Virology and Bioinformatics from Virology.ca
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Genomic Variation in Seven Khoe-San Groups Reveals Adaptation and Complex African History

"The history of click-speaking Khoe-San, and African populations in general, remains poorly understood. We genotyped ∼2.3 million SNPs in 220 southern Africans and found that the Khoe-San diverged from other populations ≥100,000 years ago, but structure within the Khoe-San dated back to about 35,000 years ago. Genetic variation in various sub-Saharan populations did not localize the origin of modern humans to a single geographic region within Africa; instead, it indicated a history of admixture and stratification. We found evidence of adaptation targeting muscle function and immune response, potential adaptive introgression of UV-light protection, and selection predating modern human diversification involving skeletal and neurological development. These new findings illustrate the importance of African genomic diversity in understanding human evolutionary history."

 

Ex Africa, semper aliquid novi...or old, in this case!

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Virology and Bioinformatics from Virology.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: | Virology and Bioinformatics from Virology.ca | 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, 6:13 AM
Great work. Keep it going.
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Codon optimization of antigen coding sequences improves the immune potential of DNA vaccines...

Highly pathogenic avian influenza viruses are a serious threat to domestic poultry and can be a source of new human pandemic and annual influenza strains. Vaccination is the main strategy of protection against influenza, thus new generation vaccines, including DNA vaccines, are needed. One promising approach for enhancing the immunogenicity of a DNA vaccine is to maximize its expression in the immunized host. Results: The variant of the DNA vaccine containing almost 100 % of the GC content in the third position of codons stimulated strongest immune response in two animal models, mice and chickens. These results indicate that such modification can improve not only gene expression but also immunogenicity of DNA vaccine. Conclusion: Enhancement of the GC content in the third position of the codon might be a good strategy for development of a variant of a DNA vaccine against influenza that could be highly effective in distant hosts, such as birds and mammals, including humans.

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Standing on the Shoulders of Giant Viruses: Five Lessons Learned about Large Viruses Infecting Small Eukaryotes and the Opportunities They Create

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PHYPred: a tool for identifying bacteriophage enzymes and hydrolases

Bacteriophages are viruses that attack bacteria and kill them through the lytic replication cycle. Many studies have reported that phages are more specific to bacteria than antibiotics are; thus, phage therapy has many potential applications in human medicine, with the advantage of having few side effects (Keen, 2012). Investigating the mechanisms of bacteria-killing phages will therefore aid in the development of antibacterial drugs. Hydrolases encoded by phages play a key role in the interaction between phages and host bacteria. These enzymes act on the bacterial cell wall to kill the host bacteria and then release progeny phages (Nielsen et al., 1999). Thus, correctly identifying the hydrolases encoded by phages can provide important clues for not only studying the lytic mechanism of the phage-bacteria system but also discovering potential antibacterial drugs. With the accumulation of proteomics data, various machine-learning methods have been applied to predict functional phage proteins. Sequritan et al. designed an artificial neural network (ANN)-based method to predict viral structural proteins using amino acid frequency (Seguritan et al., 2012). Recently, a special type of structural protein, phage virion protein, was identified using primary sequence information (Ding et al., 2014; Feng et al., 2013). However, to our knowledge, no computational method has been developed to predict phage hydrolases. Thus, the aim of this letter is to describe a powerful model for identifying phage hydrolases. We started by discrimi-nating phage enzymes from phage non-enzymes. Once a phage protein is recognized as phage enzyme, the model will determine whether the predicted enzyme is phage hydrolase.

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Researchers Succeed in Growing Norovirus in Culture

Researchers Succeed in Growing Norovirus in Culture | Virology and Bioinformatics from Virology.ca | Scoop.it
Noroviruses are common; they are the primary cause of viral gastroenteritis in people and are infamous for ruining the vacations of cruise-goers. They pres
Via Gilbert C FAURE
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Researchers Discover How Zika Virus Causes Fetal Brain Damage

Researchers Discover How Zika Virus Causes Fetal Brain Damage | Virology and Bioinformatics from Virology.ca | Scoop.it
According to a team of researchers led by Yale University, infection by the Zika virus diverts a key protein necessary for neural cell division in the developing human fetus.

 

Marco Onorati et al. describe the derivation and characterization, including single-cell RNA-seq, of neocortical and spinal cord neuroepithelial stem (NES) cells to model early human neurodevelopment and Zika virus (ZIKV)-related neuropathogenesis. By analyzing human NES cells, organotypic fetal brain slices, and a ZIKV-infected micrencephalic brain, the team shows that ZIKV infects both neocortical and spinal NES cells as well as their fetal homolog, radial glial cells (RGCs), causing disrupted mitoses, supernumerary centrosomes, structural disorganization, and cell death. ZIKV infection of NES cells and RGCs causes centrosomal depletion and mitochondrial sequestration of phospho-TBK1 during mitosis.

 

The scientists also found that nucleoside analogs inhibit ZIKV replication in NES cells, protecting them from ZIKV-induced pTBK1 relocalization and cell death. They established a model system of human neural stem cells to reveal cellular and molecular mechanisms underlying neurodevelopmental defects associated with ZIKV infection and its potential treatment.


Via Dr. Stefan Gruenwald
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Newly discovered multicomponent virus is the first of its kind to infect animals

Newly discovered multicomponent virus is the first of its kind to infect animals | Virology and Bioinformatics from Virology.ca | Scoop.it
A story about Science from Phys.org, as featured in Newsfusion's Science News app.
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Tips for effective use of BLAST and other NCBI tools

The National Center for Biotechnology Information (NCBI) provides one of the most extensive sets of web-based tools for biological research. The tools are indispensable when planning genomics experiments, including for qPCR, NGS, and CRISPR. In this presentation, Dr Matt McNeill takes a practical look at getting started with the wealth of NCBI tools, and shares some relevant tips to help you sift through the tools and options that we regularly use. In particular, he focuses on commonly adjusted parameters that will allow you to more effectively use the powerful Basic Local Alignment Algorithm Tool (BLAST) to identify off-target hybridization/annealing events. Dr McNeill also covers practical examples using NCBI tools to design assays.


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CRISPR inspires new tricks to edit genes

CRISPR inspires new tricks to edit genes | Virology and Bioinformatics from Virology.ca | Scoop.it
CRISPR/Cas9 has been a rockstar gene-editing tool for just four years and it’s already being tweaked to do more things better.
Kathleen McLeod's insight:
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The Ins and Outs of Multipartite Plant Viruses

The Ins and Outs of Multipartite Plant Viruses | Virology and Bioinformatics from Virology.ca | Scoop.it
Viruses possessing a non-segmented genome require a specific recognition of their nucleic acid to ensure its protection in a capsid. A similar feature exists for viruses having a segmented genome, usually consisting of viral genomic segments joined together into one viral entity. While this appears as a rule for animal viruses, the majority of segmented…
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Smallpox eradication 'giant' Donald Henderson dies at 87 - BBC News

Smallpox eradication 'giant' Donald Henderson dies at 87 - BBC News | Virology and Bioinformatics from Virology.ca | Scoop.it

US doctor Donald Henderson, who led a successful campaign to wipe out #smallpox worldwide, has died at the age of 87.

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ZBP1/DAI is an innate sensor of influenza virus triggering the NLRP3 inflammasome and programmed cell death pathways

ZBP1/DAI is an innate sensor of influenza virus triggering the NLRP3 inflammasome and programmed cell death pathways | Virology and Bioinformatics from Virology.ca | Scoop.it
People infected with influenza get sick not only because of the presence of virus but also because of the inflammatory immune response. Now, Kuriakose et al . report that the protein ZBP1/DAI (Z-DNA binding protein 1/DNA-dependent activator of IFN regulatory factors) senses influenza A virus (IAV) and may contribute to this inflammatory pathogenesis. They found that ZBP1/DAI triggered cell death and inflammatory responses after IAV infection, and that ZBP1/DAI deficiency protected mice from IAV-related mortality. These mice had decreased inflammation and less epithelial damage than control animals. If these findings hold true in humans, ZBP1/DAI may be a host-directed target to decrease the severity of IAV pathogenesis.
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Deep mutational scanning identifies sites in influenza nucleoprotein that affect viral inhibition by MxA

bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution
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Development of Potent Antiviral Drugs Inspired by Viral Hexameric DNA-Packaging Motors with Revolving Mechanism

The intracellular parasitic nature of viruses and the emergence of antiviral drug resistance necessitate the development of new potent antiviral drugs. Recently, a method for developing potent inhibitory drugs by targeting biological machines with high stoichiometry and a sequential-action mechanism was described. Inspired by this finding, we reviewed the development of antiviral drugs targeting viral DNA-packaging motors. Inhibiting multisubunit targets with sequential actions resembles breaking one bulb in a series of Christmas lights, which turns off the entire string. Indeed, studies on viral DNA packaging might lead to the development of new antiviral drugs. Recent elucidation of the mechanism of the viral double-stranded DNA (dsDNA)-packaging motor with sequential one-way revolving motion will promote the development of potent antiviral drugs with high specificity and efficiency. Traditionally, biomotors have been classified into two categories: linear and rotation motors. Recently discovered was a third type of biomotor, including the viral DNA-packaging motor, beside the bacterial DNA translocases, that uses a revolving mechanism without rotation. By analogy, rotation resembles the Earth's rotation on its own axis, while revolving resembles the Earth's revolving around the Sun (see animations at http://rnanano.osu.edu/movie.html). Herein, we review the structures of viral dsDNA-packaging motors, the stoichiometries of motor components, and the motion mechanisms of the motors. All viral dsDNA-packaging motors, including those of dsDNA/dsRNA bacteriophages, adenoviruses, poxviruses, herpesviruses, mimiviruses, megaviruses, pandoraviruses, and pithoviruses, contain a high-stoichiometry machine composed of multiple components that work cooperatively and sequentially. Thus, it is an ideal target for potent drug development based on the power function of the stoichiometries of target complexes that work sequentially.
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The Mutational Robustness of Influenza A Virus

Author Summary Like other RNA viruses, influenza virus has a very high mutation rate. While high mutation rates may increase the rate at which influenza virus will adapt to a new host, acquire a new route of transmission, or escape from host immune surveillance, data from model systems suggest that most new viral mutations are either lethal or highly detrimental. Mutational robustness refers to the ability of a virus to tolerate, or buffer, these mutations. The mutational robustness of a virus will determine which mutations are maintained in a population and may have a greater impact on viral evolution than mutation rate. We defined the mutational robustness of influenza A virus by measuring the fitness of a large number of viruses, each with a single point mutation. We found that the overall robustness of influenza was similar to that of poliovirus and other viruses of similar size. Interestingly, mutations appeared to be more easily accommodated in hemagglutinin and neuraminidase than elsewhere in the genome. This work will inform models of influenza evolution at the global and molecular scale.
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New Virus Breaks The Rules Of Infection

New Virus Breaks The Rules Of Infection | Virology and Bioinformatics from Virology.ca | Scoop.it
A virus is generally like a little ball with a few genes. Now scientists have found one that's broken up into five little balls — as if it were dismembered.

Via Ian M Mackay, PhD
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Swine flu virus in India 'has become more virulent' since 2009 outbreak

Swine flu virus in India 'has become more virulent' since 2009 outbreak | Virology and Bioinformatics from Virology.ca | Scoop.it
Since December 2014, swine flu has claimed the lives of over 1,300 people in India, making it the worst outbreak of the virus in the country since 2009.
Via Ed Rybicki
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New kind of substances inhibits viruses and bacteria

New kind of substances inhibits viruses and bacteria | Virology and Bioinformatics from Virology.ca | Scoop.it

A new class of substances is effective against both the AIDS pathogen, HIV, and antibiotics-resistant MRSA bacteria. These two pathogensoften occur together. Scientists hope that it may be possible to control them with a single drug in the future. Scientists of the Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) developed so-called dual agents that inhibit the growth of both types of pathogens. They describe their findings in the renowned Journal of Medicinal Chemistry. The HIPS is the Saarbrücken branch of the Helmholtz Centre for Infection Research (HZI), which has its headquarters in Braunschweig. It was founded jointly by the HZI and Saarland University in 2009.

 

The human immunodeficiency virus HIV is one of the most dangerous and widespreadpathogens throughout the world. Some 37 million people are host to the virus and 1.2 million were killed by this disease in 2014 alone. Meanwhile, both the proliferation of the pathogen and the progression of the disease can be halted through a combination therapy, but the viruses show an increasing trend to develop resistance and no longer respond to the medications used against them.

 

The notorious MRSA bacteria, i.e. methicillin-resistant Staphylococcus aureus strains, show similar persistence as many common antibiotics have become ineffective. HIV patients, whose immune systemhas already been weakened by the disease, are often additionally afflicted by MRSA pathogens. These co-infections are very problematic and difficult to treat. "Resistance to the common therapies is quite widespread amongst both the viruses and the MRSA bacteria, which means that the co-infection is very difficult to control," explains HZI scientist Prof Rolf Hartmann, who is the head of the "Drug Design and Optimization" department at the HIPS. "In addition, it is necessary to carefully consider the interactions between the medications given to the patients."


Via Dr. Stefan Gruenwald
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Virus hunters search for the next deadly outbreak

Virus hunters search for the next deadly outbreak | Virology and Bioinformatics from Virology.ca | Scoop.it
Meet the researchers who enter the depths of the earth in search of deadly pathogens with the potential to cause outbreaks.

Via Ian M Mackay, PhD, Ed Rybicki
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Ed Rybicki's curator insight, August 25, 10:41 AM
And here in South Africa, what's more!! Although as a former explorer of bat-infested caves, I think rats may be a better target?
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Non-selective Packaging of Rift Valley Fever Virus Genome Segments

Author Summary The bunyavirus family is one of the largest virus families on Earth, of which several members cause severe disease in humans, animals or plants. Little is known about the mechanisms that facilitate the production of infectious bunyavirus virions, which should contain at least one copy of the small (S), medium (M) and large (L) genome segment. In this study, we investigated the genome packaging process of the Rift Valley fever virus (RVFV) by visualizing individual genome segments inside infected cells and virions. Experiments performed with wild-type virus, two- and four-segmented variants, and a variant with a codon-shuffled M segment showed that the production of infectious virions is a non-selective process and is unlikely to involve the formation of a supramolecular viral RNA complex. These observations have broad implications for understanding the bunyavirus replication cycle and may facilitate the development of new vaccines and the identification of novel antiviral targets.
Ed Rybicki's insight:
So: pretty much random, then? Interesting!
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Exploring the virome of diseased horses

Exploring the virome of diseased horses | Virology and Bioinformatics from Virology.ca | Scoop.it
Metagenomics was used to characterize viral genomes in clinical specimens of horses with various organ-specific diseases of unknown aetiology. A novel parvovirus as well as a previously described hepacivirus closely related to human hepatitis C viru

Via Bradford Condon
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Zika Virus: Two or Three Lineages?

Zika Virus: Two or Three Lineages? | Virology and Bioinformatics from Virology.ca | Scoop.it

Via Ed Rybicki
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Ed Rybicki's curator insight, August 23, 9:54 AM
This is interesting for a number of reasons: one, because it nails down slightly more convincingly where Zika came from; two, because it introduces the concept of a wider range of genotypes than we knew about; three, because vaccines that might be expected to protect against Asian and African 1 types, might conceivably not protect against African II. And given the lesson of dengue types and vaccines and the potential for ADE, that might not be a good thing....
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Fc receptors in antibody-dependent enhancement of viral infections - Taylor - 2015 - Immunological Reviews - Wiley Online Library

Fc receptors in antibody-dependent enhancement of viral infections - Taylor - 2015 - Immunological Reviews - Wiley Online Library | Virology and Bioinformatics from Virology.ca | Scoop.it

Via Gilbert C FAURE, Kenzibit
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Analysis of cis and trans Requirements for DNA Replication at the Right-End Hairpin of the Human Bocavirus 1 Genome

Analysis of cis and trans Requirements for DNA Replication at the Right-End Hairpin of the Human Bocavirus 1 Genome | Virology and Bioinformatics from Virology.ca | Scoop.it
IMPORTANCE Human bocavirus 1 (HBoV1) causes acute respiratory tract infections in young children. The duplex HBoV1 genome replicates in HEK293 cells and produces progeny virions that are infectious in well-differentiated airway epithelial cells. A recombinant AAV2 vector pseudotyped with an HBoV1 capsid has been developed to efficiently deliver the cystic fibrosis transmembrane conductance regulator gene to human airway epithelia. Here, we identified both cis-acting elements and trans-acting proteins that are required for HBoV1 DNA replication at the right-end hairpin in HEK293 cells. We localized the minimal replication origin, which contains both NS1 nicking and binding sites, to a 46-nucleotide sequence in the right-end hairpin. The identification of these essential elements of HBoV1 DNA replication acting both in cis and in trans will provide guidance to develop antiviral strategies targeting viral DNA replication at the right-end hairpin and to design next-generation recombinant HBoV1 vectors, a promising tool for gene therapy of lung diseases.

Ed Rybicki's insight:
Interesting because it throws a little doubt into long-established models of parvovirus replication - because it's an autonomously-replicating virus
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