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Biotechnology

Chapter 17 section 1 (only)

5-16-16

Learning Goals for Today:

• Explain how DNA profiling can identify individuals

• Interpret data from DNA electrophoresis

• Discuss genetically modified organisms

• Explain some ways DNA can be recombined in nature

What Is Biotechnology?

• Biotechnology is the use of organisms, cells, or biological molecules to produce food, drugs, or other goods – Yeast: fermentation (10,000 years ago)– Selective breeding of animals/plants (between 6

and 15,000 years ago)– cloning– genetic engineering– Finger-printing– Genome sequencing– Diagnosing and treating diseases

• Merriam Webster’s definition of natural: “being in accordance with or determined by nature”

Is all this natural?

According to nature

Lemon

Corn

Banana

PigDog

Things that we assume com straight from nature, do not!

ALL dogs come from the wolf!

All these veggies come from wild mustard!

Genetically Modified Organism (GMO):

– an organism that contains foreign DNA

– w/ altered characteristic(s)

– does not occur naturally because the selection pressure in for human benefit

– obtained via cloning technology

9

Genetic engineering

• Recombinant DNA - combining DNA molecules not found together in nature; via cloning

How Does DNA Recombine in Nature?

• Bacteria and yeast: can take in DNA from the environment– Transformation

• DNA piece can come from a the same or a different species

plasmid

plasmid

bacterial

chromosome

(a) Bacterium

DNA

fragments

bacterial

chromosome

(b) Transformation with a DNA fragment

(c) Transformation with a plasmid

A DNA fragment is

incorporated into

the chromosome

bacterial

chromosome

The plasmid replicates

in the cytoplasm

1 micrometer

Transformation in Bacteria

Fig. 13-1

Bacteria can take in DNA from their environment

New DNA might code for anything

Big Issue: Genes for antibiotic resistance

Viruses Also Transfer DNA

Fig. 13-2

The virus releases itsDNA into the host cell; some viral DNA (red) may be incorporated intothe host cell’s DNA (blue)

The virus enters the host cell

Viral genes encode the synthesis of viral proteins and viral gene replication; some host cell DNA may attach to the replicated viral DNA (red/blue combination)New viruses assemble;

some host cell DNA is carried by recombinant viruses

The host cell bursts open, releasing newly assembled viruses; if recombinant viruses infect a second cell, they may transfer genes from the first cell to the second cell

viral proteinsrecombinant virus

virus

viral DNA

viral DNA

A virus attaches to a susceptible host cell

host

cell

host cell DNA

2

3

1

4

5

6

Types of Cloning

• Molecular cloning (DNA cloning)

– Manipulating a small piece of DNA, typically using bacteria as host

• Therapeutic cloning

– Creating stem cell lines with same DNA as a patient, used for treating diseases and disorders

• Reproductive cloning

– Technique used to generate an animal with exact genetic makeup (DNA) as another animal

Genetic Engineering

Recombinant DNA - combining DNA molecules not found together in nature; via cloning

DNA Cloning –

– Molecular cloning

– Inserting foreign DNA from one organism into another

what is it?

15

Bacteria can transfer DNA into plants

• Agrobacterium infects plants

• Physically injects part of its own DNA into the plant cell

• Plant will grow a gall at the infection site– Bacteria live in the gall

– Plant synthesizes nutrients for the bacteria

• Similar process with Rhizogenes bacteria but the end result benefits the plant

Agrobacterium is a natural, and

commonly used, plant genetic engineer

The “gene gun” is also used to introduce

DNA into cells

After cells are

modified, they

are induced to

regenerate into

whole plants

Where are GM foods?

The Marketplace

– 60 to 70% of processed food contains GMO

In the US:

– Corn ~45% is GM

– Soybean ~85% is GM

– Cotton ~76% is GM

– Canola ~60% is GM

20

Biotech crops widespread, rapidly

adopted: Grown on >10% arable land on planet,

extensive uptake in developing world

http://www.isaaa.org/resources/publications/briefs/46/pptslides/Brief46slides.pdf

Four crops dominate,

8+ crops in USA

http://www.isaaa.org/resources/publications/briefs/46/pptslides/Brief46slides.pdf

Two traits dominate worldwide

http://www.isaaa.org/resources/publications/briefs/46/pptslides/Brief46slides.pdf

Newly approved GE crop varieties in

USA • Soybean – insect resistant (Apr. 2014)

• Alfalfa – reduced lignin (Nov. 2014)

• Potato – reduced black spot bruise and low acrylamide production (Nov. 2014), reduced browning and disease resistant as well (August 2015)

• Soybean and cotton – new herbicide tolerances (Jul. 2014 – Jan. 2015)

• Apple – non-browning (Feb. 2015)

• Plum – virus resistant (2014)

Non-browning “Arctic Apple” Reduced spoilage/waste, improved quality – USDA

approved

Courtesy of Jennifer Armen, Okanagan Specialty Fruits, Canada

Non-browning “Arctic Apple” Time lapse video

“Innate” potato approved – reduced browning

and acrylamide (↓waste, ↑safety)

“Innate” potato in my hands for teaching

One hour after cutting – Control vs. Innate

Two days after cutting – Innate vs. Control

“Innate” potato 2.0 – late blight resistant,

reduced acrylamide, reduced sprouting and

browning (↓ waste, ↑ safety, ↓ pesticide, ↑ yield)

Dramatic change in color of chips,

highly prized by consumers

Provided by Walter De Jong, Cornell University

Scientific AmericanMarch, 2013

Resistance transgenes promising solution/s to devastating ‘citrus greening’

Face the “wall of opposition” ?

Defensin-like proteins from spinach

for citrus greening disease resistance

Courtesy of Eric Mirkov, Texas A & M

Helping forests: American Chestnut

restoration by genetic modification

March 2014 issue - Scientific American

Forest health a major and growing

concern

Diverse pipeline of biofortification

products = enhancement of critical

vitamins or nutrients

Many more examples funded by Gates Foundation / other sources

• Rice

• Cassava

• Sorghum

• Banana

Biotech methods useful where breeding is

ineffective or slow

RiceCassava

Management of monocultures

• Mismanagement promotes the proliferation of weeds resistant to herbicides and bugs resistant to pesticide– Many weeds have developed resistance to glyphosate

(RoundUp)

– Rootworms have also developed resistance to Bt

• Herbicide can kills plants that are not weeds– Milkweed supplies Monarch butterflies eat

• Rotating crops, eliminate volunteers, and creating havens with no pesticide

Cloned Stem Cells• Immune system will recognize & destroy cells with different DNA

• Therefore, stem cells need to contain same DNA as patient

• Cloned Stem Cells -

• Somatic Cell Nuclear Transfer

“Therapeutic Cloning”

Somatic cells = all body cells

Nucleus = region of cell containing DNA

Transfer = remove and replace

Somatic Cell Nuclear Transfer

https://www.youtube.com/watch?v=tELZEPcgKkE

Induced Pluripotent Stem cells

(iPScells)

• Reprogramming somatic cells (skin) so they

behave as stem cells

• Can replace embryo harvesting

• Human cloning not needed

• Used for therapeutic cloning

• Must add new proteins (transcription factors)

to reprogram

https://www.youtube.com/watch?v=Q9-

4SMGiKnE

https://www.youtube.com/watch?v=Q6U5kf5By

NE

How Is Biotechnology Used in Forensic Science?

• DNA identification: huge role in criminal investigations

• Individual have unique DNA sequences

– DNA “fingerprint”

• How to we figure out a person’s DNA “fingerprint”?

Differences in short tandem repeats (STRs) can identify individuals by their DNA

• STRs: noncoding DNA

– STRs are not transcribed into mRNA

– Short sequence of 2-5 nucleotides

– Repeated many times (up to 50)

– All in a row (in tandem)

• Number of repeats varies (different alleles)

Example of a STR

Fig. 13-4

Eight side-by-side (tandem) repeats

of the same four-nucleotide sequence

Using STRs to Identify Individuals

• Different people may have different alleles of the STRs – Allele: number of repeats

• U.S. Department of Justice – 13 standard STRs tested

• Over a trillion possible combinations of alleles

– Exact match needed for conviction

https://www.youtube.com/watch?v=9bEAJYnVVBA

Question for Thought:

• DNA fingerprinting is very useful– Paternity/mate

rnity testing– Criminal

investigations

• Should there be a national database of everyone’s DNA?

How do we figure out someone’s DNA “fingerprint?”

• DNA sequence cannot be read directly

• Sequencing entire genomes is expensive and takes time

• Sometimes there isn’t much DNA in the sample

• PCR: a technique for making lots of DNA copies of specified pieces of DNA

PCR: the Polymerase Chain Reaction• Modern version developed by Kary Mullis

• Only need a tiny amount of starting DNA

• Makes lots of copies of DNA of interest

DNA Learning Center, Cold Spring Harbor Laboratory

Gel electrophoresis: a method to examine PCR results

• After PCR: a lot of pieces of DNA

– Often alleles are different sizes

• Gel electrophoresis: a method to separate DNA based on size

Example of DNA Profiling for one STR

DNA samples from

13 different people

15

14

13

12

11

10

9

8

D16: An STR on chromosome 16

Nu

mb

er

of

rep

eat

s

Why do some people have 1 band and some people have 2 bands?

DNA Profiling

Fig. 13-7

STR name

Penta D

CSF

D16

D7

Mutations

• Substitutions or point mutations

• Insertions

• Deletions

• Inversions

• Translocations

Due to errors during replication (1 in 100,000, but proof-reading fixes 99%) or external factors like toxins and radiation

Mutations in STRs

• STRs: Sequence Tandem Repeats (forensics)

• Errors are due to replication slippage

• Slippage occurs in STRs about 1 per 1000 generations

Replication slippage

Other uses for gene sequencing

• Genes other than the STRs are often sequenced

– Health-related tests

– Studying gene function