Thermal effects in stretching of Go-like models of titin and secondary structures

The effect of temperature on mechanical unfolding of proteins is studied using a Go-like model with a realistic contact map and Lennard-Jones contact interactions. The behavior of the I27 domain of titin and its serial repeats is contrasted to that of simple secondary structures. In all cases, thermal fluctuations accelerate the unraveling process, decreasing the unfolding force nearly linearly at low temperatures. However, differences in bonding geometry lead to different sensitivity to temperature and different changes in the unfolding pattern. Due to its special native-state geometry, titin is much more thermally and elastically stable than the secondary structures. At low temperatures, serial repeats of titin show a parallel unfolding of all domains to an intermediate state, followed by serial unfolding of the domains. At high temperatures, all domains unfold simultaneously, and the unfolding distance decreases monotonically with the contact order, that is, the sequence distance between the amino acids that form the native contact.     

Passive restoration in Araucaria Forest: useful ecological indicators in monitoring successional advancement in exotic tree plantation landscapes

Monitoring successional advancement is a complex field involving a constant search for applied ecological indicators which facilitate monitoring of secondary forests for both active and passive restoration. In this study, the authors investigate the successional advancement of floristics and tree structure within Araucaria Forest (AF) fragments under passive restoration in a context where exotic tree plantations (mainly Pinus L. genus) dominate the landscape. The ecological indicators used were floristic dissimilarity (β‐diversity inferences), indicator species, ecological groups of species, basal area, and species abundance distribution (SAD) models (α‐diversity inferences). A total of 182 tree species belonging to 91 genera and 43 botanical families were identified. A high β diversity was verified for which each site has indicator species (for the locations CD—Dicksonia sellowiana; CO—Cryptocarya aschersoniana; and PG—Pinus taeda), where pioneer species contributed to much of the abundance. Different SAD models are useful for describing passive restoration sites in exotic tree plantation landscapes, namely Lognormal, Mandelbrot, and Zipf. SAD models together with basal area, taxonomic group (e.g. Myrtaceae assemblage), and tree abundance in ecological groups are strategic ecological indicators for monitoring successional advancement in AF.     

Mechanistic insights into the inhibition of prostate specific antigen by beta-lactam class compounds

Prostate Specific Antigen (PSA) is a biomarker used in the diagnosis of prostate cancer and to monitor therapeutic response. However, its precise role in prostate carcinogenesis and metastasis remains largely unknown. A number of studies arguing in the favor of an active role of PSA in prostate cancer development and progression have implicated this serine protease in the release and activation of growth factors such as insulin-like growth factor 1 (IGF1) through cleavage of insulin like growth factor binding protein 3 and Transforming Growth Factor beta (TGF-beta) through cleavage of Latent TGF-beta. In contrast, other studies suggest that PSA activity might hinder tumor development and progression. In light of these contradictory findings, efficient inhibitors of PSA are needed for exploring its biological role in tumor development and metastasis. Towards the goal of developing potent inhibitors of PSA, we have explored the molecular mechanism of a series of beta-lactam based compounds on binding to PSA using activity assays, matrix assisted laser desorption ionization with a time-of-flight mass spectrometry, and GOLD docking methodology. The mass spectrometry experiments and the activity assays confirmed the time-dependent and covalent nature of beta-lactam binding. To gain insights on the reaction intermediates at the molecular level, we docked beta-lactam inhibitors to a homology modeled PSA using the GOLD docking program in noncovalent and covalent binding modes. The docking studies elucidated the molecular details of the early noncovalent Michaelis complex, the acyl-enzyme covalent complex, and the nature of conformational reorganization required for the long term stability of the covalent complex. Additionally, the molecular basis for the effect of stereochemistry of the lactam ring on the inhibitory potency was elucidated through docking of beta-lactam enantiomers. As a validation of our docking methodology, two novel enantiomers were synthesized and evaluated for their inhibitory potency using fluorogenic substrate based activity assays. Additionally, cis enantiomers of eight beta-lactam compounds reported in a previous study were docked and their GOLD scores and binding modes were analyzed in order to assess the general applicability of our docking results. The close agreement of our docking results with the experimental data validates the mechanistic insights revealed through the docking studies and paves the way for the design and development of potent and specific inhibitors of PSA.     

非线性接触率和种群动力学对SI传染病模型的影响

本文研究了具有一般非线性接触率和易感类中具有Logistic增长的SI传染病模型的正不变集、平衡位置以及平衡位置的稳定性．     

A dynamic model of thoracic differentiation for the control of turning in the stick insect

Leg movements of stick insects (Carausius morosus) making turns towards visual targets are examined in detail, and a dynamic model of this behaviour is proposed. Initial results suggest that front legs shape most of the body trajectory, while the middle and hind legs just follow external forces (Rosano H, Webb B, in The control of turning in real and simulated stick insects, vol. 4095, pp 145–156, 2006). However, some limitations of this explanation and dissimilarities in the turning behaviour of the insect and the model were found. A second set of behavioural experiments was made by blocking front tarsi to further investigate the active role of the other legs for the control of turning. The results indicate that it is necessary to have different roles for each pair of legs to replicate insect behaviour. We demonstrate that the rear legs actively rotate the body while the middle legs move sideways tangentially to the hind inner leg. Furthermore, we show that on average the middle inner and hind outer leg contribute to turning while the middle outer leg and hind inner leg oppose body rotation. These behavioural results are incorporated into a 3D dynamic robot simulation. We show that the simulation can now replicate more precisely the turns made by the stick insect. This work was supported by CONACYT México and the European Commission under project FP6-2003-IST2-004690 SPARK.     

Multiscale landscape genomic models to detect signatures of selection in the alpine plant Biscutella laevigata

Plant species are known to adapt locally to their environment, particularly in mountainous areas where conditions can vary drastically over short distances. The climate of such landscapes being largely influenced by topography, using fine‐scale models to evaluate environmental heterogeneity may help detecting adaptation to micro‐habitats. Here, we applied a multiscale landscape genomic approach to detect evidence of local adaptation in the alpine plant Biscutella laevigata. The two gene pools identified, experiencing limited gene flow along a 1‐km ridge, were different in regard to several habitat features derived from a very high resolution (VHR) digital elevation model (DEM). A correlative approach detected signatures of selection along environmental gradients such as altitude, wind exposure, and solar radiation, indicating adaptive pressures likely driven by fine‐scale topography. Using a large panel of DEM‐derived variables as ecologically relevant proxies, our results highlighted the critical role of spatial resolution. These high‐resolution multiscale variables indeed indicate that the robustness of associations between genetic loci and environmental features depends on spatial parameters that are poorly documented. We argue that the scale issue is critical in landscape genomics and that multiscale ecological variables are key to improve our understanding of local adaptation in highly heterogeneous landscapes.     

Host plant quality,selection history and trade-offs shape the immune responses of Manduca sexta

Immune defences are an important component of fitness. Yet susceptibility to pathogens is common, suggesting the presence of ecological and evolutionary limitations on immune defences. Here, we use structural equation modelling to quantify the direct effects of resource quality and selection history, and their indirect effects mediated via body condition prior to an immune challenge on encapsulation and melanization immune defences in the tobacco hornworm, Manduca sexta. We also investigate allocation trade-offs among immune defences and growth rate following an immune challenge. We found considerable variation in the magnitude and direction of the direct effects of resource quality and selection history on immune defences and their indirect effects mediated via body condition and allocation trade-offs. Greater resource quality and evolutionary exposure to pathogens had positive direct effects on encapsulation and melanization. The indirect effect of resource quality on encapsulation mediated via body condition was substantial, whereas indirect effects on melanization were negligible. Individuals in better condition prior to the immune challenge had greater encapsulation; however, following the immune challenge, greater encapsulation traded off with slower growth rate. Our study demonstrates the importance of experimentally and analytically disentangling the relative contributions of direct and indirect effects to understand variation in immune defences.