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      CommentAuthorJohn Skylar
    • CommentTimeJul 27th 2010 edited
    After gracious clearance from Mr. Ellis, here we are with a thread to discuss the biology of exotic viruses and what interesting technologies there are out there involving viruses.

    I can field questions, of course, but I don't really want this to become Lecture Time starring John Skylar. Not the place for it. In a way I'm hoping that the creative consciousness of Whitechapel is going to spur me to new ways of thinking about the work that I do.

    Anyway, to launch the thread, I want to share a couple of resources that are good for quickly familiarizing yourself with some of the cool things in virology.

    The first is virology blog, by Dr. Vincent Racaniello. Dr. Racaniello also has a podcast called THIS WEEK IN VIROLOGY, which comes highly recommended. It's also really accessible, so you can jump right in no matter what you know.

    There is also a totally open journal called Public Library of Science (PLoS), started by the decorated Dr. Harold Varmus. No paywalls here! PLoS has a subjournal called PLoS Pathogens, and their "Pearls" column includes short, entry-level introductions to various topics. They are collected here.

    Oh, and I almost forgot to mention INTERFERON FORCE, a comic put out by a company that makes reagents for studying the immune system. It's a fun, kinda cheesy summary of innate immunity, which is important against viruses. It would be nice if it credited any of its authors or artists more prominently, but it's a reagent supply company, I don't think they know from comics.

    Anyhow, that's a bunch of reading and I'm sure others will have things they want to share. I have to get back to working on this virus that makes monkeys foam blood out of their noses (Nipah virus as portrayed in a recent paper, link with photos if you're curious)
    • CommentTimeJul 27th 2010
    Can you talk a little about the use of viruses as a delivery mechanism for engineered genetic material into living cells?

    Is there a state of the art that isn't well reported? Are there any therapies in human patients yet that use this technique?
  1.  (8634.3)
    Ah, the ol' gene therapy question. Virus-vectored genetic engineering is great in experimental applications. We use it all the time to make genetically engineered cell lines or mice.

    So far in humans, though? Has a nasty habit of causing cancer. The new viral genes stick themselves into something useful a lot of the time. A couple of kids died in 2005, after a trial of that sort of thing, and it's kind of hampered the field.

    But I think herpes viruses, if we ever come to understand them better, might end up as a viable method of gene therapy, because their genomes don't integrate. It's a pet theory though. Dunno if anybody agrees.

    One thing that I think is under-reported is oncolytics. Aka, using viruses to kill cancer. The immune system usually alerts the body to an infected cell using the inflammatory Type I Interferon (IFN) system, which usually causes the immune system to kill infected cells. Turns out, cancer is inflammatory too, so the cancers that survive are often ones with mutations in the IFN system. So, viruses that are stopped by IFN and don't make you sick, are often very good at killing cancer cells. There's a couple of human trials with this, one of them using a thing called reovirus, by a group in Canada. There's also a group in New York using a bird virus called Newcastle Disease Virus for certain oncolytic applications. So yeah...virus infections to cure cancer. Kind of blows my mind.

    Anybody know of a thing I forgot?
    • CommentTimeJul 28th 2010
    Curious about the potential for spectacle in viral gene therapy - curing cancer is of course way more spectacular than cosmetic applications, but a viral infection that, say, changes your skin pigmentation or makes you grow feathers is probably going to cause just as much or more hoo-hah. What are the theoretical limits in current understanding?
    • CommentTimeJul 28th 2010
    Cool stuff! Gotta say that Nipah virus does not look like fun at all.

    A friend of mine recently completed a PhD looking at applications of network theory in epidemiology. Turns out networks can help to predict virus spread in a population, and can also identify the number of immune individuals required in a population to provide "herd immunity" (i.e. enough individuals are immune that the virus dies out in that population). Text is here for those interested. Useful for humans and livestock, but not so good for viruses in wild animal populations.

    I'm an aquatic ecologist, so don't do any virology work myself, but do find it fascinating. I'm also keen on the potential for gene therapy, as it currently looks like the only possible way to solve a few of my own medical problems. Shame about the tumours!
      CommentAuthorJohn Skylar
    • CommentTimeJul 28th 2010 edited
    @nygaard Well, currently, with the risks of viral vectored gene therapy, it's not worth it to have cosmetic applications, as any gene therapy could potentially cost you your life.

    However, let's say we got past that obstacle. We will eventually, I suspect. Changing the colour of your skin or adding feathers are two very different things that illustrate the limitations of this technology. I'm sure a lot of you remember Alpha Centauri, the computer game from the 90s. There was one tech that had this quote:

    "Remember, genes are NOT blueprints. This means you can't, for example, insert 'the genes for an elephant's trunk' into a giraffe and get a giraffe with a trunk. There are no genes for trunks. What you CAN do with genes is chemistry, since DNA codes for chemicals. For instance, we can in theory splice the native plants' talent for nitrogen fixation into a terran plant."

    Macro-structures take a complex program of genes to make, so feathers would be pretty hard to do. Most viruses are a pretty small package, and so inserting multiple genes is really tricky. Bigger viruses have their own issues with gene therapy. So feathers, or other things like them, would not be easy.

    Skin pigments? Easy, just one gene. I expect that'll be one of the first things that gets made once the technology is robust and safe.

    @smileyfish Yeah, Nipah's no fun at all.

    Combining network theory and epidemiology is something that's been on my mind for a long time. Someday I'd like to see epidemiologists using simulators not just to respond to existing pathogens, but to predict when and where new pathogens are going to emerge, so that we can defend ourselves proactively. Your friend's work sounds awesome.

    How do you feel about J. Craig Venter's explorations of genomes in the sea? I thought the number of viruses they pulled out was outright staggering.

    EDIT: Actually, come to think of it, the first outbreak of Nipah virus occurred on a farm and went from bats to pigs to humans. Your friend's network theory applications could really help in predicting and preventing the spread of future Nipah outbreaks, given their tendency to happen on farms.
    • CommentAuthorZeebo
    • CommentTimeJul 28th 2010
    Hope you don't mind if an immunologist jumps into the mix.

    I'd just like to mention another powerful technology paradigm that's growing thanks to viral genetic engineering: induced pluripotent cells (iPS). We're still not sure if they're true stem cells or not, but I think this method could prove more useful for many of the organismal changes when people think of "genetic engineering."

    For a quick primer, genetic engineering obviously edits genes, which internally control the behavior of the cell. Another less-talked about option is developmental engineering. If you have some stem cells, it's theoretically easier to grow them in specified environments that encourage the development of particular cell types. This environment often mimics the localized environment of an organ developing in a fetus.

    So, another option for people who hope to some day have horns and demonic hemipenises, developmental engineering coupled with modern medicine's amazing surgical capabilities might be an easier approach than viral engineering. Granted, surgery and in vitro growth have their own pitfalls, but it's an idea.

    Anyway, back to this idea of iPS. It's been all the rage in the news because it's a potential for unlimited sources of patient-specific stem cells. How do you make stem cells from fully developed cells? You insert the DNA for 3 or 4 developmental genes into them. Once you "kick start" this developmental program, the cell's innate machinery takes over and maintains a stem-cell-like state. Viruses are great at inserting DNA, but you have the problem of cancer, as detailed earlier. There are a lot of ways of getting around this now. One way is to create a self-excising virus, which pairs perfectly with the fact that cells can maintain the stem cell state once they've been converted. Another option is non-integrating viruses that create their products, but aren't inserted into the genome. There are more exotic ways of doing things too, like mechanically punching holes into cells and letting DNA diffuse into them.

    As for Venter, he does a lot of crazy and interesting stuff, but I think much of his acclaim comes from being a very good salesman. His oceanic sequencing project is a great idea and pulled out a lot of interesting data, but, unfortunately, it has very little metadata associated with it. Lots of conclusions can still be reached from raw, loosely-ordered data sets, but they're harder to link to previously-discovered information. Then again, that's kind of a hand-wavey argument.
    • CommentAuthorkozmund
    • CommentTimeJul 28th 2010
    I think, if anything, viral vectors are closer to cosmetic use than clinical use. You'll have to forgive me for the next sentence which is annotated in parenthesis for clarification. When you're talking about an incompetent (it can't create new copies of itself) virus that either doesn't revert to wild type (you don't end up with original, harmful viruses) or where the wild type isn't a concern (something that's more like a fairly harmless adenovirus or a lentivirus rather than HIV, as long as the virus only infects cells with minimal access to vasculature (not near blood flow to shed off cancer cells) which also stay with you for a short period of time, it's my understanding that there's not a pronounced risk. I mean, when compared to DIY magnet-insertion surgery, conjuctive tattooing, turning your cock into a crazed fucking predator face, etc.

    That is to say, applying a gene vector viruses to the epidermis isn't so risky as to put it out of the equation for the body mod crowd, if there was the available expertise and gear. Applying a vector where they'd be fairly permanent is a different matter. I'm still waiting to see the first EGFP temporary tattoo.

    (P.S. Not to be insensitive, but I would personally take leukemia over SCID any day of the week.)
    (P.P.S. Nothing in this post should be understood as medical advice. Always consult your physician before using a viral vector to modify the DNA in any of your cells.)
      CommentAuthorJohn Skylar
    • CommentTimeJul 29th 2010 edited

    Ooh! An immunologist! Good to see ya. I'm tempted to joke about how I expect you'll provide a strong response in 5-9 days, but maybe that's too much.

    Yeah, iPS is a great technology. Of course, I think that viral gene "therapy" will be useful in the context of iPS cells too, to edit the cells in culture before they're differentiated and returned to the patient. Still, there's the problem with any stem cells that they can fail to differentiate in-patient and cause cancer too. The tech needs to be worked out.

    I tend to agree with you on Venter's showmanship. I got my undergrad from a lot of people who worked with Leroy Hood, and they were no big fans of Venter, so I'm a little biased. Calling the human genome his IP...I mean really....


    The DNA changes that are caused in gene therapy are heritable to the cells' progeny, so your theory doesn't really fly. Actually I'd say the *least* dangerous application is in cell types that divide slowly or don't divide at all, because then if the cell goes haywire it might die via apoptosis before bad things happen. Bone marrow divides slowly, and the SCID trial patients only got leukemia a couple years after treatment. If it had been skin cells, I imagine they would have gotten the cancer to manifest a lot faster.

    I think, actually, that there are techniques involving electroporation of injected DNA that the body mod crowd might want to see. But the viral vectors? I'd say it's more dangerous, not less, than other applications.

    (Electroporation: a technique where you use electrical current to force DNA into cells, making them express whatever the DNA codes for. The results last for a few days before they clear up. It's being used for vaccine development right now.)

    And while I would also take leukemia over SCID if offered the choice, I'd take SCID over *incurable* leukemia.

    On an unrelated note, I think smileyfish asked me a question about lyssaviruses in another thread. I mean, aside from Rabies being basically the zombie virus (makes you go crazy, mindless, and bite people), I don't really study them. They're similar in replication to Nipah, though. But there are some key points of difference, specifically that the genomes are smaller and they tend to form visible replication complexes.
    • CommentAuthorBrazen
    • CommentTimeJul 29th 2010
    Howdy, Biochemist/Cell Physiologist here.

    I've noticed the bulk of this conversation has been about retroviruses (viruses that incorporate their DNA into a host's genome). What about Adenoviruses? These are viruses that drop a genomic payload (which modern science can program) into a host. This payload does not incorporate into the host genome and is therefore transient. That said, infection is silly efficient across most cell types and you wouldn't have to worry about cancer risks. Think about it, you could temporarily pump yourself full of some gene... say flourescent GFP for a couple weeks.

    Relating to Adenoviruses there is a movement in biotech to engineer a viable hybrid adeno-lentivirus which would have the high infection potential of an adenovirus, as well as the ability to stably incoporate DNA into a hosts genome like a retrovirus. It would be the best of both worlds (sans the cancer risk).

    Also, since this thread seems to have a genetic engineering slant, the curious should check out cre-lox technology. This stuff represents the bleeding edge of transgenic animal engineering. Essentially you add DNA sequences (lox sites) to a gene of interest that are recognized by a recombinase (cre). Cre recombinase then chops out the DNA inbetween these two sites. This allows site directed deletions of DNA (losses of function), or with some extra engineering, site directed activation of genes. Cre recombinase can be coupled to specific gene promotors which can limit recombination events to specific cell types, or specific developmental stages giving spatial control of events. There are also inducible cre recombinase derivatives that only "turn on" (get transported into the nuclease) with the addition of chemicals (or other stimulation) giving spatial control of recombination too. This is what I'm currently doing to study gene function in multicellular animals... so much mouse breeding.

    The thing that always blows me away about cre lox is that with available human embryonic stem cells, one can grow humans with suicide switches built into their genome. They recieve the right chemical dead. They fail to recieve treatment with a chemical dead. This is something that could ACTUALLY be done. Scary eh?

    Another neat genetic engineering tool in its embryonic stage is modular engineered proteins. The only example I know of is are the zinc finger nucleases which can be programmed to cleave DNA at any specific DNA sequence. Here is a movie by the people who make them. While only useful for knockouts right now, I think that this kind of thing could be thing that makes gene therapy actually possible.
    • CommentAuthorBrazen
    • CommentTimeJul 29th 2010
    Crumbs! Forgot to mention that there are targetted adenovriuses out there now that selectively infect the a specific organ... like the kidneys or pancreas. Which is pretty useful.
    • CommentTimeJul 29th 2010 edited
    Personally, I'm leery of touching any of this flavor of biotech until the intellectual property rights get thrashed out. You've still got farmers getting sued for infringement from patented seeds that were blown in from the neighbor's fields. I hate to think of the legal crap that will have to get thrashed out with intellectual property that is actively contagious. I'm not looking forward to losing the rights to my own genome because I caught a case of Monsanto.

    (ETA: I'm a former instructor in biomedical ethics and do take this seriously) .
  2.  (8634.13)
    So you're saying I'm going to need some oncolytics to cure the cancer I get from my genetically engineered demonic hemipenises?
  3.  (8634.14)
    The first part is directed to Brazen.

    They recieve the right chemical dead. They fail to recieve treatment with a chemical dead.

    I believe we already have humans like this. Strangely, all of them tend to die when you give them the chemical "cyanide" and live unless deprived of the chemical "water." It seems like it would be too time intensive and useless to engineer people who were keyed to dying on condition of something else, unless you're making Replicants. But it's not really virology, so I'll move on.

    So, when it comes to Adenoviruses, I think you might have a misconception of how gene therapy is supposed to work. For gene therapeutics to persist, you have to achieve integration of the viral genome into the host. Otherwise, the viral genome degrades and you lose the correction and after enough transient treatments you're immune to all the adenovirus serotypes. Host integrases, or engineered integrases, can make adenoviruses a good vector for gene therapy, but unless you integrate, it's not a good therapy. But with integration, you get all the problems of retroviral gene therapy. So, no, that's not a safer alternative.

    Protein engineering is pretty fascinating, though! I'm especially excited about groups making proteins with atypical amino acids.

    Anyway, moving away from that response, a great paper turned up today about Ebola virus and Marburg virus sequences that have integrated into host genomes. This is really amazing, because they are RNA viruses and strictly speaking that should never happen. Even more interestingly, the proteins that are found in the host genomes are truncated versions that contain only the parts of the Ebola/Marburg proteins that SHUT DOWN IMMUNITY. And these sequences have apparently wandered around with their hosts for 48 million years. I'm puzzled and amazed.
    • CommentAuthorBrazen
    • CommentTimeJul 31st 2010 edited
    @ John Skylar:

    Fair enough on the suicide switch. Also, I'm aware that Adenoviruses are poor candidates for gene therapy. I was just saying they have a number of cool genetic engineering applications is all.

    I did misspeak about the organ specific Adenoviruses though. I meant to say that they are Adeno-associated Viruses (AAV). These are apparently the gene therapy golden standard now. The lab nextdoor to mine uses a specific AAV to selectively infect pancreatic islets for gene therapy applications. AAV's are highly efficient at infection, can infect dormant or dividing cells, and certain types of AAVs are tissue specific (pancreas and brain for instance). Not only this but they do not cause any pathogenic symptoms in mammals infected with the virus. MOST IMPORTANTLY they are able to stably integrate their genetic payloads in a SPECIFIC genetic site (AAVS1) with no known side effects and extremely low off site integration. How cool is that?
    • CommentAuthorZeebo
    • CommentTimeAug 2nd 2010
    RE Adenoviruses:
    I think adenoviruses could also be very useful in the future once we've done more systems biological mapping of human development. Then you could use adenoviruses to "kick start" a certain cellular program, much the same as iPS technology does now.

    Fun fact: stem cells are often very good at silencing retroviruses (IE stem cells can eliminate or strongly decrease the expression of retroviruses in their genome). This is one of the key reasons iPS cells work without a bunch of strange growth aberrations. The retrovirus is incorporated into an adult cell, it causes the cell to become a stem cell, and then the stem cell "program" silences the retrovirus while using its own machinery to maintain the stem cell state.

    AAVs are awesome, but I wouldn't call them the ubervirus. As far as I know, their genetic payload is relatively small, which limits their usefulness. Though they don't cause much active immune response, they do seem to elicit a strong neutralizing antibody response, which would probably decrease their whole-animal infection capacity significantly.

    As far as cre-lox, I wouldn't really call it bleeding edge any more. It's a fairly old technology in mice and human cells do fairly well using the mouse proteins it requires. (That portage was actually part of my thesis project). Even more interesting is the games people have started to play with cre-lox and flp-frt. Both do essentially the same thing, as described above, but they do it different ways. This lets you do things like build logic gates. Here's a simplified diagram (the area between two similar sites is cut out):

    If the cell is exposed to Cre first (it eliminates the region between lox sites), then Coolstuff1 and Coolstuff2 are eliminated and Coolstuff3 becomes permanent. If the cell receives Flp first, then some cells will lose Coolstuff3, some will lose Coolstuff2, and some will lose both. But, in cells that lose Coolstuff2, Coolstuff1 becomes permanent, whereas those that only lose Coolstuff3, Coolstuff1 and 2 can still be eliminated by Cre. I know it's a little confusing, but it lets you build some really gnarly If-Then statements and such.

    But, this is all kind of getting away from the exotic virology subject and delving more into genetic engineering. As far as viruses go, how about mimi/mamaviruses, the largest ever discovered. As far as I know, they have many similarities with bacteria as far as complexity of function and size are concerned. I'm not sure about the current evolutionary thinking though. I know they were once touted as the "missing link" between viruses and bacteria, but I'm not sure if that's still a possibility. I've always thought that viruses developed from bacteria rather than the other way around since viruses all need a host to replicate and it's far more likely they had a host during evolution than all of them discarding their self-sustaining traits.
      CommentAuthorJohn Skylar
    • CommentTimeAug 3rd 2010 edited
    I'm down with AAV, but like Zeebo said, the capacity is rather limited. You know what would be cool? If we could figure out why AAV's integration site is where it is, and force that into some larger vector. I'm sure there's an engineer working on that somewhere.

    At least it's not a paramyxovirus like Nipah. If it was, the genome size would always have to be divisible by six. Weird stuff.

    Viral origins, though, now that's exotic. I've heard the idea of mimiviruses being a primordial virus, but I'm not sure I buy into it. TWiV, which I linked to up top, has covered mimis, mamas, and pseudomimis in the past, and kind of flirted with the theory that a virus that huge could be a viral progenitor.

    Now, that's one theory. Other theories suggest that viruses arose sort-of on their own, or that they were an accident. That might be legit, too.

    I have a slightly different theory, though. It's not supported by data, it's not mainstream. Don't take it as expertise. It's just speculation.

    But what if viruses are an ancient means of cell-cell communication that went horribly wrong? What if they're responsible for a lot of the diversity that we see today, and maybe even still generate diversity, but we don't know about it because we've only paid attention to the viruses that make us sick?

    There might be millions of human viruses that don't cause any symptoms. There might be some that save your life. I just don't know.

    So maybe, just maybe, cells traded genetic information via viruses at some point in the past. Or maybe they still do. And perhaps a couple of defective viruses made this into a process that can make people sick.

    I'd like to know what other people think about that idea.
    • CommentTimeAug 3rd 2010
    @John Skylar
    I don't know much of anything about virology, or science in general for that matter, so I don't know if this will be at all helpful. But I just have to say, I think that idea is awesome.
    I was just mostly skimming this thread because I'm so busy this week, but that caught my eye. It sounds like someone needs to write some fiction with that idea in there at the very least.
    How could you test this theory of yours?
  4.  (8634.19)

    Thanks! I come up with a lot of scientific ideas I'd like to use in my fiction, but with biology it's typically pretty hard to work them in. "Viruses are an ancient means of cell-cell communication" needs a bigger idea before it can get worked into a whole plot. Though, if anybody has ideas, I'd love to co-write something involving my theory.

    The smoking gun would be to discover a virus that has some beneficial effect on its hosts, in terms of a genetic enhancement. Basically, if there's a virus that does naturally-occurring gene therapy, that's a strong argument for my theory. But it's hard with experiments on origins to show anything other than "this idea is possible." Nobody was there, so it's hard to say "this happened." The best you can do is either showing proof of concept or ruling out alternatives.

    There is some evidence that the existence of genome-altering viruses like HIV has a positive effect on a species' fitness, though. So in a way that supports my idea.

    I think it would take a lot of effort (might be possible, though) to rule out enough alternative options to say that any one theory of viral origins is "the" theory.
      CommentAuthorJohn Skylar
    • CommentTimeAug 17th 2010 edited
    I thought I'd share this blog post from Virology Blog. It's about a new book called INSIDE THE OUTBREAKS, which documents the activities of the Epidemic Intelligence Service of the US Centers for Disease Control. The cover is set up to be comic-book style, but I fear the inside is not so much. However, it does contain a bunch of exciting anecdotes and highlights from the EIS's's not really supposed to be a chronology, more of a collection of "war stories."

    Either way, the EIS is one of the most interesting things around. They're the guys who are on-site when there is a disease about and you don't know what it is. I know a few people who have gone through the training program, and they've all come out with some solid, real-world experience. Students with an interest in virology might want to try this one out.

    Anyhow, enjoy. I'll probably pick up a copy of this myself eventually.