Unit 1

1. Biotechnology and Microbiology Unit 1

2. Definition Biotechnology • Biotechnology is broadly defined as the science of using living organisms or the products of living organisms for the benefit of humans and their surroundings.

3. Biotechnology The Biotechnology Revolution - NOVA • http://www.youtube.com/watch?v=bukTqyWgaM8

4. Lesson 1 • Lecture and Discussion: Introduction to classical and modern biotechnology, interdisciplinary nature of biotechnology, and ethics in biology. • Assessment: Create a concept map from lecture.

5. History of Biotechnology • What is the difference between • classical biotechnology • and modern biotechnology?

6. Classical biotechnology • Our ancient ancestors used two classic biotechnology techniques: • Fermentation – use of microorganisms to make food and beverages. • Selective Breeding – breeding of animals and plants with desirable traits.

7. Fermentation • Do you remember this? • http://people.cst.cmich.edu/schul1te/animations/fermentation.swf

8. Fermentation • Actual existence of micro-organisms and their role in contaminating food are recent discoveries, dating back 200 years ago. • Bread baking - Earliest breads were unleavened (pita bread). - Fermented dough probably discovered by accident. - Egyptians and Romans both used fermented dough to make a lighter, leavened bread.

9. Fermentation • Lactic Acid and Acetic Acid Fermentation • 5,000 BC, milk curd to make cheese was made in Mesopotamia. • By 4,000 BC, Chinese used fermentation to make yogurt, cheese, and vinegar.

10. Fermentation • Beverages • Beer Making - Egyptians probably began beer making around 6,000 BC. - Babylonians used barley to make beer. - Brewing became an art form by the 14th century AD. • Wine making - Originated in valley of the Tigris River, date unknown. - First made by accident with grapes contaminated by yeast. - Egyptians, Greeks, and Romans made wine.

11. Selective Breeding • About 10,000 years ago, people established agrarian societies. • Origins of biotechnology date back to this time. • People settled and began domesticating both animals and plants. • Both animals and plants, were artificially selected for valuable traits.

12. Selective Breeding • Animals - Babylonians, Egyptians, and Romans selectively bred livestock. - Romans have left written descriptions of their livestock selective breeding practices. - British white cattle (on right) can trace its ancestry back to the Roman empire.

13. Selective Breeding • Plants - Superior seeds, cuttings, and tubers have been selected for thousands of years to save for the next planting. - Sumarians, Egyptians, and Romans collected and traded superior seeds and plants. - (On right) Evolutionary changes in corn from 5,000 BC to 1,500 AD in Mexico.

14. Modern Biotechnology • Advances in genetics and molecular biology have led to innovations and new applications in biotechnology. • Classical biotechnology took advantage of natural microbial processes or artificially selected phenotypes. Genetics of these selected organisms proceeded naturally. • Modern biotechnology uses - Genetic Engineering - Gene Cloning

15. Modern Biotechnology • Genetic Engineering - Ability to manipulate DNA of an organism. Manipulation due to Recombinant DNA Technology. Recombinant DNA technology combines DNA from different sources. • Gene Cloning – The ability to identify and reproduce a gene of interest.

16. Modern Biotechnology • Recombinant DNA technology has dominated modern biotechnology. Has led to: - Production of disease resistant plants. - Genetically engineered bacteria to degrade environmental pollutants and to produce antibiotics. • Gene cloning and recombinant DNA technology have impacted human health through the Human Genome Project.

17. Discussion questions • What are the differences between classical and modern biotechnology? Be sure to discuss the processes involved • Discuss the differences with a partner. • Class discussion will follow.

18. Biotechnology – A science of many disciplines • What disciplines contribute to the science of biotechnology?

19. Biotechnology – A science of many disciplines. • The roots of biotechnology are formed by: - Human, animal, and plant physiology - Mathematics - Molecular and cell biology - Immunology - Statistics - Microbiology - Biochemistry - Genetics - Physics - Chemical Engineering - Computer Science

20. Biotechnology- A science of many disciplines • The “root” subjects pieced together can lead to genetic engineering approached with applications in: - Drug development - Environmental and Aquatic Biotechnology - Agricultural Biotechnology - Forensics and Detection - Medical Biotechnology - Regulatory Approval and Oversight.

21. Biotechnology – A science of many disciplines • A typical example of interdisciplinary nature of biotechnology. - Scientific microbiology research discovers a gene or gene product of interest. - Biochemical, molecular, and genetic techniques are used to determine the role of the gene. - Bioinformatics (computer data bases) are used to study gene sequence or analyze protein structure. - Gene then used in a biotechnology application.

22. Ethics in Biotechnology • What are the ethical concerns in biotechnology?

23. Ethics in Biotechnology • Powerful applications and potential promise of biotechnology raises ethical concerns. • Not everyone is a fan of biotechnology. • The wide range of legal, social, and ethical issues are cause for debate and discussion among scientists, the general public, clergy, politicians, lawyers, and many others. • Some questions of concern: - Should human cloning be permitted? - Will genetically modified foods be harmful to the environment? - Should we permit the development of synthetic genomes?

24. Ethics in Biology • We will be looking at and discussing some of the ethical concerns in biotechnology. • Our goal is not to tell you what to think but to empower you with the knowledge you can use to make your own wise decisions.

25. Discussion questions • What is a typical example of biotechnology as an interdisciplinary science? • What is bioinformatics? • What is our goal with respect to making ethical decisions about biotechnology?

26. Create a Concept Map • Read how to create a concept map. • http://www.libraries.psu.edu/psul/lls/students/research_resources/conceptmap.html • Create a concept map which incorporates the following terms: Agricultural biotechnology Animal Applications Beverage making Biochemistry Bioinformatics Biotechnology Bread making Classical biotechnology Computer Science DNA recombinant technology Drug development Environmental biotechnology Ethical Fermentation Forensics Gene cloning Genetic engineering Immunology Interdisciplinary science Issues in biotechnology Lactic/acetic acid fermentation Legal Medical biotechnology Microbiology Molecular biology Plant Root sciences Selective breeding Social

27. Lesson 2 • Case Study : A Glimpse into the Futre • Start by viewing the video: http://bigthink.com/ideas/16344 • Read case study: “ A Glimpse into the Future,” by Lee Silver a molecular biologist at Princeton University. • Work in groups of 4 students and discuss the focus questions: What arguments does Silver give for thinking that human genetic enhancement be regarded as morally permissible? What arguments are used by opponents of genetic enhancement? • Complete: Student self and group evaluation of group participation • Whole class discussion: How we make ethical decisions, as well as any points of clarification needed by students. • Write an individual persuasive 5 paragraph essay supporting your opinion on use of genetic enhancement.

28. Lesson 2 – Work Groups Term 1

29. A Framework for Ethical Decisions 1. Recognize an Ethical Issue • Could this decision or situation be damaging to someone or to some group? Does this decision involve a choice between a good and bad alternative, or perhaps between two "goods" or between two "bads"? • Is this issue about more than what is legal or what is most efficient? If so, how?

30. A Framework for Ethical Decisions 2. Get the Facts • What are the relevant facts of the case? What facts are not known? Can I learn more about the situation? Do I know enough to make a decision? • What individuals and groups have an important stake in the outcome? Are some concerns more important? Why? • What are the options for acting? Have all the relevant persons and groups been consulted? Have I identified creative options?

31. A Framework for Ethical Decisions 3. Evaluate Alternative Actions • Evaluate the options by asking the following questions: • Which option will produce the most good and do the least harm? (The Utilitarian Approach) • Which option best respects the rights of all who have a stake? (The Rights Approach) • Which option treats people equally or proportionately? (The Justice Approach) • Which option best serves the community as a whole, not just some members? (The Common Good Approach) • Which option leads me to act as the sort of person I want to be? (The Virtue Approach)

32. A Framework for Ethical Decisions 4. Make a Decision and Test It • Considering all these approaches, which option best addresses the situation? • If I told someone I respect-or told a television audience-which option I have chosen, what would they say?

33. A Framework for Ethical Decisions 5. Act and Reflect on the Outcome • How can my decision be implemented with the greatest care and attention to the concerns of all stakeholders? • How did my decision turn out and what have I learned from this specific situation?

34. Lesson 3 • Individually read the Powerpoint slides for lesson 3 and respond to the questions. • Create 7 groups. • Each group will be assigned one of the following topics and a corresponding article: 1. Microbial Biotechnology 2. Agricultural Biotechnology 3. Animal Biotechnology 4. Forensic Biotechnology 5. Bioremediation 6. Marine Biotechnology 7. Medical Biotechnology • Read the article and work together to create an accurate summary of the article • One member from each group will then present their assigned section of the powerpoint and provide a summary of their article. Write your article title on the whiteboard.

35. Microbial Biotechnology • Microbes have been used in many ways that affect society. • Manipulating microbial DNA has created organisms that manufacture food. • Manipulated microbes are used to make - enzymes - vaccines - antibiotics - insulin and growth hormones - detectors for bioterrorism - decontamination processes for industrial waste.

36. Agricultural Biotechnology • Plants have been bioengineered for - Drought resistance - Cold tolerance - Pest resistance - Greater food yield • Plants have been used for molecular pharming. Plants are bioengineered to produce recombinant proteins. • Downside: Gene transfer from engineered plants to non- target plants in the environment has produced some super weeds.

37. Animal Biotechnology • Goats, cattle, sheep, and chickens are being used to produce antibodies and other medically needed proteins. • Transgenic animals become bioreactors. They contain genes from another sources and produce these proteins in their milk. • Animals are used in “knockout” experiments. Genes are disrupted and much is learned about gene function. • Many animals have been cloned; possible uses for using cloned animals for genetically engineered organs have been explored.

38. Forensic Biotechnology • DNA fingerprinting, methods to detect unique DNA patterns are being used in: - Law enforcement - Paternity testing - Poaching of endangered species - Tracking AIDS, Lyme disease, West Nile virus, TB. - Testing of food products to see if food substitutes are being used.

39. Bioremediation • Microbial processes are used to degrade natural and man made substances. • Bioremediation is used in the clean up of massive oil spills; cleans up shorelines three times faster than traditional clean up methods.

40. Marine Biotechnology • Aquaculture – raising fish or shellfish in controlled conditions to use as food sources. - Genetically engineered disease resistant oysters - Vaccine against viruses that infect fish - Transgenic salmon injected with growth hormone that have extraordinary growth rates. • Bioprospecting – Identifying marine organisms with novel properties to exploit for commercial purposes. Ex. Snails are a rich source of anti-tumor molecules.

41. Medical Biotechnology • New drugs and vaccines have been developed. • Human Genome Project is helping to identify defective genes and in the creation of new genetic tests. • Gene Therapy – Inserting normal genes into a patient to replace defective ones. • Stem Cell Technology – Possible use in the development of new tissues to replaced damaged tissues.

42. Lesson 4 • View the video “Microbial Evolution” and respond to student worksheet • Lecture: Species Concept and Evolutionary Domains. Response to questions. • Lecture: Phenotypic Classifcation. Complete Powerpoint review of lecture • At the end of the lesson, write for 2 minutes about what you learned in Lesson 4.

43. Microbial evolution • http://www.youtube.com/watch?v=XawzIjX72U0 • http://www.youtube.com/watch?v=YPgxEl9jzRU&feature=relmfu • http://www.youtube.com/watch?v=aF5sLLLalm8&feature=relmfu • http://www.youtube.com/watch?v=vghlsa7oD_8&feature=relmfu • 4 parts of video

44. Lesson 4 • What is a species? • A species is defined as a population that can naturally interbreed and produce fertile offspring, and that is reproductively isolated from other species. • Right! • Well, maybe not……..

45. Species Concept - Microbiology • A bacterial species is a prokaryote whose 16S ribosomal RNA sequence differs by no more that 3%. • http://www.microbeworld.org/careers/tools-of-the-trade/genetic-tools-and-techniques/16s-rrna • That is, at least 97% of the rRNA sequence is identical in a bacterial species. • A bacteria whose rRNA differs by more than 3% usually turns out to be a different species.

46. Species Concept- Microbiology • Prokaryotes do not fit the biological species concept because they are haploid and reproduce asexually. • They cannot produce “fertile offspring” like plants and animals can. • In microbiology, evolutionary (molecular)chronometers measure evolutionary change. • In other words, differences in nucleotide or amino acid sequences of functionally similar (homologous) macromolecules are a function of their evolutionary distance. • The greater the number of differences in a sequence the more distantly related the two species are.

47. Species Concept - Microbiology • Molecular Chronometers • The chronometer must be present in all groups being classified and it must be functionally homologous (not many sequence differences). • The following genes and proteins are most frequently used to classify bacteria. - ribosomal RNA - ATPase proteins (synthesize ATP)  - RecA (enzyme facilitates genetic recombination) - Certain translation proteins.

48. Species Concept- Microbiology • Ribosomal RNA is the most widely used chronometer for identifying bacterial species : - It is relatively large. - Universally distributed - Has many nucleotide sequences that are conserved. • 16S rRNA are part of the small subunit (SSU) of the ribosome; used to classify prokaryotes.

49. Evolutionary Tree - Microbiology Phylogenetic Tree of Life - rRNA

50. Three Domains - Microbiology • Bacteria • At least 40 phyla of bacteria in this domain. • Most of the phyla are related from a phylogenetic standpoint but have little in common in terms of phenotype. • Proteobacteria contain species which are the ancestors of mitochondria.