Viruses, Immunology & Bioinformatics from 4Virology.net
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A baculovirus-mediated strategy for full-length plant virus coat protein expression and purification

A baculovirus-mediated strategy for full-length plant virus coat protein expression and purification | Viruses, Immunology & Bioinformatics from 4Virology.net | Scoop.it
Background

Garlic production is severely affected by virus infection, causing a decrease in productivity and quality. There are no virus-free cultivars and garlic-infecting viruses are difficult to purify, which make specific antibody production very laborious. Since high quality antisera against plant viruses are important tools for serological detection, we have developed a method to express and purify full-length plant virus coat proteins using baculovirus expression system and insects as bioreactors.

Conclusions

The expression of a plant virus full-length coat protein fused to the baculovirus Polyhedrin in recombinant baculovirus-infected insects was shown to produce high amounts of the recombinant protein which was easily purified and efficiently used to generate specific antibodies. Therefore, this strategy can potentially be used for the development of plant virus diagnostic kits for those viruses that are difficult to purify, are present in low titers or are present in mix infection in their plant hosts.

 

Baculovirus image from own collection

Ed Rybicki's insight:

I love the way plant virology / biotechnology now makes use of the whole spectrum of mol biol: this paper uses cDNA clones of an RNA plant virus, via E coli, to make recombinant baculoviruses, to express a fusion protein in insect cells - to make sera for detection of the plant virus by ELISA and other serological assays.

I'm biased because my lab uses ALL of these techniques (and I would have made the protein via agroinfiltration in plants), but this sort of science has really come of age.  One that I have lived through, incidentally, as cloning was VERY young when I started out - and ELISA had only just been invented.

I also know Renato quite well - so parabens, meu amigo!

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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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How to Build Community Trust to Fight Ebola in the Democratic Republic of Congo | Oxfam International Blogs

How to Build Community Trust to Fight Ebola in the Democratic Republic of Congo | Oxfam International Blogs | Viruses, Immunology & Bioinformatics from 4Virology.net | Scoop.it
The world’s second-biggest Ebola outbreak is still raging in DRC, with more than 1,400 cases and 900 deaths. Research has shown that distrust is one of the biggest obstacles in this Ebola fight. Oxfam’s Andrea Vera Nava outlines three ways to work with local communities to build their trust and...
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New giant virus may help scientists better understand the emergence of complex life

New giant virus may help scientists better understand the emergence of complex life | Viruses, Immunology & Bioinformatics from 4Virology.net | Scoop.it
The discovery of the Medusavirus holds clues to the evolution of more complex life. A paper published in the Journal of Virology earlier this year has been creating waves because of the ability of the Medusavirus to turn ...
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Does porcine circovirus type 3 (PCV3) interfere with porcine circovirus type 2 (PCV2) vaccine efficacy? 

PCV2 is globally spread pathogen involved in in a number of diseases (PCVD). Commonly used vaccines against PCV2 are proved to be highly efficacious. The role of recently discovered PCV3 for pig health and interference with PCV2 remains unknown. The study performed on serum samples from 7 farms vaccinated against PCV2 and 4 non-vaccinated showed very low prevalence of PCV2 viremia in the former (3 out of 106 positive serum pools) and high prevalence of PCV2 viremia in the latter (35 out of 60 positive pools). Mean log10 PCV2 genome equivalents were lower in vaccinated farms (4.8±0.6 log10 copies/ml) than in non-vaccinated farms (6.3±1.3 log10 copies/ml). PCV3 was detected in 31 out of 106 and 12 out of 60 serum pools from vaccinated and non-vaccinated farms, respectively. Mean log10 PCV3 genome equivalents were significantly (p<0.05) lower in vaccinated farms (3.9±0.8 log10 copies/ml) than in non-vaccinated farms (4.4±0.6 log10 copies/ml). Concurrent PCV2 and PCV3 infection was rare and found only in 1 out of 529 and 4 out of 292 individual serum samples from vaccinated and non-vaccinated farms, respectively. Our results showed lack of impact of PCV3 circulation on PCV2 vaccine efficacy. On the other hand, intensive PCV2 circulation and high viremia detected in non-vaccinated farms did not seem to increase the level of PCV3 infection. This article is protected by copyright. All rights reserved.

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Ebola Deaths Top 1,000 in Congo Amid Clinic Attacks - The New York Times

Ebola Deaths Top 1,000 in Congo Amid Clinic Attacks - The New York Times | Viruses, Immunology & Bioinformatics from 4Virology.net | Scoop.it
Hostility toward health workers continued to hamper efforts to contain the second-deadliest outbreak of the virus.
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Ten quick tips for biocuration

Shortcomings in data utility, reusability, and quality can be addressed by biocuration, which is the process of identifying, organising, correcting, annotating, standardising, and enriching biological data [1]. The primary aim of biocuration is to extract valuable knowledge from the corpus of available biological data and to accurately represent it in a computable manner so that it may be easy to understand and disseminate. Such knowledge includes experimental data on genes and proteins (both structural and functional) and on biological concepts like pathways, as well as experimental metadata, which provides important context for data interpretation and integrative analytics.
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Molluscum contagiosum virus MC80 sabotages MHC-I antigen presentation by targeting tapasin for ER-associated degradation. - PubMed - NCBI

Molluscum contagiosum virus MC80 sabotages MHC-I antigen presentation by targeting tapasin for ER-associated degradation. - PubMed - NCBI | Viruses, Immunology & Bioinformatics from 4Virology.net | Scoop.it
PLoS Pathog. 2019 Apr 29;15(4):e1007711. doi: 10.1371/journal.ppat.1007711. [Epub ahead of print]
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NGPhylogeny.fr: new generation phylogenetic services for non-specialists

Phylogeny.fr, created in 2008, has been designed to facilitate the execution of phylogenetic workflows, and is nowadays widely used. However, since its development, user needs have evolved, new tools and workflows have been published, and the number of jobs has increased dramatically, thus promoting new practices, which motivated its refactoring. We developed NGPhylogeny.fr to be more flexible in terms of tools and workflows, easily installable, and more scalable. It integrates numerous tools in their latest version (e.g. TNT, FastME, MrBayes, etc.) as well as new ones designed in the last ten years (e.g. PhyML, SMS, FastTree, trimAl, BOOSTER, etc.). These tools cover a large range of usage (sequence searching, multiple sequence alignment, model selection, tree inference and tree drawing) and a large panel of standard methods (distance, parsimony, maximum likelihood and Bayesian). They are integrated in workflows, which have been already configured (‘One click’), can be customized (‘Advanced’), or are built from scratch (‘A la carte’). Workflows are managed and run by an underlying Galaxy workflow system, which makes workflows more scalable in terms of number of jobs and size of data. NGPhylogeny.fr is deployable on any server or personal computer, and is freely accessible at https://ngphylogeny.fr.
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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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Fighting staph infections with the body's immune system

Fighting staph infections with the body's immune system | Viruses, Immunology & Bioinformatics from 4Virology.net | Scoop.it
Researchers have gained a greater understanding of the biology of staphylococcus skin infections in mice and how the mouse immune system mobilizes to fight them. A study appears this week in the PNAS.

Via Krishan Maggon
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‘Massive’ Ebola Outbreak In Congo Has Killed 1,136 And Is ‘Out Of Control’ Due To Violence, ‘Political Games’

‘Massive’ Ebola Outbreak In Congo Has Killed 1,136 And Is ‘Out Of Control’ Due To Violence, ‘Political Games’ | Viruses, Immunology & Bioinformatics from 4Virology.net | Scoop.it
The second-worst Ebola outbreak in history is only getting worse, even though a new vaccine has proven more than 97 percent effective, experts say. Despite a new vaccine against the deadly Ebola ...
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Naproxen Exhibits Broad Anti-influenza Virus Activity in Mice by Impeding Viral Nucleoprotein Nuclear Export - FluTrackers News and Information

Naproxen Exhibits Broad Anti-influenza Virus Activity in Mice by Impeding Viral Nucleoprotein Nuclear Export - FluTrackers News and Information | Viruses, Immunology & Bioinformatics from 4Virology.net | Scoop.it
Cell Rep. (https://www.ncbi.nlm.nih.gov/pubmed/31067470#) 2019 May 7;27(6):1875-1885.e5. doi: 10.1016/j.celrep.2019.04.053. Naproxen Exhibits Broad Anti-influenza Virus Activity in Mice by Impeding Viral Nucleoprotein Nuclear Export.
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Herpes Virus Kills 2nd Young Elephant at Indianapolis Zoo

Herpes Virus Kills 2nd Young Elephant at Indianapolis Zoo | Viruses, Immunology & Bioinformatics from 4Virology.net | Scoop.it
Just a week after the death of their 6-year-old African elephant, Nyah, the Indianapolis Zoo delivered another sad message: Its other youngest African elephant, 8-year-old Kalina, has died.
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Rabies: CDC temporarily bans dogs from Egypt

Rabies: CDC temporarily bans dogs from Egypt | Viruses, Immunology & Bioinformatics from 4Virology.net | Scoop.it
On Friday, the Centers for Disease Control and Prevention (CDC) issued a temporary ban on the importation of  dogs from Egypt due to the risk of importing rabies.Given three recent cases of rabid dogs imported from Egypt since May of 2015, CDC is taking this action to protect public health and prevent...
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An HRM Assay to Differentiate Sheeppox Virus Vaccine Strains from Sheeppox Virus Field Isolates and other Capripoxvirus Species

An HRM Assay to Differentiate Sheeppox Virus Vaccine Strains from Sheeppox Virus Field Isolates and other Capripoxvirus Species | Viruses, Immunology & Bioinformatics from 4Virology.net | Scoop.it
As live poxviruses may cause adverse reactions in vaccinated animals, it is imperative to develop new diagnostic tools for the differentiation of SPPV field strains from attenuated vaccine strains. Within the capripoxvirus (CaPV) homolog of the variola virus B22R gene, we identified a unique region in SPPV vaccines with two deletions of 21 and 27 nucleotides and developed a High-Resolution Melting (HRM)-based assay. The HRM assay produces four distinct melting peaks, enabling the differentiation between SPPV vaccines, SPPV field isolates, GTPV and LSDV. This HRM assay is sensitive, specific, and provides a cost-effective means for the detection and classification of CaPVs and the differentiation of SPPV vaccines from SPPV field isolates.
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Development of vaccines against African swine fever virus. - PubMed - NCBI

Development of vaccines against African swine fever virus. - PubMed - NCBI | Viruses, Immunology & Bioinformatics from 4Virology.net | Scoop.it
Virus Res. 2019 May;265:150-155. doi: 10.1016/j.virusres.2019.03.022. Epub 2019 Mar 25. Review
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DNAscan: personal computer compatible NGS analysis, annotation and visualisation

"We developed a fast and efficient bioinformatics pipeline that allows for the analysis of DNA sequencing data, while requiring little computational effort and memory usage. DNAscan can analyse a whole exome sequencing sample in 1 h and a 40x whole genome sequencing sample in 13 h, on a midrange computer. The pipeline can look for single nucleotide variants, small indels, structural variants, repeat expansions and viral genetic material (or any other organism). Its results are annotated using a customisable variety of databases and are available for an on-the-fly visualisation with a local deployment of the gene.iobio platform. DNAscan is implemented in Python. Its code and documentation are available on GitHub:
https://github.com/KHP-Informatics/DNAscan"

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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...
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Phylodynamics applications to crack the transmission in community, nice read for the Bayesian approach enthusiasts!!
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