Molecular Microbiology Laboratory
Instructor:
Dr.
Office Hours: by appointment
Teaching Assistants:
Required Texts:
Molecular Microbiology Laboratory
by W. Ream, B. Geller, J. Trempy & K. Field,
Academic Press, 2013 (ISBN: 978-0-12-397044-2)
How to Write & Publish a Scientific Paper,
7th Edition by R. A. Day and B. Gastel,
Greenwood Press, 2011 (ISBN: 978-0-39195-8)
Attendance is mandatory.
1 unexcused absence = -5%
>2 absences = Incomplete.
15 minutes late = ½ absence
Excused absences considered case-by-case.
You must complete missed assignments.
Please do not attend class if you
have a contagious illness.
To request an excused absence,
contact me before class.
Final Grade:
A
= 94-100% of top score
A= 90-93%
B+
= 87-89%
B
= 83-86%
B= 80-82%
C+
= 76-79%
C
= 70-75%
C= 65-69%
D
= 50-65%
F
= < 50%
Lab Reports = 20% each x 4 = 80%
Test
= 20%
No partial credit for problems
that involve calculations.
Details are important.
Decorum is important.
End personal conversations
when class begins.
Limit conversations to classrelated matters.
Attend class on time; stay entire class.
Read assignments & procedures before
class.
Bring lab & writing manual to class.
Participate in class writing activities.
Complete assignments on time.
Prepare flow chart before experiment.
You may not begin without a flow chart.
Ask questions if you do not understand.
Sample Flow Chart
1 ml O/N cult. strain DH5 in LB
dilute 1 x 10-2
10 ml LB in 125 ml Erlenmeyer
shake 30 C @ 150 rpm
A600 = 0.2
1 ml
store
on ice
dump
supernatant
9 ml
spin 5 min microfuge @ RT
pellet
Goals
Teach molecular biology techniques
commonly used in life sciences.
Develop scientific writing skills.
Experiment 1:
Plasmid Purification &
Restriction Mapping
Experiment 2:
Affinity Purification of HistidineTagged Fibronectin-Binding
Protein
Experiment 3:
Polymerase Chain Reaction
&
DNA Sequence Analysis of
Bacterial Ribosomal RNA Genes
Experiment 4:
Restriction Fragment Length
Polymorphism Analysis of
Ribosomal RNA Genes from
Uncultured Bacterial
Communities
Wear lab coat and safety glasses.
Do not pipette by mouth.
Do not eat, drink, or chew gum in lab.
Disinfect bench before & after work.
Wash your hands after working.
All bacteria you use may cause disease.
Disinfect contaminated equipment
& surfaces.
Place liquid cultures, supernatant solutions
& glassware in autoclave containers.
Discard plastic tubes, tips & plates in
autoclave bags.
Discard phenol & chloroform in organic
waste containers.
Lab coats & safety glasses are
REQUIRED when you use phenol.
Do not wear shorts or sandals.
Phenol causes severe chemical
burns; wash with water to remove
phenol.
Preparing a Lab Report
Name
Title: concise and specific.
Date
Purpose: 1-2 sentences. Be specific.
Methods: List procedures used; cite lab
manual pages. Note modifications.
Results:
Begin with 1-2 sentences
outlining experiment.
Describe what you observed.
Do not repeat methods section.
Include graphs, tables, photographs
& sequencing electropherograms.
Figures & tables need title, number &
legend explaining symbols, etc.
Specify units on axes of graphs.
Label columns and rows in tables.
Number lanes on photographs of gels.
In legend describe contents of lanes.
Place figure ASAP after first cited.
Discussion:
Begin with purpose of experiment.
Interpret data in results section.
Discuss meaning of observations.
Mention alternative interpretations;
indicate which you think is correct.
Discuss all results, even if unexpected
or negative.
If experiment did not work, indicate
what went wrong.
Conclusions:
Summarize meaning of results;
2-3 sentences.
References:
List references used to prepare report.
Questions:
Include answers at end of report.
Show calculations.
It has been shown that
Helicobacter pylori causes
stomach ulcers (1).
It has been shown that
Helicobacter pylori causes
stomach ulcers (1).
Helicobacter pylori causes
stomach ulcers (1).
Phrases to Avoid
Use:
"is"
"were"
instead of:
"is known to be"
"were found to be"
"were observed to be"
"were determined to be"
"was"
"was identified as being"
"it was observed that"
"may be" "is thought to be"
Eliminate: "It was found that"
"The results show that"
"The purpose of this study was "
An uninformative title:
Terminal Restriction Fragment
Length Polymorphism Analysis of
16S Ribosomal RNA Genes from
Uncultured Bacterial Communities
An informative title:
Streptococcus, Prevotella, and
Veillonella species predominate in
the gastric microbiota of patients
with inflammatory bowel disease
and in control patients
Proposal Abstract
Collect bacteria from environment (p. 51).
You decide what to sample.
Write 1-2 page proposal to justify choice
(due class 6).
See lab book for guidelines (xxxiii-xxxvi)
& examples (pages 129-133).
Proposals should:
Have a title (see Day, Chapter 7).
Cite peer-reviewed papers.
State question you want to answer.
Indicate why work is important.
Show how work will answer question.
Dr. Ream,
I just had to tell you that the textbook (Day &
Gastel) we used in 311 came with me to
Bermuda, helped me write my CV, my proposal,
my progress reports, my proposal to Steve, and
my final REU paper and thesis. It is amazingly
helpful and I've pretty much read it cover to
cover. That doesn't make me a perfect writer!
But what a great resource. One of those things
Professors always tell you that you don't believe
till after the fact.
Many thanks, Carmen Denman