Molecular Microbiology Laboratory

Front-matter_2013_Molecular-Microbiology-Laboratory
	MOLECULAR MICROBIOLOGY LABORATORY
Copyright_2013_Molecular-Microbiology-Laboratory
	Copyright
Introduction_2013_Molecular-Microbiology-Laboratory
	Introduction
		I Writing-Intensive Course
			A Goals
			B Means
		II Schedule
		III Attendance and Grading Policies
			A Attendance
			B Grading
			C Partial Credit
		IV Laboratory Rules
		V Decorum
		VI Flowcharts
			A How to Prepare a Flowchart
			B Sample Flowchart
		VII Laboratory Reports
			A Preparing a Laboratory Report
			B Sections of a Laboratory Report
		VIII How to Evaluate Laboratory Reports
			A Peer Review Checklist
			B Criteria for Grading Laboratory Reports
			C Checklist for Grading Laboratory Reports
		IX Proposals to Study Environmental Bacterial Populations: Writing Assignment (Class 6)
			A Overview
			B Site Selection
			C Peer Review of Proposals to Study Environmental Bacterial Populations
			D Instructions for Reviewing Proposals
				Written Reviews
				Panel Discussion
			E Proposal Review Forms
		X How to Read a Journal Article
			A Organization
			B Order in Which to Read an Article
			C Information Contained in Each Section
		XI Writing Tips
			A Begin Each Paragraph with a Topic Sentence
				Example 1
				Example 2
				Example 3
				Example 4
					Walt’s Version:
			B Write an Informative Title
			C Avoid Wordy Phrases and the Passive Voice
			D Avoid Jargon and Colloquial Wording
			E Avoid Pretentious Wording
			F Do Not Use Nouns as Adjectives
			G Revise Sentences That Do Not Make Sense
			H Place Modifiers Properly
			I Shorten Run-on Sentences
				Example 1
				Example 2
			J Convert Fragments into Complete Sentences
			K Follow Established Conventions
			L Use Which and That Correctly
				Example 1
				Example 2
			M Do Not End a Sentence with a Preposition
			N Use the Correct Homophone
			O Do Not Use the Same Word Twice in One Sentence
		Acknowledgments
Experiment-1---Plasmid-Purification-and-Restr_2013_Molecular-Microbiology-La
	Experiment 1 Plasmid Purification and Restriction Mapping
		I Introduction
		II Background: Plasmid DNA Preparation
			Micropipettor Technique
		III Procedure
			A Purify Plasmid pKN800 DNA (Class 2)
			B Restriction of Plasmid pKN800 (Class 2)
			C Agarose Gel Electrophoresis of PstI-Digested pKN800 (Class 3)
			D Transform E. coli Strain DH5α with pKN800 DNA (Class 3)
			E Observe Luciferase Reporter Gene Expression (Day after Class 3)
		IV Laboratory Report [Class 4 (Draft) and Class 5]
		V Questions (Class 5)
		VI In-Class Writing Exercise (Class 2)
		VII Restriction Mapping Exercises (Class 3)
		VIII In-Class Writing Exercise (Class 4)
Experiment-2---Affinity-Purification-of-Histidin_2013_Molecular-Microbiology
	Experiment 2 Affinity Purification of Histidine-Tagged FnbA Protein
		I Introduction
		II Background
		III Procedure
			A Lyse Bacteria (Class 5)
			B Adsorb Histadine-Tagged FnbA Protein to Nickel-Agarose (Class 5)
			C Wash Resin and Elute Histidine-Tagged FnbA Protein (Class 5)
			D SDS-Polyacrylamide Gel Electrophoresis (Class 6)
			E Stain Gel (Class 6)
		IV Laboratory Report
			A Draft (Class 8)
			B Questions (Class 9)
		V Critique of Paper by Bush et al.
Experiment-3---Polymerase-Chain-Reaction-and-DNA-Sequ_2013_Molecular-Microbi
	Experiment 3 Polymerase Chain Reaction and DNA Sequence Analysis of Bacterial Ribosomal RNA Genes
		I Introduction
		II Background
		III Procedure
			A Sample Collection for Experiments 3 and 4 (Class 7)
			B Gram Stain and Light Microscopy (Class 8)
			C Freeze Cultures (Class 9)
			D Purify Genomic DNA (Class 9)
			E PCR Amplification of 16S rRNA Genes (Class 10)
			F Purify PCR Product (Class 11)
			G Electrophoretic Analysis of PCR Product (Class 12)
			H DNA Sequence Analysis (Class 14)
		IV Laboratory Report [Class 16 (Draft) and Class 17]
		V Questions (Class 17)
		VI In-class writing exercise (class 10)
Experiment-4---Terminal-Restriction-Fragment-Length-Polym_2013_Molecular-Mic
	Experiment 4 Terminal Restriction Fragment Length Polymorphism Analysis of 16S Ribosomal RNA Genes from Uncultured Bacteria...
		I Introduction
		II Background
		III Procedure
			A Sample Collection for Experiments 3 and 4 (Class 7)
			B Extract DNA from an Uncultured Bacterial Community (Class 7)
			C PCR Amplification of 16S rRNA Genes for Terminal Restriction Fragment Length Polymorphism Analysis (Class 14)
			D Purify PCR Product (Class 15)
			E Ligate PCR Product to Plasmid: Topoisomerase-Mediated Cloning Reaction (Class 15)
			F Transform Ligated DNA (Class 15)
			G Electrophoretic and Spectrophotometric Analyses of PCR Product (Class 15)
			H Restrict Purified PCR Product (Class 16)
			I Plasmid DNA Purification (Class 16)
		IV Laboratory Report
		V Questions (Class 20)
		VI Writing Exercise: Editorial on Genetically Modified Crops [Class 14 (Draft) and Class 15]
		VII Writing Assignment: Literature Search Problem [Class 14 (Begin) and Class 20]
		VIII In-Class Writing Exercise (Class 15)
Appendix-A---Sample-Laboratory-Reports_2013_Molecular-Microbiology-Laborator
	Appendix A Sample Laboratory Reports
		Questions
	Questions
	Appendix A.A
		The additional DNA sequences of the plasmid DNA from T7 promoter primer
	Appendix A.B
		Lengths of the corresponding T-RFLP fragments for each enzyme (MspI and RsaI restriction enzymes) in the additional sequenc...
Appendix-B---Sample-Proposals_2013_Molecular-Microbiology-Laboratory
	An Outstanding Proposal
		Isolation of Antibiotic-Producing Streptomyces from Soil
	References
	A Poor Proposal
		Polution: Man made? Natural? A combination of both?
Appendix-C---Sample-Tests_2013_Molecular-Microbiology-Laboratory
	Appendix C Sample Tests
		Sample Test for This Book
			Question 1 (50 points)
			Question 2 (30 points)
			Question 3 (70 points)
			Question 4 (25 points)
			Question 5 (10 points)
			Question 6 (10 points)
			Question 7 (15 points)
		Study Questions from Day and Gastel
			Chapter 1
			Chapter 2
			Chapter 3
			Chapter 4
			Chapter 5
			Chapter 6
			Chapter 7
			Chapter 8
			Chapter 9
			Chapter 10
			Chapter 11
			Chapter 12
			Chapter 13
			Chapter 14
			Chapter 15
			Chapter 16
			Chapter 17
			Chapter 24
			Chapter 26
			Chapter 30
			Chapter 31
			Chapter 33
			Chapter 37
			Chapter 40
			Appendix C.A
Appendix-D---Guidance-for-Presentation_2013_Molecular-Microbiology-Laborator
	Appendix D Guidance for Presentations
Appendix-E---Revised-Paragraph-from-J--Biol--Che_2013_Molecular-Microbiology
	Appendix E Revised Paragraph from J. Biol. Chem. 266: 3811–3814 (1991)
Appendix-F---Abstract-from-Appl--Environ--Microbi_2013_Molecular-Microbiolog
	Appendix F Abstract from Appl. Environ. Microbiol. 63: 2647–2653 (1997)
Appendix-G---Sequence-Editing-Tutorial_2013_Molecular-Microbiology-Laborator
	Appendix G Sequence Editing Tutorial
		Sequence from the M13r Primer
		Steps in Analysis
		Analysis of Sequences that Contain the Reverse Complement of the 8–27F Primer
		Sequence from the T7 Primer
		Steps in Analysis
Appendix-H---Peak-Scanner-Tutorial_2013_Molecular-Microbiology-Laboratory
	Appendix H Peak Scanner Tutorial
Appendix-I---Adding-Size-Standards-to-Peak-_2013_Molecular-Microbiology-Labo
	Appendix I Adding Size Standards to Peak Scanner
Appendix-J---PRIMER-Tutorial_2013_Molecular-Microbiology-Laboratory
	Appendix J PRIMER Tutorial
		Nonmetric Multidimensional Scaling Using Primer
Appendix-K---Checklist-for-Grading-Laborator_2013_Molecular-Microbiology-Lab
	Appendix K Checklist for Grading Laboratory Reports
Appendix-L---Peer-Review-Checklist_2013_Molecular-Microbiology-Laboratory
	Appendix L Peer Review Checklist
Appendix-M---Career-Advice_2013_Molecular-Microbiology-Laboratory
	Appendix M Career Advice
Appendix-N---Molecular-Microbiology-Laboratory-_2013_Molecular-Microbiology-
	Appendix N Molecular Microbiology Laboratory Preparation Manual
		Media Room Preparation Manual
			Experiment 1: Plasmid Purification and Restriction Mapping
				One Week before Class 2
				Week 1
					Class 2: Plasmid Purification and Restriction
				Week 2
					Class 3: Agarose Gel Electrophoresis and Transformation
					Beginning of Week 2
					Ordering Information
				Week 3
					Experiment 2: Affinity Purification of a Histidine-Tagged Protein
						Class 5: Lyse Cells and Bind His-Tagged Protein To Ni Resin
						Class 6: SDS-Polyacrylamide Gel Electrophoresis
				Week 4
					Experiment 3: PCR and DNA Sequence Analysis of Bacterial RNA Genes, and Experiment 4: Extract Metagenomic DNA from Environm...
						Class 7: Isolate Bacteria from Environment (Unit 3) and Extract DNA from Environmental Samples (Unit 4)
						Class 8: Gram Stain/Microscopy and Inoculate Broth
				Week 5
					Class 9: Isolate Genomic DNA and Freeze Cultures
					Class 10: PCR
				Week 6
					Class 11: Purify PCR Product
					Class 12: Agarose Gel Electrophoresis and Template Preparation
				Week 7
					Class 13: No Lab Exercise; Midterm Exam. Free Day for Tas
				Week 7
					Class 14: PCR for T-RFLP
				Week 8
					Class 15: Purify T-RFLP PCR Product; Topoisomerase-Mediated Ligation to Plasmid pCR4-Topo and Transformation; 1% Agarose Ge...
				Week 8
					Class 15+1 Day: Inoculate Broth with Transformant (White Colony)
					Class 16: Restrict Amplicon; Inoculate Broth with Colony
					Class 16: Plasmid DNA Purification
		Teaching Assistant Preparation Manual
			Four Days before Class 2
			Experiment 1: Plasmid Purification and Restriction Mapping
				Week 1
					Class 1: Meet Students in Lab at Start of Class 1
				Week 2
					Class 3: Agarose Gel Electrophoresis and Transformation
					Class 3+1 Day
					Class 4: No Laboratory Exercise. Free Day for Tas
				Week 3
					Class 5: Lyse Cells and Bind His-Tagged Protein to NI Resin
					Class 6: SDS-Polyacrylamide Gel Electrophoresis
			Experiment 3: PCR and DNA Sequence Analysis of Bacterial rRNA Genes, and Experiment 4: Extract Metagenomic DNA from Environ...
				Week 4
					Class 7: Isolate Bacteria from Environment (Unit 3) and Extract DNA from Environmental Samples (Unit 4)
				Week 4
					Class 8: Gram Stain/Microscopy and Inoculate Broth
					Class 8+1 Day
				Week 5
					Class 9: Isolate Genomic DNA and Freeze Cultures
					Class 10: PCR
				Week 6
					Class 11: Purify PCR Product
					Class 12: Agarose Gel Electrophoresis and Template Preparation
					Preparing Purified DNA
					Customer Provided Primers
					Class 13: No Lab Exercise; Midterm Exam. Tas Needed to Monitor Small Lab
				Week 7
					Class 14: PCR for T-RFLP
				Week 8
					Class 15: Purify T-RFLP PCR Product; Topoisomerase-Mediated Ligation to Plasmid pCR4-Topo and Transform Ligation; 1% Agaros...
					Class 15+1 Day: Inoculate Broth with Transformant (White Colony)
					Class 16: Restrict Amplicon; Prepare Plasmid DNA from Broth Culture
					Class 16: Plasmid DNA Purification
			Preparing Purified DNA
		Strain Curator Preparation Manual
			Experiment 1: Plasmid Purification and Restriction Mapping
				Six Days Before Class 2
				Four Days Before Class 2
	Week 1
		Three Days Before Class 2
		Two Days Before Class 2
		Class 2: Plasmid Purification and Restriction
No-title-available_2013_Molecular-Microbiology-Laboratory1
	Bibliography
No-title-available_2013_Molecular-Microbiology-Laboratory
	Index