The antagonistic pleiotropy of insulin‐like growth factor 1

While insulin‐like growth factor‐1 (IGF‐1) is a well‐established modulator of aging and longevity in model organisms, its role in humans has been controversial. In this study, we used the UK Biobank (n = 440,185) to resolve previous ambiguities in the relationship between serum IGF‐1 levels and clinical disease. We examined prospective associations of serum IGF‐1 with mortality, dementia, vascular disease, diabetes, osteoporosis, and cancer, finding two generalized patterns: First, IGF‐1 interacts with age to modify risk in a manner consistent with antagonistic pleiotropy; younger individuals with high IGF‐1 are protected from disease, while older individuals with high IGF‐1 are at increased risk for incident disease or death. Second, the association between IGF‐1 and risk is generally U‐shaped, indicating that both high and low levels of IGF‐1 may be detrimental. With the exception of a more uniformly positive relationship between IGF‐1 and cancer, these effects were remarkably consistent across a wide range of conditions, providing evidence for a unifying pathway that determines risk for most age‐associated diseases. These data suggest that IGF‐1 signaling could be harmful in older adults, who may actually benefit from the attenuation of biological growth pathways.     

Funnel hunting in a rough terrain: learning and discriminating native energy funnels

Protein folding and binding is commonly depicted as a search for the minimum energy conformation. Modeling of protein complex structures by RosettaDock often results in a set of low-energy conformations near the native structure. Ensembles of low-energy conformations can appear, however, in other regions, especially when backbone movements occur upon binding. What then characterizes the energy landscape near the correct orientation? We applied a machine learning algorithm to distinguish ensembles of low-energy conformations around the native conformation from other low-energy ensembles. The resulting classifier, FunHunt, identifies the native orientation in 50/52 protein complexes in a test set. The features used by FunHunt teach us about the nature of native interfaces. Remarkably, the energy decrease of trajectories toward near-native orientations is significantly larger than for other orientations. This provides a possible explanation for the stability of association in the native orientation.     

The effect of <Emphasis Type="Italic">Cercidium praecox</Emphasis> and <Emphasis Type="Italic">Prosopis laevigata</Emphasis> on vertical distribution of soil free-living nematode communities in the Tehuacán Desert,Mexico

Vegetation cover is known to act as an abiotic mediator influencing the structure of soil fauna communities in arid and semi-arid ecosystems. The aim of the current research was to determine the spatial dispersion of the soil free-living nematode community under the canopy of Cercidium praecox and Prosopis laevigata during the rainy season. These shrubs are the dominant plant associations in the western part of the Tehuacán-Cuicatlán Valley in Mexico. Soil samples were taken from each 10-cm depth between 0 and 50 cm in August 2004. Our results demonstrated that the abundance and structure of the soil free-living nematode communities in the study area were strongly dependent on plant effects, specified by limited factors such as soil moisture and organic matter availability. The greatest degree of abundance of soil-free-living nematodes (88%) was found in the upper (0–10 cm) soil layer. Plant parasites were the most abundant trophic group under the two plants (58 and 36% under Parkinsonia (Cercidium) praecox and Prosopis laevigata, respectively), whereas omnivore-predators were the most dominant (96%) in inter-plant spaces. The fungivore/bacterivore (F/B) ratio was found to be the most useful tool of the ecological indices tested in the present study, reflecting the vertical distribution of the free-living nematode communities beneath different plant species in the different soil layers. The soil free-living nematode communities and their vertical distribution were found to be affected by plant ecophysiological adaptation, soil moisture, and the interaction between them.     

Stress-protective signalling of prion protein is corrupted by scrapie prions

Studies in transgenic mice revealed that neurodegeneration induced by scrapie prion (PrP(Sc)) propagation is dependent on neuronal expression of the cellular prion protein PrP(C). On the other hand, there is evidence that PrP(C) itself has a stress-protective activity. Here, we show that the toxic activity of PrP(Sc) and the protective activity of PrP(C) are interconnected. With a novel co-cultivation assay, we demonstrate that PrP(Sc) can induce apoptotic signalling in PrP(C)-expressing cells. However, cells expressing PrP mutants with an impaired stress-protective activity were resistant to PrP(Sc)-induced toxicity. We also show that the internal hydrophobic domain promotes dimer formation of PrP and that dimerization of PrP is linked to its stress-protective activity. PrP mutants defective in dimer formation did not confer enhanced stress tolerance. Moreover, in chronically scrapie-infected neuroblastoma cells the amount of PrP(C) dimers inversely correlated with the amount of PrP(Sc) and the resistance of the cells to various stress conditions. Our results provide new insight into the mechanism of PrP(C)-mediated neuroprotection and indicate that pathological PrP conformers abuse PrP(C)-dependent pathways for apoptotic signalling.     

Protein localization by actin treadmilling and molecular motors regulates stereocilia shape and treadmilling rate

We present a physical model that describes the active localization of actin-regulating proteins inside stereocilia during steady-state conditions. The mechanism of localization is through the interplay of free diffusion and directed motion, which is driven by coupling to the treadmilling actin filaments and to myosin motors that move along the actin filaments. The resulting localization of both the molecular motors and their cargo is calculated, and is found to have an exponential (or steeper) profile. This localization can be at the base (driven by actin retrograde flow and minus-end myosin motors), or at the stereocilia tip (driven by plus-end myosin motors). The localization of proteins that influence the actin depolymerization and polymerization rates allow us to describe the narrow shape of the stereocilia base, and the observed increase of the actin polymerization rate with the stereocilia height.     

Physical model of contractile ring initiation in dividing cells

We present a physical mechanism to describe initiation of the contractile ring during cell division. The model couples the membrane curvature with the contractile forces produced by protein clusters attached to the membrane. These protein clusters are mobile on the membrane and possess either an isotropic or an anisotropic spontaneous curvature. Our results show that under these conditions the contraction force gives rise to an instability that corresponds in a closed cellular system to the initiation of the contractile ring. We find a quantization of this process at distinct length-scales, which we compare to available data for different types of eukaryote cells.     

Broad phylogeny and functionality of cellulosomal components in the bovine rumen microbiome

The cellulosome is an extracellular multi‐enzyme complex that is considered one of the most efficient plant cell wall‐degrading strategies devised by nature. Its unique modular architecture, achieved by high affinity and specific interaction between protein modules (cohesins and dockerins) enables formation of various enzyme combinations. Extensive research has been dedicated to the mechanistic nature of the cellulosome complex. Nevertheless, little is known regarding its distribution and abundance among microbes in natural plant fibre‐rich environments. Here, we explored these questions in bovine rumen microbial communities, specialized in efficient degradation of lignocellulosic plant material. We bioinformatically screened for cellulosomal modules in this complex environment using a previously published ultra‐deep fibre‐adherent rumen metagenome. Intriguingly, a large portion of the functions of the dockerin‐containing proteins were related to alternative biological processes, and not necessarily to the classic fibre degradation function. Our analysis was experimentally validated by characterizing specific interactions between selected cohesins and dockerins and revealed that cellulosome is a more generalized strategy used by diverse bacteria, some of which were not previously associated with cellulosome production. Remarkably, our results provide additional proof of similarity among rumen microbial communities worldwide. This study suggests a broader and widespread role for the cellulosomal machinery in nature.