Viruses, Immunology & Bioinformatics from 4Virology.net
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Viruses, Immunology & Bioinformatics from 4Virology.net
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 4Virology.net | Scoop.it

get in touch if you want to help curate this topic

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Bwana Moses's comment, May 25, 2016 11:13 AM
Great work. Keep it going.
Bwana Moses's comment, March 7, 2017 5:46 PM
Thank You.
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AbPredict 2: a server for accurate and unstrained structure prediction of antibody variable domains | Bioinformatics | Oxford Academic

AbPredict 2: a server for accurate and unstrained structure prediction of antibody variable domains | Bioinformatics | Oxford Academic | Viruses, Immunology & Bioinformatics from 4Virology.net | Scoop.it
AbstractSummary. Methods for antibody structure prediction rely on sequence homology to experimentally determined structures. Resulting models may be accurate
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GeneSpy, a user-friendly and flexible genomic context visualizer | Bioinformatics | Oxford Academic

GeneSpy, a user-friendly and flexible genomic context visualizer | Bioinformatics | Oxford Academic | Viruses, Immunology & Bioinformatics from 4Virology.net | Scoop.it
AbstractSummary. The exploration and comparison of genome organization is routinely used in the frame of genomic and phylogenomic analyses. As a consequence, i
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Accurate multiple alignment of distantly related genome sequences using filtered spaced word matches as anchor points | Bioinformatics | Oxford Academic

Accurate multiple alignment of distantly related genome sequences using filtered spaced word matches as anchor points | Bioinformatics | Oxford Academic | Viruses, Immunology & Bioinformatics from 4Virology.net | Scoop.it
AbstractMotivation. Most methods for pairwise and multiple genome alignment use fast local homology search tools to identify anchor points, i.e. high-scoring l
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Epstein-Barr virus and schizophrenia linked by abnormal immune response

Epstein-Barr virus and schizophrenia linked by abnormal immune response | Viruses, Immunology & Bioinformatics from 4Virology.net | Scoop.it
Individuals with schizophrenia also have higher level of antibodies against the Epstein-Barr virus, according to new research.
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Statistical and integrative system-level analysis of DNA methylation data | Nature Reviews Genetics

Review
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Ten quick tips for sharing open genomic data

Ten quick tips for sharing open genomic data | Viruses, Immunology & Bioinformatics from 4Virology.net | Scoop.it
As sequencing prices drop, genomic data accumulates—seemingly at a steadily increasing pace. Most genomic data potentially have value beyond the initial purpose—but only if shared with the scientific community. This, of course, is often easier said than done. Some of the challenges in sharing genomic data include data volume (raw file sizes and number of files), complexities, formats, nomenclatures, metadata descriptions, and the choice of a repository. In this paper, we describe 10 quick tips for sharing open genomic data.
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Porcine circovirus 2 (PCV-2) genotype update and proposal of a new genotyping methodology

Porcine circovirus 2 (PCV-2) genotype update and proposal of a new genotyping methodology | Viruses, Immunology & Bioinformatics from 4Virology.net | Scoop.it
Porcine circovirus 2 (PCV-2) is one of the most widespread viral infections of swine, causing a remarkable economic impact because of direct losses and indirect costs for its control. As other ssDNA viruses, PCV-2 is characterized by a high evolutionary rate, leading to the emergence of a plethora...
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Toll-like receptor 4 in acute viral infection: Too much of a good thing

Toll-like receptor 4 in acute viral infection: Too much of a good thing | Viruses, Immunology & Bioinformatics from 4Virology.net | Scoop.it
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iCn3D, a Web-based 3D Viewer for the Visualization of Biomolecular Structure and Sequence Annotation

iCn3D (I-see-in-3D) is a web-based 3D molecular structure viewer implemented in JavaScript. It invites users to explore sequence-structure relationships by displaying 3D structures, protein and nucleotide sequences, and biological annotations such as protein domains, Single Nucleotide Variations, functional sites, molecular contacts, as well as user defined features. Customized and user-annotated displays can be shared with colleagues or publishers via a simple URL, or embedded in web pages as live 3D displays. iCn3D is unique in its ability to simultaneously show 3D structure, 2D molecular networks and interactions, and 1D protein and nucleotide sequences through an integrated sequence/annotation browser. Arbitrary molecular features can be selected in any of the 1D/2D/3D windows as sets of molecules or residues, utilizing flexible user interfaces. These selections are synchronized dynamically in all displays. They can, for example, be shown as tracks in the 1D sequence/annotation browser with simultaneous 3D representations. They can be saved and reused throughout a single user session, or exported for subsequent sessions and further external analysis. iCn3D is rich in structural analysis and visualization features and has a built-in user interface that supports both command line- and menu-driven operation. Session commands can be saved, replayed and shared. iCn3D can display superimposed structures obtained from NCBI's VAST+ structural alignment resource, for comparative analysis of tertiary or quaternary structure. iCn3D can also display electron density maps for crystal structures and export files for 3D printing. The following example URL exemplifies some of the 1D/2D/3D representations: https://www.ncbi.nlm.nih.gov/Structure/icn3d/full.html?mmdbid=1TUP&showanno=1&show2d=1&showsets=1
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Genomics, Medicine, and Pseudoscience: Russian homeopathy, hiding in plain sight

Genomics, Medicine, and Pseudoscience: Russian homeopathy, hiding in plain sight | Viruses, Immunology & Bioinformatics from 4Virology.net | Scoop.it
It turns out that Russia has its very own brand of bogus medicine:"release-active drugs," or RADs. Dozens of scientific articles hav
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A De Novo Shape Motif Discovery Algorithm Reveals Preferences of Transcription Factors for DNA Shape Beyond Sequence Motifs

Building on the recent line of research that DNA shape encodes specificity signals
for transcription factor (TF)-DNA binding, Samee et al. developed an algorithm to
identify enriched patterns of DNA shape directly from DNA shape profiles of TF-bound
regions. These patterns, or “shape motifs,” correspond well with conventional sequence
motifs, but often include additional nucleotides flanking the sequence motifs. They
also show that apparent mismatches to the sequence motif can have similar shape to
the shape motif and are potential targets for TF binding. While the observations still
need experimental validation, the work shows that motif models that capture additional
structural and biophysical aspects are necessary to understand the mechanism of TF-DNA
binding.
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SLIDE – a web-based tool for interactive visualization of large-scale – omics data | Bioinformatics | Oxford Academic

SLIDE – a web-based tool for interactive visualization of large-scale – omics data | Bioinformatics | Oxford Academic | Viruses, Immunology & Bioinformatics from 4Virology.net | Scoop.it
AbstractSummary. Data visualization is often regarded as a post hoc step for verifying statistically significant results in the analysis of high-throughput dat
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CoMSA: compression of protein multiple sequence alignment files | Bioinformatics | Oxford Academic

CoMSA: compression of protein multiple sequence alignment files | Bioinformatics | Oxford Academic | Viruses, Immunology & Bioinformatics from 4Virology.net | Scoop.it
AbstractMotivation. Bioinformatics databases grow rapidly and achieve values hardly to imagine a decade ago. Among numerous bioinformatics processes generating
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A peek behind the paper – Prof. Mohamed El Zowalaty on arboviral infections

A peek behind the paper – Prof. Mohamed El Zowalaty on arboviral infections | Viruses, Immunology & Bioinformatics from 4Virology.net | Scoop.it
Take a look behind the scenes of a recent Future Virology paper on the challenges facing the field of arboviruses both in South Africa and across the world.
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First clinical trial for intravenous phage therapy gets FDA approval

First clinical trial for intravenous phage therapy gets FDA approval | Viruses, Immunology & Bioinformatics from 4Virology.net | Scoop.it
The first clinical trial to use intravenously-administered bacteriophage therapy in hopes of combatting resistant bacteria has recieved FDA approval.
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Genomics, Medicine, and Pseudoscience: The flu vaccine is working well this year. It's not too late to get it.

Genomics, Medicine, and Pseudoscience: The flu vaccine is working well this year. It's not too late to get it. | Viruses, Immunology & Bioinformatics from 4Virology.net | Scoop.it
Current flu trends for 2018-19. Brown shows H1N1 strains, red shows H3N2, and yellow indicates the strain was not genotyped. The flu i
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HEALTH CARE's curator insight, January 14, 3:55 PM
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What is bioinformatics?

What is bioinformatics? | Viruses, Immunology & Bioinformatics from 4Virology.net | Scoop.it
Bioinformatics is a growing field of research, existing at the cutting-edge of the biological sciences. But what is it?
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Conserved and Differential Features of TNF Superfamily Ligand Expression on APC Subsets over the Course of a Chronic Viral Infection in Mice

Conserved and Differential Features of TNF Superfamily Ligand Expression on APC Subsets over the Course of a Chronic Viral Infection in Mice | Viruses, Immunology & Bioinformatics from 4Virology.net | Scoop.it
There is currently much interest in how different APC subsets shape the immune response. We recently described a division of labor between classical dendritic cells (cDC) and inflammatory monocyte-derived APC in provision of costimulatory ligands to T cells early during chronic lymphocytic choriomeningitis clone 13 (LCMV 13) infection in mice. At day 2 of LCMV 13 infection, cDC preferentially express CD80 and CD86, whereas TNF superfamily ligands GITRL, 4-1BBL, CD70, and OX40L are preferentially induced by type I IFN on inflammatory monocyte-derived APC, with minimal expression on cDC. In this study, we further investigate the expression of TNF and B7 family ligands on APC over the course of LCMV 13 infection. OX40L and 4-1BBL remain above baseline through the chronic stage of infection, with predominant expression on inflammatory APC compared with cDC in the spleen, partially blocked by anti–IFN-γR Ab pretreatment. Conversely, CD70, like GITRL, returns to baseline on the APC within a few days postinfection. In the lung, TNF family ligands were also preferentially expressed on inflammatory monocyte-derived APC. CD86 was generally higher on cDC than inflammatory APC in the spleen, but in the lung CD86 was highest on inflammatory APC. Moreover, in the spleen, CD80 levels on different APC subsets fluctuated over the course of the infection. We also show that LPS induction of TNF superfamily ligands is largely mediated through type I IFN. This study highlights the importance of IFNs and monocyte-derived APC in TNF superfamily ligand expression in both secondary lymphoid organs and tissues during chronic viral infection.

Via Gilbert C FAURE
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SonicParanoid: fast, accurate and easy orthology inference | Bioinformatics | Oxford Academic

SonicParanoid: fast, accurate and easy orthology inference | Bioinformatics | Oxford Academic | Viruses, Immunology & Bioinformatics from 4Virology.net | Scoop.it
AbstractMotivation. Orthology inference constitutes a common base of many genome-based studies, as a pre-requisite for annotating new genomes, finding target g
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Scientists identify vast underground ecosystem containing billions of micro-organisms | Science | The Guardian

Scientists identify vast underground ecosystem containing billions of micro-organisms | Science | The Guardian | Viruses, Immunology & Bioinformatics from 4Virology.net | Scoop.it
Global team of scientists find ecosystem below earth that is twice the size of world’s oceans
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Iterons homologous to helper geminivirus are essential for efficient replication of betasatellite

Betasatellites associated with geminiviruses can be replicated promiscuously by distinct geminiviruses but exhibit a preference for cognate helper viruses. However, the cis elements responsible for betasatellite origin recognition have not been characterized. In this study, we identified an iteron-like repeated sequence motif, 5′-GAGGACC-3′, in a tobacco curly shoot betasatellite (TbCSB) associated with tobacco curly shoot virus (TbCSV). Competitive DNA binding assays revealed that two core repeats 5′-GGACC-3′ are required for specific binding to TbCSV Rep, TbCSB iteron mutants accumulated to greatly reduced levels and lost the cognate helper-mediated replication preference. Interestingly, TbCSV also contains identical repeated sequences that are essential for specific Rep binding and in vivo replication. To gain an insight into the mechanism by which TbCSB has acquired the cognate iterons, we performed a SELEX assay to identify the high-affinity Rep binding ligands from a large pool of randomized sequences. Analysis of SELEX winners showed that all of the sequences contained at least one core iteron-like motif, suggesting that TbCSB has evolved to contain cognate iterons for high-affinity Rep binding. Further analyses of various betasatellite sequences revealed a region upstream of the satellite conserved region replete with iterative sequence motifs, including species-specific repeats and a general repeat 5′-GGTAAAT-3′. Remarkably, the species-specific repeats in many betasatellites are homologous to their respective cognate helper begomoviruses, whereas the general repeat is widespread in most of betasatellite molecules analyzed. These data collectively suggest that many betasatellites have evolved to acquire homologous iteron-like sequences for cognate helper virus-mediated efficient replication.

IMPORTANCE Geminivirus-encoded replication initiator protein (Rep) binds to repeated sequence elements (also known as iterons) in the origin of replication that serve as essential cis elements for specific viral replication. Betasatellites associated with begomoviruses can be replicated by cognate or noncognate helper viruses, but the cis elements responsible for betasatellite origin recognition have not been characterized. Using a betasatellite (TbCSB) associated with tobacco curly shoot virus (TbCSV) as a model, we identify two tandem repeats (iterons) in the Rep-binding motif (RBM) as required for specific Rep binding and efficient replication, and show that identical iteron sequences present in the TbCSV are also necessary for Rep binding and replication of helper virus. Extensive analysis of begomovirus/betasatellite sequences show that many betasatellites contain iteron-like elements homologous to their respective cognate helper begomoviruses. Our data suggest that many betasatellites have evolved to acquire homologous iteron-like sequences for cognate helper virus-mediated efficient replication.
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Commonly misunderstood parameters of NCBI BLAST and important considerations for users | Bioinformatics | Oxford Academic

Commonly misunderstood parameters of NCBI BLAST and important considerations for users | Bioinformatics | Oxford Academic | Viruses, Immunology & Bioinformatics from 4Virology.net | Scoop.it
Raúl A González-Pech, Timothy G Stephens, Cheong Xin Chan, John Hancock; Commonly misunderstood parameters of NCBI BLAST and important considerations for users
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