A re-evaluation of some basic structural and functional properties of Pseudomonas cytochrome oxidase

Determinations of iron content and dry-weight measurements on samples of Pseudomonas cytochrome oxidase were coupled with sodium dodecyl sulphate/polyacrylamide-gel-electrophoresis studies of both the native protein and covalently cross-linked oligomers in order to estimate the enzyme's molecular weight and spectral absorption coefficients. A value of epsilon(ox.) (410)=282x10(3) litre.mol(-1).cm(-1) was calculated for a dimeric protein molecule having a total molecular weight of 122000 (based on iron analysis). Steady-state kinetic observations of the enzyme-catalysed oxidation of reduced azurin by nitrite indicated a marked increase in enzyme inactivation as the pH was raised from 5.7 to 7.2. Since NO, a product of the nitrite reductase activity of Pseudomonas cytochrome oxidase, is known to bind to the enzyme, a study was undertaken to try to assess the potential of NO as a product inhibitor. Investigations showed that samples of the oxidized protein at pH values 4, 5 and 6 bound NO to both haem c and d(1) components, but oxidized enzyme samples at pH7 and above formed their reduced ligand-bound forms when placed under an atmosphere of the gas. Ascorbate-reduced enzyme samples at pH4, 5, 6 and 7 were also found to bind NO at both haem components, although at pH7 the rate of haem c binding was very slow. At pH8 and 9 only the ferrohaem d(1) bound NO. Titration experiments on the reduced protein over the pH range 5-7, with nitrite as a precursor of NO, showed that the haem d(1) had a much higher affinity than the haem c: experiments at pH5.2 and 5.9 with NO-equilibrated solutions revealed the same pattern of behaviour with the oxidized enzyme.     

Evaluating factors that predict the structure of a commensalistic epiphyte–phorophyte network

A central issue in ecology is the understanding of the establishment of biotic interactions. We studied the factors that affect the assembly of the commensalistic interactions between vascular epiphytes and their host plants. We used an analytical approach that considers all individuals and species of epiphytic bromeliads and woody hosts and non-hosts at study plots. We built models of interaction probabilities among species to assess if host traits and abundance and spatial overlap of species predict the quantitative epiphyte–host network. Species abundance, species spatial overlap and host size largely predicted pairwise interactions and several network metrics. Wood density and bark texture of hosts also contributed to explain network structure. Epiphytes were more common on large hosts, on abundant woody species, with denser wood and/or rougher bark. The network had a low level of specialization, although several interactions were more frequent than expected by the models. We did not detect a phylogenetic signal on the network structure. The effect of host size on the establishment of epiphytes indicates that mature forests are necessary to preserve diverse bromeliad communities.     

Von Willlebrand Adhesion to Surfaces at High Shear Rates Is Controlled by Long-Lived Bonds

Von Willebrand factor (vWF) adsorbs and immobilizes platelets at sites of injury under high-shear-rate conditions. It has been recently demonstrated that single vWF molecules only adsorb significantly to collagen above a threshold shear, and here we explain such counterintuitive behavior using a coarse-grained simulation and a phenomenological theory. We find that shear-induced adsorption only occurs if the vWF-surface bonds are slip-resistant such that force-induced unbinding is suppressed, which occurs in many biological bonds (i.e., catch bonds). Our results quantitatively match experimental observations and may be important to understand the activation and mechanical regulation of vWF activity during blood clotting.     

Birds see the true colours of fruits to live off the fat of the land

Communication is a characteristic of life, but its reliability and basic definition are hotly debated. Theory predicts that trade among mutualists requires high reliability. Here, we show that moderate reliability already allows mutualists to optimize their rewards. The colours of Mediterranean fleshy-fruits indicate lipid rewards (but not other nutrients) to avian seed dispersers on regional and local scales. On the regional scale, fruits with high lipid content were significantly darker and less chromatic than congeners with lower lipid content. On the local scale, two warbler species (Sylvia atricapilla and Sylvia borin) selected fruit colours that were less chromatic, and thereby maximized their intake of lipids—a critical resource during migration and wintering. Crucially, birds were able to maximize lipid rewards with moderate reliability from visual fruit colours (r² = 0.44–0.60). We suggest that mutualisms require only that any association between the quality and sensory aspects of signallers is learned through multiple, repeated interactions. Because these conditions are often fulfilled, also in social communication systems, we contend that selection on reliability is less intense than hitherto assumed. This may contribute to explaining the extraordinary diversity of signals, including that of plant reproductive displays.     

GRAPES: A Software for Parallel Searching on Biological Graphs Targeting Multi-Core Architectures

Biological applications, from genomics to ecology, deal with graphs that represents the structure of interactions. Analyzing such data requires searching for subgraphs in collections of graphs. This task is computationally expensive. Even though multicore architectures, from commodity computers to more advanced symmetric multiprocessing (SMP), offer scalable computing power, currently published software implementations for indexing and graph matching are fundamentally sequential. As a consequence, such software implementations (i) do not fully exploit available parallel computing power and (ii) they do not scale with respect to the size of graphs in the database. We present GRAPES, software for parallel searching on databases of large biological graphs. GRAPES implements a parallel version of well-established graph searching algorithms, and introduces new strategies which naturally lead to a faster parallel searching system especially for large graphs. GRAPES decomposes graphs into subcomponents that can be efficiently searched in parallel. We show the performance of GRAPES on representative biological datasets containing antiviral chemical compounds, DNA, RNA, proteins, protein contact maps and protein interactions networks.     

Effects of induced variation in anuran larval development on postmetamorphic energy reserves and locomotion

Anuran larvae exhibit high levels of phenotypic plasticity in growth and developmental rates in response to variation in temperature and food availability. We tested the hypothesis that alteration of developmental pathways during the aquatic larval stage should affect the postmetamorphic performance of the Iberian painted frog (Discoglossus galganoi). We exposed tadpoles to different temperatures and food types (animal- vs. plant-based diets) to induce variation in the length of the larval period and body size at metamorphosis. In this species, larval period varied with temperature but was unaffected by diet composition. In contrast, size at metamorphosis was shaped by the interaction between food quality and temperature; tadpoles fed on an animal-based diet became bulkier metamorphs than those fed on plant-based food at high (22°C) but not at low (12°C) temperature. Body condition of newly metamorphosed frogs was unrelated to the temperature or food type experienced during the premetamorphic stage. Frogs maintained at high temperature during the larval period showed reduced jumping ability, especially when fed on the plant-based diet. However, when considering size-independent jumping ability, cold-reared individuals exhibited the lowest performance, and herbivores reared at 17°C the highest. Cold-reared (12°C) frogs accumulated larger amounts of energy reserves than individuals raised at 17°C or 22°C. This was still the case after correction for differences in body mass, thus indicating some size-independent effect of developmental temperature. Despite the higher lipid content of the carnivorous diet, the differences in energy reserves between herbivores and carnivores were relatively weak and associated with differences in body size. These results suggest that the consequences of environmental variation in the larval habitat can extend to the terrestrial phase and influence juvenile growth and survival.