ERVs
sa smith | October 21, 2011If there is one ERV I genuinely love talking about on ERV, its PERVs-- Porcine Endogenous Retroviruses.
And you all should care about them too-- Pigs and their PERVs (or, lack of PERVs, or lack of infectious PERVs) might one day have a direct impact on you or your friends/family.
Clinical trials involving tissue from genetically distinct pigs has already started Down Under, and apparently research in the US and UK is now considered 'imminent'.
Very, very cool update-- Im glad the PERVs are under control and this kind of research can move forward.
Of course, there are ethical positions to…
sa smith | May 27, 2011Like BlagHag, I have a soft-spot for astrology. Not that I ever 'believed' in it, I have just always loved the stars and the moon and zodaic stuff is just fun. Via that, Ive also always had a soft-spot for cows. I am a Taurus, and I just think cows are pretty:
I also love zodiac for the lulz.
Example #1:
*in an argument with person Im dating*
Me: You should have known I wouldnt like you changing plans on a whim like that. You KNOW Im a Taurus. *angry face*
Person: *stops argument dead in tracks in disbelief I just said that*
Me: LOL PWND!
Example #2:
Literally everyone Ive dated has had…
sa smith | May 26, 2011I LOVE talking about PERVs on ERV.
PERVs.
PERVs.
EVEN MOAR PERVs.
I LOVE PERVs!
Well... PERVs as in Piggie Porcine Endogenous Retroviruses. Not pervs as in Catholic Priests and Teh Popes advisers. Thats a different story.
Because the need for organs for transplants is so high, and because pigs are pretty great sources for transplants in humans, and because of recent successes with minimal PERV-pigs down-under, a lot of research has gone into PERVs to really try to nail down just how big of a threat they are to humans.
The problem is, PERVs can 'infect' human cells. But as some of you who…
sa smith | May 24, 2011So I got the idea to do this after stumbling across a bunch of viral/farmyard stories this week. I know its currently Tuesday, not Sunday, so, SURPRISE!!! BARNYARD WEEK!
If you ERV readers are anything like me, you have spent countless nights tossing and turning in bed, unable to sleep, unable to stop pondering one of lifes greatest mysteries:
Why are some chickens white?
I finally accepted the fact that this question was ultimately unanswerable, like "What is the meaning of life?" or "Why did anyone ever think Jim Carrey was funny?". Then I found out that the question actually had an…
sa smith | May 19, 2011SQUEEEEEEEEE!!!!!!!!
The first sequenced carnivore genome shows complex host-endogenous retrovirus relationships.
ONE note of dismay: They did not include a picture of the boxer they sequenced. WTF???
Substitute picture:
see more dog and puppy pictures
Fun quickies!
Despite Arnies love of getting into the garbage, dogs have much less junk DNA via proviral ERVs than humans (them <0.15%, us 0.8%)
Of the 407 kinda ERVs, most are gammas (313) and betas (28)
Only 44 had potentially fully open gag-pol-env
Only 36 still had their LTRs
Their ERVs are backwards! With DNA, there really is no '…
sa smith | May 13, 2011CTL-based vaccines and HIV-1.
Ive written about them quite a few times here on ERV.
Quick recap-- All of your cells fly 'flags' that show circulating cytotoxic T-cells what proteins they are making. Normally, a virus-infected cell will put up virus/pirate 'flags', the T-cell will 'see' something is wrong, and convince the infected cell to commit suicide. This process is thwarted by HIV-1 numerous ways, so infected cells arent killed. Some people can 'see' the HIV-1 'pirate flags', so they (kind of) control HIV better, but HIV is evolving ways around this. As a whole, the HIV-1 population…
sa smith | March 8, 2011Amyotrophic Lateral Sclerosis, aka Lou Gherigs disease. Pretty much sounds like hell, to me. Your mind is fine, while your body is collapsing around you-- slowly but surely paralyzing you, taking away your ability to eat and breathe, while your mind is fine and dandy so you are acutely aware of what is happening to you. If youre lucky, youre dead in 3 years. Not so lucky, it can go on for 6 or more. Terrifying.
What makes it even more terrifying, is that the vast, vast majority of people who develop ALS have no family history of it whatsoever. Wikipedia says 95%.
There is *a* drug for…
sa smith | November 19, 2010I guess Im going to have to change the name of 'ERV'.
Before I was just concerned.
Now, ERVs are officially not so special at all.
Viruses, all kinds of viruses, are all over the place in genomes-- from insects to humans.
Endogenous Viral Elements in Animal Genomes
Carl Zimmers take: Your inner viruses: the trickle becomes the flood
My quick-and-dirty take:
Every form of virus-- retrovirus, ssRNA(-), ssRNA(+), dsRAN, dsDNA, ssDNA-- every form of virus has an endogenous component now.
Theyre all over the place. Every organism has these 'alternative' endogenous viruses. Theyre inserted all…
sa smith | November 11, 2010Even though the real ERV is a) hiding in an undisclosed location and b) blinded by a week long migraine from this stress, you can still enjoy me via video taken at the Texas Freethought Convention!
First of all, that was an absolutely fantastic introduction. I loved it! I felt like a total ass for changing my topic at the last minute :-/
Aaaaaand I was totally terrified. The largest group of normal people I think Ive talked to, ever. And not just normal people. Normal people who really like science and were really excited to learn something new. My inner thoughts as I was walking up the…
sa smith | November 5, 2010The endogenous retroviruses in your genome are dead.
Dead.
Junk.
They no longer code for functional, infectious viruses.
Those viruses are also extinct. They were floating around thousands, millions of years ago, infecting stuff, and now they are hanging out in your genome instead (100% of humans are infected, *wink*).
ERVs are viruses that we have, functionally, tamed. We have overcome them.
Thus, it would be useful to 'bring ERVs back to life' so we can study them and figure out how we conquered them, hopefully giving us idea how to treat modern day infections.
"OMFG!" a crazy person…
sa smith | October 27, 2010This is a repost from the old ERV. A retrotransposed ERV :P
Its Halloween time, and we just got a BRAND NEW FRANKENSTEIN ERV! To prime you all for that post, heres a repost on an OLD FRANKENSTEIN ERV!
Remember, ERVs are junk. These are not zombie viruses. Scientists are not taking totally functional but silenced DNA or totally functional specially created by The Designer but coopted by evolution and doing stuff with it. There are ERV families-- take all the ones that are related and still have a gag or a env, figure out what their common ancestor looks like, and then do experiments with…
sa smith | October 18, 2010Now COMMON.
COMMON.
What is this nonsense?
COMMON.
...
How am I supposed to have a blog titled 'ERV', crowing on about how awesome and special endogenous retroviruses are, when scientists keep friggen unearthing endogenous NON-retroviruses.
COMMON!!
First there were Borna disease viruses.
Then there were filoviruses.
Then there were hepadnaviruses.
And NOW, NOW there are endogenous parvoviruses:
Discovery and Characterization of Mammalian Endogenous Parvoviruses
OMGWTFBBQ??
Im sure almost all of you have heard the term 'parvo' or 'parvo virus'. Its a disease that ravages pets worldwide (the…
sa smith | September 29, 2010Hepatitis B is my favorite non-retrovirus.
Why?
Because its a retrovirus :-D
Heres another reason for me to love it-- Its viral family, Hepadnaviridae, inserted themselves into bird genomes 19 million years ago.
Genomic Fossils Calibrate the Long-Term Evolution of Hepadnaviruses
*happy-prospector-dance* Okay, this is like, the billionth time this has happened in the past few months-- Finding endogenous versions of viruses that arent 'supposed' to endogenize. THIS IS SO AMAZING!
We do not have viral fossils for us to study what a kind of virus looked like 100, 1000, 1000000000 years ago.…
sa smith | September 15, 2010Creationists cant deal with ERVs. They have no answer to the problems ERVs pose to Creationism. They have no alternative explanation for the weight ERVs lend to evilution.
However, this doesnt stop Creationists from bluffing/lying to save face in front of the True Believers.
One of the more baffling responses Ive gotten to ERVs is 'ERVs dont exist. They arent really ancient retroviral fossils.' The most common response is 'ERVs arent junk DNA! See, this one gene (out of 1,000,000 similar genes that are clearly junk) has been co-opted for use by the host! So, YAY JESUS!'
Real world, real…
sa smith | July 29, 2010Ummmmmmm...
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... :-/
sa smith | July 26, 2010Human 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…
sa smith | July 8, 2010One of the scary things about filoviruses (eg Ebola, Marburg)... is that we dont know where they comes from. We know how polio is transmitted. We know how HIV-1 is transmitted. We know how influenza is transmitted. We know how rabies is transmitted.
Even if you dont have good vaccines or good therapies, if you know where a virus comes from or how it is transmitted, you can take steps to prevent illness.
But filoviruses....?
One hypothesis is that small mammals are the natural reservoir. A way to look for that would be to study the immunology of lots of small mammals-- Do they have…
sa smith | June 24, 2010There is not really a good way to get rid of the junk in your genome. Pretty much, once its in there, its in there-- there is no organized biochemical system that says "Oy! This 'eres crap!" and cuts out the useless bits, cleaning up residual transposable elements like a chimney sweep. We just keep accumulating this stuff.
An exception to this is recombination.
Your chromosomes dont always line up just perfectly during meiosis, so when you have lots of repetitive elements (junk DNA-- transposable elements, ERVs, etc), you can 'accidentally' cut out (or duplicate!) parts of your genome.…
sa smith | June 22, 2010As if you all needed one more reason to want Junk DNA to stay JUNK, I just read a couple of neato papers on the impact of wayward ERV and LINE activity in testes/sperm development:
MOV10L1 is necessary for protection of spermatocytes against retrotransposons by Piwi-interacting RNAs
Mouse MOV10L1 associates with Piwi proteins and is an essential component of the Piwi-interacting RNA (piRNA) pathway
Turns out that mice that lack MOV10L1 (a protein named after a retrovirus, but not retroviral-- its totally a host protein, long story), grow up to be nice normal mice... except for the fact the…
sa smith | June 10, 2010Im glad this reader was persistent in poking me with this Q, its a really good un!
Dear ERV--
I always thought that ERVs were some of the best evidence for evolution, but I always wondered if there was an additional aspect to the story that is not usually told. I imagined that different strains of viruses have existed at different times over the last few million years, so if some of the ERVs we share with chimps (or other animals) were caused by retroviruses that HAVE NOT existed since modern humans evolved, this would really put the nail in the coffin to some of the Creationist arguments…