Viruses, Immunology & Bioinformatics from 4Virology.net
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Vaccination with Adenovirus Serotypes 35, 26, and 48 Elicits Higher Levels of Innate Cytokine Responses than Adenovirus Serotype 5 in Rhesus Monkeys

Vaccination with Adenovirus Serotypes 35, 26, and 48 Elicits Higher Levels of Innate Cytokine Responses than Adenovirus Serotype 5 in Rhesus Monkeys | Viruses, Immunology & Bioinformatics from 4Virology.net | Scoop.it

"These data demonstrate that Ad35, Ad26, and Ad48, which utilize CD46 as their primary cellular receptor, induce significantly greater innate cytokine responses than Ad5, which uses the coxsackievirus and adenovirus receptor (CAR). These differences in innate triggering result in markedly different immunologic milieus for the subsequent generation of adaptive immune responses by these vaccine vectors."

 

Important news for the vectored vaccine community in general, and for HIV vaccine in particular: Ad5 was the vehicle of choice; now it looks as though it shouldn't be.

 

Adenovirus graphic courtesy of Russell Kightley Media

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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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Bemol Sido's comment, October 10, 2015 5:28 AM
Thanks. Nice.
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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ORCA: A Comprehensive Bioinformatics Container Environment for Education and Research | Bioinformatics | Oxford Academic

ORCA: A Comprehensive Bioinformatics Container Environment for Education and Research | Bioinformatics | Oxford Academic | Viruses, Immunology & Bioinformatics from 4Virology.net | Scoop.it
AbstractSummary. The ORCA bioinformatics environment is a Docker image that contains hundreds of bioinformatics tools and their dependencies. The ORCA image an
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Uganda reports Crimean Congo Hemorrhagic Fever (CCHF) fatality in Wakiso District

Uganda reports Crimean Congo Hemorrhagic Fever (CCHF) fatality in Wakiso District | Viruses, Immunology & Bioinformatics from 4Virology.net | Scoop.it
The Uganda Ministry of Health issued a press release Monday saying that there was one confirmed Crimean Congo Hemorrhagic Fever (CCHF) case who died on Apr. 11. The deceased was a 32-year-old man from Bendegere village, Kasenyi Parish-Katabi sub country in Wakiso District.
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Motto: Representing motifs in consensus sequences with minimum information loss | bioRxiv

bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution
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Ten quick tips for creating an effective lesson

Author summary As a species, we know as much about teaching and learning as we do about public health, but most people who teach at the postsecondary level are never introduced to even the basics of evidence-based pedagogy. Knowing just a few key facts will help you build more effective lessons in less time and with less pain and will also make those lessons easier for your peers to find and reuse. This paper presents 10 tips that you can apply immediately and explains why they work.
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Bayesian inference of transmission chains using timing of symptoms, pathogen genomes and contact data

Bayesian inference of transmission chains using timing of symptoms, pathogen genomes and contact data | Viruses, Immunology & Bioinformatics from 4Virology.net | Scoop.it
Author summary Reconstructing the history of transmission events in an infectious disease outbreak provides valuable information for informing infection control policy. Recent years have seen considerable progress in the development of statistical tools for the inference of such transmission trees...
Fredrick Nindo's insight:
Phylodynamics applications to crack the transmission in community, nice read for the Bayesian approach enthusiasts!!
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Virus tricks the immune system into ignoring bacterial infections

Virus tricks the immune system into ignoring bacterial infections | Viruses, Immunology & Bioinformatics from 4Virology.net | Scoop.it
The finding could explain why the body tolerates some microbes ― and lead to better treatments for chronic infections.

Via Krishan Maggon , Gilbert C FAURE
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Viruses | Free Full-Text | Immune Activation, Inflammation, and Non-AIDS Co-Morbidities in HIV-Infected Patients under Long-Term ART

Viruses | Free Full-Text | Immune Activation, Inflammation, and Non-AIDS Co-Morbidities in HIV-Infected Patients under Long-Term ART | Viruses, Immunology & Bioinformatics from 4Virology.net | Scoop.it
Despite effective antiretroviral therapy (ART), people living with HIV (PLWH) still present persistent chronic immune activation and inflammation. This condition is the result of several factors including thymic dysfunction, persistent antigen stimulation due to low residual viremia, microbial translocation and dysbiosis, caused by the disruption of the gut mucosa, co-infections, and cumulative ART toxicity. All of these factors can create a vicious cycle that does not allow the full control of immune activation and inflammation, leading to an increased risk of developing non-AIDS co-morbidities such as metabolic syndrome and cardiovascular diseases. This review aims to provide an overview of the most recent data about HIV-associated inflammation and chronic immune exhaustion in PLWH under effective ART. Furthermore, we discuss new therapy approaches that are currently being tested to reduce the risk of developing inflammation, ART toxicity, and non-AIDS co-morbidities.

Via Gilbert C FAURE
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CIRCUS: a package for Circos display of structural genome variations from paired-end and mate-pair sequencing data | BMC Bioinformatics | Full Text

CIRCUS: a package for Circos display of structural genome variations from paired-end and mate-pair sequencing data | BMC Bioinformatics | Full Text | Viruses, Immunology & Bioinformatics from 4Virology.net | Scoop.it
Detection of large genomic rearrangements, such as large indels, duplications or translocations is now commonly achieved by next generation sequencing (NGS) approaches. Recently, several tools have been developed to analyze NGS data but the resulting files are difficult to interpret without an additional visualization step. Circos (Genome Res, 19:1639–1645, 2009), a Perl script, is a powerful visualization software that requires setting up numerous configuration files with a large number of parameters to handle. R packages like RCircos (BMC Bioinformatics, 14:244, 2013) or ggbio (Genome Biol, 13:R77, 2012) provide functions to display genomic data as circular Circos-like plots. However, these tools are very general and lack the functions needed to filter, format and adjust specific input genomic data. We implemented an R package called CIRCUS to analyze genomic structural variations. It generates both data and configuration files necessary for Circos, to produce graphs. Only few R pre-requisites are necessary. Options are available to deal with heterogeneous data, various chromosome numbers and multi-scale analysis. CIRCUS allows fast and versatile analysis of genomic structural variants with Circos plots for users with limited coding skills.
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Immunotherapy kicks and kills HIV by exploiting a common virus

Immunotherapy kicks and kills HIV by exploiting a common virus | Viruses, Immunology & Bioinformatics from 4Virology.net | Scoop.it
Credit: Donna Stolz, Ph.D./University of Pittsburgh, Center for Biologic Imaging PITTSBURGH, April 3, 2019 - In a first on the quest to cure HIV, University of Pittsburgh Graduate School of Public Hea | Bioengineering...

Via Krishan Maggon
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Educational Material about Influenza Viruses

Educational Material about Influenza Viruses | Viruses, Immunology & Bioinformatics from 4Virology.net | Scoop.it
To supplement a special edition of the journal Viruses, entitled “What’s New with Flu?”, influenza virus researchers have worked together to generate simple educational material to communicate their science to school students.

Via Ed Rybicki
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Many in Congo Do Not Believe Ebola Virus Is Real

Many in Congo Do Not Believe Ebola Virus Is Real | Viruses, Immunology & Bioinformatics from 4Virology.net | Scoop.it
The area currently has the second-deadliest Ebola outbreak in history.
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Protein Multiple Alignments: Sequence-based vs Structure-based Programs | Bioinformatics | Oxford Academic

Protein Multiple Alignments: Sequence-based vs Structure-based Programs | Bioinformatics | Oxford Academic | Viruses, Immunology & Bioinformatics from 4Virology.net | Scoop.it
AbstractMotivation. Multiple sequence alignment programs have proved to be very useful and have already been evaluated in the literature yet not alignment prog
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Full genome sequence analysis and putative host-shifting of Milk vetch dwarf virus infecting tobacco (Nicotiana tabacum) in China | Virology Journal | Full Text

Full genome sequence analysis and putative host-shifting of Milk vetch dwarf virus infecting tobacco (Nicotiana tabacum) in China | Virology Journal | Full Text | Viruses, Immunology & Bioinformatics from 4Virology.net | Scoop.it
Tobacco production in China has been affected by plant viruses with Milk vetch dwarf virus (MDV) as a recent invader posing serious concern. According to most of the studies, MDV mainly infects hosts from Fabaceae family but in our previous study we reported its infection in tobacco plant...
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EMBL-EBI search and sequence analysis tools APIs in 2019 | Nucleic Acids Research | Oxford Academic

EMBL-EBI search and sequence analysis tools APIs in 2019 | Nucleic Acids Research | Oxford Academic | Viruses, Immunology & Bioinformatics from 4Virology.net | Scoop.it
Abstract. The EMBL-EBI provides free access to popular bioinformatics sequence analysis applications as well as to a full-featured text search engine with powe
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Meet the scientist painter who turns deadly viruses into beautiful works of art

Meet the scientist painter who turns deadly viruses into beautiful works of art | Viruses, Immunology & Bioinformatics from 4Virology.net | Scoop.it
David Goodsell’s scientifically precise watercolor paintings of the cells and microbes he studies grace journal covers and impress colleagues
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Microbes May Take Some of the Blame for the Reproducibility Crisis

Microbes May Take Some of the Blame for the Reproducibility Crisis | Viruses, Immunology & Bioinformatics from 4Virology.net | Scoop.it
Scientists find varied microbiota among the same strain of mice from four vendors--and that variability affects their susceptibility to infection.
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Systems Immunology: Understanding Responses to Vaccination and Infection

The Scientist is bringing together a panel of experts to discuss their research and experiences in using systems immunology to gain new insights into immune responses to infection through single-cell data analysis, and into innate immune dysfunction in HIV infection.

Via Gilbert C FAURE
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CD4+ resident memory T cells dominate immunosurveillance and orchestrate local recall responses

CD4+ resident memory T cells dominate immunosurveillance and orchestrate local recall responses | Viruses, Immunology & Bioinformatics from 4Virology.net | Scoop.it
This study examines the extent to which memory CD4+ T cells share immunosurveillance strategies with CD8+ resident memory T cells (TRM). After acute viral infection, memory CD4+ T cells predominantly used residence to survey nonlymphoid tissues, albeit not as stringently as observed for CD8+ T...

Via Gilbert C FAURE
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TagGraph reveals vast protein modification landscapes from large tandem mass spectrometry datasets

TagGraph reveals vast protein modification landscapes from large tandem mass spectrometry datasets | Viruses, Immunology & Bioinformatics from 4Virology.net | Scoop.it
A string-based computational tool enables swift, robust identification of post-translational modifications in MS/MS datasets.
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HPV vaccine linked to 'dramatic' drop in cervical disease

HPV vaccine linked to 'dramatic' drop in cervical disease | Viruses, Immunology & Bioinformatics from 4Virology.net | Scoop.it
Researchers said the vaccine has nearly wiped out cases of cervical pre-cancer in young women since an immunisation programme was introduced 10 years ago.

They found the vaccine had led to a 90% cut in pre-cancerous cells.
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Avoiding preventable deaths: The scourge of counterfeit rabies vaccines - ScienceDirect

Avoiding preventable deaths: The scourge of counterfeit rabies vaccines - ScienceDirect | Viruses, Immunology & Bioinformatics from 4Virology.net | Scoop.it
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Ebola Treatment Center in Congo Reopens After Attack 

Ebola Treatment Center in Congo Reopens After Attack  | Viruses, Immunology & Bioinformatics from 4Virology.net | Scoop.it
Center run by MSF in district of Katwa was set on fire Feb.24 by unknown attackers...
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Illumina sequencing of clinical samples for virus detection in a public health laboratory

Illumina sequencing of clinical samples for virus detection in a public health laboratory | Viruses, Immunology & Bioinformatics from 4Virology.net | Scoop.it
High-throughput sequencing (HTS) provides the opportunity, once a diagnostic result is obtained, to extract additional information from a virus-containing sample. Hence, it offers advantages over established quantitative amplification technology, such as quantitative PCR, particularly in a public health environment. At this early stage of its clinical application, there have been limited studies comparing HTS performance to that of the more established quantitative PCR technology for direct detection of viruses. In this pilot-scale study, we tested HTS with a range of viruses and sample types routinely encountered in a public health virology laboratory. In comparison with quantitative PCR, our HTS method was able to sensitively (92%) detect all viruses in any sample type with the exception of certain tissues. Moreover, sufficient nucleotide sequence information was obtained to enable genotyping of strains detected, thus providing additional useful epidemiological information. While HTS sensitivity may not yet match that of PCR, the added value through enhanced epidemiological data has considerable potential to enable real-time surveillance of circulating strains so as to facilitate rapid and appropriate response to outbreaks and virus zoonotic spillover events.
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