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Biol1414: Introduction to Biotechnology I

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Biol1414: Introduction to Biotechnology I BIOL1414: INTRODUCTION TO BIOTECHNOLOGY I Exercise Workbook & Lab Guide Dr. Jack O’Grady 2019-2020 Acknowledgments This manual could not have been possible without the dedication of the faculty, staff, and students of Austin Community College’s Biotechnology Program, in addition to our valuable educational partners, and numerous grants. Some lab material provided by the following educational partners: Bio-Link, Bio-Rad, Dolan Learning Center, and Edvotek. A special thank you to our amazing lab technicians Evelyn Apple and Jeremy Garza. Copyright This lab manual was created by Jack O’Grady. This manual can be openly shared and printed. Please send comments, derivatives, or corrections to [email protected]. The content in this lab manual is compiled from various open copyright, public domain, and commercial sources, which are all cited within, and maybe copyright protected. Funding This material was developed with the assistance of the following grants: 1. Sabbatical Funding (2018-19), Austin Community College 2. Bio-link award number 9850325 (2014-2016), 1400721 (2013), 0903317 (2010) 3. Texas Education Agency (2004-2015) 4. National Science Foundation, Award Number 0053296 (2004-2006) Table of Contents LAB UNIT 1: INTRODUCTION TO BIOL1414 ..................................................................................... 1 LAB UNIT 2: ESSENTIAL TOOLS IN THE BIOTECHNOLOGY LABORATORY ....................................... 19 LAB UNIT 3: PREPARING SOLUTIONS ............................................................................................. 35 LAB UNIT 4: DNA BARCODING – ISOLATING GENOMIC DNA ........................................................ 51 LAB UNIT 5: DNA BARCODING – PCR AMPLIFICATION .................................................................. 77 LAB UNIT 6: DNA BARCODING - SEQUENCING & BIOINFORMATICS ............................................. 89 LAB UNIT 7: PCR-BASED VNTR ANALYSIS OF HUMAN DNA ........................................................... 97 LAB UNIT 8: RECOMBINANT DNA TECHNOLOGY ......................................................................... 105 LAB UNIT 9: PLASMID DNA ISOLATION ........................................................................................ 129 LAB UNIT 10: RESTRICTION ENZYME DIGEST .............................................................................. 139 LAB UNIT 11: COLUMN CHROMATOGRAPHY .............................................................................. 147 LAB UNIT 12: POLYACRYLAMIDE GEL ELECTROPHORESIS ........................................................... 157 LAB UNIT 13: ENZYME-LINKED IMMUNOSORBENT ASSAY (ELISA) .............................................. 169 LAB UNIT 14: PREPARING FOR A CAREER IN BIOTECHNOLOGY .................................................. 183 APPENDIX .................................................................................................................................... 191 BIOL1414: Laboratory Report Rubric ....................................................................................... 193 Employability Skills Evaluation Form ........................................................................................ 195 Solution Preparation Form ....................................................................................................... 197 SOP Template ........................................................................................................................... 199 LAB UNIT 1: INTRODUCTION TO BIOL1414 J. O’Grady, EdD., L. Fletcher, Ph.D., A. Wheeler, M.S., & P. Phelps, Ph.D. OBJECTIVES In this lab activity, students will: ✓ Describe biotechnology ✓ Identify potential careers in biotechnology ✓ Create a lab notebook to use throughout the semester ✓ Learn proper PPE and lab policies expected during every lab class ✓ Complete lab-specific safety and security training ✓ Locate safety equipment & laboratory instruments that will be used throughout the semester Welcome to your first course in biotechnology! What an exciting time to learn about biotechnology! Whether you are taking this course for general interest or you want to obtain a job working in a biotechnology lab, this course is designed to provide you with a foundation of biotechnology skills. Throughout this course, students will: ✓ Discover the field of biotechnology, and potential careers in the biosciences ✓ Learn basic laboratory techniques of a biotechnology or bioscience lab ✓ Develop skills in using basic biosciences laboratory equipment ✓ Cultivate critical thinking skills ✓ Encourage teamwork, accountability, and taking charge of your learning ✓ Practice accuracy in calculations, performing experiments, and in writing scientifically ✓ Learn how to work in a regulated bioscience work environment This workbook is designed to provide students with an active learning discovery experience. Please bring it to every class. It will guide you through the course and tie in concepts between the lecture and laboratory. Before every class, students may be asked to read a chapter from the textbook, research information online, watch a video or animation, or complete quiz exercises. It is important to follow the syllabus schedule to plan and complete assigned activities. In this first lab unit, students will begin exploring the field of biotechnology and become acquainted with lab organization, policies, and safety training. Before working in an ACC laboratory, students must first: 1. View the ACC Science Safety video. 2. Review safety policies and procedures. 3. Tour the laboratory with the instructor and locate emergency equipment. 4. Sign a safety contract, by which students agree to comply with safety regulations. We hope that you enjoy your experience in this introductory course. The following is a discussion of biotechnology and a description of some of the activities that you may be performing this semester! J. O’GRADY, 2019-20 BIOL1414: INTRODUCTION TO BIOTECHNOLOGY I 1 | P a g e PART I: WHAT IS BIOTECHNOLOGY? Strictly speaking, biotechnology is the use of a living organism to create a useful product. By this definition, biotechnology would date back to the very beginnings of civilization, when humankind first learned to cultivate crops and domesticate animals in a system of agriculture. When one thinks of modern biotechnology, however, DNA manipulation and pharmaceutical products take center stage. The modern biotechnology revolution came when scientists first learned how to isolate and clone genes, allowing for genetic engineering in the 1970s. However, today, the biotechnology industry has grown and expanded to improve and enrich our daily lives. Below is an excerpt from Bio.org discussing the ever-expanding applications of biotechnology in healthcare, agriculture, and energy (http://www.bio.org). Biotechnology: Healing, Fueling, and Feeding the World (bio.org, 2014) At its simplest, biotechnology is technology based on biology - biotechnology harnesses cellular and biomolecular processes to develop technologies and products that help improve our lives and the health of our planet. We have used the biological processes of microorganisms for more than 6,000 years to make useful food products, such as bread and cheese, and to preserve dairy products. Modern biotechnology provides breakthrough products and technologies to combat debilitating and rare diseases, reduce our environmental footprint, feed the hungry, and use cleaner (and less!) energy, and have safer, cleaner and more efficient industrial manufacturing processes. Currently, there are more than 250 biotechnology healthcare products and vaccines available to patients, many for previously untreatable diseases. More than 13.3 million farmers around the world use agricultural biotechnology to increase yields, prevent damage from insects and pests, and reduce farming's impact on the environment. Moreover, more than 50 biorefineries are being built across North America to test and refine technologies to produce biofuels and chemicals from renewable biomass, which can help reduce greenhouse gas emissions. Recent advances in biotechnology are helping us prepare for and meet society’s most pressing challenges. Let’s Explore! Watch this! New approaches to Biotechnology: 3D Bio-Printing video https://youtu.be/peeWHtYsmdM In your own words, what is 3D Bioprinting? Figure 1-1: 3-D Bio-printing a human ear J. O’GRADY, 2019-20 BIOL1414: INTRODUCTION TO BIOTECHNOLOGY I 2 | P a g e TEST YOUR KNOWLEDGE! WHAT IS BIOTECHNOLOGY? 1. In your own words define Biotechnology: 2. Can you think of a biotechnology product that has improved your life? What do you think your life would be like without this product? What makes it a biotechnology product? Modern Biotechnology The modern definition of Biotechnology usually means the manipulation of DNA to create useful products. Deoxyribonucleic acid (DNA) is the carrier of genetic information in our cells. During this course, you will learn to isolate and manipulate DNA from several different organisms, including your own! Let’s try it out! Extract your own DNA! You can easily isolate DNA from your cheek cell using common materials found at home. Follow the instructions here on this website (Nova). Your instructor may have these materials for you in the lab today or may ask you to try it at home! http://www.planet-science.com/categories/experiments/biology/2012/03/extract-your-own-dna.aspx What you need: 500ml bottled water 2 x clear plastic cups or glasses Dish soap 1 tbsp. table salt (3 salt packets)
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