ERVs

We now have the complete pig (aka Sus scrofa) genome!  You know what that means..........!!! PERVs!!!! Analyses of pig genomes provide insight into porcine demography and evolution While I am a huge fan of all ERVs, including PERVs, PERVs hold a special place in my heart. Literally. Physicians can use pig parts and organs for human transplants.  Thanks to a pig, someone I love very much is alive today.  It would be fantastic if pigs could be used to their full medical potential... but because of PERVs, some people who could benefit from a pig transplant, cannot. Pigs have ERVs just like…
Technically, its the immune response to the HERVs that can control the HIVs, not the HERVs directly. :-D Ive written about the proposed connection between ERVs and HIV a couple times before-- Briefly, viruses do lots of things by accident.  Things just happen.  Sometimes viruses make us blind for no good reason, or give us cancer for no good reason, 'bad' things happen to us because of viruses we are infected with that are actually 'bad' for the virus too.  But when you are dealing with the population/infection numbers we deal with in virology, and all the blind randomness going on, 'bad'…
This is not overly helpful information for MS patients, but its still good news: No additional copies of HERV-Fc1 in the germ line of multiple sclerosis patients. Previous research has indicated that there are endogenous retroviruses that are disregulated and leading to detectable production of ERV proteins in MS patients.  They found the bugger involved-- an ERV they named HERV-Fc1. We do not know whether this protein is causing MS, or just a side-effect we might (might not) be able to capitalize on for diagnostic purposes, or whether its a bit of both. But with all of this previous research…
Ive 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…
Paleovirology 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…
Well 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…
Arnie 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...…
Time 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,…
The 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…
If 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…
Carl 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-…
The 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…
I wasnt super thrilled about the last ERV-->MS paper I wrote about, but I really like this new one:Human endogenous retrovirus type W envelope expression in blood and brain cells provides new insights into multiple sclerosis disease. Those of you who have been following the XMRV fiasco will find this intro paragraph very interesting:When the first descriptions of retrovirus-like particles with reverse-transcriptase (RT) activity in leptomeningeal and macrophage cell cultures from patients with multiple sclerosis (MS) were published they were thought to be related to a new human T-…
Its 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,…
Common 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…
ERVs 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…
Let 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…
Arnie 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: **…
I 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…
Quick 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…