Land eco-security evaluation in the Shule River Basin during 2005–2014 in Gansu Province,China

The Shule River Basin is an ecologically fragile area in arid zone. To understand the state of land eco-security, the Environment-Economic-Society model was applied to build a land eco-security evaluation index system in the Shule River Basin. An entropy-weighted and matter-element model was built for eco-security evaluation from 2005 to 2014. Principal component analysis was used to quantitatively study the limiting factors of land ecological security. The result showed: the direction of development of the state of land eco-security in the Shule River Basin from 2005 to 2014 was characterized by “unsafe (No₄) → safe (No₁),” and presented an upward trend. The land eco-security status during 2005–2007 was in the “Unsafe” state and the state changed to “Critical Safe” in 2008–2009, “Safer” in 2010–2011, but “Safe” in 2012–2014. The key factors that affected land eco-security in the Shule River Basin were Per Capita Arable Land, Forest Cover Rate, Per Capita Water Resources, Water Production Modulus, the Tertiary Industry Output Value, and GDP Ratio and Water Consumption. Among them, Forest Cover Rate and Water Production Modulus had the greatest impact, with principal component loads of up to 0.973 and 0.968, respectively. The result of this study is expected to serve as reference and support for the conservation and management of Shule River Basin to ensure sustainable development.     

Reinterpreting maximum entropy in ecology: a null hypothesis constrained by ecological mechanism

Simplified mechanistic models in ecology have been criticised for the fact that a good fit to data does not imply the mechanism is true: pattern does not equal process. In parallel, the maximum entropy principle (MaxEnt) has been applied in ecology to make predictions constrained by just a handful of state variables, like total abundance or species richness. But an outstanding question remains: what principle tells us which state variables to constrain? Here we attempt to solve both problems simultaneously, by translating a given set of mechanisms into the state variables to be used in MaxEnt, and then using this MaxEnt theory as a null model against which to compare mechanistic predictions. In particular, we identify the sufficient statistics needed to parametrise a given mechanistic model from data and use them as MaxEnt constraints. Our approach isolates exactly what mechanism is telling us over and above the state variables alone.     

Crystal structures exploring the origins of the broader specificity of escherichia coli heat-labile enterotoxin compared to cholera toxin

Cholera toxin (CT) and Escherichia coli heat-labile enterotoxin (LT) are structurally and functionally related and share the same primary receptor, the GM1 ganglioside. Despite their extensive similarities, these two toxins exhibit distinct ligand specificities, with LT being more promiscuous than CT. Here, we have attempted to rationalize the broader binding specificity of LT and the subtle differences between the binding characteristics of LTs from human and porcine origins (mediated by their B subunit pentamers, hLTB and pLTB, respectively). The analysis is based on two crystal structures of pLTB in complexes with the pentasaccharide of its primary ligand, GM1, and with neolactotetraose, the carbohydrate determinant of a typical secondary ligand of LTs, respectively. Important molecular determinants underlying the different binding specificities of LTB and CTB are found to be contributed by Ser95, Tyr18 and Thr4 (or Ser4 of hLTB), which together prestabilize the binding site by positioning Lys91, Glu51 and the adjacent loop region (50-61) containing Ile58 for ligand binding. Glu7 and Ala1 may also play an important role. Many of these residues are closely connected with a recently identified second binding site, and there appears to be cross-talk between the two sites. Binding to N-acetyllactosamine-terminated receptors is further augmented by Arg13 (present in pLT and some hLT variants), as previously predicted.     

Congeneric but still distinct: how closely related trypsin ligands exhibit different thermodynamic and structural properties

A congeneric series of benzamidine-type ligands with a central proline moiety and a terminal cycloalkyl group—linked by a secondary amine, ether, or methylene bridge—was synthesized as trypsin inhibitors. This series of inhibitors was investigated by isothermal titration calorimetry, crystal structure analysis in two crystal forms, and molecular dynamics simulations. Even though all of these congeneric ligands exhibited essentially the same affinity for trypsin, their binding profiles at the structural, dynamic, and thermodynamic levels are very distinct. The ligands display a pronounced enthalpy/entropy compensation that results in a nearly unchanged free energy of binding, even though individual enthalpy and entropy terms change significantly across the series. Crystal structures revealed that the secondary amine-linked analogs scatter over two distinct conformational families of binding modes that occupy either the inside or of the outside the protein's S3/S4 specificity pocket. In contrast, the ether-linked and methylene-linked ligands preferentially occupy the hydrophobic specificity pocket. This also explains why the latter ligands could only be crystallized in the conformationally restricting closed crystal form whereas the derivative with the highest residual mobility in the series escaped our attempts to crystallize it in the closed form; instead, a well-resolved structure could only be achieved in the open form with the ligand in disordered orientation. These distinct binding modes are supported by molecular dynamics simulations and correlate with the shifting enthalpic/entropic signatures of ligand binding. The examples demonstrate that, at the molecular level, binding modes and thermodynamic binding signatures can be very different even for closely related ligands. However, deviating binding profiles provide the opportunity to optimally address a given target.     

Superbinding: Spatio-temporal oscillatory dynamics

This paper presents superbinding, a concept that represents integrative oscillatory dynamics over the time and space axes. Principle of superposition describes integration over the temporal axis; selectively distributed and selectively coherent oscillatory neural populations describe integration over the spatial axis. Integrative activity is a function of the coherences between spatial locations of the brain; these coherences vary according to the type of sensory and or cognitive event and possibly the consciousness state of the species. Complex percepts and integrative activity in general that is achieved by superbinding supported by the neurons-brain theory may replace the Sherringtonian integrative brain function that is achieved through the single neuron doctrine.

Results of recent experiments related to the percept of the grandmother-face support our concept of super-synergy in the whole brain in order to explain manifestation of Gestalts and Memory-Stages. The strategies of the Grandmother paradigm may open new horizons in search of memories or evolving memories, and possibly provide relevant clinical applications.     

An integrated approach for thermal stabilization of a mesophilic adenylate kinase

Thermally stable proteins are desirable for research and industrial purposes, but redesigning proteins for higher thermal stability can be challenging. A number of different techniques have been used to improve the thermal stability of proteins, but the extents of stability enhancement were sometimes unpredictable and not significant. Here, we systematically tested the effects of multiple stabilization techniques including a bioinformatic method and structure‐guided mutagenesis on a single protein, thereby providing an integrated approach to protein thermal stabilization. Using a mesophilic adenylate kinase (AK) as a model, we identified stabilizing mutations based on various stabilization techniques, and generated a series of AK variants by introducing mutations both individually and collectively. The redesigned proteins displayed a range of increased thermal stabilities, the most stable of which was comparable to a naturally evolved thermophilic homologue with more than a 25° increase in its thermal denaturation midpoint. We also solved crystal structures of three representative variants including the most stable variant, to confirm the structural basis for their increased stabilities. These results provide a unique opportunity for systematically analyzing the effectiveness and additivity of various stabilization mechanisms, and they represent a useful approach for improving protein stability by integrating the reduction of local structural entropy and the optimization of global noncovalent interactions such as hydrophobic contact and ion pairs. Proteins 2014; 82:1947–1959. © 2014 Wiley Periodicals, Inc.     

Burial of nonpolar surface area and thermodynamic stabilization of globins as a function of chain elongation

Proteins are biosynthesized from N to C terminus before they depart from the ribosome and reach their bioactive state in the cell. At present, very little is known about the evolution of conformation and the free energy of the nascent protein with chain elongation. These parameters critically affect the extent of folding during ribosome‐assisted biosynthesis. Here, we address the impact of vectorial amino acid addition on the burial of nonpolar surface area and on the free energy of native‐like structure formation in the absence of the ribosomal machinery. We focus on computational predictions on proteins bearing the globin fold, which is known to encompass the 3/3, 2/2, and archaeal subclasses. We find that the burial of nonpolar surface increases progressively with chain elongation, leading to native‐like conformations upon addition of the last C‐terminal residues, corresponding to incorporation of the last two helices. Additionally, the predicted folding entropy for generating native‐like structures becomes less unfavorable at nearly complete chain lengths, suggesting a link between the late burial of nonpolar surface and water release. Finally, the predicted folding free energy takes a progressive favorable dip toward more negative values, as the chain gets longer. These results suggest that thermodynamic stabilization of the native structure of newly synthesized globins during translation in the cell is significantly enhanced as the chain elongates. This is especially true upon departure of the last C‐terminal residues from the ribosomal tunnel, which hosts ca., 30–40 amino acids. Hence, we propose that release from the ribosome is a crucial step in the life of single‐domain proteins in the cell. Proteins 2014; 82:2318–2331. © 2014 Wiley Periodicals, Inc.     

Where the bears roam in Majella National Park,Italy

The Brown bear (Ursus arctos Linnaeus, 1758) occupies contiguous areas in Eastern and Northern Europe. In Western Europe, the largest remnant populations occur in Cantabria, Spain and the Apennines, Italy. Under Italian law the bear and its occupied range are protected. The occupied range of the Apennine brown bear includes Majella National Park. However, information on the distribution within Majella NP is extrapolated and inconsistent, thus precluding evidence-based protected area and species management. To address this lack of information, bear presence records (1996–2010) were collated and corrected for observational bias. Multiple Species Distribution Models (SDMs) were created at 800 m resolution to predict year-round and seasonal bear distribution. A hierarchical, stepwise maxent SDM approach was applied using climatic, terrain, vegetation, and anthropogenic predictors of bear distribution. Occupied ranges were identified by point density analysis of bear presence. Our climate-only SDMs predicted bear presence in areas with relatively low snowfall and temperate temperatures. Year-round bear distribution was also accurately predicted by using temperate-montane elevations and mesic, mesotrophic vegetation substrates, irrespective of vegetation. Ski-resorts were negative predictors of year-round bear occurrence. Bears were predicted in autumn and winter by beech forest, in spring by meadows and in summer by a variety of vegetation categories. The regional and our local models predicted bear throughout the south. However, our predicted and occupied range in the north includes the Orta valley and exclude alpine heights, contrary to the regional models. Only our summer bear range is similar to a regional SDM. We demonstrated that multiple maxent SDMs using a modest number of observations and a comprehensive set of environmental variables may generate essential distributional information for protected area and species management where full wildlife and food source censuses are lacking.     

Functional diversity of leaf nitrogen concentrations drives grassland carbon fluxes

Little is known about the role of plant functional diversity for ecosystem‐level carbon (C) fluxes. To fill this knowledge gap, we translocated monoliths hosting communities with four and 16 sown species from a long‐term grassland biodiversity experiment (‘The Jena Experiment’) into a controlled environment facility for ecosystem research (Ecotron). This allowed quantifying the effects of plant diversity on ecosystem C fluxes as well as three parameters of C uptake efficiency (water and nitrogen use efficiencies and apparent quantum yield). By combining data on ecosystem C fluxes with vegetation structure and functional trait‐based predictors, we found that increasing plant species and functional diversity led to higher gross and net ecosystem C uptake rates. Path analyses and light response curves unravelled the diversity of leaf nitrogen concentration in the canopy as a key functional predictor of C fluxes, either directly or indirectly via LAI and aboveground biomass.