ERVs
sa smith | October 9, 2015Theyre figuring out what the heck is going on in the saga of ERVs and ALS!
2011:
ERVs and ALS
2015:
Human endogenous retrovirus-K contributes to motor neuron disease
1-- Of the many ERVs in your genome, the ones they found activated in the brains of people with ALS are HERV-Ks, at two positions: one on chromosome 7 and one on chromosome 10. ERVs degrade a lot over time, but they could find transcripts for all the major retroviral proteins, gag, pol, and env.
Why is this important?
At first, they could only find activity from the chromosome 7 locus, only in some patients. HERV-K activity from…
sa smith | January 25, 2015A paper was recently brought to my attention via a Creationist. It was the usual 'HAHAHA! Oh you silly Creationist! This paper says the opposite of what you think it says!', and I was going to write a blog post along that usual theme.
Fazale Rana, 'Vice President' of 'Research and Apologetics' at Reasons to Believe said on Facebook:
What happens when the best evidence for biological evolution becomes evidence for intelligent deign?
Retroviruses, long thought to be junk DNA, play a role in regulating gene expression in the brain (link to ScienceDaily about the article)
The article has some…
sa smith | December 5, 2014For some reason, pop news became enamored with this paper last month (unfortunately while I was away at a conference):
HIV infection en route to endogenization: two cases
Inexplicable media frenzy--
Scientists find mechanism for spontaneous HIV cure
French scientists find genetic mechanism by which two men were spontaneously cured of HIV.
HIV discovery offers new lead in finding cure
I have a lot of problems with this paper. Starting with the first sentence.
The long-term spontaneous evolution between humans and the human immunodeficiency virus (HIV) is not well characterized.
"Spontaneous…
milhayser | December 1, 2014In a phenomenon known as Peto's paradox, large mammals do not develop cancer more often than small mammals, despite having more cells that could go haywire. On Life Lines, Dr. Dolittle writes "Some researchers suggested that perhaps smaller animals developed more oxidative stress as a result of having higher metabolisms. Others proposed that perhaps larger animals have more genes that suppress tumors." But a new hypothesis argues that large mammals have evolved to minimize the activity of ERVs, which are ancient viral elements integrated into our DNA. Active ERVs can cause cancer and possibly…
sa smith | October 23, 2014The title of this article by Answers In Genesis is a good question:
Where Did Ebola Come From?
*shrug* Look, I love making fun of Creationists, but this is a great question!
Ebola is not 'supposed' to be a human pathogen. Like many emerging infectious diseases, the natural reservoir for ebola is bats. Specifically, fruit bats.
By studying the genomes of many small mammals, we have determined that ebola-like viruses have existed on Earth, infecting small mammals, for 12 to 24 million years.
YAY! Straight forward answer to an interesting, valid question.
...... But with Creationists, things are…
sa smith | September 24, 2014For quite a while, now, there has been a connection between Endogenous Retroviruses and HIV. For some unknown reason, some of the young ERVs in humans, the ones that can still code for a protein here and there, are reactivated in HIV+ patients. Scientists have found ERV RNA in HIV+ patient plasma, and they have even found cytotoxic T-cells that target ERV proteins.
HIVs controlled by HERVs
This lead some scientists to believe that maybe, maybe, ERVs could be a good target for an anti-HIV therapy.
HIV changes a lot. It is really hard to train your immune system to fight it.
ERVs are 'human',…
sa smith | June 24, 20141-- Herpes viruses are old. They are ooooooold. Like, hundreds of millions of years old. Specifically, about 400 million years old.
2-- Herpes viruses are everywhere. Fish, reptiles, birds, cows, humans, everywhere. And there are lots of different kinds that humans have to deal with-- CMV, EBV, HHV-8, VZV, HSV...
3-- And, though herpes viruses should not be inserted into the genome of their host cell, generally, some herpes viruses can. Its called 'strategic somatic genome integration', and some herpes viruses (and only a small percentage of cells infected with that virus) do insert.
So…
sa smith | December 18, 2013Okay, I have written a LOT about the connection between wayward ERV activity and Multiple Sclerosis. This is something scientists have been investigating for a long time... but we still do not know exactly what is going on.
It seems the running hypothesis is that 'something'/'somethings' alter the epigenetic profile of individuals DNA, allowing for expression of an endogenous retroviral Envelope protein, especially in the brains of (future) MS patients. These proteins are pro-inflammatory, start causing all sorts of trouble, like MS.
Its gotten to the point where other scientists are trying…
sa smith | November 21, 2013Well, some of you! And maybe me!
Last year, scientists combed through Neanderthal and Denisovian DNA sequences (yeah, those exist!) and found fourteen ERVs that were in Neanderthals and/or Denisovians, but NOT humans.
Neandertal and Denisovan retroviruses
SUMMARY:
Modern humans (Homo sapiens) last shared a common ancestor with two types of archaic hominins, Neandertals and Denisovans, roughly 800,000 years ago, and the population leading to modern H. sapiens separated from that leading to Neandertals and Denisovans roughly 400,000 years ago [1,2,3,4]. Genome sequences for these two types of…
sa smith | November 14, 2013I love viruses, and I love ERVs, but I am not the only one :-D
Here are some links to pieces people have written about these lovely pirates, from three different perspectives.
1-- Nicholas Covington at Humes Apprentice (formerly AIG Busted!) is more a philosopher than a scientist, but even as a 'layman', he gets what ERVs are, and their place in evolutionary biology:
Proving Darwin: Fun with Endogenous Retroviruses!
2-- Carl Zimmer is no stranger to viruses. While he is still a 'layman', he has turned a personal fascination into a professional interest in viruses and ERVs. I love his…
sa smith | November 13, 2013I have written quite a bit about the connection between wayward expression of an ERV, and Multiple Sclerosis.
ERVs and Multiple Sclerosis
ERVs and Multiple Sclerosis, #2
ERVs and Multiple Sclerosis, #3
ERVs and Multiple Sclerosis, #4
ERVs and Multiple Sclerosis, #5
I am very comfortable saying there is a connection between ERV expression and MS. I am not confident in saying 'If we destroy the cells producing this ERV, we will stop MS.'
I totally get that the ERV protein in question, an Env, can be inflammatory in the brain, so knocking that out might stop some inflammation/damage in the brain…
sa smith | November 11, 2013I have no idea how the leopard got its spots, but scientists have figured out how horses got their leopard spots!
Evidence for a Retroviral Insertion in TRPM1 as the Cause of Congenital Stationary Night Blindness and Leopard Complex Spotting in the Horse
Get this!
Scientists have known for a few years that it is mutations within 'transient receptor potential cation channel subfamily M member 1' (TRPM1), that cause leopard spots and sometimes night blindness in horses. It turns out the bugger causing both of these phenotypes is a retrovirus that decided to plop into TRPM1.
The retrovirus did…
sa smith | September 11, 2013After I cleared up everyones confusion on why chicken gonads are lopsided, and why we have white chickens, I thought I would tackle another one of lifes great mysteries.
Admit it. Youve wondered where the hell blue chicken eggs come from.
Source: http://www.lespetitesgourmettes.com/recipes/gorgeous/
I 'get' brown eggs. I 'get' white, kinda. BUT WHERE THE HELL DID BLUE COME FROM?
'Well, you see when a chicken lays an egg mid-flight on a bright, sunny day, predators on the ground have a harder time seeing the blue egg...'
WAT?
No, seriously, whats up with blue chicken eggs?
Turns out it is a…
sa smith | February 15, 2013This idea... this idea might be absolute genius...
Immunogenicity of bivalent human papillomavirus DNA vaccine using human endogenous retrovirus envelope-coated baculoviral vectors in mice and pigs.
The 'best' vaccines are live attenuated vaccines. Weakened/Misadapted viruses that can replicate a little bit, and get your immune system to generate a B-cell response (what you get with most vaccines) and a CTL response (what you really need a 'live' virus for).
But with some viruses, it isnt practical/possible to make an attenuated version (think HIV-1. aint nobody ever going to get an…
sa smith | February 14, 2013The connection between ERVs and placentas is already well established.
Without a shadow of a doubt, the ability of mammals to generate placentas was, in part, accomplished by domesticating an endogenous retroviral env protein. In humans, we call this protein syncytin, or ERVWE1.
This new paper in Nature Genetics takes the ERV-Placenta connection a step further:
Endogenous retroviruses function as species-specific enhancer elements in the placenta.
Even though all mammals have placentas, mammalian placentas are different, even between species we would think should be very similar, like the…
sa smith | February 13, 2013Here is a nice open access review article on ERVs and their association with cancer:
Human endogenous retroviruses and cancer prevention: evidence and prospects
While thats wonderfully interesting, what I want to focus on is a bit at the end. More information I have never heard before--
An amino acid sequence similar to HERV-K-MEL, recognized to cause a significant protective effect against melanoma, is shared by the antigenic determinants expressed by some vaccines such as BCG, vaccinia virus and the yellow fever virus.
...
A recent epidemiological study provided provisional evidence of how…
sa smith | February 12, 2013I was actually unaware of this-- But melanoma is Yet Another Disease that has been associated with wayward ERV transcription and translation. Scientists have found inappropriate ERV RNA, protein, and anti-ERV antibodies in melanoma patients.
This is the first paper to break down 'melanoma' into subtypes (like 'cancer' is not monolithic, all 'melanomas' are not the same), and to compare those subtypes to normal tissue and benign naevus (non-cancerous birthmarks and moles).
Human endogenous retrovirus K (HERV-K) rec mRNA is expressed in primary melanoma but not in benign naevi or normal skin.…
sa smith | February 11, 2013ERMAHGERD! IM GONNA TALK ABOUT ERVS ALL WEEK!!!
I have a love/hate relationship with the ERV-[insert brain/CNS disorder] 'connection'. Labs from all over the world, with independent protocols and patient cohorts, see there is something going on with, for example, ERVs and multiple sclerosis. So there is *something* going on there, we just arent sure what yet. Sometimes I think the researchers are on the right track, and sometimes I think subsequent papers are a backslide, but *something* is going on.
I am totally sympathetic to the folks who do research with brains and other precious body…
sa smith | February 6, 2013I recently got to chat with the guys of Skeptiles this weekend about viruses, vaccines/anti-vaxers, HIV, HepC, Creationists-- We were all over the place, and it was so much fun!
Skeptiles: Episode 21 – Abbie Smith
sa smith | December 12, 2012Uh oh. VIRAL NOMENCLATURE WAR!!!
CERV vs CERV!!!
Chimpanzee vs Crocodile!!!
Its gonna be a THROWDOWN!!!
... Or we can just read a neat open-access article about ERVs in crocodiles :)
Strong purifying selection in endogenous retroviruses in the saltwater crocodile (Crocodylus porosus) in the Northern Territory of Australia
Specifically, Crocodylus porosu, saltwater crocodiles, one of the many terrifying creatures that inhabits Australia.
They used PCR to fish around the genomes of 47 crocs from all over Northern Australia for the gag-pol portion of some ERVs. They successfully got sequences…