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[Music]

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[Applause]

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hello my name is Anton Mohammed I'm from

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Oakland University in Michigan and I'm a

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master student and I'm working with dr.

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favia but the suit see on domain

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signatures of genome complexity and

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extremophiles so what are extremophiles

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extremophiles are those interesting and

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unique organisms that live in extreme

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environments and they live in hot and

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cold niches and they also live in acid

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solutions alkaline solutions salty

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environments and they include members of

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all they glued members of all domain all

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domains of life are kiai eukaryotes and

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bacteria and archaea is the major group

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that survive in extreme environments and

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although members of this group are less

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versatile than bacteria and eukaryotes

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they're quite skilled at adapting to

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extreme conditions and extremophiles

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exist in all of the archaeal phyla and

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in our data we only have the

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crenarchaeota the URI archaea and the

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thumb mark iota and these are some

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examples of the extremophiles we have

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the hyperthermophiles in red and then

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the thermo files in green and then we

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have the psycho files in blue and then

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piezo files also called viral files in

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black and as you may know that the

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extreme environments are unstable

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environments so that they're likely to

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lead to high variability at the genomic

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level so on any sort of adaptation or

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surviving strategy is likely to have

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genomic signatures and here we're

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looking at these genomic signatures and

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the organisms and part of these genomic

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signatures which are part of the bigger

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group are LCR's the low-complexity

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regions and LCR's have been known to be

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evolutionarily significant because they

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provide genomes and individual genes

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with adjustable turning knobs for

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efficient adaptation so previous

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research has been done by hearting

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Golding and showed that LCR's are not

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conserved regions and that they

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accumulate mutations so here

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number zero we have the LCR's and these

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are the number of mutations they

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accumulate the proportion of snips the

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single nucleotide polymorphisms and the

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different colors here and the graph

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shows the different conditions they

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tested the LCR Xen and genomic

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variability has been tested in

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eukaryotes and viruses and in the

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viruses it was suggested that LCR's are

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an important source of genomic

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variability for the lengthy virus and

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that they're an important source for

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antigenic variability in the HIV

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populations so what are the low

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complexity regions the LCR's are

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repetitive sequences that contain few

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nucleotides or amino acid types and some

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regions contain few different

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nucleotides or amino acids while others

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only contain one and LCR's have various

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configurations ranging from periodic to

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a periodic motives and they have

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different nomenclatures ranging from low

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complexity sequences tandem repeats

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simple sequence repeats amino acid

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repeats but they all basically share the

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same low complex or low diverse sequence

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so LCR's are ubiquitous in eukaryotes

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about still the function and

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evolutionary forces that act on these

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regions are unknown and are poorly

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understood and here on the right we have

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examples of LCR's and different

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eukaryotic species so for example in the

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homo sapiens the humans we have about

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18% and then in the Plasmodium

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falciparum the malaria agent we have

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about 50% so the proportion of genes

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that contain LCR's is highly variable

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across the different eukaryotic species

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so all the information that we have so

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far on LCR's is a result of research on

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eukaryotes and here you can see the

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eukaryotic tree and the parts that are

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marked with a star are the ones that

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have been studied for LCR's

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and even those form the minority in

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comparison to the other eukaryotic

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species and no one actually has looked

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at prokaryotes for LCR's and although

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the prokaryotes formed the majority of

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the fully sequenced genomes thus they

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provide us with a huge set of data

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to analyze and work with and prokaryotes

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also also form two out of the three

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three main domains of life and all the

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analysis that has been done so far was

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done on model eukaryotic species so in

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order to study a full domain we need to

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develop new testing methods and analysis

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in order to automate the process so we

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decided to focus on archaea in our

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research because archaea has about 200

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species while bacteria have 13,000

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species so when we study our km we will

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be able to develop these new testing

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methods and to automate the process in

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our future research so what we actually

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did we got the fully sequenced genomes

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of archaea from ncbi and it was about

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221 species and then we did basic

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statistics to see the LCR patterns and

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trends in the archaea and at that point

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we don't really know if LCR's even

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exists in archaea so now i'm going to be

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talking about the LCR patterns that we

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explored in archaea and the LCR

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frequency LCR length versus protein

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length the LCR frequency versus the GC

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content the amino acid composition and

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usage and the LCR location the proteins

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so to calculate the LCR frequency we

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just followed a simple equation a number

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of proteins with LCR's over the total

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number of proteins times 100 around this

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tree you can see the red are the

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temperature extremophiles and then the

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yellow are the temperature meter files

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and the orange bars are the LCR

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frequency so on average the healthy our

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frequency arranged between three and

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seven percent and when we looked

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specifically at certain groups for

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example the halobacteria the salt loving

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extremophiles we saw that they have the

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highest LCR frequency which was about

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14% and halobacteria else our salt

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loving extremophiles they live in salt

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extreme environments and the red water

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here shows the halobacteria and then

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when we looked at other groups such as

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the clan RKO de which are temperature

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extremophiles and to be exact

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hyperthermophiles and they all

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so have a high LCR frequency but it's

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lower than the halobacteria and there's

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range between 10 and 12 percent so we

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decide we are compared the LCR frequency

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between these groups to see if there is

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any significant difference and as you

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can see we saw that the halobacteria

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have a higher LCR frequency than the

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crenarchaeota and they have a higher LCR

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frequency than the URI RK Ora and the

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URI are Keota in this case includes both

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extremophiles and Misa files so the main

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question here is is this high LCR

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frequency a characteristic of salt

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extremophiles or temperature

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extremophiles or extremophiles in

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general so to answer this question we

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did a further analysis comparing the LCR

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frequency between halobacteria and

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archaea and as you can see we saw that

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halobacteria has a higher LCR frequency

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than archaea in general and even when we

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compared the needs of files and

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extremophiles in the URI our Keota we

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see that the Mesa files have a higher

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LCR frequency than the extremophiles so

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this suggests that the high LCR

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frequency is a characteristic and D

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salt-loving extremophiles and there are

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actually a few possible explanations to

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this trend that we just saw and one of

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them is that LCR's are an emergent

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property of proteins meaning longer

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proteins will have longer LCR's

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and when we compared them we didn't see

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this correlation between them so if the

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LCR s are not an emergent property of

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proteins the LCR's might be driven by

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the GC content of the genome whether

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it's high or low GC content so previous

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research done by TN showed that the LCR

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frequency is driven by the 80 content of

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the genome in eukaryotes and in our data

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as you can see the hello bacteria and

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the yellow temperature extremophiles in

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blue temperature mesa files in red they

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all follow the same trend and when we

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did a comparison for significant

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differences we saw that the halobacteria

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has a higher GC content than all of the

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other groups that Grande URI and then

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all of the archaea in general and even

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the mesa files had a higher GC content

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than the extremophiles so that means yes

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the patterns of GC and LC are

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frequencies are the same

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and that they'll see our frequency is

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driven by the GC content of the genome

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then we looked at the specific amino

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acid usage between extremophiles and

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mizore files and we saw that they both

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use our GC rich amino acids but

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extremophiles also use a T rich amino

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acids which is expected as we saw they

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have a lower GC content every one we

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looked specifically at the hello

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bacteria we saw that they use similar

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amino acids to the miso files and there

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are GC rich amino acids and then we

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compared in the amino acids usage

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between the halobacteria and the urea

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Ark iota and we found that they have

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different amino acids in their

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composition and actually previous

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research in eukaryotes showed that the

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amino acid composition is species

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specific and it's different between the

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groups and as you can see these are

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three different research done on

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vertebrates drosophila and Plasmodium

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falciparum and if you look closely all

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of them use different amino acid

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composition in their LCR's

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and the reason actually behind this

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difference is still unknown

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so up to this point just to summarize we

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saw that the LCR's are driven by the GC

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content of the genome and the amino acid

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composition confirmed this as we saw

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that they use GC rich amino acids so

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this suggests the neutrality of these

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regions and that there are functionless

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regions so we decided to look at the LCR

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locations in the proteins because this

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might be a sign of potential selection

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so we followed a previously developed

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methods where we divided the protein

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into three segments the n-terminal the

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middle and then the c-terminal and then

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we calculated the difference between the

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observed distribution of the middle

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point of the LCR's and the expected

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distribution to locate where HL c our

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sequence would fall and our null

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hypothesis suggests that the LCR's are

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randomly distributed and our alternative

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hypothesis suggests that they are not

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randomly distributed and that means that

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there is a potential biological function

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for them so the results of our

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chi-square shows that in extremophiles

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we have 82 percent and in the mesial

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files we have 75% significant

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which means that the LCR's do prefer

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certain locations and that they're not

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randomly distributed and when we look at

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the extremophiles in the Misa files we

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see that they both follow the same trend

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where the LCR's are located at the

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terminal of the proteins and when we

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look at the halobacteria specifically we

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also see that they follow the same trend

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and the LCR's are at the terminal of the

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proteins and this actually follows a

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previous trend that was found in

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research in eukaryotes and this one

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specifically in the drosophila where it

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shows that the LCR's prefer to be at the

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extremities of the protein rather than

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in the middle and this suggests that

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there might be a potential function for

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these regions and that they're not

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functionalist regions so do LCR's

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actually help extremophiles to survive

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well maybe but we do know the LCR's are

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a common feature in archaea and that

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they exist in salt-loving extremophiles

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and a higher frequency than the other

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extremophiles we also saw that the LCR's

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are are driven by the GC content of the

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genome and this was confirmed with the

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amino acid usage as we saw that they use

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gc-rich

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amino acids and we also saw that the

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amino acid usage is species specific and

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different between the groups so all of

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that with the non-random distribution of

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the LCR's we can say that the LCR's

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maybe creating genomic variability for

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the halobacteria the salt-loving

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extremophiles specifically so they can

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survive and there are extreme

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environment but we did not really see

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this trend in the temperature

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extremophiles so this suggests that they

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may be using different adaptive

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strategies to survive in their extreme

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environments so I'd like to thank

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Oakland University central for

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biomedical research NASA and IH for

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funding this program and I would like to

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thank dr. Sheila Sheila Randall Westrick

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and all of my lab members for helping me

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in this research thank you for attention

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[Applause]

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[Music]

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[Applause]

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all right Thank You Anton so we're

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running a little bit short on time but

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we have time I'm sorry we have time for

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thanks for the good talk

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my name is Tian from the University of I

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was wondering if you looked at the

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distribution of other hit archaea

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halophiles we looked specifically at the

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fully sequenced genomes so these were

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the only ones that were available on

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NCBI to look for their distribution

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they're like two or three other hello

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Felix lineages of like really weird GC

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content so well there was actually a

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paper back in 2008 that explained the

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high GC content and the hallow files and

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that convergent evolution have to do

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with this weird GC content in the hallow