erv

Horribleness2

Sat, 10 Apr 2010 14:36:09 -0500

How to make something totally awesome and geeky even MOAR AWESOME AND GEEKY?

Stylize 'Dr. Horribles Sing Along Blog' into an old-school Nintendo game:

AAAAAAAH I HOPE HE DOES ALL THREE ACTS!!!

H/T to Phage Integrase!

Read the comments on this post...

Arnies long-lost cousin

Thu, 08 Apr 2010 16:00:30 -0500

Since Arnie was a street dog when I found him, his parentage has always been in question. It doesnt help that he is a 'pit bull', which could mean any number of things-- line up 50 'pit bulls' and you will get short-and-stout to long-and-lean and everything in between. Black, white, red, big spots, small spots, brown with black stripes, black with brown stripes, everything. 'Pit bulls' are like a Dr. Seuss book.

Arnies round, doe-eyes and alligator smile definitely put him in the 'pit' camp, but his ears/profile are rather labrador-ish, and I think from watching this obedience training video that Arnie almost certainly has boxer in him as well:

Read the comments on this post...

Steven Pinker at USAO (live-stream available!)

Thu, 08 Apr 2010 11:30:29 -0500

Steven Pinker will be speaking tonight at the University of Science and Arts of Oklahoma in Chicasha!

Steven Pinker asks audacious questions about the human mind -- then boldly sets out to answer them. Recently named one of TIME magazine's 100 Most Influential People in The World, he is enormously popular in the media and highly respected in scientific circles. On April 8, he takes center stage in Chickasha as the keynote speaker for the fourth annual Emerson-Wier Liberal Arts Symposium. The evening presentation is scheduled at 7:30 p.m. in Te Ata Memorial Auditorium on the campus of the University of Science and Arts of Oklahoma.

If you cant make it down to Chicasha by 7.30, it looks like they are going to have a live-stream available (OK is on Central Time, for those of you way far away that wanna listen in)! WHOO! I love that! Go USAO!

Well dammit, I guess some panel was live-streamed, not the 7.30 lecture! WTF!

Lame!

Read the comments on this post...

Using HSV-1 to cure metastatic melanoma

Wed, 07 Apr 2010 12:00:39 -0500

Metastatic melanoma is definately one of the Cancers That Suck.

We basically have the same treatment options in 2010 as they had back in 1975... and not because we have chemotherapy/immunotherapy that works super great, no reason to change it. Our treatment options just suck, with horrible consequences-- Say you have 100 friends that are diagnosed with Stage IV metastatic melanoma today. One year from today, only about 25, 26 of those friends will still be alive.

~25.

Out of 100.

Survive one year after diagnosis.

Maybe fewer (this paper Im reading says 25.5%, Wikipedia says 9-15%).

Melanomas expression of ERV proteins might help us develop new therapies/vaccines in the future, but weve got a vaccine available right now that, apparently, cures some Stage IV metastatic melanoma!

Phase II Clinical Trial of a Granulocyte-Macrophage Colony-Stimulating Factor-Encoding, Second-Generation Oncolytic Herpesvirus in Patients With Unresectable Metastatic Melanoma

Read the rest of this post... | Read the comments on this post...

Quasispecies: A Wrinkle in Time

Tue, 06 Apr 2010 12:30:04 -0500

Super awesome review of viral quasispecies and what they mean, historically and currently:

Unfinished stories on viral quasispecies and Darwinian views of evolution.

They touch on so many good points, I could write about this review for a week! But just read it, cause I think you all can access it for free :P

One point I love: Quasispecies are like A Wrinkle in Time, connecting the origin of life to modern day viruses:

(on the origin of the quasispecies concept) First, there was the interaction between ideas from different fields of science such as physical chemistry and biological evolution. Second, there was the discovery that the concept of organizing genetic information in the form of quasispecies had relevance far beyond the idea of the origin of life. It was as though a time loop had joined microscopic and macroscopic knowledge together in our view of the world and established a link between the remote-in-time origin of life and current concepts about the genetic organization of RNA viruses.

Also, quasispecies give us a real-world framework by which we can test evolutionary/information theory concepts that were previously theoretical:

The addition of aspects arising from information theory complemented the theoretical framework. A multidimensional hypercube (cubes within cubes, as in a Russian nesting doll) served as a "space" for the theoretical representation of all the possible variants in a viral sequence. An important property of the space, referred to as a sequence space, is that all the variant sequences of a virus can be theoretically represented according to their kinship relation to the remaining variants. This framework served as a support for representing the fitness of each variant sequence in the sequence space (the fitness space) and for visualizing the correlation between fitness space and the distribution of the variants.

... Thus, several classic genetic principles applied to the evolution of the biological species, such as the Red Queen hypothesis, Muller Ratchet theory, and competitive exclusion, held up to experimentation and proved useful in viral quasispecies analysis. In contrast, experimental findings showed that the classic genetic concepts of wild type and mutant may not be applicable to molecular viral elements and that the idea of individuality does not relate to single, replicative RNA molecules but instead must be viewed in terms of a "clan" or quasispecies.

Theyve got a huge section on random mutation, fitness, and antiviral resistance, which several Creationists need to read.

And, a pretty funny commentary on the development of antivirals:

A drug reaches the last phases of development because it is predicted to have a reasonably good chance of being effective. Nonetheless, these predictions can fail when unexpected viral mutations that confer on the virus the ability to evade treatment develop. This outcome is so frequent that it raises the question of why scientists have been surprised again and again for decades by this "strange" phenomenon, instead of being surprised by the lack of flexibility of our concepts.

...There is enough experimental work to propose that at the RNA self-replication level, the "resistant" mutation is no more accidental than the "norm".

...Despite the fact that the concept of quasispecies was initially developed as a deterministic theory, chance is an essential element in all of these theories, conferring plasticity on the systems described.

EXACTLY! This is a point I have really tried to drive home on ERV:

The moral of this story, children, is that HIV-1 does NOT need to 'evolve' resistance to all the drugs in HAART therapy. The drug resistance mutations are already there, in every patient, for no reason at all. Just chance. Its just a matter of how fit those resistant viruses are, and they do regain fitness over time. In some unfortunate patients, their quasispecies contains viruses that are resistant and very fit-- you must change their drug regime immediately.

Random mutations, chance, are what a quasispecies is all about. The fact there are variants within a quasispecies that are resistant to any drug you happen to think up is 100% totally normal. Its not 'miraculous' or 'proof of a Designer' any more than water freezing at 32 F.

Thats just what quasispecies do. Thats just what water does. Its chemistry, not magic.

Fantastic review of quasispecies-- You all should read it :)

Read the comments on this post...

BALLS!

Sat, 03 Apr 2010 17:04:08 -0500

From my post on testicular cancer and ERVs earlier this week, to Randys balls in the last episode of South Park, the word of the week appears to be "BALLS!"

This trend is continuing, considering Judy Mikovits/the Chronic Fatigue communities vociferous support for anti-vaccination cranks:

The increasing incidence of mumps orchitis: a comprehensive review-- There has been a recent increase in mumps orchitis among pubertal and postpubertal males. These outbreaks can be attributed to a reduction in the uptake of measles-mumps-rubella (MMR) vaccine during the early to mid-1990s in children who have now matured. The mumps virus is commonly associated with extra-salivary complications. Unvaccinated postpubertal males diagnosed with mumps virus frequently develop complications such as mumps orchitis. Therefore, it is important that urologists are familiar with the diagnosis, treatment and complications of this condition. Here we review the epidemiology, clinical presentation, diagnostic methods, treatment options and complications of mumps orchitis, as a complication of mumps virus, with particular emphasis on testicular atrophy, subfertility and infertility.

SPOILER: All those little boys not getting their MMR? They grow up, go to college/work/military, and get mumps. Little boys sometimes get swollen balls as the result of mumps infection, but young adult/adult males get it often (40% of men who get mumps, get swollen, inflamed balls. 'most common complication') and really bad. End result? Sub- or total infertility. 40% of men who get mumps.

Also, their balls shrink.

:-/

A very big problem is that physicians arent really used to diagnosing mumps-induced orchitis. Im not dude, but I can think of lots of reasons why a dude might have swollen balls. Mumps orchitis hasnt really been a problem since the MMR vaccine was developed, so why would it be their first thought when a guy walks into their office with swollen balls? I mean, how many of todays physicians could readily diagnose a reemerging nonparalytic polio virus vs a simple influenza infection? Its just not something a modern physician thinks about.

To top this off, swollen balls might not show up until 6 weeks after the guy has mumps! With all the other symptoms long-since resolved, Doc would have no reason at this point to think something viral is going on.

Diagnosing mumps orchitis is a problem for physicians. Theyre needing to remind one another what to look for/how to treat the pathology of mumps.

So even though the mumps vaccine was invented in 1949, because of anti-vaxers, we still get publications in the 'British Journal of Urology' like this, reminding everyone of the "epidemiology, aetiology, clinical presentation, diagnosis, treatment, and complications" of mumps in relation to balls, in 2010.

Way to go, Ace!

Read the comments on this post...

Not all CD4+ T-cells are created equal

Thu, 01 Apr 2010 10:30:15 -0500

One of the coolest things I learned last week in Banff is the 'why' behind an odd AIDS phenomena:

So you all might know that the cut-off, the mark for being diagnosed with AIDS (and not just 'HIV-1+') is a CD4+ T-cell count of <200 cells/mm3.

Okay, so, you lose all your CD4+ T-cells, your immune system loses its ability to work properly, and you start getting all these secondary infections-- infections that 'healthy' people get, but they arent a big deal. But secondary infections are a big deal to AIDS patients, I mean, thats what they die of, not the HIV-1 specifically.

What is weird, is that HIV-1+ patients get Tuberculosis before they hit that '200 cells/mm3' mark. In fact, its one of the first signs of HIV-1 infection, a random 'healthy' person getting TB. Conversely, Cytomegalovirus doesnt reactivate until you are waaaaay below 200. You dont lose your ability to defend yourself against CMV until you are basically running on empty.

It appears as if the CD4+ T-cells that 'remember' TB are more susceptible to HIV-1 infection, while CD4+ T-cells that 'remember' CMV are protected from HIV-1 infection.

But how the heck would that work??

Early depletion of Mycobacterium tuberculosis-specific T helper 1 cell responses after HIV-1 infection

CD4+ T-cells that 'remember' TB secrete chemical messages that keep them in more of an 'active' state... precisely the kind of cell HIV-1 LOVES to infect.

On the other hand:

Autocrine Production of β-Chemokines Protects CMV-Specific CD4+ T Cells from HIV Infection

CD4+ T-cells that 'remember' CMV secrete chemical messages that are protective, mainly, one called MIP-1β. MIP-1β is the ligand to CCR5, one of the co-receptors HIV-1 needs to infect cells. So if MIP-1β is taking up all the available CCR5 slots, or the bounty of MIP-1β around causes the cell to downregulate CCR5, those cells would be protected from HIV-1 infection!

Similar research from another lab backs this up:

'Self-Protection' of Individual CD4+ T Cells against R5 HIV-1 Infection by the Synthesis of Anti-Viral CCR5 Ligands

This has a huge impact on how we design HIV-1 vaccines! What would be the point in making a vaccine against HIV-1, if all your CD4+ T-cells that 'remember' HIV-1 are killed off in the first round of HIV-1 infection?

So now all we have to do is figure out how to make a vaccine that generates CMV-like CD4+ T-cells, not TB-like cells! Easy-peasy... right?

Read the comments on this post...

ERVs, Epigenetics, and Testicular Cancer

Tue, 30 Mar 2010 13:00:17 -0500

Once again, ERVs, the best goddamn workhorse in the stable, have provided another great example for explaining How the World Works. This time? How a functional ERV protein interacts with normal cellular proteins to cause epigenetic changes that lead to cancer:

Human Endogenous Retrovirus Protein Rec interacts with the Testicular Zinc Finger Protein and Androgen Receptor.

WARBLEGARBLE!!! FUNCTIONAL ERVs!

WARBLEGARBLE!!! EPIGENETICS!

EVERYTHING YOUVE BEEN TOLD ABOUT EVILUTION IS WRONG!

JESUS IS LORD!

heh.

That title/abstract looks scary (okay, it is scary. there is a reason I didnt go into cell bio), but the basic premise of the paper is super easy and really cool.

Read the rest of this post... | Read the comments on this post...

XMRV and chronic fatigue syndrome: PI FAIL, revisited

Tue, 23 Mar 2010 16:21:08 -0500

Oh for fucks sake.

Just after Jenny McCarthys 'keynote address' at an 'autism' conference sponsored by AUTISMONE and Generation Rescue, Judy Mikovits is going to talk to everyone about XMRV (3-4 pm).

Judy, you are one pathetic excuse of a 'scientist'.

Read the comments on this post...

The Great Banff Adventure!!

Mon, 22 Mar 2010 15:21:45 -0500

They wouldnt let us pay for gas or anything, so the best I can do is Blog Props: Mark and his Super Awesome Girlfriend are AWESOME!!!

There is this company that offers tours around Banff-- White Mountain Adventures, something like that. Yeah... all the trips they offer? MARK AND HIS SUPER AWESOME GIRLFRIEND TOOK ME AND BOSSMAN ON ALL OF THEM. ALL OF THEM. AWESOME!

Technically, they didnt take us on a dog-sledding tour, but the substitution was better-- I got to have two snuggly weenie dogs curled up on my lap for part of the trip. Two snuggly puppies, enjoying the beautiful scenery, this was my thing.

But Bossman, Mark, and Marks Super Awesome Girlfriend were wild mountain trekking all over the place! There are hysterical photos (and possibly video) in the works of Abbie looking like a clumsy giraffe...

But it was great!

THANK YOU MARK AND HIS SUPER AWESOME GIRLFRIEND!!!

Read the comments on this post...

The Great Banff Adventure!

Sat, 20 Mar 2010 21:53:04 -0500

OMG you guys! I have had such a day (in a good way)!

1-- We barely made it out of OKC. Barely. As in, our plane left, and then they shut down Will Rogers Airport for a while, cause our plane had to be de-iced three times to get off the ground.

2-- We barely made it on to our flight to Calgary. Seeing as the plane from OKC was 2 hours late, and we factored in a 2 hour layover (just in case), we should have missed this flight. Except, by Teh Grayce of GAWD, the flight to Calgary was held up for a random 15 minutes, allowing us enough time to careen to the appropriate gate.

3-- Since we barely made it on the plane to Calgary, we expected our luggage to arrive, oh, about June-ish. Dudes. Dudes. The luggage was there waiting for us in the carousel in Calgary! !!!!!!!

4-- We were starving (no time for food since 5 am), we hunted down Banffs only Indian resteraunt. They werent open yet. So we got beer. I tried that 'honey wheat something or another'. AWESOME!!!!

5-- SHAME ON ALL YOU BANFFIANS! None of you recommended the Indian place, AND IT WAS FUCKING AWESOME!!!! We creeped the hell out of our poor waitress by telling her how we had been fantasizing about her food for hours, making erotic noises at the table, etc. MASALA. GO THERE IF YOU VISIT BANFF. AWESOME!!!!

6-- I am now sitting in a jacuzzi, blogging... unfortunately on crappy slow $10-a-day internet. Might not renew every day... But otherwise... AWESOME!!!

---
Edited to add:
BLARG I almost forgot another good thing!!

7-- I have never, in the history of ever, flown without pain. Cabin pressure going up/coming down causes these constant, stabbing needle pains in my ears. After I land at the desired location, I cant hear anything for about a day. Needless to say, I dont enjoy flying, and avoid it whenever possible... UNTIL I FOUND EARPLANES. OMFG you guys. OMFG. They were a pain in the ass to put in (was I supposed to get the childs sized ones? these things are huge), but once I got it-- my ears felt normal. On both flights. The whole time. No stabbie-needle pain. No stuffy ears. I am shocked this life-long problem was solved so easily.

Also, another bad thing-- ALLERGIES. WTF. I thought I was leaving the cedar pollen behind in OKC! Ever since I got here, my eyes have been itchy, sneezing, stuffy nose. What is this crap??

Read the comments on this post...

HIV Denier FAIL

Sat, 20 Mar 2010 06:08:55 -0500

AAAAAAAHAHAHAHAHAHA!

Know how a while back, when I let that 'House of Numbers' spam through for the lulz?

Well, apparently that spam was sent by a real human, not a spambot. Like, a real breathing human with no life.

Cause humanspambot took that comment going through as an opportunity to spam numerous other posts on ERV, sometimes the same post repeatedly. The exact, same, message.

Since I approved the other spam, poor ERV thought it was supposed to let them all through, so I had to manually trash them all. I then sent a short polite email to the email address associated with the comments:

Stop spamming my blog, pig fucker.

--Abbie

This, naturally, is BIG TIEM NEWS for loser manual humanspambot:

Guess "House of Numbers" can't have an opinion on HIV/AIDS on scienceblogs.com without a Hostile reaction from the host.

You can comment on ERV all you want. You can even ignore my HIV-Denier challenge and keep bitching about ANTIRETROVIRULZ BE POISEON!!

But you cant spam, pigfucker.

Read the comments on this post...

Varmus head of National Cancer Institute!

Fri, 19 Mar 2010 13:07:32 -0500

WHOO!!

Harold Varmus is gonna be the next head of the National Cancer Institute (probably, still a non-confirmed nerd rumor)!

*excited peter griffin giggle*

Read the comments on this post...

Backwards day: Using ERVs to treat cancer

Fri, 19 Mar 2010 11:00:42 -0500

Retroviruses cause cancer.

Like how HPV causes cancer, its not really 'on purpose', its just a side-effect of their life-cycle-- insert DNA randomly into a genome enough times, and eventually youre going to plop somewhere you aint supposed to be, and cause cancer.

Thus I am terribly amused when Creationists bawww about how ERVs are perfect and special (not junk!)... cause if those ERVs werent rendered junk by mutagenesis or epigenetics, we would all be dead (technically, never born).

Found a paper in Nature Cancer Gene Therapy that kinda turns this issue upside down:

Fusogenic membrane glycoproteins induce syncytia formation and death in vitro and in vivo: a potential therapy agent for lung cancer

Theyre exploring ways to use envelope (from ERVs and retroviruses) to kill cancer!

Read the rest of this post... | Read the comments on this post...

Banff!

Wed, 17 Mar 2010 09:45:10 -0500

Next week Im going to be in Banff, Alberta.

Its just a generic resort town, so I dont suppose any of *you* would be there to party, but I was hoping some of you might have visited and know some tips/tricks/things to see/things to avoid.

My plans so far: soak in hot springs for a week

Read the comments on this post...