2.  Describe the science of Biotechnology and its product domains  List the steps to producing a GMO through use of rDNA  Outline the steps of producing and delivering a product made through recombinant DNA technology  Identify the important labs and agencies in the US, and what they’re mainly responsible for

3.  Apply the strategy for values clarification to bioethical issues  Identify products made through biotechnology

4.  Insulin  Biotechnology  DNA  rDNA technology  PCR  Cloning  Fermentation  Diabetes  Antibiotics  Restriction enzyme  DNA ligase  rDNA  Proteases  Antibodies  Pharmaceutical  R&D  Pure Science  NIH  CDC  DNA Fingerprinting  Microbial agents  Virus  Applied science

5.  Moral  GMO  E. coli  Plasmid  t-PA  Efficacy  Clinical trials  FDA  Cystic fibrosis  Biochemistry  Molecular biology  Genetics  ethics  Therapeutic  EPA  USDA  Data  Hypothesis  Variable  Control  Positive control  Negative control  Concentration  Journals  Genome  bioethics

6.  We have been manipulating entire organisms for thousands of years through selective breeding to produce plant and animal products that are  Bigger  Healthier  More productive  Have novel phenotypes  Scientists recently learned to manipulate not only whole organisms, but also the molecules, cells, tissues, and organs of which they are built

7.  Insulin is a protein produced in healthy individuals that facilitates the uptake of sugar from the blood stream into specific tissues  In some diabetic patients, the ability to produce insulin is impaired  In the past diabetic patients had to take injections of Bovine (cow) insulin to regulate their blood sugar

8.  Problem: getting insulin from cows is not very efficient, it’s time consuming and expensive, and can lead to improper immune stimulation of the recipients  Solution: Biotechnology  We have learned to manufacture large amounts of specific molecules, such as human insulin in bacterial cells  Cost effective  Convenient  Fast

9. PAST PRESENT  Selective breeding  Fermentation: a process by which in an oxygen deprived environment a cell converts sugar into lactic acid or ethyl alcohol (ethanol)  DNA technology  Recombinant DNA (rDNA) technology  PCR  Cloning  Proteomics

10.  Since biotechnology is constantly changing there is no one definitive definition  In 2003 in an international treaty on biotechnology, modern biotechnology was defined as :  “the application of techniques that overcome natural physiological reproductive or recombination barriers and that are not techniques used in traditional breeding and selection “ including  In vitro nucleic acid techniques  The fusion of cells beyond taxonomic family

11.  One major discovery that propelled the biotechnology science and industry was the discovery of restriction enzymes  Restriction enzymes: enzymes that cut DNA at specific recognition nucleotide sequences known as restriction sites  They were discovered in bacteria & are thought to have evolved to provide a defense mechanism against invading viruses

12.  Restriction enzymes allow us to cut and recombine DNA molecules, often from different species  “cutting”  Reminder  DNA (deoxyribonucleic acid) is a double stranded helical molecule that that stores genetic information for the production of all of an organisms proteins  DNA Ligase: an enzyme that binds the disconnected strands of DNA together  “pasting”  If you put DNA into an organisms cell, that cell will produce the protein that DNA codes for!

14.  Advances in rDNA technology allow biotechnologists to manufacture a wide variety of products either previously unavailable or that could only otherwise be made in small quantities  Examples:  Insulin : for treatment of diabetes  Proteases : function in breaking down other proteins  Antibodies : proteins normally developed by the immune system for recognizing specific molecules called antigens on infectious agents and so limiting their infectious ability

15.  PCR: Polymerase Chain Reaction is a technique that involves copying short pieces of DNA and using them as templates to make millions of copies in a very short amount of time  Cloning: method of asexual reproduction that produces identical organisms  Done mainly in bacteria and some fungi  Only happens in animals if manipulated by scientists to do so

16. Cao Yilin, a plastic surgery expert in Shanghai, successfully reproduces a human ear on the body of a little white mouse on Friday, April 4, 1997 in Shanghai. Dolly, right, the first cloned sheep produced through nuclear transfer from differentiated adult sheep cells, and Polly, the world's first transgenic lamb, are in their pen at the Roslin Institute in Edinburgh, Scotland, in early December, 1997.

17.  Biotechnology is practiced in a variety of settings, and in general the setting determine the major emphasis  Private companies: focus is making money so they tend to emphasize the development and manufacture of products that will yield high profit margins  The do have a Research & Development department, but they will only fund research that has potential for financial pay off  Universities & Government agencies focus on research  More involved in Pure science The main difference between companies and university or government labs is that companies must provide a product or service that results in earnings, a nonprofit research facility does not

18.  Pure-science: Scientific research whose main purpose is to enrich the scientific knowledge base  This is the type of science nonprofit labs focus on  Applied Science: the practice of utilizing scientific knowledge for practical purposes, including the manufacture of a product  This is the type of research forprofit labs focus on

19.  Pharmaceutical  Agricultural  Industrial  Research or production instruments, reagents, or data  Some companies sell their services rather than product  Example: 23 and Me23 and Me  See figure 1.13

20.  Research & Development : refers to the early stages of product development that includes discovery of the structure and function of a potential product and the initial small scale production  Quality Control is a measure of precision or how well the measurement system reproduces the same result over time and under varying operating conditions

21.  National Institute of Health (NIH): the federal agency that funds and conducts biomedical research  Centers for Disease Control & Prevention (CDC): National research center for developing and applying disease prevention control, environmental health, and health promotion and educationactivities to promote public health

22.  By the 1970’s scientists had developed new methods including the use of restriction enzymes and DNA ligase to create new combinations of genetic information, or rDNA  rDNA can be inserted into cells giving these cells a new genotype phenotype  Organisms containing these modified cells are called Genetically Modified Organisms (GMOs)

23.  GMO’s contain DNA from another organism and will produce the new proteins encoded in the acquired DNA  The 1 st GMO’s to produce a human protein were Escherichia coli ( E. coli ) bacteria  E. coli bacteria are the work horse of molecular biology, no other bacteria is used as frequently as this one

24.  Were given pieces of human DNA (genes) containing instructions to produce a human growth hormone called somatostatin  The somatostatin gene was carried into the E. coli cells on tiny pieces of bacterial DNA called Plasmids  These recombinant DNA plasmids contained both bacterial and human DNA  The E. coli cells read the human DNA and produced the human protein somatostatin, which could then be harvested and purified for use

25.  One of the 1 st genetically engineered products to be sold was t-PA  t-PA is a blood clot dissolving enzyme that can be used immediately after a heart attack to clear blocked blood vessels  The body produces only small amounts of t-PA  To produce enough t-PA for therapeutic use scientists genetically engineered mammalian cells using Chinese Hamster Ovary (CHO) cells

26.  Ovary cells are grown in culture and engineered with the gene that provides the instructions to make the t-PA enzyme  By subjecting the cells to the right conditions, the CHO cells accept and incorporate the foreign DNA and begin the process of transcription and translation  Large amounts of t-PA can then be extracted and purified  See figure 1.18

27.  Applications of rDNA and genetic engineering have resulted in the creation of hundreds of Biotech companies, specializing in all kinds of GMOs and their protein products including  Proteins used in pregnancy tests  Enzymes that increase the amount of juice that can be extracted from an apple  Molecules used in vaccines  In 2004 there were already over 370 drug products created from rDNA techniques undergoing clinical trials  Strawberry plants that can grow in freezing weather

29.  Biotechnological advances will enable patients to submit tissue samples and receive a treatment regimen designed specifically for them. This is calle Personalized medicine, or pharmacogenomics  pharmacogenomics: pharmaceuticals based on genomics  Present research based on broad characteristics such as ethnicity, gender, and family history has already been performed and treatments have been modofied accordingly

30.  The human genome project was an international effort to sequence and map all the DNA on the 23 pairs of human chromosomes  We know the sequence of the human genome, but we still do not know  all of the sequences that code for proteins  For the ones we do know about, we don’t completely understand how, when, and where they are turned on or off  This is called differential gene expression  DNA intro DNA intro

31.  As sequencing human genomes becomes more cost effective, there will come a time when drug regimen is determined by the genotype of the patient or the tumor being targeted  One of the 1 st drugs to accomplish this is the drug Herceptin which will only target breast cancer cells that produce too much of the protein HER2  The decision to administer Herceptin as part of the chemotherapy regimen is based on a single gene

32.  Some drugs, like chemotherapeutic agents, have serious side effects because they treat the whole organism and not just the diseased tissue  Advances in biotechnology have enabled the development of therapies that can be delivered directly to diseased tissue and greatly reduce side effects  Rexin-G: a drug that targets pancreatic cancer is delivered by a genetically engineered viral particle that is designed to seek out and kill metastasized cancer cells is in clinical trials now

33.  Research & Development  No matter what the product, the goal is to make it and market it as quickly as possible  The R&D phase for a new pharmaceutical often takes from 10-15 years for a company to move a product through the “pipeline”

34.  A drug must demonstrate “proof of concept” data in the research phase before being allowed to move to the development phase, including  Is it feasible to manufacture in amounts sufficient to treat people  What needs to be done to ensure safety  What characteristics indicate it will be effective  And unfortunately, what is the profit margin  This is accomplished with a Product development Plan

35.  Does the product meet the following criteria  Does the product meet a critical need?  Is there a market large and wealthy enough to produce enough sales  Does preliminary data support that the product will work?  Can patent protection be secured  Can the company make a profit?  Each product in a pipeline will be reviewed regularly and dropped from production if the answers to these questions are unsatisfactory  See figure 1.21

36.  Projects then enter clinical development  Testing is done small scale before large scale production is pursued  All pharmaceuticals have to undergo at least 3 rounds of strict clinical trials under the guidance of the FDA before being marketed  Example: Pulmozyme is manufactured by Genentech Inc and is an enzyme used to treat patients with Cystic Fibrosis  People with CF experience a build up of mucus in the lungs and intestines and is often fatal by the age 30  Pulmozyme reduces the amount of mucus produced In 2003 Pulmozyme had sales of $167million

37.  All biotechnology products have regulations governing their production in the product pipeline  Environmental Protection Agency (EPA)  The federal agency that enforces environmental laws including the production and use of microorganisms, herbicides, pesticides, and GMOs  United States Department of Agriculture (USDA)  Federal agency that regulates the use and production of plants, plant products, plant pests, veterinary supplies and medications, and genetically modified plants and animals

38.  Being able to distinguish between right and wrong and to make decisions based on that knowledge is considered having good morals  Problem: not all people have the same list of right and wrong, and so we often have different morals  Example: Vegans don’t eat or use any animal products, and many consider it immoral to do so  Fact: most people eat and use animal products on a daily basis without any qualms Also Fact: those same people that don’t have any problem eating meat and using animal products would be horrified to think of going home and cooking their pet dog Sparky or their new kitten Mittens for dinner

39.  The study of moral standards and how they effect conduct is called ethics  Bioethics is a term that has been coined to describe the study of decision making as it applies to moral decisions that need to be made because of advances in biology, medicine, and technology

40.  Many of the new biotechnologies are controversial because they force people to think about what they believe is right or wrong  Examples:  Harvesting and manipulating embryonic stem cells  It kills the human embryo  Genetically modifying food  Are they really safe to eat  Prenatal genetic testing/ engineering  Playing God

41.  New technologies generate ethical questions  The positions one takes on ethical issues are based on how you feel about the knowledge and understanding you have of a subject  There is often not a clear right or wrong answer  Most of the time you have to make a choice between the lesser of 2 evils  So how do we decide what’s “right” But sometimes people are!

42.  Identify and understand the problem or issue.  List all the possible solutions to the issue  Identify the pros and cons of each of the solutions  Consider legal, financial, medical, personal, social, and environmental aspects  Based on the pros and cons for each solution, rank all the solutions from best to worst  Decide if the problem is important enough to take a position. If it is, decide your position and be prepared to describe and defend it

43.  There is no 1 correct scientific method  The scientific method is really just a series of common sense steps and techniques that scientists use to solve a problem or answer a question  There are several practices used by most scientists when conducting experimental research

44.  State a testable scientific question or problem based on some information or observation  Develop a testable hypothesis  Plan a valid experiment  Multiple replicates  Control groups  Conduct the outlined experiment and collect and organize data  Formulate conclusions based on experimental data and error analysis

45. POSITIVE CONTROLSNEGATIVE CONTROLS  A group that will give a predictable positive result  A group that will give a predictable negative result

46.  A good approach to writing an experimental conclusion is to use the REE/PE/PA method  REE: Results with Evidence and Explanation  PE: Possible Errors  Identify the sources of expreimental design errors that would or could lead to false or misleading data, and explain possible implications from such errors  PA: Practical Applications:  discuss the meaning or value of experimental results in the short and long term.  Identify how the findings could be valuable clinically, to the company, or to the community  Identify the direction the experiment will go take from here

47.  Biotechnology: The study and manipulation of living things or their component molecules, cells, tissues, or organs  Product Domains  Pharmaceutical  Agricultural  Industrial  Research or production instruments, reagents, or data

48.  Identify a gene of interest  Treat gene of interest and plasmid vectors with a restriction enzyme  Use DNA ligase to glue gene of interest to plasmid  Insert plasmid into host organism (plant, animal, or bacteria) through various mechanisms  The rDNA will be used by the host organism to produce the new protein of interest

49.  Come up with an Idea  Research and Development  Proof of Concept through a Product Development Plan  Will it work  Is there a market for it  Can we make it in sufficient quantities  Large Scale Production  Clinical Trials  FDA approval

50.  NIH: the federal agency that funds and conducts biomedical research  CDC: National research center for developing and applying disease prevention control, environmental health, and health promotion and education activities to promote public health  EPA: The federal agency that enforces environmental laws including the production and use of microorganisms, herbicides, pesticides, and GMOs  USDA: Federal agency that regulates the use and production of plants, plant products, plant pests, veterinary supplies and medications, and genetically modified plants and animals

51.  Identify /understand the issue  List all the possible solutions  Identify the pros and cons of each considering  legal  financial,  Medica  personal  Social  environmental aspects  Rank solutions from best to worst  Decide and defend your position

52.  T-PA  Human insulin  Strawberry plants that can grow in freezing weather  Pulmozyme