Sunday, November 27, 2011

Viral etiquette tips: the epigenetic effects of life-long guests!

there is an interesting post from Nicole Kelesoglu on the E3 blog regarding how viruses modify host epigenomes to avoid detection by the immune can read about it by clicking here!

Friday, November 18, 2011

so let's get this straight; CFS patients don't have XMRV or MLVs, but if they did, it would explain the neuromuscular pathology....

Dusty Miller, greatly respected in the retroviral community, has just published a paper in the Journal of Virology describing how, if it really existed in humans, XMRV could induce apoptosis of human neuroblastoma cells - presenting a potential mechanism for the neuromuscular pathology seen in patients with chronic fatigue syndrome.  I don't normally blog about XMRV or other MLVs that might be capable of infecting humans - but we did just publish a paper showing how easy it would be to get false-negative results when attempting to PCR amplify the GAG region of viruses like these, which would be especially relevant if the titer or copy number of the virus in various tissues was low.  While several journals considered this scientifically worthy work, they all thought the "interest" in this paper would be low.  By publishing in an open access journal, we've now had 850 accesses to our paper in 3 weeks - suggesting at least some people are in fact interested in it.  I then wonder if anyone actually did find polytropic/xenotropic MLVs in human disease, would they be able to publish it? Would it not get held back by virtue of the already published negative data, which in most cases was poorly controlled for or maybe not the appropriate source of tissue?  Just a thought.  It just seems highly coincidental that the virus (family) that apparently is so ubiquitous in the lab - from reported contamination in heparin blood tubes to DNA extraction kits...can in some cases infect human cells...and can reproduce the symptoms seen in CFS patients, whom at one point were thought to carry the virus.  Its just a can read the paper, an epub, here - Xpr1 is an Atypical G-protein Coupled Receptor that Mediates Xenotropic and Polytropic Murine Retrovirus Neurotoxicity

Global DNA Demethylation During Mouse Erythropoiesis in Vivo

Previously, it was thought that global DNA demethylation just occurs in germ cells and the preimplantation embryo, however here, Socolovsky's lab at U Mass show that in fact, global demethylation of DNA occurs during erythropoiesis (red cell development), and that it is dependent on replication - which is contrary to the idea of active DNA demethylation that has been put forward in some models.  Read about it in today's Science magazine Shearstone et al.

Thursday, November 17, 2011

The New Einsteins Will Be Scientists Who Share From cancer to cosmology, researchers could race ahead by working together—online and in the open

Michael Nielsen on Networked Science - -- 

this is a short but sweet article extolling the virtues of online networking for scientists -- it's definitely the way of the future, and I imagine that in a few short years manuscript impact factors will be a measure of the past -- instead people will look at how many other scientists read and cited your works -- open sharing of manuscripts by using the BMC and PLoS styles of journals will also help to rapidly disseminate information -- the trick now is getting everyone involved in the discussion, from senior faculty who aren't quite trusting of the internet, to postdocs and grad students who have possibly never been to the medical library in their institution - but visit it virtually online multiple times a day -- people can pretend but no one has the answers to everything, even if they are the expert in the area -- so why not start a discussion online about our favorite topic - and maybe we can all get to the answers sooner!  And speaking of the value of open access journals -- we published a manuscript in BMC Research Notes a couple of weeks ago - it went immediately into the ":highly accessed" classification - having garnered over 700 downloads in the first two weeks online -- tell me a single hard-print journal that can match that...

Wednesday, November 16, 2011

False negative results from using regular PCR reagents!

This is actually a new publication from our own lab, one of those "why did you run that control, and why did it turn out like that?" kind of moments, which led us to figure out that there are some serious problems with standard PCR techniques.  So what happened? We were testing human DNA samples to detect contaminating mouse DNA (recent reports have suggest mouse DNA gets into just about everything...including DNA isolation kits...) -- so we spiked some human DNA with varying amounts of mouse DNA to check our assay sensitivity-- then we wanted to test if carryover PCR product contamination (from previously generated reactions) could be eliminated by using a master-mix with uracil-DNA-glycosylase (UNG) -- it should do, because that's what is for -- so someone in the lab tested this, by adding mouse PCR product to the human DNA, but also added mouse DNA as well.  Huh! that reaction shouldn't tell us anything, because even if the PCR product was eliminated by the UNG, the mouse DNA would still amplify. Except that it didn't.  Even when the amount of PCR product added was minute, equivalent to femtoliters, and the mouse DNA was present in huge quantities (60ng) -- it still didnt' amplify!  We looked into this further to find that in fact, even primer-dimers from previously generated reactions will effectively inhibit new PCR reactions, even when the legitimate target is present in high copy number - who knew?  But how is this important?  Like all assays, its important to know what you are dealing with, the strenghths, and weaknesses of the technique -- in this case, if your target is limiting, you could have a huge problem, notably false-negative results.  We use the currently highly controversial example of murine leukemia virus-type sequences, that are either present (or not) in a variety of human tissue and serum samples, depending on who you talk to.  As we show in our paper - even two million copies of this virus can go undetected, if as much as 1 in 10000th of a microliter of a previously generated negative control PCR reaction contaminates the sample.  Maybe no one gets contaminated ever.  But as any lab that has ever tried to do nested PCRs  would likely attest to -- it is virtually impossible to never get contamination with previously generated reactions -- especially at the levels we are talking about here - anyway, read all about it, by clicking here (it's free!)

Tuesday, November 15, 2011

Vitamin D and cancer prevention! upcoming webinar from the experts, free!

As part of the frontiers in nutrition and cancer prevention webinar series put on by the Nutritional Sciences Research group at NCI, experts in the area of Vitamin D and Cancer will be speaking --
Presenters JoAnn E. Manson, MD, MPH, DrPH

Donald L. Trump, MD, FACP

James C. Fleet, PhD

register online at