Is Is There a Ge Genetic Ba Basi sis t s to R Race? Exam - - PowerPoint PPT Presentation

Is Is There a Ge Genetic Ba Basi sis t s to R Race?

Exam amining human an var ariation an and an ancestry usi using ng mt mtDNA

CCSF Mission Campus February 10, 2018

No Note t to t teache achers: : the following slides are background info for teachers as given during a BABEC workshop. Student sections start on slide #9.

Objectives (for teac achers)

• 1. Beta-test of new template-go over lesson packet
• 2. New approach that addresses NGSS 3-Dimensions
• 3. New curricular concepts – why?

a. Popularity of personal genomics/commercial ancestry tests b. Uses scientific evidence to dispel societal misconceptions c. Uses the potentially charged topic of race to connect and engage students with modern society and current methods in genetics d. Idea: Genetic variation within any race is greater than between races

We want YOUR feedback!

Ho How we e de devel eloped ped thi his les esson

Power of Illusion PBS Documentary New updated version with approachable bioinformatics Genetic Origins curriculum from DNA Learning

BABEC’s ad adap aptation

• Prompts students to examine their assumptions about the link

between genetics and race

• Provides an opportunity for students to examine their own deep

ancestry by discovering their haplogroup

• Examines whether students’ own mtDNA is more/less similar to their

peers

• Analyzes similarity in DNA sequences using a bioinformatics platform

widely used by the scientific community (CLUSL Omega)

• Follows 3-Dimensions of NGSS

Thr Three ee Dimens ensions ns of NGSS

HS-LS3-2 Make and defend a claim based on evidence that heritable genetic variation may result from: (1) new genetic combinations through meiosis, (2) viable errors occurring during replication, and/or (3) mutations by environmental factors. SEP: Engaging in Argument from Evidence DCI: LS3.B Variation of Traits Cross-Cutting Concept: Cause and Effect Evidence Statement from HS-LS3-2

Le Let’s Star art! t!

Is Is There a Ge Genetic Ba Basi sis t s to R Race?

Exam amining human an var ariation an and an ancestry usi using ng mt mtDNA

Read th the challenge statement t below:

Th There i is a s a g genetic b basi sis t s to r race.

Do you agree or disagree and why?

Ø Write your answer on your lab notebook. Ø Discuss…

Video: Race, the Power of Illusion, Episode 1 Newsreel (0:45-4:37)

https://www.youtube.com/watch?v=Y8MS6zubIaQ&t=3s

Ø Watch Video Ø Fill out the worksheet, answering… Ø Who in this room are you most biologically similar to? Ø Who are you least biologically similar to? Ø Why do you think so? Discuss… Ø Next step, Lab activity!

Lab ab Activity Workflow

1) Extract your cheek cell DNA using Chelex 2) Amplify 440-nucleotide sequence from the D-loop

• f your mt genome

3) Submit PCR samples for sequencing at CSUEB 4) Analyze your mtDNA sequence using bioinformatics

PCR is DNA Replication in a a Test Tube!

Polymerase Chain Reaction Cellular DNA Replication What are we copying? How do we separate the DNA? What is doing the copying? How do we fish out the sequence? What does the work? DNA DNA Heat Enzymes Taq polymerase Human polymerase Primers Primers Thermal cycler Cell

Individual genes are present in amounts too low to be detected in vivo. PCR amplification allows for their detection and measurement from a very small sample It produces the double amount of product from the previous cycle, for an exponential increase Cycle 1 Cycle 2 Cycle 3 After 30 cycles, DNA is amplified

• ver a billion fold.

Wh Why y do we do PCR?

DNA DNA Sequencin cing – its eas asy!

San anger Sequencing Animations

From DNALC https://www.dnalc.org/resources/animations/sangerseq.html DNA Sequencing in 3D https://www.youtube.com/watch?v=ONGdehkB8jU The Di-deoxy Approach https://www.youtube.com/watch?v=bEFLBf5WEtc

Sequence Data a Results & Bioinformatics

• You will receive sequence files from CSUEB with the extension “.ab1”
• These files need special software to open

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!

Sequence chromatogram Sequence text file

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Once you get your text file, you can do all kinds of fun stuff!

SnapGene is open source

But first – the lab activity!

Boil

Lab Flowchart: Chelex DNA Isolation Procedure

Rinse mouth with saline Resuspend Mix Store on ice Fall 2011, page 1 Pour off liquid Centrifuge Centrifuge Transfer saline Transfer cells into Chelex Transfer DNA

• ut of Chelex

A microfuge tube has a total volume of 1.5 milliliters (ml), or 1500 microliters (µl).

1500µl 1000µl 500µl 100µl

Fill the tube with your saline rinse to a volume

• f 1000µl to 1500µl

(step 4)

1000µl 1500µl

Introduction to microfuge tubes

Fall 2011, page 2

Ideal Centrifuging Method

Orient the hinge of the tube to point outward and away from the middle of the centrifuge. This allows for solid material to settle to the bottom of the tube directly below the hinge. Hinge of tube points out All spins should be performed at 10,000 x g, which is about 10,000 rpm depending on the centrifuge If you have a less powerful centrifuge, spin longer than 5 minutes After centrifuging, look below the hinge for the solid material (pellet)

Fall 2011, page 3

After you centrifuge the saline rinse, your cheek cells will settle to the bottom of the tube. This is called a cell pellet. The cell pellet will be white. Observe your cell pellet. If you do not see one, add more saline rinse and repeat. The clear liquid above the cell pellet is called the supernatant. It does not contain any cells. When you place your tube in the centrifuge, have the hinge of the tube facing outward. Then you can find your cell pellet directly underneath the hinge.

Cell pellet side view Cell pellet back view

Supernatant Cell Pellet

The Cell Pellet

Fall 2011, page 4

The supernatant can be poured out of the tube by inverting it. The cell pellet will stick to the bottom

• f the tube while you pour.

(step 6) Observe cell pellet stuck to the bottom of the tube while you pour. If you do not see one, repeat with more saline rinse.

Decanting the Supernatant

Fall 2011, page 5

To resuspend means to dislodge the cell pellet and mix in into the liquid using your pipette. There will be about 100µl of supernatant remaining in the tube after you pour. Look at the 0.1 line on the bottom of the tube and add more saline if it is not at that level. (step 7) After resuspension, the solution will be cloudy. This is because you have concentrated your cells into a smaller volume than what you started with. 100µl

Resuspending the Cell Pellet

Fall 2011, page 6

Chelex is made of very small white beads. They are heavy and settle to the bottom on the tube. Chelex cant be pipetted with a P20 or P200 tip. It will shear the beads. Use a P1000. Chelex beads mixed with your cell suspension (step 9) Tiny Chelex beads

Chelex

Fall 2011, page 7

After heating and centrifuging, DNA is in the supernatant. Chelex beads & cell debris DNA is in the supernatant Remove DNA with a pipette (step 13) Keep the pipette tip near the surface of the liquid so as to not touch the Chelex beads. Keep pipette tip near the top

• f the liquid while aspirating

Removing the DNA

Fall 2011, page 8

PCR Reaction Set-up

ü 20 µl of Master Mix Contains buffer, dNTPs, MgCl2, AmpliTaq Gold ü 20 µl of Primer Mix Contains the forward and reverse primers, diluted to the proper concentration ü 10 µl of your own DNA

For every experiment, a positive and negative control should be done in order to produce credible data. ü Positive control: human DNA of known genotype

• Will produce a result that shows all possible positive results in an experiment
• Will show that the reagents are working as expected

ü Negative control: water in place of DNA

• This reaction lets us know if we have any contaminated reagents

Experimental controls

Start on page 4 of the new curricula, and we would love your feedback!

Knowledge an and bioinformatics section

ØBackground Lecture ØBioinformatics Activities üHaplogroups using Mitomap üSequence comparison using Clustal Omega ØElectrophoresis Results

Mitochondria, a, our “second” genome

Food + O2 = Energy + CO2 + H2O (glucose) (ATP)

Images: DNLC & Genebase

Powerhouse of the Cell

mt mtDNA Co Control R Region / / D D-Loop p / Hype ypervariabl ble Regi gion

A gene-free region of ≈1,000 nts like a promoter or origin of replication accumulates point mutations at 10x rate of nuclear DNA It is our fastest evolving DNA sequence!

Over evolutionary time, many more mutations have accumulated in the D-Loop than the coding region. Why?

Image: Genebase

mt mtDNA is Maternal ally In Inherited

Why is this significant for ancestral studies?

1) It is not subject to recombination: stays the same throughout generations 2) Changes only occur through mutation, which is passed on 3) Has a strict line of descent from mother to child

Image: Genebase

Uni Unique que Proper perties es of mt mtDNA

We have many more copies of mtDNA than other DNA Large amount of mtDNA & its small size = excellent candidate for anthropological studies of old or degraded samples Maternal inheritance gives us specific information about human migration & evolution Because they don't mix with genes from the father's line, mt genes can be used to trace a sort of lineage right the way back to when our first ancestors came out of Africa. The region we sequence has a high mutation rate. It is our fastest evolving DNA sequence!

De Deep Ance cestr try

Common Maternal Ancestors people with the same mtDNA SNPs as you

Images: Wikipedia, BBC

Ancestral Marker a mutation that occurred a long time ago Single Nucleotide Polymorphism

• ne nucleotide replaced by another

SNPs are the mutations found in mtDNA

Deep Ancestry: ancestry from tens of thousands of years ago

Bioinformatics Activities for Mitochondrial DNA

Lab ab Activity Workflow

1) Extract your cheek cell DNA using Chelex 2) Amplify 440-nucleotide sequence from the D-loop

• f your mt genome

3) Submit PCR samples for sequencing at CSUEB 4) Analyze your mtDNA sequence using bioinformatics

Bi Bioi

• inform
• rmatics Ac

Activity 1 1 mtDNA Haplogroups & Human Origins

≈27 major groups compromise the human race

mtDNA Haplogroups & Human Origins

Haplogroup Groups or people with similar haplotypes - they share a common ancestor Haplotype inheritance of a cluster of single nucleotide polymorphisms (SNPs)

Learn where your line diverged

Bioinformatics Activity 1 – determine your haplogroup We will use sample sequences today, then we will email you your actual results in 2-3 weeks

Bi Bioi

• inform
• rmatics Ac

Activity 2 2 Similarity of DNA

• The human genome is over 3

billion base pairs long

• Two random people are 99.9%

identical

• However, that still leaves 3

MILLION base pairs that can be different

Ho How we e descr escrib ibe e DNA NA dif iffer eren ences ces SNPs – Single Nucleotide Polymorphisms

Sickle cell anemia: TàA Tay-Sachs disease: insertion cystic fibrosis: deletion

Genetic similar arity exam ample

• Which pair of people is the most genetically similar?
• Which pair of people is the least genetically similar?

AGTG ACTG AGAG AGAT AGTG

Emma Laura Marcus Leslie Martin

Genetic similar arity

• Who is most genetically similar?
• People who have identical sequences
• 4/4 bases same = 100% similarity
• Who is least genetically similar?
• ACTG and AGAT
• They only have 1 base in common, which

is the A in the beginning

• 1/4 bases same = 25% similarity

AGTG

Emma

AGTG

Marcus

ACTG

Leslie

AGAT

Martin

How can an we determine genetic similar arity?

• Sequence the entire genome
• f everyone in the class?
• Problems:

Way too long Too Expensive Too Complicated

• Solution:

Look at a small region with lots of variability à mtDNA HRV

Similarity Matrix

I am most similar to _________ I am least similar to _________

Me Tony Selina Deanne Hector Me 100% 94.44% 92.44% 88.24% 86.79% Tony 94.44% 100% 88.89% 82.35% 100% Selina 92.44% 88.89% 100% 82.35% 92.44% Deanne 88.24% 82.35% 82.35% 100% 88.24% Hector 86.79% 100% 92.44% 88.24% 100%

Are there any siblings on this table?

Anal alyzing & In Interpreting the Data

• What was the range of genetic similarity in this

experiment?

• “Most similar” typically 98%+
• “Least similar” typically 80% - 98%
• Sometimes more than one “most similar”

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ATCC GTCC ATCG 75% similar 75% similar

Online Sequence Alignment

ID # Observed or Self-reported Phenotype or Nationality 1 Algerian 2 Brazilian 3 South Asian (India) 4 North/West European 5 Chinese 6 Russian 7 South Asian (India) 8 Chinese 9 North/West European 10 Vietnamese 11 North/West European 12 North/West European 13 South Asian (India) 14 North/West European 15 Chinese 16 Latinx 17 North/West European 18 Samoan 19 African American 20 Latinx 21 Vietnamese 22 Latinx 23 Latinx 24 Ethiopian 25 Chinese

Activity #1

Refer to: https://drive.google.com/drive/folders/10tuxHwrzCrchOWNfjqnu3T0YMIAayFVC

Activity #2

ID Nationality Haplogroup Group # 2 Chinese M7b 1 3 Chinese D4a 1 5 Chinese M76 1 35 North/West European H39 1 36 North/West European H13a 1 42 North/West European M33c 1 47 North/West European T 1 55 Chinese M30 1 9 Venezuela C1 2 11 South Asian (India) K2b 2 15 South Asian (India) M10a 2 31 Taiwanese F2a 2 32 Taiwanese F2a 2 33 South Asian (India) D4e 2 38 Venezuela U7 2 50 South Asian (India) M7b 2 28 China B4a 3 62 Samoan A2 3 63 African American U5b 3 64 African American B4a 3 68 Latinx A2w 3 73 Vietnamese L3e 3 80 Ethiopian U2d 3 87 African American L2b 3

Refer to: https://drive.google.com/drive/folders/10tuxHwrzCrchOWNfjqnu3T0YMIAayFVC

Go back to the challenge statement – IS IS THE HERE a a GE GENETIC IC BASIS IS TO O RACE?

• Agree/disagree, why? provide evidence

Review Ten things everyone should know about race. http://www.pbs.org/race/000_About/002_04-background-01- x.htm

After bioinformatics analysis, Watch Video: Power of Illusion, Episode 1, clip 2

https://www.youtube.com/watch?v=GyuKJA G11Cw

Re Resources

Power of Illusion (2003) http://www.pbs.org/race/000_General/000_00-Home.htm http://www.pbs.org/race/000_About/002_04-teachers-03.htm BioSeq Website: from Tufts University (2017)

• http://ase.tufts.edu/chemistry/walt/sepa/geneticsofrace.html
• Article: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5459240

insert in your folder)

Perspectives on rac ace

American Anthropological Association:

“Evidence from the analysis of genetics (e.g., DNA) indicates that most physical variation, about 94%, lies within so-called racial groups. Conventional geographic "racial" groupings differ from one another only in about 6% of their genes. This means that there is greater variation within "racial" groups than between them. …These facts render any attempt to establish lines of division among biological populations both arbitrary and subjective.”

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Perspectives on rac ace

Human Genome Project:

“DNA studies do not indicate that separate classifiable subspecies (races) exist within modern humans…People who have lived in the same geographic region for many generations may have some alleles in common, but no allele will be found in all members of one population and in no members of any other.”

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Is Is rac ace mean aningful…

• … genetically?
• … in society?
• … in the justice system?
• … on surveys (like the US census or standardized tests)?

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