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INTRODUCTORY MICROBIOLOGY LABORATORIES

Northern Arizona University


Department of Biological Sciences
College of Engineering, Forestry, and Natural Sciences
BIO 205L Microbiology Laboratory
1 Credit Hour
Science Lab Facility Building 17
Room 112, 116, or 118

Spring 2015
Tentative Syllabus
The required published reading materials for the BIO 205 laboratories include:
Fundamental Experiments and Techniques in Microbiology; an "in-house"
publication.
A Photographic Atlas for the Microbiology Laboratory; M.J. Leboffe and B.E.
Pierce, 4th Edition, 2011.
Grading: (500 points possible)
5 Staining Techniques & Wet Mount (5 points each)....................
Aseptic Technique Quiz...................................................................
Gram Stain Unknown Quiz.............................................................
Bacterial Enumeration Data Analysis Assignment........................
Phage One-step Growth Worksheet................................................
Transformation Worksheet.............................................................
Environmental Isolate Assignment................................................
Lab Practical....................................................................................
Technique Points1............................................................................
Professionalism Points 2...................................................................
7 Quizzes (10 points each; lowest quiz score dropped) 3...............
Total
500 points

30 points
10 points
50 points
50 points
25 points
25 points
100 points
100 points
25 points
25 points
60 points

Please note
a) You will be expected to work in the laboratory at times other than
your regularly scheduled lab period to practice techniques, to record
the results of lab exercises, to make fresh cultures, and to place
cultures in the refrigerator.
b) Attendance is mandatory. Unexcused absences may result in an
administrative drop from the course. Missed assignments, quizzes,
and lab exercises cannot be made up. If you miss the laboratory
exercise for a worksheet or other assignment, you will lose ten (10)
points on that assignment.
c) If you need BIO 305W, the junior-level writing course for biology
majors, you are strongly encouraged to enroll in BIO 305W Writing in
Biology and in BIO 205L Microbiology Laboratory during the same
semester.
1

Techniques include (but are not limited to) microscope care and use, proper use of sterile
technique throughout the semester, appropriate disposal of waste, etc.

Professionalism includes (but is not limited to) coming to lab prepared and on time with
your printed pre-lab assignment, wearing your lab coat and other appropriate personal
protective equipment (including eye protection when working with living cultures),
following directions, paying attention, etc.

There will be seven (7) quizzes administered during the semester covering material from
previous and upcoming labs. One quiz grade will be dropped. Missed quizzes cannot
be made up.

Academic Dishonesty (including, but not limited to, plagiarism and cheating):
Please see "Academic Integrity" in NAUs policy statements below. Penalties for
plagiarism are up to and including an F in the lab and/or lecture. Microbiology
laboratory exercises are often conducted in groups of two or more students. Group
discussion and examination of research questions, hypotheses, methodology, and
data analysis is encouraged, but this collaboration ends when the written
component begins. Each student will independently complete his or her own
assignments and papers.
NAUs Emergency Textbook Loan Program: To help students acquire the materials they
need to be successful in class, NAU has partnered with Follett to create the Emergency
Textbook Loan program. The program is administered by the LEADS Center. The
program assists students with unmet financial need in obtaining required textbook(s)
and other materials for courses. Students must apply and meet eligibility criteria before
textbooks are purchased on their behalf. Textbooks must be returned at the end of the
term in which the textbooks were loaned. More information can be found online:
http://nau.edu/LEADS-Center/Textbook-Loan-Program/
NORTHERN ARIZONA UNIVERSITY
POLICY STATEMENTS
NAUs Safe Working and Learning Environment Policy prohibits sexual harassment and
assault, and discrimination and harassment on the basis of sex, race, color, age,
national origin, religion, sexual orientation, gender identity, disability, or veteran status
by anyone at this university. Retaliation of any kind as a result of making a complaint
under the policy or participating in an investigation is also prohibited. The Director of
the Office of Affirmative Action & Equal Opportunity (AA/EO) serves as the universitys
compliance officer for affirmative action, civil rights, and Title IX, and is the ADA/504
Coordinator. AA/EO also assists with religious accommodations. You may obtain a copy
of this policy from the college deans office or from the NAUs Affirmative Action website
nau.edu/diversity/. If you have questions or concerns about this policy, it is important
that you contact the departmental chair, deans office, the Office of Student Life (928523-5181), or NAUs Office of Affirmative Action (928) 523- 3312 (voice), (928) 5239977 (fax), (928) 523-1006 (TTD) or aaeo@nau.edu.
STUDENTS WITH DISABILITIES
If you have a documented disability, you can arrange for accommodations by
contacting Disability Resources (DR) at 523-8773 (voice) or 523-6906 (TTY),
dr@nau.edu (e-mail) or 928-523-8747 (fax). Students needing academic
accommodations are required to register with DR and provide required disability related
documentation. Although you may request an accommodation at any time, in order for
DR to best meet your individual needs, you are urged to register and submit necessary
documentation (www.nau.edu/dr) 8 weeks prior to the time you wish to receive
accommodations. DR is strongly committed to the needs of student with disabilities and
the promotion of Universal Design. Concerns or questions related to the accessibility of
programs and facilities at NAU may be brought to the attention of DR or the Office of
Affirmative Action and Equal Opportunity (523-3312).

ACADEMIC CONTACT HOUR POLICY


Based on the Arizona Board of Regents Academic Contact Hour Policy (ABOR Handbook,
2-224), for every unit of credit, a student should expect, on average, to do a minimum
of three hours of work per week, including but not limited to class time, preparation,
homework, studying.
ACADEMIC INTEGRITY
Integrity is expected of every member of the NAU community in all academic
undertakings. Integrity entails a firm adherence to a set of values, and the values most
essential to an academic community are grounded in honesty with respect to all
intellectual efforts of oneself and others. Academic integrity is expected not only in
formal coursework situations, but in all University relationships and interactions
connected to the educational process, including the use of University resources. An NAU
students submission of work is an implicit declaration that the work is the students
own. All outside assistance should be acknowledged, and the students academic
contribution truthfully reported at all times. In addition, NAU students have a right to
expect academic integrity from each of their peers.
Individual students and faculty members are responsible for identifying potential
violations of the universitys academic integrity policy. Instances of potential violations are
adjudicated using the process found in the university Academic Integrity Policy
(https://policy.nau.edu/policy/policy.aspx?num=100601).
RESEARCH INTEGRITY
The Responsible Conduct of Research policy is intended to ensure that NAU personnel
including NAU students engaged in research are adequately trained in the basic
principles of ethics in research. Additionally, this policy assists NAU in meeting the RCR
training and compliance requirements of the National Science Foundation (NSF)-The
America COMPETES Act (Creating Opportunities to Meaningfully Promote Excellence in
Technology, Education and Science); 42 U.S.C 18620-1, Section 7009, and the National
Institutes of Health (NIH) policy on the instruction of the RCR (NOT-OD-10-019; Update
on the Requirement for Instruction in the Responsible Conduct of Research). For more
information on the policy and the training activities required for personnel and students
conducting research, at NAU, visit: http://nau.edu/Research/Compliance/ResearchIntegrity/
SENSITIVE COURSE MATERIALS
University education aims to expand student understanding and awareness. Thus, it
necessarily involves engagement with a wide range of information, ideas, and creative
representations. In the course of college studies, students can expect to encounter
and critically appraisematerials that may differ from and perhaps challenge familiar
understandings, ideas, and beliefs. Students are encouraged to discuss these matters
with faculty.
CLASSROOM DISRUPTION POLICY
Membership in the academic community places a special obligation on all participants
to preserve an atmosphere conducive to a safe and positive learning environment. Part
of that obligation implies the responsibility of each member of the NAU community to
maintain an environment in which the behavior of any individual is not disruptive.
Instructors have the authority and the responsibility to manage their classes in
accordance with University regulations. Instructors have the right and obligation to
confront disruptive behavior thereby promoting and enforcing standards of behavior
necessary for maintaining an atmosphere conducive to teaching and learning.
Instructors are responsible for establishing, communicating, and enforcing reasonable
expectations and rules of classroom behavior. These expectations are to be
communicated to students in the syllabus and in class discussions and activities at the

outset of the course. Each student is responsible for behaving in a manner that
supports a positive learning environment and that does not interrupt nor disrupt the
delivery of education by instructors or receipt of education by students, within or
outside a class. The complete classroom disruption policy is in Appendices of NAUs
Student Handbook (http://nau.edu/student-life/Student-Handbook/).
Effective Summer 2014
Approved UCC 1/28/14 Approved UGC 2/12/14

Schedule of Laboratory Exercises, Reading Assignments, Assessments, and


Outcomes
(TENTATIVE)
Reading Assignments
Week 1

Exercise 1

Orientation and Introduction


Laboratory Protocol and Safety
Required Materials
Microscopy
Begin Environmental Isolate:
- collect microbes from outside

McMillan Readings for 305W

Introduction to McMillan (p. 1-4)


Reading Scientific Papers (p. 21-26)
Literature Cited Section (p. 133143)
Example Literature Cited Section
(p. 101-103)

Photoatlas
for 205L
Introduction
(p. 1-4)
Microscopy
(p. 31-34)

Week of
305W:
01/12 Course introduction
Introduce scientific papers
Literature search
References section

Assign Mini Writing


Assignment 1 (MWA1):
Literature Search &
References Section
Reading Assignments
Week 2

Exercise 2

McMillan Readings for 305W

Photoatlas
for 205L

Week of
01/19

Staining:
- dry mount & heat-fix
- simple vs. differential stains
- positive & negative stain
- methylene blue, Gram, & capsule
Environmental Isolate:
- record colony morphology on
original plates
- first isolation streak

Research Questions & Hypothesis


(p. 27-28)
Writing Lab Reports: Title (p. 61-65)
Introduction Section (p. 69-70)
Example Title Page & Introduction
Section (p. 94-97)
Citing Sources in the Text (p. 125133)

Streak plate
isolation
(p. 5-6)
Bacterial
growth
patterns &
colony
morphology
(p. 19-26)
Simple stains
& cell
morphology
(p. 37-44)

305W:
Scientific papers continued
Questions about MWA1
Title page
Introduction Section
Assign Mini Writing
Assignment 2: Title Page &
Introduction Section
Read scientific papers for next
week

Gram stain
(p. 45-48)
Capsule
stain
(p. 51)

Reading Assignments
Week 3

Week of
01/26

Exercise 3
Continue differential staining:
- acid fast
- endospore
Sterile/Aseptic Technique (Part I)
Environmental Isolate
- record colony morphology on first
isolation streak
- second isolation streak

McMillan Readings for 305W

Ch. 7: Writing & Revising (p. 144171)

Photoatlas
for 205L
Acid-fast
(p. 49-50)
Endospore
(p. 51-54)
Bacterial
growth
patterns &
colony
morphology
(p. 19-26)

305W:
MWA1 DUE on Monday,
January 26th
Introduction section continued
In-class activity: Introduction
section paragraphs
Discuss scientific papers from last
week
Reading Assignments
Week 4

Exercise 4

McMillan Readings for 305W

Photoatlas
for 205L

Dental plaque
Quizzes:
- sterile/aseptic technique
- Gram stain unknown
Environmental Isolate
- continue purification
- verify purification with wet mount
- record observations

Materials & Methods (p. 71-76)


Example Materials & Methods
Section (p. 98)
Results Section (p. 76-81)
Example Results Section (p. 98100)
Ch. 3: Tables & Figures (p. 39-60)

Week of
02/02 305W:
MWA2 DUE on Monday,
February 2nd
Materials and Methods section
Results section
In-class activity: Tables & figures
Assign Mini Writing
Assignment 3: Materials and
Methods Section & Results
Section

Gumline
smear Gram
stain
(p. 39)
More
gumline
smear Gram
stains
(p. 46-48,
238)
Wet mount
(p. 55)

Reading Assignments
Week 5

Week of
02/09

Exercise 5
Enumerating bacteria
- serial dilutions
- spread & pour plate
Environmental Isolate
- verify purification with wet mount
- start characterization with
microscopy & staining
- record observations

McMillan Readings for 305W

Discussion Section (p. 81-85)


Example Discussion (p. 100-101)
Citing Sources in the Text (p. 125133)

Photoatlas
for 205L
Standard
plate count
(viable assay)
(p. 217-219)
Direct cell
count
(p. 219-220)

305W:
MWA3 DUE on Monday,
February 9th
Discussion Section
Assign Mini Writing
Assignment 4: Discussion
Section
Reading Assignments
Week 6

Exercise 6

McMillan Readings for 305W

Photoatlas
for 205L

Week of
02/16

Standard
plate count
(viable assay)
(p. 217-219)

Enumerating bacteria data


analysis
- count colonies
- calculate titer
- record class data for 50 point
assignment DUE NEXT WEEK
Environmental isolate
- MUST HAVE PURE CULTURE
- continue microscopy & staining
- begin storage conditions
- STREAK SLANTS FOR EX. 7
BIOCHEMICALS (24 hours
before lab)

Bacterial
growth on
slants
(p. 26-27)

305W:
MWA4 DUE on Monday,
February 16th
In-class activity: Introduction &
Discussion
Overview of paper format

Assign First Submission


of Environmental Isolate
Paper
Reading Assignments
Week 7

Week of
02/23

Exercise 7
Biochemical tests on
environmental isolate
CHECK BIOCHEMICAL TEST
RESULTS
- 24 & 48 hours
- one week
TURN IN BACTERIAL
ENUMERATION DATA ANALYSIS
ASSIGNMENT INCLUDING
TABLES & FIGURES DURING LAB
Other environmental isolate work:
- finish microscopy & staining
- start or continue storage
conditions
- start using Bergey's Manual to
identify your E.I.
STREAK SLANTS FOR EX. 10
PCR (24-hr culture)
305W:
Review common errors from
MWAs

Questions for first


submission of paper

McMillan Readings for 305W

Ch. 7: Writing & Revising


(p. 144-171)
Paragraphs (start on p.
152)
Sentences (start on p.
155)
Avoid Wordiness (start
on p. 163)
Verb Tense (p. 167)
Punctuation (start on p.
167)

Photoatlas for 205L


Oxygen requirements
(p. 29-30)
Casein hydrolysis
(p. 62-63)
Catalase (p. 63-64)
Simmons citrate
(p. 64-65)
Carbohydrate
fermentation (p. 71-73)
Gelatin hydrolysis
(p. 73-74)
Kligler's iron agar
(p. 75-76)
Lipid hydrolysis
(p. 77-78)
Motility (p. 82-83)
Nitrate reduction
(p. 83-85)
Oxidase (p. 87-89)
Starch hydrolysis
(p. 92-93)
Urea hydrolysis
(p. 96-97)
Bacterial growth on
slants
(p. 26-27)

Reading Assignments
Week 8

Week of
03/02

Exercise 10
PCR: Bacterial molecular
identification of environmental
isolate
Finish biochemical tests
Other environmental isolate work:
- continue using Bergey's Manual
& other resources to identify E.I.
- discuss requirements for E.I.
assignment (and first E.I. paper)

McMillan Readings for 305W

Ch. 8: Final Draft (p. 172-181)

Photoatlas for
205L
PCR
(p. 111-112)
Gel
electrophoresis
(p. 110-111)
DNA
sequencing
(p. 112-113)

305W:
Review common errors on
environmental isolate papers
Questions for first submission of
paper
Reading Assignments
Week 9

Exercise 8

McMillan Readings for 305W

Phage plaque
assay & titer
(p. 220-221)

Bacteriophage
- one-step growth curve
- determine burst size
Week of
03/09

Photoatlas for
205L

305W:
1st Submission of
Environmental Isolate Paper
DUE on Monday, March 9th
Guidelines for second submission
of paper
Assign Second Submission of
Environmental Isolate Paper
Reading Assignments

Week
10

Spring Break

McMillan Readings for 305W

Photoatlas
for 205L

No microbiology lab this week


Week of
03/16

Enjoy spring break!


305W:
No class this week
Reading Assignments

Week
11

Exercise 9 (Exercises 8 & 10 cont.)

McMillan Readings for 305W

Photoatlas
for 205L

Week of
03/23

Phage plaque
assay & titer
(p. 220-221)

Bacterial transformation
- extract DNA
- spread & control plates
- apply DNA to cells on spread
plate only
Bacteriophage worksheet
- count plaques
- calculate titer
- plot data on semi-log graph paper
- calculate burst size
- TURN IN BACTERIOPHAGE
WORKSHEET & FIGURE
DURING LAB
DNA sequence data analysis
- UGENE
- NCBI BLAST
Environmental isolate
- start analyzing DNA sequence
data
- verify E.I. identity with DNA data
- start E.I. assignment
305W:
PCR & DNA sequence data
analysis requirements for second
submission
Questions on second submission
of paper
Reading Assignments

Week
12

Exercises 9 &10 cont.

McMillan Readings for 305W

Photoatlas
for 205L

Week of
03/30

Bacterial transformation worksheet


- observe growth & count colonies
- TURN IN BACTERIAL
TRANSFORMATION
WORKSHEET DURING LAB
Review/continue DNA sequence
data analysis
- UGENE
- NCBI BLAST
Continue DNA sequence data
analysis
Environmental isolate
- continue analyzing DNA sequence
data
- verify E.I. identity with DNA data
- continue working on E.I.
assignment
305W:
Review PCR & DNA sequence data
analysis requirements for second
submission
Questions on second submission
of paper
Reading Assignments

Week
13

Week of
04/06

Environmental Isolate Assignment

McMillan Readings for 305W

Photoatlas
for 205L

Continue DNA sequence data


analysis
Environmental isolate
- finalize DNA sequence data
analysis
- finish E.I. assignment
305W:
Review PCR & DNA sequence data
analysis requirements for second
submission
Questions on second submission
of paper
Reading Assignments

Week
14

Exercises 9 & 10 (continued)


Environmental isolate
- TURN IN E.I. ASSIGNMENT &
DATA SHEET DURING LAB

Week of
04/13 305W:
2nd Submission of
Environmental Isolate Paper
DUE on Monday, April 13th
No class this week

McMillan Readings for 305W

Photoatlas
for 205L

Reading Assignments
Week
15

Week of
04/20

Lab Practical Review

McMillan Readings for 305W

Photoatlas
for 205L

Lab practical review


- review guide
- Jeopardy review
- ask questions about lab practical
Lab cleaning
305W:
No class this week
Reading Assignments

Week
16

Reading week

Lab Practical

McMillan Readings for 305W

Photoatlas
for 205L

Lab Practical
Week Of
04/27 305W:
No class this week
Reading Assignments
Week
17

Finals Week

NO LAB
Week of
05/04 305W:
No class this week

McMillan Readings for 305W

Photoatlas
for 205L