Viruses, Immunology & Bioinformatics from Virology.uvic.ca
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Data Drive | The Scientist Magazine®

Data Drive | The Scientist Magazine® | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it

Data demands in genomics and other omics projects have helped drive development of new and improved platforms for data analysis, sharing and pooling, and transfer. Profiled by The Scientist, four such advances can help with sequencing projects and more.

 

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Viruses, Immunology & Bioinformatics from Virology.uvic.ca
Virus and bioinformatics articles with some microbiology and immunology thrown in for good measure
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It's a group effort - the curators:

It's a group effort - the curators: | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it

get in touch if you want to help curate this topic

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Bwana Moses's comment, May 25, 2016 6:13 AM
Great work. Keep it going.
Bwana Moses's comment, March 7, 2017 12:46 PM
Thank You.
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FastViromeExplorer: a pipeline for virus and phage identification and abundance profiling in metagenomics data

FastViromeExplorer: a pipeline for virus and phage identification and abundance profiling in metagenomics data | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
With the increase in the availability of metagenomic data generated by next generation sequencing, there is an urgent need for fast and accurate tools for identifying viruses in host-associated and environmental samples. In this paper, we developed a stand-alone pipeline called FastViromeExplorer for the detection and abundance quantification of viruses and phages in large metagenomic datasets by performing rapid searches of virus and phage sequence databases. Both simulated and real data from human microbiome and ocean environmental samples are used to validate FastViromeExplorer as a reliable tool to quickly and accurately identify viruses and their abundances in large datasets.
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The Neuronal Gene Arc Encodes a Repurposed Retrotransposon Gag Protein that Mediates Intercellular RNA Transfer - S0092-8674(17)31504-0.pdf

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New shingles vaccine should be free, argues seniors advocate

New shingles vaccine should be free, argues seniors advocate | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
As the cases of shingles rise, especially among seniors, advocates are pushing for provincial governments to cover the cost of a new and effective vaccine.

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Modular and configurable optimal sequence alignment software: Cola. - PubMed - NCBI

Source Code Biol Med. 2014 Jun 9;9:12. doi: 10.1186/1751-0473-9-12. eCollection 2014.
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Kenya: Late Diagnosis Causing More Deaths in HIV-Positive Children

Kenya: Late Diagnosis Causing More Deaths in HIV-Positive Children | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
By Elgar Machuka A new study is raising concern that more children infected with HIV are dying early in hospitals in spite of anti-retroviral therapy (ART)…

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Highly parallel direct RNA sequencing on an array of nanopores

Highly parallel direct RNA sequencing on an array of nanopores | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
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How good bacteria control your genes

How good bacteria control your genes | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it

Signals produced by bacteria in the gut could help prevent infections and bowel cancer


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Exosomes serve as novel modes of tick-borne flavivirus transmission from arthropod to human cells and facilitates dissemination of viral RNA and proteins to the vertebrate neuronal cells

Exosomes serve as novel modes of tick-borne flavivirus transmission from arthropod to human cells and facilitates dissemination of viral RNA and proteins to the vertebrate neuronal cells | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
results suggest that flaviviruses uses arthropod-derived exosomes as a novel means for viral RNA and protein transmission from the vector, and the vertebrate exosomes for dissemination within the host that may subsequently allow neuroinvasion and neuropathogenesis.
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Transmission of Human Respiratory Syncytial Virus in the Immunocompromised Ferret Model

Transmission of Human Respiratory Syncytial Virus in the Immunocompromised Ferret Model | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Human respiratory syncytial virus (HRSV) causes substantial morbidity and mortality in vulnerable patients, such as the very young, the elderly, and immunocompromised individuals of any age. Nosocomial transmission of HRSV remains a serious challenge in hospital settings, with intervention strategies largely limited to infection control measures, including isolation of cases, high standards of hand hygiene, cohort nursing, and use of personal protective equipment. No vaccines against HRSV are currently available, and treatment options are largely supportive care and expensive monoclonal antibody or antiviral therapy. The limitations of current animal models for HRSV infection impede the development of new preventive and therapeutic agents, and the assessment of their potential for limiting HRSV transmission, in particular in nosocomial settings. Here, we demonstrate the efficient transmission of HRSV from immunocompromised ferrets to both immunocompromised and immunocompetent contact ferrets, with pathological findings reproducing HRSV pathology in humans. The immunocompromised ferret-HRSV model represents a novel tool for the evaluation of intervention strategies against nosocomial transmission of HRSV.
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Case study: China’s Year of the Rooster looking foul

Case study: China’s Year of the Rooster looking foul | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Anhui Provinces have experie

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Phandango: an interactive viewer for bacterial population genomics | Bioinformatics | Oxford Academic

Phandango: an interactive viewer for bacterial population genomics | Bioinformatics | Oxford Academic | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
AbstractSummary. Fully exploiting the wealth of data in current bacterial population genomics datasets requires synthesizing and integrating different types of
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Construction of an infectious horsepox virus vaccine from chemically synthesized DNA fragments

Construction of an infectious horsepox virus vaccine from chemically synthesized DNA fragments | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it

Edward Jenner and his contemporaries believed that his variolae vaccinae originated in horses and molecular analyses show that modern vaccinia virus (VACV) strains share common ancestry with horsepox virus (HPXV). Given concerns relating to the toxicity of modern VACV vaccines, we asked whether an HPXV-based vaccine might provide a superior alternative. Since HPXV may be extinct and the only specimen of HPXV that has been identified is unavailable for investigation, a group of scientists now explored whether HPXV could be obtained by large-scale gene synthesis.

 

Ten large (10–30 kb) fragments of DNA were synthesized based on the HPXV sequence along with two 157 nt VACV terminal sequences, and were recombined into a live synthetic chimeric HPXV (scHPXV) in cells infected with Shope fibroma virus (SFV). Sequencing of the 212 kbp scHPXV confirmed it encoded a faithful copy of the input DNA.

 

This is the first complete synthesis of a poxvirus using synthetic biology approaches. This scHPXV produced smaller plaques, produced less extracellular virus and exhibited less virulence in mice than VACV, but still provided vaccine protection against a lethal VACV challenge. Collectively, these findings support further development of scHPXV as a novel replication-proficient smallpox vaccine.


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Classification and evolution of human papillomavirus genome variants: Alpha-5 (HPV26, 51, 69, 82), Alpha-6 (HPV30, 53, 56, 66), Alpha-11 (HPV34, 73), Alpha-13 (HPV54) and Alpha-3 (HPV61) - ScienceD...

Classification and evolution of human papillomavirus genome variants: Alpha-5 (HPV26, 51, 69, 82), Alpha-6 (HPV30, 53, 56, 66), Alpha-11 (HPV34, 73), Alpha-13 (HPV54) and Alpha-3 (HPV61) - ScienceD... | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
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After flu vaccine mismatch, calls for delayed selection intensify

After flu vaccine mismatch, calls for delayed selection intensify | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
This collection includes Reviews and Research articles from across the Nature group of journals to showcase advances in our understanding of influenza virus biology, evolution and adaptation, and in surveillance and drug and vaccine development.

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Ed Rybicki's curator insight, January 17, 4:37 AM
...and after delayed selection, A MORE MODERN AND MUCH QUICKER MEANS OF PRODUCTION?? Like - plants, maybe?
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ePlant: A Comprehensive Data Visualization Tool for Plant Biologists « Botany One

ePlant: A Comprehensive Data Visualization Tool for Plant Biologists « Botany One | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
The advent and breadth of bioinformatics resources have made scientist’s jobs easier. Before jumping into wet lab work, they are able to parse gene targets
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Transcriptome profiling of whitefly guts in response to Tomato yellow leaf curl virus infection

Transcriptome profiling of whitefly guts in response to Tomato yellow leaf curl virus infection | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Plant viruses in agricultural crops are of great concern worldwide, and over 75% of them are transmitted from infected to healthy plants by insect vectors. Tomato yellow leaf curl virus (TYLCV) is a begomovirus, which is the largest and most economically important group of plant viruses, transmitted by the whitefly Bemisia tabaci. The circulation of TYLCV in the insect involves complex insect-virus interactions, whereas the molecular mechanisms of these interactions remain ambiguous. The insect gut as a barrier for viral entry and dissemination is thought to regulate the vector specificity. However, due to its tiny size, information for the responses of whitefly gut to virus infection is limited. We investigated the transcriptional response of the gut of B. tabaci Middle East-Asia Minor 1 species to TYLCV infection using Illumina sequencing. A total of 5207 differentially expressed genes (DEGs) between viruliferous and non-viruliferous whitefly guts were identified. Enrichment analyses showed that cargo receptor and ATP-binding cassette (ABC) transporters were enriched in DEGs, and might help the virus to cross gut barrier. TYLCV could perturb cell cycle and DNA repair as a possible result of its replication in the whitefly. Our data also demonstrated that TYLCV can activate whitefly defense responses, such as antimicrobial peptides. Meanwhile, a number of genes involved in intracellular signaling were activated by TYLCV infection. Our results reveal the complex insect-virus relationship in whitefly gut and provide substantial molecular information for the role of insect midguts in virus transmission.
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Ed Rybicki's curator insight, January 17, 6:02 AM
Back to my mid-term roots in geminivirology...it is an open question as to whether geminiviruses and especially TYLCV can replicate in vector insects, seeing as they do seem to be able to set them up to be persistent circulative vectors. Some swear they do; others that they don't - but I am willing to bet that TYLCV at any rate undergoes either partial replication, or expression from "repaired" dsDNA forms of the genomic DNA, in insect cells, so as to effect some of the changes seen in insect transcription.

I have another theory concerning trans-replication of gemini- and other ssDNA virus genomes by Reps or RCR-mediating proteins endogenous to or from viruses or even bacteria co-infecting the vectors, but that is the subject for another posting.
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Meditation or exercise for preventing acute respiratory infection: a randomized controlled trial

PURPOSE:
This study was designed to evaluate potential preventive effects of meditation or exercise on incidence, duration, and severity of acute respiratory infection (ARI) illness.

METHODS:
Community-recruited adults aged 50 years and older were randomized to 1 of 3 study groups: 8-week training in mindfulness meditation, matched 8-week training in moderate-intensity sustained exercise, or observational control. The primary outcome was area-under-the-curve global illness severity during a single cold and influenza season, using the Wisconsin Upper Respiratory Symptom Survey (WURSS-24) to assess severity. Health care visits and days of missed work were counted. Nasal wash collected during ARI illness was assayed for neutrophils, interleukin-8, and viral nucleic acid.

RESULTS:
Of 154 adults randomized into the study, 149 completed the trial (82% female, 94% white, mean age 59.3 ± 6.6 years). There were 27 ARI episodes and 257 days of ARI illness in the meditation group (n = 51), 26 episodes and 241 illness days in the exercise group (n = 47), and 40 episodes and 453 days in the control group (n = 51). Mean global severity was 144 for meditation, 248 for exercise, and 358 for control. Compared with control, global severity was significantly lower for meditation (P = .004). Both global severity and total days of illness (duration) trended toward being lower for the exercise group (P=.16 and P=.032, respectively), as did illness duration for the meditation group (P=.034). Adjusting for covariates using zero-inflated multivariate regression models gave similar results. There were 67 ARI-related days of-work missed in the control group, 32 in the exercise group (P = .041), and 16 in the meditation group (P <.001). Health care visits did not differ significantly. Viruses were identified in 54% of samples from meditation, 42% from exercise, and 54% from control groups. Neutrophil count and interleukin-8 levels were similar among intervention groups.

CONCLUSIONS:
Training in meditation or exercise may be effective in reducing ARI illness burden.


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Ed Rybicki's curator insight, January 16, 5:11 AM
Surprising spoiler: may help??
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50 Adverbs to avoid in academic writing

50 Adverbs to avoid in academic writing | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Here are 50 adverbs that that you can eliminate in your writing, be it academic or professional.
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Direct Imaging of the circular chromosome of a live bacterium

New assays for quantitative imaging and sequencing have yielded great progress towards understanding the organizational principles of chromosomes. Yet, even for the well-studied model bacterium Escherichia coli, many basic questions remain unresolved regarding chromosomal (sub-)structure, its mechanics and dynamics, and the link between structure and function. Here we resolve the spatial organization of the circular chromosome of bacteria by directly imaging the chromosome in live E. coli cells with a broadened cell shape.

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Sequence motif finder using memetic algorithm

Sequence motif finder using memetic algorithm | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
De novo prediction of Transcription Factor Binding Sites (TFBS) using computational methods is a difficult task and it is an important problem in Bioinformatics. The correct recognition of TFBS plays an important role in understanding the mechanisms of gene regulation and helps to develop new drugs. We here present Memetic Framework for Motif Discovery (MFMD), an algorithm that uses semi-greedy constructive heuristics as a local optimizer. In addition, we used a hybridization of the classic genetic algorithm as a global optimizer to refine the solutions initially found. MFMD can find and classify overrepresented patterns in DNA sequences and predict their respective initial positions. MFMD performance was assessed using ChIP-seq data retrieved from the JASPAR site, promoter sequences extracted from the ABS site, and artificially generated synthetic data. The MFMD was evaluated and compared with well-known approaches in the literature, called MEME and Gibbs Motif Sampler, achieving a higher f-score in the most datasets used in this work. We have developed an approach for detecting motifs in biopolymers sequences. MFMD is a freely available software that can be promising as an alternative to the development of new tools for de novo motif discovery. Its open-source software can be downloaded at
https://github.com/jadermcg/mfmd

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Interactions between Enteric Bacteria and Eukaryotic Viruses Impact the Outcome of Infection

Interactions between Enteric Bacteria and Eukaryotic Viruses Impact the Outcome of Infection | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Enteric viruses encounter a multitude of environments as they traverse the gastrointestinal tract. The interaction of enteric eukaryotic viruses with members of the host microbiota impacts the outcome of infection. Infection with several enteric viruses is impaired in the absence of the gut microbiota, specifically bacteria. The effects of bacteria on virus biology are diverse. Poliovirus capsid stability and receptor engagement are positively impacted by bacteria and bacterial lipopolysaccharides. Norovirus utilizes histo-blood group antigens produced by enteric bacteria to attach and productively infect B cells. Lipopolysaccharides on the envelope of mouse mammary tumor virus promote a tolerogenic environment that allows for the establishment of viral persistence. Reovirus binds Gram negative and Gram-positive bacteria through bacterial envelope components to enhance virion thermostability. Through the direct engagement of bacteria and bacterial components, viruses evolved diverse ways to impact the outcome of infection.
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How Do Virus–Mosquito Interactions Lead to Viral Emergence?

'while wrapid progression and frequency of recent arbovirus outbreaks is associated with long-term changes in human behavior (globalization, urbanization, climate change), there are direct mosquito–virus interactions which drive shifts in host range and alter virus transmission'

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Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins. - PubMed - NCBI

Nucleic Acids Res. 2015 Feb 18;43(3):e15. doi: 10.1093/nar/gku1196. Epub 2014 Nov 20. Research Support, Non-U.S. Gov't
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A Completely Reimplemented MPI Bioinformatics Toolkit with a New HHpred Server at its Core. - PubMed - NCBI

A Completely Reimplemented MPI Bioinformatics Toolkit with a New HHpred Server at its Core. - PubMed - NCBI | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
J Mol Biol. 2017 Dec 16. pii: S0022-2836(17)30587-9. doi: 10.1016/j.jmb.2017.12.007. [Epub ahead of print]
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