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Yi An, Jiawei Wang, Chen Li, André Leier, Tatiana Marquez-Lago, Jonathan Wilksch, Yang Zhang, Geoffrey I Webb, Jiangning Song, Trevor Lithgow
Bacterial effector proteins secreted by various protein secretion systems play crucial roles in host-pathogen interactions. In this context, computational tools capable of accurately predicting effector proteins of the various types of bacterial secretion systems are highly desirable. Existing computational approaches use different machine learning (ML) techniques and heterogeneous features derived from protein sequences and/or structural information. These predictors differ not only in terms of the used ML methods but also with respect to the used curated data sets, the features selection and their prediction performance...
October 24, 2016: Briefings in Bioinformatics
Ursula N Broder, Tina Jaeger, Urs Jenal
Virulence of pathogenic bacteria is a tightly controlled process to facilitate invasion and survival in host tissues. Although pathways controlling virulence have been defined in detail, signals modulating these processes are poorly understood. The opportunistic pathogen Pseudomonas aeruginosa causes acute and chronic infections in humans. Disease progression is typically associated with a loss of acute virulence and the emergence of biofilms and chronic behaviour. The acute-to-chronic switch is governed by the global Gac/Rsm pathway...
October 24, 2016: Nature Microbiology
Anthony L Cunningham, Nathalie Garçon, Oberdan Leo, Leonard R Friedland, Richard Strugnell, Béatrice Laupèze, Mark Doherty, Peter Stern
In the 21st century, an array of microbiological and molecular allow antigens for new vaccines to be specifically identified, designed, produced and delivered with the aim of optimising the induction of a protective immune response against a well-defined immunogen. New knowledge about the functioning of the immune system and host pathogen interactions has stimulated the rational design of vaccines. The design toolbox includes vaccines made from whole pathogens, protein subunits, polysaccharides, pathogen-like particles, use of viral/bacterial vectors, plus adjuvants and conjugation technology to increase and broaden the immune response...
October 18, 2016: Vaccine
Kristen L Lokken, Gregory T Walker, Renée M Tsolis
Non-typhoidal Salmonella enterica serovars (NTS) are generally associated with gastroenteritis; however, the very young and elderly, as well as individuals with compromised immunity, are at risk of developing disseminated infection that can manifest as bacteremia or focal infections at systemic sites. Disseminated NTS infections can be fatal and are responsible for over 600,000 deaths annually. Most of these deaths are in sub-Saharan Africa, where multi-drug resistant NTS clones are currently circulating in a population with a high proportion of individuals that are susceptible to disseminated disease...
October 8, 2016: Pathogens and Disease
Ying Qiao, Yong Mao, Jun Wang, Ruanni Chen, Yong-Quan Su, Jia Chen, Wei-Qiang Zheng
The white-spot disease caused by marine ciliate Cryptocryon irritans hindered the sustainable development of large yellow croaker Larimichthys crocea industry. Better understandings about the parasite-host interactions in the molecular level will facilitate the prevention of mass mortality of the L. crocea caused by white-spot disease. MicroRNAs (miRNAs) are a class of small RNA molecules about 20-22 nucleotides which post-transcriptionally regulated many protein-coding genes and involved in many biological processes, especially in host-pathogen responses...
October 17, 2016: Fish & Shellfish Immunology
Johanneke D Hemmink, Sophie B Morgan, Mario Aramouni, Helen Everett, Francisco J Salguero, Laetitia Canini, Emily Porter, Margo Chase-Topping, Katy Beck, Ronan Mac Loughlin, B Veronica Carr, Ian H Brown, Mick Bailey, Mark Woolhouse, Sharon M Brookes, Bryan Charleston, Elma Tchilian
Influenza virus infection in pigs is a major farming problem, causing considerable economic loss and posing a zoonotic threat. In addition the pig is an excellent model for understanding immunity to influenza viruses as this is a natural host pathogen system. Experimentally, influenza virus is delivered to pigs intra-nasally, by intra-tracheal instillation or by aerosol, but there is little data comparing the outcome of different methods. We evaluated the shedding pattern, cytokine responses in nasal swabs and immune responses following delivery of low or high dose swine influenza pdmH1N1 virus to the respiratory tract of pigs intra-nasally or by aerosol and compared them to those induced in naturally infected contact pigs...
October 20, 2016: Veterinary Research
Kuo-Hsun Chiu, Ling-Hui Wang, Tsung-Ting Tsai, Huan-Yao Lei, Pao-Chi Liao
The secreted proteins of bacteria are usually accompanied by virulence factors, which can cause inflammation and damage host cells. Identifying the secretomes arising from the interactions of bacteria and host cells could, therefore, increase understanding of the mechanisms during initial pathogenesis. The present study used a host-pathogen coculture system of Helicobacter pylori and monocytes (THP-1 cells) to investigate the secreted proteins associated with initial H. pylori pathogenesis. The secreted proteins from the conditioned media from H...
October 20, 2016: Journal of Proteome Research
Voon Kin Chin, Tze Yan Lee, Basir Rusliza, Pei Pei Chong
Candida bloodstream infections remain the most frequent life-threatening fungal disease, with Candida albicans accounting for 70% to 80% of the Candida isolates recovered from infected patients. In nature, Candida species are part of the normal commensal flora in mammalian hosts. However, they can transform into pathogens once the host immune system is weakened or breached. More recently, mortality attributed to Candida infections has continued to increase due to both inherent and acquired drug resistance in Candida, the inefficacy of the available antifungal drugs, tedious diagnostic procedures, and a rising number of immunocompromised patients...
October 18, 2016: International Journal of Molecular Sciences
Yushu Yin, Georgia Papavasiliou, Olga Y Zaborina, John C Alverdy, Fouad Teymour
The human gastrointestinal tract is the primary site of colonization of multidrug resistant pathogens and the major source of life-threatening complications in critically ill and immunocompromised patients. Eradication measures using antibiotics carry further risk of antibiotic resistance. Furthermore, antibiotic treatment can adversely shift the intestinal microbiome toward domination by resistant pathogens. Therefore, approaches directed to prevent replacement of health promoting microbiota with resistant pathogens should be developed...
October 19, 2016: Annals of Biomedical Engineering
Kristin Surmann, Marjolaine Simon, Petra Hildebrandt, Henrike Pförtner, Stephan Michalik, Vishnu M Dhople, Barbara M Bröker, Frank Schmidt, Uwe Völker
To simultaneously obtain proteome data of host and pathogen from an internalization experiment, human alveolar epithelial A549 cells were infected with Staphylococcus aureus HG001 which carried a plasmid (pMV158GFP) encoding a continuously expressed green fluorescent protein (GFP). Samples were taken hourly between 1.5 h and 6.5 h post infection. By fluorescence activated cell sorting GFP-expressing bacteria could be enriched from host cell debris, but also infected host cells could be separated from those which did not carry bacteria after contact (exposed)...
June 2016: Data in Brief
Kayvan Etebari, Sultan Asad, Guangmei Zhang, Sassan Asgari
Long intergenic non-coding RNAs (lincRNAs) are appearing as an important class of regulatory RNAs with a variety of biological functions. The aim of this study was to identify the lincRNA profile in the dengue vector Aedes aegypti and evaluate their potential role in host-pathogen interaction. The majority of previous RNA-Seq transcriptome studies in Ae. aegypti have focused on the expression pattern of annotated protein coding genes under different biological conditions. Here, we used 35 publically available RNA-Seq datasets with relatively high depth to screen the Ae...
October 2016: PLoS Neglected Tropical Diseases
Abdul Arif Khan, Zakir Khan, Mohd Abul Kalam, Azmat Ali Khan
Microbial pathogenesis involves several aspects of host-pathogen interactions, including microbial proteins targeting host subcellular compartments and subsequent effects on host physiology. Such studies are supported by experimental data, but recent detection of bacterial proteins localization through computational eukaryotic subcellular protein targeting prediction tools has also come into practice. We evaluated inter-kingdom prediction certainty of these tools. The bacterial proteins experimentally known to target host subcellular compartments were predicted with eukaryotic subcellular targeting prediction tools, and prediction certainty was assessed...
October 6, 2016: Briefings in Bioinformatics
Alireza Banazadeh, Lucas Veillon, Kerry M Wooding, Masoud Zabet, Yehia Mechref
Glycosylation is one of the most common post-translational modifications of proteins and plays essential roles in various biological processes, including protein folding, host-pathogen interaction, immune response, and inflammation and aberrant protein glycosylation is a well-known event in various disease states including cancer. As a result, it is critical to develop rapid and sensitive methods for the analysis of abnormal glycoproteins associated with diseases. Mass spectrometry in conjugation with different separation methods, such as capillary electrophoresis, ion mobility, and high performance liquid chromatography, has become a popular tool for glycoprotein analysis, providing highly informative fragments for structural identification of glycoproteins...
October 18, 2016: Electrophoresis
Dayoung Park, Narine Arabyan, Cynthia C Williams, Ting Song, Anupam Mitra, Bart C Weimer, Emanual Maverakis, Carlito B Lebrilla
Although gut host-pathogen interactions are glycan-mediated processes, few details are known about the participating structures. Here we employ high-resolution mass spectrometric profiling to comprehensively identify and quantitatively measure the exact modifications of native intestinal epithelial cell surface N-glycans induced by S. Typhimurium infection. Sixty minutes post-infection, select sialylated structures showed decreases in terms of total number and abundances. To assess the effect of cell surface mannosylation, we selectively rerouted glycan expression on the host using the alpha-mannosidase inhibitor, kifunensine, toward overexpression of high mannose...
October 17, 2016: Molecular & Cellular Proteomics: MCP
Joana C Silva, Emmanuel Cornillot, Carrie McCracken, Sahar Usmani-Brown, Ankit Dwivedi, Olukemi O Ifeonu, Jonathan Crabtree, Hanzel T Gotia, Azan Z Virji, Christelle Reynes, Jacques Colinge, Vidya Kumar, Lauren Lawres, Joseph E Pazzi, Jozelyn V Pablo, Chris Hung, Jana Brancato, Priti Kumari, Joshua Orvis, Kyle Tretina, Marcus Chibucos, Sandy Ott, Lisa Sadzewicz, Naomi Sengamalay, Amol C Shetty, Qi Su, Luke Tallon, Claire M Fraser, Roger Frutos, Douglas M Molina, Peter J Krause, Choukri Ben Mamoun
Babesia microti, a tick-transmitted, intraerythrocytic protozoan parasite circulating mainly among small mammals, is the primary cause of human babesiosis. While most cases are transmitted by Ixodes ticks, the disease may also be transmitted through blood transfusion and perinatally. A comprehensive analysis of genome composition, genetic diversity, and gene expression profiling of seven B. microti isolates revealed that genetic variation in isolates from the Northeast United States is almost exclusively associated with genes encoding the surface proteome and secretome of the parasite...
October 18, 2016: Scientific Reports
Petya Berger, Michael Knödler, Konrad U Förstner, Michael Berger, Christian Bertling, Cynthia M Sharma, Jörg Vogel, Helge Karch, Ulrich Dobrindt, Alexander Mellmann
Escherichia coli O104:H4 (E. coli O104:H4), which caused a massive outbreak of acute gastroenteritis and hemolytic uremic syndrome in 2011, carries an aggregative adherence fimbriae I (AAF/I) encoding virulence plasmid, pAA. The importance of pAA in host-pathogen interaction and disease severity has been demonstrated, however, not much is known about its transcriptional organization and gene regulation. Here, we analyzed the pAA primary transcriptome using differential RNA sequencing, which allows for the high-throughput mapping of transcription start site (TSS) and non-coding RNA candidates...
October 17, 2016: Scientific Reports
Kan Xing Wu, Patchara Phuektes, Pankaj Kumar, Germaine Yen Lin Goh, Dimitri Moreau, Vincent Tak Kwong Chow, Frederic Bard, Justin Jang Hann Chu
Enterovirus 71 (EV71) is a neurotropic enterovirus without antivirals or vaccine, and its host-pathogen interactions remain poorly understood. Here we use a human genome-wide RNAi screen to identify 256 host factors involved in EV71 replication in human rhabdomyosarcoma cells. Enrichment analyses reveal overrepresentation in processes like mitotic cell cycle and transcriptional regulation. We have carried out orthogonal experiments to characterize the roles of selected factors involved in cell cycle regulation and endoplasmatic reticulum-associated degradation...
October 17, 2016: Nature Communications
Vincent Doublet, Robert J Paxton, Cynthia M McDonnell, Emeric Dubois, Sabine Nidelet, Robin F A Moritz, Cédric Alaux, Yves Le Conte
Regulation of gene expression in the brain plays an important role in behavioral plasticity and decision making in response to external stimuli. However, both can be severely affected by environmental factors, such as parasites and pathogens. In honey bees, the emergence and re-emergence of pathogens and potential for pathogen co-infection and interaction have been suggested as major components that significantly impaired social behavior and survival. To understand how the honey bee is affected and responds to interacting pathogens, we co-infected workers with two prevalent pathogens of different nature, the positive single strand RNA virus Black queen cell virus (BQCV), and the Microsporidia Nosema ceranae, and explored gene expression changes in brains upon single infections and co-infections...
December 2016: Genomics Data
Marcela Suárez-Esquivel, Nazareth Ruiz-Villalobos, Amanda Castillo-Zeledón, César Jiménez-Rojas, R Martin Roop Ii, Diego J Comerci, Elías Barquero-Calvo, Carlos Chacón-Díaz, Clayton C Caswell, Kate S Baker, Esteban Chaves-Olarte, Nicholas R Thomson, Edgardo Moreno, Jean J Letesson, Xavier De Bolle, Caterina Guzmán-Verri
Brucellosis is a bacterial infectious disease affecting a wide range of mammals and a neglected zoonosis caused by species of the genetically homogenous genus Brucella. As in most studies on bacterial diseases, research in brucellosis is carried out by using reference strains as canonical models to understand the mechanisms underlying host pathogen interactions. We performed whole genome sequencing analysis of the reference strain B. abortus 2308 routinely used in our laboratory, including manual curated annotation accessible as an editable version through a link at https://en...
2016: Frontiers in Microbiology
Hui-Ling Liao, Yuan Chen, Rytas Vilgalys
Ectomycorrhizal fungi (EMF) represent one of the major guilds of symbiotic fungi associated with roots of forest trees, where they function to improve plant nutrition and fitness in exchange for plant carbon. Many groups of EMF exhibit preference or specificity for different plant host genera; a good example is the genus Suillus, which grows in association with the conifer family Pinaceae. We investigated genetics of EMF host-specificity by cross-inoculating basidiospores of five species of Suillus onto ten species of Pinus, and screened them for their ability to form ectomycorrhizae...
October 2016: PLoS Genetics
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