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Turning 'crazy' into learnin-- XMRV from contaminated vaccines?

Category: Immunology

I hate how the 'new' Technorati doesnt let you see everyone whos linked to you. Sometimes, smaller blogs with less traffic write a neat post and link to me, but I dont 'see' the post unless I happen to catch one of their readers clicking to me on SiteMeter.

*FROWNY FACE AT TECHNORATI*

I just happened to catch an interesting post at this blag, Shiningthelights Blog. Dude might be nuts, I dunno. But I do like a Q they brought up (a month ago, *FROWNY FACE AT TECHNORATI*):

Is a mouse leukemia virus contaminating vaccine reagents the cause of Chronic Fatigue Syndrome?

Now, this Q might be coming from a place of deep distrust of all vaccines or the government or whatever-- I dunno. Doesnt matter. Can you answer that Q? Then its a good learnin opportunity, even if it comes from a place of crazy.

Do I think XMRV came from a contaminated cell line? It was one of my posts that got referenced, Oops: Contaminated cell-lines from the NIH.

No.

But thats partially because I think XMRV has shit (or is one of many components, almost shit) to do with Chronic Fatigue.

Its also because there are a gazillion cell lines with +gazillion uses-- And TZM-bls have nothing to do with vaccines. Like I said in that post, problems with that cell line are restricted to people using them as indicator cells for HIV-1 infection. Thats it. Thats all we use those cells for.

But still, how do we know? Can we be certain XMRV wasnt introduced to the population via vaccines?

Well, first we can wipe all the bacterial vaccines off the list (diphtheria, tetanus, pneumococcal, haemophilus influenzae type b, pertussis). Bacterial vaccines arent anywhere near cell lines.

Then we can knock out anything grown in yeast (HPV, Hepatitis B).

And measles, mumps, and influenza are grown in eggs.

Polio is a sturdy little mo-fo. The stuff we have to do to it to 'kill it' would blow the brains out of a wussy, fragile, enveloped retrovirus like XMRV (I just have to use a teeny tiny bit of formaldehyde to kill HIV-1 in the lab).

The people who have CFS now are too old to have gotten the chicken-pox or rotavirus vaccine, so Im not looking them up.

So... we are left with Rubella and Hepatitis A. They are the only ones attenuated/grown in human cells... but theyre lyophilized, and have formaldehyde... Thatll pretty much kill XMRV.

I guess technically, that evil 'formaldehyde' is actually kinda protecting you from wayward/undetected/undiscovered viruses in vaccines...

Even ignoring that the epidemiology of XMRV in vaccines-->CFS doesnt make sense, Im not concerned that vaccines meant for human use have XMRV in them.

*shrug*

But it was a good question!

Posted by ERV at 9:00 PM • 10 Comments • 0 TrackBacks

An open invitation to Bill Maher

Category: Douchebaggery!

Hi Bill!

I think Ive figured out why youve been... unresponsive... to the Skeptical communitys efforts to educate you on vaccines.

All the people addressing you have been cranky old men.

Apparently you dont swing that way.

I hearby offer to give you a personal crash-course in immunology, virology, and why scientists are so 'into' vaccines.

In my bikini.

Skeptic community gets you to quit spouting anti-vaccine BS on TV (and 'Twitter'), you get an out for admitting youre wrong ('34D! Id believe anything she said!') and can put this topic behind you.

Call my people.

Yours in Christ,
Abbie

Posted by ERV at 10:00 PM • 46 Comments • 0 TrackBacks

Virus helps save the American Chestnut tree

Category: Virology

100 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 characteristics and Asian fungus resistance (or take a shortcut and make a GMO).

Solution 2-- While Solution 1 is going, give currently surviving American Chestnut trees a therapeutic vaccine. Therapeutic vaccines dont prevent infection like the vaccines you are familiar with (like MMR, which prevents measles/mumps/rubella), they are given post-exposure to limit pathogenesis.

American Chestnut trees with Asian fungal lesions are given a 'vaccine' in the form of more fungus... but this fungus is infected with a fungal virus, hypoviridae. The virus goes on to infect all of the fungus infecting the tree, weakening the fungus so the trees immune system can kill it off!

Fleas on the backs of fleas!

You cant use virus/fungus as a prophylactic vaccine, as plants dont have an adaptive immune system like we do (they dont 'remember' pathogens theyve seen before). But this therapeutic 'vaccination' strategy can keep the American Chestnut population alive long enough for the breeders to find a permanent solution!

Posted by ERV at 8:33 AM • 17 Comments • 0 TrackBacks

Dan Barker at OU!

Category: Atheism

Dan Barker of the Freedom From Religion Foundation is going to be speaking at OU this Friday!

November 20
6:30 pm
Dale Hall

I-35 is Hell in the evening rush hour (last time I went to Norman we were going 15 mph. on an interstate. RAAAAAAGE!!), plus its a Friday, so all you OKCers make sure you leave early enough to get there on time!

Dan is going to be speaking on 'How to be good without God'.

Know what will be funny? If CFI cancels their invitation cause they insist Dans speech be pre-approved, and he wont change stuff they dont like, and then he shows up anyway, and we all beat-up/mace Annie Gaylor...

Too bad that wont happen, cause OUs CFI is made up of some fun, open-minded kids, and its not a troupe of morons.

lol!

Posted by ERV at 12:49 PM • 15 Comments • 0 TrackBacks

Modified virus lets blind kids see (and some adults too)

Category: Virology

A 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 stressors on those genes, infectious agents colliding with malfunctioning genes at just the right time...

I dont want you all to get the impression that treating/curing genetic diseases is going to be as 'easy' as the previous post made it out to be.

This is the case with a form of blindness-- Lebers congenital amaurosis (LCA). People born with this disease progressively go blind in infancy-childhood. There are numerous forms of LCA caused by a combination of 13 genes. Where do you start when youre trying to treat a multifactorial disease? Take small steps. Simplify it.

Researchers knew 6% of all LCA cases are caused by a defective RPE65 gene. Without this enzyme, you cant metabolize Vitamin A (EAT YOUR CARROTS!), you go blind.

So they started there:

Age-dependent effects of RPE65 gene therapy for Leber's congenital amaurosis: a phase 1 dose-escalation trial.

Read on »

Posted by ERV at 12:00 PM • 8 Comments • 0 TrackBacks

Three viruses join forces to treat X-linked adrenoleukodystrophy

Category: Virology

X-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 your brain and CNS.

X-linked ALD can be treated with allogeneic hematopoietic cell transplantation. You all can tell from the Wikipedia page, this isnt something you want to do unless you literally have no other options--

Hematopoietic stem cell transplantation remains a risky procedure with many possible complications; it has traditionally been reserved for patients with life-threatening diseases. While occasionally used experimentally in nonmalignant and nonhematologic indications such as severe disabling auto-immune disease and cardiovascular disease, the risk of fatal complications appears too high to gain wider acceptance.

Know what might be a better option, especially for kids who cant find transplant matches?

Retroviral gene therapy.

Hematopoietic Stem Cell Gene Therapy with a Lentiviral Vector in X-Linked Adrenoleukodystrophy

Read on »

Posted by ERV at 8:49 PM • 13 Comments • 0 TrackBacks

Ongoing witch-hunt against Oklahoma scientists

Category: General Science • Politics

Though only a handful of ERV readers are from Oklahoma, I know all of you are familiar with the handiwork of Senator Randy Brogdon.

He was the fellow who recently tried to get Creationism taught in Oklahoma public schools (FAIL).

Dude is a fucking IDiot (and just plain old idiot) who hates science:

I am also disgusted with the yearlong one-sided celebration of Darwinism that OU is sponsoring on their campus.

Disgusted? Really? Not 'disappointed', or 'dismayed', or 'intrigued, so Im going to check it out', but disgusted? Fantastic.

So what happens when you combine:
1. Anti-science
2. New found hatred of the US federal government
3. Xenophobia/racism
4. Infantile inability to delay immediate gratification for long-term goals
???

Attacks on university professors performing federally funded research!
(link-- might not work, video #1 isnt embedding, and is occasionally disappearing, way to go 'News 6')

Read on »

Posted by ERV at 10:30 AM • 41 Comments • 0 TrackBacks

Viral evilution in the lab-- 'Evolution before our eyes'

Category: Evolution • Virology

Professor 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 Biologist!

Posted by ERV at 12:00 PM • 9 Comments • 0 TrackBacks

Nef: Savior and Satan

Category: HIV/AIDS

Vpu has kinda been my accessory protein of choice here at ERV, but its not the only one with a super cool evolutionary history and super cool evolutionary implications.

Another particularly fun one is Nef.

This eeeeeeeety bitty HIV-1 protein (27 kDa) has a lot on its plate. Contrary to the 'expert' opinion of Michel Behe, who thinks viral proteins just 'gum up the works', Nef has several exceedingly specific functions--

1. Down-regulating CD4 from the host cell plasma membrane-- This is basically 'pissing on the fire hydrant'. HIV-1 requires CD4 on the surface of susceptible cells to initiate infection. HIV-1 doesnt want to share a cell with other HIV-1s, so one of the first things it does is haul all the CD4 receptors off the cell surface via clathrin coated pits (animation).


2. Down regulating MHC Class I from the host cell plasma membrane-- A simple Creationist might think that both CD4 and MHC are pulled off of the plasma membrane the same way. Since Nef just 'gums up the works', gumming up one surface receptor should gum up any surface receptor. This is soooooo not the case. MHC Class I molecules are essential components of a normal cell plasma membrane. They send up flags that say 'Everything is fine here! So dont kill me, k?' Viruses like to take down these flags, because they also can signal 'HEY! Im infected here! Better tell me to kill myself!' Viruses dont want that, so they take down the flags. Minor problem-- If no MHC Class I flags are there, another immune cell notices they are missing, and kills the cell. What Nef does, is specifically targets HLA-A and B, but leaves HLA-C and E alone, effectively keeping other immune cells from knowing anything is wrong with the infected cell. These are very very very specific interactions! Teeeeeeeeny tiny viral protein knows the difference between HLA-A and HLA-C. Thats nuts. Also, it takes these receptors off the surface an entirely different way than the CD4-- Its clathrin independent.


3. Inhibiting apoptosis-- Your immune system doesnt technically 'kill' infected cells. It tells them to commit suicide (apoptosis). Infected cells do not want to die. They want to produce progeny virus, and kill the cell in the process. Thus Nef also has the capability to inhibit a couple of the ways your immune system tries to induce apoptosis, FAS and TNF.

EEEEEEEEETY BITTY protein, all those functions.

At one point, Nef had the potential to be our savior. Between 1981 and 1984, eight people in Australia were infected with HIV-1 via blood transfusions from the same donor. This donor happened to have a mutation, where none of their viruses contained Nef. HIV-1, no nef. While this was during the height of the HIV-1 epidemic, people dying left and right, these eight patients were doing real damn good. Better than good. They were fine! None of them were progressing to AIDS, even without antiretrovirals! Scientists had hope that this meant we could make a live attenuated vaccine with delta-nef HIV-1!

Unfortunately, these patients never cleared the virus. And, three of them eventually progressed to AIDS (but responded to anti-retrovirals!) (one died from unrelated causes). Theres no way we could use that for a vaccine. *sigh*

Nef also turned into our nightmare. Know how HIV-1 always has the 'same genes that act the same way', according to Perfesser Behe? Nothing real exciting, he says? Yeah, this one time, back in the late 80's, we accidentally evolved an acutely lethal SIV.

Yes, you read that right. Acutely lethal SIV. As in, it kills you <13 days after youre infected. Not 10 years, less than 13 days.

Yeah.

Yeah.

Oops.

Scientists were passing SIV from sooty mangabeys in pig-tailed macaques. Its a stock-standard way of generating a live attenuated vaccine. Take the pathogen out of its native host, passage it in a non-native host, return the attenuated virus to the original host. The original host can usually fight it off better than the virus you started with.

Yeah, this didnt work with SIV. The 'new' SIV, 'smPBj'* had altered cell tropism, caused super friggen hyperactivated immune systems, and the monkeys basically shat their guts out and died.

All because Nef evolved a new function.

One amino acid mutation turned Nef into an ITAM, and all kinds of hell broke loose.

Happily, this variant of SIV is not found in nature, nor would we expect it to survive in nature (if you are pooping out your guts, you arent having sex to pass on the virus), but the artificial conditions we used in the lab allowed this variant to thrive.

Vpu aint the only cool eeeeeeeety bitty HIV-1 protein to have a fun evolutionary history :)

* An acutely lethal SIV, and its name makes my mind scream "ITS PEANUT BUTTER JELLY TIME! PEANUT BUTTER JELLY TIME!!!!"

Posted by ERV at 9:00 PM • 8 Comments • 0 TrackBacks