Structural and functional domains of cellobiohydrolase I from trichoderma reesei

Limited proteolysis (papain) of the cellobiohydrolase I (CBH I, 65 kDa) from Trichoderma reesei led to the seperation of two functional domains: a core protein (55 kDa) containing the active site, and a C-terminal glycopeptide (10 kDa) implicated in binding to the insoluble matrix (cellulose). The quaternary structures of the intact CBH I and its core in solution are now compared by small angle X-ray scattering (SAXS) measurements. The molecular parameters derived for the core (Rg=2.09 nm, D_max=6.5 nm) and for the intact enzyme (Rg=4.27 nm, D_max=18 nm) indicate very different shapes. The resulting models show a tadpole-like structure for the intact enzyme where the isotropic part coincides with the core protein and the flexible tail part should be identified with the C-terminal glycopeptide. Thus in this enzyme, functional differentiation is reflected in structural peculiarities.Abbreviations SAXS small angle X-ray scattering - SDS-PAGE SDS-polyacrylamide gel electrophoresis - IEF-PAG polyacrylamide gel isoelectric focusing; cellobiohydrolase (CBH, 1,4--glucan cellobio hydrolase (E.C.3.2.1.91)) - D_max maximum diameter - Rg radius of gyration     

Management of a semi‐natural grassland; results from a 15‐year‐old experiment in southern Sweden

Abstract. Vegetation changes in a semi‐natural grassland of wooded meadow type that had been grazed for centuries are described following the introduction of various management regimes: mowing each year, mowing every third year, burning, mechanical removal of woody plants, chemical treatment of woody plants, continuous grazing and abandonment. The experiment was established in southern Sweden in 1972 and has been in progress for 15 years. In 1972, 1980 and 1986 the botanical composition in these plots was investigated in permanent subplots. The study clearly demonstrates that mowing or grazing is necessary to preserve community structure and that mowing is to be preferred in cases where maintaining species richness is of primary concern. Mowing every third year delayed vegetation change and prevented woody species from spreading. Therefore, periodic mowing might be an alternative way to preserve the flora. In contrast, yearly burning does not seem to be a viable management in this type of semi‐natural grassland. To preserve the open landscape regeneration of woody plants has to be prevented. However, in plots where woody plants were removed the typical grassland flora declined. Abandonment resulted in closed forest.     

Hydrologic flowpaths influence inorganic and organic nutrient leaching in a forest soil

Hydrologic pathways through soil affect element leaching by determining the relative importance of biogeochemical processes such as sorption and decomposition. We used stable hydrogen isotopes of water (δD) to examine the influence of flowpaths on soil solution chemistry in a mature spruce–hemlock forest in coastal Oregon, USA. Soil solutions (50 cm depth, n = 13) were collected monthly for 1 year and analyzed for δD, major ions and dissolved organic carbon (DOC) and nitrogen (DON). We propose that the variability of δD can be used as an index of flowpath length and contact time. Throughfall variability in δD was much greater than soil solution variability, illustrating that soil solution integrates the variation in inputs. Lysimeters with greater variation in δD presumably have a greater proportion of flow through rapid flowpaths such as macropores. The variation in soil solution δD for individual lysimeters explained up to 53% of the variation in soil solution chemistry, and suggests that flowpaths influence leaching of some constituents. Soil solutions from lysimeters with greater δD variation had higher DOC and DON (r ² = 0.51 and 0.37, respectively), perhaps because transport via macropores reduces interaction of DOM with the soil matrix. In contrast, nitrate concentrations were highest in lysimeters with a small variation in δD, where long contact time and low DOC concentrations may yield higher net nitrification. Our results demonstrate the utility of stable isotopes to link flowpaths and soil solution chemistry, and illustrate how the spatial complexity of soils can influence ecosystem-level nutrient losses.     

How predator functional responses and Allee effects in prey affect the paradox of enrichment and population collapses

In Rosenzweig-MacArthur models of predator-prey dynamics, Allee effects in prey usually destabilize interior equilibria and can suppress or enhance limit cycles typical of the paradox of enrichment. We re-evaluate these conclusions through a complete classification of a wide range of Allee effects in prey and predator's functional response shapes. We show that abrupt and deterministic system collapses not preceded by fluctuating predator-prey dynamics occur for sufficiently steep type III functional responses and strong Allee effects (with unstable lower equilibrium in prey dynamics). This phenomenon arises as type III functional responses greatly reduce cyclic dynamics and strong Allee effects promote deterministic collapses. These collapses occur with decreasing predator mortality and/or increasing susceptibility of the prey to fall below the threshold Allee density (e.g. due to increased carrying capacity or the Allee threshold itself). On the other hand, weak Allee effects (without unstable equilibrium in prey dynamics) enlarge the range of carrying capacities for which the cycles occur if predators exhibit decelerating functional responses. We discuss the results in the light of conservation strategies, eradication of alien species, and successful introduction of biocontrol agents.     

Stress relaxation of wood partially non-crystallized using aqueous NaOH solutions

Wood samples (Picea jezoensis Carr.) were treated with aqueous NaOH solutions (0-0.20 concentration fraction, 12 conditions), and bending tests were performed to measure stress relaxation. The relationship between mechanical properties and NaOH concentration is discussed. The relaxation modulus and relaxation rate were divided into three concentration ranges. Both decreased slightly for NaOH concentrations less than 0.10, decreased drastically for concentrations between 0.11 and 0.14, and decreased slightly for concentrations greater than 0.15. The change in relaxation behavior upon NaOH treatment was due to an increase in molecular chain mobility in non-crystallized regions along the microfibril longitudinal axis in wood as well as lignin swelling. Furthermore, the molecular chain response in this region required time; thus, the dependence of crystallinity on the relaxation rate was apparent in the long time region.     

To be or not to be faithful: flexible fidelity to foraging trails in the leaf‐cutting ant Acromyrmex lobicornis

1. Ants using trails to forage have to select between two alternative routes at bifurcations, using two, potentially conflicting, sources of information to make their decision: individual experience to return to a previous successful foraging site (i.e. fidelity) and ant traffic. In the field, we investigated which of these two types of information individuals of the leaf‐cutting ant Acromyrmex lobicornis Emery use to decide which foraging route to take. 2. We measured the proportion of foraging ants returning to each trail of bifurcations the following day, and for 4–7 consecutive days. We then experimentally increased ant traffic on one trail of the bifurcation by adding additional food sources to examine the effect of increased ant traffic on the decision that ants make. 3. Binomial tests showed that for 62% of the trails, ant fidelity was relatively more important than ant traffic in deciding which bifurcation to follow, suggesting the importance of previous experience. 4. When information conflict was generated by experimentally increasing ant traffic along the trail with less foraging activity, most ants relied on ant traffic to decide. However, in 33% of these bifurcations, ants were still faithful to their trail. Thus, there is some degree of flexibility in the decisions that A. lobicornis make to access food resources. 5. This flexible fidelity results in individual variation in the response of workers to different levels of ant traffic, and allows the colony to simultaneously exploit both established and recently discovered food patches, aiding efficient food gathering.     

A three-species model explaining cyclic dominance of Pacific salmon

The four-year oscillations of the number of spawning sockeye salmon (Oncorhynchus nerka) that return to their native stream within the Fraser River basin in Canada are a striking example of population oscillations. The period of the oscillation corresponds to the dominant generation time of these fish. Various—not fully convincing—explanations for these oscillations have been proposed, including stochastic influences, depensatory fishing, or genetic effects. Here, we show that the oscillations can be explained as an attractor of the population dynamics, resulting from a strong resonance near a Neimark Sacker bifurcation. This explains not only the long-term persistence of these oscillations, but also reproduces correctly the empirical sequence of salmon abundance within one period of the oscillations. Furthermore, it explains the observation that these oscillations occur only in sockeye stocks originating from large oligotrophic lakes, and that they are usually not observed in salmon species that have a longer generation time.     

A mixed strategy model for the emergence and intensification of social learning in a periodically changing natural environment

Based on a population genetic model of mixed strategies determined by alleles of small effect, we derive conditions for the evolution of social learning in an infinite-state environment that changes periodically over time. Each mixed strategy is defined by the probabilities that an organism will commit itself to individual learning, social learning, or innate behavior. We identify the convergent stable strategies (CSS) by a numerical adaptive dynamics method and then check the evolutionary stability (ESS) of these strategies. A strategy that is simultaneously a CSS and an ESS is called an attractive ESS (AESS). For certain parameter sets, a bifurcation diagram shows that the pure individual learning strategy is the unique AESS for short periods of environmental change, a mixed learning strategy is the unique AESS for intermediate periods, and a mixed learning strategy (with a relatively large social learning component) and the pure innate strategy are both AESS's for long periods. This result entails that, once social learning emerges during a transient era of intermediate environmental periodicity, a subsequent elongation of the period may result in the intensification of social learning, rather than a return to innate behavior.     

Solution conformations of cyclosporins and magnesium-cyclosporin complexes determined by vibrational circular dichroism

Vibrational circular dichroism (VCD) spectroscopy was used to investigate the solution conformations of cyclosporins A, C, D, G, and H in CDCl(3), in the amide I and NH/OH-stretching regions, and their corresponding magnesium complexes in CD(3)CN, in the amide I region. VCD spectra are sensitive to the chiral arrangement of Cdbond;O and NH bonds in this cyclic undecapeptide. Calculations of molecular geometries, as well as IR and VCD intensities of model cyclosporin fragments that include the intramolecular hydrogen bonds of the crystal conformations of cyclosporins A and H (CsA and CsH), were carried out at the density functional theory (DFT; BPW91 functional/6-31G* basis set) level. The good agreement between IR and VCD spectra from experiment and DFT calculations provides evidence that the crystal conformation of CsA is dominant in CDCl(3) solution; CsH, however, assumes both an intramolecularly hydrogen-bonded crystal conformation and more open forms in solution. Comparisons of the experimental and calculated VCD spectra in the NH/OH-stretching region of the noncomplexed cyclosporins indicate that conformers with both free and hydrogen-bonded NH and OH groups are present in solution. Differences between the IR and VCD spectra for the metal-free and magnesium-complexed cyclosporins are indicative of strong interactions between cyclosporins and magnesium ions.     

Conformational preferences of the amylin nucleation site in SDS micelles: an NMR study

Human islet amyloid polypeptide (hIAPP), or amylin, is a 37 amino acid hormone secreted by pancreatic beta-cells. hIAPP constitutes approximately 90% of the amyloid deposits found in type II diabetic patients. It has been shown that the central region of the peptide (hIAPP(20-29)) constitutes the nucleation site for the amyloidogenic process with F23 playing a key role in the formation of the beta-pleated structures. In addition, it has been proposed that an important stage in the cytotoxicity of hIAPP is its interaction with the beta-cell membranes. As a first step toward the characterization of the interaction of hIAPP with cell membranes, we determined conformational preferences of hIAPP(20-29) in membrane-mimicking environments. We found that upon interacting with negatively charged micelles, the dominant conformation of hIAPP(20-29) is a distorted type I beta-turn centered on residues F23 and G24, with F23, A25, and I26 forming a small hydrophobic cluster that may facilitate the interaction of this peptide with the membrane bilayer. Moreover, we were able to elucidate the topological orientation of the peptide that is absorbed on the micelle surface, with the hydrophobic cluster oriented toward the hydrocarbon region of the micelles and both N- and C-termini exposed to the solvent.