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[Music]

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[Applause]

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all right still worth in progress so now

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we're at perform DNA repair alright so

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here I'm showing you our most everybody

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hear me in the back yes okay so here I

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am showing you our most current

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understanding of the phylogenetic tree

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of life with bacteria Eukarya archaea

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and I hope I'm not insulting anyone's

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intelligence here by just sort of

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reminding you how to read a phylogenetic

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tree because I will show you another one

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in the course of this talk and so you

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know the nodes and the phylogenetic tree

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places where it branches connect you

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know we consider those and burn or

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hypothesize ancestors and we can say

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that a group is monophyletic if it

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shares a unique common ancestor unto

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itself

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exclusive not including other groups so

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here are bacteria forming a monophyletic

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group now the inferred ancestor that I

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want to talk to you about today and some

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people have already brought this up in

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their talks I want to talk to you about

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the Luca the last Universal common

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ancestor of all living on earth and

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lived on their Creed's for billion years

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ago and this food probably doesn't need

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it

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put that into a pictographic perspective

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if we read this picture from from left

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to right we see early Earth on the Left

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and modern times including astronomers

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people like some of you in this room on

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the on the right then of course I'm

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okay yes and of course I'm talking about

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a time period writing here now I

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personally believe you know this is the

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the topic of this particular symposium

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is you know the Dark Ages and I have I

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believe that the look at has great

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capacity to teach us about modern

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biodiversity and also some capacity to

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help us look back further in time

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probably not something I need to

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convince folks up in this room and so

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one way we can understand what we can

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understand will Luca is by studying its

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genome its genome content and that helps

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us to understand what its metabolic

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capabilities were what its structures

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we're live in there been many studies on

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the Luca Gina and I'm showing you some

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of those here and the team's inferred to

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be present in the Luca based on these

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studies have been aggregated into a

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database called leukopenia yes so one of

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the things that fascinates me is trying

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to understand how did the Luca conduct

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its DNA processes have a palooka

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interact with its own DNA tina and so

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these studies of the leuco we know quite

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a bit about its ability to do DNA

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transcription or at least a little bit

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about ability to do DNA transcription

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depending on who you ask if it's ability

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to do DNA replication then let's

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remember that DNA replication is not

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just the ability of an organism to make

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more DNA DNA replication requires quite

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a lot of fidelity in terms of making

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that copy and so there's a lot of

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excision and repair that goes on during

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that process so it's no surprise that

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you know at least some of the genes that

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we have heard to be present in the Luca

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genome were involved in DNA replication

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and specifically in excision and

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repaired during DNA during DNA

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replication and so you know I became

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very interested more broadly in DNA

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repair enzymes that might have been

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present in the luca and so using

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Wikipedia and studies in leukopenia that

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predicted or rather you think leukopenia

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and looking at genes that were predicted

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to be present by at least four studies

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within leukopenia and considering the

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function of these gene families

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predicted to be present in my four

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studies using a gene ontology resource I

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asked them you know how many of these

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these genes you know we're involved in

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in DNA repair and out of 981 genes

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predicted presence in the Luca by at

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least four studies we

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at 14 of those gene families were

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probably involved in DNA repair and so

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what were they do it well you know some

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again were involved in DNA replication

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but some are probably acting outside of

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that DNA replication system some

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operating in meiosis and doing various

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excision repair so we decided to look in

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depth at a protein family called MGMT

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that's ubiquitous across the Tree of

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Life and therefore we assumed probably

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present in the Luca so here I'm showing

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you a representative in GMT protein now

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in e.coli MGMT has three parallels and

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they are og ta da and ato

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the og T and a da paralogs

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are pretty similar to one another they

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have an in terminal domain that does D

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alkylation of DNA phosphate so

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essentially removing methyl groups from

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DNA phosphates a form of DNA damage

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repairing that and a c-terminal domain

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so these are by functional a c-terminal

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domain that D methylates or de-escalates

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oh six wonnie or of work finding OG

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ta-daa act as monomers that is they

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don't recruit other proteins to be part

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of a complex to do these DNA repairs

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they act on their bow and

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they're sudo enzymes why I like sudo

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enzymes well after they do their job

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they D methylate or de-escalate

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something they're defunct and now they

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differ in terms of OTT is Institute

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constituents if we produce so it's

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always on where a DA is auto induced and

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in fact it becomes its own transcription

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factor now ATM is a little bit different

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it lacks this in terminal domain

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function and it has the c-terminal

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domain function it is able to bind DNA

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but it doesn't actually do demethylation

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or duty appellation instead it recruits

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other DNA repair enzymes that are not

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part of this protein family so if I'm

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related to this protein family to

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actually do the DNA repair and this new

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believe is at root in time meaning it

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can be reused and in terms of its

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production we don't know if it's always

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on or if it's an induced so why do we

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care so much about the alkylation or

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demethylation the evolution of DNA and

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one might early

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healthcare so

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thinking in terms of MGMT so remembering

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that it is going to one of its functions

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is to deep methylated des played a

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thymine or a guanine

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so these spaces become methylated or a

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belated and in fact that causes oh they

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were supposed to be a little animation

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there I apologize for its absence but in

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fact what that causes is mismatched

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pairing so T normally binds with a

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that's not news to anybody here but in

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fact when this is methylated it bonds

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with G similarly when G is methylated it

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bonds with T and these point mutations

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in DNA caused by this methylation in RF

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elation can lead to this can be computed

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through DNA replication or through

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transcription so what are the sources of

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the methyl group the methyl groups that

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cause damage to DNA well they can be

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endogenous or exogenous most most often

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in modern life their exogenous sources

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coming from the environment

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endogenous sources can include this demo

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online and so those of you that are

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familiar with this molecule know that we

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really need it it's a really important

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molecule and it does a lot of good work

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in the body however it turns out that

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this can in fact randomly methylate

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parts of the DNA transfer a methyl group

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to parts of the DNA but we don't want it

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to do that too

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and so actually causing damage and so

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one possibility is that as there was

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more methane present in the early

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atmosphere so here showing you early

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atmosphere of Earth more methane present

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and possibly membranes of early

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organisms were a bit leaky we know that

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this is a very old molecule predating

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the Luca so it's possible that there was

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more of this floating around at living

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systems anyway methylating DNA of course

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it's also possible that there were other

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sources for more fur methylation as well

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and again you know these are repair

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enzymes that we need in our systems and

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of course we're not exposed to this

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level of methane all right

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so anyway to convince ourselves that

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this in GMT protein family was president

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in the last Universal common ancestor we

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reconstructed a phylogeny using sampling

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from across the Tree of Life and rather

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from across the prokaryotic tree of life

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eukaryotes probably would not have

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contributed very much to our

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understanding here I'm sorry to say

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because I studied eukaryote before this

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and so um nevertheless

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uh we using all three of the the

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parralox

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OG t AP a and a TL and so what we

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determined is that in fact this protein

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family of G of T was present in the last

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Universal common ancestor this node here

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representing the Luca and following the

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it diversified into an RKO and bacterial

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lineage following the species Tree of

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Life are consistent with the species

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Tree of Life and it turns out that the

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og t-type enzyme was probably ancestral

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here so remember that's the one that's

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constitutively produced and by

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functional so then we have the origin of

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ABA so again that one zips operate since

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its own transcription factor arrives

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later within the bacterial lineage and a

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TL which again is recruiting other

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proteins from other prepare protein or

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rather of DNA to prepare families arise

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here later

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I should point out that this is

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primarily this ATL is primarily found in

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bacteria so probably arising due to our

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horizontal gene transfer from archaea so

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what do these things look like well so

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these images that I'm showing you here

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and I'll start these movies up here in

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just a second

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these are the MGMT paralogs

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based on crystalline structure as shown

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here from a cola and you can see I'm

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showing you here in light colors these

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are the in terminal domains that are

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doing the demethylation

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of data the phosphate in DNA and these

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darker colors here these are the

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c-terminal domains that our response

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will afford d methylating or deflating

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[Music]

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started for you so you can see the

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structure and to point out here in this

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ATL at the end of our set we see only

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this dark colored structure this is the

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homologous would be the c-terminal

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domain over here so only you know that

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function that the bonds DNA and recruits

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other enzymes to to make repairs the

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Humvee

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Wow

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there we go all right so how does the

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luca compare so we did some sequence

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reconstruction here ancestral sequence

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reconstruction as well as 3d modeling

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and so here's what we get and what you

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can see is that there is the darker

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color the darker orange here represents

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homologous with the c-terminal domain

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that is presumably performing our care

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by removing it ethyl group or a methyl

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group from wanting and fighting and then

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we have kind of a simple interval in

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terminal domain here so it's not quite

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as complexes what's going over on over

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here at OG tier 88 is lacking these beta

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sheets but still possibly some

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functionality here in the the in

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terminal domain alright so where are we

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well we came into the study knowing that

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Luca possessed enzymes acted on DNA so

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it's interacting with its own DNA genome

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and we know that these enzymes included

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enzymes for DNA repair especially within

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replication so we found was that there

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are potentially more DNA enzymes present

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in the Luca that we realized and not all

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of those are acting within the DNA

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repair system most likely such as MGMT

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in G and T in the Luca appears to have

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functions similar to og ta da so you

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know having both an n-terminal and a

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c-terminal domain possibly again dual

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functional like modern MGMT and the MGMT

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protein we saw later or present in the

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luca later diversified in both archaea

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and bacteria to produce some additional

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functionality

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so I would go on to speculate that these

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relics at least relatively simple DNA

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repair was probably possible and pre

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with the organisms so something that

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maybe so if you who are studying such

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organisms should be on the lookout for

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and that's all I have to say about this

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so we have time for one short question

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very illuminating have I was interested

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in the final hypotheses and one of the

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things in the null hypotheses in your

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final statement would be that in order

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to get Luca or a tall order to get the

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last common Universal ancestor or the

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unity of biochemistry he might have had

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a polymerases that made a lot of

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mistakes very similar to what you

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actually have in let's say viral DNA

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because that that would allow you more

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options to arrive finally at the final

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unity of biochemistry so it's just a