Niche partitioning of a pathogenic microbiome driven by chemical gradients

© 2018 The Authors, some rights reserved. Environmental microbial communities are stratified by chemical gradients that shape the structure and function of these systems. Similar chemical gradients exist in the human body, but how they influence these microbial systems is more poorly understood. Understanding these effects can be particularly important for dysbiotic shifts in microbiome structure that are often associated with disease. We show that pH and oxygen strongly partition the microbial community from a diseased human lung into two mutually exclusive communities of pathogens and anaerobes. Antimicrobial treatment disrupted this chemical partitioning, causing complex death, survival, and resistance outcomes that were highly dependent on the individual microorganism and on community stratification. These effects were mathematically modeled, enabling a predictive understanding of this complex polymicrobial system. Harnessing the power of these chemical gradients could be a drug-free method of shaping microbial communities in the human body from undesirable dysbiotic states

Formation of Amyloid-Like Fibrils by Y-Box Binding Protein 1 (YB-1) Is Mediated by Its Cold Shock Domain and Modulated by Disordered Terminal Domains

YB-1, a multifunctional DNA- and RNA-binding nucleocytoplasmic protein, is involved in the majority of DNA- and mRNA-dependent events in the cell. It consists of three structurally different domains: its central cold shock domain has the structure of a β-barrel, while the flanking domains are predicted to be intrinsically disordered. Recently, we showed that YB-1 is capable of forming elongated fibrils under high ionic strength conditions. Here we report that it is the cold shock domain that is responsible for formation of YB-1 fibrils, while the terminal domains differentially modulate this process depending on salt conditions. We demonstrate that YB-1 fibrils have amyloid-like features, including affinity for specific dyes and a typical X-ray diffraction pattern, and that in contrast to most of amyloids, they disassemble under nearly physiological conditions

Prioritizing natural product diversity in a collection of 146 bacterial strains based on growth and extraction protocols

In order to expedite the rapid and efficient discovery and isolation of novel specialized metabolites, whilst minimizing the waste of resources on rediscovery of known compounds, it is crucial to develop efficient approaches for strain prioritization, rapid dereplication, and the assessment of favored cultivation and extraction conditions. Herein we interrogated bacterial strains by systematically evaluating cultivation and extraction parameters with LC-MS/MS analysis and subsequent dereplication through the Global Natural Product Social Molecular Networking (GNPS) platform. The developed method is fast, requiring minimal time and sample material, and is compatible with high throughput extract analysis, thereby streamlining strain prioritization and evaluation of culturing parameters. With this approach, we analyzed 146 marine Salinispora and Streptomyces strains that were grown and extracted using multiple different protocols. In total, 603 samples were analyzed, generating approximately 1.8 million mass spectra. We constructed a comprehensive molecular network and identified 15 molecular families of diverse natural products and their analogues. The size and breadth of this network shows statistically supported trends in molecular diversity when comparing growth and extraction conditions. The network provides an extensive survey of the biosynthetic capacity of the strain collection and a method to compare strains based on the variety and novelty of their metabolites. This approach allows us to quickly identify patterns in metabolite production that can be linked to taxonomy, culture conditions, and extraction methods, as well as informing the most valuable growth and extraction conditions

Prioritizing natural product diversity in a collection of 146 bacterial strains based on growth and extraction protocols

In order to expedite the rapid and efficient discovery and isolation of novel specialized metabolites, whilst minimizing the waste of resources on rediscovery of known compounds, it is crucial to develop efficient approaches for strain prioritization, rapid dereplication, and the assessment of favored cultivation and extraction conditions. Herein we interrogated bacterial strains by systematically evaluating cultivation and extraction parameters with LC-MS/MS analysis and subsequent dereplication through the Global Natural Product Social Molecular Networking (GNPS) platform. The developed method is fast, requiring minimal time and sample material, and is compatible with high throughput extract analysis, thereby streamlining strain prioritization and evaluation of culturing parameters. With this approach, we analyzed 146 marine Salinispora and Streptomyces strains that were grown and extracted using multiple different protocols. In total, 603 samples were analyzed, generating approximately 1.8 million mass spectra. We constructed a comprehensive molecular network and identified 15 molecular families of diverse natural products and their analogues. The size and breadth of this network shows statistically supported trends in molecular diversity when comparing growth and extraction conditions. The network provides an extensive survey of the biosynthetic capacity of the strain collection and a method to compare strains based on the variety and novelty of their metabolites. This approach allows us to quickly identify patterns in metabolite production that can be linked to taxonomy, culture conditions, and extraction methods, as well as informing the most valuable growth and extraction conditions

The Storm of Decameter Spikes During the Event of 14 June 2012

© 2015, Springer Science+Business Media Dordrecht. An event on 14 June 2012, observed with the radio telescopes UTR-2 (Kharkov, Ukraine), URAN-2 (Poltava, Ukraine), and NDA (Nançay, France) during a joint Summer campaign, is analyzed and discussed. The high solar activity resulted in a storm of spikes, and a storm of Type III bursts, Type IIIb bursts, and a Type IV burst observed in the decameter band. During the observed time interval, the average flux of radio emission changed twice. Using spikes as a tool for diagnostics of plasma parameters, we followed variations of the coronal temperature and the coronal magnetic field in the observed time interval. Thus, in frames of the model described in this article the observed decameter spikes’ durations of 0.3 – 1 seconds correspond to the coronal plasma temperatures of ≈0.1–0.6×106K{\approx}\, 0.1\,\mbox{--}\,0.6 \times10^{6}~\mbox{K}. At the same time the spikes’ frequency bandwidths of 25 – 80 kHz give us the magnetic-field value of about 2 G.status: publishe

Paws, pads and plants: the enhanced elasticity of cell-filled load-bearing structures

Paws, fat pads and plants share a remarkable structure made up of closed cells with elastic cell walls capable of supporting large loads and deformations. A key challenge is to understand how the function of these structures is enhanced by their geometric and material design. To do so, we compare different elastic models operating in large strain deformation when the cells are empty or filled with an incompressible liquid or solid core. We demonstrate theoretically, for three different cell geometries, that the elastic modulus in a direction associated with the change of curvature in the cell wall (i) is greater when the cell is filled; (ii) increases as the internal cell pressure increases; and (iii) increases also as the thickness of the cell wall increases or when the wall is multi-layer. As these results do not depend on the choice of the strain-energy function describing the cell-wall material, they are valid for a wide range of structures made from different elastic materials. For multiple cells deforming together due to external forces, the increase in elastic modulus of the cell walls under increasing core pressure is found numerically throughout the structure