ERVs
sa smith | May 4, 2010Hey, you guys remember a while back, when Casey 'Tits' Luskin about peed his pants because 'ERVS AR BE FUNKSHUNAL!!'
Except, this is really another case of Creationists not knowing the difference between an ERV, solo LTRs, and random wayward ERV genes.
And those solo LTRs that could theoretically still act as a promoter, really dont all that often.
Well, like I have said a million times on this blog, these solo LTRs, like all endogenous retroviral bits are not usually good things, CAUSE THEY CAUSE CANCER.
Furthermore, Creationists (and wooists as a whole) are madly in love with epigenetics.…
sa smith | March 30, 2010Once 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…
sa smith | March 19, 2010Retroviruses 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…
sa smith | February 2, 2010I hesitate to write about this, as Im sure its going to be taken and amplified by Teh Crazy... but I suppose I better just get a head start...
Isolation of an Infectious Endogenous Retrovirus in a Proportion of Live Attenuated Vaccines for Pets
Well shit.
Researchers took a dozen cat/dog vaccines from manufacturers in Japan and Britain, and looked for a specific cat endogenous retrovirus, RD-114. Why this cat ERV? Cause the viruses in these vaccines are passaged in cat cell lines to attenuate them. Cat cell lines that contain and can produce ERV RD-114. Whats RD-114? Welp, um, its…
sa smith | January 21, 2010My god, epigenetics is a woo-magnet.
Its not epigenetics fault, its just science.
But the word 'epigenetics' gets put on this ('chambery thing' heh.).
And this.
And this.
And... well, just Google it. Find your own favorite bit of self-help/explain all/magic epigenetic crap.
Attention woo-meisters:
STOP WHORING UP EPIGENETICS. IT IS NOT MAGIC. ITS JUST THAT 'BORING SCIENCE CRAP' YOU HATED IN HIGH SCHOOL.
Its science and its cool because its science.
DEAL WITH IT.
THIS is epigenetics:KAP1 controls endogenous retroviruses in embryonic stem cells--
Almost half of the mammalian genome is…
sa smith | January 18, 2010The only creatures that existed in the RNA World that still exist today, are viruses.
They are the only creatures that still use RNA to store their genome-- they never upgraded to V2.0, DNA.
In fact the creatures that might have written V2.0, retroviruses, are still around today too. They carry their genomes as RNA, but convert it to DNA via reverse transcription in order to take advantage of their hosts.
Ive written a bit about reverse transcription before... its kind of a mess to describe... however every retrovirus, from simple retroviruses like Avian Leukosis Virus (only gag, pol, and…
sa smith | January 6, 2010Endogenous retroviruses are weird, but how they got into our genomes and what they mean, evolutionarily, isnt too hard to understand (unless youre an IDiot). A retrovirus has to not only accidentally infect a germ-line cell (sperm/egg), that particular egg/sperm has to successfully mediate fertilization, and where the retrovirus randomly inserts has to not cause trouble for the resulting offspring (cell cycle arrest, cancer, etc), for an endogenous retrovirus to form.
But this scenareo, while highly improbable, has happened lots and lots of times (a large portion of your genome is retroviral…
sa smith | December 23, 2009Clinical trials for using pig cells to treat diabetes are now legal Down Under!
Most countries health/medical regulatory bodies have been hesitant to approve of animal organ/part transplants because of the risk of Creating Another HIV. Theoretically endogenous retroviruses still active in pigs (PERVs) could cause trouble once they are transplanted into a human.
Happily scientists have 'optimized' some pigs to be free of the most dangerous PERVs.
So New Zealand just started clinical trials in diabetes patients who have problems controlling their blood sugar levels, even with diet/exercise/…
sa smith | December 8, 2009(this post is me laughing at Sternberg, intermittently talking about ERVs, ask Qs if Im not clear-- sorry, laughing so hard, must share this joke as well as I can between snorts)
HAHAHAHAHAHAHA!
AAAAAAAAAAHAHAHAHAHAHAHAHAHA!
RICHARD STERNBERG IS SO STUPID!
AAAAAAAAAAAAAAAAHAHAHAHAHAHAHAHAHAHAHA!
Arrogant, stupid little twat that doesnt even know what he doesnt know.
*wipes away tears*
*sniff*
I was just listening to the 'debate' between Shermer/Prothero and Meyer/Sternberg.
Prothero brought up ERVs, and how they are leftover garbage cluttering up your genome.
Sternberg was all like, "NUH UH…
sa smith | August 21, 2009The connection between wayward endogenous retroviral protein production and multiple sclerosis is tightening :D Sure its still a mess, sure we dont have all the pieces to The Puzzle-- but weve got a strong foothold now. We know we are going in the right direction.
A subtle paper just came out in 'Journal of Virological Methods'. They dont have some earth shattering revelation or sexy data to report... they have a reagent.
Novel reliable real-time PCR for differential detection of MSRVenv and syncytin-1 in RNA and DNA from patients with multiple sclerosis.
There are lots of ERVs in your…
sa smith | July 30, 2009EMAIL!
Dear ERV--
Hope you don't mind a real question instead of the stupid stuff teh idiots usually send you.
This morning we had a lecture by Salvatore DiMauro, M.D. from columbia university (he is neurolog/neuromuscular mainly mitochondrial diseases) about mitochondrial diseases.
Any evidence for ERV's in the mitochondrial genome?
Cool question!
Short answer-- No. Mitochondria have a different kind of integrated virus...
Long answer-- There are two ways mitochondria could get an ERV.
Retrovirus infected bacteria was the original endosymbiont 1.7-2 billion years ago-- Not likely. We dont…
sa smith | July 21, 2009WTF!
Did someone declare this week 'cool ERV research week.' or something?? Yet another awesome ERV paper came out:
Distribution of Endogenous Retroviruses in Crocodilians.
The title is pretty non-sexy, but what they found... AAAAH!
Okay, Jaratlerdsiri and company set out to look at ERVs in the order crocodilians. Crocodilians include the families of alligatoridae, crocodylidae, and gavialidae. Nobodys done it. So why not?
Armed with PCR primers for pol, Jaratlerdsiri went digging. Heres what they found:CERV-1: This group of ERVs werent found in gators or gharials. All of the ones they…
sa smith | July 17, 2009WEIRD COOL EXPERIMENT ALERT!
Proviral integrations and expression of endogenous Avian leukosis virus during long term selection for high and low body weight in two chicken lines
For some reason, I have no idea why (Im sure they have a good reason-- obesity research, farming research), scientists were playing a selection game with chickens.
Select the skinniest chickens. Breed them. Select the skinniest chickens. Repeat.
Select the fattest chickens. Breed them. Select the fattest chickens. Repeat.
Keep doing that until you get a population of skinny chickies and another population of fat…
sa smith | July 16, 2009So Ive been over the basics of ERVs (Intro, gag, pol, env), but Im still missing a 'basic' aspect of ERVs, even though I talk about them all the friggen time on this blag: LTRs.
In exogenous retroviruses, LTRs act as promoters. Genome has all the genes (gag, pol, env), LTRs make sure they, and genomic RNA, is made. But just as a side-effect of the reverse transcription process, every integrated retrovirus (provirus) has two identical LTRs, U3-R-U5. A viral genome just has an R-U5 on the 5' end, and a U3-R on the 3' end.
So, two promoters-- One at the 5' end, making virus, and one at the 3…
sa smith | June 22, 2009Weird science fact of the day:
Girl birds only have a left ovary. The right one kinda develops, and then regresses. Left ovary is the only one that works. All birds.
Wait... what?
What the hell?
What kind of evolutionary weirdness led to this absurdity?
I bet you guessed an ERV is involved :DOVEX1, a novel chicken endogenous retrovirus with sex-specific and left-right asymmetrical expression in gonads.
For real, you all should download and read over this one. Its in obnoxious 'pre-print' format (ie almost unreadable format. figures, figure legends, and text about figure all on different…
sa smith | June 19, 2009There is nothing wrong with not knowing something.
I dont know lots of stuff.
You dont know lots of stuff.
Its okay-- we share knowledge with each other. I dont *have* to be an expert in car repair. I dont *have* to be an expert in particle physics. You dont *have* to be an expert in retroviruses. We are a hippy commune of knowledge.
Seems like the only people who *have* to know EVERYTHING are Creationists. Pressures not on them from our end-- I dont expect Creationists to know how to feed themselves without assistance, much less the details of ERVs. No, its the Creationists who insist…
sa smith | April 28, 2009More evidence that evilution is a vast, world-wide conspiracy.Revealing the History of Sheep Domestication Using Retrovirus Integrations
Scientists from all over the world (literally, Portugal to Pakistan, Italy to Iceland, Tanzania to Texas) have used the random insertion of endogenous retroviruses, specifically, Jaagsiekte sheep retrovirus, to determine the evolutionary history of sheepies:enJSRVs can be used as highly informative genetic markers because the presence of each endogenous retrovirus in the host genome is the result of a single integration event in a single animal and is…
sa smith | April 16, 2009While Ive mentioned the connection between endogenous retroviruses and Multiple Sclerosis on teh blag before, I realized Ive never written a post on this topic. Fortunately I just read an interesting paper thats provided me with a good opportunity to do just that:
Analysis of transcribed human endogenous retrovirus W env loci clarifies the origin of multiple sclerosis-associated retrovirus env sequences
In addition to being 'cancer' viruses, it seems like another trick retroviruses are good at is screwing with our central nervous system. For example, HIV-1 infection leads to HIV associated…
sa smith | April 8, 2009Alternate post title: Why Charles Jackson is a tool who can quote papers, but doesnt understand what he is reading.
I get this question all the time, and its totally valid:
How do you tell the difference between an endogenous retrovirus that is shared because of common descent, and a retrovirus that was endogenized independently in two species?
A follow up paper to the one I wrote about here (Me, and you, and Zaboomafoo) provides a lovely example of how we do this!
So heres the back story: There are a ton of different retroviruses. Its not one big homogeneous group of 'virus kind', each…