Synchrony affects Taylor’s law in theory and data

Two widely confirmed patterns in ecology are Taylor’s law (TL), which states that the variance of population density is approximately a power of mean population density, and population synchrony, the tendency of species’ population sizes in different areas to be correlated through time. TL has been applied in many areas, including fisheries management, conservation, agriculture, finance, physics, and meteorology. Synchrony of populations increases the likelihood of large-scale pest or disease outbreaks and shortages of resources. We show that changed synchrony modifies and can invalidate TL. Widespread recent changes in synchrony, possibly resulting from climate change, may broadly affect TL and its applications

MultiMetEval: comparative and multi-objective analysis of genome-scale metabolic models

Comparative metabolic modelling is emerging as a novel field, supported by the development of reliable and standardized approaches for constructing genome-scale metabolic models in high throughput. New software solutions are needed to allow efficient comparative analysis of multiple models in the context of multiple cellular objectives. Here, we present the user-friendly software framework Multi-Metabolic Evaluator (MultiMetEval), built upon SurreyFBA, which allows the user to compose collections of metabolic models that together can be subjected to flux balance analysis. Additionally, MultiMetEval implements functionalities for multi-objective analysis by calculating the Pareto front between two cellular objectives. Using a previously generated dataset of 38 actinobacterial genome-scale metabolic models, we show how these approaches can lead to exciting novel insights. Firstly, after incorporating several pathways for the biosynthesis of natural products into each of these models, comparative flux balance analysis predicted that species like Streptomyces that harbour the highest diversity of secondary metabolite biosynthetic gene clusters in their genomes do not necessarily have the metabolic network topology most suitable for compound overproduction. Secondly, multi-objective analysis of biomass production and natural product biosynthesis in these actinobacteria shows that the well-studied occurrence of discrete metabolic switches during the change of cellular objectives is inherent to their metabolic network architecture. Comparative and multi-objective modelling can lead to insights that could not be obtained by normal flux balance analyses. MultiMetEval provides a powerful platform that makes these analyses straightforward for biologists. Sources and binaries of MultiMetEval are freely available from https://github.com/PiotrZakrzewski/MetEv​al/downloads

Reduced LRRK2 in association with retromer dysfunction in post-mortem brain tissue from LRRK2 mutation carriers

Missense mutations in leucine-rich repeat kinase 2 (LRRK2) are pathogenic for familial Parkinson's disease. However, it is unknown whether levels of LRRK2 protein in the brain are altered in patients with LRRK2-associated Parkinson's disease. Because LRRK2 mutations are relatively rare, accounting for approximately 1% of all Parkinson's disease, we accessioned cases from five international brain banks to investigate levels of the LRRK2 protein, and other genetically associated Parkinson's disease proteins. Brain tissue was obtained from 17 LRRK2 mutation carriers (12 with the G2019S mutation and five with the I2020T mutation) and assayed by immunoblot. Compared to matched controls and idiopathic Parkinson's disease cases, we found levels of LRRK2 protein were reduced in the LRRK2 mutation cases. We also measured a decrease in two other proteins genetically implicated in Parkinson's disease, the core retromer component, vacuolar protein sorting associated protein 35 (VPS35), and the lysosomal hydrolase, glucocerebrosidase (GBA). Moreover, the classical retromer cargo protein, cation-independent mannose-6-phosphate receptor (MPR300, encoded by IGF2R), was also reduced in the LRRK2 mutation cohort and protein levels of the receptor were correlated to levels of LRRK2. These results provide new data on LRRK2 protein expression in brain tissue from LRRK2 mutation carriers and support a relationship between LRRK2 and retromer dysfunction in LRRK2-associated Parkinson's disease brain

Phase Separation and Magnetic Order in K-doped Iron Selenide Superconductor

Alkali-doped iron selenide is the latest member of high Tc superconductor family, and its peculiar characters have immediately attracted extensive attention. We prepared high-quality potassium-doped iron selenide (KxFe2-ySe2) thin films by molecular beam epitaxy and unambiguously demonstrated the existence of phase separation, which is currently under debate, in this material using scanning tunneling microscopy and spectroscopy. The stoichiometric superconducting phase KFe2Se2 contains no iron vacancies, while the insulating phase has a \surd5\times\surd5 vacancy order. The iron vacancies are shown always destructive to superconductivity in KFe2Se2. Our study on the subgap bound states induced by the iron vacancies further reveals a magnetically-related bipartite order in the superconducting phase. These findings not only solve the existing controversies in the atomic and electronic structures in KxFe2-ySe2, but also provide valuable information on understanding the superconductivity and its interplay with magnetism in iron-based superconductors

The Endogenous Th17 Response in NO<inf>2</inf>-Promoted Allergic Airway Disease Is Dispensable for Airway Hyperresponsiveness and Distinct from Th17 Adoptive Transfer

Severe, glucocorticoid-resistant asthma comprises 5-7% of patients with asthma. IL-17 is a biomarker of severe asthma, and the adoptive transfer of Th17 cells in mice is sufficient to induce glucocorticoid-resistant allergic airway disease. Nitrogen dioxide (NO2) is an environmental toxin that correlates with asthma severity, exacerbation, and risk of adverse outcomes. Mice that are allergically sensitized to the antigen ovalbumin by exposure to NO2 exhibit a mixed Th2/Th17 adaptive immune response and eosinophil and neutrophil recruitment to the airway following antigen challenge, a phenotype reminiscent of severe clinical asthma. Because IL-1 receptor (IL-1R) signaling is critical in the generation of the Th17 response in vivo, we hypothesized that the IL-1R/Th17 axis contributes to pulmonary inflammation and airway hyperresponsiveness (AHR) in NO2-promoted allergic airway disease and manifests in glucocorticoid-resistant cytokine production. IL-17A neutralization at the time of antigen challenge or genetic deficiency in IL-1R resulted in decreased neutrophil recruitment to the airway following antigen challenge but did not protect against the development of AHR. Instead, IL-1R-/- mice developed exacerbated AHR compared to WT mice. Lung cells from NO2-allergically inflamed mice that were treated in vitro with dexamethasone (Dex) during antigen restimulation exhibited reduced Th17 cytokine production, whereas Th17 cytokine production by lung cells from recipient mice of in vitro Th17-polarized OTII T-cells was resistant to Dex. These results demonstrate that the IL-1R/Th17 axis does not contribute to AHR development in NO2-promoted allergic airway disease, that Th17 adoptive transfer does not necessarily reflect an endogenously-generated Th17 response, and that functions of Th17 responses are contingent on the experimental conditions in which they are generated. © 2013 Martin et al

In situ epitaxial engineering of graphene and h-BN lateral heterostructure with a tunable morphology comprising h-BN domains

Graphene and hexagonal boron nitride (h-BN), as typical two-dimensional (2D) materials, have long attracted substantial attention due to their unique properties and promise in a wide range of applications. Although they have a rather large difference in their intrinsic bandgaps, they share a very similar atomic lattice; thus, there is great potential in constructing heterostructures by lateral stitching. Herein, we present the in situ growth of graphene and h-BN lateral heterostructures with tunable morphologies that range from a regular hexagon to highly symmetrical star-like structure on the surface of liquid Cu. The chemical vapor deposition (CVD) method is used, where the growth of the h-BN is demonstrated to be highly templated by the graphene. Furthermore, large-area production of lateral G-h-BN heterostructures at the centimeter scale with uniform orientation is realized by precisely tuning the CVD conditions. We found that the growth of h-BN is determined by the initial graphene and symmetrical features are produced that demonstrate heteroepitaxy. Simulations based on the phase field and density functional theories are carried out to elucidate the growth processes of G-h-BN flakes with various morphologies, and they have a striking consistency with experimental observations. The growth of a lateral G-h-BN heterostructure and an understanding of the growth mechanism can accelerate the construction of various heterostructures based on 2D materials

Microbial ligand costimulation drives neutrophilic steroid-refractory asthma

Funding: The authors thank the Wellcome Trust (102705) and the Universities of Aberdeen and Cape Town for funding. This research was also supported, in part, by National Institutes of Health GM53522 and GM083016 to DLW. KF and BNL are funded by the Fonds Wetenschappelijk Onderzoek, BNL is the recipient of an European Research Commission consolidator grant and participates in the European Union FP7 programs EUBIOPRED and MedALL. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Peer reviewedPublisher PD

An introduction to Graph Data Management

A graph database is a database where the data structures for the schema and/or instances are modeled as a (labeled)(directed) graph or generalizations of it, and where querying is expressed by graph-oriented operations and type constructors. In this article we present the basic notions of graph databases, give an historical overview of its main development, and study the main current systems that implement them

Adaptive remodeling of the bacterial proteome by specific ribosomal modification regulates Pseudomonas infection and niche colonisation

Post-transcriptional control of protein abundance is a highly important, underexplored regulatory process by which organisms respond to their environments. Here we describe an important and previously unidentified regulatory pathway involving the ribosomal modification protein RimK, its regulator proteins RimA and RimB, and the widespread bacterial second messenger cyclic-di-GMP (cdG). Disruption of rimK affects motility and surface attachment in pathogenic and commensal Pseudomonas species, with rimK deletion significantly compromising rhizosphere colonisation by the commensal soil bacterium P. fluorescens, and plant infection by the pathogens P. syringae and P. aeruginosa. RimK functions as an ATP-dependent glutamyl ligase, adding glutamate residues to the C-terminus of ribosomal protein RpsF and inducing specific effects on both ribosome protein complement and function. Deletion of rimK in P. fluorescens leads to markedly reduced levels of multiple ribosomal proteins, and also of the key translational regulator Hfq. In turn, reduced Hfq levels induce specific downstream proteomic changes, with significant increases in multiple ABC transporters, stress response proteins and non-ribosomal peptide synthetases seen for both ΔrimK and Δhfq mutants. The activity of RimK is itself controlled by interactions with RimA, RimB and cdG. We propose that control of RimK activity represents a novel regulatory mechanism that dynamically influences interactions between bacteria and their hosts; translating environmental pressures into dynamic ribosomal changes, and consequently to an adaptive remodeling of the bacterial proteome

Local antiferromagnetic exchange and collaborative Fermi surface as key ingredients of high temperature superconductors

Cuprates, ferropnictides and ferrochalcogenides are three classes of unconventional high-temperature superconductors, who share similar phase diagrams in which superconductivity develops after a magnetic order is suppressed, suggesting a strong interplay between superconductivity and magnetism, although the exact picture of this interplay remains elusive. Here we show that there is a direct bridge connecting antiferromagnetic exchange interactions determined in the parent compounds of these materials to the superconducting gap functions observed in the corresponding superconducting materials. High superconducting transition temperature is achieved when the Fermi surface topology matches the form factor of the pairing symmetry favored by local magnetic exchange interactions. Our result offers a principle guide to search for new high temperature superconductors.Comment: 12 pages, 5 figures, 1 table, 1 supplementary materia