erv
sa smith | August 28, 2012Ive always wanted a ferret. When I was little, because of this (1m59s):
Now, because of stuff like this:
Ferrets arent just super cool pets, they also have a very rare 'gift'-- While all organisms genomes are littered with pirate DNA and endogenous retroviruses, endogenous lentiviruses have only been found in three creatures: Bunnies, lemurs, and now, ferrets!
Endogenous Lentiviral Elements in the Weasel Family (Mustelidae)
Lentiviruses are 'complex', in that they have the basics retroviruses need to survive, LTRs, gag, pol, and env, plus some bonus genes. In this case, vif, tat, and rev…
sa smith | August 27, 2012Paleovirology seems to work the opposite of the way the Creationist want. The more information we have, the further back the timeline shifts, not vice versa.
For example, we used to think HIV-1 started in humans ~1930, but after we found more 'old' HIV sequences, the clock got pushed back to 1902-1921.
We used to think Simian Immunodeficiency Virus emerged 1266-1685, but after we found more 'old' SIV sequences, the clock got pushed back 76,794 years.
After a recent finding in fish, the evolutionary history of retroviruses got pushed back... 400 million years.
An Endogenous Foamy-like Viral…
sa smith | August 14, 2012Well this is a new one:
This will sound radical to most of you, but the latest information available to us now could improve your health, should you decide to take this seriously.
Have you ever considered why Muslims and Jews are forbidden from eating pork? Both religions consider it unclean. Dr. Jeff McCombs, author of the book “Life Force,” found that by eliminating pork, there is a consequent and immediate increase in energy and health levels as well as the body’s disease-fighting capabilities.
According to health experts, the danger of eating pork is an unseen one—a retrovirus called…
sa smith | August 13, 2012Arnie got to meet horses for the first time last week :)
It was an unexpected event (horsies were out at a neighbors when we went on a walkie), so I didnt get it on film-- but I can recreate it:
Arnie: HOLY SHIT MOM! MOOOOOM! MOOOOOOOOOOOM! WHAT ARE THOSE MONSTERS??? OH GOD THEYRE WALKING TOWARDS US!!!! I WILL PROTECT YOU MOMMY!!!!!!
Horses: *SNORT* *unimpressed blink*
Arnie: AAAAAAAAHH IT SNORTED! GOD THEYRE HUGE! I DONT CARE! YOU SHALL NOT PASS, VILE BEASTS!
Me: Arnie, those horses would kick your ass. Literally. Calm yourself.
Horses: *unimpressed blink* *eat grass*
Arnie: Well...…
sa smith | July 13, 2012Time to add another disease to the list of problems associated with wayward ERV expression:
Protective Effect of Human Endogenous Retrovirus K dUTPase Variants on Psoriasis Susceptibility
Repeat after me everyone:
ERVs are junk DNA. We WANT them to be junk DNA. Yes, very rarely an ERV is domesticated for Good, but almost universally, ERV expression is BAD.
While the main idea of this paper is neat, the experimental biology in this paper isnt very satisfying at all. There is no firm, obvious experimentally derived connection between ERV protein expression and disease, here.
For instance,…
sa smith | July 5, 2012The questions I get asked most often are:
How many ERVs are there?
How many do we have in common with chimpanzees/gorillas/orangutans/etc?
Its hard to answer this. Depends on what your definition of 'ERV' is. Because sometimes scientists mean a complete/nearly complete ERV (LTR-gag, pol, env-LTR), and sometimes they mean either LTR, Gag, Pol, or Env, or any combination. There are very few of the former, and a lot of the latter.
But how many are there total? Well, its hard to say. Sure, we sequenced the human (and chimpanzee, etc) genome, but we skipped a lot of the parts that are just…
sa smith | July 3, 2012If you are reading this blog, you already know all about how a huge portion of your genome is parasitic junk DNA (~40-45%), a fraction of which is retroviral junk (ERVs, ~9%). If youre new here... SURPRISE!
Sure, we have a gene here, a promoter there (maybe) that was domesticated for human genome use, but its junk, and that is a good thing. I mean, if our genome was 9% retrovirus and every one of them was active, we would all be dead from the insertional mutagenesis alone.
So your genome and cells have evolved lots of ways to make sure your junk DNA stays junk... but I guess ERVs are like…
sa smith | June 19, 2012Carl Zimmer is, hands down, one of the best science writers out there. Its no surprise, then, that he is almost as obsessed with viruses as I am. Viruses are our past and our future, and Zimmer *gets* it.
So while I am busy in the lab this week, I will happily point you to a piece he recently wrote about ERVs and embryos.
We Are Viral From the Beginning
Regarding the paper he is writing about-- I dont think the active ERVs are 'doing' anything in embryos. I dont think we have evidence that the active 'silent' viruses are genuinely domesticated. I think the ERV activity is probably a side-…
sa smith | April 24, 2012The human genome is about 3.1 billion nucleotides long.
8-10% of your genome is retroviral-ish. We will be conservative and go with 8%-- thats 248,000,000 nucleotides of retrovirus.
The average retrovirus is about 10,000 nucleotides long. So we should have ~ 24,800 retroviral elements in our genome.
But there must be more than that, because there usually are not full-length retroviruses left in your genome (they would make retroviruses and kill you). Some have deleted genes, or deleted chunks of genes, or sometimes the entire genome is deleted except for a solo-LTR.
So, some number of…
sa smith | April 5, 2012Its not so hard to get your head around endogenous retroviruses once you get the gist of them. RNA virus turns itself into DNA, inserts itself into your genome, makes babby viruses. Sometimes the RNA virus infects an egg/sperm, turns itself into DNA, inserts itself into the genome, and that egg/sperm goes on to create an organism that has the retrovirus permanently integrated into every cell of said organism.
Other endogenous viruses are a little harder to 'get'-- there are endogenous RNA viruses. How the hell did they get there? RNA viruses have no DNA step in their lifecycle, and yet,…
sa smith | March 21, 2012Common everybody! Sing the chorus with me, you know the words!The vast, vast majority of ERVs are junk. They are genomic pirates, and your genome is doing the best it can to keep them silent. When ERVs are making noise, its a sign that something has gone wrong. Very, very wrong. Like, for example, breast cancer:
Immunotherapeutic Potential of Anti-Human Endogenous Retrovirus-K Envelope Protein Antibodies in Targeting Breast Tumors.
This paper has the potential to lead to something incredible. Lemme try to convey how cool this is...
Like I always say, cells not only making ERV RNA, but…
sa smith | March 12, 2012ERVs and Multiple Sclerosis
ERVs and Multiple Sclerosis, #2
Hmmm... This new paper on the association between 'active' ERVs and Multiple Sclerosis is a step back, and a step forward, at the same time:Expression of HERV-Fc1, a human endogenous retrovirus, is increased in patients with active Multiple Sclerosis.
If you go back and read ERVs and MS #2, youll see that we have an endogenous retroviral protein, gag, expressed in elevated levels in the brains of MS patients. The gag is from the HERV-W family of ERVs, related to syncytin.
In this paper, however, they associated Multiple Sclerosis…
sa smith | February 29, 2012Let me make this clear, for like the millionth time:You do not want transposable elements in your genome (DNA transposons, ERVs, LINEs, SINEs, etc) to be active and functional. You are happy, happy, happy that these elements are junk. Yes, occasionally a transposable element has been domesticated for the hosts purposes. Yes, I know, Creationists think this means every last nucleotide to be there For A Reason by The Designer. But if what they wanted was a reality, we would all be dead right now. Expression of the vast, vast majority of transposable elements is a sign that something has…
sa smith | February 20, 2012Arnie is a very happy dog (see photo in upper left). Its always a party when Arnie is around-- He loves everyone and everything...
... Everything, that is, except cats.
It didnt used to be like that. Arnie used to like cats just fine. But then one day, when he was a puppy...Neighbor: Hey can I introduce my new kitten to Arnie? I want to get a dog later, so I want her to be used to dogs.
Me: Sure!
Arnie: *happyhappyhappynewfriendhappyhappy*
Kitten: *squint*
Arnie: *newfriendnewfriendsofluffyhappyhappyhappy*
Kitten: *squint*
Arnie: *haaaaaaappyhappyhappy...
Kitten: **…
sa smith | November 16, 2011I love junk DNA.
Well, thats an understatement-- I mean I love is SO MUCH I created a blog dedicated to a particular form of junk DNA, endogenous retroviruses.
I love how we can learn fantastic things about organisms (and their diseases) from, basically, dumpster-diving though millions and millions of years of mistakes and accidents and chance and evolution.
So its hard not to take it a touch personally that Creationists HATE junk DNA. They spend a lot of effort trying to make it not exist anymore (seems like a silly waste of time considering the fact epigenetic control of ERVs and…
sa smith | November 15, 2011Quick recap of ERVs for new readers of ERV (or long-time readers who have forgotten!)--
ERVs are retroviruses that accidentally infected an egg/sperm cell, and became a permanent part of that egg/sperms DNA. That egg/sperm then went on to successfully generate a viable embryo, and because that retrovirus was part of the egg/sperms DNA, it also becomes a permanent part of the organisms DNA.
Though this is a very very rare, totally accidental event, on an evolutionary time-scale, random events have happened quite a few times, to the point where a large chunk of your, *your* DNA, is…
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 a…
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…