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WWW: Astrovirology - Shared screen with speaker view
Graham Lau
01:56:36
Hi all!
Esra
01:58:37
Hi everyone! Thanks for this great chance...
Ismael
01:59:31
Hi everyone!
kstedman
01:59:33
Welcome! Feel free to tweet with #Astrovirology.
Mario_Rivas
02:09:08
Hello everyone!
Cindy
02:11:13
Hi!
Nadim Ajami
02:13:47
Can we share the workshop link via twitter?
Graham Lau
02:14:03
Ha. Too late :)
pboston
02:14:17
Thanks Graham!
Nadim Ajami
02:14:24
thanks, Ken!
trubl1
02:14:30
#Astrovirology
Graham Lau
02:54:47
Yup
sstrathdee
02:54:49
Was wondering what people think of the utility of Neveu's Ladder of Life criteria ?
kstedman
02:58:34
Great question, I would ask Steve Benner directly.
Graham Lau
03:02:54
sstrathdee: I like that Marc and co-authors pointed out our understanding that measuring Darwinian natural selection would be impractical for measurement through a spacecraft mission, but I’m not sure if I’m on-board with Steve’s position that having apparently evolvable molecules would allow us to detect evolution without measuring it.
pboston
03:06:48
Graham, I agree. I’m struggling with this idea also.
cconley
03:07:22
A couple of people have their microphones un-muted, and are talking — could people maybe please check their mute buttons? Thanks!
Marco Presentation
03:09:33
i've muted all participants-- will turn on the ability to unmute during q+a.
kstedman
03:09:53
Thanks Marco
Graham Lau
03:10:35
Poor bird
cconley
03:12:02
Are there any viruses that are not parasites?
trubl1
03:12:09
anthropogenic virus evolution...
kstedman
03:13:33
Depends on how you define parasites. All viruses require cells as an environment to replicate.
trubl1
03:14:07
Great Q. I think it depends on how we view parasitism. A virus can be in a host and not "harming it"...sometimes helping it...for periods of time
cconley
03:14:12
Those are the ones we’ve been studying, I know — but if all people studied were tapeworms, they’d never think of hydrothermal vent animals…
Mexico
03:14:13
Only 1% of all viruses are parasites and make sick their hosts. The most of them are commensals or symbionts
Mexico
03:14:55
You can read Marilyn Roosink articles about "viruses that are Good"
trubl1
03:15:07
but does pathogenicity = parasitism?
cconley
03:16:37
Rephrasing my question: are there any conditions under which people could imagine that viruses (perhaps not yet discovered) would replicate without requiring a prokaryotic or eukaryotic cell?
Siobain Duffy
03:17:08
Agree that the melts are going to bring these layers to the surface… but we can detect preserved DNA more easily than preserved intact viral capsids I assume (these ssDNA viruses aren’t as durable as the tobamoviruses). What are the chances that most permafrost viruses would still be infectious, compared to we could (as Arvind did) resurrect them through reverse genetics? Are we overplaying the risk in nature?
kstedman
03:18:20
In terms of virus detection (Astrovirology) maybe detecting capsid folds would be useful.
trubl1
03:20:08
Also, does the permafrost need to thaw for a virus to be active? In my talk I will highlight viruses active in permafrost (phage)
cconley
03:22:39
Antibodies detect folds without knowing what amino acids are making them…
Nadim Ajami
03:22:57
#FoldIt
timothyrogers
03:23:12
Shivam needs to mute his mic
timothyrogers
03:23:25
thier*
timothyrogers
03:23:35
yep
pboston
03:24:24
cconley, I can imagine such a circumstance but then the entity would be a free-living entity but of a very minute size. Would that make it a not-virus at that point?
cconley
03:25:59
That’s an aspect of the question I’m asking people — is it more important to the definition of a ‘virus’ that it have capsid proteins and function the way a virus does, etc., or that it has to replicate inside a membrane-bound cell with ribosomes & chromosomes, etc.?
Rijul Kochhar
03:26:48
Admin question: will these fantastic slides be shared with participants?
kstedman
03:28:22
I believe yes.
Ismael
03:32:37
Yes! Please.
Siobain Duffy
03:34:04
Great summary of a decade of work from diverse labs!!
cconley
03:34:12
Accidentally hit return before editing my question, so here’s a re-phrased version: One way to define organisms by how they replicate and perform other ‘life’ processes, yet another is what they’re made of and the things they use to build the structures that enable them to do what they do as organisms. The viruses studied so far are distinguished from cellular organisms in what types of proteins they use to build their ‘bodies’ — and also that they co-opt the same mechanisms that cellular organisms use to generate those proteins. Is it imaginable that an organism built of the kinds of proteins that we find in ‘viruses’ might have invented ways to replicate that don’t require them to co-opt a pro- or eukaryotic cell?
Diana Rivera
03:34:22
Are these talks being recorded?, maybe can be upload to youtube
pboston
03:34:36
We will ask all participants for their permission to post the slide decks. Of course, they have the option to decline, but most folks are agreeable.
pboston
03:34:56
Yes they are being recorded, but as NASA materials, we will post them to our own website not YouTube
Ariel Petchel
03:35:26
Can't hear the speaker's audio for some reason
Marco Boldt
03:36:32
Ariel- maybe try rejoining the zoom meeting
Arvind Varsani
03:46:29
@cconley - antibodies bind to liner or conformationl epitopes = protein sequences. Homologous proteins can be 30% similar at protein sequence level and yet have the same fold but the sequence is different and thus antibodies will not necessarily bind both.
pboston
03:47:26
So Britt, Resistance Is Futile???
Arvind Varsani
03:47:36
@cconley - mitoviruses are RNA fungal viruses that do not encode CPs and replicate in the mitochondria of fungi.
joman
03:50:41
I missed most of it :(((, but I learned a lot, thanks
sawsan wehbi
03:52:30
i have a question about the definition of a virus. if we were to investigate whether certain viruses ( maybe giant viruses) had an abiogenic origin where they evolved on early earth prior to the emergence of life mainly through chemically driven self assembly of prebiotic proteins that happened to encapture freely swimming nucleic acids ( and that process kept happening under the environmental conditions). would we at the point consider viruses as a mere combination of protein capsids and some nucleic acids ( minus the additional accessories)?
cconley
03:53:40
Sawsan — that’s exactly the idea my colleagues and I have been wondering about…
sawsan wehbi
03:55:57
ahh yes just readd parts of the chat i missed
Arvind Varsani
03:56:01
@britt - please speak to @Pacifica as her cryoconite work may help - or ping me and i will introduce you to pacifica and she can share some of our work on Antarctic cryoconites
sawsan wehbi
03:56:03
and thats exactly my point
sawsan wehbi
03:58:32
i direct way to test that is through an extensive geo biological study to dig up the weirdest/ oldest viruses possible and check if any predate the most ancient form of life we found
sawsan wehbi
03:58:39
A*
Alonso
03:59:38
@sawsan wehbi - "would we at the point consider viruses as a mere combination of protein capsids and some nucleic acids ( minus the additional accessories)?- I don't see why not, what would you propose as an alternative definition or concept?
brittkoskella
03:59:41
Thanks @arvind, I do not know her work so will definitely follow up with you. Also, yes @pboston, resistance is often futile, and yet it is often selected for - so the arms race is futile but unavoidable (evolution is not forward-looking after all!)
sawsan wehbi
04:02:51
@Alonso the alternative would be an entity that is purely dependent on cellular mechanisms to exist and evolve
Yashas
04:13:23
Hey @Arvind Varsani, @kstedman and everyone,My questions are1) what's the probability that viral genomes are integrated into the human genome ??2) Are there any scientific evidences and significant impact so far ??Cheers..
trubl1
04:13:28
This is one of my favorite papers that shows lineage-specific virus–host dynamics with CRISPR. https://www.nature.com/articles/s41564-018-0312-6?WT.feed_name=subjects_bacteriophages
Ariel
04:15:12
@Yashas I'm only an undergrad so I may be wrong but I believe there already are parts of viral genomes in our DNA. I think certain races are more likely to have the viral genomes but it's possible or probably everyone has some
evelien
04:16:59
@Yashas The human genome has incorporated endogenous retrovirus sequences https://genomebiology.biomedcentral.com/articles/10.1186/gb-2001-2-6-reviews1017
Alonso
04:17:18
@Yashas - Like Ariel said, the probability is 1 since it already happened. As for the impact, that would depend on the context, virus have been considered very important drives for evolution so there's that.
cconley
04:17:42
These discussions are highlighting a form of reductionism that’s certainly endemic in evolutionary biology as I’m familiar with it — there’s a bias to assume that evolution by descent and selection is the primary mode, despite the fact that viruses were present and affecting fitness for a very large fraction of the total period that life has existed on Earth. Is anyone working on the scope and implications of non-‘Darwinian’ contributions to evolution writ large? There’s a nice 2019 hypothesis paper by Moelling and Broecker in Frontiers in Microbiology that reviews some aspects of this question — but I’ve not heard much about the question, previously.
timothyrogers
04:17:49
@Yashas: There are, I believe, three events with placental mammals of viral integration. If it wasn’t for these, its likely live birth would not be seen in placental mammals
brittkoskella
04:19:18
Hi @cconley, I agree that HGT and viral-mediated traits are an important part of evolution, but I am always wary of using the term “non-‘Darwinian’” as this would still be evolution by natural selection, right?
brittkoskella
04:20:11
I agree that the descent part becomes wobbly, but most of the principles still apply, no?
Marco Boldt
04:20:38
Is Joshua Weitz online? Not seeing in the attendee list but might be under a different name
timothyrogers
04:20:43
@brittkoskella sexual selection is a type of evolution outside of natural selection, I believe…could be wrong though
Luis Zaman
04:20:57
Sex is part of Nature, no?
Luis Zaman
04:21:02
;)
Alonso
04:21:22
I'm very interested in the first part of this section, is CRISPR spacer paleontology the next step?
timothyrogers
04:21:39
Yes, but natural selection has a particular definition that sexual selection is outside of
brittkoskella
04:21:51
It is, yes. But my issue is with thinking about HGT as non-Darwinian. I know people do describe this as Lamarkian… but I can’t help but think Darwin would have been cool with incorporating HGT had he known about it : )
Siobain Duffy
04:21:53
sexual selection is part of natural selection, Darwin artificially separated the two. It’s all about whatever leaves the most descendents, and sometimes that’s being very sexy and not very good at other things.
timothyrogers
04:21:59
Again, I maybe mistaken though
cconley
04:22:47
It’s the ‘descent’ part of Darwin’s hypothesis I’m questioning, not the ‘natural selection’ part...
timothyrogers
04:22:48
Yeah your right. Sexual selection is under the umbrella of natural selection… I stand corrected
Siobain Duffy
04:22:57
*where descendants are not kids, but grandkids and beyond.
Luis Zaman
04:23:47
Also, HEY Ya’ll! Great to see some familiar names floating around :)
cconley
04:34:42
The current bias towards genetic hereditary descent may be a residual reaction to Lysenkoism — but traits transmitted by viral infections could (arguably) qualify as LaMarckian…
Madhan
04:35:23
mobile elements perhaphs add a lamarckian component to the whole idea
pboston
04:36:13
I agree that the “classical” boundaries between organisms and how descent occurs are increasing blurring, and while this is fabulous and interesting, it does present us with a much more complex picture to analyze. I think these are critical points for the article/white paper.
Luis Zaman
04:36:55
I agree!
Luis Zaman
04:38:12
@cconley and @Madhan, I don’t think I would call this Lamarckian but I’ll expand in a bit
Luis Zaman
04:38:45
CRISPR, though, is Lamarckian (as our current speaker would argue)
pboston
04:38:52
I think that the Lamarckian ideas had an element of teleology, in that an organism already living “needed” some capability and “strived” in some way to obtain it. Mobility elements have their own rationale.
Madhan
04:39:00
caveat though: phages are specific to the bacteria they infect - are there phages/viruses that have more than one target(s)?
Rachel Whitaker
04:40:19
viruses infect populations of bacteria. Many diverse target strains.
Siobain Duffy
04:40:26
some phages are specific to the F-pilus, so can infect virtually any bacteria with it
Siobain Duffy
04:41:08
It’s also clear that phage specificity is rapidly selected when you bring phage into the lab and grow it on a single strain, host ranges of phage in nature seem larger
Madhan
04:41:19
phage therapy which is making a comeback in recent years is successful mainly coz of specific phages for specific strains (say antibiotic resistant clostridium etc as an example)- isn’t that so?
Madhan
04:41:47
ok thanks for the input on selection of phage specificity
Siobain Duffy
04:42:22
phages are absolutely more narrow spectrum than chemical antibiotics.
Alonso
04:42:45
You don't require specificity for therapy in the same way you don't require for your antibiotics.
cconley
04:44:10
The other bias illustrated here is the almost-exclusive focus on nucleic acid as ‘the’ information-carrying molecule — despite the fact that structural information is carried in the 3D arrangement of organismal contents, that (except for viruses and prions) *is* transmitted in obligate fashion from parent to progeny, all the way back to the initial organism.
steffanie strathdee
04:45:30
Weighing in on the phage therapy issue raised above, some phage have a wider host tropism than others (e.g., those infecting staph), whereas others have very narrow host range (e.g., those infecting A.baumannii).
Alonso
04:45:31
@cconley - Could you elaborate?
cconley
04:46:40
You’ll never get a functional ribosome if you take the denatured amino acid and nucleic acid chains, and mix them in a test-tube…
Madhan
04:50:11
@cconley thats an interesting point you have raised - one of the biggest challenges is how prebiotic conditions with the catalog of molecules gave rise to a minimal PTC (peptidyl transferase center) (which is at the ‘heart ‘of the ribosome in the large subunit
Madhan
04:50:21
and is very ancient
cconley
04:55:24
Ribosomes are only one, rather closely-related-to-central-dogma, example. Where in the DNA is a golgi body encoded, or what amino acid sequence will tell you where to add the sugars and other cofactors that permits photosynthesis or exocytosis to work?
cconley
04:57:12
Conversely — what is it about viral genomes and capsids that allows them to be recreated from nucleic acid sequence plus cellular translation machinery?
trubl1
05:01:04
Lytic to temperate switching of viral communities by Knowles et al. (2016): https://www.nature.com/articles/nature17193. Response to Knowles et al. (2016), entitled "Lysis, lysogeny and virus–microbe ratios" : https://www.nature.com/articles/nature23295.pdf?draft=journal
Max Showalter
05:02:19
Do we have any good estimates of prevalence of chronic infection in the environment?
Arvind Varsani
05:32:00
In case anyone is interested in the dynamics of plant virus evolution and ecology please see - https://www.nature.com/articles/s41579-019-0232-3
Sheila Roitman
05:34:55
This was great! Thank you very much, see you tomorrow :)
ellistorrance
05:35:40
Thank you so much for making these talks to accessible and FREE! Wonderful workshop!
Dyanna Louyakis
05:37:21
This was great. Thank you to all the organizers! -Gogarten Lab
Madhan
05:37:26
is there a viral equivalent of LUCA?
Dyanna Louyakis
05:37:30
*And all the speakers!