Human interactome of the influenza B virus NS1 protein

This work was partially supported by NIAID grant U19AI106754, and by CRIP (Center for Research in Influenza Pathogenesis), an NIAID funded Center of Excellence for Influenza Research and Surveillance (CEIRS, contract #HHSN272201400008C) to A. G-S. Work at the University of Zurich was supported by the Swiss National Science Foundation (grant 31003A_159993 to BGH).NS1 proteins of influenza A and B viruses share limited sequence homology, yet both are potent manipulators of host cell processes, particularly interferon (IFN) induction. Although many cellular partners are reported for A/NS1, only a few (e.g. PKR and ISG15) have been identified for B/NS1. Here, affinity-purification and mass spectrometry were used to expand the known host interactome of B/NS1. We identified 22 human proteins as new putative targets for B/NS1, validating several, including DHX9, ILF3, YBX1 and HNRNPC. Consistent with two RNA-binding domains in B/NS1, many of the identified factors bind RNA and some interact with B/NS1 in an RNA-dependent manner. Functional characterization of several B/NS1 interactors identified SNRNP200 as a potential positive regulator of host IFN responses, while ILF3 exhibited dual roles in both IFN induction and influenza B virus replication. These data provide a resource for future investigations into the mechanisms underpinning host cell modulation by influenza B virus NS1.Publisher PDFPeer reviewe

Recombinant vacuolar iron transporter family homologue PfVIT from human malaria-causing Plasmodium falciparum is a Fe2+/H+ exchanger

This work was funded in part by a Royal Society Wolfson Research Merit Award (to J.P.D). It was also supported by the Wellcome Trust (grant number WT079272AIA) which funded the MALDI TOF-TOF analyser at the BSRC Mass Spectrometry and Proteomics Facility, University of St Andrews. P.L was supported by a Northern Ireland Department of Employment and Learning (DEL) postgraduate studentship.Vacuolar iron transporters (VITs) are a poorly understood family of integral membrane proteins that can function in iron homeostasis via sequestration of labile Fe2+ into vacuolar compartments. Here we report on the heterologous overexpression and purification of PfVIT, a vacuolar iron transporter homologue from the human malaria-causing parasite Plasmodium falciparum. Use of synthetic, codon-optimised DNA enabled overexpression of functional PfVIT in the inner membrane of Escherichia coli which, in turn, conferred iron tolerance to the bacterial cells. Cells that expressed PfVIT had decreased levels of total cellular iron compared with cells that did not express the protein. Qualitative transport assays performed on inverted vesicles enriched with PfVIT revealed that the transporter catalysed Fe2+/H+ exchange driven by the proton electrochemical gradient. Furthermore, the PfVIT transport function in this system did not require the presence of any Plasmodium-specific factor such as post-translational phosphorylation. PfVIT purified as a monomer and, as measured by intrinsic protein fluorescence quenching, bound Fe2+ in detergent solution with low micromolar affinity. This study of PfVIT provides material for future detailed biochemical, biophysical and structural studies to advance understanding of the vacuolar iron transporter family of membrane proteins from important human pathogens.Publisher PDFPeer reviewe

Investigation of the blood proteome in response to spinal cord injury in rodent models

We would like to thank the Institute of Orthopaedics and the Midlands Centre for Spinal Cord Injury (MCSI) for funding this research. This work was also supported by the Wellcome Trust [grant number 094476/Z/10/Z] which funded the purchase of the TripleTOF 5600 mass spectrometer at the BSRC Mass Spectrometry and Proteomics Facility, University of St Andrews.Study Design: Explanatory and mechanistic study. Objective: A better understanding of the 'whole-body' response following spinal cord injury (SCI) is needed to guide future research aimed at developing novel therapeutic interventions and identifying prognostic indicators for SCI. This study aimed to characterise the blood proteome following contusion or complete SCI compared to a sham injury in rat models. Setting: United Kingdom. Methods: Pooled blood samples from one and seven days after a contusion (serum; n = 5) or from 14 days and 112 days post-complete transection SCI (plasma; n = 8) and their sham-injured counterparts were subjected to independent iTRAQ nanoflow liquid chromatography tandem mass-spectrometry proteomic analyses. Pathway analyses of the proteins that were differentially abundant between SCI and their matched sham injured counterparts were completed to indicate biological pathways that may be changed in response to SCI. Results: Eleven and 42 proteins were differentially abundant (≥±2.0 FC; p ≤ 0.05) between the contusion SCI and sham injured animals at 24 h and seven days post-injury, respectively. Seven and tweleve proteins were differentially abundant between complete and sham injured rats at 14 and 112 days post-injury, respectively. Acute-phase response signalling and Liver X Receptor/Retinoic X Receptor activation were identified as differentially regulated pathways in both models of SCI. Conclusions: We have utilised longitudinal preclinical SCI models to provide an insight into the blood proteome changes that result following SCI and to highlight a number of biological pathways of interest for future studies.Publisher PDFPeer reviewe

Contaminants in commercial preparations of ‘purified’ small leucine-rich proteoglycans may distort mechanistic studies

The authors are grateful to Genodisc (EC’s 7th Framework Programme (FP7, 2007-2013) under grant agreement no. HEALTH-F2-2008-201626) and the Orthopaedic Institute Ltd for funding.This paper reports the perplexing results that came about because of seriously impure commercially available reagents. Commercial reagents and chemicals are routinely ordered by scientists and are expected to have been rigorously assessed for their purity. Unfortunately, we found this assumption to be risky. Extensive work was carried out within our laboratory using commercially-sourced preparations of the small leucine-rich proteoglycans, decorin and biglycan, to investigate their influence on nerve cell growth. Unusual results compelled us to analyse the composition and purity of both preparations of these proteoglycans using both mass spectrometry and Western blotting, with and without various enzymatic deglycosylations. Commercial ‘decorin’ and ‘biglycan’ were found to contain a mixture of proteoglycans including not only both decorin and biglycan but also fibromodulin and aggrecan. The unexpected effects of ‘decorin’ and ‘biglycan’ on nerve cell growth could be explained by these impurities. Decorin and biglycan contain either chondroitin or dermatan sulphate glycosaminoglycan chains whilst fibromodulin only contains keratan sulphate and the large (>2,500 kDa), highly glycosylated aggrecan, contains both keratan and chondroitin sulphate. The different structure, molecular weights and composition of these impurities significantly affected our work and any conclusions that could be made. These findings beg the question as to whether scientists need to verify the purity of each commercially obtained reagent used in their experiments. The implications of these findings are vast, since the effects of these impurities may already have led to inaccurate conclusions and reports in the literature with concomitant loss of researchers’ funds and time.Publisher PDFPeer reviewe

Financial leverage and stock returns: evidence from an emerging economy

The aim of this research was to examine the propositions of Campbell et al. and Mirza et al. on pricing of leverage in stock returns using a comprehensive set of firms listed on the Karachi Stock Exchange (KSE) over a period of 13 years. Our results suggest that while size, value and, more importantly, financial leverage are systematic in nature, market risk premium is not a relevant factor. The results confirm the notion of leverage premium and have important implications for financial managers, investment analysts and other market participants who use asset pricing frameworks for investment appraisals. These findings have global relevance, notably for other emerging and developing economies where default risk is of importance due to cyclical nature of cash flows and low recovery rates owing to weaknesses of legal structure

Linking microbial community structure and function during the acidified anaerobic digestion of grass

This research was funded by the Irish Higher Education Authority Program for Research in Third Level Institutions Cycle 5: – PRTLI-5 ESI Ph.D. ENS Program. This work was also supported by the Wellcome Trust (grant number 094476/Z/10/Z for the TripleTOF 5600 mass spectrometer at the University of St Andrews), NERC (grant number NE/L011956/1), and a Royal Irish Academy Mobility Grant.Harvesting valuable bioproducts from various renewable feedstocks is necessary for the critical development of a sustainable bioeconomy. Anaerobic digestion is a well-established technology for the conversion of wastewater and solid feedstocks to energy with the additional potential for production of process intermediates of high market values (e.g. carboxylates). In recent years, first-generation biofuels typically derived from food crops have been widely utilised as a renewable source of energy. The environmental and socioeconomic limitations of such strategy, however, have led to the development of second-generation biofuels utilising, amongst other feedstocks, lignocellulosic biomass. In this context, the anaerobic digestion of perennial grass holds great promise for the conversion of sustainable renewable feedstock to energy and other process intermediates. The advancement of this technology however, and its implementation for industrial applications, relies on a greater understanding of the microbiome underpinning the process. To this end, microbial communities recovered from replicated anaerobic bioreactors digesting grass were analysed. The bioreactors leachates were not buffered and acidic pH (between 5.5 and 6.3) prevailed at the time of sampling as a result of microbial activities. Community composition and transcriptionally active taxa were examined using 16S rRNA sequencing and microbial functions were investigated using metaproteomics. Bioreactor fraction, i.e. grass or leachate, was found to be the main discriminator of community analysis across the three molecular level of investigation (DNA, RNA and proteins). Six taxa, namely Bacteroidia, Betaproteobacteria, Clostridia, Gammaproteobacteria, Methanomicrobia and Negativicutes accounted for the large majority of the three datasets. The initial stages of grass hydrolysis were carried out by Bacteroidia, Gammaproteobacteria and Negativicutes in the grass biofilms, in addition to Clostridia in the bioreactor leachates. Numerous glycolytic enzymes and carbohydrate transporters were detected throughout the bioreactors in addition to proteins involved in butanol and lactate production. Finally, evidence of the prevalence of stressful conditions within the bioreactors and particularly impacting Clostridia was observed in the metaproteomes. Taken together, this study highlights the functional importance of Clostridia during the anaerobic digestion of grass and thus research avenues allowing members of this taxon to thrive should be explored.Publisher PDFPeer reviewe

Insights into the mechanism of the cyanobactin heterocyclase enzyme

The work is supported by the European Research Council NCB-TNT (339367), Biotechnology and Biological Sciences Research Council (BB/K015508/1 and BB/M001679/1).Cyanobactin heterocyclases share the same catalytic domain (YcaO) as heterocyclases/cyclodehydratases from other ribosomal peptide (RiPPs) biosynthetic pathways. These enzymes process multiple residues (Cys/Thr/Ser) within the same substrate. The processing of cysteine residues proceeds with a known order. We show the order of reaction for threonines is different and depends in part on a leader peptide within the substrate. In contrast to other YcaO domains, which have been reported to exclusively break down ATP into ADP and inorganic phosphate, cyanobactin heterocyclases have been observed to produce AMP and inorganic pyrophosphate during catalysis. We dissect the nucleotide profiles associated with heterocyclization and propose a unifying mechanism, where the γ-phosphate of ATP is transferred in a kinase mechanism to the substrate to yield a phosphorylated intermediate common to all YcaO domains. In cyanobactin heterocyclases, this phosphorylated intermediate, in a proportion of turnovers, reacts with ADP to yield AMP and pyrophosphate.Publisher PDFPeer reviewe

Djelatnost Odsjeka za povijest hrvatske glazbe Zavoda za povijest hrvatske književnosti, kazališta i glazbe HAZU u 2016. godini

<i>Geobacter sulfurreducens</i> is a dissimilatory metal-reducing bacterium capable of forming thick electron-conducting biofilms on solid electrodes. Here we employ for the first time comparative proteomics to identify key physiological changes involved in <i>G. sulfurreducens</i> adaptation from fumarate-respiring planktonic cells to electron-conducting biofilms. Increased levels of proteins involved in outer membrane biogenesis, cell motility, and secretion are expressed in biofilms. Of particular importance to the electron-conducting biofilms are proteins associated with secretion systems of Type I, II, V and Type IV pili. Furthermore, enzymes involved in lipopolysaccharide and peptidoglycan biosynthesis show increased levels of expression in electron-conducting biofilms compared with planktonic cells. These observations point to similarities in long-range electron-transfer mechanisms between <i>G. sulfurreducens</i> and <i>Shewanella oneidensis</i> while highlighting the wider significance of secretion systems beyond that of Type IV pili identified to date in the adaptation of <i>G. sulfurreducens</i> to electrode respiration

hSSB1 (NABP2/OBFC2B) is regulated by oxidative stress

The maintenance of genome stability is an essential cellular process to prevent the development of diseases including cancer. hSSB1 (NABP2/ OBFC2A) is a critical component of the DNA damage response where it participates in the repair of double-strand DNA breaks and in base excision repair of oxidized guanine residues (8-oxoguanine) by aiding the localization of the human 8-oxoguanine glycosylase (hOGG1) to damaged DNA. Here we demonstrate that following oxidative stress, hSSB1 is stabilized as an oligomer which is required for hSSB1 to function in the removal of 8-oxoguanine. Monomeric hSSB1 shows a decreased affinity for oxidized DNA resulting in a cellular 8-oxoguanine-repair defect and in the absence of ATM signaling initiation. While hSSB1 oligomerization is important for the removal of 8-oxoguanine from the genome, it is not required for the repair of double-strand DNA-breaks by homologous recombination. These findings demonstrate a novel hSSB1 regulatory mechanism for the repair of damaged DNA.Publisher PDFPeer reviewe

Short Prolegomena of a »Right to a Home« in the Consumer Bankruptcy Act

Kriza identiteta modela »socijalne države« otvorila je niz pitanja za teoretičare i praktičare. Ovi problemi, naravno, nisu zaobišli niti sustav potrošačko stečajne zaštite kojoj je primarni cilj ekonomska i socijalna »rehabilitacija« potrošača što je differentia specifica u odnosu na primarni cilj korporativnog stečaja, namirenje vjerovnika. Prostor koji ovdje imamo ne dopušta detaljnu raščlambu ove problematike, pa smo prinuđeni ograničiti se isključivo na jedno od ključnih pitanja novog potrošačko stečajnog zakonodavstva: prava na dom. Pritom se posebno analizira praksa Europskog suda za ljudska prava (dalje: Europski sud) u postupcima prema čl. 8. Europske konvencije za zaštitu ljudskih prava i temeljnih sloboda (»Pravo na dom«) jer polazimo od pretpostavke da saznanja o ovome mogu biti ključna za razumijevanje problematike rada, kao i za pravilnu primjenu instituta prava na dom. U cilju što sveobuhvatnijeg odgovora na samu temu, uz uvažavanje prethodno navedenog, struktura i koncept rada je tome morao biti prilagođen. Ovaj rad mogao je biti podijeljen na tri dijela što će se i vidjeti tijekom njegovog čitanja, ali to formalno nije učinjeno.The identity crisis of a »welfare state» model has raised a number of questions for theorists and practitioners. These problems, of course, have not surpassed the system of consumer bankruptcy protection which has the primary objective - economic and social »rehabilitation« of consumers and which is differentia specifica in relation to the primary objective of corporate bankruptcy − settlement of creditors. The scope of this paper does not permit a detailed analysis of these issues, and we are forced to limit ourselves exclusively to one of the key issues of the new consumer bankruptcy law: the right to a home. We specifically analyze the practice of the European Court of Human Rights (hereinafter: European Court) in proceedings under Art. 8 of the European Convention for the Protection of Human Rights and Fundamental Freedoms ("Right to a Home") because we assume that it is a key to understanding the paper subject, as well as to the proper application of the institute of “right to a home”. With respect to the foregoing, in order to have a comprehensive answer to the subject, the structure and concept of paper had to be adjusted. This paper could have been divided into three parts, but it has not been formally done