Using national FADN database to describe Italian farms and arable fields. A comparison of sustainability level between organic versus conventional regimes.

The study defines a new farm classification and identifies the arable land management. These aspects and several indicators are taken into account to estimate the sustainability level of farms, for organic and conventional regimes. The data source is Italian Farm Account Data Network (RICA) for years 2007-2011, which samples structural and economical information. An environmental data has been added to the previous one to better describe the farm context. The new farm classification describes holding by general informations and farm structure. The general information are: adopted regime and farm location in terms of administrative region, slope and phyto-climatic zone. The farm structures describe the presence of main productive processes and land covers, which are recorded by FADN database. The farms, grouped by homogeneous farm structure or farm typology, are evaluated in terms of sustainability. The farm model MAD has been used to estimate a list of indicators. They describe especially environmental and economical areas of sustainability. Finally arable lands are taken into account to identify arable land managements and crop rotations. Each arable land has been classified by crop pattern. Then crop rotation management has been analysed by spatial and temporal approaches. The analysis reports a high variability inside regimes. The farm structure influences indicators level more than regimes, and it is not always possible to compare the two regimes. However some differences between organic and conventional agriculture have been found. Organic farm structures report different frequency and geographical location than conventional ones. Also different connections among arable lands and farm structures have been identified.

Structural basis for the regulation of cysteine-protease activity by a new class of protease inhibitors in Plasmodium

Plasmodium cysteine proteases are essential for host-cell invasion and egress, hemoglobin degradation, and intracellular development of the parasite. The temporal, site-specific regulation of cysteine-protease activity is a prerequisite for survival and propagation of Plasmodium. Recently, a new family of inhibitors of cysteine proteases (ICPs) with homologs in at least eight Plasmodium species has been identified. Here, we report the 2.6 A X-ray crystal structure of the C-terminal, inhibitory domain of ICP from P. berghei (PbICP-C) in a 1:1 complex with falcipain-2, an important hemoglobinase of Plasmodium. The structure establishes Plasmodium ICP as a member of the I42 class of chagasin-like protease inhibitors but with large insertions and differences in the binding mode relative to other family members. Furthermore, the PbICP-C structure explains why host-cell cathepsin B-like proteases and, most likely, also the protease-like domain of Plasmodium SERA5 (serine-repeat antigen 5) are no targets for ICP.

Functional, structural and molecular plasticity of mammalian skeletal muscle in response to exercise stimuli

Biological systems have acquired effective adaptive strategies to cope with physiological challenges and to maximize biochemical processes under imposed constraints. Striated muscle tissue demonstrates a remarkable malleability and can adjust its metabolic and contractile makeup in response to alterations in functional demands. Activity-dependent muscle plasticity therefore represents a unique model to investigate the regulatory machinery underlying phenotypic adaptations in a fully differentiated tissue. Adjustments in form and function of mammalian muscle have so far been characterized at a descriptive level, and several major themes have evolved. These imply that mechanical, metabolic and neuronal perturbations in recruited muscle groups relay to the specific processes being activated by the complex physiological stimulus of exercise. The important relationship between the phenotypic stimuli and consequent muscular modifications is reflected by coordinated differences at the transcript level that match structural and functional adjustments in the new training steady state. Permanent alterations of gene expression thus represent a major strategy for the integration of phenotypic stimuli into remodeling of muscle makeup. A unifying theory on the molecular mechanism that connects the single exercise stimulus to the multi-faceted adjustments made after the repeated impact of the muscular stress remains elusive. Recently, master switches have been recognized that sense and transduce the individual physical and chemical perturbations induced by physiological challenges via signaling cascades to downstream gene expression events. Molecular observations on signaling systems also extend the long-known evidence for desensitization of the muscle response to endurance exercise after the repeated impact of the stimulus that occurs with training. Integrative approaches involving the manipulation of single factors and the systematic monitoring of downstream effects at multiple levels would appear to be the ultimate method for pinpointing the mechanism of muscle remodeling. The identification of the basic relationships underlying the malleability of muscle tissue is likely to be of relevance for our understanding of compensatory processes in other tissues, species and organisms.

The impact of structural conditions in communes on sports behaviour of adolescents and young adults in Switzerland

Young peoples’ sport activity in Switzerland differs considerably depending on the linguistic region (Lamprecht, Fischer, & Stamm, 2008). This appears to be based on cultural as well as on structural differences. The question then arises how differing structural conditions in communes (e.g. sport facilities, significance of the municipal promotion of sport) across different linguistic regions of Switzerland cause variation in sport behaviour. Based on the theory of social action (Coleman, 1990), it is assumed that individual behaviour is not only determined by individual but also by structural and socio-cultural factors in which a person is socially embedded. In two case studies, multilevel data was gathered analysing possible influences of structural factors on sports behaviour. Using an online survey, 15 to 25 year old inhabitants (N = 205) living in a German and French speaking commune were questioned about their sports participation in and outside of their commune, as well as their perception of sport-related structural characteristics in their commune. To collect information about communes’ sport facilities, the sport providers (N = 23) were interviewed. Sport-related characteristics of the communes were also collected through two interviews with representatives of the municipal administration. As expected, sport participation is significantly lower in the French speaking commune (Chi2 (1, N = 205) = 3.84, p < .05). Adolescents and young adults living in the French speaking commune are less satisfied with the sport infrastructure (F(1,135) = 9.65, p < .01) and evaluate the opportunities to be physically active in their commune significantly worse (F(1,144) = 15.33, p < .01) than their German-speaking counterparts. These first findings show the impact of structural conditions in communes on sport participation of adolescents and young people. However, it must be noted that this study is explorative and further communes would need to be examined in order to generalize the results. References Coleman, J. S. (1990). Foundations of social theory. Cambridge, MA: Belknap. Lamprecht, M., Fischer, A. & Stamm, H. (2008). Sport Schweiz 2008. Das Sportverhalten der Schweizer Bevölkerung. Magglingen: BASPO.

The impact of structural conditions in communes on physical activity and sports behaviour of adolescents and young adults in Switzerland

Introduction The physical activity of the Swiss population differs considerably depending on the linguistic region. German speakers are more often physically active than people living in the French- or Italian-speaking part of Switzerland (Stamm & Lamprecht, 2008). This study analyses how differing structural conditions in communes (e.g. sport facilities, significance of the municipal promotion of sport) across different linguistic regions of Switzerland correlate with physical activity and sports participation for adolescents and young adults. Methodological approach Based on the theory of social action (Coleman, 1990), it is assumed that individual behaviour is not only determined by individual but also by structural and socio-cultural factors in which a person is socially embedded. In two case studies, multilevel data was gathered analysing possible influences of structural factors on sports behaviour. Using an online survey, 15 to 25 year old inhabitants (N = 205) living in a German- and French-speaking commune were questioned about their sports participation in and outside of their commune, as well as their perception of sport-related structural characteristics in their commune. To collect information about communes’ sport facilities, the sport providers (N = 23) were interviewed. Sport-related characteristics of the communes were also collected through two interviews with representatives of the municipal administration. Results and discussion Physical activity is significantly higher (Chi2 (1, N = 183) = 4.78, p < .05) and sport participation is significantly lower in the French speaking commune (Chi2 (1, N = 205) = 3.84, p < .05). Adolescents and young adults in the French speaking commune (M = 3.15, SD = 1.23) are less satisfied with the opportunities to be physically active in the environment than their counterparts living in the German speaking commune (p < .001, Mann-Whitney U – test). These first findings show the impact of structural conditions in communes on physical activity and sport participation of adolescents and young people. However, it must be noted that this study is explorative and further communes would need to be examined in order to generalize the results. References Coleman J S (1990). Foundations of social theory. Belknap, Cambridge, MA. Stamm H, Lamprecht M (2008). EJSS, 8(1+2), 15-29.

The impact of structural conditions in communes on sports behaviour of adolescents and young adults in Switzerland

Young peoples’ sport activity differs considerably depending on the linguistic region in Switzerland (Lamprecht, Fischer, & Stamm, 2014). This appears to be based on cultural as well as on structural differences. The question then arises how differing structural conditions in communes (e.g. sport facilities, significance of the municipal promotion of sport) across different linguistic regions of Switzerland cause variation in sport behaviour. Based on the theory of social action (Coleman, 1990), it is assumed that individual behaviour is not only determined by individual but also by structural and socio - cultural factors in which a person is socially embedded . In 33 municipalities of the German and French speaking region of Switzerland, multilevel data was gathered analysing possible influences of structural factors on sports behaviour. Using an online survey, 15 to 30 year old inhabitants (N=3677) were questi oned about their sports participation, as well as their perception of sport - related structural characteristics in their commune. To collect information about communes’ sport facilities, sport providers as well as representatives of the municipal administra tion were interviewed and document analyses were conducted. Representatives of the municipal administration attach more importance to sport promotion in the German speaking than in French - speaking municipalities. Young people living in the French speaking commune are less satisfied with the sport facilities (F(1,3266)=31.31, p<.01) and they are less physically active than their German - speaking counterparts (Chi2(1,N=3537)=22.51, p<.05). These first findings show the impact of structural conditions in commun es on sport participation of adolescents and young people. However, further multilevel analyses will be conducted for a better understanding of correlations between structural conditions and different sports behaviour of young people. References Coleman, J. S. (1990). Foundations of social theory. Cambridge, MA: Belknap. Lamprecht, M., Fischer, A. & Stamm, H. (2014). Sport Schweiz 2014. Sportaktivität und Sportinteresse der Schweizer Bevölkerung. Magglingen: BASPO.

A structural census of the current population of protein sequences

We examine the occurrence of the ≈300 known protein folds in different groups of organisms. To do this, we characterize a large fraction of the currently known protein sequences (≈140,000) in structural terms, by matching them to known structures via sequence comparison (or by secondary-structure class prediction for those without structural homologues). Overall, we find that an appreciable fraction of the known folds are present in each of the major groups of organisms (e.g., bacteria and eukaryotes share 156 of 275 folds), and most of the common folds are associated with many families of nonhomologous sequences (i.e., >10 sequence families for each common fold). However, different groups of organisms have characteristically distinct distributions of folds. So, for instance, some of the most common folds in vertebrates, such as globins or zinc fingers, are rare or absent in bacteria. Many of these differences in fold usage are biologically reasonable, such as the folds of metabolic enzymes being common in bacteria and those associated with extracellular transport and communication being common in animals. They also have important implications for database-based methods for fold recognition, suggesting that an unknown sequence from a plant is more likely to have a certain fold (e.g., a TIM barrel) than an unknown sequence from an animal.

Structural assignments to the Mycoplasma genitalium proteins show extensive gene duplications and domain rearrangements

The parasitic bacterium Mycoplasma genitalium has a small, reduced genome with close to a basic set of genes. As a first step toward determining the families of protein domains that form the products of these genes, we have used the multiple sequence programs psi-blast and geanfammer to match the sequences of the 467 gene products of M. genitalium to the sequences of the domains that form proteins of known structure [Protein Data Bank (PDB) sequences]. PDB sequences (274) match all of 106 M. genitalium sequences and some parts of another 85; thus, 41% of its total sequences are matched in all or part. The evolutionary relationships of the PDB domains that match M. genitalium are described in the structural classification of proteins (SCOP) database. Using this information, we show that the domains in the matched M. genitalium sequences come from 114 superfamilies and that 58% of them have arisen by gene duplication. This level of duplication is more than twice that found by using pairwise sequence comparisons. The PDB domain matches also describe the domain structure of the matched sequences: just over a quarter contain one domain and the rest have combinations of two or more domains.

PseudoBase: structural information on RNA pseudoknots

PseudoBase is a database containing structural, functional and sequence data related to RNA pseudo­knots. It can be reached at http://wwwbio.LeidenUniv.nl/∼Batenburg/PKB.html. For each pseudoknot, thirteen items are stored, for example the relevant sequence, the stem positions of the pseudoknot, the EMBL accession number of the sequence and the support that can be given regarding the reliability of the pseudo­knot. Since the last publication, information on sizes of the stems and the loops in the pseudoknots has been added. Also added are alternative entries that produce surveys of where the pseudoknots are, sorted according to stem size or loop size.