Are streamside buffers edge-affected habitat for ground-dwelling forest beetle assemblages?

Reservation of forest in riparian buffers is common practice in commercial forestry areas worldwide, potentially providing valuable habitat for biodiversity dependent on mature forest. However, the habitat value of narrow reserve corridors can be compromised by edge effects. We investigated the habitat value of streamside buffers in wet eucalypt forest for ground-dwelling beetles in Tasmania, Australia. Beetles were collected with pitfall traps in five replicates of four habitats: unlogged corridors of mature forest in streamside reserves (buffers) with clearfelling-derived logging regeneration either side; continuous mature upslope forest; continuous mature riparian forest; and <20-year-old upslope clearfelling-derived logging regeneration. Streamside reserve widths on each side of the stream were on average 40 ± 6 m (±95% CI) from reserve edge to stream. Beetle assemblages in logging regeneration differed substantially from those in the unlogged habitats, including the streamside reserves. Streamside reserve assemblages nevertheless differed from those of the continuous unlogged areas. Assemblage composition in streamside reserves was most similar to that in continuous mature riparian forest, although beetle diversity was higher in the reserves. Our results suggest that although streamside reserves provide habitat for the majority of commonly collected beetle species occurring in continuous mature forest, wider reserve corridors in the wet eucalypt forests of Tasmania may be required to provide habitat that is not edge-affected.     

Proton decay kinetics for vesicles containing buffers—an analytical solution

The problem of predicting the kinetics of proton efflux and the decay of the internal proton concentration for vesicles containing one or more buffers for which the internal proton concentration is initially higher than that of the surrounding medium is examined. An analytical solution is derived that describes the time course of the proton efflux from vesicles and the decay of the internal proton concentration under conditions of zero transmembrane electric potential. The effect of the internal buffers is to increase the time required for the proton concentration gradient to equilibrate across the membrane. To simplify the analysis we assume that the equilibration of the internal and external proton activity is due primarily to proton diffusion through the membrane, and not to hydroxyl ion flux. For a vesicle containing a single buffer the solution requires six independent physical parameters: the initial internal proton concentration, the external proton concentration, the ratio of the vesicle surface area to the internal volume, the permeability coefficient of the membrane for protons, the total concentration of the internal buffer, and the equilibrium constant for the dissociation of the internal buffer. Determination of these physical values is sufficient to predict the time dependence of the internal proton concentration and of the proton efflux. Over a pH range that is below or near the pK of the internal buffer the solution is complex. However, if the initial pH is one unit or more higher than the pK of the internal buffer the kinetics of the internal proton concentration and proton efflux can be described by a pseudo first order reaction. In this case the apparent rate constant depends linearly on the permeability coefficient and is dominated by the total internal buffer concentration and its pK. For example, increasing the internal buffer concentration inside a vesicle by 10-fold results in an approximately 10-fold increase in the half-time of the proton efflux kinetics. The theoretical analysis is applied to thylakiod vesicles using experimentally determined values for the physical parameters. The predictions of the analysis are compared to experimentally observed kinetics.     

Do calcium buffers always slow down the propagation of calcium waves?

Calcium buffers are large proteins that act as binding sites for free cytosolic calcium. Since a large fraction of cytosolic calcium is bound to calcium buffers, calcium waves are widely observed under the condition that free cytosolic calcium is heavily buffered. In addition, all physiological buffered excitable systems contain multiple buffers with different affinities. It is thus important to understand the properties of waves in excitable systems with the inclusion of buffers. There is an ongoing controversy about whether or not the addition of calcium buffers into the system always slows down the propagation of calcium waves. To solve this controversy, we incorporate the buffering effect into the generic excitable system, the FitzHugh–Nagumo model, to get the buffered FitzHugh–Nagumo model, and then to study the effect of the added buffer with large diffusivity on traveling waves of such a model in one spatial dimension. We can find a critical dissociation constant ( $K=K(a)$ ) characterized by system excitability parameter $a$ such that calcium buffers can be classified into two types: weak buffers ( $K\in (K(a),\infty )$ ) and strong buffers ( $K\in (0,K(a))$ ). We analytically show that the addition of weak buffers or strong buffers but with its total concentration $b_0^1$ below some critical total concentration $b_{0,c}^1$ into the system can generate a traveling wave of the resulting system which propagates faster than that of the origin system, provided that the diffusivity $D_1$ of the added buffers is sufficiently large. Further, the magnitude of the wave speed of traveling waves of the resulting system is proportional to $\sqrt{D_1}$ as $D_1\rightarrow \infty $ . In contrast, the addition of strong buffers with the total concentration $b_0^1>b_{0,c}^1$ into the system may not be able to support the formation of a biologically acceptable wave provided that the diffusivity $D_1$ of the added buffers is sufficiently large.     

Phosphate and HEPES buffers potently affect the fibrillation and oligomerization mechanism of Alzheimer's Aβ peptide

The oligomerization of Aβ peptide into amyloid fibrils is a hallmark of Alzheimer’s disease. Due to its biological relevance, phosphate is the most commonly used buffer system for studying the formation of Aβ and other amyloid fibrils. Investigation into the characteristics and formation of amyloid fibrils frequently relies upon material formed in vitro, predominantly in phosphate buffers. Herein, we examine the effects on the fibrillation and oligomerization mechanism of Aβ peptide that occur due solely to the influence of phosphate buffer. We reveal that significant differences in amyloid fibrillation are observed due to fibrillation being initiated in phosphate or HEPES buffer (at physiological pH and temperature). Except for the differing buffer ions, all experimental parameters were kept constant. Fibril formation was assessed using fluorescently monitored kinetic studies, microscopy, X-ray fiber diffraction and infrared and nuclear magnetic resonance spectroscopies. Based on this set up, we herein reveal profound effects on the mechanism and speed of Aβ fibrillation. The three histidine residues at positions 6, 13 and 14 of Aβ(1–40) are instrumental in these mechanistic changes. We conclude that buffer plays a more significant role in fibril formation than has been generally acknowledged.     

How deep must we dig? Sampling depth effects on root biomass assessments in Mediterranean riparian buffers

Abstract

Root turnover is a relevant process controlling carbon and nutrient cycles. Furthermore, root biomass could influence the effectiveness of riparian buffer systems with regard to immobilizing and processing soil water pollutants and improving soil quality. However, sampling root biomass presents many technical problems, because there is as yet no well-established method for assessment thereof. In the present study, we evaluated the effects of limited sampling depth on biomass assessment in four riparian buffers and on two different dates (January and June): a poplar forest, two mixed deciduous afforestations of different ages, and a grassy area. Although, for all systems, most root biomass was limited to the first 30 cm, detection of differences in root biomass among vegetation types depended strongly on sampling depth for both sampling dates. Furthermore, although the poplar forest presented one of the most stable root systems in terms of total biomass between the sampling dates, it was one of the most seasonally dynamic in terms of the amount and distribution with depth of root biomass. The results of this study suggest that a minimum sampling depth should be established for each study according to seasonal variation in vertical distribution of root biomass.     

Are buffers boring? Uniqueness and asymptotical stability of traveling wave fronts in the buffered bistable system

Traveling waves of calcium are widely observed under the condition that the free cytosolic calcium is buffered. Thus it is of physiological interest to determine how buffers affect the properties of calcium waves. Here we summarise and extend previous results on the existence, uniqueness and stability of traveling wave solutions of the buffered bistable equation, which is the simplest possible model of the upstroke of a calcium wave. Taken together, the results show that immobile buffers do not change the existence, uniqueness or stability of the traveling wave, while mobile buffers can eliminate a traveling wave. However, if a wave exists in the latter case, it remains unique and stable.      

Localized or delocalized protons in photophosphorylation? On the accessibility of the thylakoid lumen for ions and buffers

The deposition of protons inside thylakoids after flash excitation was measured photometrically with neutral red as pH indicator. In continuation of previous work (Junge, W., Ausländer, W., McGeer, A. and Runge, T. (1979) Biochim. Biophys. Acta 546, 121–141), we studied the influence of salts on neutral red binding and on the pK of the heterogeneous protonation-deprotonation of inside-bound neutral red as a function of salts. With freeze-thawed (cryoprotective dimethyl sulphoxide) or aged chloroplasts, we observed that the heterogeneous pK of inside-bound neutral red was salt dependent in a way which suggested that neutral red was bound close to the plane of negative fixed charges and that the adjacent inner aqueous phase could accommodate an extended ionic double layer. This, together with the known extremely rapid proton exchange between surface layer and adjacent bulk phase, led us to conclude that inside-deposited protons rapidly reached an aqueous inner bulk phase. This conclusion was corroborated by the observation that extremely hydrophilic buffers like phosphate quenched the transient internal acidification independent of whether proton deposition was due to water oxidation or to plastohydroquinone oxidation. Very different behaviour was observed for freshly prepared chloroplasts with broken outer envelope. Here, inside-bound neutral red was seemingly unaffected by salts and hydrophilic buffers failed to quench the internal acidification. The electrical conductivity and proton permeability of the thylakoid membrane, on the other hand, were as usual. We attributed the seeming inaccessibility of the internal phase to the failure to accommodate a sufficiently extended ionic cloud between the tightly appressed membranes. In such material we observed hindered lateral mobility of protons at the outer side of the thylakoid membrane. This was tentatively attributed to multiple binding-debinding at buffering groups. The consequences for the chemiosmotic theory are: There is one type of damaged chloroplast material, which is competent in photophosphorylation and where protons are deposited into an internal aqueous bulk phase in the orthodox sense. In more intact material, however, the internal space lacks the characteristic properties of an aqueous bulk phase and there is evidence for lateral diffusion limitation for protons. Here, the thermodynamics of photophosphorylation may be inadequately described by the proton-motive force between two aqueous phases which are each isopotential.     

Secondary forest buffers the effects of fragmentation on aerial insectivorous bat species following 30 years of passive forest restoration

Passive forest restoration can buffer the effects of habitat loss on biodiversity. We acoustically surveyed aerial insectivorous bats in a whole-ecosystem fragmentation experiment in the Brazilian Amazon over a 2-year period, across 33 sites, comprising continuous old-growth forest, remnant fragments, and regenerating secondary forest matrix. We analyzed the activity of 10 species/sonotypes to investigate occupancy across habitat types and responses to fragment size and interior-edge-matrix (IEM) disturbance gradients. Employing a multiscale approach, we investigated guild (edge foragers, forest specialists, flexible forest foragers, and open space specialists) and species-level responses to vegetation structure and forest cover, edge, and patch density across six spatial scales (0.5–3 km). We found species-specific habitat occupancy patterns and nuanced responses to fragment size and the IEM disturbance gradient. For example, Furipterus horrens had lower activity in secondary forest sites and the interior and edge of the smallest fragments (1 and 10 ha) compared to continuous forest, and only two species (Pteronotus spp.) showed no habitat preference and no significant responses across the IEM and fragment size gradients. Only the Molossus sonotype responded negatively to vegetation structure. We uncovered no negative influence of forest cover or edge density at guild or species-level. Our results indicate that reforestation can buffer the negative effects of fragmentation and although these effects can still be detected in some species, generally aerial insectivorous bats appear to be in recovery after 30 years of passive forest restoration. Our findings reinforce the need to protect regenerating forests while conserving vast expanses of old-growth forest.     

Redox cycling compounds generate H2O2 in HTS buffers containing strong reducing reagents--real hits or promiscuous artifacts?

Redox cycling compounds (RCCs) generate μM concentrations of hydrogen peroxide (H(2)O(2)) in the presence of strong reducing agents, common buffer components used to maintain the catalytic activity and/or folding of target proteins for high throughput screening (HTS) assays. H(2)O(2) generated by RCCs can indirectly inhibit the catalytic activity of proteins by oxidizing accessible cysteine, tryptophan, methionine, histidine, or selenocysteine residues, and indeed several important classes of protein targets are susceptible to H(2)O(2)-mediated inactivation; protein tyrosine phosphatases, cysteine proteases, and metalloenzymes. The main sources of H(2)O(2) in cells are the Nox enzyme/SOD systems, peroxisome metabolism, and the autoxidation of reactive chemicals by enzyme mediated redox cycling at both the microsomal and mitochondrial sites of electron transport. Given the role of H(2)O(2) as a second messenger involved in the regulation of many signaling pathways it is hardly surprising that compounds that can generate intracellular H(2)O(2) by enzyme mediated redox cycling would have pleiotropic effects. RCCs can therefore have serious negative consequences for the probe and/or lead generation process: primary HTS assay hit rates may be inflated by RCC false positives; crucial resources will be diverted to develop and implement follow up assays to distinguish RCCs from real hits; and screening databases will become annotated with the promiscuous activity of RCCs. In an attempt to mitigate the serious impact of RCCs on probe and lead generation, two groups have independently developed assays to indentify RCCs.     

Practical acid dissociation constants,temperature coefficients,and buffer capacities for some biological buffers in solutions containing dimethyl sulfoxide between 25 and −12 °C

Acid dissociation constants (K_a), usually expressed as pK_a (-logK_a) can be considered as indices of acid-base equilibria in solution and their evaluation under the solution conditions that exist during the exposure of biological systems to low temperatures are as important as the measurement of pH per se. The assignment of pH1 standards to define pH1 scales in the binary mixed solvent, dimethyl sulfoxide-water (27), has provided the basis for measuring the pK_a1 values of some biological buffers in mixtures of Me₂SO and H₂O which have particular relevance to studies which demonstrate the “pH-dependent” recovery of smooth muscle after low-temperature storage (9, 31). “Practical” ionization conslants in water (pK′_a) and in 20% ($\text{w}\text{w}$) and 30% ($\text{w}\text{w}$) dimethylsulfoxide-water (pK_a1) have been measured by potentiometric titration of a range of zwitterionic buffer compounds at 25, 0, ?5.5, and ?12 °C together with the respective buffer capacities and temperature coefficients. Measurements have been made with reference to the relevant standard states for each solvent system, thereby endowing the values with as much thermodynamic significance as possible.     

Free metal ion depletion by “good's” buffers: II. N-(2-acetamido)-2-aminoethanesulfonic acid (ACESH): Complexes with Calcium(II), Magnesium(II), Manganese(II), Cobalt(II), Zinc(II), Nickel(II), and Cooper(II)

Potentiometric, visible, and infrared studies of the complexation of N-(2-acetamido)-2-aminoethanesulfonic acid (ACESH) by Ca(II), Mg(II), Mn(II), Co(II), Zn(II), Ni(II), and Cu(II) are reported. Ca(II), Mg(II), and Mn(II) were found not to complex with ACES^?, while Co(II), Zn(II), Ni(II), and Cu(II) were found to form 2:1, ACES^? to M²⁺, complexes, and [Cu(ACES)₂] was found to undergo stepwise deprotonation of the amide groups to form [Cu(H_?1ACES)₂^2?]. Formation (affinity) constants for the various metal complexes are reported, and the probable structures of the various metal chelates in solution are discussed.