July 29, 2010
Category: ERVs • Virology
Ummmmmmm...
Hmmm...
Filoviruses are ancient and integrated into mammalian genomes
Hmmmmmm...
Unexpected Inheritance: Multiple Integrations of Ancient Bornavirus and Ebolavirus/Marburgvirus Sequences in Vertebrate Genomes--
This first comprehensive study of its kind demonstrates that the sources of genetic inheritance in vertebrate genomes are considerably more diverse than previously appreciated.
No... no... PLOS received this paper first, but BMC Evolutionary Biology published their paper first... so... no...
Its still neat, but... :-/
Posted by ERV at 8:27 PM • 0 Comments • 0 TrackBacks
July 28, 2010
Category: GMO NOMS • Vaccines
While poop jokes are all in good fun here in the US (and in other developed parts of the world), diarrhea really isnt all that funny for most of the planet. Dehydration due to diarrhea is the second leading cause of death for babies, worldwide (it was #1 until we started aggressive education/re-hydration efforts). Hundreds of thousands of people die from cholera and enterotoxigenic E. coli (ETEC) infection every year.
Thats not funny :(
So scientists have been working really hard to create vaccines to cholera and ETEC, and a group of folks have figured out a really cool strategy-- genetically modify rice to express part of the cholera toxin. When someone eats the vaccine rice, their immune system gets a cheat-sheet for what the real toxin will look like. Their body starts secreting IgA, antibodies that recognize the toxin, in their mouth/tears/digestive tract/breast milk. If that person is exposed to real cholera, they already have antibodies around to neutralize the toxin, thus are able to prevent or limit the extent of that infection!
BONUS: If the person who gets the vaccine is a breast-feeding mom, these beneficial anti-cholera-toxin IgA antibodies are passed down to their babies via breast milk, thus also protect their babies from cholera!
BONUS BONUS: This plant-based vaccine strategy is also beneficial because it requires no sterile needles, no freezing/refrigeration, and the vaccine would have a ridiculous shelf-life of at least three years.
What have the scientists named this awesome GMO-rice-product?
MucoRice.
*gag*... *gaaaag* Oh gross... Christ... LOL! I know its supposed to be 'muco' for 'mucosal immunity', but all I think is 'mucus', and I dont want to eat that... uuuuugh... LOL!
Ignoring the gross name, theyve put a lot of effort into this vaccine-- here is just their latest paper, 'proving' that the secreted anti-cholera-toxin IgA antibodies are why this vaccine works:
Secretory IgA-mediated protection against V. cholerae and heat-labile enterotoxin-producing enterotoxigenic Escherichia coli by rice-based vaccine
Read on »
Posted by ERV at 12:00 PM • 23 Comments • 0 TrackBacks
July 26, 2010
Category: ERVs • Evolution
Human beta globin has held a special place in my heart due to its rather prominent role in the Evolution-Creation 'debate'. It just got a neat evolutionary upgrade :)
Humans have one kind of hemoglobin when they are infants which has a higher affinity for O2 (alpha globin + gamma globin), because it makes it easier to steal O2 from their mom. Once the babies are out in the real world for a few months, they slowly but steadily shift from making the gamma globin to beta globin, the adult hemoglobin (alpha globin + beta globin).
This transition is a problem for kids with sickle-cell. Their gamma globin subunit is totally fine... but once they transition to using the beta subunit, all hell breaks loose. The mutated betas get together to form fibers that misshape red blood cells (ie, sickle-shaped).
Gene therapy, replacing the 'bad' gene with a normally functioning gene, would be a marvelous future option for people with sickle-cell (or designer babies for people who carry the gene), but an option we are pursuing today is how to get people with sickle cell to stop/reduce their production of the beta subunit, and go back to using their fully normal gamma subunit. Even if you can only slightly alter the ratio of gamma:beta, you could provide a useful therapeutic effect for people with sickle-cell-- If there is a lot of gamma subunit floating around, then the malfunctioning beta subunits cannot form those fibers as easily.
A neat paper came out earlier this month that help explains the how/why of the gamma-->beta subunit switch in humans, and might give us some ideas on how to alter it:
Long-range function of an intergenic retrotransposon
Read on »
Posted by ERV at 12:00 PM • 3 Comments • 0 TrackBacks
July 24, 2010
Category: Shillerations!
Lets say you are a super hero. You are in cognito at this huge fancy party the Mayor is throwing, and you get word that one of the party guests is really a mad scientist/evil genius whos about to do something really mad/evil. You can stop them, but the mad scientist/evil genius is in cognito too. How do you pick them out of the crowd?
One handy physical identifier of a mad scientist/evil genius is their crazy hair*.
Go on, Google Image 'mad scientist'.
We have crazy hair.
Its not just the antisocial aspect of it (dont touch me), but we just dont have time for this sort of thing. My last haircut was sometime last September or October. I remember back in March thinking "Ugh, I need to get a haircut." And then in May when it got really hot I was like "Shit. I need to get a hair cut." Finally, today, at the end of July, I got another hair cut.
But a problem I had March-->today was what to do with my crazy compound Mormon-length hair. Certainly cant wear it down at work. Braids look dowdy. Pony-tails got saggy. I loved doing a Lara Croft braid, but that gets old. What I really would have loved to do was wrap all my hair up in a chignon, but my hair is so fine and super thick, all the bobby-pins in the world wouldnt hold it.
UNTIL NOW!!
SPIN CLIPS by Goody are freaking amazing*! Check out YouTube-- Chicks are freaking out over these things, with good reason. So, once again, I had creepy compound Mormon-length hair. Super fine. Super thick. These two stupid little clips kept my hair in a bun not only through an entire day of work, but through 45 minutes of boxing! With no ponytail holder or any other hair apparatus. I tried them several times to make sure the boxing thing wasnt a fluke-- But it wasnt. These are two tough little stupid clips.
So now I have a nice normal haircut again, and Ive got spin clips, so I can blend seamlessly into crowds :-D YAY!!
* DOES NOT WORK for bald mad scientists/evil geniuses.
Posted by ERV at 4:39 PM • 18 Comments • 0 TrackBacks
July 23, 2010
Category: General Science • Science Outreach
WARBLEGARBLETHISISSOCOOLYALL!
Where to start?
You all are aware of the fact we have 'science education issues' here in Oklahoma? Well not everyone here is sitting on their hands, shaking their heads, bemoaning what a shame it is. A fellow who lives in Stillwater, Monty Harper, is actually trying to do something about it in a really cool way (weve praised him on SciBlogs before)!
Monty is a childrens song writer and self-professed science geek, so once a month he and a local scientist put on a show for local elementary school kids (3-5th grades)-- he writes a song about that scientist, and they talk about their research! For real, check out the fantastic programs hes run at the Stillwater Public Library! I wanna go...
Anyway, Monty has built up enough of a song-base now, he wants to make an album so he can help kids everywhere get excited about science. It will include songs on topics like phototaxic bacteria, stress hormones, wheat genomics, bacterial biofilms, bat taxonomy, x-ray crystallography, and luminescence dating! For real.
Here is where you can help--
If you think this is a neato idea and would like to help it become reality, check out Montys page over at kickstarter.
Look at the donation tiers, and see where you want to help-- you can donate and free CDs will be sent to a local school, you can get a CD for yourself for your kids (Im giving mine to my nieces), you can get all kinds of insider exclusives, get your name in the CD booklet as an official donor, or at the highest tier-- you can get a custom song of your very own, written about YOUR research or your FAVORITE branch of science if you arent a scientist, and be included on the CD!
If Monty doesnt reach his funding goal by August 21 (HIS BIRTHDAY), you wont be charged anything, Monty loses the window his producer has open, and he has to start all over.
Im not much for talk (*cough**Mooney**cough*)-- Im all about action, and I really have to get behind a guy who may not be a scientist, but he is using his passion and talent to actually DO something to promote science literacy and getting kids excited about science.
"My goal is to give kids a chance to talk to real working scientists about their research," said Harper. "I want kids to come away feeling that they talked to a scientist who's doing important work and I want them to picture themselves doing similar work in their own lives."
Posted by ERV at 10:30 AM • 8 Comments • 0 TrackBacks
July 21, 2010
Category: HIV/AIDS
Im 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, immunological/genetic barriers (not enough people who are delta-CCR5, certainly not enough have the genetic diversity to be an appropriate match for everyone with HIV-1).
A new idea has come up that doesnt help with the first two problems (but technology does get cheaper over time), but it helps with the last problem-- What if we could make any bone marrow donor delta-CCR5?
Generation of human induced pluripotent stem cells bearing an anti-HIV transgene by a lentiviral vector carrying an internal murine leukemia virus promoter
How this would theoretically work:
1. Find an appropriate genetic bone marrow match for the HIV-1+ patient, OR, get bone marrow from the patient him/herself (though some say bone marrow is infectable with HIV-1, so this might not be possible)
2. Treat the bone marrow with a lentivirus that contains an MLV promoter for an anti-CCR5 gene
3. Bone marrow transplant to HIV-1+ patient
4. The bone marrow will generate new immune cells.
5. The new immune cells are genetically modified by the viral vector to express the anti-sense CCR5 RNA, which will bind to the normal CCR5 mRNA. This double-stranded RNA PISSES OFF the cell, so it destroys it. Thus CCR5 mRNA is never translated into CCR5 proteins. The person is functionally, if not genetically, deltaCCR5.
6. PROFIT!!!
Of course, things really arent that straight forward. Bone marrow transplants arent a casual deal-- over 10% of the people who get them die from complications. You cannot get one unless its life-or-death, and if youve got HIV-1 thats under control with meds, you arent gonna get one-- Just people with HIV-1 AND leukemia/lymphoma.
And then theres the gene therapy side of it. MLV has a great promoter we can pirate to get the anti-CCR5 RNA made, and it knows to keep its mouth shut in the pluripotent state, so their wayward gene expression doesnt screw up the normal development of various cell types... but it causes... leukemia and lymphomas (except when it doesnt). But lentiviral vectors have some advantages over MLV. So they cut/pasted a lentivirus with the MLV promoter with the anti-CCR5 message (previous post on cutting/pasting viruses together to make better gene therapy vectors).
And, everything in this paper is in culture dishes. Not people, yet. What if the stem cells (or their progeny) just quit making the anti-CCR5 message? Does that happen in one year in people? One month? Ten years? We dunno. We dont really know what controls latency in regular retroviruses yet, certainly not ones we are screwing around with. Nothing would be as disappointing as going through this ordeal, surviving it, thinking youre 'cured', and things go to shit again in a few months/years.
But as far as tissue culture work goes, this is nice. And even if we cant ultimately use it for HIV-1, we might be able to use the technology these folks are working on for any number of diseases.
Posted by ERV at 8:30 PM • 13 Comments • 0 TrackBacks
July 20, 2010
Category: Douchebaggery! • Theism
My mom and her friends have been having a fun time with recent Oklahoma weather-- We had constant ice storms that crippled the city this winter. Spring gave us loads of tornadoes and of course, the sideways baseball-sized hail. This summer has been 'filled' with flooding...
Mom & Co. giggle: "Better stock up on OFF!. I heard next you all are going to have a plague of locusts." "What the hell is Oklahoma doing to piss off God??" "The only thing keeping Oklahoma from being obliterated by God is the few Chosen People who manage to live there. Way to keep God from killing Oklahoma, Abbie!"
So you can imagine their peels of laughter when they found out 'Reclaiming America for Christ' held a rally right here in OKC last week. And that 'Reclaiming Oklahoma for Christ' has, quite possibly, one of the most terrifying, designed-by-a-serial-killer-looking websites on the internet. But for Christs sake, SOMEONE has to bring this state of heathens to Christ before we are permanently obliterated from the planet, and if it has to be the owners of one of the creepiest websites on Earth, so be it!!
So while they were laughing, I was totally pissed off. KEN HAM was here in OKC, and NOBODY thought it might have been nice to invite ME. KEN HAM. You selfish mother fuckers at Trinity Baptist Church in Yukon. Dan Fisher, you suck.
Now today I find out that the Westboro Baptist crew are going to be like 2 blocks away from me, and Ive got to, get this, WORK! WTF!!
5:00 PM - 5:30 PM Oklahoma City, OK
Oklahoma State Capital 2300 N Lincoln Blvd WBC to picket the Oklahoma State Capital. Like their spiritual forefather, Haman, these rulers have passed a law that is mischief and mayhem with the agenda of their father the devil at the heart. They hope to kill (literally) the servants of God. They have passed a law which basically gives the brutish, lawless, violent rebels of Oklahoma authority, by law, to commit crimes against WBC members when they come with words of truth to the public sidewalks of that DOOMED state, and they may not be held personally liable if they commit these crimes. Behold the face of the good old boy, Bible belt southern hypocrites. Do you fools think God is going to let you get a pass? Psalm 53:1 <> The fool hath said in his heart, There is no God. Corrupt are they, and have done abominable iniquity: there is none that doeth good. Isaiah 24:16-23 From the uttermost part of the earth have we heard songs, even glory to the righteous. But I said, My leanness, my leanness, woe unto me! the treacherous dealers have dealt treacherously; yea, the treacherous dealers have dealt very treacherously. Fear, and the pit, and the snare, are upon thee, O inhabitant of the earth. And it shall come to pass, that he who fleeth from the noise of the fear shall fall into the pit; and he that cometh up out of the midst of the pit shall be taken in the snare: for the windows from on high are open, and the foundations of the earth do shake. The earth is utterly broken down, the earth is clean dissolved, the earth is moved exceedingly. The earth shall reel to and fro like a drunkard, and shall be removed like a cottage; and the transgression thereof shall be heavy upon it; and it shall fall, and not rise again. And it shall come to pass in that day, that the LORD shall punish the host of the high ones that are on high, and the kings of the earth upon the earth. And they shall be gathered together, as prisoners are gathered in the pit, and shall be shut up in the prison, and after many days shall they be visited. Then the moon shall be confounded, and the sun ashamed, when the LORD of hosts shall reign in mount Zion, and in Jerusalem, and before his ancients gloriously. Oklahoma should be afraid, very afraid for these treacherous actions will not go unnoticed or unpunished by Our God, the Consuming Fire and the Avenger of Blood. Praise and fear Him. AMEN!
HOLY CRAP that is some FANTASTIC crazy!!!
And I gotta WORK.
*silently fumes*
Well, at least I can take heart in the fact Im studying HIV/AIDS (TEH HOMO GAY!) and evilution (ATHIEST DEEEMONS!), so, *pout* I guess Im still kinda counter protesting.
But Arnieman would have had SO MUCH FUN.
*pout*
Posted by ERV at 6:00 PM • 12 Comments • 0 TrackBacks
Category: HIV/AIDS
Sometimes 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 infected with HIV-1 are women, and the vast majority of them are infected via heterosexual contact. Not every woman has a say in when/where/how she has sex. So not every woman can speak up and say "Yeah, you are so wearing a condom, dude, lol!" Same thing goes for some men.
Ideally, we would like to be able to help the people most at risk of acquiring HIV-1 infection. Put the power in their hands, not the hands attached to the guy not putting on a condom. One way we can do this I talked about a week ago-- microbicides. A gel that could be used pre/post sex to help stop HIV-1 transmission.
Weve now got one that works. Kinda.
Effectiveness and Safety of Tenofovir Gel, an Antiretroviral Microbicide, for the Prevention of HIV Infection in Women
They gave a gel containing tenofovir to 445 women, placebo to 444. They were supposed to use it before and after sex, but no more than 2 doses in 24 hours. And they did. There was a very high compliance rate, and the women didnt mind the gel at all-- over 97% were totally cool with it.
The gel reduced HIV-1 acquisition by 39% (even higher for women who were really strict about using it properly-- 54%).
Thats no 80-90%, but hell, Ill take 40-50% over someone not being able to protect themselves at all.
Also awesome: Applying the drug in small quantities where its needed in a microbicide, instead of giving oral (systemic) antiretrovirals as a prophylactic means you get to avoid a lot of unwanted physical side effects. The 'worst' they got with this microbicide? Some people got diarrhea. No renal failure.
What I am actually interested in discussing about this, is the evolutionary aspect. If we put this drug in microbicides, arent we just going to get lots of drug resistant HIV-1 spreading?
NO.
Read on »
Posted by ERV at 1:30 AM • 17 Comments • 0 TrackBacks
July 15, 2010
Category: BLAG
I was so scared this was gonna happen while I was at the dentist this morning, but some time this afternoon/evening, New ERV (not including Old ERV) is gonna get its one millionth visitor!
YAY!
Normally I would demand sacrifices and lulz for a big celebration, but I got Lortab, so... Im going to go to sleep now... But I would appreciate lulz in the comments when I wake up...
YAY!!!
Posted by ERV at 1:02 PM • 56 Comments • 0 TrackBacks
I'm a graduate student studying the molecular and biochemical evolution of HIV within patients and within populations. I also study epigenetic control of ERVs.
