The Fundamentals of Scientific Research: An Introductory Laboratory Manual

The Fundamentals of Scientific Research: An Introductory Laboratory Manual is a laboratory manual geared toward first–semester undergraduates enrolled in general biology courses focusing on cell biology. This laboratory curriculum centers on studying a single organism throughout the entire semester Serratia marcescens or S. marcescens a bacterium unique in its production of the red pigment prodigiosin.

The manual separates the laboratory course into three separate modules. The first two modules familiarizes students with the organism and lab equipment by performing growth curves, Lowry protein assays, quantifying prodigiosin and ATP production, and by performing complementation studies to understand the biochemical pathways responsible for prodigiosin production. Students learn how to use Microsoft Excel to prepare and present data in graphical format and how to calculate their data into meaningful numbers that can be compared across experiments. The third module requires that the students employ UV mutagenesis to generate hyper–pigmented mutants of S. marcescens for further characterization. Students use experimental data and protocols learned in the first module to help them develop their own hypotheses and experimental protocols, and to analyze their own data.

Before each laboratory, students are required to answer questions designed to probe their understanding of required pre–laboratory reading materials. Questions also guide the students through the development of hypotheses and predictions. Following each laboratory, students then answer a series of post–laboratory questions to guide them through the presentation and analysis of their data, and how to place their data into the context of primary literature. Students are also asked to review their initial hypotheses and predictions to determine if their conclusions are supportive. A formal laboratory report is also to be completed after each module, in a format similar to that of primary scientific literature.

The Fundamentals of Scientific Research: An Introductory Laboratory Manual is an invaluable resource to undergraduates majoring in the life sciences.

Text focuses on one organism, S. marcescens, throughout the semester with a focused goal: to enhance the organism s production of prodigiosin

Teaches students how to use laboratory equipment correctly and effectively

Follows structure of laboratory curriculum similar to professional research environment

Prompts first–year undergraduates to read, evaluate, and use their own data in the context of primary scientific literature

Preface xi

Acknowledgments xv

About the Companion Website xvii

Introduction xix

Module 1 Working with and Learning About Common Laboratory Techniques and Equipment 1

Exercise 1A Using Common Laboratory Tools to Evaluate Measurements Pre–laboratory Thinking Questions 3

Exercise 1B Using Common Laboratory Tools to Evaluate Measurements 4

Exercise 1C Using Common Laboratory Tools to Evaluate Measurements Post–laboratory Thinking Questions 18

Exercise 2A Using Microscopy to Evaluate Cell Size and Complexity Pre–laboratory Thinking Questions 19

Exercise 2B Using Microscopy to Evaluate Cell Size and Complexity 20

Exercise 2C Using Microscopy to Evaluate Cell Size and Complexity Post–laboratory Thinking Questions 32

Exercise 3A The Bacterial Growth Curve Pre–laboratory Thinking Questions 35

Exercise 3B The Bacterial Growth Curve 36

Exercise 3C The Bacterial Growth Curve Post–laboratory Thinking Questions 55

Module 2 Working with and Learning About Serratia marcescens in the Laboratory 57

Exercise 4A Protein Concentration Versus Growth Stage Pre–laboratory Thinking Questions 59

Exercise 4B Protein Concentration Versus Growth Stage 60

Exercise 4C Protein Concentration Versus Growth Stage Post–laboratory Thinking Questions 69

Exercise 5A Measuring Prodigiosin Pre–laboratory Thinking Questions 71

Exercise 5B Measuring Prodigiosin 72

Exercise 5C Measuring Prodigiosin Post–laboratory Thinking Questions 84

Exercise 6A Conditions Affecting the Growth of and Prodigiosin Production by Serratia marcescens Pre–laboratory Thinking Questions 87

Exercise 6B Conditions Affecting the Growth of and Prodigiosin Production by S. marcescens 91

Exercise 6C Formal Laboratory Report Describing the Conditions Affecting the Growth of and Prodigiosin Production by S. marcescens 95

Exercise 7A Biochemistry of Prodigiosin Production Pre–laboratory Thinking Questions 101

Exercise 7B Biochemistry of Prodigiosin Production 102

Exercise 7C Biochemistry of Prodigiosin Production Post–laboratory Thinking Questions 112

Exercise 8A The Probability Basis for Mutation Rate Calculation: A Dice ]Roll Exercise Pre–laboratory Thinking Questions 113

Exercise 8B The Probability Basis for Mutation Rate Calculation: A Dice ]Roll Exercise 114

Exercise 8C The Probability Basis for Mutation Rate Calculation: A Dice ]Roll Exercise Post–laboratory Thinking Questions 120

Exercise 9A Understanding Evolution by the Generation of UV Light ]Induced Prodigiosin Mutants Pre–laboratory Thinking Questions 121

Exercise 9B Understanding Evolution by the Generation of UV Light ]Induced Prodigiosin Mutants 122

Exercise 9C Understanding Evolution by the Generation of UV Light ]Induced Prodigiosin Mutants Post–laboratory Thinking Questions 131

Exercise 10A Understanding the Energy Spilling Properties of Prodigiosin Pre–laboratory Thinking Questions 137

Exercise 10B Understanding the Energy Spilling Properties of Prodigiosin 139

Exercise 10C Understanding the Energy Spilling Properties of Prodigiosin Post–laboratory Thinking Questions 146

Module 3 Initial Characterization of Novel Serratia marcescens Prodigiosin Mutants 147

Exercise 11A Prodigiosin Mutant Study Part 1 Pre–laboratory Thinking Questions 149

Exercise 11B Prodigiosin Mutant Study Part 1 150

Exercise 11C Prodigiosin Mutant Study Part 1 Post–laboratory Thinking Questions 153

Exercise 12A Prodigiosin Mutant Study Part 2 Pre–laboratory Thinking Questions 155

Exercise 12B Prodigiosin Mutant Study Part 2 156

Exercise 12C Formal Laboratory Report 2: Prodigiosin Mutant Study 158

Appendix A CSE Citation and Reference List Format Guidelines 163

Appendix B Prodigiosin Biosynthesis 165

References 167

Index 169

Marcy A. Kelly is Professor and Assistant Chair of the Department of Biology at Pace
University in New York, NY, USA.

Pryce L. Haddix is an Associate Professor of Biology at Auburn University in Montgomery,
AL, USA.