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Health News - Common virus is a new target for cancer treatment

Health News - Common virus is a new target for cancer treatment | Virology and Bioinformatics from Virology.ca | Scoop.it

"Treatment for the common cytomegalovirus (CMV) has been shown to give seriously ill cancer patients a much improved prognosis."

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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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Genetically Modified Mosquitoes Pave the Way for Dengue Fever Prevention | Viruses101 | Learn Science at Scitable

Genetically Modified Mosquitoes Pave the Way for Dengue Fever Prevention | Viruses101 | Learn Science at Scitable | Virology and Bioinformatics from Virology.ca | Scoop.it
Over 40% of the word's population is at risk of contracting Dengue Fever, a mosquito borne virus. Scientists are now using genetically modified mosquitoes to try and prevent the spread of Dengue Fever.
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▶ Jonathan Yewdell - How to Succeed in Science - YouTube

Jonathan Yewdell M.D., Ph.D. (NIH) -- leading immunologist and head of NIAID Cell Biology and Viral Immunology -- delivers a grantsmanship lecture on "How to...
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Marburgvirus Resurgence in Kitaka Mine Bat Population after Extermination Attempts

Marburgvirus Resurgence in Kitaka Mine Bat Population after Extermination Attempts | Virology and Bioinformatics from Virology.ca | Scoop.it

Marburg virus (MARV) and Ravn virus (RAVV), collectively called marburgviruses, cause Marburg hemorrhagic fever (MHF) in humans. In July 2007, 4 cases of MHF (1 fatal) occurred in miners at Kitaka Mine in southern Uganda. Later, MHF occurred in 2 tourists who visited Python Cave, ≈50 km from Kitaka Mine. One of the tourists was from the United States (December 2007) and 1 was from the Netherlands (July 2008); 1 case was fatal (1,2,3). The cave and the mine each contained 40,000–100,000 Rousettus aegyptiacus bats (Egyptian fruit bats).

Longitudinal investigations of the outbreaks at both locations were initiated by the Viral Special Pathogens Branch of the Centers for Disease Control and Prevention (CDC, Atlanta, GA, USA, and Entebbe, Uganda) in collaboration with the Uganda Wildlife Authority (UWA) and the Uganda Virus Research Institute (UVRI). During these studies, genetically diverse MARVs and RAVVs were isolated directly from bat tissues, and infection levels of the 2 viruses were found to increase in juvenile bats on a predictable bi-annual basis (4,5). However, investigations at Kitaka Mine were stopped when the miners exterminated the bat colony by restricting egress from the cave with papyrus reed barriers and then entangling the bats in fishing nets draped over the exits. The trapping continued for weeks, and the entrances were then sealed with sticks and plastic. These depopulation efforts were documented by researchers from UVRI, the CDC, the National Institute of Communicable Diseases (Sandringham, South Africa), and UWA during site visits to Kitaka Mine (Technical Appendix[PDF - 124 KB - 1 page] Figure). In August 2008, thousands of dead bats were found piled in the forest, and by November 2008, there was no evidence of bats living in the mine; whether 100% extermination was achieved is unknown. CDC, UVRI, and UWA recommended against extermination, believing that any results would be temporary and that such efforts could exacerbate the problem if bat exclusion methods were not complete and permanent (6,7).

 

Ed Rybicki's insight:

So there's the bats' revenge: exterminate us, and we'll come back with a higher prevalence - with more diverse viruses!

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SearchSmallRNA: a graphical interface tool for the assemblage of viral genomes using small RNA libraries data - Virology Journal

SearchSmallRNA: a graphical interface tool for the assemblage of viral genomes using small RNA libraries data - Virology Journal | Virology and Bioinformatics from Virology.ca | Scoop.it
Next-generation parallel sequencing (NGS) allows the identification of viral pathogens by sequencing the small RNAs of infected hosts. Thus, viral genomes may be assembled from host immune response products without prior virus enrichment, amplification or purification. However, mapping of the vast information obtained presents a bioinformatics challenge.
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Ten Simple Rules for Better Figures

Ten Simple Rules for Better Figures | Virology and Bioinformatics from Virology.ca | Scoop.it

"Scientific visualization is classically defined as the process of graphically displaying scientific data. However, this process is far from direct or automatic. There are so many different ways to represent the same data: scatter plots, linear plots, bar plots, and pie charts, to name just a few. Furthermore, the same data, using the same type of plot, may be perceived very differently depending on who is looking at the figure. A more accurate definition for scientific visualization would be a graphical interface between people and data. In this short article, we do not pretend to explain everything about this interface; rather, see [1], [2] for introductory work. Instead we aim to provide a basic set of rules to improve figure design and to explain some of the common pitfalls."

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ImmunizeCA App - Immunize Canada

ImmunizeCA App - Immunize Canada | Virology and Bioinformatics from Virology.ca | Scoop.it
The Canadian Public Health Association, Immunize Canada and the Ottawa Hospital Research Institute collaborated to develop an app for mobile devices that will help Canadians keep track of their vaccinations. The app is FREE and can be downloaded from iTunes, Google Play of BlackBerry World.
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Microbiology: Bacteria get vaccinated

Microbiology: Bacteria get vaccinated | Virology and Bioinformatics from Virology.ca | Scoop.it
Infection by defective bacterial viruses that cannot replicate has now been found to be the key feature enabling bacteria to rapidly develop adaptive immunity against functional viruses.
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A fish, a rabbit — same thing, to a creationist

A fish, a rabbit — same thing, to a creationist | Virology and Bioinformatics from Virology.ca | Scoop.it
JBS Haldane is said to have responded to a question about how evolution could be disproved by saying, “A Precambrian rabbit”. What was meant by this, of course, is any substantial discovery that greatly disrupted the evidence for the chronological pattern of descent observed in Earth’s life. That pattern of descent is one of the…
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A single vertebrate DNA virus protein disarms invertebrate immunity to RNA virus infection

A single vertebrate DNA virus protein disarms invertebrate immunity to RNA virus infection | Virology and Bioinformatics from Virology.ca | Scoop.it

Virus-host interactions drive a remarkable diversity of immune responses and countermeasures. We found that two RNA viruses with broad host ranges, vesicular stomatitis virus (VSV) and Sindbis virus (SINV), are completely restricted in their replication after entry into Lepidopteran cells. This restriction is overcome when cells are co-infected with vaccinia virus (VACV), a vertebrate DNA virus. Using RNAi screening, we show that Lepidopteran RNAi, Nuclear Factor-κB, and ubiquitin-proteasome pathways restrict RNA virus infection. Surprisingly, a highly conserved, uncharacterized VACV protein, A51R, can partially overcome this virus restriction. We show that A51R is also critical for VACV replication in vertebrate cells and for pathogenesis in mice. Interestingly, A51R colocalizes with, and stabilizes, host microtubules and also associates with ubiquitin. We show that A51R promotes viral protein stability, possibly by preventing ubiquitin-dependent targeting of viral proteins for destruction. Importantly, our studies reveal exciting new opportunities to study virus-host interactions in experimentally-tractable Lepidopteran systems.

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Human Immunodeficiency Virus gag and protease: partners in resistance

Human Immunodeficiency Virus gag and protease: partners in resistance | Virology and Bioinformatics from Virology.ca | Scoop.it

Human Immunodeficiency Virus (HIV) maturation plays an essential role in the viral life cycle by enabling the generation of mature infectious virus particles through proteolytic processing of the viral Gag and GagPol precursor proteins. An impaired polyprotein processing results in the production of non-infectious virus particles. Consequently, particle maturation is an excellent drug target as exemplified by inhibitors specifically targeting the viral protease (protease inhibitors; PIs) and the experimental class of maturation inhibitors that target the precursor Gag and GagPol polyproteins. Considering the different target sites of the two drug classes, direct cross-resistance may seem unlikely. However, coevolution of protease and its substrate Gag during PI exposure has been observed both in vivo and in vitro. This review addresses in detail all mutations in Gag that are selected under PI pressure. We evaluate how polymorphisms and mutations in Gag affect PI therapy, an aspect of PI resistance that is currently not included in standard genotypic PI resistance testing. In addition, we consider the consequences of Gag mutations for the development and positioning of future maturation inhibitors.

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Estimates of the reproduction number for seasonal, pandemic, and zoonotic influenza: a systematic review of the literature - BMC Infectious Diseases

Background

The potential impact of an influenza pandemic can be assessed by calculating a set of transmissibility parameters, the most important being the reproduction number (R), which is defined as the average number of secondary cases generated per typical infectious case.

Methods

We conducted a systematic review to summarize published estimates of R for pandemic or seasonal influenza and for novel influenza viruses (e.g. H5N1). We retained and summarized papers that estimated R for pandemic or seasonal influenza or for human infections with novel influenza viruses.

Results

The search yielded 567 papers. Ninety-one papers were retained, and an additional twenty papers were identified from the references of the retained papers. Twenty-four studies reported 51 R values for the 1918 pandemic. The median R value for 1918 was 1.80 (interquartile range [IQR]: 1.47-2.27). Six studies reported seven 1957 pandemic R values. The median R value for 1957 was 1.65 (IQR: 1.53-1.70). Four studies reported seven 1968 pandemic R values. The median R value for 1968 was 1.80 (IQR: 1.56-1.85). Fifty-seven studies reported 78 2009 pandemic R values. The median R value for 2009 was 1.46 (IQR: 1.30-1.70) and was similar across the two waves of illness: 1.46 for the first wave and 1.48 for the second wave. Twenty-four studies reported 47 seasonal epidemic R values. The median R value for seasonal influenza was 1.28 (IQR: 1.19-1.37). Four studies reported six novel influenza R values. Four out of six R values were <1.

Conclusions

These R values represent the difference between epidemics that are controllable and cause moderate illness and those causing a significant number of illnesses and requiring intensive mitigation strategies to control. Continued monitoring of R during seasonal and novel influenza outbreaks is needed to document its variation before the next pandemic.

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Ecology and evolution of viruses infecting uncultivated SUP05 bacteria

Ecology and evolution of viruses infecting uncultivated SUP05 bacteria | Virology and Bioinformatics from Virology.ca | Scoop.it

Viruses modulate microbial communities and alter ecosystem functions. However, due to cultivation bottlenecks specific virus-host interaction dynamics remain cryptic. Here we examined 127 single-cell amplified genomes (SAGs) from uncultivated SUP05 bacteria isolated from a marine oxygen minimum zone (OMZ) to identify 69 viral contigs representing five new genera within dsDNACaudoviralesand ssDNAMicroviridae. Infection frequencies suggest that ~1/3 of SUP05 bacteria are viral-infected, with higher infection frequency where oxygen-deficiency was most severe. ObservedMicroviridaeclonality suggests recovery of bloom-terminating viruses, while systematic co-infection between dsDNA and ssDNA viruses posits previously unrecognized cooperation modes. Analyses of 186 microbial and viral metagenomes revealed that SUP05 viruses persisted for years, but remained endemic to the OMZ. Finally, identification of virus-encoded dissimilatory sulfite reductase suggests SUP05 viruses reprogram their host's energy metabolism. Together these results demonstrate closely coupled SUP05 virus-host co-evolutionary dynamics with potential to modulate biogeochemical cycling in climate-critical and expanding OMZs.

 


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How to bury your academic writing

How to bury your academic writing | Virology and Bioinformatics from Virology.ca | Scoop.it
Book chapters can allow freedom to think about your work in line with broader theoretical issues, but if you're tempted to write a book chapter for an edited collection, it might be best to reconsi...
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Ebola - WakaWaka

Ebola - WakaWaka | Virology and Bioinformatics from Virology.ca | Scoop.it
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Ten Simple Rules for Better Figures

Ten Simple Rules for Better Figures | Virology and Bioinformatics from Virology.ca | Scoop.it
PLOS Computational Biology is an open-access
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Filoviruses Require Endosomal Cysteine Proteases for Entry but Exhibit Distinct Protease Preferences

Ken Yaw Agyeman-Badu's insight:

Filoviruses are enveloped viruses that cause sporadic outbreaks of severe hemorrhagic fever [CDC, MMWR Morb. Mortal. Wkly. Rep. 50:73–77, 2001; Colebunders and Borchert, J. Infect. 40:16–20, 2000; Colebunders et al., J. Infect. Dis. 196(Suppl. 2):S148–S153, 2007; Geisbert and Jahrling, Nat. Med. 10:S110-S121, 2004]. Previous studies revealed that endosomal cysteine proteases are host factors for ebolavirus Zaire (Chandran et al., Science 308:1643–1645, 2005; Schornberg et al., J. Virol. 80:4174–4178, 2006). In this report, we show that infection mediated by glycoproteins from other phylogenetically diverse filoviruses are also dependent on these proteases and provide additional evidence indicating that they cleave GP1 and expose the binding domain for the critical host factor Niemann-Pick C1. Using selective inhibitors and knockout-derived cell lines, we show that the ebolaviruses Zaire and Cote d'Ivoire are strongly dependent on cathepsin B, while the ebolaviruses Sudan and Reston and Marburg virus are not. Taking advantage of previous studies of cathepsin B inhibitor-resistant viruses (Wong et al., J. Virol. 84:163–175, 2010), we found that virus-specific differences in the requirement for cathepsin B are correlated with sequence polymorphisms at residues 47 in GP1 and 584 in GP2. We applied these findings to the analysis of additional ebolavirus isolates and correctly predicted that the newly identified ebolavirus species Bundibugyo, containing D47 and I584, is cathepsin B dependent and that ebolavirus Zaire-1995, the single known isolate of ebolavirus Zaire that lacks D47, is not. We also obtained evidence for virus-specific differences in the role of cathepsin L, including cooperation with cathepsin B. These studies strongly suggest that the use of endosomal cysteine proteases as host factors for entry is a general property of members of the family Filoviridae.

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Ken Yaw Agyeman-Badu's curator insight, September 14, 11:22 PM

Filoviruses are enveloped viruses that cause sporadic outbreaks of severe hemorrhagic fever [CDC, MMWR Morb. Mortal. Wkly. Rep. 50:73–77, 2001; Colebunders and Borchert, J. Infect. 40:16–20, 2000; Colebunders et al., J. Infect. Dis. 196(Suppl. 2):S148–S153, 2007; Geisbert and Jahrling, Nat. Med. 10:S110-S121, 2004]. Previous studies revealed that endosomal cysteine proteases are host factors for ebolavirus Zaire (Chandran et al., Science 308:1643–1645, 2005; Schornberg et al., J. Virol. 80:4174–4178, 2006). In this report, we show that infection mediated by glycoproteins from other phylogenetically diverse filoviruses are also dependent on these proteases and provide additional evidence indicating that they cleave GP1 and expose the binding domain for the critical host factor Niemann-Pick C1. Using selective inhibitors and knockout-derived cell lines, we show that the ebolaviruses Zaire and Cote d'Ivoire are strongly dependent on cathepsin B, while the ebolaviruses Sudan and Reston and Marburg virus are not. Taking advantage of previous studies of cathepsin B inhibitor-resistant viruses (Wong et al., J. Virol. 84:163–175, 2010), we found that virus-specific differences in the requirement for cathepsin B are correlated with sequence polymorphisms at residues 47 in GP1 and 584 in GP2. We applied these findings to the analysis of additional ebolavirus isolates and correctly predicted that the newly identified ebolavirus species Bundibugyo, containing D47 and I584, is cathepsin B dependent and that ebolavirus Zaire-1995, the single known isolate of ebolavirus Zaire that lacks D47, is not. We also obtained evidence for virus-specific differences in the role of cathepsin L, including cooperation with cathepsin B. These studies strongly suggest that the use of endosomal cysteine proteases as host factors for entry is a general property of members of the family Filoviridae.

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PolyCTLDesigner: a computational tool for constructing polyepitope T-cell antigens - BMC Research Notes

Construction of artificial polyepitope antigens is one of the most promising strategies for developing more efficient and safer vaccines evoking T-cell immune responses. Epitope rearrangements and utilization of certain spacer sequences have been proven to greatly influence the immunogenicity of polyepitope constructs. However, despite numerous efforts towards constructing and evaluating artificial polyepitope immunogens as well as despite numerous computational methods elaborated to date for predicting T-cell epitopes, peptides binding to TAP and for antigen processing prediction, only a few computational tools were currently developed for rational design of polyepitope antigens.

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Chimpanzee adenovirus vaccine generates acute and durable protective immunity against ebolavirus challenge : Nature Medicine : Nature Publishing Group

A chimpanzee adenovirus-based vaccination approach elicits acute and long-term protection against ebolavirus challenge in nonhuman primates.

Via Mel Melendrez-Vallard
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Emerging Viral Diseases: Confronting Threats with New Technologies

Abstract

Emerging viral diseases pose ongoing health threats, particularly in an era of globalization; however, new biomedical research technologies such as genome sequencing and structure-based vaccine and drug design have improved our ability to respond to viral threats.

 
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Rabies Rapid Transit System

Rabies Rapid Transit System | Virology and Bioinformatics from Virology.ca | Scoop.it
Rabies virus hijacks the transport systems of neurons, manipulating axonal transport machinery to get to the central nervous system at maximum speed.
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Reverse genetics system could ease norovirus research

Reverse genetics system could ease norovirus research | Virology and Bioinformatics from Virology.ca | Scoop.it
Finding may allow scientists to manipulate viral genome.
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Major alteration in coxsackievirus B3 genomic RNA structure distinguishes a virulent strain from an avirulent strain

Coxsackievirus B3 (CV-B3) is a cardiovirulent enterovirus that utilizes a 5′ untranslated region (5′UTR) to complete critical viral processes. Here, we directly compared the structure of a 5′UTR from a virulent strain with that of a naturally occurring avirulent strain. Using chemical probing analysis, we identified a structural difference between the two 5′UTRs in the highly substituted stem-loop II region (SLII). For the remainder of the 5′UTR, we observed conserved structure. Comparative sequence analysis of 170 closely related enteroviruses revealed that the SLII region lacks conservation. To investigate independent folding and function, two chimeric CV-B3 strains were created by exchanging nucleotides 104–184 and repeating the 5′UTR structural analysis. Neither the parent SLII nor the remaining domains of the background 5′UTR were structurally altered by the exchange, supporting an independent mechanism of folding and function. We show that the attenuated 5′UTR lacks structure in the SLII cardiovirulence determinant.

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MxB binds to the HIV-1 core and prevents the uncoating process of HIV-1

The IFN-α-inducible restriction factor MxB blocks HIV-1 infection after reverse transcription but prior to integration. Genetic evidence suggested that capsid is the viral determinant for restriction by MxB. This work explores the ability of MxB to bind to the HIV-1 core, and the role of capsid-binding in restriction

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TWiV 301: Marine viruses and insect defense

TWiV 301: Marine viruses and insect defense | Virology and Bioinformatics from Virology.ca | Scoop.it
Vincent speaks with Carla and Curtis about RNA interference and antiviral defense in fruit flies, and viruses in the sea, the greatest biodiversity on Earth.

Via Ed Rybicki
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Inferring Heterogeneous Evolutionary Processes Through Time: from Sequence Substitution to Phylogeography

Molecular phylogenetic and phylogeographic reconstructions generally assume time-homogeneous substitution processes. Motivated by computational convenience, this assumption sacrifices biological realism and offers little opportunity to uncover the temporal dynamics in evolutionary histories. Here, we propose an evolutionary approach that explicitly relaxes the time-homogeneity assumption by allowing the specification of different infinitesimal substitution rate matrices across different time intervals, called epochs, along the evolutionary history. We focus on an epoch model implementation in a Bayesian inference framework that offers great modeling flexibility in drawing inference about any discrete data type characterized as a continuous-time Markov chain, including phylogeographic traits. To alleviate the computational burden that the additional temporal heterogeneity imposes, we adopt a massively parallel approach that achieves both fine- and coarse-grain parallelization of the computations across branches that accommodate epoch transitions, making extensive use of graphics processing units. Through synthetic examples, we assess model performance in recovering evolutionary parameters from data generated according to different evolutionary scenarios that comprise different numbers of epochs for both nucleotide and codon substitution processes. We illustrate the usefulness of our inference framework in two different applications to empirical data sets: the selection dynamics on within-host HIV populations throughout infection and the seasonality of global influenza circulation. In both cases, our epoch model captures key features of temporal heterogeneity that remained difficult to test using ad hoc procedures. [Bayesian inference; BEAGLE; BEAST; Epoch Model; phylogeography; Phylogenetics.]

 
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