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Small World Initiative: Research Protocols and Research Guide to Microbial and Chemical Diversity Package
- Research Protocols print (Paperback: 66 pages) and eBook access
- Research Guide print (Paperback: 116 pages) and eBook access
Package ISBN: 978-1-50669-699-7
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About the Book
This guide is part of the official materials used in the Small World Initiative™ (SWI). Formulated at Yale University in 2012 by the author, Dr. Jo Handelsman, SWI is an innovative program that inspires and retains students in the sciences while addressing a worldwide health threat—the diminishing supply of effective antibiotics. SWI centers around a discovery-based introductory biology course in which students from around the world perform hands-on field and laboratory research on soil samples in the hunt for new antibiotics. This is particularly relevant since over two thirds of antibiotics originate from soil bacteria or fungi.
Differentiating itself from traditional courses, SWI’s biology course provides original research opportunities rather than relying on cookbook experiments with predetermined results. Through a series of student-driven experiments, students collect soil samples, isolate diverse bacteria, test their bacteria against clinically relevant microorganisms, and characterize those showing inhibitory activity. SWI’s approach also provides a platform to crowdsource antibiotic discovery by tapping into the intellectual power of many student researchers concurrently addressing a global challenge and advances promising candidates into the drug development pipeline. This unique class approach harnesses the power of active learning to achieve both educational and scientific goals.
About the Authors
Over the past four years, SWI has grown rapidly to include 167 participating schools across 35 U.S. states, Puerto Rico, and 12 countries. The program seeks to inspire the next generation of Partner Instructors and collaborators who will pledge to further SWI’s mission to transform science education and promote antibiotic discovery through the curiosity and creativity of young scientists around the world. SWI’s Partner Instructors are committed to making meaningful and measurable improvements in the education landscape and expanding opportunities for their students while addressing real-world health challenges.
If you are interested in learning more about the Small World Initiative, please visit www.smallworldinitiative.org.
Table of Contents
Lab Safety and Best Practices
Agarose Gel Electrophoresis
Aligning and Combining 16S rRNA Gene Sequences
Analyzing Organic Extracts for Antibiotic Production
Analyzing Sequences with BLAST Search
Antibiotic Resistance Test
MacConkey Agar Test
Making Glycerol Stocks
Obtaining Soil Sample
Picking and Patching Colonies
Plating Soil Sample
Screen for Isolate Antibiotic Production #1—Patch/Patch
Screen for Isolate Antibiotic Production #2—Spread/Patch
Screen for Isolate Antibiotic Production #3—Top Agar
Silica Column Chromatography Protocol
Sulfide and Indole Production and Motility
Thin Layer Chromatography (TLC)
Typical Media Menu
Small World Initiative™ Overview
Introduction: The Antibiotic Crisis
Section 1: Living on a Bacterial Planet: Experiment 1: Devise a method to transfer microbes from a soil sample to a medium in the lab
Section 2: More Than Just “Dirt:” Experiment 2: Find a local soil environment you wish to sample
Section 3: Redefining “Growth” and “Culture:” Experiment 3: Find a method to isolate single colonies of bacteria from your soil sample
Section 4: Bacteria Are What They Eat, Too: Experiment 4: Choose your own media and culture conditions
Section 5: Solid Versus Liquid Cultures: Experiment 5: Isolate unique colonies to test for antibiotic production
Section 6: Meet the ESKAPE Pathogens: Experiment 6: Understand the significance of the ESKAPE pathogens and using safe relatives in the lab
Section 7: Antibiotic Discovery, Structure, & Targets: Experiment 7: Design a method to screen for antibiotic producers
Section 8: Getting to Know Your Isolates: Experiment 8: Conduct initial identification of your antibiotic-producing isolate
Section 9: It All Comes Down to Chemistry: Experiment 9: Test an organic extract of your isolate for antibiotic activity
Section 10: Resisting Antibiotics: Experiment 10: Test your isolate’s resistance to common antibiotics
Section 11: “Classic” versus “Modern:” Experiment 11: Conduct biochemical characterization of your isolates
Section 12: Bacteria in Context: Experiment 12: Assess your isolate’s activity against eukaryotes, potential use as biological control, and ecological relationships with other organisms