Bad week

I have the swine flu.

Well, some kind of flu, anyway. I woke up at about 5am on Saturday with a cough, sore throat, aching joints, and low-grade fever. I seem to already be past the worst of the fever and aches, but that cough is just nasty, and while I'm not actually short of breath, my breathing doesn't feel as free and easy as usual. So I stayed home on the sofa all weekend while Mr E Man went to an awesome Hallowe'en party/sleepover on the Sunshine Coast.

I'm still too sick to do any useful work - I had to lie down for an hour after doing one load of laundry yesterday. My colleague has just emailed to confirm that our flu guidelines mean I'm not allowed into work all this week, even if I feel better. (I'm based in the research building, but the clinical building is just over the road, and there's a lot of traffic (patients and staff) between the two). As soon as my 7 day isolation period is up, I'll be getting on a plane... so I'm going to be horribly, horribly behind when we get back from vacation! Oh well, if I feel better later in the week I'll get one of my colleagues to send me some of the documents I was working on last week. And I can call into my various meetings, if my colleagues don't mind listening to me cough.

I'm thankful for two things though: the timing (the WHO's 7 day isolation recommendation means I'll be OK by the time our flight takes off at 10pm on Saturday), and the fact that (so far!) I haven't had the gastric symptoms that some people have been getting. I hate throwing up, almost to the point of phobia.

So, it could be worse. I have movies, internet, podcasts, books, and kitties to keep me entertained, and Mr E Man has stocked the cupboards and fridge with soup, fruit, juice, and lots of different kinds of tea. I forgot to ask him to pick up some honey, though, and as it turns out, lemon tea with maple syrup is NOT going to be the Next Big Thing. Worth trying though!

I might even get caught up on my blog reading!

Dear Mr Norovirus,

OK, so you ruined Christmas Day. Rather than eating delicious turkey and socialising with the neighbours, I spent the day alternating between throwing up and shivering under a duvet with a hot water bottle.

I think we can call that Round One to you.

And I know what you were thinking when I woke up to the sound of our house guest* throwing up at 3 am last weekend, because I was thinking the same thing:

"Hmm, that must be the same thing his kid had a few days ago. Infectious, then. Oh bloody hell, it's my old friend Mr Norovirus. Let me see, person with highly infectious virus throwing up repeatedly in our one and only bathroom. Aerosols, all surfaces will be infected... oh, and I bet that's the same noise that woke me up half an hour ago, so I was in there immediately after him without realising. I washed my hands, but then I used the towel and touched the door handle. 24-48 hour incubation period, hmm, it's my birthday on Monday, I guess I'll be spending that the same way as Christmas. Oh, fuck, citizenship test on Tuesday, if I miss that it'll set me back by months. And even if by some miracle I'm not already infected, he'll still be infectious for at least another three or four days... which, if I'm not careful, would see me getting sick on Saturday, big birthday dinner... this is gonna SUCK."

But! Fool me once, shame on you. Fool me twice, shame on ME. I've learned a few things since our last encounter:

• I boiled my toothbrush for 10 minutes before using it. And I brushed my teeth in the kitchen for a whole week.
  
• I threw out my contact lenses a few days early, and switched to a new case when I opened the new pair of lenses.
  
• I've washed my hands so often and so well, my skin is cracked and painful despite all the lotion.
  
• I abandoned all environmental principles and bought some bleach spray. I've sprayed it on all hard surfaces in the bathroom at regular intervals for a week.

WE CAN'T GET FOOLED AGAIN!

As of today - eight days after that dark, dark night - I am symptom free. 

Round Two to me.

Infect THAT, mo fo.

Yeah, OK, so the CDC says that "some people" are infectious for up to three weeks after symptoms stop. Too bad it doesn't say which people... So FYI I will not be dropping my guard any time soon. 

But even if you DO make me sick some time this month, the joke will be on YOU, because I enjoyed my birthday AND my birthday dinner AND I took my citizenship test on schedule. So while I will curse your name from my battle station in the bathroom, victory will still me mine. Mwa ha ha ha!

You are a worthy adversary. And I'm sure we will meet again.  I will be forewarned, forearmed, and ready to kick your butt.

Now if you will excuse me, I need to write a letter of complaint to Mr Sangria. His behaviour last night was really quite appalling.

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*Friend of Mr E Man's, staying with us indefinitely while he navigates his way through a particularly vicious divorce. And that is all I have to say about that.

Snowed under...

I'm back! Ever so slightly hungover, but the jet lag has gone. Staying out until after 2 am on our first full day back seemed to reset my system.

This is what happens when you leave your car outside for two weeks during record snow falls... this is NOT normal weather for Vancouver! And it's still snowing!

I hope everyone had an excellent Christmas or other festive break. Our first week in the UK was awesome, but unfortunately the second week was spoiled by a 24-hour norovirus that my sister brought with her from London and that swept through the entire family. It hit me next, at about 11.30 pm on Christmas Eve, so I was the only one to miss Christmas dinner. I did get to open my two stockings though - chocolate, fruit, chocolate, whiskey, more chocolate... just what I needed! Mr E Man and my Dad went down next, and my Mum was just getting over it as we left. Lovely.

Still, at least I lost some weight over Christmas, for the first time in my life...

So, back to reality - I worked from home yesterday, and am due back in the office tomorrow. As usual when coming home from a trip, I'm feeling a bit snowed under with laundry, other household chores, work stuff, and an avalanche of blog posts - I'll get to them soon, I promise!

Like Mr E Man, I need to start digging out. If only it would stop fucking snowing...

Happy New Year, everyone!

Endogenous retroviruses and evolution: redux

While chatting with Propter Doc last week, I realised that most of my current readers weren't around to witness this blog's finest hour. Way back in June 2007, I posted an explanation of why a paper of mine that had appeared on a creationist website actually provided evidence in support of evolution. The post earned me many links, including one from PZ Myers at Pharyngula* (as Propter said, it's like getting a link from God! I got an email too!). It also made the front page of Reddit; these two internet forces combined to bring in over 3,000 unique visitors in one day. The post also spawned a crazy comments thread, featuring some nice juicy arguments with creationists (you can see it here at the original post), and is the most frequently Googled post on the entire blog. As my sidebar poll comes to a close, more than 50% of all respondents have indicated that they planned to use the material in the post in their own arguments with creationists. In fact I've already seen the link appear in several internet discussion forums.

Oh, and they eventually took my paper off the website: details here. Score!

The text of the original post is below if you're interested...

*Another conversation with Propter: is it Pha-RING-you-lah (my interpretation) or Pha-rin-GOOL-ah (hers?)
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Here is my description of the part of my research that has been misrepresented by the Reasons to Believe website. See this post for an explanation.

My paper concerns the regulation of a human gene by DNA derived from an endogenous retrovirus (ERV). An ERV is a viral sequence that has become part of the infected animal's genome. Upon entering a cell, a retrovirus copies its RNA genome into DNA, and inserts the DNA copy into one of the host cell's chromosomes. Different retroviruses target different species and types of host cells; the retrovirus only becomes endogenous if it inserts into a cell whose chromosomes will be inherited by the next generation, i.e. an ovum or sperm cell. The offspring of the infected individual will have a copy of the ERV in the same place in the same chromosome in every single one of their cells.

This happens more often than you might think; 8% of the modern human genome is derived from ERVs. Repeated sequences of this kind were formerly considered to be non-functional, or "junk" DNA. However, we're gradually finding more and more examples of viral sequences that appear to have some kind of function in human cells. For example, many ERV sequences play a role in human gene regulation. ERVs contain viral genes, and also sequences - known as promoters - that dictate when those genes should be switched on. When an ERV inserts into the host's chromosome, its promoter can start to interfere with the regulation of any nearby human genes. In the example that I researched, the ERV promoter has become responsible for most of the expression of a particular human gene in the large intestine.

Creationists and intelligent design advocates like to think that because some ERVs have useful functions in the human genome, they must have been deliberately put there by a creator / designer with that particular purpose in mind. Of course, no-one can explicitly prove that that is incorrect - it's not a falsifiable hypothesis, and therefore it's not science. What we can show is that ERVs provide evidence in support of the theory of evolution.

Let's imagine how ERVs would behave within a model of evolution by common descent. An ancient creature, let's call it the common ancestor of all modern mammals, is infected by a retrovirus that becomes endogenous. All of the animal's descendants (i.e. all mammals) would be expected to carry the same ERV insertion (ERV1) in the same chromosomal location.

Fast forward in evolutionary time. Different lineages have evolved and diverged from the original common ancestor and there are now many different types of mammal in existence, all carrying ERV1. A small rodent, let's call it the common ancestor of mice and rats, is again infected by a species-specific retrovirus that becomes endogenous. This is ERV2. In a parallel event in a different lineage, the common ancestor of all great apes acquires a third insertion, ERV3.

Moving forward again, a fourth ERV appears in some of these new-fangled human thingies that are running around in Africa, but not in their hairier relatives who will eventually evolve into modern chimpanzees. The early humans spread out, and a fifth and (don't worry) final ERV arises in a population that is isolated in a discrete geographical location. The infection does not spread to other human populations.

So what would we expect? Humans, chimps, mice and rats should all possess ERV1. The mouse and rat genomes will also contain ERV2, the virus that infected their common ancestor, but not the primate-specific ERV3, 4 or 5 insertions. All great apes will share an identical ERV3 insertion; all humans will also possess an ERV4 insertion that is not found in chimps or other apes. In addition, some, but not all, humans will carry an insertion of ERV5. The rodent-specific ERV2 insertion will not be found in any primate species.

Now that several genomes have been sequenced, we have begun to test these predictions. The patterns of ERV insertions observed in modern species exactly match the predictions made by the model described above. Some insertions are shared between humans and mice and represent truly ancient viral infections. Others are found only in primates, and not in other species, obviously derived from an infection of the ancestral primate species after its divergence from other lineages. More modern insertions are found only in humans, while the youngest ERVs of all are found in some humans, but not in all. We do not find any examples of ERV insertions shared by, say, humans and mice, but not by chimps. Insertions are always shared by all species, and only by those species, that have a common ancestor. ERV insertions therefore provide excellent support for the theory of evolution by common descent.

My particular favourite ERV is found in various primate species, and therefore must be at least 25 - 30 million years old. I compared the sequences and activities of the same ERV promoter in the human, chimp, gorilla, and baboon genomes. Despite some minor "single-letter" point mutations caused by DNA copying errors, the promoter had essentially the same function in all four species. I struggle to understand why any kind of designer would decide to use different codes to perform the same function in different species, but there it is. I hypothesised that the ERV was only allowed to persist (that is, its meddling in gene regulation didn't kill the first organism in which it inserted, which was therefore able to pass the insertion on to its offspring) because the incoming ERV promoter behaved in a very similar way to the original host cell's gene promoter. I wasn't able to do the experiments I wanted in order to investigate this point, but another group subsequently did, and their findings supported my hypothesis. That's what happens when you make and test falsifiable predictions.

I could go on and on about the role of ERVs in genome evolution, but this post is too long already. I would encourage anyone who's interested to search for "endogenous retrovirus" AND evolution in the PubMed database of peer-reviewed research papers. You won't find much in there about creationism or intelligent design.

Viral Sneakiness

Viruses are fascinating little buggers. They sneak into cells and take over their entire machinery and pathways for their own use, sometimes with as few as three genes. The amazing thing is that every virus has evolved a different way in which to do this. This week's papers are from the same issue of Cell Host and Microbe, and describe the MOs of two different classes of virus. (I love it when I find pairs of complementary papers in the same journal issue; it makes my job so much easier.)

The first paper, by George Katsafanas and Bernard Moss at the National Institute of Allergy and Infectious Diseases in Maryland, concerns poxvirus replication. It has been known for almost sixty years that poxviruses, unlike many other DNA-based viruses, do not replicate in the cell nucleus where the host's DNA replication machinery resides. Instead, the infectious particles that enter the cell contain several viral enzymes; these proteins allow the poxvirus genome to replicate in the cell's cytoplasm. This process occurs in distinct cytoplasmic regions known as DNA factories.

The authors began with high-resolution visualisation of viral DNA factories. Dual colour staining revealed cavities and tunnels within each factory that appeared to contain RNA, the cell's intermediate between DNA and protein. This suggested that transcription (DNA→RNA) and translation (RNA→protein) may also occur within the factories.

A direct test of this hypothesis would have been technically very tricky, as RNA is notoriously unstable and difficult to work with. An alternative approach is to determine whether molecules that are associated with transcription and translation co-localise to the viral DNA factories. Indeed, viral and host proteins that are known to be involved in viral transcription and translation were found in the RNA cavities within the DNA factories.

As the authors wrote in the Discussion section of their paper: “Although the presence of translation initiation factors... provided circumstantial evidence that protein synthesis occurs in the factory, more compelling data were needed”. But how do you prove that viral proteins are made in the factory, rather than being produced elsewhere and then imported? One solution is to insert a foreign gene that encodes a visible protein into the viral genome, and to track the accumulation of the protein over time. In fact, the blue marker protein was synthesised within the viral DNA factory, as predicted by the presence of translation machinery components. Further experiments with other coloured proteins revealed that a single virus genome is often transcribed and translated within a single DNA factory.

Packaging everything needed for viral transcription, translation and DNA replication into a distinct cell region makes sense in terms of increasing the efficiency of viral replication. However, a secondary effect is to sequester vital molecules away from the cell's own DNA and RNA, decreasing the efficiency of host transcription and translation. So increasing your own replication efficiency also helps to suppress the host's immune responses. I told you these things were sneaky.

The second paper concerns a modern media darling, the West Nile Virus (WNV). Although this small RNA-based virus is very different to the large DNA-based poxvirus, WNV also replicates in distinct structures outside the cell nucleus – in this case, in specialised cell membrane subdomains¹ – and knocks out aspects of the host's immune system. Jason Mackenzie and colleagues from the University of Queensland, Australia, spotted similarities between the WNV-induced membrane structures and those that arise when the cell's usual cholesterol levels are disrupted, and investigated whether disruption of cholesterol synthesis is part of the viral arsenal. And just like that, a brand new avenue of investigation was opened...

The first finding was that cholesterol is distributed differently in WNV-infected cells. There was less overall cholesterol present in infected cell membranes, and the remaining cholesterol molecules clustered in the membrane subdomains associated with viral replication. By observing the effects of various cholesterol-modulating chemicals, the researchers concluded that WNV replication depends on a key enzyme that is usually involved in cholesterol synthesis, and that is upregulated when the host cell detects the virus-induced changes in cholesterol distribution.

Cholesterol is also involved in communication between some cell membrane proteins. The redistribution of membrane cholesterol by WNV severely hampered that communication in one specific molecular pathway – yes, you've guessed it, a pathway that usually participates in anti-viral immune responses. While supplementing the cell with additional cholesterol did help to restore the usual immune response, don't resort to eating deep fried Mars Bars² if you get bitten by a mosquito - just trust that this potential treatment for WNV will be followed up.

The tactics of WNV and the poxvirus family are, then, strikingly similar: infect a cell, claim a specific region of the cell as your own, sequester cellular molecules away into those regions in order to replicate efficiently, and in doing so, deprive your host of the means to mount an effective response against you. Two very different viruses converging on a very similar solution (using different pathways) to the same problem. A double double whammy of viral sneakiness. So what are you waiting for? Go out there and evolve some resistance, why don't you?

1. Imagine the membrane as an oily bag that surrounds the cell. Molecules such as cholesterol and various proteins are embedded into this layer; the molecules are mobile and can move through the oil to contact one another. Some embedded proteins connect to the outside of the cell, and some to the inside, allowing communication between cells.

2. Imagine the deep fried Mars Bar as an oily bag that surrounds the artery... seriously, they exist, I've eaten one, it was tasty. And gross. Don't try this at home.

HERVs and Multiple Sclerosis, part 2

Well, after a short period of distraction, I have just finished reading the new paper from Christopher Power's lab at the University of Alberta. This study follows on from an earlier paper that suggested a causal link between the expression of Syncytin-1, a gene derived from a human endogenous retrovirus (HERV), and multiple sclerosis (MS). The new paper sought to identify the mechanisms by which Syncytin-1 mediates central nervous system damage.

I found it extremely interesting to revisit a subject that I'd read about in detail a few years ago, but ignored ever since. I've clearly managed to neglect a lot of new research; Antony et al. cited a whopping 87 papers, and incorporated new advances in the fields of infectious virology, neurology, biochemistry and immunology into their research.

Much of the work described in the paper focused on the effects of Syncytin-1 on the expression of other cellular proteins; candidate proteins were chosen on the basis of known or predicted involvement in the pathophysiology of MS and other relevant disorders. The Power lab and their Canadian, Japanese and French collaborators approached the problem from various angles. RNA transcript and protein levels were compared in human brain tissue, cultured cells, and transgenic mice that express human Syncytin-1 in specific areas of the brain. After establishing some initial correlations between MS and altered protein expression, the team went on to develop tools to differentiate cause and effect. They were able to manipulate the level of Syncytin-1 protein in cultured cells, either by forced over-expression or by targeted degradation of the corresponding RNA transcript, and show that certain other cellular proteins were specifically misregulated as a result. In this way, the mechanisms of neural damage by Syncytin-1 gradually emerged. The initial event appears to be generation of an inflammatory response, which in turn induces altered expression of proteins involved in cell stress. Ultimately, and as a direct result of Syncytin-1 expression, the myelin coating that protects the nerve fibres becomes damaged - a hallmark of MS.

I've compressed the results of a staggering amount of work into the single paragraph above. This is one of the most comprehensive studies I have ever read – every single finding was confirmed using at least two different methods, sometimes more. Some parts of this paper could easily have stood alone as a full publication. I've seen many a paper based entirely on comparative gene expression analysis in normal versus diseased tissue, or on development of a transgenic mouse model, tools that were both used here as only two parts of a much bigger puzzle. I am hugely impressed. I must admit that when Antony's first paper came out I was somewhat sceptical as I started to read it, having read many other studies showing correlations between HERV expression and diseases such as MS, cancer and schizophrenia. I was always inclined to think that such correlations were more likely to be the result of general transcriptional chaos in some disease states than of pathological HERV sequences. But, in this case at least, it appears that I was wrong; the combined results of these two papers present a very convincing case for the role of Syncytin-1 in the development of MS.

Now that the case has been made so clearly, the field can progress and address some new questions. How does Syncytin-1 expression affect the immune cells that play such an important role in MS? Why does Syncytin-1, a protein usually confined to the placenta, sometimes appear in central nervous system cells and trigger MS? A quick PubMed search brought up some interesting hints. Syncytin-1 expression can be upregulated by viral infection, a condition which is suspected to trigger some cases of MS, and by some signalling molecules associated with MS. In addition, the placental expression of human and rhesus monkey Syncytin-1 changes during pregnancy, suggesting a role for female hormones such as progesterone. As I alluded to in an earlier post, this may explain some aspects of gender-specific MS epidemiology. I hope someone somewhere is working on this problem – not only does it have important consequences for the understanding of this devastating disease, but I also want to know if I managed to be right this time.

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Canada has one of the highest rates of MS in the world. For more information, including how to make a donation, see the MS Society of Canada's website.

HERVs and Multiple Sclerosis, part 1

I have a new paper sitting on my desk that I plan to summarise in the near future. The study investigates the relationship between syncytin, a human endogenous retroviral protein, and MS. I actually wrote a review of an earlier paper by the same group for my former lab's newsletter in December 2004. Leaving myself open to ridicule and correction, I have copied my original report word for word below without reading the new paper first. I wonder if the new study addresses any of the points I made in the final paragraph?

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Human endogenous retrovirus (HERV) transcripts are usually repressed by DNA methylation, but have been detected in patients with Multiple Sclerosis (MS) and other autoimmune diseases. The nature of this relationship remains unclear. Does re-expression of viral proteins trigger an autoimmune response? Can antibodies produced in response to another virus cross-react with HERV antigens? (Viral infections may be a trigger of MS). Or is expression of HERVs merely a result of reprogrammed DNA methylation, with no causal link to the disease? A recent Nature Neuroscience paper has finally provided some evidence for a causal relationship.

The paper focuses on syncytin, a HERV envelope protein. Syncytin was specifically up-regulated in the brain, demyelinating lesions and neuroinflammatory cells of MS patients. Expression of syncytin in cultured cells reproduced some aspects of the MS phenotype, including oligodendrocyte death and induction of proinflammatory molecules. Reproduction of these effects in cultured cells suggests that syncytin protein function, rather than an autoimmune response, may be involved in at least the initial neuroinflammatory aspects of MS.

The region of the mouse brain corresponding to that most affected in human MS was in infected with a syncytin expression vector. Infection reproduced some of the effects of human MS, including myelin damage, decreased numbers of oligodendrocytes, and induction of neuroinflammatory molecules. Infected mice performed poorly in behavioural tests, indicating muscle weakness and unsteady gait. Interestingly, treatment with antioxidants significantly reduced the molecular and behavioural effects of syncytin in infected mice and cultured cells. There is some anecdotal evidence that antioxidants can help control the symptoms of MS, but no large-scale clinical trials have been completed.

So there you have it – finally, some evidence to support the theory that HERVs are involved in MS. Personally, I'm most interested in the association that the authors didn't make. Syncytin is usually expressed mainly in the placenta, which may explain some aspects of MS epidemiology. Women are approximately twice as likely as men to develop MS, and the frequency of MS relapses can change during and after pregnancy. More work is needed to determine the mechanisms of syncytin activation in the placenta and in MS, and specifically the role of female hormones in this process. No doubt the paper by Antony et al will stimulate this, and other, avenues of investigation and debate.

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Canada has one of the highest rates of MS in the world. For more information, including how to make a donation, see the MS Society of Canada's website.

Field dispatches from the war on viruses

I have yet to be formally challenged, so I will take the initiative to venture ever so slightly away from the very centre of my usual comfort zone...

I have written before about the ongoing arms race between viruses and the host species they infect. This week's Journal Club will cover one story from each side of the struggle. The first paper, by Andreas Ackermann and colleagues from the University of Freiburg, concerns the evolution of the Borna disease virus (BDV) to enable infection of a new host species.

BDV infects many bird and mammal species, causing a severe neurological disorder, but does not usually infect mice. However, virus extracted from monkey cells grown in the lab can be injected into rat brain, where it will cause disease symptoms within a few weeks. Extracts from the rat's brain can then be injected into mice, which will display some signs of neuronal infection, but no symptoms. Extracts from the mouse brains are then injected into new mice, and so on until the virus eventually evolves to become infectious and pathogenic in the mouse host.

To determine how this process happens, Ackermann et al. sequenced the genomes of viruses that had successfully adapted to mouse hosts. They found three point mutations (single-letter typos) that were each present in around 80 – 100% of evolved viruses. The mutations mapped to proteins within the polymerase complex that is responsible for transcribing the viral genes into RNA. Two of the mutations arose twice independently, indicating that they confer a strong selective advantage to viruses that are in the process of adaptation to mouse cells.

The researchers engineered viruses that contained either a single mutation, or a combination of two or three of the original mutations. The mutated viruses were then put through their paces in a series of tests for replication in cultured cells and in living mouse brains. While each mutation individually improved the ability of BDV to infect mouse cells, the viruses that combined two or three different mutations grew the most aggressively. Not surprisingly, the viruses that multiplied the fastest caused the most severe symptoms in infected mice.

So how do polymerase mutations enable BDV to infect mice? One possible mechanism is interference with the normal interactions between different members of the polymerase protein complex. Indeed, one of the evolved changes essentially blocked the mutated protein subunit from binding to a partner that usually inhibits polymerase activity. The result is increased transcription of the viral RNA, which appears to be enough to overcome the mouse cell's normal barriers to BDV infection. This is not the only route by which viruses can evolve new host specificities, but it is certainly an effective one.

The second paper is from the same issue of the Journal of Virology, and involves host resistance to HIV. Lokesh Agrawal, from the Indiana University School of Medicine, worked with colleagues in China and France to study why some Caucasians are resistant to HIV infection, and how that resistance can sometimes fail.

The first thing that HIV needs to do before infecting a cell is to bind to its surface. This requires the presence of two proteins on the cell's surface membrane – CD4, and usually CCR5 or CXCR4. In other words, the virus needs to fit keys into two different locks in order to enter the cell. Some Caucasians carry a mutation in CCR5 that prevents the protein from reaching the cell surface and contacting the virus; one of the two locks closes, and the virus can not enter. Around 1% of the Caucasian population have two copies of the mutated CCR5 protein, and therefore have no CCR5 protein on the surface of their cells. HIV infection is very rare in these individuals, but a few cases are known. Agrawal and colleagues wanted to know how these patients' usual defenses had failed.

The first phase of the study examined the amount of CCR5 and CXCR4 protein expression on the surface of cells from various individuals. HIV negative subjects with 2 mutated copies of CCR5 (known as CCR5^-/-) did not express CCR5 on the surface of their cells, as expected. They also expressed CXCR4 less strongly than normal, presumably because the mutated CCR5 protein is known to bind CXCR4 and hold it captive inside the cell, preventing it from reaching the surface. This represents a double line of defense against both CCR5- and CXCR4-specific viral strains. However, HIV positive CCR5^-/- patients expressed normal levels of CXCR4 on their cell surfaces, suggesting that HIV infection somehow prevents the mutated CCR5 protein from retaining the CXCR4 protein inside the cell. The researchers showed that the increased level of surface CXCR4 protein made HIV positive CCR5^-/- cells more susceptible to viral cell penetration.

As expected, cells that contained more copies of the mutated CCR5 protein were generally the most resistant to HIV infection. However, the stability of the mutant protein also played an important role. Some HIV positive CCR5^-/- patients' cells remained susceptible to viral entry despite artificially increasing their level of mutated CCR5 protein expression, as the protein was too short-lived to perform its usual protective function. The paper's discussion section speculates on several potential mechanisms by which HIV infection could destabilise the mutated CCR5 protein, and hence reopen the CXCR4 lock to allow viral cell entry. One such mechanism is targeted destruction of the mutated CCR5 protein by Tat, a viral protein that is known to increase the expression of CXCR4. The authors look to have a lot of painstaking work ahead of them in order to identify exactly how CCR5^-/- individuals' usual HIV resistance sometimes breaks down.

Meanwhile, the arms race will continue. Viruses such as BDV, SARS and avian influenza will evolve ways to target new species. Hosts will evolve novel defense mechanisms that will in turn be breached by mutated viruses. However, understanding the underlying processes gives us a slight advantage that we can potentially leverage in the form of new anti-viral drugs and targeted treatments for people with different genetic profiles. We may never win the war, but tactical advances might just win us a few battles.

Endogenous retroviruses and the evidence for evolution

Here is my description of the part of my research that has been misrepresented by the Reasons to Believe website. See this post for an explanation.

My paper concerns the regulation of a human gene by DNA derived from an endogenous retrovirus (ERV). An ERV is a viral sequence that has become part of the infected animal's genome. Upon entering a cell, a retrovirus copies its RNA genome into DNA, and inserts the DNA copy into one of the host cell's chromosomes. Different retroviruses target different species and types of host cells; the retrovirus only becomes endogenous if it inserts into a cell whose chromosomes will be inherited by the next generation, i.e. an ovum or sperm cell. The offspring of the infected individual will have a copy of the ERV in the same place in the same chromosome in every single one of their cells.

This happens more often than you might think; 8% of the modern human genome is derived from ERVs. Repeated sequences of this kind were formerly considered to be non-functional, or "junk" DNA. However, we're gradually finding more and more examples of viral sequences that appear to have some kind of function in human cells. For example, many ERV sequences play a role in human gene regulation. ERVs contain viral genes, and also sequences - known as promoters - that dictate when those genes should be switched on. When an ERV inserts into the host's chromosome, its promoter can start to interfere with the regulation of any nearby human genes. In the example that I researched, the ERV promoter has become responsible for most of the expression of a particular human gene in the large intestine.

Creationists and intelligent design advocates like to think that because some ERVs have useful functions in the human genome, they must have been deliberately put there by a creator / designer with that particular purpose in mind. Of course, no-one can explicitly prove that that is incorrect - it's not a falsifiable hypothesis, and therefore it's not science. What we can show is that ERVs provide evidence in support of the theory of evolution.

Let's imagine how ERVs would behave within a model of evolution by common descent. An ancient creature, let's call it the common ancestor of all modern mammals, is infected by a retrovirus that becomes endogenous. All of the animal's descendants (i.e. all mammals) would be expected to carry the same ERV insertion (ERV1) in the same chromosomal location.

Fast forward in evolutionary time. Different lineages have evolved and diverged from the original common ancestor and there are now many different types of mammal in existence, all carrying ERV1. A small rodent, let's call it the common ancestor of mice and rats, is again infected by a species-specific retrovirus that becomes endogenous. This is ERV2. In a parallel event in a different lineage, the common ancestor of all great apes acquires a third insertion, ERV3.

Moving forward again, a fourth ERV appears in some of these new-fangled human thingies that are running around in Africa, but not in their hairier relatives who will eventually evolve into modern chimpanzees. The early humans spread out, and a fifth and (don't worry) final ERV arises in a population that is isolated in a discrete geographical location. The infection does not spread to other human populations.

So what would we expect? Humans, chimps, mice and rats should all possess ERV1. The mouse and rat genomes will also contain ERV2, the virus that infected their common ancestor, but not the primate-specific ERV3, 4 or 5 insertions. All great apes will share an identical ERV3 insertion; all humans will also possess an ERV4 insertion that is not found in chimps or other apes. In addition, some, but not all, humans will carry an insertion of ERV5. The rodent-specific ERV2 insertion will not be found in any primate species.

Now that several genomes have been sequenced, we have begun to test these predictions. The patterns of ERV insertions observed in modern species exactly match the predictions made by the model described above. Some insertions are shared between humans and mice and represent truly ancient viral infections. Others are found only in primates, and not in other species, obviously derived from an infection of the ancestral primate species after its divergence from other lineages. More modern insertions are found only in humans, while the youngest ERVs of all are found in some humans, but not in all. We do not find any examples of ERV insertions shared by, say, humans and mice, but not by chimps. Insertions are always shared by all species, and only by those species, that have a common ancestor. ERV insertions therefore provide excellent support for the theory of evolution by common descent.

My particular favourite ERV is found in various primate species, and therefore must be at least 25 - 30 million years old. I compared the sequences and activities of the same ERV promoter in the human, chimp, gorilla, and baboon genomes. Despite some minor "single-letter" point mutations caused by DNA copying errors, the promoter had essentially the same function in all four species. I struggle to understand why any kind of designer would decide to use different codes to perform the same function in different species, but there it is. I hypothesised that the ERV was only allowed to persist (that is, its meddling in gene regulation didn't kill the first organism in which it inserted, which was therefore able to pass the insertion on to its offspring) because the incoming ERV promoter behaved in a very similar way to the original host cell's gene promoter. I wasn't able to do the experiments I wanted in order to investigate this point, but another group subsequently did, and their findings supported my hypothesis. That's what happens when you make and test falsifiable predictions.

I could go on and on about the role of ERVs in genome evolution, but this post is too long already. I would encourage anyone who's interested to search for "endogenous retrovirus" AND evolution in the PubMed database of peer-reviewed research papers. You won't find much in there about creationism or intelligent design. ERVs are also the subject of their own blog, a decent novel (although the sequel was disappointing) and a post on This Week in Evolution!