HIV/AIDS
sa smith | September 2, 2010A long time ago, I think on Pharyngula, Richard Dawkins said something that really pissed me off. Its been so long ago I cant find the right comment thread anymore, but Dawkins said something regarding epigenetics along the lines of "Um... isnt this just a fancy word for transcription regulation? Stuff weve been studying for years and years..." And I went all WARBLEGARBLE "OMG NO EPIGENETICS IS SO NEW AND DIFFERENT AND SO MUCH COOLER THAN TRANSCRIPTIONAL REGULATION OMFG RICHARD DAWKINS UR SUCH A N00B!!!"
Yeah...
Yeah......
I totally get it now. Ive slowly been getting it since that…
sa smith | August 29, 2010EDIT-- TIME ZONE FAIL! 11 am Central! LOL!!!
So this weekend there is a live blogtv blogathon to raise money for HIV Research!
I am not a member of the blogtv culture, so I have no idea whats going on, LOL, but you can watch it here!devchelle2- Broadcast your self LIVE
And you can donate here!
I will be on live at 10 am Central time to talk about HIV-1 and answer some Qs!
NOTE: To stop the echo, click on the mute in the inner window!
sa smith | August 3, 2010FINALLY!
A free paper that explains the basics of viral quasispecies!!! YAAAAAY!!!Quasispecies Theory and the Behavior of RNA Viruses
ARG! I have been wanting a paper like this to come out for AGES! I dont back down from explaining complex topics to you guys, but 'quasispecies' is just so weird...
I am going to reference this thing all the time now!
Eeeeeeeeeeeeeee!!!! Survival of the flattest!
**HAPPY-DANCE**
sa smith | July 21, 2010Im sure you all remember the guy I wrote about a while back, who had HIV-1 and leukemia. While that is actually pretty common, what wasnt common was his treatment-- a bone marrow transplant from a match who happened to lack the CCR5 gene, thus lacked one of the co-receptors HIV-1 needs to infect cells. This was a death-blow to the HIV-1 in this guys system. The virus in him simply has no (or very few) place else to go, so it burned out.
But this is simply a non-viable idea for 'curing HIV/AIDS' for basically everyone else on the planet. Financial barriers, technological barriers,…
sa smith | July 19, 2010Sometimes I am the worlds worst advocate for my own research.
Yes, its fantastically cool.
Yes, we learn more about the world and how life evolves on it.
But THE REASON I do HIV-1 research is to help ultimately create an HIV-1 vaccine. The only way we are going to beat HIV-1 is to stop new infections, and to stop new infections, we need a vaccine...
Or, everyone could just wear condoms, which reduce HIV-1 transmission ~85%, and we could cut this bastard off at its head in a few generations and I can go do something else.
*blink*
Well, the thing is, things arent that simple. Half the people…
sa smith | July 14, 2010A few weeks ago, Slate ran this pointed article about the FDAs refusal to allow homosexual men to donate blood. Quick summary: Yes, homosexual men are 'at risk' for HIV-1 infection. But the majority of HIV-1+ homosexual men are aware of their status, thanks to increased HIV-1 awareness in their social community. African Americans also have an increased risk of being HIV-1+... but very few know they are positive. So if you are going to ban homosexuals for 'being at an increased risk of being HIV positive' (but not people who have sex with prostitutes or IV drug users), why not blacks too…
sa smith | July 9, 2010Antibody Discovered for 91% of HIV Strains
*sigh*
For all intents and purposes, Ive talked about this before.
Not *this* antibody, but other SUPER AWESOME ANTIBODIES OMFG BREAKTHROUGH!
Your adaptive immune system operates by, what I would call, picoevolution. It is chance + random mutations + natural selection.
Lets say both you and I get infected with the exact same variant of swine flu. We both fight it off successfully, and generate a potent neutralizing antibody response to swine flu. My neutralizing antibodies are nothing like your neutralizing antibodies. Chance, randomization, and…
sa smith | June 9, 2010Read on my GoogleNews today:Taliban Reportedly Adding HIV-Infected Needles to Explosive Devices
Hypodermic syringes are reportedly hidden below the surface of explosive devices, pointing upwards to prick bomb squad experts as they hunt for devices.
The needles are feared to be contaminated with hepatitis and HIV. And if the bomb goes off, the needles become deadly flying shrapnel.
Some viruses/bacteria can live a long time outside of the human body. Bacteria sporulate so that can survive in harsh conditions (think anthrax spores), and some viruses can survive outside of a host okay (polio,…
sa smith | May 18, 2010Hey do you guys remember Michael Behe? Massive douche, wrote books about how EVILUTION IS IMPOSSI-BLEH! Gave school boards/teachers an excuse to teach Creationism in public school classrooms and pretend they were teaching science? He was like, the cock-of-the-walk when 'Darwins Black Box' came out, but then he made a total ass of himself testifying in Dover, and then he wrote that massive abortion, 'Edge of Evolution', and now dude has pretty much disappeared off Planet Earth?
Well, while Michael 'Lilo' Behe might be gone, he has not been forgotten!
Ancient adaptive evolution of Tetherin…
sa smith | May 13, 2010This post is really frustrating to write.
Its frustrating because this paper could (should) be FANTASTICALLY COOL, but it was just really frustrating to read:
Mosaic HIV-1 vaccines expand the breadth and depth of cellular immune responses in rhesus monkeys
You all know there is a TON of genetic diversity in HIV-1. That has been a huge barrier for vaccine design. You put one HIV-1 variant in a vaccine, people are exposed to another, they still get sick. Our vaccines are eliciting a very narrow immune response. Our immune systems are only seeing exactly what our vaccine tells it to see.
We…
sa smith | April 1, 2010One 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
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+…
sa smith | March 15, 2010[insert random collection of Ray Comfort jokes here]
Well, this is a welcome bit of good news!
A lectin isolated from bananas is a potent inhibitor of HIV replication.
Lectins are proteins that bind to specific sugars. For example, in humans, lets say you are infected with Staphylococus aureus. Your human lectins ignore 'your' sugar, but they recognize that the bacteria are making the 'wrong' sugar, and stick to them. This sets off a cascade of events that ends with the bacteria getting blown up.
Swanson et al have found a lectin in bananas ('BanLec', heh) that really likes high-mannose…
sa smith | March 3, 2010Your immune system is like an onion ogre parfait.
Its has lots and lots of layers.
You have intrensic immunity-- Abilities every single one of your cells has to defend itself from viruses. VpuTetherin would be a good example of this, as would APOBEC and Trim5a. Pick a cell in your body-- it can make these proteins. Doesnt have to be a special immune cell.
Then you have innate immunity-- Certain immune cells are not specific for any particular pathogen, but they can identify patterns that are 'wrong'. They see things your body knows aint right, like double-stranded RNA (your body doesnt…
sa smith | March 1, 2010HIV-1 deniers-- They love Orac. They love Tara. Even like haunting the Hoofnagle brothers a bit.
They dont like ERV.
Never have.
*sad face*
I really cant figure out why. (I bet its cause Im mean and kannut com00nicates scienz).
Three years ago, today, I posted a challenge to HIV-1 Deniers. A simple test of basic HIV-1 literacy and competency. Three years ago... and it only has three comments. One from a supporter, one from me, and one from an HIV-1 Denier... who didnt answer the question. Just linked to the nutty Perth Group and hoped something Perth said stuck (nothing on the linked…
sa smith | February 25, 2010From building bridges with anti-vaxers to building bridges with animal liberation maniacs, Chris Mooneys 'building bridges' plan is revolutionizing the way scientists interact with insane people!
Its even changing the playing field with HIV-1 Deniers.
Long-time readers know I have relatively little patience with HIV-1 Deniers. Everyone involved with HIV Denial, from the 'professional scientists' to the 'Average Joe snake-oil salesman' are complete and utter morons. So, frankly, they are only good for one thing: lulz.
So while I like writing about the latest HIV-1 findings on ERV, I rarely…
sa smith | February 15, 2010Last week I wrote about a disappointing study where they found that treating people infected with HIV-1 and HSV-2 with acyclovir didnt decrease their rates of HIV-1 transmission to their partners... even though they had lower HIV-1 viral loads, and fewer HSV-2 outbreaks.
Really disappointing.
Well, that same group reanalyzed their data from a different angle: The people who got acyclovir, how did that effect their progression to AIDS?
Daily aciclovir for HIV-1 disease progression in people dually infected with HIV-1 and herpes simplex virus type 2: a randomised placebo-controlled trial--Our…
sa smith | February 11, 2010I refer to this so often-- I need to make a name for it.
A name for how Creationists are always parading about saying protein structures are so perfect and pretty colorful Lego blocks, and they all snap together perfectly, but reality is SO not like that? Reality is a buzzing, floppy, invisible mess?
Invisible is the key word here-- Scientists cant look into their microscopes and watch 'Inner Life of a Cell' in real-time.
Figuring out what protein structures 'look like' is really damn hard.
Example #1: VSV, Vesicular Stomatitis Virus? It is like, and old-school virus. Old-school. Like,…
sa smith | February 9, 2010Acyclovir and Transmission of HIV-1 from Persons Infected with HIV-1 and HSV-2.
--Daily acyclovir therapy did not reduce the risk of transmission of HIV-1, despite a reduction in plasma HIV-1 RNA of 0.25 log10 copies per milliliter and a 73% reduction in the occurrence of genital ulcers due to HSV-2.
Well crap.
Im sure you all can figure out from that one sentence in that abstract why this is disappointing, but let me give you the back story.
Way back in the 1990s, scientists noticed that HIV-1 and HSV-2 were able to form this awful, unholy alliance. Proteins made by HSV-2 could increase…
sa smith | January 4, 2010I havent mentioned anything about Ugandas Evangelical-driven quest to kill homosexuals.
I figured that you dont really need to have my expertise in HIV-1 to recognize that these people are fucking psycho.
But, it doesnt take a whole lot of effort for me to demonstrate that on a scientific level, these people are wrong (not surprising since its religious nuts fueling this fire, and they think the universe began 6000 years ago and believe in talking snakes and shit)-- killing every homosexual in Uganda would have little effect on HIV-1 infections/deaths.
Anyway, heres the deal.
Percentage of…
sa smith | November 3, 2009Vpu 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--
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…