Assembling novel protein folds from super-secondary structural fragments

The results of applying a fragment-based protein tertiary structure prediction method to the prediction of 14 CASP5 target domains are described. The method is based on the assembly of supersecondary structural fragments taken from highly resolved protein structures using a simulated annealing algorithm. A number of good predictions for proteins with novel folds were produced, although not always as the first model. For two fold recognition targets, FRAGFOLD produced the most accurate model in both cases, despite the fact that the predictions were not based on a template structure. Although clear progress has been made in improving FRAGFOLD since CASP4, the ranking of final models still seems to be the main problem that needs to be addressed before the next CASP experiment

"Just as fragments are part of a vessel": a translation into medieval Occitan of the life of Alexander the Great

This article examines a 14th-c. translation into Old Occitan prose of a late-antique life of Alexander the Great: Justin’s Epitome of the 'Historia Philippicae' of Pompeius Trogus. The article argues that it is the work of translators whose knowledge of pagan Latin materials was incomplete and whose use of their native tongue rested on non-literary bases. This text has not been edited before, and examining its uneven treatment of its source provides important new insights into the work of translators in the later Middle Ages. In conclusion, the article suggests some new approaches to the understanding of translation as a process of reconstruction and adaptation.

Samuel Beckett, the Gate Theatre Dublin, and the contemporary Irish independent theater sector: fragments of performance history

From 1991, when the Dublin Gate Theatre launched their Samuel Beckett Festival featuring nineteen of Beckett’s stage plays, to more recent years, the Gate dominated Irish productions of Beckett’s theater. The Gate Beckett Festival was remounted in 1996 at the Lincoln Center, New York, and at the Barbican Centre, London, in 1999, and individual or grouped productions have toured regularly since then in Ireland and internationally. However, since the Irish premiere of Waiting of Godot at the Pike Theatre in 1955, in addition to several Beckett plays mounted by the National Theatre, many independent Irish theater companies, such as Focus Theatre, Druid Theatre, and more recently Pan Pan Theatre, Blue Raincoat Theatre, The Corn Exchange, and Company SJ (under director Sarah Jane Scaife), have produced Beckett’s drama. While acknowledging earlier Irish productions, this essay will consider the role of the Dublin Gate Beckett Festival and the Beckett Centenary celebrations in Dublin in 2006 in greatly enhancing the marketability of Beckett’s work, and will discuss the proliferation of productions of Beckett’s stage plays (as opposed to stage adaptations of the prose work, which is a topic for another essay) in the independent theater sector in the Republic of Ireland since 2006. In addition to giving an overview of these recent productions, the essay will consider some issues at stake in creating or constructing performance histories

First Results with the RISING active stopper

This paper outlines some of the physics opportunities available with the GSI RISING active stopper and presents preliminary results from an experiment aimed at performing beta-delayed gamma-ray spectroscopic studies in heavy-neutron-rich nuclei produced following the projectile fragmentation of a 1 GeV per nucleon 208Pb primary beam. The energy response of the silicon active stopping detector for both heavy secondary fragments and beta-particles is demonstrated and preliminary results on the decays of neutron-rich Tantalum (Ta) to Tungsten (W) isotopes are presented as examples of the potential of this technique to allow new structural studies in hitherto experimentally unreachable heavy, neutron-rich nuclei. The resulting spectral information inferred from excited states in the tungsten daughter nuclei are compared with results from axially symmetric Hartree–Fock calculations of the nuclear shape and suggest a change in ground state structure for the N = 116 isotone 190W compared to the lighter isotopes of this element.

New insights into the structure of exotic nuclei using the RISING active stopper

This conference paper outlines the operation and some of the preliminary physics results using the GSI RISING active stopper. Data are presented from an experiment using combined isomer and beta‐delayed gamma‐ray spectroscopy to study low‐lying spectral and decay properties of heavy‐neutron‐rich nuclei around A∼190 produced following the relativistic projectile fragmentation of 208Pb primary beam. The response of the RISING active stopper detector is demonstrated for both the implantation of heavy secondary fragments and in‐situ decay of beta‐particles. Beta‐delayed gamma‐ray spectroscopy following decays of the neutron‐rich nucleus 194Re is presented to demonstrate the experimental performance of the set‐up. The resulting information inferred from excited states in the W and Os daughter nuclei is compared with results from Skyrme Hartree‐Fock predictions of the evolution of nuclear shape.

Is bird incidence in Atlantic forest fragments influenced by landscape patterns at multiple scales?

The degree to which habitat fragmentation affects bird incidence is species specific and may depend on varying spatial scales. Selecting the correct scale of measurement is essential to appropriately assess the effects of habitat fragmentation on bird occurrence. Our objective was to determine which spatial scale of landscape measurement best describes the incidence of three bird species (Pyriglena leucoptera, Xiphorhynchus fuscus and Chiroxiphia caudata) in the fragmented Brazilian Atlantic forest and test if multi-scalar models perform better than single-scalar ones. Bird incidence was assessed in 80 forest fragments. The surrounding landscape structure was described with four indices measured at four spatial scales (400-, 600-, 800- and 1,000-m buffers around the sample points). The explanatory power of each scale in predicting bird incidence was assessed using logistic regression, bootstrapped with 1,000 repetitions. The best results varied between species (1,000-m radius for P. leucoptera; 800-m for X. fuscus and 600-m for C. caudata), probably due to their distinct feeding habits and foraging strategies. Multi-scale models always resulted in better predictions than single-scale models, suggesting that different aspects of the landscape structure are related to different ecological processes influencing bird incidence. In particular, our results suggest that local extinction and (re)colonisation processes might simultaneously act at different scales. Thus, single-scale models may not be good enough to properly describe complex pattern-process relationships. Selecting variables at multiple ecologically relevant scales is a reasonable procedure to optimise the accuracy of species incidence models.

Relief influence on tree species richness in secondary forest fragments of Atlantic Forest, SE, Brazil

(Relief influence on tree species richness in secondary forest fragments of Atlantic Forest, SE, Brazil). The aim of this work was to explore the relationship between tree species richness and morphological characteristics of relief at the Ibiuna Plateau (SE Brazil). We sampled 61 plots of 0.30 ha, systematically established in 20 fragments of secondary forest (2-274 ha) and in three areas within a continuous secondary forest site, Morro Grande Reserve (9,400 ha). At each plot, 100 trees with diameter at breast height > 5 cm were sampled by the point centered quarter method, and total richness and richness per dispersal and succession class were obtained. The relief was characterized by the mean and variance of slope, elevation, aspect and slope location. There was no significant relationship between relief heterogeneity and tree species richness. Relief parameters generally did not affect tree richness, but elevation was particularly important especially in the continuous forest. Despite the limited range of altitudinal variation (150 m), species richness increases with elevation. The highest areas were also those with the largest forest cover and the lowest disturbance degree, which should contribute to the greater richness of those sites. Our results suggest an indirect influence of relief, due to the fact that deforestation is less intense in higher regions, rather than a direct influence of abiotic factors related to the altitudinal gradient.

Fragmentation drives tropical forest fragments to early successional states: A modelling study for Brazilian Atlantic forests

Land use leads to massive habitat destruction and fragmentation in tropical forests. Despite its global dimensions the effects of fragmentation on ecosystem dynamics are not well understood due to the complexity of the problem. We present a simulation analysis performed by the individual-based model FORMIND. The model was applied to the Brazilian Atlantic Forest, one of the world`s biodiversity hot spots, at the Plateau of Sao Paulo. This study investigates the long-term effects of fragmentation processes on structure and dynamics of different sized remnant tropical forest fragments (1-100 ha) at community and plant functional type (PFT) level. We disentangle the interplay of single effects of different key fragmentation processes (edge mortality, increased mortality of large trees, local seed loss and external seed rain) using simulation experiments in a full factorial design. Our analysis reveals that particularly small forest fragments below 25 ha suffer substantial structural changes, biomass and biodiversity loss in the long term. At community level biomass is reduced up to 60%. Two thirds of the mid- and late-successional species groups, especially shade-tolerant (late successional climax) species groups are prone of extinction in small fragments. The shade-tolerant species groups were most strongly affected; its tree number was reduced more than 60% mainly by increased edge mortality. This process proved to be the most powerful of those investigated, explaining alone more than 80% of the changes observed for this group. External seed rain was able to compensate approximately 30% of the observed fragmentation effects for shade-tolerant species. Our results suggest that tropical forest fragments will suffer strong structural changes in the long term, leading to tree species impoverishment. They may reach a new equilibrium with a substantially reduced subset of the initial species pool, and are driven towards an earlier successional state. The natural regeneration potential of a landscape scattered with forest fragments appears to be limited, as external seed rain is not able to fully compensate for the observed fragmentation-induced changes. Our findings suggest basic recommendations for the management of fragmented tropical forest landscapes. (C) 2011 Elsevier B.V. All rights reserved.

Sex ratio and morphological characteristics of Rufous Gnateaters, Conopophaga lineata (Aves, Passeriformes) in Atlantic forest fragments

Unequal sex ratios lead to the loss of genetic variability, decreasing the viability of populations in the long term. Anthropogenic activities often disturb the natural habitats and can cause alterations in sex ratio and morphological characteristics of several species. Forest fragmentation is a major conservation concern, so that understanding its effects in natural populations is essential. In this study, we evaluated the sex ratio and the morphological characteristics of Rufous Gnateaters (Conopophaga lineata (Wied, 1831)) in small and large forest fragments in Minas Gerais, Brazil. Birds (n = 89) were sexed by plumage characteristics and molecular markers. The molecular analysis showed that plumage is not a totally reliable method for sexing Rufous Gnateaters. We observed that sex ratio did not differ between large and small forest fragments, but birds in small fragments had larger wings and tarsus. Wing and tarsus changes may affect the movement ability of individuals within and among forest fragments. In conclusion, Rufous Gnateaters have been able to survive in both small and large Atlantic rain forest fragments without altering their sex ratio, but morphological changes can be prejudicial to their long term survival.

Autolytic Mycobacterium leprae Hsp65 fragments may act as biological markers for autoimmune diseases

Investigating the proteolytic activity of the recombinant Mycobacterium leprae Heat Shock Protein of 65 kDa (rHsp65), chaperonin 2 (cpn2), we observed that it displays high instability. The fragmentation process starts at the C-terminus followed by progressive degradation of the N-terminus, which leads to a stable fragment comprising the middle region of the molecule. Urea was able to prevent autolysis, probably due to its denaturing action, while EDTA increased degradation levels indicating the need for metal ions. Peptides originated from autolysis were purified and analyzed by mass spectrometry, generating a continuous map. Since the bacteria and mammalian Hsp60 are known to be targets of the immune response and have been implicated in autoimmune diseases and chronic inflammation, the in vivo effect of rHsp65 peptides was evaluated in the spontaneous Systemic Lupus Erythematosus (SLE) model developed by the (NZB/NZW)F(1) mouse hybrids, and their individual anti-rHsp65 IgG2a/IgG1 antibody titer ratio was determined. The results showed orientation toward a T(H)1 responsiveness, and the treatment with the rHsp65 peptides diminished the environmental variance of the survival time of treated animals. These results outline the fact that environmental factors may also act through the modified stability expression of Heat Shock Proteins intervening during autoimmune processes. (C) 2011 Elsevier Ltd. All rights reserved.