Probiotic<i> Bacillus subtilis</i> protects against α-synuclein aggregation in <i>C. elegans</i>

How the gut microbiome affects Parkinson's disease remains unclear. Goya et al. show that the probiotic B. subtilis strain PXN21 inhibits and clears α-synuclein aggregation in a C. elegans model. The bacterium acts via metabolites and biofilm formation to activate protective pathways in the host, including DAF-16/FOXO and sphingolipid metabolism.Fil: Goya, María Eugenia. University of Edinburgh; Reino UnidoFil: Xue, Feng. University of Edinburgh; Reino UnidoFil: Sampedro Torres Quevedo, Cristina. University of Edinburgh; Reino UnidoFil: Arnaouteli, Sofia. University Of Dundee; Reino UnidoFil: Riquelme Dominguez, Lourdes. University of Edinburgh; Reino UnidoFil: Romanowski, Andrés. University of Edinburgh; Reino Unido. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; ArgentinaFil: Brydon, Jack. University of Edinburgh; Reino UnidoFil: Ball, Kathryn L.. University of Edinburgh; Reino UnidoFil: Stanley-Wall, Nicola R.. University Of Dundee; Reino UnidoFil: Doitsidou, Maria. University of Edinburgh; Reino Unid

Identification of novel interferon responsive protein partners of human leukocyte antigen A (HLA-A) using cross-linking mass spectrometry (CLMS) approach

The interferon signalling system elicits a robust cytokine response against a wide range of environmental pathogenic and internal pathological signals, leading to induction of a subset of interferon-induced proteins. We applied DSS (disuccinimidyl suberate) mediated cross-linking mass spectrometry (CLMS) to capture novel protein–protein interactions within the realm of interferon induced proteins. In addition to the expected interferon-induced proteins, we identified novel inter- and intra-molecular cross-linked adducts for the canonical interferon induced proteins, such as MX1, USP18, OAS3, and STAT1. We focused on orthogonal validation of a cohort of novel interferon-induced protein networks formed by the HLA-A protein (H2BFS-HLA-A-HMGA1) using co-immunoprecipitation assay, and further investigated them by molecular dynamics simulation. Conformational dynamics of the simulated protein complexes revealed several interaction sites that mirrored the interactions identified in the CLMS findings. Together, we showcase a proof-of-principle CLMS study to identify novel interferon-induced signaling complexes and anticipate broader use of CLMS to identify novel protein interaction dynamics within the tumour microenvironment

Nutrition for the ageing brain: towards evidence for an optimal diet

As people age they become increasingly susceptible to chronic and extremely debilitating brain diseases. The precise cause of the neuronal degeneration underlying these disorders, and indeed normal brain ageing remains however elusive. Considering the limits of existing preventive methods, there is a desire to develop effective and safe strategies. Growing preclinical and clinical research in healthy individuals or at the early stage of cognitive decline has demonstrated the beneficial impact of nutrition on cognitive functions. The present review is the most recent in a series produced by the Nutrition and Mental Performance Task Force under the auspice of the International Life Sciences Institute Europe (ILSI Europe). The latest scientific advances specific to how dietary nutrients and non-nutrient may affect cognitive ageing are presented. Furthermore, several key points related to mechanisms contributing to brain ageing, pathological conditions affecting brain function, and brain biomarkers are also discussed. Overall, findings are inconsistent and fragmented and more research is warranted to determine the underlying mechanisms and to establish dose-response relationships for optimal brain maintenance in different population subgroups. Such approaches are likely to provide the necessary evidence to develop research portfolios that will inform about new dietary recommendations on how to prevent cognitive decline

Clinical utility and diagnostic accuracy of faecal calprotectin for IBD at first presentation to gastroenterology services in adults aged 16–50 years

BACKGROUND: Distinguishing inflammatory bowel disease (IBD) from functional gastrointestinal (GI) disease remains an important issue for gastroenterologists and primary care physicians, and may be difficult on the basis of symptoms alone. Faecal calprotectin (FC) is a surrogate marker for intestinal inflammation but not cancer. AIM: This large retrospective study aimed to determine the most effective use of FC in patients aged 16–50 presenting with GI symptoms. METHODS: FC results were obtained for patients presenting to the GI clinics in Edinburgh between 2005 and 2009 from the Edinburgh Faecal Calprotectin Registry containing FCs from >16,000 patients. Case notes were interrogated to identify demographics, subsequent investigations and diagnoses. RESULTS: 895 patients were included in the main analysis, 65% female and with a median age of 33 years. 10.2% were diagnosed with IBD, 7.3% with another GI condition associated with an abnormal GI tract and 63.2% had functional GI disease. Median FC in these three groups were 1251, 50 and 20 μg/g (p < 0.0001). On ROC analysis, the AUC for FC as a predictor of IBD vs. functional disease was 0.97. Using a threshold of ≥ 50 μg/g for IBD vs. functional disease yielded a sensitivity of 0.97, specificity of 0.74, positive predictive value of 0.37 and negative predictive value of 0.99. Combined with alarm symptoms, the sensitivity was 1.00. CONCLUSIONS: Implementation of FC in the initial diagnostic workup of young patients with GI symptoms, particularly those without alarm symptoms, is highly accurate in the exclusion of IBD, and can provide reassurance to patients and physicians

Investigation into the structural mechanisms underlying functional diversity of interferon-alpha subtypes

Interferons (IFNs) were discovered by Isaacs and Lindeman in 1957, and were found to be the mediators of viral interference; as such they are central to innate immunity. They are expressed robustly upon recognition of viral pathogens, and effect proteomic changes in target cells which establish a virus-restrictive state. IFN-Is include the subtype IFNα, itself a family of 12 proteins in humans. These also play roles in anti-cancer immunity via their anti-proliferative and immune-modulatory effects. IFNα2 and IFNβ have been developed as therapeutics for chronic virus infection and several malignancies, but with limitations due to severe side effects. Here, the functional diversity of the IFNα subtypes was investigated, as a basis for development of further IFNα therapeutics. IFNα14 was a particular focus due to its established high potency across several metrics, and high affinity for the IFN receptor. The viral restriction, anti-proliferative effects, signalling cascades, and proteomic changes effected by IFNα subtypes were compared in order to understand the distinct functional profiles of IFNα subtypes. IFNs’ interactions with their receptor were assessed computationally and biophysically, to identify a structural-functional mechanism explaining their differential effects. These investigations led to the development of a high-throughput IFNAR2 binding screen for synthetic and mutant IFNαs. The higher affinity of IFNα14 was linked to faster intracellular signal generation and increased anti-viral and anti-proliferative efficacy vs other subtypes. Differences between the receptor interactions of each IFN were identified, which may be the basis for different signal propagation across the plasma membrane

Generation of photocaged nanobodies for intracellular applications in an animal using genetic code expansion and computationally guided protein engineering**

Nanobodies are becoming increasingly popular as tools for manipulating and visualising proteins in vivo. The ability to control nanobody/antigen interactions using light could provide precise spatiotemporal control over protein function. We develop a general approach to engineer photo‐activatable nanobodies using photocaged amino acids that are introduced into the target binding interface by genetic code expansion. Guided by computational alanine scanning and molecular dynamics simulations, we tune nanobody/target binding affinity to eliminate binding before uncaging. Upon photo‐activation using 365 nm light, binding is restored. We use this approach to generate improved photocaged variants of two anti‐GFP nanobodies that function robustly when directly expressed in a complex intracellular environment together with their antigen. We apply them to control subcellular protein localisation in the nematode worm Caenorhabditis elegans. Our approach applies predictions derived from computational modelling directly in a living animal and demonstrates the importance of accounting for in vivo effects on protein‐protein interactions

Hammett Structural Relationships Revealed in Chalcogen Bonded Co-crystals of Electron Rich Pyridines with 4′-Substituted Ebselen Derivatives

In this work, a detailed Hammett structure-structure correlation was applied to a range of chalcogen bonded co-crystals prepared by combining 4′-substituted derivatives of the selenium-based drug ebselen with three different 4-amino-substituted pyridine based chalcogen bond acceptors of differing basicities. This established that the N · · · Se chalcogen bond distance is well within the sum of the van der Waals radii of Se and N and is sensitive to the electronic nature of the substituent. Thus N · · · Se distances ranging from 2.2424(5)–2.4496(9) Å were observed with the shorter distances being observed in co-crystals of ebselen substituted with electron withdrawing groups. Associated with trends of the N · · · Se distance as a function of the 4′-substituent was lengthening of the internal Se−N bond distance consistent with a significant covalent contribution to N · · · Se chalcogen bonding in these derivatives. We define a covalency quotient for the chalcogen bond as the negative slope of the plot of the internal Se−N bond distance vs the external N · · · Se chalcogen bond distance. A value of 0.31 was obtained implying a significant covalent contribution to N · · · Se chalcogen bond. A similar result was obtained by an analysis of chalcogen bonded selenium containing molecules harvested from the Cambridge Crystallographic Database. The covalency quotient is extended to the general case for sigma-hole interactions including halogen bonding and hydrogen bonding, and we show that the covalent component of such interactions can be inferred from the lengthening of the donor bond. The degree of charge transfer in a smaller number of chalcogen bonded co-crystals of ebselen was established by measuring experimental electron density using high-resolution x-ray diffraction to more accurately measure the degree of electron transfer and hence covalency. This showed that in the most strongly bound systems, up to 1 electron worth of charge is transferred from the Lewis base to the Ch-bond donor, which again clearly points to significant covalent character