MedWorm.com provides a medical RSS filtering service. Over 6000 RSS medical sources are combined and output via different filters. This feed contains the latest items from the 'VBRC Blog' source. Tue, 06 Jan 2009 11:12:36 +0100 http://athena.bioc.uvic.ca/node/876 In the recently published article  Molecular profiling of T-helper immune genes during dengue virus infection  in Virology Journal (Source: VBRC Blog) VBRC Blog blogs http://www.medworm.com/rss/comments.php?id=2081826 Tue, 06 Jan 2009 08:31:04 +0100 2081826 http://athena.bioc.uvic.ca/node/873               Well January first has been missed by about 10 hours, but we here at VBRC would still like to wish you a good 2009. There are a lot of exciting things happening here. We look to continue our funding from NIH with our Alabama collaborators with a grant renewal application due early this year.  We've got some really neat new tools and new additions to old tools on the go and with our new website we hope to engage with the science community. read more (Source: VBRC Blog) VBRC Blog blogs http://www.medworm.com/rss/comments.php?id=2077098 Fri, 02 Jan 2009 18:12:54 +0100 2077098 http://athena.bioc.uvic.ca/node/869 George Rohrmann has complied a detailed annotation of the AcMNPV genome that concisely summarizes known information concerning function and conservation of genes across the Baculoviridae. You can find it here: http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=bacvir&part=ch11 read more (Source: VBRC Blog) VBRC Blog blogs http://www.medworm.com/rss/comments.php?id=2068150 Sat, 27 Dec 2008 22:20:36 +0100 2068150 http://athena.bioc.uvic.ca/node/868 I am sure that anyone working with proteins is familiar with at least some of the many analytic options available.  There are so many different applications for visualizing data in different ways that it can be daunting. In a blog post on Freelancing science Pawel Szczesny describes how he navigates the largely visual field of protein bioinformatics and the direction that he sees it going in.  (Source: VBRC Blog) VBRC Blog blogs http://www.medworm.com/rss/comments.php?id=2063160 Tue, 23 Dec 2008 07:08:08 +0100 2063160 http://athena.bioc.uvic.ca/node/867 Smith SK, Olson VA, Karem KL, Jordan R, Hruby DE, Damon IK Abstract read more (Source: VBRC Blog) VBRC Blog blogs http://www.medworm.com/rss/comments.php?id=2063161 Tue, 23 Dec 2008 06:44:04 +0100 2063161 http://athena.bioc.uvic.ca/node/866 Viral evolution is likely the most fruitful area of evolutionary biology because of the rapid rate at which viral genomes change, especially RNA viruses.  In his recent review "Evolutionary History and Phylogeography of Human Viruses" Edward Holmes discusses the study of evolution of human viruses in light of some of the major factors effecting it.  AbstractUnderstanding the evolutionary history of human viruses, along withthe factors that have shaped their spatial distributions, is one of the read more (Source: VBRC Blog) VBRC Blog blogs http://www.medworm.com/rss/comments.php?id=2063162 Tue, 23 Dec 2008 05:25:09 +0100 2063162 http://athena.bioc.uvic.ca/node/865 There is an exciting new feature available on Base-By-Base that allows for the visualization of genomic subsequences alongside genomes.  Under the ‘File’ menu, the ‘Import Analysis from File...’ option allows users to specify a file containing a list of subsequences of interest (promoter elements or conserved domains, for instance) which then get marked in the Base-by-Base visualization window alongside the selected genome.  read more (Source: VBRC Blog) VBRC Blog blogs http://www.medworm.com/rss/comments.php?id=2054764 Sat, 20 Dec 2008 04:56:06 +0100 2054764 http://athena.bioc.uvic.ca/node/861 Virus Particle Explorer database (VIPERdb) is designed to provide the user with all the tools they need to look at the structure of a number of viruses.  This database currently contains 264 viruses, giving access to capsid structures created based on Cryo-EM data and X-ray crystallography data.  VIPERdb also provides access to a range of tools to help you compare capsid structures, find background information on the virus, analyze specific residues in the capsid and perform numerous other tasks.  The basics of how to use this resource and its most popular functions are introduc read more (Source: VBRC Blog) VBRC Blog blogs http://www.medworm.com/rss/comments.php?id=2048836 Thu, 18 Dec 2008 20:01:44 +0100 2048836 http://athena.bioc.uvic.ca/node/860 BioData Mining read more (Source: VBRC Blog) VBRC Blog blogs http://www.medworm.com/rss/comments.php?id=2042830 Wed, 17 Dec 2008 05:40:03 +0100 2042830 http://athena.bioc.uvic.ca/node/859 Drupal read more (Source: VBRC Blog) VBRC Blog blogs http://www.medworm.com/rss/comments.php?id=2042831 Tue, 16 Dec 2008 00:39:24 +0100 2042831 http://athena.bioc.uvic.ca/node/852 Arenaviruses cause a significant risk to human health in a number of ways:  The ability of Arenaviruses to cause serious neurological disease is well documented.  The virus family can cause hemorrhagic fever.  It even has a global distribution and a successful animal reservoir - rodents. read more (Source: VBRC Blog) VBRC Blog blogs http://www.medworm.com/rss/comments.php?id=2019296 Thu, 04 Dec 2008 05:12:00 +0100 2019296 http://athena.bioc.uvic.ca/node/851 Becker et al. have recently announced that they have successfully synthesized the bat SARS-CoV, which is the likely progenitor to the human SARS-CoV.  The importance of synthetic viruses is that they allow the study of how animal viruses become zoonotic.  The article in which they present their findings is available through PNAS and has been further discussed by Brandon Kiem on the WIRED Science blog. (Source: VBRC Blog) VBRC Blog blogs http://www.medworm.com/rss/comments.php?id=2008192 Wed, 03 Dec 2008 19:31:25 +0100 2008192 http://athena.bioc.uvic.ca/node/850 African swine fever (ASF) is the only member of the Asfarviridae family, as such it has many genes not observed in other viruses.  Salguero et al. work to elucidate the role of one of these genes in their recent paper "Cytokine mRNA expression and pathological findings in pigs inoculated with African swine fever virus (E-70) deleted on A238L".  They prepared a virus deficient in the gene of interest and infected a natural host, in this way they were able to find its role in virulence.  For details of the approach and a discussion of their findings check out the (Source: VBRC Blog) VBRC Blog blogs http://www.medworm.com/rss/comments.php?id=2008193 Wed, 03 Dec 2008 02:58:06 +0100 2008193 http://athena.bioc.uvic.ca/node/849 There are two proposed evolutionary paths of Nucleocytopasmic large DNA viruses (NCLDV).  The first being a bacterial origins and subsequent simplification and the second being gene acquisition by a DNA virus.  In a paper just published, Filee et al. study the phylogenetics of NCLDV.  Their findings shed some light on the ongoing debate of the origins of NCLDV.  To find out more check out the paper. (Source: VBRC Blog) VBRC Blog blogs http://www.medworm.com/rss/comments.php?id=2008194 Tue, 02 Dec 2008 07:56:02 +0100 2008194 http://athena.bioc.uvic.ca/node/848 Drinking water is routinely tested for the presence of fecal contamination via coliform testing as a matter of protecting public health.  It is widely held that these bacterial indicators are not adequate indicators for the presence of enteric viruses.  A recent publication by Griffin et al. suggests the non-pathogenic Torque teno virus (TTV) may be more representative of viral contamination in drinking water.  The authors' outline the necessary steps for TTV testing to be implimented.  You can find their paper here read more (Source: VBRC Blog) VBRC Blog blogs http://www.medworm.com/rss/comments.php?id=2008195 Tue, 02 Dec 2008 04:40:00 +0100 2008195 http://athena.bioc.uvic.ca/node/847 Erbar et al. in their recent paper "Selective receptor expression restricts Nipah virus infection of endothelial cells" describe the limitation on infection of endothelial cells by Nipah virus based on the expression of cellular markers. read more (Source: VBRC Blog) VBRC Blog blogs http://www.medworm.com/rss/comments.php?id=2008196 Tue, 02 Dec 2008 03:10:02 +0100 2008196 http://athena.bioc.uvic.ca/node/846 Just uploaded this ebolavirus genome into our database. Here is a blog about it that is definitely worth reading; you will find a link to the paper there. (Source: VBRC Blog) VBRC Blog blogs http://www.medworm.com/rss/comments.php?id=1997547 Sat, 29 Nov 2008 05:49:03 +0100 1997547 http://athena.bioc.uvic.ca/node/845 We are all familiar with hospital-acquired infections and the risk of getting such an infection.  Post-transplant viral infections, most often caused by cytomegalovirus and Epstein-Barr virus, can lead to serious illness and even death.  In his review article "Emerging Viruses in Transplantation: There Is More to Infection After Transplant Than CMV and EBV" Fisher discusses several emerging viral pathogens in transplant patients.  He describes the symptoms, diagnoses and possible treatments for many recently described viral infections.   read more (Source: VBRC Blog) VBRC Blog blogs http://www.medworm.com/rss/comments.php?id=1997548 Fri, 28 Nov 2008 08:22:08 +0100 1997548 http://athena.bioc.uvic.ca/node/843 In a recent review of a 2002 article by Chinchar we learned about the global impact Ranavirus is having on populations of fish, reptiles and amphibians (if you haven't read that blog article go read it now).  In a paper published earlier this year Ridenhour and Storfer have focused on a specific Ranavirus, Ambystoma tigrinum, looking at the evolution of host-pathogen interactions.  Although this newer study is focused on the Ranavirus-salamander relationship, the authors point out that it could provide insight into the evolu read more (Source: VBRC Blog) VBRC Blog blogs http://www.medworm.com/rss/comments.php?id=1997549 Fri, 28 Nov 2008 03:57:09 +0100 1997549 http://athena.bioc.uvic.ca/node/844 With increased distribution and incidence Dengue viruses have risen to global importance.  Arujo et al. study the phylogeography of three major dengue genotypes.  The aim of this study is to understand the spread and evolution of one of the most rapidly changing serotypes (DENV-3) on a global scale over the last 50 years.  They estimate that DENV-3 originated in the late 19th century, with current major genotypes emerging in the 1960's and 1970's. read more (Source: VBRC Blog) VBRC Blog blogs http://www.medworm.com/rss/comments.php?id=1997550 Thu, 27 Nov 2008 21:08:46 +0100 1997550 http://athena.bioc.uvic.ca/node/842 With increased distribution and incidence Dengue viruses have risen to global importance.  Arujo et al. study the phylogeography of three major dengue genotypes.  The aim of this study is to understand the spread and evolution of one of the most rapidly changing serotypes (DENV-3) on a global scale over the last 50 years.  They estimate that DENV-3 originated in the late 19th century, with current major genotypes emerging in the 1960's and 1970's. read more (Source: VBRC Blog) VBRC Blog blogs http://www.medworm.com/rss/comments.php?id=1993713 Thu, 27 Nov 2008 05:35:06 +0100 1993713 http://athena.bioc.uvic.ca/node/841 Previously thought to be a non-functional remnant of F proteins the authors suggest that the F-like protein Ac23 is a pathogenicity factor required for their virus construct to achieve full levels of infectivity.  read more (Source: VBRC Blog) VBRC Blog blogs http://www.medworm.com/rss/comments.php?id=1993714 Wed, 26 Nov 2008 08:22:08 +0100 1993714 http://athena.bioc.uvic.ca/node/840 Edan R. Tulman and Daniel L. Rock Abstract Current work is beginning to reveal the complex mechanisms by which African swine fever virus interacts with its swine and tick hosts. This work includes the identification of novel viral genes that mediate virulence and host range, and influence important cellular regulatory pathways. read more (Source: VBRC Blog) VBRC Blog blogs http://www.medworm.com/rss/comments.php?id=1993715 Wed, 26 Nov 2008 06:30:03 +0100 1993715 http://athena.bioc.uvic.ca/node/839 In a chilling review Chinchar exposes just how deadly Ranaviruses can be. read more (Source: VBRC Blog) VBRC Blog blogs http://www.medworm.com/rss/comments.php?id=1993716 Wed, 26 Nov 2008 05:37:09 +0100 1993716 http://athena.bioc.uvic.ca/node/838 Jehle JA, Blissard GW, Bonning BC, Cory JS, Herniou EA, Rohrmann GF, Theilmann DA, Thiem SM, Vlak JM Abteilung Phytomedizin, DLR Rheinpfalz, Neustadt/Wstr, Germany. read more (Source: VBRC Blog) VBRC Blog blogs http://www.medworm.com/rss/comments.php?id=1993717 Wed, 26 Nov 2008 03:45:08 +0100 1993717 http://athena.bioc.uvic.ca/node/837 (Source: VBRC Blog) VBRC Blog blogs http://www.medworm.com/rss/comments.php?id=1985833 Tue, 25 Nov 2008 09:35:03 +0100 1985833 http://athena.bioc.uvic.ca/node/836 Abstract Over the past 30 years, Zaire and Sudan ebolaviruses have been responsible for large hemorrhagic fever (HF) outbreaks with case fatalities ranging from 53% to 90%, while a third species, Côte d'Ivoire ebolavirus, caused a single non-fatal HF case. In November 2007, HF cases were reported in Bundibugyo District, Western Uganda. read more (Source: VBRC Blog) VBRC Blog blogs http://www.medworm.com/rss/comments.php?id=1985834 Tue, 25 Nov 2008 06:47:00 +0100 1985834 http://athena.bioc.uvic.ca/node/833 Here you have it, people encouraging critical, proof-based thinking through blogs and twitter. This Blog Post written by Steven Salzberg contains what is in my opinion and excellent critical review of a study done for the drug Crestor.  The post outlines a drug that has become almost a media darling with studies that claim healthy people will significantly benefit from taking Crestor.  read more (Source: VBRC Blog) VBRC Blog blogs http://www.medworm.com/rss/comments.php?id=1982210 Sat, 22 Nov 2008 04:32:06 +0100 1982210 http://athena.bioc.uvic.ca/node/831 <Note: No, this isn't actually serious> Recently, research performed years ago has been coming to light with far-reaching and grave consequences.  While I only just came across these papers myself, it isn't hard to draw conclusions between their findings and the global economic slowdown.  Nobel prizes cannot be far off for these fine academics. These astounding papers include: read more (Source: VBRC Blog) VBRC Blog blogs http://www.medworm.com/rss/comments.php?id=1977422 Thu, 20 Nov 2008 05:00:03 +0100 1977422 http://athena.bioc.uvic.ca/node/830 We examined the spectrum of clinical presentations, neuroimaging findings, and clinical outcomes of children with congenital LCMV infection. read more (Source: VBRC Blog) VBRC Blog blogs http://www.medworm.com/rss/comments.php?id=1970865 Tue, 18 Nov 2008 04:35:04 +0100 1970865 http://athena.bioc.uvic.ca/node/829 As has been mentioned in the past, VBRC uses Connotea for bookmarking articles of interest.  You can find those articles in our News feeds. For more information on Connotea please see This Post. In an effort to keep updated on the current happenings of Web 2.0 and the bioinformatics online community, we have started using twitter to let people know what we are up to.  Cupton1 is Dr. Upton's user name and from there you will find most of our lab. read more (Source: VBRC Blog) VBRC Blog blogs http://www.medworm.com/rss/comments.php?id=1962563 Sat, 15 Nov 2008 07:24:09 +0100 1962563 http://athena.bioc.uvic.ca/node/828 Antiviral Res. 2008 Nov;80(2):87-93. Epub 2008 Jul 9. Mouse models of dengue virus infection and disease. read more (Source: VBRC Blog) VBRC Blog blogs http://www.medworm.com/rss/comments.php?id=1962564 Fri, 14 Nov 2008 06:28:00 +0100 1962564 http://athena.bioc.uvic.ca/node/826 A new deadly virus has been identified in South Africa, after having infected and killed three people in September. The outbreak was confined to the patient and hospital staff and fortunately should not affect others. The virus was initially classified as an Old World arenavirus, but sequencing data suggests it is a new virus. We hope to learn more about the evolution and the virulence of arenaviridae from this virus. I look forward to seeing it.. in our database. read more (Source: VBRC Blog) VBRC Blog blogs http://www.medworm.com/rss/comments.php?id=1956552 Wed, 12 Nov 2008 22:28:22 +0100 1956552 http://athena.bioc.uvic.ca/node/821 It has been a few months since Huss et al., thoughtful template for the future "A Gene Wiki for Community Annotation of Gene Function" in the July's edition of PLoS Biology.  The authors introduced the idea of a Gene Wiki, a collection of informal gene articles on an online encyclopedia Wikipedia. read more (Source: VBRC Blog) VBRC Blog blogs http://www.medworm.com/rss/comments.php?id=1941011 Fri, 07 Nov 2008 04:51:07 +0100 1941011 http://athena.bioc.uvic.ca/node/819 Another of Alan Cann's posts: Clustering of dengue virus infections « MicrobiologyBytes Powered by ScribeFire. (Source: VBRC Blog) VBRC Blog blogs http://www.medworm.com/rss/comments.php?id=1941012 Thu, 06 Nov 2008 00:51:00 +0100 1941012 http://athena.bioc.uvic.ca/node/818 The visualization of biological pathways is useful in learning and teaching biological concepts. Programs like GenMAPP have already allowed researchers to create, visualize and analyze these data. PathVisio, a new program, has been released, and it is intended to extend the functionalities of GenMAPP. Among its features: Java-based and thus multi-platform; Integration with other Java bioinformatic tools; Backward compatible with the MAPP format from GenMAPP; read more (Source: VBRC Blog) VBRC Blog blogs http://www.medworm.com/rss/comments.php?id=1922177 Thu, 30 Oct 2008 22:12:47 +0100 1922177 http://athena.bioc.uvic.ca/node/816 Denison's recent article in PLoS Biology on Seeking Membranes:  Positive-Strand RNA Virus Replication Complexes explores the evolution of viral cell biology. read more (Source: VBRC Blog) VBRC Blog blogs http://www.medworm.com/rss/comments.php?id=1918666 Thu, 30 Oct 2008 03:44:03 +0100 1918666 http://athena.bioc.uvic.ca/node/814 Although it has been around for a few years, this incredible animation is well worth taking a look at if you haven't already.  Developed for Harvard Biology students, it features a beautiful and in-depth look at the various mechanisms of the cell, including everything from microtubule formation and vesicle transport to cell adhesion and lipid raft formation.  Visualizing all of these processes in action is nothing short of amazing. read more (Source: VBRC Blog) VBRC Blog blogs http://www.medworm.com/rss/comments.php?id=1915861 Wed, 29 Oct 2008 19:27:34 +0100 1915861 http://athena.bioc.uvic.ca/node/808 Rev Med Virol. 2008 Sep-Oct;18(5):331-46. read more (Source: VBRC Blog) VBRC Blog blogs http://www.medworm.com/rss/comments.php?id=1887427 Sat, 18 Oct 2008 03:18:09 +0100 1887427 http://athena.bioc.uvic.ca/node/807 Transbound Emerg Dis. 2008 Sep;55(7):263-72. read more (Source: VBRC Blog) VBRC Blog blogs http://www.medworm.com/rss/comments.php?id=1887428 Sat, 18 Oct 2008 03:07:02 +0100 1887428 http://athena.bioc.uvic.ca/node/804 Immunol Res. 2008 Oct 8. [Epub ahead of print] Tick-borne flaviviruses: dissecting host immune responses and virus countermeasures. read more (Source: VBRC Blog) VBRC Blog blogs http://www.medworm.com/rss/comments.php?id=1863767 Thu, 09 Oct 2008 21:29:34 +0100 1863767 http://athena.bioc.uvic.ca/node/803 The emergence of Nipah virus, a highly pathogenic paramyxovirus. J Clin Virol. 2008 Oct 1; Authors: Lo MK, Rota PA read more (Source: VBRC Blog) VBRC Blog blogs http://www.medworm.com/rss/comments.php?id=1863768 Thu, 09 Oct 2008 04:05:02 +0100 1863768 http://athena.bioc.uvic.ca/node/802 I was given the following list of free citation handling software: Are there any open source alternatives to EndNote? Yes. Most of the open source alternatives listed below are citation generators, which means they don’t store the citations for you, but they do automatically format them in a particular citation style after you’ve entered all the relevant information (author, title, etc.). A few others are markup languages, and one—Zotero—allows you to cite and store sources within your web browser. read more (Source: VBRC Blog) VBRC Blog blogs http://www.medworm.com/rss/comments.php?id=1860639 Wed, 08 Oct 2008 07:23:06 +0100 1860639 http://athena.bioc.uvic.ca/node/799 Ribosomal frameshifting and the world of hidden genes is mushrooming up in the field of bioinformatics!  read more (Source: VBRC Blog) VBRC Blog blogs http://www.medworm.com/rss/comments.php?id=1860640 Wed, 08 Oct 2008 06:05:00 +0100 1860640 http://athena.bioc.uvic.ca/node/786 The Canadian Bioinformatics Help Desk is an endeavor by Genome Canada to unite a large number of Bioinformatics resources in one common forum.  Among many useful features, the CBHD site hosts a directory of Bioinformatics researchers, a software repository and also a newsletter containing a software spotlight, job postings, and upcoming meeting read more (Source: VBRC Blog) VBRC Blog blogs http://www.medworm.com/rss/comments.php?id=1857371 Tue, 07 Oct 2008 21:08:04 +0100 1857371 http://athena.bioc.uvic.ca/node/787 Genetika. 2008 Aug;44(8):1029-44. [Molecular evolution of poxviruses] [Article in Russian] [No authors listed] Previous restriction fragment length polymorphism analysis divided variola virus(VARV) strains into two subtypes, one of which included West Africanand South American isolates. This allowed a dating to be introduced for read more (Source: VBRC Blog) VBRC Blog blogs http://www.medworm.com/rss/comments.php?id=1857370 Tue, 07 Oct 2008 21:08:03 +0100 1857370 http://athena.bioc.uvic.ca/node/794 This month's issue of BMC Bioinformatics has seen the unveiling of FOSTA, a database and tool which provides access to a much needed library of Functionally Equivalent Proteins (FEPs). Excerpt from the Abstract (found here): read more (Source: VBRC Blog) VBRC Blog blogs http://www.medworm.com/rss/comments.php?id=1857369 Tue, 07 Oct 2008 21:08:03 +0100 1857369 http://athena.bioc.uvic.ca/node/796 Are we ready? read more (Source: VBRC Blog) VBRC Blog blogs http://www.medworm.com/rss/comments.php?id=1857368 Tue, 07 Oct 2008 21:08:03 +0100 1857368 http://athena.bioc.uvic.ca/node/797 A recent study published in Nature has made a significant step towards the mapping of those Human genes involved in the cellular propagation of West Nile virus.  Through the use of RNA interference, 21,121 human genes were silenced and the effect on a WNV infection was monitored, yielding 305 host proteins that either positively or negatively affect viral synthesis. read more (Source: VBRC Blog) VBRC Blog blogs http://www.medworm.com/rss/comments.php?id=1857367 Tue, 07 Oct 2008 21:08:02 +0100 1857367 http://athena.bioc.uvic.ca/node/784 Jonathan Eisen over at the Tree of Life blog recently posted this blog.  It seems that researchers are conducting an online survey about user's values surrounding privacy and are looking to get a few thousand people to complete the survey.  This should take little of your time and you're helping websites tailor their policies to your needs and values :). read more (Source: VBRC Blog) VBRC Blog blogs http://www.medworm.com/rss/comments.php?id=1848996 Fri, 03 Oct 2008 19:29:39 +0100 1848996