Virology and Bioinformatics from Virology.ca
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$1000 Genomes for $2000

$1000 Genomes for $2000 | Virology and Bioinformatics from Virology.ca | Scoop.it
Getting an accurate genome sequence requires that you collect the data at least twice argue Robasky, Lewis, and Church in their recent opinion piece in Nat. Rev. Genetics [1]. The DNA sequencing world kicked off 2014 with an audacious start.
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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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Tools to annotate genes and genetic variants 

Tools to annotate genes and genetic variants  | Virology and Bioinformatics from Virology.ca | Scoop.it

Recently published in Genome Biology, Ginger Tsueng and colleagues discuss two high-performance web services for querying gene and variant annotation. Ginger explains more in this blog about the ideas behind the software, and how they advance the field.


Via Integrated DNA Technologies
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Nature Microbiology: Fungal pathogenesis: Host modulation every which way (2016)

Nature Microbiology: Fungal pathogenesis: Host modulation every which way (2016) | Virology and Bioinformatics from Virology.ca | Scoop.it

The plant pathogenic fungus Fusarium oxysporum secretes an effector that is similar to a plant peptide hormone, underscoring the variety of mechanisms that plant pathogens have evolved to tamper with host physiology.

 

Plant pathogens cause devastating diseases of crop plants and threaten food security in an era of continuous population growth. Annual losses due to fungal and oomycete diseases amount to enough food calories to feed at least half a billion people. Understanding how plant pathogens infect and colonize plants should help to develop disease-resistant crops. It appears that plant pathogens are sophisticated manipulators of their hosts. They secrete effector molecules that alter host biological processes in a variety of ways, generally promoting the pathogen lifestyle. A new study by Masachis, Segorbe and colleagues describes a new mechanism by which plant pathogens interfere with plant physiology. They discovered that the root-infecting fungus F. oxysporum secretes a peptide similar to the plant regulatory peptide RALF (rapid alkalinization factor) to induce host tissue alkalinization and enhance plant colonization. This study demonstrates that in addition to secreting classical plant hormones (or mimics thereof), fungi have also evolved functional homologues of plant peptides to alter host cellular processes.


Via Kamoun Lab @ TSL, Franc Viktor Nekrep
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CDC Head Tom Frieden Delivers Emotional Plea For Zika Funding

CDC Head Tom Frieden Delivers Emotional Plea For Zika Funding | Virology and Bioinformatics from Virology.ca | Scoop.it
"Three months in an epidemic is an eternity."
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Tiny Wire Can Detect A Single Virus In Your Urine

Tiny Wire Can Detect A Single Virus In Your Urine | Virology and Bioinformatics from Virology.ca | Scoop.it
Testing technique could make a versatile new diagnostic tool

Via Ed Rybicki, Kenzibit
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Determinants of Arbovirus Vertical Transmission in Mosquitoes

Determinants of Arbovirus Vertical Transmission in Mosquitoes | Virology and Bioinformatics from Virology.ca | Scoop.it
Vertical transmission (VT) and horizontal transmission (HT) of pathogens refer to parental and non-parental chains of host-to-host transmission.
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Sweet Honey Is Bacteria's Worst Nightmare

Sweet Honey Is Bacteria's Worst Nightmare | Virology and Bioinformatics from Virology.ca | Scoop.it
Honey contains multiple defense systems for fighting off bacteria, making it a natural and powerful antibacterial agent.
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Omics! Omics!: Around the World in Amino Acids

This post is pure whimsy, growing out of killing time on a train ride. The not-so-serious question: what is the geography of amino acids?  If I search for them by name in Google Maps, what will I find?  With just Google Maps, plus some Google Translate thrown in, I found a few surprises.

Alanine
Marche Alanine, Goma, Congo
This was the first search and perhaps the most striking surprise -- why is there a market deep in Africa named Alanine?  
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Both CD8+ and CD4+ T-Cells Contribute to Corneal Clouding and Viral Clearance Following Vaccinia Virus Infection in C57BL/6 Mice

Potentially blinding eye infections can occur after vaccination for Smallpox. Very little is known about the pathologic mechanisms that are involved and the information that is available was generated using rabbit models. The lack of immunological reagents for rabbits makes such studies difficult. We have characterized a mouse model of vaccinia virus ocular disease using C57BL/6 mice and strain WR and show that both CD4+ and CD8+ T-cell subsets play a role in the blinding eye disease and controlling virus replication. Based on these results vaccinia virus keratitis is significantly different from Herpes simplex virus keratitis and further studies using this model should generate novel insights into immunopathological responses to viral ocular infection.
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The Zombie Literature

The Zombie Literature | Virology and Bioinformatics from Virology.ca | Scoop.it
its authors maintain the voracity and robustness of its findings
Ed Rybicki's insight:
As they should, for a zombie lit paper B-)
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Can Zika Be Misdiagnosed? The Virus Shares Similar Markers With Dengue Fever

Can Zika Be Misdiagnosed? The Virus Shares Similar Markers With Dengue Fever | Virology and Bioinformatics from Virology.ca | Scoop.it
The Zika virus has rapidly spreading throughout South America and the Caribbean over the past year, and recently it’s slowly been making its way into the
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For Zika-infected pregnancies, microcephaly risk may be as high as 13 percent

For Zika-infected pregnancies, microcephaly risk may be as high as 13 percent | Virology and Bioinformatics from Virology.ca | Scoop.it
untries where Zika is being transmitted locally have suffered the same spike in microcephaly -- but that could change soon. "If the risk of infection and adverse outcomes is similar in the other geographic areas where Zika virus has since spread, many more cases of microcephaly and other adver

Via Ian M Mackay, PhD
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Recent Advances in Immunotherapy for Kidney Cancer

Recent Advances in Immunotherapy for Kidney Cancer | Virology and Bioinformatics from Virology.ca | Scoop.it
Abstract: Immunotherapy has been a mainstay of treatment for metastatic renal cell carcinoma (mRCC) since the introduction of high-dose interleukin-2. Recently, improved knowledge of immune regulation and tumor-host immune interactions has led to the development of several novel immunotherapies. Immune checkpoint blockade showed promise in early clinical trials - eventually leading to FDA approval of nivolumab (anti-PD-1) as a second-line treatment for mRCC. Despite encouraging results, PD-1 blockade alone does not achieve durable responses in the majority of patients treated. Improved biomarkers for patient selection, tumor vaccines and combination therapy may augment the efficacy of existing immunotherapies. This review summarizes recent progress in immunotherapy for RCC, focusing on a discussion of emerging agents.

Via Krishan Maggon
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WHO rejects call to move Rio Olympics because of Zika

WHO rejects call to move Rio Olympics because of Zika | Virology and Bioinformatics from Virology.ca | Scoop.it
Health experts urged the UN agency to act over concern that the games will speed up spread of virus linked to birth defects
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Bacterial Outer Membrane Vesicles Mediate Cytosolic Localization of LPS and Caspase-11 Activation: Cell

Bacterial Outer Membrane Vesicles Mediate Cytosolic Localization of LPS and Caspase-11 Activation: Cell | Virology and Bioinformatics from Virology.ca | Scoop.it
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Will Zika virus cast a shadow over the Rio Olympics?

Will Zika virus cast a shadow over the Rio Olympics? | Virology and Bioinformatics from Virology.ca | Scoop.it
travellers will be returning well before our peak periods of mosquito activity in central and north Queensland where those mosquitoes are present. Notwithstanding the preparedness of local authorities

Via Ian M Mackay, PhD
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Targeted virus detection in next-generation sequencing data using an automated e-probe based approach

Targeted virus detection in next-generation sequencing data using an automated e-probe based approach | Virology and Bioinformatics from Virology.ca | Scoop.it
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Structure of the T4 baseplate and its function in triggering sheath contraction

Structure of the T4 baseplate and its function in triggering sheath contraction | Virology and Bioinformatics from Virology.ca | Scoop.it
Several systems, including contractile tail bacteriophages, the type VI secretion system and R-type pyocins, use a multiprotein tubular apparatus to attach to and penetrate host cell membranes. This macromolecular machine resembles a stretched, coiled spring (or sheath) wound around a rigid tube with a spike-shaped protein at its tip. A baseplate structure, which is arguably the most complex part of this assembly, relays the contraction signal to the sheath. Here we present the atomic structure of the approximately 6-megadalton bacteriophage T4 baseplate in its pre- and post-host attachment states and explain the events that lead to sheath contraction in atomic detail. We establish the identity and function of a minimal set of components that is conserved in all contractile injection systems and show that the triggering mechanism is universally conserved.
Ed Rybicki's insight:
REALLY cool stuff: I've been fascinated by the "nanosyringe" character of phages with contractile tails since I was an undergraduate - and now 42 years later, we're seeing how those mechanisms actually work!
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Why humans (and not mice) are susceptible to Zika - Scienmag

Why humans (and not mice) are susceptible to Zika - Scienmag | Virology and Bioinformatics from Virology.ca | Scoop.it
Flaviviruses--such as Zika, dengue, and yellow fever--have emerged as human (and other primate) pathogens because of their ability to specifically overcome our anti-viral defenses. In the case of Zika..
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Gilbert C FAURE's curator insight, May 20, 1:45 AM
zika anf IFNs!
... one of the virus's seven non-structural proteins (NS5) is singularly responsible for blocking the action of interferons (proteins that stop viral replication) in human cells, while mouse cells are unaffected.
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Newly discovered microbe does something textbooks say is impossible: it lives without mitochondria

Newly discovered microbe does something textbooks say is impossible: it lives without mitochondria | Virology and Bioinformatics from Virology.ca | Scoop.it
Cells have adapted to find new ways of life.
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Evaluation of hybrid and non-hybrid methods for de novo assembly of nanopore reads. - PubMed - NCBI

AVAILABILITY:
https://github.com/kkrizanovic/NanoMark CONTACT: mile.sikic@fer.hr SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Becoming Acculturated: culturing the dark matter of microbiomes

Becoming Acculturated: culturing the dark matter of microbiomes | Virology and Bioinformatics from Virology.ca | Scoop.it
Techniques for deep dives into the microbial dark matter
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Viral quasispecies complexity measures

Mutant spectrum dynamics (changes in the related mutants that compose viral populations) has a decisive impact on virus behavior. The several platforms of next generation sequencing (NGS) to study viral quasispecies offer a magnifying glass to study viral quasispecies complexity. Several parameters are available to quantify the complexity of mutant spectra, but they have limitations. Here we critically evaluate the information provided by several population diversity indices, and we propose the introduction of some new ones used in ecology. In particular we make a distinction between incidence, abundance and function measures of viral quasispecies composition. We suggest a multidimensional approach (complementary information contributed by adequately chosen indices), propose some guidelines, and illustrate the use of indices with a simple example. We apply the indices to three clinical samples of hepatitis C virus that display different population heterogeneity. Areas of virus biology in which population complexity plays a role are discussed.
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