Conservation and developmental expression of ubiquitin isopeptidases in Schistosoma mansoni

Several genes related to the ubiquitin (Ub)-proteasome pathway, including those coding for proteasome subunits and conjugation enzymes, are differentially expressed during the Schistosoma mansoni life cycle. Although deubiquitinating enzymes have been reported to be negative regulators of protein ubiquitination and shown to play an important role in Ub-dependent processes, little is known about their role in S. mansoni . In this study, we analysed the Ub carboxyl-terminal hydrolase (UCHs) proteins found in the database of the parasite’s genome. An in silicoana- lysis (GeneDB and MEROPS) identified three different UCH family members in the genome, Sm UCH-L3, Sm UCH-L5 and SmBAP-1 and a phylogenetic analysis confirmed the evolutionary conservation of the proteins. We performed quantitative reverse transcription-polymerase chain reaction and observed a differential expression profile for all of the investigated transcripts between the cercariae and adult worm stages. These results were corroborated by low rates of Z-Arg-Leu-Arg-Gly-Gly-AMC hydrolysis in a crude extract obtained from cercariae in parallel with high Ub conjugate levels in the same extracts. We suggest that the accumulation of ubiquitinated proteins in the cercaria and early schistosomulum stages is related to a decrease in 26S proteasome activity. Taken together, our data suggest that UCH family members contribute to regulating the activity of the Ub-proteasome system during the life cycle of this parasite.

Conserving biodiversity in production landscapes.

Alternative land uses make different contributions to the conservation of biodiversity and have different implementation and management costs. Conservation planning analyses to date have generally assumed that land is either protected or unprotected, and that the unprotected portion does not contribute to conservation goals. We develop and apply a new planning approach that explicitly accounts for the contribution of a diverse range of land uses to achieving conservation goals. Using East Kalimantan (Indonesian Borneo) as a case study, we prioritize investments in alternative conservation strategies and account for the relative contribution of land uses ranging from production forest to well-managed protected areas. We employ data on the distribution of mammals and assign species-specific conservation targets to achieve equitable protection by accounting for life history characteristics and home range sizes. The relative sensitivity of each species to forest degradation determines the contribution of each land use to achieving targets. We compare the cost effectiveness of our approach to a plan that considers only the contribution of protected areas to biodiversity conservation, and to a plan that assumes that the cost of conservation is represented by only the opportunity costs of conservation to the timber industry. Our preliminary results will require further development and substantial stakeholder engagement prior to implementation; nonetheless we reveal that, by accounting for the contribution of unprotected land, we can obtain more refined estimates of the costs of conservation. Using traditional planning approaches would overestimate the cost of achieving the conservation targets by an order of magnitude. Our approach reveals not only where to invest, but which strategies to invest in, in order to effectively and efficiently conserve biodiversity.

One billion years of bZIP transcription factor evolution: conservation and change in dimerization and DNA-binding site specificity.

The genomic era has revealed that the large repertoire of observed animal phenotypes is dependent on changes in the expression patterns of a finite number of genes, which are mediated by a plethora of transcription factors (TFs) with distinct specificities. The dimerization of TFs can also increase the complexity of a genetic regulatory network manifold, by combining a small number of monomers into dimers with distinct functions. Therefore, studying the evolution of these dimerizing TFs is vital for understanding how complexity increased during animal evolution. We focus on the second largest family of dimerizing TFs, the basic-region leucine zipper (bZIP), and infer when it expanded and how bZIP DNA-binding and dimerization functions evolved during the major phases of animal evolution. Specifically, we classify the metazoan bZIPs into 19 families and confirm the ancient nature of at least 13 of these families, predating the split of the cnidaria. We observe fixation of a core dimerization network in the last common ancestor of protostomes-deuterostomes. This was followed by an expansion of the number of proteins in the network, but no major dimerization changes in interaction partners, during the emergence of vertebrates. In conclusion, the bZIPs are an excellent model with which to understand how DNA binding and protein interactions of TFs evolved during animal evolution.

Assessing the pH and DP of canvasses with NIR spectroscopy

The canvas support in easel paintings is composed mainly of cellulose. One of the maindegradation paths of cellulose is acid-catalysed hydrolysis, which means that in an acidic environment (low pH), its degradation proceeds at a faster rate (Strlič et al., 2005).The main effect of acid-catalysed hydrolysis is the breaking up of the polymer chains,measured by the “Degree of Polymerisation” (DP). The lowering of the DP value impliesa lower mechanical strength of the textile (Scicolone, 1993), and thus this parameter canbe used to monitor degradation. Knowing these two parameters can, therefore, be veryinformative regarding the condition of the canvas support.

A study of the effects of PVAC on works of art on paper and wood: pH and colour change

This paper presents the preliminary findings of pH and colour measurements carried out on artworks on paperand on wood that had been treated with a poly(vinyl acetate) (PVAC) based adhesive in the 1980s. In both cases, areas treated with PVAC proved to be less acidic than untreated areas. Contrary to expectations, the conservation treatments have not, as yet, increased acidity levels in the objects under study. Colour measurements of the works on paper showed that those that had been backed with a cotton fabric using a mixture of methylcellulose and PVAC were less yellow than those from the same print run that had not been backed. This finding suggests that the backing somehow prevented the natural degradation of the support. In view of these preliminary results, further research is clearly needed. This study forms part of a broader ongoing project to assess the role of PVAC in the conservation of a range of cultural assets.

Assessing the pH and DP of canvasses with NIR spectroscopy

The canvas support in easel paintings is composed mainly of cellulose. One of the maindegradation paths of cellulose is acid-catalysed hydrolysis, which means that in an acidic environment (low pH), its degradation proceeds at a faster rate (Strlič et al., 2005).The main effect of acid-catalysed hydrolysis is the breaking up of the polymer chains,measured by the “Degree of Polymerisation” (DP). The lowering of the DP value impliesa lower mechanical strength of the textile (Scicolone, 1993), and thus this parameter canbe used to monitor degradation. Knowing these two parameters can, therefore, be veryinformative regarding the condition of the canvas support.

A study of the effects of PVAC on works of art on paper and wood: pH and colour change

This paper presents the preliminary findings of pH and colour measurements carried out on artworks on paperand on wood that had been treated with a poly(vinyl acetate) (PVAC) based adhesive in the 1980s. In both cases, areas treated with PVAC proved to be less acidic than untreated areas. Contrary to expectations, the conservation treatments have not, as yet, increased acidity levels in the objects under study. Colour measurements of the works on paper showed that those that had been backed with a cotton fabric using a mixture of methylcellulose and PVAC were less yellow than those from the same print run that had not been backed. This finding suggests that the backing somehow prevented the natural degradation of the support. In view of these preliminary results, further research is clearly needed. This study forms part of a broader ongoing project to assess the role of PVAC in the conservation of a range of cultural assets.

Forest owners' acceptance of incentive based policy instruments in forest biodiversity conservation : a choice experiment based approach

Abstract

A study of the effects of PVAC on works of art on paper and wood: pH and colour change

This paper presents the preliminary findings of pH and colour measurements carried out on artworks on paperand on wood that had been treated with a poly(vinyl acetate) (PVAC) based adhesive in the 1980s. In both cases, areas treated with PVAC proved to be less acidic than untreated areas. Contrary to expectations, the conservation treatments have not, as yet, increased acidity levels in the objects under study. Colour measurements of the works on paper showed that those that had been backed with a cotton fabric using a mixture of methylcellulose and PVAC were less yellow than those from the same print run that had not been backed. This finding suggests that the backing somehow prevented the natural degradation of the support. In view of these preliminary results, further research is clearly needed. This study forms part of a broader ongoing project to assess the role of PVAC in the conservation of a range of cultural assets.

A study of the effects of PVAC on works of art on paper and wood: pH and colour change

This paper presents the preliminary findings of pH and colour measurements carried out on artworks on paperand on wood that had been treated with a poly(vinyl acetate) (PVAC) based adhesive in the 1980s. In both cases, areas treated with PVAC proved to be less acidic than untreated areas. Contrary to expectations, the conservation treatments have not, as yet, increased acidity levels in the objects under study. Colour measurements of the works on paper showed that those that had been backed with a cotton fabric using a mixture of methylcellulose and PVAC were less yellow than those from the same print run that had not been backed. This finding suggests that the backing somehow prevented the natural degradation of the support. In view of these preliminary results, further research is clearly needed. This study forms part of a broader ongoing project to assess the role of PVAC in the conservation of a range of cultural assets.

Conservation and management of the Common Quail (Coturnix coturnix) in Europe: past, present and future.

En el presente estudio hacemos una revisión del estado de conservación y las tendencias poblacionales de la codorniz común (Coturnix coturnix) desde 1900 hasta nuestros días. Algunos de los datos de los que disponemos son contradictorios con respecto al estado de la especie, que presenta ciertas características que dificultan el poder proporcionar estimas poblacionales fiables. Datos recientes sugieren claramente, tanto a escala local como a escala transnacional, que las poblaciones atlánticas de codorniz común han permanecido estables en las dos últimas décadas y que la práctica de liberar codornices criadas en granjas (híbridas con la codorniz japonesa, Coturnix japonica) con finalidades cinegéticas, no afectan significativamente a nuestras estimas. Por otra parte, los complejos patrones de desplazamiento de esta especie requieren especial atención. En este sentido, el análisis de recuperaciones de anillas puede aportar información relevante, especialmente de los movimientos nomádicos de codornices a la búsqueda de hábitats adecuados, tras la destrucción de los cultivos invernales de cereales debido a la siega. Así, al desarrollar un modelo de distribución de cría para esta especie, se debe incorporar continuamente información actualizada de los cambios estacionales de hábitat y clima, con el fin de obtener unas predicciones óptimas. En este sentido, por ejemplo, la inclusión de datos quincenales de índices de vegetación en los modelos de distribución ha dado muy buenos resultados. La obtención de predicciones fiables de los cambios de la distribución de la especie y de sus desplazamientos durante la estación de cría puede ser muy útil para un mejor conocimiento del estado de conservación y las tendencias poblacionales de la especie, así como para el diseño de futuras medidas de gestión.

Statistical Methods for Conservation and Alignment Quality in Proteins

Construction of multiple sequence alignments is a fundamental task in Bioinformatics. Multiple sequence alignments are used as a prerequisite in many Bioinformatics methods, and subsequently the quality of such methods can be critically dependent on the quality of the alignment. However, automatic construction of a multiple sequence alignment for a set of remotely related sequences does not always provide biologically relevant alignments.Therefore, there is a need for an objective approach for evaluating the quality of automatically aligned sequences. The profile hidden Markov model is a powerful approach in comparative genomics. In the profile hidden Markov model, the symbol probabilities are estimated at each conserved alignment position. This can increase the dimension of parameter space and cause an overfitting problem. These two research problems are both related to conservation. We have developed statistical measures for quantifying the conservation of multiple sequence alignments. Two types of methods are considered, those identifying conserved residues in an alignment position, and those calculating positional conservation scores. The positional conservation score was exploited in a statistical prediction model for assessing the quality of multiple sequence alignments. The residue conservation score was used as part of the emission probability estimation method proposed for profile hidden Markov models. The results of the predicted alignment quality score highly correlated with the correct alignment quality scores, indicating that our method is reliable for assessing the quality of any multiple sequence alignment. The comparison of the emission probability estimation method with the maximum likelihood method showed that the number of estimated parameters in the model was dramatically decreased, while the same level of accuracy was maintained. To conclude, we have shown that conservation can be successfully used in the statistical model for alignment quality assessment and in the estimation of emission probabilities in the profile hidden Markov models.