1. Issues in Biotechnology: The Way We Work With Life
Dr. Albert P. Kausch
life edu.org
OnCampus Live
BCH 190, MIC 190, AFS 190, NRS 190, PLS 190
OnLine BCH 190
A Sweeping General Survey on Life and Biotechnology
A Public Access College Course
The University of Rhode Island
Issues in Biotechnology:
Biotechnology, Our Society and Our Future

2. Issues in Biotechnology: The Way We Work With Life
Dr. Albert Kausch
Kimberly Nelson
BCH 190
Section I. The Mechanics of DNA: What is Life?
Section II. The Applications of Biotechnology
A Sweeping General Survey on Life and Biotechnology
A Public Access College Course
The University of Rhode Island
life edu.org

3. Issues in Biotechnology: The Way We Work With Life
Dr. Albert P. Kausch
life edu.org
The Mechanics of DNA: What is Life?
5. The Trends, Patterns and Relationships In Biology
6. Some More Techniques in Biotechnology
A Sweeping General Survey on Life and Biotechnology
The University of Rhode Island
Lectures 5 & 6

4. Issues in Biotechnology: The Way We Work With Life
Dr. Albert P. Kausch
life edu.org
The Mechanics of DNA: What is Life?
6. Some More Techniques in Biotechnology
A Sweeping General Survey on Life and Biotechnology
The University of Rhode Island
Some More Techniques in Biotechnology
Lecture 6

5. Bio 104: Issues in Biotechnology
FDA requires special labeling when a food is produced under certain conditions: when biotechnology’s use introduces an allergen or when it substantially changes the food’s nutritional content... Otherwise special labeling is not required. Would you say that you support or oppose this policy of FDA?
Support
Oppose
Neither support or oppose
Don’t know
Refuse to answer
© life_edu
Feb 20a: Agricultural Biochechnology

6. Current FDA labeling policy supported by majority
Bio 104: Issues in Biotechnology
Current FDA labeling policy supported by majority
FDA requires special labeling when a food is produced under certain conditions: when biotechnology’s use introduces an allergen or when it substantially changes the food’s nutritional content... Otherwise special labeling is not required. Would you say that you support or oppose this policy of FDA?
© life_edu
Feb 20a: Agricultural Biochechnology

7. Constitutive expression of rainbow trout growth factor hormone
A Success Story: Genetically Modified Salmon
Constitutive expression of rainbow trout growth factor hormone
All salmon shown are fourteen months old, those at the bottom are the controls

8. Transgenic Atlantic salmon produced by Aqua Bounty Inc.
Growth rate, not ultimate
size is enhanced.
Commercial production of Aqua Bounty salmon is
being reviewed by FDA. First transgenic meat product.

9. Would you order genetically modified salmon at a restaurant if you also had a choice of wild salmon?
Yes
No.
Doesn’t matter
Undecided

10. Tools and Techniques
used in Biotechnology

11. Tools of the Trade The eppendorf tube and the pipetman
are the standard stock
and trade in the daily
work of a molecular
Biologist
“On the body of the traditional P-Series pipet it says, in relief, “Gilson.” Warren Gilson, who earned his MD in 1940 at the Univ. of Wisconsin, invented and patented the mechanical basis for the popular adjustable pipet (US Patent No. 3,827,305, 1974), Nearly 30 yrs. After the patent, the Pipetman continues to be manufactured in France in a factory started by Gilson’s colleague, Eugene Marteau D’Autry. Shortly before Gilson’s patent issued Gilson sold the marketing and sales rights to Ken Rainin President of Rainin Instrument, because, Gilson says, ‘He was a good salesman.’”

12. Gene transfer from one organism to another is not new
Image of two species of
bacteria transferring viral
phage particles
Bacteria transfer genes
to other bacteria and plants.
Now in nature there
is another organism
capable of
Transferring DNA:
we call that organism
a human being.

13. Innovative technologies
become biotech products
“Eppendorf tubes
And Pipetteman
For the Gold Rush”

14. Issues in Biotechnology
A Pipetman is:
(A) the new biomedical device made by tissue engineering and now used to treat the damaged blood vessels of heart attack victims
(B) a radical group of bioengineered superheroes in the Hollywood movie GATTACCA
(C) a molecular biology tool used in the lab to measure small volumes of liquid common in biotechnology
(D) a new type of bio-engineered crop plants that are drought tolerant
(E) a new surgical tool used in to extract cancer cells

15. Separation Techniques: The need to separate the components of Life
Precipitation/Dissolution
Filters
Centrifugation
Affinity
Blots
Magnetics
Electrophoresis
Etc.

16. Gel Electrophoresis: the separation of molecules,
DNA, RNA and proteins
by charge and size
Electro refers to the energy of
electricity. Phoresis, from the
Greek verb phoros, means
"to carry across." Thus, gel
electrophoresis refers to the
technique in which molecules are forced across a span of gel,
motivated by an electrical current.

17. What is a Gel?

18. Agarose is a long chain of sugar molecules,
a polymer, derived from algae
used in electrophoresis to separate molecules
Two types of gel:
Agarose (horizontal type)
Polyacrylamide (vertical type)

19. How are Gels Loaded and Run?

20. Applications of Gel Electrophoresis
DNA Fingerprinting
DNA Recombinant Technology
Forensics
The Human Genome Project

21. DNA carries a net negative charge; it is negatively charged because the phosphates (red circles) that form the sugar-phosphate backbone of a DNA molecule have a negative charge.

22. The gel matrix acts as a sieve for DNA molecules
The gel matrix acts as a sieve for DNA molecules. Large molecules have difficulty getting through the holes in the matrix. Small molecules move easily through the holes. Because of this, large fragments will lag behind small fragments as DNA migrates through the gel.

23. As the separation process continues, the separation between the larger and smaller fragments increases.

24. Molecular weight markers are often electrophoresed with DNA.
Molecular weight markers are usually a mixture of DNAs with known molecular weights
Molecular weight markers are used to estimate the sizes of DNA fragments in a DNA sample

25. Issues in Biotechnology
Gel electrophoresis is an important tool in molecular biology and biotechnology. Electro refers to the energy of electricity. Phoresis, from the Greek verb phoros, means "to carry across." Thus, gel electrophoresis refers to the technique in which molecules are forced across a span of gel, motivated by an electrical current. Gel electrophoresis allows for
(A) the separation of biological molecules, including DNA, RNA and proteins by their charge and size
(B) all of the answers are correct
(C) the identification of DNA markers now commonly used in forensics to implicate or exonerate persons accused of various crimes
(D) the rapid visualization of the products of PCR
(E) the acceleration of DNA into cells for genetic engineering purposes

26. Molecular Biotechnology
The Techniques of
Molecular Biotechnology
Technology has created new Fields
DNA detection Genomics
DNA synthesis Bioinformatics
DNA sequencing Pharmacogenomics
DNA cloning Transgenics
Expression cassette Computational
construction Biology
RNA detection Population Genetics
Protein detection Proteomics

27. Molecular Biotechnology
Techniques of
Molecular Biotechnology
Polymerase Chain Reaction
Southern Blot Analysis
Northern Blot Analysis
Western Blot Analysis
cDNA Library Construction
DNA Sequencing
Gene Isolation
Gene Vector Construction

28. PCR

29. The Polymerase Chain Reaction
PCR
The Polymerase Chain Reaction

30. PCR was used on the "BLUE DRESS"
and showed President Clinton's association with
Monica Lewinsky.

31. Polymerase Chain Reaction
Nobel laureate in Chemistry,
1994
PCR is Amplification

32. THERE ARE MILLIONS OF DIFFERENT GENES OR SEQUENCES WITHIN ANY DNA SAMPLE (BLOOD, TISSUE, PLANT, ETC.).
A SPECIFIC SEQUENCE IS SELECTED TO BE AMPLIFIED (RED ABOVE). THIS SEQUENCE CAN BE ANY GENE OF INTEREST OR A NON-CODING MARKER REGION OF DNA.

33. IN ORDER TO COPY THE SEQUENCE OR GENE, A SHORT SEQUENCE ON EITHER SIDE OF THE SECTION MUST BE KNOWN. THIS REGION (BLUE ABOVE) WILL SERVE AS A PRIMER ATTACHMENT SITE TO COPY THE DNA TARGET SEGMENT.

34. IN ORDER TO AMPLIFY A SPECIFIC FRAGMENT OF DNA, SEVERAL THINGS ARE NEEDED, INCLUDING PRIMERS AND DNA POLYMERASE,
AN ENZYME WHICH COPIES DNA. PRIMERS ARE SHORT PIECES OF DNA OR RNA DESIGNED TO PAIR WITH GENOMIC DNA AT A SPECIFIC ATTACHMENT SITE FOR THE MAIN PURPOSE OF HELPING THE DNA POLYMERASE BIND AT THE DESIRED SECTION.

35. WITHOUT A SHORT PIECE OF DNA(OR RNA) TO ATTACH TO, DNA POLYMERASE CAN NOT COPY A DNA STRAND.

36. NUCLEOSIDE TRIPHOSPHATES, THE BUILDING BLOCKS OF DNA ARE ALSO NEEDED.
EACH NUCLEOSIDE TRIPHOSPHATE CONSISTS OF:
A BASE (ADENINE, THYMINE, CYTOSINE OR GUANINE).
A SUGAR AND THREE PHOSPHATES.

37. PCR REQUIRES SEVERAL CYCLES OF AMPLIFICATION. EACH CYCLE CONSISTS OF
THREE TEMPERATURE CHANGES.
THE STARTING TEMPERATURE (95 C) SEPARATES THE DNA STRANDS.
A LOWERED TEMPERATURE (50-60 C) ALLOWS PRIMERS TO BIND TO COMPLEMENTARY SEQUENCES IN THE DNA.
A SLIGHTLY HIGHER TEMPERATURE (72 C) ALLOWS DNA POLYMERASE TO ATTACH TO THE PRIMERS AND COPY THE DNA STRANDS (EXTENSION).

38. DNA STRANDS ARE SEPARATED BY HEATING @ 94o C.

39. THE TEMPERATURE IS LOWERED TO 54oC TO ALLOW PRIMERS TO PAIR WITH COMPLEMENTARY DNA SEQUENCES.

40. MAKING NEW DNA MOLECULES:
DNA POLYMERASE ATTACHES TO THE
72 C.
DNA POLYMERASE ADDS NUCLEOSIDE TRIPHOSPHATES TO THE PRIMERS TO COPY THE DNA STRANDS.

41. COPYING IS COMPLETED FOR EACH STRAND.

42. THE PROCESS IS REPEATED IN THE NEXT CYCLE.
THE TEMPERATURE IS RAISED AGAIN TO SEPARATE
THE DNA STRANDS.

43. THE TEMPERATURE IS LOWERED TO ALLOW PRIMERS
TO ANNEAL. DNA POLYMERASE ATTACHES TO
THE PRIMERS AND DNA IS COPIED TO MAKE
4 STRANDS OF DNA.

44. THE PROCESS OF COPYING DNA STRANDS IS REPEATED
32-35 TIMES. WITH EACH AMPLIFICATION CYCLE,
THE NUMBER OF COPIES OF THE DNA SEQUENCE IS
DOUBLED UNTIL MILLIONS OF COPIES HAVE BEEN MADE.

45. The stability of TAQ Polymerase allows for this amplification process through the three temperature changes.

46. Issues in Biotechnology
A method used to copy small amounts of DNA many times over was invented by Dr. Kary Mullis in the 1980s and is called PCR. PCR stands for:
(A) Protein Chromosomal Replication
(B) Polymerase Chain Reaction
(C) Pipetman California Reaction
(D) Peptide Catalytic Reactors
(D) Polysaccharide Catalyst Repair

47. Forensic applications of DNA based technologies
DNA Fingerprinting
since OJ Simpson
Identification
Paternity
Crime Solving
World wide
data base

48. Forensic Identification: Basic Principles
Each of us is genetically unique.
If enough genetic variation is tested, each of us can be uniquely identified.
DNA is found in nearly all cells (blood, semen, hair, etc.).
DNA from an evidentiary sample can be matched with DNA from a suspect to implicate or exonerate.

49. STRs Are Used in Identity Testing
...atatatacaacttactaccatata
ccgattacgatcgaattataccgcgga
cgtagtaatgacgatgaagtaactata
tatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatat
atactacctaccagggaggagata...
“Short
Tandem
Repeat
sequence”

50. Laboratory PCR Instrument
INPUT:
Sample DNA, PCR enzymes,
primers, individual nucleotide
building blocks (and maybe
fluorescent labels)
OUTPUT:
Specific DNA fragments amplified
millions of times for easy visualization
With sizes that vary between individuals
Here is a picture of one kind of PCR instrument. This one has the ability to do PCR on 96 samples at a time. Small tubes are inserted that contain the sample DNA, and all the ingredients to do PCR. The instrument cycles the temperature so that specific enzymes can unzip the DNA and make copies.
The output after thermal cycling is a tube with the original ingredients plus millions of copies of the DNA segment of interest.
It is now possible to set up the sample so that many different regions are copied all at the same time: called multiplex PCR.

51. After PCR, DNA Fragments are Separated on a Gel
PCR products for each sample - +
TIME 5 45 15 10 40 20 25 30 35
Minutes
Fragment
Size
100
180
120
110
170
130
140
150
160
DNA fragments move through
gel based on their size
After amplifying (copying) the DNA in the two regions by PCR, the copied DNA is loaded on a gel, and separated by size. This process is called electrophoresis. When an electrical charge is placed on the gel, the DNA will move through the gel, with the smallest DNA fragments moving the fastest. In this example, samples from 5 different individuals DNA have been tested. Size standards are added at both sides of this example gel image.
After a few minutes, the different fragments can be seen to separate by size, producing the spots shown here. Because we have 2 chromosomes, and the # of repeats is likely to be different on each chromosome, we usually see 2 spots for each DNA fragment being tested. In sample #5 however, only one green spot is seen, and the intensity of this spot would indicate that that individual has the same # of CGA repeats on both chromosomes.
(Bring a gel box with a gel to show on camera)

52. Identity Testing Using PCR
Analysis of four different sections of the DNA
Possible conclusions:
A. Suspect 1 DNA was
at the scene
B. Suspect 2 DNA was
C. Suspect 3 DNA was
D. None were at the scene
E. Multiple suspects
were at the scene
F. Data are inconclusive
S = size standards
V = victim’s DNA
1 = suspect #1 blood
2 = suspect #2 blood
3 = suspect #3 blood
E = evidence #1

53. A complete match! S V 1 2 3 E S S = size standards V = victim’s DNA
450
S = size standards
V = victim’s DNA
1 = suspect #1 blood
2 = suspect #2 blood
3 = suspect #3 blood
E = evidence #1
400
A complete match!
350
300
250
200
150
100 50

54. PCR was used on the "BLUE DRESS"
and showed President Clinton's association with
Monica Lewinsky.

55. Congratulations!!!!!
You have $100,000.00!!!!!!!
To Invest in Biotech.

56. Issues in Biotechnology
Stock Project The idea is to select five biotechnology companies and invest $100,000 (fictitiously, of course).

57. Issues in Biotechnology
Stock Project
You can spread your money evenly across five companies (i.e. $20,000 each) or not. For example, if a company is trading at $20/share you can purchase 1,000 shares for $20, 000. Look up companies on Google (e.g.: type Monsanto stock) and record their stock ticker designation (e.g.. MON of the New York Stock Exchange, NYSE). Observe their performance over the past year. Record current trading price per share and calculate how many shares you can buy. You must choose your companies and the number of shares. Submit a single page summary on these results. Toward the end of the course you will look up these same companies and determine the cost per share at that time. Calculate your losses or gains for each company and your total losses and gains. This project will be summarized at the end of the course in a one page summary of losses and gains.

58. Biotechnology Stocks Project
Congratulations!!!!!
You have $100,000.00!!!!!!!
To Invest in Biotech.
1. Select and Research five Biotech companies
2. Print and submit the current stock quote and for each company
3. Invest chosen amounts in each. Calculate the number of shares in each. (Submit a One page summary)
4. Contact company to receive investors information (Optional)
5. Monitor Stock during the course
6. Calculate gains and losses. Submit report with final exam

59. Biotechnology and Industry
“In retrospect, recombinant-DNA may rank as the safest revolutionary technology ever developed.”
- James D. Watson, Nobel Prize Winner, 1953

60. Biotechnology is directly linked with Industry
The Development of
Biotechnology is directly
linked with Industry
The application of the
biological sciences has moved
from academia to the private
sector.
Driven by profits and the
promise of profits.
The distinction between
Basic and Applied Science
is blurred.
Basic science is immediately
applied in today’s biotech.

61. Biotech Industry
Red vs Green companies
pharmaceuticals vs
agriculture
(blood vs chlorophyll)
Information Sciences
Genomics
Proteomics
Phenomics
Bioinformatics
Population Genetics
Clinical trials

62. The Role of Companies in the Development of Biotechnology
Technology Development
Patents
Markets and Products
Market-driven Innovation

63. Genomics Companies Celera Incyte Genome Therapeutics Corp Millenium
Paradigm Genetics
DuPont
Genaissance
Monsanto

64. Technology Companies Invitrogen Stratagene Qiagen Packard
PE Biosystems
Kairos
BioRobotics

65. Biotechnology Industry Advertisement of services
in international journals
NATURE
Science
Nature Biotechnology
“Picks and shovels
for the Gold Rush”

66. And look at the ads! Innovative technologies become biotech products
Big money in licenses
Commercialization of
biotech products requires
Freedom to Operate (FTO)
with all the technologies
used.
And look at the ads!

67. Agricultural Productivity Product Pipeline Benefits of Our Products
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68. » View Biotechnology Videos
Roundup RReady2Yield™ Soybeans — Another Step Closer to Farmers' Fields Read More
2007 Farm Progress Show — "Road to Success" — Monsanto Technology Showcase Read More
Delta & Pine Land — Monsanto Company Begins Combining Delta & Pine Land Business Read More
Featured Story
$21 Million Data Center Completed
High-tech center will provide global IT support for Monsanto's growing data analysis needs Read More
View All Featured Stories
Recent News
Mon, 17 Sep 2007 — Monsanto Increases Ongoing Earnings Per Share Guidance, Provides Free Cash Flow Guidance For Fiscal Year 2007
Fri, 14 Sep 2007 — Monsanto, Dow Agreement Paves the Way for Industry's First-Ever, Eight-Gene Stacked Offering in Corn
Thu, 13 Sep 2007 — Monsanto to Provide Information to Iowa Attorney General Concerning Seed, Trait and Chemistry Business

70. Biotechnology Companies:
AstraZeneca
Active Motif
Aventis
Adventa
Celera PE
Incyte
Invitrogen
Pfizer
Merck
Smith Kline Beecham
Novartis
Monsanto
Qiagen
Roche
Paradigm Genetics
Chemicon International Trevigen
Avigen
Metabasis Therapeutics
Pintex Pharmaceuticals
BioGen
Garst
Pioneer
DuPont
Pharmacia
Bristol-Myers
Squibb
Eli Lilly
Cistem Molecular Corp.
Operon Technologies

71. Biotechnology Companies:
DNX Transgenic Sciences
Chemdex
MWGAG BIOTECH
Double Twist
Larova Biochemie
Greiner Labortechnik
Sungene
Molecular Devices Corp.
Evotec BioSystems AG
BIACORE
TIB MOLBIOL
PE Biosystems
Bruker Daltonics Inc.
Eppendorf Scientific
Curagen
Cargill
Dow Agri Sciences
Dow Chemical Co.
AmGen
Bayer
Dynal
Noxxon Pharma
Schering
Boehringer
Rhein Biotech
Hyseq
Genome Therapeutics

72. O sweet spontaneous
earth how often have
the doting  fingers of
purient philosophers pinched
and poked thee
,has the naughty thumb
of science prodded
thy  beauty    how
often have religions taken
thee upon their scraggy knees
squeezing and
buffeting thee that thou mightest conceive
gods
        (but
true to the incomparable
couch of death thy
rhythmic lover
          thou answerest
them only with
                        spring) e.e. cummings

73. 20. Of the following techniques, which would be most unlikely to be used in a biotechnology laboratory?
(A) gel electrophoresis
(B) PCR
(C) DNA cloning
(D) use of the Hubble telescope
(E) antibiotic resistant bacteria

74. 21. Many of the molecular reactions used in biotechnology occur in volumes less than a milliliter. A Pipetman is:
(A) the new biomedical device made by tissue engineering and now used to treat the damaged blood vessels of heart attack victims
(B) a radical group of bioengineered superheroes in the Hollywood movie GATTACCA
(C) a molecular biology tool used in the lab to measure small volumes of liquid
(D) a new type of bio-engineered crop plants that are drought tolerant
(E) a new surgical tool used in to extract cancer cells

75. 22. Gel Electrophoresis is used for:
(A) the separation of molecules, DNA, RNA and proteins by charge and size
(B) separation of various cell types in blood samples
(C) viewing cells at a high magnification
(D) as a home pregnancy test
(E) fusing cells during the process for cloning animals

76. 23. Every time a cell divides it copies all of its DNA
23. Every time a cell divides it copies all of its DNA. A method used commonly in many applications of biotechnology today is called PCR. PCR:
(A) is used to study life on other planets
(B) stands for the PolyChromal Repercussions that occur in cell division
(C) is a type of digital processing used in DNA sequencing
(D) uses a heat stable DNA polymerase to copy DNA
(E) is a dangerous prescription drug

77. 24. Basic Forensic principles include:
(A) Each of us is genetically unique.
(B) If enough genetic variation is tested, each of us can be uniquely identified.
(C) DNA is found in nearly all cells (blood, semen, hair, etc.).
(D) DNA from an evidentiary sample can be matched with DNA from a suspect to implicate or exonerate
(E) All of the above

78. 25. Given DNA samples from three suspects, the victims DNA and DNA evidence from a crime scene the possible conclusions are:
(A) Suspect 1's DNA was at the scene; or Suspect 2's DNA was at the scene; or Suspect 3' DNA was at the scene
(B) None were at the scene
(C) Multiple suspects were at the scene
(D) Data are inconclusive
(E) Any of the above

79. 26. A method used to copy small amounts of DNA many times over was invented by Dr. Kary Mullis in the 1980s and is called PCR. PCR stands for:
(A) Protein Chromosomal Replication
(B) Polymerase Chain Reaction
(C) Pipetman California Reaction
(D) Peptide Catalytic Reactors
(D) Polysaccharide Catalyst Repair

80. 27. STR stand for
(A) Separation of Trans Replicators
(B) Scientists for True Religion
(C) Short Tandem Repeats
(D) Standard Test for Recidivism
(E) Seek To Reach assay

81. 28. The development of Biotechnology is directly linked with Industry
28. The development of Biotechnology is directly linked with Industry. Which of the following is not true?
(A) The application of the biological sciences has largely moved from academia to the private sector.
(B) The application of biotechnology is driven by profits and the promise of profits
(C) The distinction between Basic and Applied Science is often blurred.
(D) Basic Science is nearly immediately applied in today’s biotech fields.
(E) Basic Science has not yet applied in any of today’s biotech fields.

82. 29. The development of Biotechnology is
(A) driven by application
(B) has been banned in Europe by governments in the EU
(C) has disproven the Theory of Evolution
(D) destroying medicine as we know it
(E) finally leveling off

83. 30. The process of creating genetically modified organisms (GMOs)
(A) has been applied to salmon
(B) has been applied to crop plants
(C) has not been commercialized for beef
(D) has been not demonstrated in peer review journals to cause health issues
(E) all of the answers shown are correct