Influence of thermal motion on 1H chemical shifts in proteins: the case of bovine pancreatic trypsin inhibitor.

The possible influence of thermal motion on 1H chemical shifts is discussed for a small stable protein, the bovine pancreatic Kunitz trypsin inhibitor (BPTI). The thermal effects on the aromatic side chains and on the backbone are treated separately. The thermal motion of the aromatic side chains is accounted for in terms of their rotation around the C(alpha)-C(beta) bond and the motion of each individual proton is interpreted as a ratio between the amount of ordered and quite disordered states. The influence of hydrogen bonds is introduced as an extra contribution to the chemical shifts of the bonded proton. Their contribution to the chemical shifts resulting from the polarization of the peptide bond is investigated, as is their influence on local flexibility. Finally, the relative importance of each contribution to the chemical shift information is compared.     

Nutrient use by tropical ant communities varies among three extensive elevational gradients: A cross-continental comparison

Aim

Many studies demonstrate that climate limits invertebrates along tropical elevational gradients, but we have only a rudimentary understanding of the role of nutrient limitation and climatic seasonality. Here we examined the relationships between ant community structure, nutrient use and season along three undisturbed elevational gradients, each from a different continent.

Location

Ecuador (South America), Papua New Guinea (PNG: Oceania), Tanzania (Africa).

Time period

2011–2014.

Major taxa studied

Ants.

Methods

Along each of the three gradients, we placed six distinct nutrient types (amino acid, sucrose, sucrose + amino acid, lipid, NaCl, H₂O). In total, we distributed 2370 baits at 38 sites from 203 m to 3972 m. We used generalized linear models to test for the effects of elevation and season on ant species richness and activity and relative nutrient use. We also tested if changes in ant trophic guilds corresponded to changes in the use of particular nutrients.

Results

Both species richness and activity decreased with elevation along each gradient. However, there were significant interaction effects among elevation, region and season, as ant activity in the dry season was higher in Ecuador and Tanzania but lower in PNG. Relative nutrient use varied among regions: ant preference for some nutrients changed with increasing elevation in Ecuador (decrease in lipid use) and Tanzania (decrease in amino acid and H₂O use), while season affected nutrient use in PNG. There were common trends in trophic guilds along the three elevational gradients (e.g. proportional increase of predators), but these did not explain most of the nutrient use patterns.

Main conclusion

While the structure of ant communities changed similarly with elevation, both the seasonal and elevational effects on nutrient use by ants differed between continents. We argue that regional differences in climate and nutrient availability rather than ant functional composition shape nutrient use by ants.     

Clockwise and counterclockwise hysteresis characterize state changes in the same aquatic ecosystem

Incremental increases in a driver variable, such as nutrients or detritus, can trigger abrupt shifts in aquatic ecosystems that may exhibit hysteretic dynamics and a slow return to the initial state. A model system for understanding these dynamics is the microbial assemblage that inhabits the cup‐shaped leaves of the pitcher plant Sarracenia purpurea. With enrichment of organic matter, this system flips within three days from an oxygen‐rich state to an oxygen‐poor state. In a replicated greenhouse experiment, we enriched pitcher‐plant leaves at different rates with bovine serum albumin (BSA), a molecular substitute for detritus. Changes in dissolved oxygen (DO) and undigested BSA concentration were monitored during enrichment and recovery phases. With increasing enrichment rates, the dynamics ranged from clockwise hysteresis (low), to environmental tracking (medium), to novel counter‐clockwise hysteresis (high). These experiments demonstrate that detrital enrichment rate can modulate a diversity of hysteretic responses within a single aquatic ecosystem, and suggest different management strategies may be needed to mitigate the effects of high vs. low rates of detrital enrichment.     

Melatonin Shifts Human Orcadian Rhythms According to a Phase-Response Curve

A physiological dose of orally administered melatonin shifts circadian rhythms in humans according to a phase-response curve (PRC) that is nearly opposite in phase with the PRCs for light exposure: melatonin delays circadian rhythms when administered in the morning and advances them when administered in the afternoon or early evening. The human melatonin PRC provides critical information for using melatonin to treat circadian phase sleep and mood disorders, as well as maladaptation to shift work and transmeridional air travel. The human melatonin PRC also provides the strongest evidence to date for a function of endogenous melatonin and its suppression by light in augmenting entrainment of circadian rhythms by the light-dark cycle.     

An ecological resilience perspective on cancer: Insights from a toy model

In this paper we propose an ecological resilience point of view on cancer. This view is based on the analysis of a simple ODE model for the interactions between cancer and normal cells. The model presents two regimes for tumor growth. In the first, cancer arises due to three reasons: a partial corruption of the functions that avoid the growth of mutated cells, an aggressive phenotype of tumor cells and exposure to external carcinogenic factors. In this case, treatments may be effective if they drive the system to the basin of attraction of the cancer cure state. In the second regime, cancer arises because the repair system is intrinsically corrupted. In this case, the complete cure is not possible since the cancer cure state is no more stable, but tumor recurrence may be delayed if treatment is prolongued. We review three indicators of the resilience of a stable equilibrium, related with size and shape of its basin of attraction: latitude, precariousness and resistance. A novel method to calculate these indicators is proposed. This method is simpler and more efficient than those currently used, and may be easily applied to other population dynamics models. We apply this method to the model and investigate how these indicators behave with parameters changes. Finally, we present some simulations to illustrate how the resilience analysis can be applied to validated models in order to obtain indicators for personalized cancer treatments.     

Ontogenetic niche shifts in the Mesozoic bird Confuciusornis sanctus

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Temporal variation in foraging group structure of a size-structured stream fish community

Temporal variation in foraging group structure of a fish assemblage was examined in a flood-prone stream in southern Hokkaido, Japan. Foraging behaviour was observed underwater for four species which inhabit the water column: ayu, Plecoglossus altivelis, white-spotted charr, Salvelinus leucomaenis, masu salmon, Oncorhynchus masou, and Japanese dace, Tribolodon hakonensis, with each species being categorized into five size classes (species-size group; SSG). Based on foraging behaviour, each SSG of the fish assemblage was classified into one of four foraging groups: algae grazers, drift foragers, benthos-drift foragers, and omnivores, defined as SSG exhibiting similar foraging behaviour. All size classes of ayu, and of charr and salmon were categorized as algae grazers and drift foragers, respectively, throughout the study period. In contrast, size classes of dace were categorized as drift foragers, benthos-drift foragers, or omnivores with the same size classes often assigned to different foraging groups from month to month. Digestive tract contents of the fishes in the four foraging groups reflected their observed foraging behaviour, and foraging groups were therefore regarded as representing trophic groups. Abundance and membership of each foraging group varied in accordance with changes in abundance of SSG due to their growth, immigration, emigration, and/or mortality. Moreover, due to numerical dominance within the assemblage, plasticity in foraging behaviour of small- and medium-sized dace also played a key role in determining variability in the foraging group structure. Relative frequencies of two types of foraging behaviour, algae nipping and benthos foraging, of the small-sized dace were significantly correlated with the level of each resource, whereas no significant relationship was detected between foraging frequencies of the medium-sized dace and either resource. Fluctuations in foraging group structure within this assemblage occurred through niche shifts of some component members and by changes in SSG composition.     

Bivariate Sign Tests Sensitive to Homeo- and Heteropoetic Treatment Effects

Starting from N paired differences of a continuous variable, BENNETT 's (1962) bivariate sign test is identified as a test against so called homeopoetic treatment effects (or location shifts in one or both variables X and Y). As a complement, a new sign test is identified to be sensitive to so called heteropoetic treatment effects (shifts in dispersion). Both tests are shown to be important in biomedical and psychosocial research. A numerical example is given from psychopharmacology using the new bivariate sign test.