters (wind speed, turbulent heat flux, river discharge) have shown the important role of atmospheric forcings in transporting particulate matter through the submarine canyon and towards the deep sea. Indeed, atmospheric forcing during 2009 2010 and 2010 2011 winter months showed differences in both intensity and persistence that led to distinct oceanographic responses. Persistent dry northern winds caused strong heat losses (14.2 × 103 W m−2) in winter 2009 2010 that triggered a pronounced sea surface cooling compared to winter 2010 2011 (1.6 × 103 W m−2 lower). As a consequence, a large volume of dense shelf water formed in winter 2009 2010, which cascaded at high speed (up to ∼1 m s−1) down Cap de Creus Canyon as measured by a current-meter in the head of the canyon. The lower heat losses recorded in winter 2010 2011, together with an increased river discharge, resulted in lowered density waters over the shelf, thus preventing the formation and downslope transport of dense shelf water. High total mass fluxes (up to 84.9 g m−2 d−1) recorded in winter-spring 2009 2010 indicate that dense shelf water cascading resuspended and transported sediments at least down to the middle canyon. Sediment fluxes were lower (28.9 g m−2 d−1) under the quieter conditions of winter 2010 2011. The dominance of the lithogenic fraction in mass fluxes during the two winter-spring periods points to a resuspension origin for most of the particles transported down canyon. The variability in organic matter and opal contents relates to seasonally controlled inputs associated with the plankton spring bloom during March and April of both years.

Open Apps: Opening Teaching Experiences and Applications

The Universitat Oberta de Catalunya (Open University of Catalonia, UOC) is an online university that makes extensive use of information and communication technologies to provide education. Ever since its establishment in 1995, the UOC has developed and tested methodologies and technological support services to meet the educational challenges posed by its student community and its teaching and management staff. The know-how it has acquired in doing so is the basis on which it has created the Open Apps platform, which is designed to provide access to open source technical applications, information on successful learning and teaching experiences, resources and other solutions, all in a single environment. Open Apps is an open, online catalogue, the content of which is available to all students for learning purposes, all IT professionals for downloading and all teachers for reusing.To contribute to the transfer of knowledge, experience and technology, each of the platform¿s apps comes with full documentation, plus information on cases in which it has been used and related tools. It is hoped that such transfer will lead to the growth of an external partner network, and that this, in turn, will result in improvements to the applications and teaching/learning practices, and in greater scope for collaboration.Open Apps is a strategic project that has arisen from the UOC's commitment to the open access movement and to giving knowledge and technology back to society, as well as its firm belief that sustainability depends on communities of interest.

Foliar photochemical processes and carbon metabolism under favourable and adverse winter conditions in a Mediterranean mixed forest, Catalonia (Spain)

Evergreen trees in the Mediterranean region must cope with a wide range of environmental stresses from summer drought to winter cold. The mildness of Mediterranean winters can periodically lead to favourable environmental conditions above the threshold for a positive carbon balance, benefitting evergreen woody species more than deciduous ones. The comparatively lower solar energy input in winter decreases the foliar light saturation point. This leads to a higher susceptibility to photoinhibitory stress especially when chilly (< 12 C) or freezing temperatures (< 0 C) coincide with clear skies and relatively high solar irradiances. Nonetheless, the advantage of evergreen species that are able to photosynthesize all year round where a significant fraction can be attributed to winter months, compensates for the lower carbon uptake during spring and summer in comparison to deciduous species. We investigated the ecophysiological behaviour of three co-occurring mature evergreen tree species (Quercus ilex L., Pinus halepensis Mill., and Arbutus unedo L.). Therefore, we collected twigs from the field during a period of mild winter conditions and after a sudden cold period. After both periods, the state of the photosynthetic machinery was tested in the laboratory by estimating the foliar photosynthetic potential with CO2 response curves in parallel with chlorophyll fluorescence measurements. The studied evergreen tree species benefited strongly from mild winter conditions by exhibiting extraordinarily high photosynthetic potentials. A sudden period of frost, however, negatively affected the photosynthetic apparatus, leading to significant decreases in key physiological parameters such as the maximum carboxylation velocity (Vc,max), the maximum photosynthetic electron transport rate (Jmax), and the optimal fluorometric quantum yield of photosystem II (Fv/Fm). The responses of Vc,max and Jmax were highly species specific, with Q. ilex exhibiting the highest and P. halepensis the lowest reductions. In contrast, the optimal fluorometric quantum yield of photosystem II (Fv/Fm) was significantly lower in A. unedo after the cold period. The leaf position played an important role in Q. ilex showing a stronger winter effect on sunlit leaves in comparison to shaded leaves. Our results generally agreed with the previous classifications of photoinhibition-tolerant (P. halepensis) and photoinhibitionavoiding (Q. ilex) species on the basis of their susceptibility to dynamic photoinhibition, whereas A. unedo was the least tolerant to photoinhibition, which was chronic in this species. Q. ilex and P. halepensis seem to follow contrasting photoprotective strategies. However, they seemed equally successful under the prevailing conditions exhibiting an adaptive advantage over A. unedo. These results show that our understanding of the dynamics of interspecific competition in Mediterranean ecosystems requires consideration of the physiological behaviour during winter which may have important implications for long-term carbon budgets and growth trends.

Bioinformatics: making large-scale science happen

Bionformatics is a rapidly evolving research field dedicated toanalyzing and managing biological data with computational resources. This paperaims to overview some of the processes and applications currently implementedat CCiT-UB¿s Bioinformatics Unit, focusing mainly on the areas of Genomics,Transcriptomics and Proteomics

Applications of stochastic analysis in finance and statistical inference

First: A continuous-time version of Kyle's model (Kyle 1985), known as the Back's model (Back 1992), of asset pricing with asymmetric information, is studied. A larger class of price processes and of noise traders' processes are studied. The price process, as in Kyle's model, is allowed to depend on the path of the market order. The process of the noise traders' is an inhomogeneous Lévy process. Solutions are found by the Hamilton-Jacobi-Bellman equations. With the insider being risk-neutral, the price pressure is constant, and there is no equilibirium in the presence of jumps. If the insider is risk-averse, there is no equilibirium in the presence of either jumps or drifts. Also, it is analised when the release time is unknown. A general relation is established between the problem of finding an equilibrium and of enlargement of filtrations. Random announcement time is random is also considered. In such a case the market is not fully efficient and there exists equilibrium if the sensitivity of prices with respect to the global demand is time decreasing according with the distribution of the random time. Second: Power variations. it is considered, the asymptotic behavior of the power variation of processes of the form _integral_0^t u(s-)dS(s), where S_ is an alpha-stable process with index of stability 0&alpha&2 and the integral is an Itô integral. Stable convergence of corresponding fluctuations is established. These results provide statistical tools to infer the process u from discrete observations. Third: A bond market is studied where short rates r(t) evolve as an integral of g(t-s)sigma(s) with respect to W(ds), where g and sigma are deterministic and W is the stochastic Wiener measure. Processes of this type are particular cases of ambit processes. These processes are in general not of the semimartingale kind.

Genetic diversity and species richness patterns in Baetidae (Ephemeroptera) in the Montseny Mountain range (North-East Iberian Peninsula)

This study aimed to describe patterns of diversity of Baetidae (Ephemeroptera) at the ommunity and population levels within the Montseny Mountain range (North-East Iberian Peninsula). We studied both the distribution of 4 species of baetids in 20 sites among three catchments along the altitudinal gradient (350-1700 masl); and the genetic diversity of the mtDNA cytochrome c oxidase subunit I (cox1) gene of the two common species Baetis alpinus and Baetis rhodani. We found a gradual replacement of the dominant species along the altitudinal gradient. Baetis alpinus inhabited sites at high-altitudes, and this species was replaced by B. rhodani when the altitude decreased. Baetis melanonyx and Alainites muticus attained low abundance at all river sections, and no clear altitudinal trend appeared. Our hypothesis at the population level was that genetic structuring is associated with geographic distance and limited by drainage boundaries among the three studied catchments because of the short-time dispersion of adults. Unexpectedly, analyses of molecular variance (AMOVA) and isolation-bydistance (IBD) showed genetic diversity was unstructured by distance for both species, which may be explained by the relatively short spatial scale studied and small topographic barriers among the three catchments. The Generalized Mixed Yule-Coalescent (GMYC) model showed that B. rhodani had two differentiated genetic lineages that co-occurred in all sites. Overall, diversity of baetids was structured at the community level along the altitudinal gradient, whereas it was unstructured at the population level within the Montseny Mountain range.

Genetic diversity and species richness patterns in Baetidae (Ephemeroptera) in the Montseny Mountain range (North-East Iberian Peninsula)

This study aimed to describe patterns of diversity of Baetidae (Ephemeroptera) at the ommunity and population levels within the Montseny Mountain range (North-East Iberian Peninsula). We studied both the distribution of 4 species of baetids in 20 sites among three catchments along the altitudinal gradient (350-1700 masl); and the genetic diversity of the mtDNA cytochrome c oxidase subunit I (cox1) gene of the two common species Baetis alpinus and Baetis rhodani. We found a gradual replacement of the dominant species along the altitudinal gradient. Baetis alpinus inhabited sites at high-altitudes, and this species was replaced by B. rhodani when the altitude decreased. Baetis melanonyx and Alainites muticus attained low abundance at all river sections, and no clear altitudinal trend appeared. Our hypothesis at the population level was that genetic structuring is associated with geographic distance and limited by drainage boundaries among the three studied catchments because of the short-time dispersion of adults. Unexpectedly, analyses of molecular variance (AMOVA) and isolation-bydistance (IBD) showed genetic diversity was unstructured by distance for both species, which may be explained by the relatively short spatial scale studied and small topographic barriers among the three catchments. The Generalized Mixed Yule-Coalescent (GMYC) model showed that B. rhodani had two differentiated genetic lineages that co-occurred in all sites. Overall, diversity of baetids was structured at the community level along the altitudinal gradient, whereas it was unstructured at the population level within the Montseny Mountain range.