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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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How Investigating Bacteria Will Change Health Care In Hospitals

How Investigating Bacteria Will Change Health Care In Hospitals | Virology and Bioinformatics from Virology.ca | Scoop.it
Preventing the spread of disease and infection through microbes.

 

We often think of the world around us as sterile and static, especially when we are in a hospital. In reality, every surface on earth is literally teeming with millions of bacteria.
Jack Gilbert, a microbiologist from the University of Chicago, has spent his career investigating these invisible companions all around us. This year, Gilbert and a group of microbiologists will take over a brand new hospital in an experiment called the "Hospital Microbiome."

Read more: http://www.businessinsider.com/investigating-the-bacteria-that-plague-a-hospital-2012-10#ixzz2AzYCir9Q

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#Genotype #Phenotype Progress in #Biophysics and Molecular Biology - From sequence to consequence and back

#Genotype #Phenotype Progress in #Biophysics and Molecular Biology - From sequence to consequence and back | Virology and Bioinformatics from Virology.ca | Scoop.it

The genotype–phenotype relation is at the core of theoretical biology. It is argued why a mathematically based explanatory structure of this relation is in principle possible, and why it has to embrace both sequence to consequence and consequence to sequence phenomena. It is suggested that the primary role of DNA in the chain of causality is that its presence allows a living system to induce perturbations of its own dynamics as a function of its own system state or phenome, i.e. it capacitates living systems to self-transcend beyond those morphogenetic limits that exist for non-living open physical systems in general. Dynamic models bridging genotypes with phenotypic variation in a causally cohesive way are shown to provide explanations of genetic phenomena that go well beyond the explanatory domains of statistically oriented genetics theory construction. A theory originally proposed by Rupert Riedl, which implies that the morphospace that is reachable by the standing genetic variation in a population is quite restricted due to systemic constraints, is shown to provide a foundation for a mathematical conceptualization of numerous evolutionary phenomena associated with the phenotypic consequence to sequence relation. The paper may be considered a call to arms to mathematicians and the mathematically inclined to rise to the challenge of developing new formalisms capable of dealing with the deep defining characteristics of living systems.

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Hunting dark matter with DNA

Hunting dark matter with DNA | Virology and Bioinformatics from Virology.ca | Scoop.it

Particle physicists propose a new way to detect dark matter using the molecule of life


Via Integrated DNA Technologies
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An integrated map of genetic variation from 1,092 human genomes : Nature : Nature Publishing Group

An integrated map of genetic variation from 1,092 human genomes : Nature : Nature Publishing Group | Virology and Bioinformatics from Virology.ca | Scoop.it

By characterizing the geographic and functional spectrum of human genetic variation, the 1000 Genomes Project aims to build a resource to help to understand the genetic contribution to disease. Here we describe the genomes of 1,092 individuals from 14 populations, constructed using a combination of low-coverage whole-genome and exome sequencing. By developing methods to integrate information across several algorithms and diverse data sources, we provide a validated haplotype map of 38|[thinsp]|million single nucleotide polymorphisms, 1.4|[thinsp]|million short insertions and deletions, and more than 14,000 larger deletions. We show that individuals from different populations carry different profiles of rare and common variants, and that low-frequency variants show substantial geographic differentiation, which is further increased by the action of purifying selection.

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Study reveals dangerous levels of contamination on hospital keyboards

Study reveals dangerous levels of contamination on hospital keyboards | Virology and Bioinformatics from Virology.ca | Scoop.it

In the largest study of its kind, an investigation into the extent of contamination of computer keyboards in hospital setting has shown that 58% are contaminated with harmful bacteria. The study sampled 230 keyboards across 3 different ward types in 4 separate hospitals. Contamination rates were similar for all hospitals and wards.


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Synthetic Viral Genomics: Risks and Benefits for Science and Society

by

Ralph S. Baric

"Viral disease outbreaks have long inspired fear in human populations. Highly pathogenic infectious disease has shaped world history, primarily by impacting the outcome of wars and other global conflicts and precipitating human movement. Historic accounts have documented the catastrophic consequences and human suffering associated with widespread viral outbreaks like smallpox virus, yellow fever virus, measles virus, human immunodeficiency virus (HIV), the severe acute respiratory syndrome coronavirus (SARS-CoV), the 1918 influenza virus and others (51). News accounts and film have reinforced the serious threat posed by the emergence of new viral diseases as well as the catastrophic consequences of intentional release of highly pathogenic viruses in human populations. As illustrated by the SARS epidemic and the continuing evolution of the H5N1 avian influenza, global and national infectious disease outbreaks can overwhelm disaster medical response networks and medical facilities, disrupt global economies, and paralyze health and medical services by targeting health care workers and medical staff (21). This review focuses on viruses of humans, animals and plants that are viewed as potential weapons of mass disruption to human populations, critical plant and animal food sources, and national economies; and will consider whether and how the availability of synthetic genomics technologies will change this landscape.
Biological warfare (BW) agents are microorganisms or toxins that are intended to kill, injure or incapacitate the enemy, elicit fear and devastate national economies. Because small amounts of microorganisms might cause high numbers of casualties, they are classified as weapons of mass destruction. A number of naturally occurring...."

http://bit.ly/Se6Z33

#syntheticbiology #synbio


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De novo assembly of the pepper #transcriptome (Capsicum annuum): a benchmark for in silico discovery of SNPs, SSRs and candidate genes

Molecular breeding of pepper (Capsicum spp.) can be accelerated by developing DNA markers associated with transcriptomes in breeding germplasm.
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Computational Challenges in the Field Bioinformatics ...

Computational Challenges in the Field Bioinformatics ... | Virology and Bioinformatics from Virology.ca | Scoop.it
Bioinformatics training: a review of challenges, actions and support requirements. Briefings In Bioinformatics,11(6), 544-551. doi:10.1093/bib/bbq021. Stein, L. (2010). The case for cloud computing in genome informatics.

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Benefit and harm from immunity to respiratory syncytial virus (RSV)

Human respiratory syncytial virus (RSV) infection is a major cause of morbidity in children and of morbidity and mortality in elderly or immunocompromised adults. Given prophylactically, antibody can protect against infection, but natural levels are poorly protective. Vaccination may enhance disease, and there is no well tolerated and effective vaccine or antiviral treatment. Despite over 50 years of research, therapy remains nonspecific and supportive.

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PLOS Neglected Tropical Diseases: Ebola and Marburg Hemorrhagic Fevers: Neglected Tropical Diseases?

PLOS Neglected Tropical Diseases: Ebola and Marburg Hemorrhagic Fevers: Neglected Tropical Diseases? | Virology and Bioinformatics from Virology.ca | Scoop.it
PLOS Neglected Tropical Diseases is an open-access journal publishing peer-reviewed research on the world\'s most neglected tropical diseases, such as elephantiasis, river blindness, leprosy, hookworm, schistosomiasis, and African sleeping sickness...
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Deaths from Symptomatically Identifiable Furious Rabies in India: A Nationally Representative Mortality Survey

Deaths from Symptomatically Identifiable Furious Rabies in India: A Nationally Representative Mortality Survey | Virology and Bioinformatics from Virology.ca | Scoop.it

"Rabies remains an avoidable cause of death in India. As verbal autopsy is not likely to identify atypical or paralytic forms of rabies, our figure of 12,700 deaths due to classic and clinically identifiable furious rabies underestimates the total number of deaths due to this virus. The concentrated geographic distribution of rabies in India suggests that a significant reduction in the number of deaths or potentially even elimination of rabies deaths is possible."

 

Isn't it really, really about time we had REALLY cheap rabies vaccines - to stop preventable deaths from a ghastly disease?  I think so.

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Sending DNA Messages Inside Viruses

Sending DNA Messages Inside Viruses | Virology and Bioinformatics from Virology.ca | Scoop.it

Given its power, it is no surprise that synthetic biologists want to harness the power of intercellular communication.


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Video Tip of the Week: AnimalTFDB for transcription factors | The OpenHelix Blog

Transcription factor details--and sources of information about them and their binding sites--are definitely among the the most common questions we hear in...
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Prochloron - MicrobeWiki

Prochloron - MicrobeWiki | Virology and Bioinformatics from Virology.ca | Scoop.it

Species of the Prochloron genus are oxyphotobacteria, or oxygenic photosynthetic prokaryotes. They are most prominent in tropical waters as symbionts with ascidians, commonly known as sea squirts. These organisms' unique photosynthetic morphology make them interesting to scientists who study the evolution of the features in photosynthesizers.

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7 Great #YouTube Channels for #Science

7 Great #YouTube Channels for #Science | Virology and Bioinformatics from Virology.ca | Scoop.it

Dedicated Science YouTube channels with some really great videos covering pretty much all topics within the curriculum.


Via Karen Innes
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Free Technology for Teachers: MIT Video - More Than 10,000 Educational Videos

Free Technology for Teachers: MIT Video - More Than 10,000 Educational Videos | Virology and Bioinformatics from Virology.ca | Scoop.it

MIT Video is a giant collection of more than 10,000 educational videos organized into more than 150 channels. The largest channel is the Open Courseware channel that contains more than 2,300 lectures from MIT's open courses.

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Psychic pair fail scientific test

Psychic pair fail scientific test | Virology and Bioinformatics from Virology.ca | Scoop.it

University researchers test the abilities of two professional mediums. who are unable to demonstrate they have special psychic powers.


Via Luca Baptista
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Current Opinion in Virology - Composition of plant virus RNA replicase complexes

Current Opinion in Virology - Composition of plant virus RNA replicase complexes | Virology and Bioinformatics from Virology.ca | Scoop.it

The replication of the genome of positive-strand RNA viruses depends on their own RNA replicase complexes. Substantial advances in the experimental approaches used to determine the composition of the viral replicase complexes revealed that the replicase complexes of eukaryotic positive-strand RNA viruses are assembled in a host-membrane-derived microenvironment and that this process is regulated by orchestrated interactions between viral proteins, viral genomic RNAs, and co-opted host factors, including molecular chaperones, RNA-binding proteins, and proteins associated with membrane remodeling and lipid synthesis. This review focuses on recent progress in our understanding of how plant RNA viruses organize viral and host factors to form their replicase complexes.

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A neutral theory of molecular function

A neutral theory of molecular function | Virology and Bioinformatics from Virology.ca | Scoop.it
In 1968 Motoo Kimura published a short article in Nature in which he argued that “most mutations produced by nucleotide replacement are almost neutral in natural selection”. This fantastic paper is generally viewed as having established the “neutral theory” of molecular evolution, whose central principle was set out by Jack King and Lester Jukes in a Science paper the following year:

Evolutionary change at the morphological, functional, and behavioral levels results from the process of natural selection, operating through adaptive change in DNA. It does not necessarily follow that all, or most, evolutionary change in DNA is due to the action of Darwinian natural selection.

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Mechanism found for destruction of key allergy-inducing complexes, researchers say

Mechanism found for destruction of key allergy-inducing complexes, researchers say | Virology and Bioinformatics from Virology.ca | Scoop.it

Researchers have learned how a man-made molecule destroys complexes that induce allergic responses — a discovery that could lead to the development of highly potent, rapidly acting interventions for a host of acute allergic reactions.

 

The new inhibitor disarms IgE antibodies, pivotal players in acute allergies, by detaching the antibody from its partner in crime, a molecule called FcR. (Other mechanisms lead to slower-developing allergic reactions.)

 

“It would be an incredible intervention if you could rapidly disconnect IgE antibodies in the midst of an acute allergic response,” said Ted Jardetzky, PhD, professor of structural biology and senior investigator for the study. It turns out the inhibitor used by the team does just that. A myriad of allergens, ranging from ragweed pollen to bee venom to peanuts, can set off IgE antibodies, resulting in allergic reactions within seconds. The new inhibitor destroys the complex that tethers IgE to the cells responsible for the reaction, called mast cells. Severing this connection would be the holy grail of IgE-targeted allergy treatment.

 

 


Via Dr. Stefan Gruenwald
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The proteins came in two by two - Protein pairing essential for male fruit fly survival

The proteins came in two by two - Protein pairing essential for male fruit fly survival | Virology and Bioinformatics from Virology.ca | Scoop.it

Female fruit flies have two copies of the X chromosome, while males have only one.


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Virology - Tools from viruses: Bacteriophage successes and beyond

Virology - Tools from viruses: Bacteriophage successes and beyond | Virology and Bioinformatics from Virology.ca | Scoop.it

Viruses are ubiquitous and can infect any of the three existing cellular lineages (Archaea, Bacteria and Eukarya). Despite the persisting negative public perception of these entities, scientists learnt how to domesticate some of them. The study of molecular mechanisms essential to the completion of viral cycles has greatly contributed to deciphering fundamental processes in biology. Nowadays, viruses have entered the biotechnological era and numerous applications have already been developed.

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Transient Activation of the PI3K-AKT Pathway by HCV to Enhance Viral Entry

The PI3K-AKT signaling pathway plays an important role in cell growth and metabolism. Here we report that HCV transiently activates the PI3K-AKT pathway. This activation was observed as early as 15 minutes post-infection, peaked by 30 minutes, and became undetectable at 24 hours post-infection. The activation of AKT could also be mediated by UV-inactivated HCV, HCV pseudoparticle (HCVpp) and the ectodomain of the HCV E2 envelope protein.

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Sharing and re-use of phylogenetic trees (and associated data) to facilitate synthesis

Recently, various evolution-related journals adopted policies to encourage or require archiving of phylogenetic trees and associated data.
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Ancient Viruses Wreak New Havoc | The Scientist Magazine®

Ancient Viruses Wreak New Havoc | The Scientist Magazine® | Virology and Bioinformatics from Virology.ca | Scoop.it

Fragments of ancient viruses buried in the genomes of mammals and other vertebrates typically lay dormant but can awaken in immune-compromised mice and may cause cancers, according to a new study published today (October 24) in Nature.

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