Lab Tour with Dr. DeSalle

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En provenance du cours de American Museum of Natural History

Genetics and Society: A Course for Educators

76 notes

American Museum of Natural History

Genetics and Society: A Course for Educators

76 notes

How have advances in genetics affected society? What do we need to know to make ethical decisions about genetic technologies? This course includes the study of cloning, genetic enhancement, and ownership of genetic information. Course participants will acquire the tools to explore the ethics of modern genetics and learn how to integrate these issues into their classrooms.

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Genomics in Medicine

You will see how genetic information is being used to individualize medical treatments and take a video tour of the Sackler Institute for Comparative Genomics at the American Museum of Natural History. You will also apply the Science and Engineering practices from A Framework for K-12 Science Education and the Next Generation Science Education Standards in considering how to engage students in discussion about ethics.

Lab Tour with Dr. DeSalle7:18

Rencontrer les enseignants

Rob DeSalle, Ph.D.
Curator
Division of Invertebrate Zoology
David Randle, Ph.D.
Senior Manager of Professional Development
Education Department

[MUSIC].

Hi, I'm Rob DeSalle and

we're in the

Sackler Institute

for Comparative Genomics Labs here at the American Museum of Natural History.

What I want to do today is show you some

of the techniques and technology that are used in generating

genome sequences.

And the first step in generating any genome sequence is to obtain tissues.

And then, to isolate DNA from those tissues.

So, the first thing to do is to get a tissue sample.

And this is just a little bit of salt in, in distilled water.

And I'm just going to put it in my mouth and swish it around in my mouth.

>>

[SOUND]

>> And that's the end of the gross part.

>>

[SOUND]

>> Now what I have in this tube is just a bunch of cells from my mouth.

And this'll include.

Cells from me, but also cells from anything that I've eaten for

breakfast or anything that I've eaten for lunch, and also

any of the 500 or so species of, of bacteria that live in my mouth.

The next step is to simply lice the cells in the, in the mouthwash.

And we use a simple detergent called SDS to do that.

And you just simply add it, and you might see a little bit of clearing

of the solution, and that's because the at first, that's because the.

SDS is actually blowing the cells apart and

making this illusion a little bit more translucent and

now the final step is simply to add ethanol

and to precipitate the DNA away from the solution.

And you can start to see the DNA strands coming out of the cell there.

And you should start to see the DNA coming

out of solution by swirling it a little bit.

Now this DNA is, after it's purified, is then

carried through a series of steps that allow us to

determine the sequence of a's, g's, t's, and c's

on the strands of DNA that are in this tube.

The next step is to take the DNA

samples that you've made from a hundred different people.

And, each of the wells, on this plate, has a

DNA sample in it.

And again, we just need to deliver the sequencing chemistry to

each one of them, and, to do that we use a robot.

[SOUND]

Now we're moving to the next step of DNA

sequencing and we're doing what is called Sanger sequencing.

We've taken our plate of 100 samples and put it on this robot.

And the robot is simply delivering different

chemicals and different solutions to our DNA sample.

And chemical reactions are going on in the plates,

and these chemical reactions are labeling the

DNA with fluorescent molecules One for each of

the different bases, g, a, t, c and the chemical reactions are splitting the DNA

up, making ladders of DNA so that we can then read the g's, a's, t's,

and c's in the order that they appear on the DNA fragments that we're sequencing.

And then allows us to move to the

third step of the procedure, which is to place them on the sequencing machine.

So, this is the plate with the chemical and biochemical reactions

that we did to do the dna sequencing, with the four

different fluorescences for g, a, t, and c And the fragments have been

separated in the chemical reactions, and this machine, the ABI3730,

now will allow us to separate the fragments by size

and then, read the florescences from the fragments to give

us the sequence of g's, a's, t's and c's in

all of the wells that we see on this plate.

Now once the sequence run has been done on the 3730 with your Sanger

sequences, you need to process them and

to look for a singular nucleotide polymorphisms.

So, in my sequence, you can see in this region right

here a black peak, a green peak, and a blue peak.

That's my sequence.

And then in, in this individual, it's a black peak, green peak, blue peak.

But in this individual, it's a black peak, green peak, red

peak.

This particular, sequence right here, where it's a c in,

in my sequence, a c in this other reference sequence.

And a t in this bottom sequence.

What this means is that we have a polymorphism in this position right here.

That is what we call a single nucleotide polymorphism.

And these single nucleotide polymorphisms, or snips, are what

we use in the genetic technology and the genetic techniques

that we described in lecture.

These chromatographs are relatively hard to look at,

so what the computer also does, the programs

also do, is they transform this peak information

into actual DNA sequence information, into the g's

t's a's and c's, so that this region right here that my finger is pointing to,

is the same region we talked about when

we were looking at the pigs in the chromatagraph.

So my sequence has a c. The middle reference sequence

has a c and the bottom reference sequence

has a t indicating a single nucleotide polymorphism which

is the main thing that you use in

doing genomic analysis that we talked about in lecture.

So now were sitting next to a

next generation sequencing machine here, there 454

machine, and this machine can sequence DNA

fragments much more efficient than other methods.

and this machine, what it does is it uses small beads

where the DNA that you're trying to sequence are attached to.

And then those beads are placed onto this tiny plate.

Now if we could look at this plate under a microscope we would see that there are

hundreds of thousands of little depressions in the

plate and the beads fall into these little depressions.

On each of the beads, we'll do a sequencing reaction and

we do them in a highly parallel fashion, about 100,000 reactions at a time.

In this way, the process of DNA sequencing

has been sped up several orders of magnitude.

There are other next generation sequencing machines

that are even much more powerful than this.

That, use different technology.

but also generate thousands times more sequence than the previous

generation sequencers.

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