i i don't know i feel um bad calling it computational biology because i can't actually do any coding so that's good so it's hard for me to get over that and call it computation

so um in order for a retrovirus to get into the the genome it has to access the germline whether that's through infection of one of the spermatocytes an egg a sperm or a developing embryo at an early stage infection has to occur in some lineage that will then develop into the next generations super matasites or oocytes to pass on the the pro viral dna

and we're just looking at the the dna that exists in the genome now so there's after the initial endogenization event there's a number of selective forces that are shaping what we're seeing in the genome sequences that we have available

e of those are endogenous retroviruses but others are retro elements that were there before retroviruses came on the scene is that a fair statement

the vast majority of the endogenous retroviral sequence itself in the human genome is comprised of solitary long terminal repeats ltrs

retroviruses could be a billion years old we don't really know

endogenization is something that it's hard to see but right now it's happening in koalas

by doing appropriate phylogenetics you can distinguish amongst these ideas

this family when it integrates it makes a five nucleotide target site duplication

what we did was search through all of the genomes that were available at the time and there was about 50 of them so you're looking just at sequences where you have whole genomes no these were any genomes that were available so they were like the human was very very good at the time mouse was very good chimpanzee's very good baboon rhesus were okay but some of them were a little more than a lot of context there might be might have been a lot of sequence there but they were really short and very fragmented

so the first thing that we did really is looking at how conserved each one of the the pro protein coding sequences are and one would expect that the the highly important rt the capsid the other structural genes those things should be very conserved and that's what we found there's very little um well i shouldn't say very little because it's still quite divergent in the scale of like a human gene um but it's in terms of viral evolution very conserved in those genes

so then we went on from there and did some actual phylogenies to figure out what sequences were most related to others and we show that there are certainly species in which the uh the sequence of irv fcs are mostly most closely related such as humans and non-human primates or at least old world primates they show very similar viruses in their genome so they probably even though they're not you know vertically transmitted they probably pass the viruses back and forth between themselves

the next thing we wanted to do was to figure out uh more specifically how these uh viruses jumped species and the way that you do that analysis is to compare a known host phylogeny to the phylogeny that we've produced for this virus you can do the same thing for any any parasite so we compare the the two trees and you connect the dots between species right so you have i don't know a mouse or a rat you connect it from the host to the the viral sequence and you look to see where those lines that you're connecting overlap indicating that there was certainly a cross species jump that happened to put the irv fc in that particular species

There is evidence of cross-species transmission and endogenization of IRV FC, including the transmission of the virus between carnivores and other species, such as primates and rodents.

The initial endogenization events of IRV FC were estimated to have occurred around 35 million years ago in carnivores and 30 million years ago in new world primates. The oldest IRV FCs are found in carnivores, and the youngest endogenization event was also found in a carnivore, the dog.

The species that we now associate exclusively with Australia don't have these IRV FCs, which may suggest that geography played a role in the spread of the virus. However, it's also possible that the virus was able to spread across the globe through various means, including carnivores and other animals.

The continents have undergone significant changes over the past 35 million years, including the separation of North and South America, the connection of South America to Antarctica, and the formation of land bridges between Asia and North America.

There is evidence of recombination and mixing of IRV FC with other viruses, including HERV W and beta retroviruses. This has resulted in the exchange of envelope sequences and potentially broadened the tropism of IRV FC.

it then got back into a number of species including dogs and ferrets and seems to in both of those cases uh recombined um to gain a gag of the pre-existing type so for this paper we're calling the the chimeric virus irv fc1 and the prototypical irv fc irv fc2

recombination is occurring when you have co-infection of a cell with two different viruses right or yeah co-packaging yeah so packaging from a producer cell right so they're two pro viruses in a in a genome and they're both back yeah right so it's unclear whether this is going to be exogenous virus

he found individual instances where an envelope a nerve fc viral envelope gene was still completely intact from start codon to stop codon even when the pro virus surrounding it was clearly old and highly degraded and that would strongly suggest that that particular envelope gene has been preserved by selection for some wow

so we can in some cases express the protein and then ask whether or not it's still processed correctly and whether it's still functional and so some of that early data suggests that the protein probably can't still function as a viral envelope protein but can still interact with its receptor

it would be nice to be able to go back and do some wet lab experiments yes to figure out um some of the observations that we made indicate that for instance like the the p12 region may be a place where it interacts with host factors and that's why it's evolved so yeah

the dyson dispersed much more uh virus particles compared to the other two i mean the the paper towels were really insignificant very low plaques and dispersal of the phage but as you might expect this dyson uh throws around uh a lot of pfu

there's a place on the bottom where you initially put your hands in and they're dripping yeah and there's it's wet in the bottom so even the guy before you who used the the the hand dryer you go in and the hand dryer's contaminated okay yeah and it blows it all up into your face and all over the place and the the magnitude of the effect is is huge we're talking i mean not just a little difference a big difference between uh the dyson air blade and the and the regular hand dryer and the paper towel

there's papers on this going back at least till to 1987 there's a paper in 1987 on hot electric hand dryers compared with paper towels for spread of bacteria this is from the uk and they concluded that hot air hand dryers appear safe from a bacteriological viewpoint

the r naught as you know if is the number of other people that one sick person is likely to infect so if it's the number is greater than one then the virus will be transmitted and if uh or perpetuated and if the virus if the r naught is less than one then that won't happen and of course measles is uh very high 11 to 18

an npr report that is entitled accidental brilliance and science and it's kind of going over you know what i i happened upon in the irv fc story is that you don't necessarily have to have a hypothesis when you go into something if you follow it up and it doesn't make sense

the person is a woman a scientist at university of hawaii named hope geren and the book is called lab girl and it's um so i've started to read it i haven't i haven't got very far into it but it's very personal sort of biography of of her life and how she came to be a scientist

of the main themes of the book sounds great and i the link i put there actually instead of i don't know if you've been to powell's bookstore in portland oregon it's an awesome bookstore and their website they have an essay that she that she wrote and so instead of a link directly to the buddha book i put a link to her essay

my pick has to do with the weather which is a theme here on twitter and it's a harsh technical article and if you've ever got nws forecasts you know on your phone or on your computer you know they're all on capitals as if they're yelling at you

now we have two listener picks first is from basel who writes dear twiv ohms following up on the units used to report temperature during weather updates i'd like to participate with the pick of the week the gimli glider and the mars climate orbiter two major accidents due to measuring unit communication

and one from ken here's a very nice comic book about vaccination uh vaccines work here are the facts and you know you can't get enough of these it's a really good comic book yeah it is very good graphic novel type thing

um by the way it isn't that easy to find the twit email address at microbe.tv twiv all right look microbe i think you've made it easier since he wrote that email because i had that complaint at first also every uh well actually it's not on the the body of the page but it's in every post right