5 ms·
On the 3.2kbytes in Influenza A
- ars 17y agoSince this virus mutates so often, shouldn't they sequence a few hundred versions of it? And clearly I need to install a firewall to close some of those open ports.
- robinhouston 17y agoAt the institute where I work, we're sequencing H1N1 isolates from (IIRC) fifty UK patients. There are also emergency plans to start sequencing flu samples on a massive scale if it turns into a major epidemic. I would be astonished if large sequencing centres in other countries were not doing similar things. In other words: yes you're right, and it's already being done.
- jballanc 17y agohttp://www.ncbi.nlm.nih.gov/genomes/FLU/FLU.html http://www.ncbi.nlm.nih.gov/genomes/FLU/FLU.html There are literally thousands of strains that have been sequenced.
- silentOpen 17y agoSo, those of us with the mutation that causes lungs to ignore the H5 port would have a better chance of surviving an Avian flu infection, whereas as those of us that open port H5 on the lungs have no chance to survive make your time / all your base pairs are belong to H5N1.
- jbyers 17y agoThat's the most interesting not-really-about-computers article I've read on HN in the last two years.
- jhickner 17y agoIf you thought of organisms as computers with IP addresses, each functional group of cells in the organism would be listening to the environment through its own active port. So, as port 25 maps specifically to SMTP services on a computer, port H1 maps specifically to the windpipe region on a human. Interestingly, the same port H1 maps to the intestinal tract on a bird. Could anyone expand a bit on this subject? I found this completely fascinating, but I'm having trouble finding further reading on the underlying mechanics of "ports", as the article calls them.
- xel02 17y agoDifferent species have a different type from the protein family Hemagglutinin(HA)(they all look similar to each other) these proteins are similar to services offered on a port. Viruses like Influenza target HA but only of certain types. In the case of Influenza HA doesn't actually act as a port, its not designed to allow things to go into the cell, the virus however uses HA as a recognition marker for where it will attack. As a side note H1N1 means HA type 1, and Neuraminidase (NA) type 1. NA is a necessary protein for Influenza to leave the cell after replication.
- jballanc 17y agoNot entirely correct. Hemagglutinin is the protein on the virus coat. It binds to sialic acid on the surface of the cells. Sialic acids can have different glycosidic linkages. In humans, the predominant linkage type is alpha-1,6. In birds the predominant linkage is alpha-1,4. Pigs have a fairly even mix of both alpha-1,4 and alpha-1,6 which explains why they make good hosts for recombination.
- stuntgoat 17y agoI am under the impression that once a virus binds to a site, it attempts to push itself into the cell. Would it be possible or practical to make a filter media, or throat spray using sialic acid to catch H1N1 viruses and fool them into 'thinking' they have reached a target location? The goal being to selectively trap or destroy as the virus attempts to enter a fake target cell. Could something like this help prevent infection or help to quell severe infections? Would this be the computer analogous metaphor for a 'honey pot'.
- jballanc 17y agoWell, this doesn't really get at the heart of the article (or the matter), but to be rather pedantic, the virus genome encodes much more than just 3.2KB. Keep in mind that most of what the genome accomplishes is done with proteins. In that case, you have to take codons (sets of 3 bases) and convert to one of the 20 amino acids. This effectively takes 64 bits of information and reduces it to 20... EXCEPT that proteins are 3-dimensional entities. Their exact 3D configuration is encoded in the amino acid sequence encoded by the DNA. We still don't fully understand how this encoding works, but it is, in effect, the most awesome compression algorithm imaginable!
- sketerpot 17y agoThere's some redundancy in the mapping of codons to amino acids. Some of the most common point mutations will cause a codon to map to the same amino acid, or a functionally similar one. That's some information that would be lost if you represented DNA as an amino acid sequence.
- Robin_Message 17y ago(Disclaimer: I am not a biologist) DNA can only have four bases (ACGT), so each DNA base can only encode 2 bits of information. 20 amino acids could be encoded in 4 and a bit bits, not 20 bits (actually, you need a stop code, so 21 codes are needed). As it is, DNA uses 3 bases, 6 bits to encode each amino acid, so there is a little redundancy. See http://en.wikipedia.org/wiki/Genetic_code#RNA_codon_table http://en.wikipedia.org/wiki/Genetic_code#RNA_codon_table for the mapping. Proteins are 3D entities, but their shape is determined by the amino acids, which are determined by the DNA - so there is no awesome compression here. To put it another way, the words "booktitle:Dune" encode a novel, which is much more than 14 bytes, but I cannot encode any arbitrary stream of bytes in this way.
- jballanc 17y agoPlease, please, PLEASE Don't take the author's advice of trying to catch H1N1!!! I realize that comment was tongue-in-cheek, but still... There are a lot of people who do believe that they'll be better off catching it, and this is only likely to make things worse.
- imajes 17y agowell, since most of us get flu at least once every couple of years, it's kind of hard to avoid H1N1, the most popular form of influenza going around. Of course, if we were to catch the very specific form of H1N1 with the genetic coding that matches the swine flu epidemic, that'd be worse. It's worth remembering that in almost all cases, it's not the flu that kills you - it's the onset pneumonia, diarrhea and dehydration that takes you down. The best survivalist method is to remind yourself how to treat cold/flu symptoms, stock up on meds, and sweat it out. Helps if your health insurance is up to date too. :)
- jballanc 17y agoTrue, many will become infected naturally. The problem is that the antigenic shift of influenza is affected by transmission rate. That is, the more times a virus gets passed from person to person, the more it can mutate. The vaccines that are developed are based on a "normal" rate of antigenic shift. If large groups of people try to get infected, there is a risk that they will throw off this rate.
- kqr2 17y agoInteresting use of computer analogies: DNA : Program stored on disk RNA : Program loaded in RAM Amino Acid : Pixel in a frame buffer Protein : Image output from the RNA program Organism : Computer with an IP address Functional : An application which listens to a particular socket Group of Cells
- eru 17y agoYes interesting. Though Proteins are much more active than images. Perhaps an analogy with robots would be more apt.
- stuntgoat 17y agoJoel, can I help you build a stackoverflow for virologists, please? I want to call it antigenoverflow.
- flinc 17y agothe best resource on H1N1 (and virology in general) I've found to counter the news hysteria http://www.twiv.tv/ http://www.twiv.tv/