Green nanosilicas for monoaromatic hydrocarbons removal from air

We demonstrate a novel application of green nanosilicas (GN), prepared via an environmentally friendly route, in removing volatile organic compounds (VOCs). Herein, we aim to establish GN as viable alternatives to traditional mesoporous silicas for the removal of monoaromatic hydrocarbons (MAHC). The results show that the GN have high extraction efficiencies comparable to those previously reported for mesoporous silicas. It was demonstrated that bespoke GN can be syntheised readily with the ability to tailor their physical properties and MAHC adsorption. In order to understand the MAHC adsorption by GN, their porosity, morphology and pore structure were characterised. It was observed that the combination of broad pore size distribution and, in particular, the presence of meso- and micro-porosity in GN contributed to high MAHC extraction efficiencies and selectivity. Although from a commercial viewpoint, further optimisation of GN is desirable in order to replace traditional sorbents, this work clearly highlights a new family of “green” sorbents, which can be prepared with a substantial reduction in secondary pollution with potential applications in selective gas separation

IHMCIF: An Extension of the PDBx/mmCIF Data Standard for Integrative Structure Determination Methods

IHMCIF (github.com/ihmwg/IHMCIF) is a data information framework that supports archiving and disseminating macromolecular structures determined by integrative or hybrid modeling (IHM), and making them Findable, Accessible, Interoperable, and Reusable (FAIR). IHMCIF is an extension of the Protein Data Bank Exchange/macromolecular Crystallographic Information Framework (PDBx/mmCIF) that serves as the framework for the Protein Data Bank (PDB) to archive experimentally determined atomic structures of biological macromolecules and their complexes with one another and small molecule ligands (e.g., enzyme cofactors and drugs). IHMCIF serves as the foundational data standard for the PDB-Dev prototype system, developed for archiving and disseminating integrative structures. It utilizes a flexible data representation to describe integrative structures that span multiple spatiotemporal scales and structural states with definitions for restraints from a variety of experimental methods contributing to integrative structural biology. The IHMCIF extension was created with the benefit of considerable community input and recommendations gathered by the Worldwide Protein Data Bank (wwPDB) Task Force for Integrative or Hybrid Methods (wwpdb.org/task/hybrid). Herein, we describe the development of IHMCIF to support evolving methodologies and ongoing advancements in integrative structural biology. Ultimately, IHMCIF will facilitate the unification of PDB-Dev data and tools with the PDB archive so that integrative structures can be archived and disseminated through PDB

Outcome of the First wwPDB Hybrid / Integrative Methods Task Force Workshop

Structures of biomolecular systems are increasingly computed by integrative modeling that relies on varied types of experimental data and theoretical information. We describe here the proceedings and conclusions from the first wwPDB Hybrid/Integrative Methods Task Force Workshop held at the European Bioinformatics Institute in Hinxton, UK, on October 6 and 7, 2014. At the workshop, experts in various experimental fields of structural biology, experts in integrative modeling and visualization, and experts in data archiving addressed a series of questions central to the future of structural biology. How should integrative models be represented? How should the data and integrative models be validated? What data should be archived? How should the data and models be archived? What information should accompany the publication of integrative models

Altered aryl-hydrocarbon-receptor signalling affects regulatory and effector cell immunity in autoimmune hepatitis

BACKGROUND & AIMS: In autoimmune hepatitis (AIH) imbalance between Treg and Th17-cells has been linked to low levels of CD39, an ectoenzyme that hydrolyses ATP ultimately generating immunosuppressive adenosine. Upregulation of CD39 results from activation of aryl-hydrocarbon-receptor (AHR), which mediates toxin responses to modulate T-cell immunity. Upon binding to exogenous or endogenous ligands, AHR dimerizes with the aryl-hydrocarbon-receptor-nuclear-translocator (ARNT) or other ‘non-canonical’ binding factors like oestrogen-receptor-α (Erα) to modulate gene transcription. The AHR/ARNT complex is in turn regulated by hypoxia-inducible-factor-1α (HIF-1α) and the aryl-hydrocarbon receptor-repressor (AHRR). In this study we investigated whether altered AHR signalling underlies defective CD39 expression and function in AIH Treg and Th17-cells, therefore contributing to regulatory/effector cell imbalance. METHODS: Treg and Th17-cells, obtained from the peripheral blood of 49 AIH patients and 21 healthy subjects (HS), were tested for response to AHR endogenous and exogenous ligands. RESULTS: When compared to HS, AIH Treg and Th17-cells displayed impaired response to AHR activation, as reflected by impaired upregulation of CD39, delayed increase in ectoenzymatic activity and defective Treg suppressive function. These impairments resulted, at least in part, from heightened levels of AHRR and Erα in Treg and high HIF-1α in Th17-cells and were reverted upon molecular blockade. Importantly, in AIH Treg, the binding affinity of AHR was higher for Erα than ARNT. CONCLUSIONS: In AIH, high levels of AHRR and HIF-1α inhibit AHR signalling in Treg and Th17-cells. AHR non-canonical binding to Erα further amplifies lack of effective CD39 upregulation. Blockade of these inhibitory and/or non-canonical activation pathways represents a potential therapeutic approach to restore CD39 and immunohomeostasis in AIH