A knowledge resource to understand virus diversity...
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The notion that sequence homology implies functional similarity underlies much of computational biology. In the case of protein-protein interactions, an interaction can be inferred between two proteins on the basis that sequence-similar proteins have been observed to interact. The use of transferred interactions is common, but the legitimacy of such inferred interactions is not clear. Here we investigate transferred interactions and whether data incompleteness explains the lack of evidence found for them.
The American Society for Microbiology is dedicated to the utilization of microbiology and microbiological sciences for the promotion of human welfare and for the accumulation of knowledge.
ASM has extended the discounted student member rate through the Institutional Student Membership program through December 31, 2012. Professors, department chairs, mentors, or anyone working with students can purchase four student memberships for the price of three, or for $15 each - a discount of $5 per student membership. This offer is good until December 31, 2012, so act fast!
If you ever have to explain which data viz technique to use under what circumstance to someone - then Stanford's Visualization Zoo tour is well worth a few minutes. The tour showcases techniques for visualizing and interacting with diverse data sets. In many situations, not only will simple data graphics suffice, they may be preferable. However the tour also includes some of the more sophisticated and unusual techniques that have been developed to deal with complex data sets. Well worth reading. Click on the image or the title to learn more
|Scooped by Ed Rybicki|
"Plant-mediated interactions between herbivorous arthropods and pathogens transmitted by herbivores are important determinants of the population dynamics of both types of organisms in the field. The role of plant defence in mediating these types of tripartite interactions have been recognized but rarely examined especially at the physiological and molecular levels. Our previous work shows that a worldwide invasive whitefly can establish mutualism with the begomovirus Tomato yellow leaf curl China virus (TYLCCNV) via crop plants. Here, we show that TYLCCNV and betasatellite co-infection suppresses jasmonic acid defences in the plant. Impairing or enhancing defences mediated by jasmonic acid in the plant enhances or depresses the performance of the whitefly. We further demonstrate that the pathogenicity factor βC1 encoded in the betasatellite is responsible for the initiation of suppression on plant defences and contributes to the realization of the virus–vector mutualism. By integrating ecological, mechanistic and molecular approaches, our study reveals a major mechanism of the plant-mediated mutualism between a virus and its vector. As the test plant is an important economic crop, the results also have substantial implications for developing novel strategies for management of crop viruses and the insect vectors associated with them."
I noted previously in Virology News and here that researchers in China had found in 2007 that the B biotype of Bemisia tabaci greatly enhanced its own survival by transmitting begomoviruses - and now this group have figured out why. Fascinating interaction between a tiny virus, an even smaller satellite DNA, and host plants and insect vectors. The original paper, BTW, can be found here:
Family-wide molecular diagnostic assays are valuable tools for initial identification of viruses during outbreaks and to limit costs of surveillance studies. Recent discoveries of paramyxoviruses have called for such assay that is able to detect all known and unknown paramyxoviruses in one round of PCR amplification. We have developed a RT-PCR assay consisting of a single degenerate primer set, able to detect all members of the Paramyxoviridae family including all virus genera within the subfamilies Paramyxovirinae and Pneumovirinae.
Influenza virus is pleiomorphic, producing both spherical (100-nm-diameter) and filamentous (100-nm by 20-μm) virions. While the spherical virions are known to enter host cells through exploitation of clathrin-mediated endocytosis, the entry pathway for filamentous virions has not been determined, though the existence of an alternative, non-clathrin-, non-caveolin-mediated entry pathway for influenza virus has been known for many years. In this study, we confirm recent results showing that influenza virus utilizes macropinocytosis as an alternate entry pathway. Furthermore, we find that filamentous influenza viruses use macropinocytosis as the primary entry mechanism. Virions enter cells as intact filaments within macropinosomes and are trafficked to the acidic late-endosomal compartment. Low pH triggers a conformational change in the M2 ion channel protein, altering membrane curvature and leading to a fragmentation of the filamentous virions. This fragmentation may enable more-efficient fusion between the viral and endosomal membranes.
|Scooped by Ben Hetman|
|Scooped by Ed Rybicki|
Influenza virus neuraminidase (NA) cleaves terminal sialic acid residues on oligosaccharide chains that are receptors for virus binding, thus playing an important role in the release of virions from infected cells to promote the spread of cell-to-cell infection. In addition, NA plays a role at the initial stage of viral infection in the respiratory tract by degrading hemagglutination inhibitors in body fluid which competitively inhibit receptor binding of the virus. Current first line anti-influenza drugs are viral NA-specific inhibitors, which do not inhibit bacterial neuraminidases. Since neuraminidase producing bacteria have been isolated from oral and upper respiratory commensal bacterial flora, we posited that bacterial neuraminidases could decrease the antiviral effectiveness of NA inhibitor drugs in respiratory organs when viral NA is inhibited. Using in vitro models of infection, we aimed to clarify the effects of bacterial neuraminidases on influenza virus infection in the presence of the NA inhibitor drug zanamivir. We found that zanamivir reduced progeny virus yield to less than 2% of that in its absence, however the yield was restored almost entirely by the exogenous addition of bacterial neuraminidase from Streptococcus pneumoniae. Furthermore, cell-to-cell infection was severely inhibited by zanamivir but restored by the addition of bacterial neuraminidase. Next we examined the effects of bacterial neuraminidase on hemagglutination inhibition and infectivity neutralization activities of human saliva in the presence of zanamivir. We found that the drug enhanced both inhibitory activities of saliva, while the addition of bacterial neuraminidase diminished this enhancement. Altogether, our results showed that bacterial neuraminidases functioned as the predominant NA when viral NA was inhibited to promote the spread of infection and to inactivate the neutralization activity of saliva. We propose that neuraminidase from bacterial flora in patients may reduce the efficacy of NA inhibitor drugs during influenza virus infection.
That's potentially pretty serious - especially in coinfections.
Social media is an important technological trend that has big implications for how researchers (and people in general) communicate and collaborate. Researchers have a huge amount to gain from engaging with social media in various aspects of their work.
Alan Cann talks a bout a paper: Every year I get excitied and rant at my virology students about how amazing it is that a virus can have more than more host, i.e. for viruses which undergo propagative transmission, replicating in both the “host” and the “vector”. For the most part, the students humour me, trying to pretend it’s not happening. When we reach that point in the course this year, I suspect arms will get waved wildly in the direction of this paper.
R&D site in Laval, Canada, to close with loss of 170 jobs...
The site specialises in virology, a research area that Boehringer is now leaving because ‘the demands for medical innovation are shifting significantly’ and the emphasis is now on prevention through vaccination, an area in which the company is not active.
Bats are natural hosts for a large variety of zoonotic viruses. This study aimed to describe the range of bat viromes, including viruses from mammals, insects, fungi, plants, and phages, in 11 insectivorous bat species (216 bats in total) common in six provinces of China.
In a stunning technical feat, an international team of scientists has sequenced the genome of an archaic Siberian girl 31 times over, using a new method that amplifies single strands of DNA. The sequencing is so complete that researchers have as sharp a picture of this ancient genome as they would of a living person's, revealing, for example that the girl had brown eyes, hair, and skin. "No one thought we would have an archaic human genome of such quality," says Matthias Meyer, a postdoc at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany. "Everyone was shocked by the counts. That includes me."
That precision allows the team to compare the nuclear genome of this girl, who lived in Siberia's Denisova Cave more than 50,000 years ago, directly to the genomes of living people, producing a "near-complete" catalog of the small number of genetic changes that make us different from the Denisovans, who were close relatives of Neandertals. "This is the genetic recipe for being a modern human," says team leader Svante Pääbo, a paleogeneticist at the institute.
Ironically, this high-resolution genome means that the Denisovans, who are represented in the fossil record by only one tiny finger bone and two teeth, are much better known genetically than any other ancient human—including Neandertals, of which there are hundreds of specimens. The team confirms that the Denisovans interbred with the ancestors of some living humans and found that Denisovans had little genetic diversity, suggesting that their small population waned further as populations of modern humans expanded. "Meyer and the consortium have set up the field of ancient DNA to be revolutionized—again," says Beth Shapiro, an evolutionary biologist at the University of California, Santa Cruz, who was not part of the team. Evolutionary geneticist Sarah Tishkoff of the University of Pennsylvania agrees: "It's really going to move the field forward."
A method has been established to sequentially delete combinations of genes from the ASFV genome to test the effect on virus replication and host responses to infection. Initially the ASFV genes MGF505 2R and MGF505 3R and a truncated MGF360 9L gene were deleted from the genome of the tissue-culture adapted ASFV strain BA71V and replaced with bacteriophage loxP sequences flanking the beta-glucuronidase (GUS) marker gene to create recombinant virus VΔMGF-GUS. Subsequently the GUS gene was removed by site-specific recombination between the two loxP sites involving expression of the bacteriophage Cre recombinase enzyme to create recombinant virus VΔMGFΔGUS. The EP402R and EP153R genes were subsequently deleted from the genome of VΔMGFΔGUS, using the same GUS marker gene, to construct virus VΔMGFΔCD2-Lectin-GUS. These sequential deletions of ASFV genes were shown not to alter virus replication significantly.
Health officials around the world are on alert after the discovery of a new virus in two patients with pneumonia. The agent belongs to the coronavirus group, which includes several common cold viruses but also the virus that causes SARS, a severe disease that killed more than 700 people during a fast-moving global outbreak in 2002 and 2003 before it was contained.
|Scooped by Jeff Habig|
|Scooped by Ben Hetman|
A new word, phylodynamics, was coined to emphasize the interconnection between phylogenetic properties, as observed for instance in a phylogenetic tree, and the epidemic dynamics of viruses, where selection, mediated by the host immune response, and transmission play a crucial role...
This video was produced by youth participating in the 2012 Science in Action Summer Intensive. A project of the Academy’s Digital Learning Department, generously funded by the Gordon and Betty Moore Foundation.
SERIOUSLY good graphics of dengue virions, change in envelope glycoprotein conformation, and entry into the cell.