Development of a protocol for the auto-generation of explicit aqueous-phase oxidation schemes of organic compounds
description: This paper presents a new CAPRAM–GECKO-A protocol for mechanism auto-generation of aqueous-phase organic processes. For the development, kinetic data in the literature were reviewed and a database with 464 aqueous-phase reactions of the hydroxyl radical with organic compounds and 130 nitrate radical reactions with organic compounds has been compiled and evaluated. Five different methods to predict aqueous-phase rate constants have been evaluated with the help of the kinetics database: gas–aqueous phase correlations, homologous series of various compound classes, radical reactivity comparisons, Evans–Polanyi-type correlations, and structure–activity relationships (SARs). The quality of these prediction methods was tested as well as their suitability for automated mechanism construction. Based on this evaluation, SARs form the basis of the new CAPRAM–GECKO-A protocol. Evans–Polanyi-type correlations have been advanced to consider all available H atoms in a molecule besides the H atoms with only the weakest bond dissociation enthalpies (BDEs). The improved Evans–Polanyi-type correlations are used to predict rate constants for aqueous-phase NO3 and organic compounds reactions. Extensive tests have been performed on essential parameters and on highly uncertain parameters with limited experimental data. These sensitivity studies led to further improvements in the new CAPRAM–GECKO-A protocol but also showed current limitations. Biggest uncertainties were observed in uptake processes and the estimation of Henry's law coefficients as well as radical chemistry, in particular the degradation of alkoxy radicals. Previous estimation methods showed several deficits, which impacted particle growth. For further evaluation, a 1,3,5-trimethylbenzene oxidation experiment has been performed in the aerosol chamber “Leipziger Aerosolkammer” (LEAK) at high relative humidity conditions and compared to a multiphase mechanism using the Master Chemical Mechanism (MCMv3.2) in the gas phase and…
creator: P. Bräuer, C. Mouchel-Vallon, A. Tilgner, A. Mutzel, O. Böge, M. Rodigast, L. Poulain, D. van Pinxteren, R. Wolke, B. Aumont, H. Herrmann
source: Atmospheric Chemistry and Physics
publisher: Copernicus Publications
date: 2019
language: EN
identifier: DOI: 10.5194/acp-19-9209-2019
coverage: Physics, Chemistry

Multi-Organ Damage in Human Dipeptidyl Peptidase 4 Transgenic Mice Infected with Middle East Respiratory Syndrome-Coronavirus.
description: The Middle East Respiratory Syndrome Coronavirus (MERS-CoV) causes severe acute respiratory failure and considerable extrapumonary organ dysfuction with substantial high mortality. For the limited number of autopsy reports, small animal models are urgently needed to study the mechanisms of MERS-CoV infection and pathogenesis of the disease and to evaluate the efficacy of therapeutics against MERS-CoV infection. In this study, we developed a transgenic mouse model globally expressing codon-optimized human dipeptidyl peptidase 4 (hDPP4), the receptor for MERS-CoV. After intranasal inoculation with MERS-CoV, the mice rapidly developed severe pneumonia and multi-organ damage, with viral replication being detected in the lungs on day 5 and in the lungs, kidneys and brains on day 9 post-infection. In addition, the mice exhibited systemic inflammation with mild to severe pneumonia accompanied by the injury of liver, kidney and spleen with neutrophil and macrophage infiltration. Importantly, the mice exhibited symptoms of paralysis with high viral burden and viral positive neurons on day 9. Taken together, this study characterizes the tropism of MERS-CoV upon infection. Importantly, this hDPP4-expressing transgenic mouse model will be applicable for studying the pathogenesis of MERS-CoV infection and investigating the efficacy of vaccines and antiviral agents designed to combat MERS-CoV infection.
creator: Guangyu Zhao, Yuting Jiang, Hongjie Qiu, Tongtong Gao, Yang Zeng, Yan Guo, Hong Yu, Junfeng Li, Zhihua Kou, Lanying Du, Wen-Jie Tan, Shibo Jiang, Shihui Sun, Yusen Zhou
source: PLoS ONE
publisher: Public Library of Science (PLoS)
date: 2015
language: EN
identifier: DOI: 10.1371/journal.pone.0145561
coverage: Science, Medicine

From the Beginning Until Today: Current Status of SARS
subject: severe acute respiratory syndrome virus, coronavirus, Respiratory syndrome, Severe, Acute
creator: Can Polat EYIGUN
source: Flora Infeksiyon Hastalıkları ve Klinik Mikrobiyoloji Dergisi
publisher: Bilimsel Tip Yayinevi
date: 2005
language: EN, TR
coverage: Infectious and parasitic diseases, Microbiology

Genome Wide Identification of SARS-CoV Susceptibility Loci Using the Collaborative Cross.
description: New systems genetics approaches are needed to rapidly identify host genes and genetic networks that regulate complex disease outcomes. Using genetically diverse animals from incipient lines of the Collaborative Cross mouse panel, we demonstrate a greatly expanded range of phenotypes relative to classical mouse models of SARS-CoV infection including lung pathology, weight loss and viral titer. Genetic mapping revealed several loci contributing to differential disease responses, including an 8.5Mb locus associated with vascular cuffing on chromosome 3 that contained 23 genes and 13 noncoding RNAs. Integrating phenotypic and genetic data narrowed this region to a single gene, Trim55, an E3 ubiquitin ligase with a role in muscle fiber maintenance. Lung pathology and transcriptomic data from mice genetically deficient in Trim55 were used to validate its role in SARS-CoV-induced vascular cuffing and inflammation. These data establish the Collaborative Cross platform as a powerful genetic resource for uncovering genetic contributions of complex traits in microbial disease severity, inflammation and virus replication in models of outbred populations.
creator: Lisa E Gralinski, Martin T. Ferris, David L Aylor, Alan C. Whitmore, Richard Green, Matthew B. Frieman, Damon Deming, Vineet D. Menachery, Darla R. Miller, Ryan J Buus, Timothy A. Bell, Gary A. Churchill, David W. Threadgill, Michael G. Katze, Leonard McMillan, William Valdar, Mark T. Heise, Fernando Pardo-Manuel de Villena, Ralph S. Baric
source: PLoS Genetics
publisher: Public Library of Science (PLoS)
date: 2015
language: EN
identifier: DOI: 10.1371/journal.pgen.1005504
coverage: Genetics

Reconstruction of family-level phylogenetic relationships within Demospongiae (Porifera) using nuclear encoded housekeeping genes.
description: Demosponges are challenging for phylogenetic systematics because of their plastic and relatively simple morphologies and many deep divergences between major clades. To improve understanding of the phylogenetic relationships within Demospongiae, we sequenced and analyzed seven nuclear housekeeping genes involved in a variety of cellular functions from a diverse group of sponges.We generated data from each of the four sponge classes (i.e., Calcarea, Demospongiae, Hexactinellida, and Homoscleromorpha), but focused on family-level relationships within demosponges. With data for 21 newly sampled families, our Maximum Likelihood and Bayesian-based approaches recovered previously phylogenetically defined taxa: Keratosa(p), Myxospongiae(p), Spongillida(p), Haploscleromorpha(p) (the marine haplosclerids) and Democlavia(p). We found conflicting results concerning the relationships of Keratosa(p) and Myxospongiae(p) to the remaining demosponges, but our results strongly supported a clade of Haploscleromorpha(p)+Spongillida(p)+Democlavia(p). In contrast to hypotheses based on mitochondrial genome and ribosomal data, nuclear housekeeping gene data suggested that freshwater sponges (Spongillida(p)) are sister to Haploscleromorpha(p) rather than part of Democlavia(p). Within Keratosa(p), we found equivocal results as to the monophyly of Dictyoceratida. Within Myxospongiae(p), Chondrosida and Verongida were monophyletic. A well-supported clade within Democlavia(p), Tetractinellida(p), composed of all sampled members of Astrophorina and Spirophorina (including the only lithistid in our analysis), was consistently revealed as the sister group to all other members of Democlavia(p). Within Tetractinellida(p), we did not recover monophyletic Astrophorina or Spirophorina. Our results also reaffirmed the monophyly of order Poecilosclerida (excluding Desmacellidae and Raspailiidae), and polyphyly of Hadromerida and Halichondrida.These results, using an independent nuclear gene set, confirm…
creator: Malcolm S. Hill, April L Hill, José López, Kevin J Peterson, Shirley Pomponi, María C. Díaz, Robert W. Thacker, Maja Adamska, Nicole Boury-Esnault, Paco Cárdenas, Andia Chaves-Fonnegra, Elizabeth Danka, Bre-Onna De Laine, Dawn Formica, Eduardo Hajdu, Gisele Lôbo-Hajdu, Sarah Klontz, Christine C Morrow, Jignasa Patel, Bernard Picton, Davide Pisani, Deborah Pohlmann, Niamh E Redmond, John Reed, Stacy Richey, Ana Riesgo, Ewelina Rubin, Zach Russell, Klaus Rützler, Erik A Sperling, Michael di Stefano, James E Tarver, Allen G. Collins
source: PLoS ONE
publisher: Public Library of Science (PLoS)
date: 2013
language: EN
identifier: DOI: 10.1371/journal.pone.0050437
coverage: Science, Medicine

Lung epithelial cells have virus-specific and shared gene expression responses to infection by diverse respiratory viruses.
description: The severity of respiratory viral infections is partially determined by the cellular response mounted by infected lung epithelial cells. Disease prevention and treatment is dependent on our understanding of the shared and unique responses elicited by diverse viruses, yet few studies compare host responses to viruses from different families while controlling other experimental parameters. Murine models are commonly used to study the pathogenesis of respiratory viral infections, and in vitro studies using murine cells provide mechanistic insight into the pathogenesis observed in vivo. We used microarray analysis to compare changes in gene expression of murine lung epithelial cells infected individually by three respiratory viruses causing mild (rhinovirus, RV1B), moderate (coronavirus, MHV-1), and severe (influenza A virus, PR8) disease in mice. RV1B infection caused numerous gene expression changes, but the differential effect peaked at 12 hours post-infection. PR8 altered an intermediate number of genes whose expression continued to change through 24 hours. MHV-1 had comparatively few effects on host gene expression. The viruses elicited highly overlapping responses in antiviral genes, though MHV-1 induced a lower type I interferon response than the other two viruses. Signature genes were identified for each virus and included host defense genes for PR8, tissue remodeling genes for RV1B, and transcription factors for MHV-1. Our comparative approach identified universal and specific transcriptional signatures of virus infection that can be used to distinguish shared and virus-specific mechanisms of pathogenesis in the respiratory tract.
creator: James T VanLeuven, Benjamin J. Ridenhour, Andres J Gonzalez, Craig R. Miller, Tanya A. Miura
source: PLoS ONE
publisher: Public Library of Science (PLoS)
date: 2017
language: EN
identifier: DOI: 10.1371/journal.pone.0178408
coverage: Science, Medicine

Short (16-mer) locked nucleic acid splice-switching oligonucleotides restore dystrophin production in Duchenne Muscular Dystrophy myotubes.
description: Splice-switching antisense oligonucleotides (SSOs) offer great potential for RNA-targeting therapies, and two SSO drugs have been recently approved for treating Duchenne Muscular Dystrophy (DMD) and Spinal Muscular Atrophy (SMA). Despite promising results, new developments are still needed for more efficient chemistries and delivery systems. Locked nucleic acid (LNA) is a chemically modified nucleic acid that presents several attractive properties, such as high melting temperature when bound to RNA, potent biological activity, high stability and low toxicity in vivo. Here, we designed a series of LNA-based SSOs complementary to two sequences of the human dystrophin exon 51 that are most evolutionary conserved and evaluated their ability to induce exon skipping upon transfection into myoblasts derived from a DMD patient. We show that 16-mers with 60% of LNA modification efficiently induce exon skipping and restore synthesis of a truncated dystrophin isoform that localizes to the plasma membrane of patient-derived myotubes differentiated in culture. In sum, this study underscores the value of short LNA-modified SSOs for therapeutic applications.
creator: Vanessa Borges Pires, Ricardo Simões, Kamel Mamchaoui, Célia Carvalho, Maria Carmo-Fonseca
source: PLoS ONE
publisher: Public Library of Science (PLoS)
date: 2017
language: EN
identifier: DOI: 10.1371/journal.pone.0181065
coverage: Science, Medicine

Alterations in nerve-evoked bladder contractions in a coronavirus-induced mouse model of multiple sclerosis.
description: Patients with neurodegenerative diseases such as multiple sclerosis, Parkinson's, and Alzheimer's often present with lower urinary tract symptoms (LUTS, urinary frequency, urgency, nocturia and retention) resulting from damage to the peripheral and central nervous systems. These studies were designed to examine the changes in the function of the bladder that may underlie neurogenic bladder dysfunction using a mouse model of demyelination in the CNS.Bladders from 12 week old male C57BL/6J mice with coronavirus-induced encephalomyelitis (CIE, a chronic, progressive demyelinating disease model of human MS), and age-matched controls, were cut into 5-7 strips and suspended in physiological muscle baths for tension measurement in response to agonists and electric field stimulation (EFS). Experiments were performed on intact and denuded (with mucosa removed) bladder strips.The maximum effect of EFS was not significantly different between CIE and control bladders. Nerve-evoked EFS contractions (tetrodotoxin-sensitive) were blocked by a combination of atropine (cholinergic antagonist) and α,β-methylene ATP (an ATP analog that desensitizes purinergic receptors). In response to EFS, the α,β-methylene ATP-resistant (cholinergic) component of contraction was significantly reduced, while the atropine-resistant (purinergic) component was significantly increased in CIE bladders. Removal of the mucosa in CIE bladders restored the cholinergic component. Bethanechol (muscarinic receptor agonist) potency was significantly increased in CIE bladders.Our data demonstrate a deficit in the nerve-evoked cholinergic component of contraction that is not due to the ability of the smooth muscle to respond to acetylcholine. We conclude that neurodegenerative bladder dysfunction in this model of multiple sclerosis may be due, in part, to pathologic changes in the mucosa that causes suppression of muscarinic receptor-mediated contractile response and augmentation of purinergic response of the under…
creator: Neil S Lamarre, Alan S Braverman, Anna P Malykhina, Mary F. Barbe, Michael R Ruggieri
source: PLoS ONE
publisher: Public Library of Science (PLoS)
date: 2014
language: EN
identifier: DOI: 10.1371/journal.pone.0109314
coverage: Science, Medicine

Role of fomites in SARS transmission during the largest hospital outbreak in Hong Kong.
description: The epidemic of severe acute respiratory syndrome (SARS) had a significant effect on global society in the early 2000s and the potential of its resurgence exists. Studies on the modes of transmission of SARS are limited though a number of outbreak studies have revealed the possible airborne route. To develop more specific and effective control strategies, we conducted a detailed mechanism-based investigation that explored the role of fomite transmission in the well-known Ward 8A outbreak. We considered three hypothetical transmission routes, i.e., the long-range airborne, fomite and combined routes, in 1,744 scenarios with combinations of some important parameters. A multi-agent model was used to predict the infection risk distributions of the three hypothetical routes. Model selection was carried out for different scenarios to compare the distributions of infection risk with that of the reported attack rates and select the hypotheses with the best fitness. Our results reveal that under the assumed conditions, the SARS coronavirus was most possible to have spread via the combined long-range airborne and fomite routes, and that the fomite route played a non-negligible role in the transmission.
creator: Shenglan Xiao, Yuguo Li, Tze-wai Wong, David S.C. Hui
source: PLoS ONE
publisher: Public Library of Science (PLoS)
date: 2017
language: EN
identifier: DOI: 10.1371/journal.pone.0181558
coverage: Science, Medicine

An evaluation of emergency guidelines issued by the World Health Organization in response to four infectious disease outbreaks.
description: BACKGROUND:The production of high-quality guidelines in response to public health emergencies poses challenges for the World Health Organization (WHO). The urgent need for guidance and the paucity of structured scientific data on emerging diseases hinder the formulation of evidence-informed recommendations using standard methods and procedures. OBJECTIVES:In the context of the response to recent public health emergencies, this project aimed to describe the information products produced by WHO and assess the quality and trustworthiness of a subset of these products classified as guidelines. METHODS:We selected four recent infectious disease emergencies: outbreaks of avian influenza A-H1N1 virus (2009) and H7N9 virus (2013), Middle East respiratory syndrome coronavirus (MERS-CoV) (2013), and Ebola virus disease (EVD) (2014 to 2016). We analyzed the development and publication processes and evaluated the quality of emergency guidelines using AGREE-II. RESULTS:We included 175 information products of which 87 were guidelines. These products demonstrated variable adherence to WHO publication requirements including the listing of external contributors, management of declarations of interest, and entry into WHO's public database of publications. For guidelines, the methods for development were incompletely reported; WHO's quality assurance process was rarely used; systematic or other evidence reviews were infrequently referenced; external peer review was not performed; and they scored poorly with AGREE II, particularly for rigour of development and editorial independence. CONCLUSIONS:Our study suggests that WHO guidelines produced in the context of a public health emergency can be improved upon, helping to assure the trustworthiness and utility of WHO information products in future emergencies.
creator: Susan L. Norris, Veronica Ivey Sawin, Mauricio Ferri, Laura Reques Sastre, Teegwendé V. Porgo
source: PLoS ONE
publisher: Public Library of Science (PLoS)
date: 2018
language: EN
identifier: DOI: 10.1371/journal.pone.0198125
coverage: Science, Medicine