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PLOS Computational Biology: The Roots of Bioinformatics in ISMB

PLOS Computational Biology: The Roots of Bioinformatics in ISMB | Virology and Bioinformatics from Virology.ca | Scoop.it
PLOS Computational Biology is an open-access
Nicolas Palopoli's insight:

Besides the interesting recall of the Intelligent Systems for Molecular Biology (ISMB) annual conferences on computational biology, it offers a nice insight into current state-of-the-art methodologies and upcoming trends in the discipline.

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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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Missing link in evolution of complex cells discovered

Missing link in evolution of complex cells discovered | Virology and Bioinformatics from Virology.ca | Scoop.it
Biologists have discovered a new microbe that represents a missing link in the evolution of complex life. The study provides a new understanding of how, billions of years ago, the complex cell types that comprise plants, fungi, but also animals and humans, evolved from simple microbes.
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Scientists Have Found A Way To Kill HIV

Scientists Have Found A Way To Kill HIV | Virology and Bioinformatics from Virology.ca | Scoop.it
A newly created "can opener" molecule is capable of opening HIV and allowing the body's own immune system to kill the infection.
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Cardiac Safety of Modified Vaccinia Ankara for Vaccination against Smallpox in a Young, Healthy Study Population

Cardiac Safety of Modified Vaccinia Ankara for Vaccination against Smallpox in a Young, Healthy Study Population | Virology and Bioinformatics from Virology.ca | Scoop.it

Background Conventional smallpox vaccines based on replicating vaccinia virus (VV) strains (e.g. Lister Elstree, NYCBOH) are associated with a high incidence of myo-/pericarditis, a severe inflammatory cardiac complication. A new smallpox vaccine candidate based on a non-replicating Modified Vaccinia Ankara (MVA) poxvirus has been assessed for cardiac safety in a large placebo-controlled clinical trial.

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Nature Reviews Microbiology: The damage-response framework of microbial pathogenesis (2003)

Nature Reviews Microbiology: The damage-response framework of microbial pathogenesis (2003) | Virology and Bioinformatics from Virology.ca | Scoop.it

All other curves are derived from this basic curve. The arrow indicates that the position of the curve is variable, and depends on the particular host–microorganism interaction. The y-axis denotes host damage as a function of the host response. In this scheme, host damage can occur throughout the host response, but is magnified at both extremes. The host response is represented by a continuum from 'weak' to 'strong'. 'Weak' and 'strong' are terms that can encompass both quantitative and qualitative characteristics of the host response and are used as the best available terms to denote the spectrum of host response as more precise terms are limiting. Weak responses are those that are insufficient, poor or inappropriate — that is, they are not strong enough to benefit the host. Strong responses are those that are excessive, overly robust or inappropriate — that is, they are too strong and can damage the host. When a threshold amount of damage is reached, the host can become symptomatic and if damage is severe, death can ensue. Green, yellow and purple represent health, disease and severe disease, respectively.


Via Kamoun Lab @ TSL
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Proteomics identifies DNA repair toolbox

Proteomics identifies DNA repair toolbox | Virology and Bioinformatics from Virology.ca | Scoop.it

Various repair mechanisms help our cells to revert continuous damage to their DNA. If they fail, mutations accumulate in the genome that can lead to devastating diseases. DNA repair defects underlie predisposition to certain cancers, such as familial breast cancer, and promote the transformation process in other spontaneous cancers. DNA repair requires many factors, but so far there have not been comprehensive analyses of the intricate pathways involved. Using novel and highly sensitive proteomic technologies, scientists of the Max Planck Institute (MPI) of Biochemistry in Martinsried near Munich now report in the journal Sciencethe first global analysis of the protein recruitment dynamics underlying a critical DNA repair pathway. Their results shed light on the repair mechanism and identified new proteins and drug targets that could be important in maintaining genomic stability and preventing cancer.


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Mol Biol Evol: Genomic signature of selective sweeps illuminates adaptation of Medicago truncatula to root-associated microorganisms (2015)

Mol Biol Evol: Genomic signature of selective sweeps illuminates adaptation of Medicago truncatula to root-associated microorganisms (2015) | Virology and Bioinformatics from Virology.ca | Scoop.it

Medicago truncatula is a model legume species used to investigate plant-microorganism interactions, notably root symbioses. Massive population genomic and transcriptomic data now available for this species open the way for a comprehensive investigation of genomic variations associated with adaptation of M. truncatula to its environment. Here we performed a fine-scale genome scan of selective sweep signatures in Medicago truncatula using more than 15 million SNPs identified on 283 accessions from two populations (Circum and Far West), and exploited annotation and published transcriptomic data to identify biological processes associated with molecular adaptation. We identified 58 swept genomic regions with a 15 kb average length and comprising 3.3 gene models on average. The unimodal sweep state probability distribution in these regions enabled us to focus on the best single candidate gene per region. We detected two unambiguous species-wide selective sweeps, one of which appears to underlie morphological adaptation. Population genomic analyses of the remaining 56 sweep signatures indicate that sweeps identified in the Far West population are less population-specific and probably more ancient than those identified in the Circum population. Functional annotation revealed a predominance of immunity-related adaptations in the Circum population. Transcriptomic data from accessions of the Far West population allowed inference of four clusters of co-regulated genes putatively involved in the adaptive control of symbiotic carbon flow and nodule senescence, as well as in other root adaptations upon infection with soil microorganisms. We demonstrate that molecular adaptations in Medicago truncatula were primarily triggered by selective pressures from root-associated micro-organisms.


Via Christophe Jacquet, Kamoun Lab @ TSL, Francis Martin
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Mammals Harbor At Least 320,000 Undiscovered Viruses

Mammals Harbor At Least 320,000 Undiscovered Viruses | Virology and Bioinformatics from Virology.ca | Scoop.it

Humans have been playing defense against viruses for much of history. Think about it, -people mainly take action against a virus once it has already become a threat. Just recently, researchers have switched tactics and taken the offensive. A team of scientists lead by Simon Anthony of Columbia University released a study this month in the journal mBio estimating the number of novel viruses in all mammalian species to be 320,000. Anthony and his colleagues' estimate of mammalian viruses is the first ever to be statistically supported. With this information scientists may discover potentially dangerous viruses before they transition from wildlife to humans.


Roughly 70% of all new viruses infecting humans originated in other animals. Viruses that originate in mammals are particularly hazardous because they are easily transferable to people; their exposure to other mammalian species allows them to skillfully "navigate our own warm-blooded bodies." The knowledge of just how many viruses may be lurking in mammals helps scientists assess the threat viruses pose to society. In order to calculate the number of viruses, scientists studied one species of flying fox (a type of bat) known as Pteropus giganteus. Found in Bangladesh, the flying fox is a known carrier of multiple viruses, such as Nipah, and was therefore well-suited for the study. Scientists repeatedly took biological samples - 1,900 in all - from bat populations over a five year span. From those samples fifty-five different viruses from nine viral families were identified. Only five of the viruses found were previously known to scientists! Calculating that another three unknown viruses were not accounted for in the study, the researchers estimated that flying foxes alone harbor 58 viruses. If all 5,486 known species of mammals carried 58 different viruses, then the total number of undiscovered mammalian viruses is at least 320,000.


To clarify, 320,000 viruses is a very rough estimate. The scientists assumed that every mammal carries 58 viruses based on their findings with flying foxes. The problem with this figure is that flying foxes, and bats in general, are virus friendly animals. The lifestyle factors that predispose bats to be good viral carriers are living in large communities, long distance travel and dispersal throughout the world. It is unlikely that the remaining 5,485 other mammals also carry exactly 58 viruses. Scientists are not sure by what factor the estimate could be off. Dr. Anthony explains "it is very likely that 320,000 viruses under-estimates the actual number of viruses, but we have no way of knowing by how much. It is for this very reason that we need to expand and repeat these systematic studies, and only then will we be able to refine our estimations with greater confidence." This study is significant because it presents the first statistically supported estimate of mammalian viruses.


Before now, some scientists speculated there to be millions of undiscovered mammalian viruses. Only 320,000 mammalian viruses is a much more reassuring and manageable number than ten million. Now that the number of estimated viruses has dropped from the millions to hundred thousands, identifying each one is feasible. The researchers' goal is to track down every single mammalian virus and catalogue it. Dr. Anthony predicts that all mammalian viruses can be identified over a 10 year period for a mere $6.3 billion. You may not think of $6.3 billion as a small amount, but in comparison to the cost of pandemics it's not too outlandish. The SARS outbreak alone cost $16 billion dollars. For just $1.2 billion the scientists estimate that 85% of mammalian viruses can be identified.


Via Dr. Stefan Gruenwald
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Eric Vincill's curator insight, May 1, 7:42 AM

"....Think about it, -people mainly take action against a virus once it has become a threat."   Very interesting article on viral-mammalian interactions that we are just now starting to identify

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Rubella Virus Declared Eliminated in the Americas

Rubella Virus Declared Eliminated in the Americas | Virology and Bioinformatics from Virology.ca | Scoop.it
Effective vaccination programs mean German measles are no longer considered a threat in the Americas.

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Ed Rybicki's curator insight, April 30, 5:00 AM

And only the third virus for which this is true - after smallpox and polio.  Now for the rest of the world - IF the antivax people will let it happen!

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Escape of non-enveloped virus from intact cells

Escape of non-enveloped virus from intact cells | Virology and Bioinformatics from Virology.ca | Scoop.it
The primary mode of exit for non-enveloped viruses is cell lysis. However, more complex exit strategies are possible.
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Integrating alignment-based and alignment-free sequence similarity measures for biological sequence classification

Integrating alignment-based and alignment-free sequence similarity measures for biological sequence classification | Virology and Bioinformatics from Virology.ca | Scoop.it
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Is a small artificial virus fragment the key to a Chikungunya vaccine?

Is a small artificial virus fragment the key to a Chikungunya vaccine? | Virology and Bioinformatics from Virology.ca | Scoop.it
Chikungunya virus (CHIKV) is transmitted by Aedes mosquitoes and causes Chikungunya fever. CHIKV occurs in the tropical and subtropical parts of the world. Regions where it has already caused epide...
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Revision of Begomovirus taxonomy based on pairwise sequence comparisons

Revision of Begomovirus taxonomy based on pairwise sequence comparisons | Virology and Bioinformatics from Virology.ca | Scoop.it

Viruses of the genus Begomovirus (family Geminiviridae) are emergent pathogens of crops throughout the tropical and subtropical regions of the world. By virtue of having a small DNA genome that is easily cloned, and due to the recent innovations in cloning and low-cost sequencing, there has been a dramatic increase in the number of available begomovirus genome sequences. Even so, most of the available sequences have been obtained from cultivated plants and are likely a small and phylogenetically unrepresentative sample of begomovirus diversity, a factor constraining taxonomic decisions such as the establishment of operationally useful species demarcation criteria. In addition, problems in assigning new viruses to established species have highlighted shortcomings in the previously recommended mechanism of species demarcation. Based on the analysis of 3,123 full-length begomovirus genome (or DNA-A component) sequences available in public databases as of December 2012, a set of revised guidelines for the classification and nomenclature of begomoviruses are proposed. The guidelines primarily consider a) genus-level biological characteristics and b) results obtained using a standardized classification tool, Sequence Demarcation Tool, which performs pairwise sequence alignments and identity calculations. These guidelines are consistent with the recently published recommendations for the generaMastrevirus and Curtovirus of the family Geminiviridae. Genome-wide pairwise identities of 91 % and 94 % are proposed as the demarcation threshold for begomoviruses belonging to different species and strains, respectively. Procedures and guidelines are outlined for resolving conflicts that may arise when assigning species and strains to categories wherever the pairwise identity falls on or very near the demarcation threshold value.

 

Ed Rybicki's insight:

Ah, that takes me back: nice all the young ones carry on what we started, back when we invented those generic names!

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Core services: Reward bioinformaticians

Core services: Reward bioinformaticians | Virology and Bioinformatics from Virology.ca | Scoop.it
Biological data will continue to pile up unless those who analyse it are recognized as creative collaborators in need of career paths, says Jeffrey Chang.
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TreeSeq, a Fast and Intuitive Tool for Analysis of Whole Genome and Metagenomic Sequence Data

TreeSeq, a Fast and Intuitive Tool for Analysis of Whole Genome and Metagenomic Sequence Data | Virology and Bioinformatics from Virology.ca | Scoop.it
Next-generation sequencing is not yet commonly used in clinical laboratories because of a lack of simple and intuitive tools. We developed a software tool (TreeSeq) with a quaternary tree search structure for the analysis of sequence data. This permits rapid searches for sequences of interest in large datasets. We used TreeSeq to screen a gut microbiota metagenomic dataset and a whole genome sequencing (WGS) dataset of a strain of Klebsiella pneumoniae for antibiotic resistance genes and compared the results with BLAST and phenotypic resistance determination. TreeSeq was more than thirty times faster than BLAST and accurately detected resistance gene sequences in complex metagenomic data and resistance genes corresponding with the phenotypic resistance pattern of the Klebsiella strain. Resistance genes found by TreeSeq were visualized as a gene coverage heat map, aiding in the interpretation of results. TreeSeq brings analysis of metagenomic and WGS data within reach of clinical diagnostics.
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The "First Replicon" on Earth? A Chat With Virologist Ricardo Flores

The "First Replicon" on Earth? A Chat With Virologist Ricardo Flores | Virology and Bioinformatics from Virology.ca | Scoop.it

Ricardo Flores thinks viruses may be  "the most important faction of the [planet's] biomass" and that a viroid-like entity is a prime candidate for the first replicon on Earth. Viroids are subviral world parasites, non-protein coding RNAs. Excerpts of our interview follow.

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Researchers develop computer model of bacterial colony interactions

Researchers develop computer model of bacterial colony interactions | Virology and Bioinformatics from Virology.ca | Scoop.it
(Phys.org)—One of the remarkable properties of bacterial colonies is the self-ordering aggregation and orientation of bacterial cells. Bacteria secrete extracellular polymeric substances (EPS) that form biofilm-like structures in which the cells aggregate. Due to the density of such systems, researchers ...
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Haloviruses of archaea, bacteria, and eukaryotes

Hypersaline environments up to near saturation are rich reservoirs of extremophilic viruses. One milliliter of salt water may contain up to 109 viruses which can also be trapped inside salt crystals. To date, most of the ∼100 known halovirus isolates infect extremely halophilic archaea, although a few bacterial and eukaryotic viruses have also been described. These isolates comprise tailed and tailless icosahedral, pleomorphic, and lemon-shaped viruses which have been classified according to features such as host range, genome type, and replication. Recent studies have revealed that viruses can be grouped into a few structure-based viral lineages derived from a common ancestor based on conserved virion architectural principles and the major capsid protein fold.


Via Ed Rybicki
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Ed Rybicki's curator insight, May 4, 8:06 AM

...and we're looking for them...B-)  Hey, Flavia and Maya?!

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New Chapter in Epigenetics

New Chapter in Epigenetics | Virology and Bioinformatics from Virology.ca | Scoop.it

Unsuspected DNA modification raises possibility of new carrier of heritable epigenetic information


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Researchers captured the first 3-D video of a living algal embryo turning itself inside out

Researchers captured the first 3-D video of a living algal embryo turning itself inside out | Virology and Bioinformatics from Virology.ca | Scoop.it

Researchers have captured the first 3D video of a living algal embryo (Volvox sp.) turning itself inside out, from a sphere to a mushroom shape and back again. The results could help unravel the mechanical processes at work during a similar process in animals, which has been called the "most important time in your life."

Researchers from the University of Cambridge have captured the first three-dimensional images of a live embryo turning itself inside out. The images, of embryos of a green alga called Volvox, make an ideal test case to understand how a remarkably similar process works in early animal development.


Using fluorescence microscopy to observe the Volvox embryos, the researchers were able to test a mathematical model of morphogenesis - the origin and development of an organism's structure and form - and understand how the shape of cells drives the process of inversion, when the embryo turns itself from a sphere to a mushroom shape and back again. Their findings are published today (27 April) in the journal Physical Review Letters.


The processes observed in the Volvox embryo are similar to the process of gastrulation in animal embryos - which biologist Lewis Wolpert called "the most important event in your life." During gastrulation, the embryo folds inwards into a cup-like shape, forming the primary germ layers which give rise to all the organs in the body. Volvox embryos undergo a similar process, but with an additional twist: the embryos literally turn themselves right-side out during the process.


Gastrulation in animals results from a complex interplay of cell shape changes, cell division and migration, making it difficult to develop a quantitative understanding of the process. However, Volvox embryos complete their shape change only by changing cell shapes and the location of the connections between cells, and this simplicity makes them an ideal model for understanding cell sheet folding.


In Volvox embryos, the process of inversion begins when the embryos start to fold inward, or invaginate, around their middle, forming two hemispheres. Next, one hemisphere moves inside the other, an opening at the top widens, and the outer hemisphere glides over the inner hemisphere, until the embryo regains its spherical shape. This remarkable process takes place over approximately one hour.


Via Dr. Stefan Gruenwald
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A more effective shingles vaccine could be on the way for people who need it

A more effective shingles vaccine could be on the way for people who need it | Virology and Bioinformatics from Virology.ca | Scoop.it
GSK says new shingles vaccine shows effectiveness across all age ranges, even those in their 70s.

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Virology Journal | Full text | Diversity of coronavirus in bats from Eastern Thailand

Bats are reservoirs for a diverse range of coronaviruses (CoVs), including those closely related to human pathogens such as Severe Acute Respiratory Syndrome (SARS) CoV and Middle East Respiratory Syndrome CoV. There are approximately 139 bat species reported to date in Thailand, of which two are endemic species. Due to the zoonotic potential of CoVs, standardized surveillance efforts to characterize viral diversity in wildlife are imperative.
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John Oliver calls Dr. Oz "the worst person in scrubs who has ever been on television"

The HBO host encapsulates everything that's wrong with The Dr. Oz Show in one segment.
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BMC Infectious Diseases | Abstract | Medical student’s attitude towards influenza vaccination

Influenza vaccination is recommended for all healthcare personnel (HCP) and most institutions offer vaccination for free and on site. However, medical students do not always have such easy access, and the predictors that might guide the motivation of medical students to get vaccinated are largely unknown.
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The Ebola Epidemic Crystallizes the Potential of Passive Antibody Therapy for Infectious Diseases

The Ebola Epidemic Crystallizes the Potential of Passive Antibody Therapy for Infectious Diseases | Virology and Bioinformatics from Virology.ca | Scoop.it

The current Ebola epidemic provides a dramatic example of the potential of passive antibody therapy for infectious diseases that is also instructive of the hurdles and limitations involved in wide-scale reintroduction of this powerful anti-infective strategy. Passive antibody therapy was first used in the 1890s as "serum therapy" and was the first effective anti-infective therapy. Serum therapy was largely discontinued with the advent of antibiotic therapy in the early 1940s because it could not compete with regards to cost or ease of administration and had additional complexities, including that it had to be administered early in disease, it manifested lot-to-lot variation, and its efficacy required immune donors and the availability of a specific microbiological diagnosis so sera could be matched to the disease-causing microorganism [1]. Serum therapy using heterologous sera was also associated with "serum sickness," a syndrome caused by the formation of antigen-antibody complexes. However, antibiotic therapy was never shown to be superior in efficacy to antibody therapy and there were some conditions, such as pneumococcal pneumonia, where it may have had some advantages. Despite their wholesale abandonment, antibody therapies did retain a niche for certain conditions where no drugs were available, such as the prevention and/or treatment of tetanus, botulism, and certain viral diseases. The development of hybridoma technology and monoclonal antibodies (mAbs) in the mid-1970s promised to solve many of the problems of serum therapy, but, to date, there has not been formal reintroduction of antibody therapies for infectious diseases despite considerable and ongoing efforts to develop such therapies against viral diseases, such as HIV infection, and bacterial diseases, such as those caused byPseudomonas aeruginosa and Staphylacoccous aureus. In contrast, mAbs have revolutionized the treatment of many cancers and rheumatic diseases and dozens have been licensed. Here we analyze why Ab-based therapies remain so underdeveloped for infectious diseases through the prism of the Ebola epidemic.

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Krishan Maggon 's curator insight, April 24, 7:15 AM

Citation: Casadevall A, Pirofski L-a (2015) The Ebola Epidemic Crystallizes the Potential of Passive Antibody Therapy for Infectious Diseases. PLoS Pathog 11(4): e1004717. doi:10.1371/journal.ppat.1004717