How context dependent are species interactions?

The net effects of interspecific species interactions on individuals and populations vary in both sign (?, 0, +) and magnitude (strong to weak). Interaction outcomes are context‐dependent when the sign and/or magnitude change as a function of the biotic or abiotic context. While context dependency appears to be common, its distribution in nature is poorly described. Here, we used meta‐analysis to quantify variation in species interaction outcomes (competition, mutualism, or predation) for 247 published articles. Contrary to our expectations, variation in the magnitude of effect sizes did not differ among species interactions, and while mutualism was most likely to change sign across contexts (and predation least likely), mutualism did not strongly differ from competition. Both the magnitude and sign of species interactions varied the most along spatial and abiotic gradients, and least as a function of the presence/absence of a third species. However, the degree of context dependency across these context types was not consistent among mutualism, competition and predation studies. Surprisingly, study location and ecosystem type varied in the degree of context dependency, with laboratory studies showing the highest variation in outcomes. We urge that studying context dependency per se, rather than focusing only on mean outcomes, can provide a general method for describing patterns of variation in nature.     

Is T-wave alternans T-wave amplitude dependent?

The possible dependence of T-wave alternans (TWA) on T-wave amplitude was investigated in 3 orthogonal leads (X, Y, Z) 20-min resting ECG recordings and in the derived vector magnitude (VM) from 176 healthy (H) subjects and 200 coronary-artery-disease (CAD) patients. After application of our adaptive-match-filter based method for parameterization of TWA in terms of its amplitude (TWA_A) and product-magnitude (TWA_PM, defined as the product of TWA_A times TWA duration), and once a TW_A parameter was defined for T-wave amplitude quantification, the existence of intra- and inter-subjects relationships of TWA_A and TWA_PM vs. TW_A was tested. Compared to the H-population, the CAD-population showed a significant (P < 0.05) increase of TWA_A (62 ± 38 μV vs. 54 ± 25 μV) and TWA_PM (4029 ± 2974 beat μV vs. 3107 ± 1976 beat μV) and a significant decrease of TW_A (298 ± 194 μV vs. 467 ± 246 μV). These repolarization changes, however, occurred with no significant intra- or inter-subjects relationships of TWA_A and TWA_PM vs. TW_A. Thus, in our CAD and H populations there was no evidence of TWA dependence on T-wave amplitude.     

Phospho-tyrosine dependent protein–protein interaction network

Post-translational protein modifications, such as tyrosine phosphorylation, regulate protein–protein interactions (PPIs) critical for signal processing and cellular phenotypes. We extended an established yeast two-hybrid system employing human protein kinases for the analyses of phospho-tyrosine (pY)-dependent PPIs in a direct experimental, large-scale approach. We identified 292 mostly novel pY-dependent PPIs which showed high specificity with respect to kinases and interacting proteins and validated a large fraction in co-immunoprecipitation experiments from mammalian cells. About one-sixth of the interactions are mediated by known linear sequence binding motifs while the majority of pY-PPIs are mediated by other linear epitopes or governed by alternative recognition modes. Network analysis revealed that pY-mediated recognition events are tied to a highly connected protein module dedicated to signaling and cell growth pathways related to cancer. Using binding assays, protein complementation and phenotypic readouts to characterize the pY-dependent interactions of TSPAN2 (tetraspanin 2) and GRB2 or PIK3R3 (p55γ), we exemplarily provide evidence that the two pY-dependent PPIs dictate cellular cancer phenotypes.     

Length dependent state of activation — Length change dependent kinetics of cross bridges in skinned insect flight muscle

Stretch induced activation and release induced deactivation of single glycerol-extracted insect flight muscle fibres were investigated. The results are interpreted to indicate that the muscle length controls the number of acting cross bridges, whereas their attachment-detachment kinetics in mainly determined by the state of strain of the cross bridges. It is concluded that the net detachment rate of the cross bridges is enhanced if the muscle is released thereby “unloading” the cross bridges. This behaviour of the unloaded cross bridge is a basic postulation of most of the molecular muscle contraction models.

1. The delayed tension rise induced by stretches of different amplitudes could be restored to the level before the stretch by a release to the initial length.
2. The delayed tension decrease induced by a release of moderate (up to δL=1.5% L _i)amplitude is quantitatively restored within the delayed increase induced by the restretch to the initial length.
3. Stiffness, which decreased during the delayed tension drop after release, is restored during a delayed stiffness increase effected by a restretch to the initial length.
4. The rate and the extent of the stiffness drop after release increased with increasing amplitude of the release and with increasing temperature.
5. After the deactivation, i.e., after tension and stiffness achieved a new steady level after the release, the attached cross bridges are already in the same state of strain as they were before the release. This finding is interpreted to indicate that within the deactivation phase all cross bridges attached prior the release are replaced by cross bridges attached after the release.
6. The rate of tension and stiffness decay after release does not depend on the absolute muscle length but on the amplitude of the release which induced the deactivation.

     

Is proteolysis dependent on phosphorus in fresh water?

Abstract HPA proteolytic assay was used to study the dependence of proteolysis on phosphorus in fresh water. Inorganic phosphate (P_i) stimulated the growth of bacteria producing proteases in water when P was limiting factor, but did not affect the biochemical activity of enzymes which were P-in-dependent. In proteolytic assays, bacteria utilised nitrogen and carbon from HPA. Therefore, during long incubations, significant increases in microbial biomass were observed. The original HPA procedure [12] gives artificial and non-realistic values of proteolytic rates in aquatic habitats due to accelerated and uncontrolled bacterial growth and enzyme production during the assay. The use of toluene to prevent microbial growth in HPA assays is recommended [10].     

Hydration dependent dynamics in sol–gel encapsulated myoglobin

In this work we study the effect of hydration on the dynamics of a protein in confined geometry, i.e. encapsulated in a porous silica matrix. Using elastic neutron scattering we investigate the temperature dependence of the mean square displacements of non-exchangeable hydrogen atoms of sol-gel encapsulated met-myoglobin. The study is extended to samples at 0.2, 0.3 and 0.5 g water/g protein fractions and comparison is made with met-myoglobin powders at the same average hydration and with a dry powder sample. Elastic data are analysed using a model of dynamical heterogeneity to take into account deviations of elastic intensity from gaussian behaviour in a large momentum transfer range and reveal a specific, model independent, effect of sol-gel confinement on protein dynamics, consisting mainly in a reduction of large-scale motions that are activated at temperatures larger than approximately 230 K. Surprisingly, the effect of confinement depends markedly on hydration and has a maximum at about 35% water/protein fraction corresponding to full first shell hydration. The presence of hydration-dependent MSD also in encapsulated met-Mb strongly supports the idea that the effect of sol-gel confinement on protein dynamics involves a modification of the structural/dynamical properties of the co-encapsulated solvent more than direct protein-matrix interactions.     

A size dependent predator-prey interaction: who pursues whom?

We investigate the properties of an (age, size) -structured model for a population of Daphnia that feeds on a dynamical algal food source. The stability of the internal equilibrium is studied in detail and combined with numerical studies on the dynamics of the model to obtain insight in the relation between individual behaviour and population dynamical phenomena. Particularly the change in the (age, size)-relation with a change in the food availability seems to be an important behavioural mechanism that strongly influences the dynamics. This influence is partly stabilizing and partly destabilizing and leads to the coexistence of a stable equilibrium and a stable limit cycle or even coexistence of two stable limit cycles for the same parameter values. The oscillations in this case are characterized by drastic changes in the size-structure of the population during a cycle. In addition the model exhibits the usual predator-prey oscillations that characterize Lotka-Volterra models.     

Which conditions promote negative density dependent selection on prey aggregations?

Negative density dependent selection on individuals in prey aggregations (negative DDS, the preferential selection by predators of spatially isolated prey) is assumed to contribute in many cases to the evolution and maintenance of aggregation. Both positive and negative DDS on prey groups have been documented in nature but there is no existing framework to predict when each of these forms of natural selection is most likely. By exploiting the tendency of artificial neural networks to exhibit consumer-like emergent behaviours, I isolate at least two environmental factors impinging on the consumer organism that may determine which form of density dependent natural selection is shown: the distribution of prey group size attacked by the predator and the spatial conformation (dispersed or compacted) of the prey group. Numerous forms of DDS on artificial prey (positive, negative, and non-DDS) are displayed through different combinations of these factors. I discuss in detail how the predictions of the model may be tested by empiricists in order to assess the usefulness of the framework presented. I stress the importance of understanding DDS on prey groups given the recent emergence of these systems as test beds for ideas on biological self-organisation.     

Amino acid–dependent stability of the acyl linkage in aminoacyl-tRNA

Aminoacyl-tRNAs are the biologically active substrates for peptide bond formation in protein synthesis. The stability of the acyl linkage in each aminoacyl-tRNA, formed through an ester bond that connects the amino acid carboxyl group with the tRNA terminal 3′-OH group, is thus important. While the ester linkage is the same for all aminoacyl-tRNAs, the stability of each is not well characterized, thus limiting insight into the fundamental process of peptide bond formation. Here, we show, by analysis of the half-lives of 12 of the 22 natural aminoacyl-tRNAs used in peptide bond formation, that the stability of the acyl linkage is effectively determined only by the chemical nature of the amino acid side chain. Even the chirality of the side chain exhibits little influence. Proline confers the lowest stability to the linkage, while isoleucine and valine confer the highest, whereas the nucleotide sequence in the tRNA provides negligible contribution to the stability. We find that, among the variables tested, the protein translation factor EF-Tu is the only one that can protect a weak acyl linkage from hydrolysis. These results suggest that each amino acid plays an active role in determining its own stability in the acyl linkage to tRNA, but that EF-Tu overrides this individuality and protects the acyl linkage stability for protein synthesis on the ribosome.     

Thyroid dependent maturation of β-adrenergic receptors in the rat lung

β-Adrenergic receptors were identified in membranes of fetal and postnatal rat lung with (?)-[³H]dihydroalprenolol, [³H]DHA. β-Receptor number (Bmax) increased 11-fold from day 18 of gestation to adult levels by day 28 of postnatal life. The increase of β-adrenergic receptors occurring between postnatal days 15 and 28 was dependent on thyroxine (T4) in propylthiouracil treated pups. β-Adrenergic receptors on day 28 were identical in euthyroid (PTU + T4) as compared to normal control pups (489±31 and 491±30 femtomoles·mg^?1) however receptors were markedly reduced in 28 day hypothyroid pups (PTU alone), Bmax = 294±21.5, m±S.E. p<0.01. Treatment of the hypothyroid pups with T4 for three days on postnatal day 25 increased β-adrenergic receptors approximately two-fold by day 28. This thyroid hormone dependent increase in lung β-adrenergic receptors occurs between postnatal days 15 and 28 coincident with the known increase in thyroid gland activity in the rat pup.     

Frequency‐dependent selection: a diversifying force in microbial populations

The benefits of “bet‐hedging” strategies have been assumed to be the main cause of phenotypic diversity in biological populations. However, in their recent work, Healey et al ( 2016 ) provide experimental support for negative frequency‐dependent selection (NFDS) as an alternative driving force of diversity. NFDS favors rare phenotypes over common ones, resulting in an evolutionarily stable mixture of phenotypes that is not necessarily optimal for population growth.     

Does the voltage dependent anion channel modulate cardiac ischemia-reperfusion injury?

The voltage dependent anion channel (VDAC) provides exchange of metabolites, anions, and cations across the outer mitochondrial membrane. VDAC provides substrates and adenine nucleotides necessary for electron transport and therefore plays a key role in regulating mitochondrial bioenergetics. VDAC has also been suggested to regulate the response to cell death signaling. Emerging data show that VDAC is regulated by protein-protein interactions as well as by post-translational modifications. This review will focus on the regulation of VDAC and its potential role in regulating cell death in cardiac ischemia-reperfusion. This article is part of a Special Issue entitled: VDAC structure, function, and regulation of mitochondrial metabolism.     

Heterotrimeric G proteins demonstrate differential sensitivity to β-arrestin dependent desensitization

G15 is a heterotrimeric G protein of the Gq/11 family. In this study, we describe its exceptional poor sensitivity to the general regulatory mechanism of G protein-coupled receptor (GPCR) desensitization.Enhancing β2 adrenergic receptor desensitization by arrestin overexpression, did not affect signalling to G15. Similarly, increased levels of arrestin did not affect G15 signalling triggered by the activation of V2 vasopressin and δ opioid receptors.Furthermore, co-immunoprecipitation experiments showed that G15 α subunit (as opposed to Gαq and Gαs) is recruited to a V2 vasopressin receptor mutant that is constitutively desensitized by β-arrestin. Interestingly, co-expression of Gα15 partially rescued cell surface localization and signalling capabilities of the same mutant receptor and reduced β2 adrenergic receptor internalization.Taken together, these findings provide evidence for a novel mechanism whereby GPCR desensitization can be bypassed and G15 can support sustained signalling in cells chronically exposed to hormones or neurotransmitters.