virology
sa smith | January 7, 2010October 16, 2009--
The science of this paper is fine. Their experiments are fine. And, there is clearly a bias for the presence of XMLV in CFS patients.
BUT, this story doesnt make sense.
October 23, 2009--
This normally 'harmless' virus is more prevalent in certain areas of the world (Africa) than in others (US), and is 'enriched' in sick populations where its not normally so prevalent (US HIV).
Similarly, XMRV was not found in 589 prostate cancer biopsies in Germany. None. Zero. In 589 biopsies, as opposed to the 233 in the XMRV+ paper I wrote about earlier.
It could be that XMRV is a US…
sa smith | January 5, 2010I volunteer my ovum in the service of cloning more Carl Zimmers.
Hes got a laymen-science appropriate-yet-not-dumbed-down-to-the-point-of-being-wrong article on the New York Times on one of the many ways we use viral evolution in the lab.
A decade ago, scientists began running experiments that suggested the idea just might work. In one study, Dr. Lawrence A. Loeb, a University of Washington geneticist, and his colleagues eradicated H.I.V. in vitro by applying a mutation-increasing drug to infected cells. Reporting their results, Dr. Loeb's group dubbed this kind of attack "lethal mutagenesis…
sa smith | December 7, 2009I was having a virus discussion with a surgeon recently:
Me-- People think to do HIV-1 research you have to gown up in those crazy suits and do all this insane safety stuff, really, the only thing I do 'really' different is I wear *two* pairs of gloves, lol!
Her-- I always double glove too, but its not the HIV-1 Im most worried about. Its Hepatitis C.
HIV-1 researchers, surgeons, people at high risk of accidental exposure to HIV-1-- we always have antiretrovirals within 5 feet of us, just in case. Get stuck with a needle, take the pills NOW, and you can stop the infection from getting a…
sa smith | December 1, 2009David Bolenski and the folks at XVIVO (yes, the same folks you all know and love) made a cool animation depicting the life-cycle of influenza!
You can find the long, 'scientific' version here, or a simplified explanation for NPR here:
H/T to Optimus Primate!
Disclaimer for stupid Creationists that want to plagiarize this animation for some reason or another-- While David & company are as scientifically accurate as possible, influenza 'doesnt really look like that'. This is an artists rendition. If you steal this, we will know. Like we knew you stole the other animation.
sa smith | November 22, 2009Invasive species suck.
Humans intentionally or unintentionally introduce some organism into a new environment... and shit hits the fan. Whether its zebra mussels in the Great Lakes or rabbits in Australia, invasive species wreak havoc on their 'new homes'.
There are lots of reasons for this, but there are only three reasons Im interested in:
1. The organism escapes from a pathogen in its native environment. No more pathogen, more reproduction.
2. The organism introduces a pathogen into its new environment. Organism has coevolved with this pathogen for ages, native organisms cant deal…
sa smith | November 16, 2009100 years ago, American Chestnut trees grew up and down the East coast. Great wood, nommy nuts, awesome! Unfortunately, an epidemic of an Asian fungus, Cryphonectria parasitica, basically wiped them out.
Asian Chestnut trees are resistant to the Asian fungus, so theoretically we could 'save' the American chestnut industry by planting Asian trees here... but they dont have the same beneficial features of the American species.
How can we save the American Chestnut?
Solution 1 (in progress)-- Keep crossing Asian Chestnut trees with American chestnut trees until you get a tree with American…
sa smith | November 13, 2009A long time ago, in a galaxy far far away, 'visionary' scientists like Francis Collins thought 'genetic diseases' were coming to an end. Because they believed in 'OGOD', 'one gene, one disease' (lol, *blink*), they were sure identifying 'disease' genes would... somehow... give us the ability to cure said diseases.
Unfortunately, even ignoring the technical issues weve had with gene therapy, OGOD isnt exactly how genetic diseases work. Yes, some are caused by one dysfunctional gene, like X-linked ALD I wrote about earlier, but many more are caused by a constellation of genes, environmental…
sa smith | November 10, 2009X-linked adrenoleukodystrophy (X-linked ALD) is a demyelination disease in little boys. The kids are usually dead before they hit adolescence.
:(
The demyelination mechanism is not the same as the demyelination disease you all have heard of, MS. With X-linked ALD, the kids dont have a functional ABCD1 gene. This means they cant break down very-long-chain fatty acids (VLCFAs) and they end up accumulating in the brain and screwing with the cells in charge of keeping up myelination, oligodendrocytes and microglia. Screw those guys up, screw up your myelin, screw up signal transduction in…
sa smith | November 4, 2009Professor Santiago Elena, one of the profs who presented at the Viral Evolution conference I went to last fall, is featured in a nifty video about watching evilution in action!
Evolution of Life: Evolution before our eyes
Just like I use evilution in the lab to understand the population dynamics of HIV-1 to create an HIV-1 vaccine, Dr. Elena uses evolution to understand how viruses evolve and adapt in plants, which will help us protect our crops.
Evolution isnt just about retarded monkey-fish-frogs. Understanding it has a direct impact on your quality of life.
Hat Tip to Teh Evilutionary…
sa smith | October 23, 2009Okaaaaaay...
*squint*
Let me preface this post by stating that I am not an MD. I dont care, particularly, about whether CFS is a 'real' disease or psychosomatic or a catch-all category for people MDs dont know how to treat. Sorry. So if you want to bitch about CFS, pro or con, dont do it in this post.
What I care about is retroviruses.
The behavior of this retrovirus in humans does not make sense as a causative agent for CF or prostate cancer.
It does not make sense.
Thus I think its an effect, not a cause.
Let me give you an example-- Human Herpes Virus 8.
The seroprevalence of HHV8 in…
sa smith | October 20, 2009One of these things is not like the others. One of these things just doesnt belong. Can you tell which thing is not like the others, by the time I finish my blag post?
#1-- Chronic Fatigue Sufferers Find Vindication in a Virus
News that chronic fatigue syndrome may be linked to a virus has been met with excitement by many sufferers whose symptoms and sanity have been doubted over the years.
#2-- Is a Virus the Cause of Fatigue Syndrome?
The new report has intrigued scientists, been seen as vindication by some patients and inspired hope for a treatment.
"I just feel like the whole future…
sa smith | October 16, 2009XMRV is so hot right now.
Read the paper on XMRV and Chronic Fatigue Syndrome last weekend:
Detection of an Infectious Retrovirus, XMRV, in Blood Cells of Patients with Chronic Fatigue Syndrome
My conclusions from the paper: XMRV is capable of infecting humans and producing viable progeny.
How this fact relates to CFS, Im still not sure.
Let me go through exactly what these researchers did.
1-- Nested PCR looking for XMRV genomes.
Nested PCR is kinda 'better' than regular PCR, especially when we are talking about retroviruses. How do you know the signal you are seeing is because of XMRV,…
grrlscientist | October 16, 2009tags: Lab Trash, recycle, molecular biology, cell biology, streaming video
I've been telling you about the perils of plastics, but some of the worst plastics offenders are molecular and cell biologists. Nearly every experiment that we do uses incredible amounts of plastics. In cell biology or molecular biology labs the emphasis is on working sterile, quickly and reproducibly. So companies have been selling all these incredibly useful products to life science labs: sterile plastic tubes of all shapes and sizes, single wrap multi-well tissue culture plates, sterile plastic dishes, sterile…
sa smith | October 15, 2009Over and over I see people concerned about the long term implications of only vaccinating against High-Risk HPV types:
If we vaccinate against types 16 and 18, wont other HPV viruses evolve to fill that empty niche? Wont other HPV step up to cause cancer?
This is a valid concern. With viruses, you need to get rid of it all, or you get rid of nothing. Say we figure out a perfect vaccine for HIV-1 Subtype C. We get rid of all HIV-1 Subtype C on this planet. Other subypes of HIV-1 will step up to fill that void... and youre back to where you started. Ugh.
But the answer to the question about HPV…
sa smith | October 12, 2009Retroviruses like to cause cancer. Its kinda their shtick.
Sometimes the viruses themselves code for oncogenes.
Sometimes the retroviral promoters accidentally upregulate an innate oncogene (the cell doesnt know its supposed to stop replicating).
And sometimes a retrovirus accidentally plops down in the middle of an important regulatory gene, and thats how you get uncontrolled replication.
MLV, murine leukemia virus, is a retrovirus that causes... leukemia... in mice.
It has also been implicated in prostate cancer in humans. This is kinda weird (target is immune cells in mice, but prostate…
sa smith | October 9, 2009There are a couple of things that Im getting over and over and over, from readers/friends/family/overheard in the grocery store, and its driving me nuts.
READ THIS NPR SUMMARY
1. Just call it swine flu. Thats what we all call it. H1N1 variants are completely normal components of generic seasonal flu. The 'new' flu is swine flu. Its just the pork industry doesnt want us to call it that in front of you all, thus we get:
We use "swine flu" as one of several names, along with "pandemic flu," "the new H1N1" and "the new flu." We try not to refer to this new virus as simply "H1N1," although…
sa smith | September 3, 2009Hey, remember a while back when I mentioned how scientists used evolution (random mutation and natural selection) in the lab to 'perfect' gene therapy vectors?
Theyve just one it again! In a BIG way!
Molecular Evolution of Adeno-associated Virus for Enhanced Glial Gene Delivery.
These folks were looking for a way to get man-made viruses to deliver therapeutic genes to infected/defective cells. Now, you dont want these viruses to infect EVERY cell of a sick person, necessarily, you want to target the specific, sick cells. A golden target for these folks is glial cells-- as their…
sa smith | August 28, 2009Since ~2006, honey bee colonies in the US have been dropping dead overnight. Literally. They call it 'colony collapse disorder'. While large populations of organisms dying is disturbing, no matter the species, we need honey bees-- they help pollinate so many of our crops. I grew up in the banks of the Missouri River, around apple and peach orchards (who always had their own bee hives, and honey) and hell, I eat everything on that list...
What is killing our bees?
People have accused GMOs and wireless internet and pesticides and antibiotics... We didnt have a clue before.
It might be…
sa smith | August 25, 2009Okay, no big shock to any of you-- bacteria are becoming resistant to our antibiotics. One of the many enteric bacteria (cause kids to poop to death), E. coli, is racking up antibiotic resistance genes like theyre McDonalds Beanie Babies.
What the hell are we going to do?
Phage therapy.
Bacteriophage are viruses that eat bacteria... lol... Bring in the gators to eat the snakes.
For a long time it was ignored as an option in the US (eh, Soviet medicine). It doesnt help that the Soviet 'science' behind phage therapy is murky-- yeah, they have commercially available phage therapies, but…
sa smith | August 11, 2009You know youre a nerd when:
1. You squeeeeee with excitement when the secretary tells you there is extra grant money you can use to order textbooks
2. You hand over a list of books you want to the secretary in ~30 seconds, because you keep a running list of stats/virus/evolution books you want
3. You squeeeeee even louder when said textbooks come in
One of the textbooks I ordered is 'Origin and Evolution of Viruses'. Bossman has the first edition, but it came out ~10 years ago. This new one is chock full of cool info... including a handy-dandy phylogenetic tree of important 'evolutions'…