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hello my name is daniel phillips i'm a

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graduate student in the go garden lab

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part of the mcb department in the

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university of connecticut

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and this is my talk on split intense and

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so first of all i would like to stress

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the important role cyanobacteria play

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in the evolution of uh earth and the

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evolution of life on earth

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were we to go back billions of years ago

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earth

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had a very different atmosphere it had a

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reducing atmosphere there was very

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little o2 uh

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that changes when we start to see

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cyanobacteria

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uh around uh two and a half two billion

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years ago where we start to see

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a gradual and then rapid rise in the

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concentration

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of o2 in earth's atmosphere until the

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level uh

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that it's at today around 20 percent and

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then

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even today around 50 of the earth's

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atmospheric oxygen

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uh can be traced back to uh

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cyanobacteria uh in the ocean

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um you know making them the true lungs

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and so in trying to learn more about the

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evolution of cyanobacteria i'm

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interested

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in the distribution and function of

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intense

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within this phylum intenes are genetic

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elements

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that reside inside important

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housekeeping genes

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in the genome so we would see in the top

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of this figure here

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we would see in red the if this is the

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dna sequence the genomic dna

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we will see the in teen coding sequence

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sandwiched between the extine the extene

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would be

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the host protein

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or the dna which would code for the host

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protein

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uh the cnn terminal of that that would

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be

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an rna

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on our on rna molecule uh combining

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of the nxt the intent and the cex team

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and then that will be translated

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together so now we have this long

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polypeptide chain

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uh containing the extine the host

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protein and the intent

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the intent will uh splice itself out

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uh spontaneously out of this uh

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polypeptide chain

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and that will leave the mature host

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protein and the now

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excised in teen

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so they're distributed fairly widely

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among uh the three domains of life

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we see them uh pretty widespread and uh

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in in bacteria and archaea

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and eukaryota they are limited to fungi

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in protists

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limited to single celled

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uh organisms and pretty much entirely

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they do

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so chloroplasts but they are absent from

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the uh nuclear genome

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of uh of all multicellular uh domains of

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life

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so there are three main types of in

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teams first we have the full length

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enteine

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uh this will contain uh the in this will

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contain a homing endonuclease domain uh

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so if you can imagine this will be

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translated uh transcribed the in team

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will self-splice itself the nsr as csr

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and terminal splicing region c terminal

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splicing you can splice itself

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out and then it can go back into the

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genome and look for a

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non-in teen containing allele if it

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finds one it will cut that

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um dna strand and then the host cell

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will

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repair it using the dna can using the

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incontaining allele

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as a template and this allows the intent

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to maintain itself in a genome making it

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much more difficult

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to be lost

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uh the mini antene of course uh will

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have uh no will have lost its

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endonuclease uh containing domain

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uh if it ever had one uh and so once

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lost from the genome it's unable to

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reinsert itself

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uh back in and then the split in team on

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what i am mostly interested in

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uh will have the n terminal and the c

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terminal uh

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located in um different loci

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of the genome and this could be tens of

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thousands of base pairs apart

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uh so you can imagine how baroque this

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process is

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um where uh we have these basically

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non-functioning

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to the host cell uh pep uh uh

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genes that are gonna be transcribed

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separately uh translated separately

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and then we have these non-functioning

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peptide chains um that have to go

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through the cytoplasm until the intense

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can link up

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combine uh excise themselves

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um connect the two host x teams host

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proteins

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uh giving the native mature functional

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so i'd like to talk more about uh the

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the split in teen particularly the dna

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e uh split in teen in cyanobacteria

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and so on the left we see an image that

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demonstrates a little bit more in depth

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of how

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uh the n terminal and the c terminal of

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the

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so as i said before this is a little bit

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of a complex process

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process and so it makes one think what

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benefit this would have

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uh to an organism well that's some quite

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uh

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these in teens have a role or not there

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are some researchers

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who think they have a unknown

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basal regulatory role uh there are other

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researchers and

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our lab is of the opinion that these are

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molecular

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parasites uh and so they are acting as

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uh

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beneficial it would be

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for parasite to make itself impossible

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to be lost

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uh for example were this were a

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dna into a dnae in teen containing

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genome um were to lose its dna e antenes

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well now it would have a non-functional

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dna e subunit

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so as we see in the figure on the on the

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left when we have these

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if we lose the intent then we have these

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two uh

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you know useless polypeptide chains that

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aren't going to make a functional

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protein

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and so as i said before these intense

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are usually found in highly conserved

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housekeeping genes means that it would

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be

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hard for a cell to lose uh genes would

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be hard for a cell

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to have these mutate or to mutate or to

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have this section of dna of their

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of uh sections of these genes lost uh

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for whatever reason so

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dnae again a very important housekeeping

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protein is a subunit

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of dna polymerase it's pointed to in red

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this is of course involved in

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uh the construction of dna uh and

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so it cannot function uh without it it

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forms the active site we see in the red

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circle in the image on the right

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with the dna strand double helix we can

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see in the middle

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buff in blue and then the dna e subunit

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highlighted

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so if this dna e split intent

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was in fact a molecular parasite and

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does not play a

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functional role uh in terms of its host

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i would expect that to be reflected in

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its level of distribution

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and conservation uh within the

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cyanobacteria phylogeny

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so here we see my current working

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phylogeny of uh

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cyanobacteria uh created with a 482 core

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proteins found using a program using get

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homologs

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consisting of a 133 complete genomes

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complete high quality genomes off ncbi

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with all cyanobacterial families

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uh represented in this tree constructed

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using iq tree

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so this dna e in team is found in about

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80

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of cyanobacteria genomes and so i first

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wanted to pay special attention

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into this clade we have highlighted in

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this strawberry and cream color

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down at the bottom so this clade uh

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consists of members of prochlorococcus

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seneca caucus

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and synovium uh this is often um

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widely accepted to be early branching uh

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or early or an early branch enclaves off

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the cyanobacteria phylogeny

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they are related to each other and most

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they are all cosmopolitan marine

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cyanobacteria and then

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in most literature it is referenced that

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prochlorococcus

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uh does not have any dna in teen

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uh in in any of its representative

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genomes

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uh there are several uh senegal caucus

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uh

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and then so i thought that would be a

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good first subject to uh to delve more

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into with the distribution of uh

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dna in teens within these genomes

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so i'd first like to show you this

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nucleotide based phylogeny

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based off dna e in

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black we see genomes that contain

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the dna e split in ten in red we see

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genomes that do not contain the intense

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and we do sort of get these interesting

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clusters uh

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as we'd expect we see uh most of the

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chlor clock is clustered together that

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do not have the in teen

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uh we see the senegal caucus and

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synovium clustering together

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that do not have the in team but we have

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a a few interesting outliers the most

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notably center caucus wh-8101

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uh that does not that does have the

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intent but it's

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matches very closely uh but it is in the

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middle of a of a non-incontaining group

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uh and the same with cengage caucus

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rs9907

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at the bottom so some interesting

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and then if we look at the amino

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acid-based phylogeny of dna so this is

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the

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in red and we see a nicer level of

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clustering although it is very

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interesting how interspersed it gets

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early on uh where we'll still see

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uh some synecococcus and prochlor caucus

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uh uh a matching uh very

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very tightly together that do not have

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the in teen uh but still

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interesting 9907 matches very closely uh

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with non-antenna containing uh proteins

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but it still has

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uh uh that in ten again top and black

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but a little bit more tightly clustered

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together than

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phylogeny

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so i would like to uh in the future and

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i am currently working on improving

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uh the cyanobacteria phytogeny i'd like

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to tighten out the nut

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tighten down the number of uh homologs

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and basing that phylogeny on

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uh removing uh genes that are prone to

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horizontal gene transfer hgt in order to

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uh

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get a tighter resolution and get higher

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bootstrap values

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uh for each of my branches i would like

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to continue search for lineages where in

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teams are lost and gained

288
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uh or if they could possibly be gained

289
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through uh hgt

290
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i would like to look for further

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lineages um

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similar to the ones we just highlighted

293
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uh where in teens are

294
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either uh we're we're in things that are

295
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either present

296
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where we have a mixture of uh in team

297
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containing and non-incontaining

298
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of related genomes and i would like to

299
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compare the phylogeny of

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dna extines to the dna in teams uh

301
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in in the consensus for dianobacteria

302
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phylogeny uh to see if we see uh

303
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a conservation of in teen sequences uh

304
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or not

305
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so thank you very much uh for listening

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i would additionally like to thank and

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acknowledge all my committee

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members all the members of the go garden

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lab and especially