keyword
MENU ▼
Read by QxMD icon Read
search

virome

keyword
https://www.readbyqxmd.com/read/27907010/viral-metagenomic-analysis-displays-the-co-infection-situation-in-healthy-and-pmws-affected-pigs
#1
Anne-Lie Blomström, Caroline Fossum, Per Wallgren, Mikael Berg
The development of high-throughput sequencing technologies have allowed the possibility to investigate and characterise the entire microbiome of individuals, providing better insight to the complex interaction between different microorganisms. This will help to understand how the microbiome influence the susceptibility of secondary agents and development of disease. We have applied viral metagenomics to investigate the virome of lymph nodes from Swedish pigs suffering from the multifactorial disease postweaning multisystemic wasting syndrome (PMWS) as well as from healthy pigs...
2016: PloS One
https://www.readbyqxmd.com/read/27902331/the-plasma-virome-of-febrile-adult-kenyans-shows-frequent-parvovirus-b19-infections-and-a-novel-arbovirus-kadipiro-virus
#2
Carolyne Ngoi, Juliana Siqueira, Linlin Li, Xutao Deng, Peter Mugo, Susan Graham, Matt Price, Eduard Sanders, Eric Delwart
Viral nucleic acids present in the plasma of 498 Kenyan adults with unexplained fever were characterized by metagenomics analysis of 51 sample pools. The highest to lowest fraction of plasma pools was positive for parvovirus B19 (75%), pegivirus C (GBV-C) (67%), alpha anellovirus (59%), gamma anellovirus (55%), beta anellovirus (41%), Dengue virus genotype 2 (DENV-2) (16%), HIV-1 (6%), HHV-6 (6%), HBV (4%), rotavirus (4%), norovirus (4%), rhinovirus C (2%), Merkel cell polyomavirus (MCPyV)(2%) and Kadipiro virus (2%)...
October 24, 2016: Journal of General Virology
https://www.readbyqxmd.com/read/27890586/exploring-the-contribution-of-bacteriophages-to-antibiotic-resistance
#3
Itziar Lekunberri, Jèssica Subirats, Carles M Borrego, José Luis Balcázar
Bacteriophages (phages) are the most abundant and diverse biological entities in our planet. They infect susceptible bacterial hosts into which they either multiply or persist. In the latter case, phages can confer new functions to their hosts as a result of gene transfer, thus contributing to their adaptation (short-term) and evolution (long-term). In this regard, the role of phages on the dissemination of antibiotic resistance genes (ARGs) among bacterial hosts in natural environments has not yet been clearly resolved...
January 2017: Environmental Pollution
https://www.readbyqxmd.com/read/27883042/two-novel-viruses-associated-with-the-apis-mellifera-pathogenic-mite-varroa-destructor
#4
Sofia Levin, Noa Sela, Nor Chejanovsky
Varroa destructor infestation of Apis mellifera colonies carries and/or promotes replication of honey bee viruses like the Deformed wing virus, the Varroa destructor virus-1, the Acute bee paralysis virus, the Israeli acute bee paralysis virus and the Kashmir bee virus that have been well described and characterized; but viruses exclusively associated with Varroa were not found. To look for viruses that may associate with- or infect V. destructor we performed deep sequencing (RNA-seq) of RNA extracted from honey bees and mites in Varroa-infested untreated colonies...
November 24, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27880830/synonymous-co-variation-across-the-e1-e2-gene-junction-of-hepatitis-c-virus-defines-virion-fitness
#5
Brendan A Palmer, Liam J Fanning
Hepatitis C virus is a positive-sense single-stranded RNA virus. The gene junction partitioning the viral glycoproteins E1 and E2 displays concurrent sequence evolution with the 3'-end of E1 highly conserved and the 5'-end of E2 highly heterogeneous. This gene junction is also believed to contain structured RNA elements, with a growing body of evidence suggesting that such structures can act as an additional level of viral replication and transcriptional control. We have previously used ultradeep pyrosequencing to analyze an amplicon library spanning the E1/E2 gene junction from a treatment naïve patient where samples were collected over 10 years of chronic HCV infection...
2016: PloS One
https://www.readbyqxmd.com/read/27880757/redefining-the-invertebrate-rna-virosphere
#6
Mang Shi, Xian-Dan Lin, Jun-Hua Tian, Liang-Jun Chen, Xiao Chen, Ci-Xiu Li, Xin-Cheng Qin, Jun Li, Jian-Ping Cao, John-Sebastian Eden, Jan Buchmann, Wen Wang, Jianguo Xu, Edward C Holmes, Yong-Zhen Zhang
Current knowledge of RNA virus biodiversity is both biased and fragmentary, reflecting a focus on culturable or disease-causing agents. Here we profile the transcriptomes of over 220 invertebrate species sampled across nine animal phyla and report the discovery of 1,445 RNA viruses, including some that are sufficiently divergent to comprise new families. The identified viruses fill major gaps in the RNA virus phylogeny and reveal an evolutionary history that is characterized by both host switching and co-divergence...
November 23, 2016: Nature
https://www.readbyqxmd.com/read/27866880/efficacy-of-sterile-fecal-filtrate-transfer-for-treating-patients-with-clostridium-difficile-infection
#7
Stephan J Ott, Georg H Waetzig, Ateequr Rehman, Jacqueline Moltzau-Anderson, Richa Bharti, Juris A Grasis, Liam Cassidy, Andreas Tholey, Helmut Fickenscher, Dirk Seegert, Philip Rosenstiel, Stefan Schreiber
BACKGROUND & AIMS: Fecal microbiota transplantation (FMT) is a highly effective therapy for recurrent Clostridium difficile infection (CDI). However, transferring undefined living bacteria entails uncontrollable risks for infectious and metabolic or malignant diseases, particularly in immunocompromised patients. We investigated whether sterile fecal filtrates (containing bacterial debris, proteins, antimicrobial compounds, metabolic products and oligonucleotides/DNA), rather than intact microorganisms, are effective in patients with CDI...
November 17, 2016: Gastroenterology
https://www.readbyqxmd.com/read/27860030/imbalance-of-bacteriome-profiles-within-the-finnish-diabetes-prediction-and-prevention-study-parallel-use-of-16s-profiling-and-virome-sequencing-in-stool-samples-from-children-with-islet-autoimmunity-and-matched-controls
#8
Ondrej Cinek, Lenka Kramna, Jake Lin, Sami Oikarinen, Katerina Kolarova, Jorma Ilonen, Olli Simell, Riitta Veijola, Reija Autio, Heikki Hyöty
BACKGROUND: We set out to explore associations between the stool bacteriome profiles and early-onset islet autoimmunity, taking into account the interactions with the virus component of the microbiome. METHODS: Serial stool samples were longitudinally collected from 18 infants and toddlers with early-onset islet autoimmunity (median age 17.4 months) followed by type 1 diabetes, and 18 tightly matched controls from the Finnish Diabetes Prediction and Prevention (DIPP) cohort...
November 17, 2016: Pediatric Diabetes
https://www.readbyqxmd.com/read/27833560/pharmacometabolomics-informs-viromics-toward-precision-medicine
#9
Angeliki Balasopoulou, George P Patrinos, Theodora Katsila
Nowadays, we are experiencing the big data era with the emerging challenge of single data interpretation. Although the advent of high-throughput technologies as well as chemo- and bio-informatics tools presents pan-omics data as the way forward to precision medicine, personalized health care and tailored-made therapeutics can be only envisaged when interindividual variability in response to/toxicity of xenobiotics can be interpreted and thus, predicted. We know that such variability is the net outcome of genetics (host and microbiota) and environmental factors (diet, lifestyle, polypharmacy, and microbiota) and for this, tremendous efforts have been made to clarify key-molecules from correlation to causality to clinical significance...
2016: Frontiers in Pharmacology
https://www.readbyqxmd.com/read/27814394/deep-sequencing-analysis-reveals-the-mycoviral-diversity-of-the-virome-of-an-avirulent-isolate-of-rhizoctonia-solani-ag-2-2-iv
#10
Anika Bartholomäus, Daniel Wibberg, Anika Winkler, Alfred Pühler, Andreas Schlüter, Mark Varrelmann
Rhizoctonia solani represents an important plant pathogenic Basidiomycota species complex and the host of many different mycoviruses, as indicated by frequent detection of dsRNA elements in natural populations of the fungus. To date, eight different mycoviruses have been characterized in Rhizoctonia and some of them have been reported to modulate its virulence. DsRNA extracts of the avirulent R. solani isolate DC17 (AG2-2-IV) displayed a diverse pattern, indicating multiple infections with mycoviruses. Deep sequencing analysis of the dsRNA extract, converted to cDNA, revealed that this isolate harbors at least 17 different mycovirus species...
2016: PloS One
https://www.readbyqxmd.com/read/27769778/a-bioinformatics-approach-reveals-seven-nearly-complete-rna-virus-genomes-in-bivalve-rna-seq-data
#11
Umberto Rosani, Marco Gerdol
Viral metagenomics (viromics) can provide a great contribution in expanding the knowledge of viruses and the relationship with their hosts. Viromic studies on marine organisms are still at a very early stage and only little efforts have been spent in the identification of viruses associated to marine invertebrates to date, leaving the complexity of marine viromes associated to bivalve hosts almost completely unexplored. However, the potential use of viromic approaches in the management of viral diseases affecting aquacultured species has been recently evidenced by the flourishing of studies on the Ostreid herpesvirus type-1, which has been associated with bivalve mortality events...
October 18, 2016: Virus Research
https://www.readbyqxmd.com/read/27761936/epigenetic-treatment-of-persistent-viral-infections
#12
Walter H Moos, Carl A Pinkert, Michael H Irwin, Douglas V Faller, Krishna Kodukula, Ioannis P Glavas, Kosta Steliou
Preclinical Research Approximately 2,500 years ago, Hippocrates used the word herpes as a medical term to describe lesions that appeared to creep or crawl on the skin, advocating heat as a possible treatment. During the last 50 years, pharmaceutical research has made great strides, and therapeutic options have expanded to include small molecule antiviral agents, protease inhibitors, preventive vaccines for a handful of the papillomaviruses, and even cures for hepatitis C virus infections. However, effective treatments for persistent and recurrent viral infections, particularly the highly prevalent herpesviruses, continue to represent a significant unmet medical need, affecting the majority of the world's population...
October 20, 2016: Drug Development Research
https://www.readbyqxmd.com/read/27731934/the-perioperative-lung-transplant-virome-torque-teno-viruses-are-elevated-in-donor-lungs-and-show-divergent-dynamics-in-primary-graft-dysfunction
#13
A A Abbas, J M Diamond, C Chehoud, B Chang, J J Kotzin, J C Young, I Imai, A R Haas, E Cantu, D J Lederer, K Meyer, R K Milewski, K M Olthoff, A Shaked, J D Christie, F D Bushman, R G Collman
Primary graft dysfunction (PGD) is a principal cause of early morbidity and mortality after lung transplantation, but its pathogenic mechanisms are not fully clarified. Thus far, studies using standard clinical assays have not linked microbial factors to PGD. We previously used comprehensive metagenomic methods to characterize viruses in lung allografts >1 month post-transplant and found that levels of Anellovirus, mainly Torque teno viruses (TTV), were significantly higher than in non-transplant healthy controls...
October 12, 2016: American Journal of Transplantation
https://www.readbyqxmd.com/read/27721694/deep-sequencing-analysis-of-apple-infecting-viruses-in-korea
#14
In-Sook Cho, Davaajargal Igori, Seungmo Lim, Gug-Seoun Choi, John Hammond, Hyoun-Sub Lim, Jae Sun Moon
Deep sequencing has generated 52 contigs derived from five viruses; Apple chlorotic leaf spot virus (ACLSV), Apple stem grooving virus (ASGV), Apple stem pitting virus (ASPV), Apple green crinkle associated virus (AGCaV), and Apricot latent virus (ApLV) were identified from eight apple samples showing small leaves and/or growth retardation. Nucleotide (nt) sequence identity of the assembled contigs was from 68% to 99% compared to the reference sequences of the five respective viral genomes. Sequences of ASPV and ASGV were the most abundantly represented by the 52 contigs assembled...
October 2016: Plant Pathology Journal
https://www.readbyqxmd.com/read/27721367/a-pair-of-identical-twins-discordant-for-myalgic-encephalomyelitis-chronic-fatigue-syndrome-differ-in-physiological-parameters-and-gut-microbiome-composition
#15
Ludovic Giloteaux, Maureen R Hanson, Betsy A Keller
BACKGROUND Patients with myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) present with profound fatigue, flu-like symptoms, pain, cognitive impairment, orthostatic intolerance, and post-exertional malaise (PEM), and exacerbation of some or all of the baseline symptoms. CASE REPORT We report on a pair of 34-year-old monozygotic twins discordant for ME/CFS, with WELL, the non-affected twin, and ILL, the affected twin. Both twins performed a two-day cardiopulmonary exercise test (CPET), pre- and post-exercise blood samples were drawn, and both provided stool samples for biochemical and molecular analysis...
October 10, 2016: American Journal of Case Reports
https://www.readbyqxmd.com/read/27699405/paucibacterial-microbiome-and-resident-dna-virome-of-the-healthy-conjunctiva
#16
Thuy Doan, Lakshmi Akileswaran, Dallin Andersen, Benjamin Johnson, Narae Ko, Angira Shrestha, Valery Shestopalov, Cecilia S Lee, Aaron Y Lee, Russell N Van Gelder
Purpose: To characterize the ocular surface microbiome of healthy volunteers using a combination of microbial culture and high-throughput DNA sequencing techniques. Methods: Conjunctival swab samples from 107 healthy volunteers were analyzed by bacterial culture, 16S rDNA gene deep sequencing (n = 89), and biome representational in silico karyotyping (BRiSK; n = 80). Swab samples of the facial skin (n = 42), buccal mucosa (n = 50), and environmental controls (n = 27) were processed in parallel...
October 1, 2016: Investigative Ophthalmology & Visual Science
https://www.readbyqxmd.com/read/27698618/an-ecological-framework-of-the-human-virome-provides-classification-of-current-knowledge-and-identifies-areas-of-forthcoming-discovery
#17
Michael T Parker
Recent advances in sequencing technologies have opened the door for the classification of the human virome. While taxonomic classification can be applied to the viruses identified in such studies, this gives no information as to the type of interaction the virus has with the host. As follow-up studies are performed to address these questions, the description of these virus-host interactions would be greatly enriched by applying a standard set of definitions that typify them. This paper describes a framework with which all members of the human virome can be classified based on principles of ecology...
September 2016: Yale Journal of Biology and Medicine
https://www.readbyqxmd.com/read/27684183/principles-of-systems-biology-no-9
#18
(no author information available yet)
Deep study of the microbiome, virome, and genetic code headline this month's Cell Systems call (Cell Systems 1, 307).
September 28, 2016: Cell Systems
https://www.readbyqxmd.com/read/27681128/bipartite-network-analysis-of-the-archaeal-virosphere-evolutionary-connections-between-viruses-and-capsidless-mobile-elements
#19
Jaime Iranzo, Eugene V Koonin, David Prangishvili, Mart Krupovic
: Archaea and particularly hyperthermophilic crenarchaea are hosts to many unusual viruses with diverse virion shapes and distinct gene compositions. As is typical of viruses in general, there are no universal genes in the archaeal virosphere. Therefore, to obtain a comprehensive picture of the evolutionary relationships between viruses, network analysis methods are more productive than traditional phylogenetic approaches. Here we present a comprehensive comparative analysis of genomes and proteomes from all currently known taxonomically classified and unclassified, cultivated and uncultivated archaeal viruses...
December 15, 2016: Journal of Virology
https://www.readbyqxmd.com/read/27639161/west-african-anopheles-gambiae-mosquitoes-harbor-a-taxonomically-diverse-virome-including-new-insect-specific-flaviviruses-mononegaviruses-and-totiviruses
#20
Joseph R Fauver, Nathan D Grubaugh, Benjamin J Krajacich, James Weger-Lucarelli, Steven M Lakin, Lawrence S Fakoli, Fatorma K Bolay, Joseph W Diclaro, Kounbobr Roch Dabiré, Brian D Foy, Doug E Brackney, Gregory D Ebel, Mark D Stenglein
Anopheles gambiae are a major vector of malaria in sub-Saharan Africa. Viruses that naturally infect these mosquitoes may impact their physiology and ability to transmit pathogens. We therefore used metagenomics sequencing to search for viruses in adult Anopheles mosquitoes collected from Liberia, Senegal, and Burkina Faso. We identified a number of virus and virus-like sequences from mosquito midgut contents, including 14 coding-complete genome segments and 26 partial sequences. The coding-complete sequences define new viruses in the order Mononegavirales, and the families Flaviviridae, and Totiviridae...
November 2016: Virology
keyword
keyword
29595
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"