Translational nucleosome positioning: A computational study

Biological and Soft Matter Physic

Understanding CO2 adsorption in a flexible zeolite through a combination of structural, kinetic and modelling techniques

In this study we show how non-trivial equilibrium and kinetic adsorption behaviour in a flexible zeolite can be understood through a combination of experimental characterisation and modelling. Flexible zeolites, such as those in the RHO-family, can exhibit unusual stepped isotherms in the presence of CO2, but their structural complexity makes it hard to attribute a clear mechanism. Here we present a structural and kinetic study on (Na,TEA)-ZSM-25, an extended member of the RHO-family, and show that by combining diffraction data, lattice fluid modelling and dynamic column experiments, we obtain a plausible mechanism for CO2 adsorption and transport in this material. It is evident that by using any single technique, the behaviour is too complex to be readily understood. This is to our knowledge the first study to measure and model the changing kinetics due to adsorption induced framework flexibility.11Nsciescopu

Spatial patterns of benthic biofilm diversity among streams draining proglacial floodplains

Glacier shrinkage opens new proglacial terrain with pronounced environmental gradients along longitudinal and lateral chronosequences. Despite the environmental harshness of the streams that drain glacier forelands, their benthic biofilms can harbor astonishing biodiversity spanning all domains of life. Here, we studied the spatial dynamics of prokaryotic and eukaryotic photoautotroph diversity within braided glacier-fed streams and tributaries draining lateral terraces predominantly fed by groundwater and snowmelt across three proglacial floodplains in the Swiss Alps. Along the lateral chronosequence, we found that benthic biofilms in tributaries develop higher biomass than those in glacier-fed streams, and that their respective diversity and community composition differed markedly. We also found spatial turnover of bacterial communities in the glacier-fed streams along the longitudinal chronosequence. These patterns along the two chronosequences seem unexpected given the close spatial proximity and connectivity of the various streams, suggesting environmental filtering as an underlying mechanism. Furthermore, our results suggest that photoautotrophic communities shape bacterial communities across the various streams, which is understandable given that algae are the major source of organic matter in proglacial streams. Overall, our findings shed new light on benthic biofilms in proglacial streams now changing at rapid pace owing to climate-induced glacier shrinkage

Lateral interactions govern self-assembly of the bacterial biofilm matrix protein BslA

The soil bacterium Bacillus subtilis is a model organism to investigate the formation of biofilms, the predominant form of microbial life. The secreted protein BslA self-assembles at the surface of the biofilm to give the B. subtilis biofilm its characteristic hydrophobicity. To understand the mechanism of BslA self-assembly at interfaces, here we built a molecular model based on the previous BslA crystal structure and the crystal structure of the BslA paralogue YweA that we determined. Our analysis revealed two conserved protein-protein interaction interfaces supporting BslA self-assembly into an infinite 2-dimensional lattice that fits previously determined transmission microscopy images. Molecular dynamics simulations and in vitro protein assays further support our model of BslA elastic film formation, while mutagenesis experiments highlight the importance of the identified interactions for biofilm structure. Based on this knowledge, YweA was engineered to form more stable elastic films and rescue biofilm structure in bslA deficient strains. These findings shed light on protein film assembly and will inform the development of BslA technologies which range from surface coatings to emulsions in fast-moving consumer goods.</p

Lateral interactions govern self-assembly of the bacterial biofilm matrix protein BslA

The soil bacterium Bacillus subtilis is a model organism to investigate the formation of biofilms, the predominant form of microbial life. The secreted protein BslA self-assembles at the surface of the biofilm to give the B. subtilis biofilm its characteristic hydrophobicity. To understand the mechanism of BslA self-assembly at interfaces, here we built a molecular model based on the previous BslA crystal structure and the crystal structure of the BslA paralogue YweA that we determined. Our analysis revealed two conserved protein-protein interaction interfaces supporting BslA self-assembly into an infinite 2-dimensional lattice that fits previously determined transmission microscopy images. Molecular dynamics simulations and in vitro protein assays further support our model of BslA elastic film formation, while mutagenesis experiments highlight the importance of the identified interactions for biofilm structure. Based on this knowledge, YweA was engineered to form more stable elastic films and rescue biofilm structure in bslA deficient strains. These findings shed light on protein film assembly and will inform the development of BslA technologies which range from surface coatings to emulsions in fast-moving consumer goods.</p

Cross-domain interactions confer stability to benthic biofilms in proglacial streams

Cross-domain interactions are an integral part of the success of biofilms in natural environments but remain poorly understood. Here, we describe cross-domain interactions in stream biofilms draining proglacial floodplains in the Swiss Alps. These streams, as a consequence of the retreat of glaciers, are characterised by multiple environmental gradients and perturbations (e.g., changes in channel geomorphology, discharge) that depend on the time since deglaciation. We evaluate co-occurrence of bacteria and eukaryotic communities along streams and show that key community members have disproportionate effects on the stability of community networks. The topology of the networks, here quantified as the arrangement of the constituent nodes formed by specific taxa, was independent of stream type and their apparent environmental stability. However, network stability against fragmentation was higher in the streams draining proglacial terrain that was more recently deglaciated. We find that bacteria, eukaryotic photoautotrophs, and fungi are central to the stability of these networks, which fragment upon the removal of both pro- and eukaryotic taxa. Key taxa are not always abundant, suggesting an underlying functional component to their contributions. Thus, we show that there is a key role played by individual taxa in determining microbial community stability of glacier-fed streams