Syllabus for MCB Microbiology Lab

Contact Information - Course Coordinator

Monika W. Oli, PhD
e-Mail: moli@ufl.edu
Office: RM 1049, MCS Building
Office Hours: TBA
Website: http://microcell.ufl.edu/directory/faculty/monika-oli/

TAs for each section will be announced on the first day of class.
Please contact your TAs for any section specific questions! Contact me any time if you
have unresolvable problem with your TAs

Course time and location

Labs will be held in the Microbiology and Cell Science Building, Museum Drive, Room 1030 and
1026 (teaching labs). On the first day please make sure you are in the right section in the
correct room. Please check on ISIS and CANVAS for your correct section before you come to the
first lab. Make sure you know who your TA is.
Labs start during the first week of classes. Labs usually last for all 3 periods!

Table of Contents
Contact Information - Course Coordinator....................................................................1
Course time and location.......................................................................................................1
Welcome!....................................................................................................................3
Course Overview..........................................................................................................4
What you will know at the end of the course........................................................................5
Laboratory Safety...................................................................................................................5
Laboratory Skills.....................................................................................................................5
Laboratory Thinking Skills......................................................................................................5
Textbooks and Required reading...........................................................................................6
Vimeo Video Channel............................................................................................................6
Quizlet Flash Cards.................................................................................................................6
Books and references.............................................................................................................6
Getting started.............................................................................................................6
Expectations of the students.................................................................................................7
Student evaluation.......................................................................................................7
Attendance and Participation (5%)...................................................................................................8
Lab Etiquette (5%).............................................................................................................................8

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 Quizzes (10%).....................................................................................................................................8
Midterm Exam (25%).........................................................................................................................9
Final Exam (10%)...............................................................................................................................9
Projects, talks (10%)..........................................................................................................................9
Electronic lab notebook (10%)..........................................................................................................9
Student Initiated Research Project (20%).......................................................................................10
Extra credit (no more than 5%).......................................................................................................10
Grading and final grades......................................................................................................10
Makeup Policy.....................................................................................................................10
Seating and Locker assignment............................................................................................11
Biosafety in the Microbiology Laboratory............................................................................11
Underlying medical conditions.............................................................................................11
Future teaching assistants for micro labs and Letter of recommendation............................11
Other UF policies.................................................................................................................12
Academic Honesty...............................................................................................................12
Software Use........................................................................................................................12
Campus Helping Resources..................................................................................................12
Services for Students with Disabilities..................................................................................13
Generic weekly schedule............................................................................................14
Databases you will use...............................................................................................16
Virtual pond dip – for wet mount identification..................................................................16
NCBI Taxonomy (no password)............................................................................................16
Gideon – to determine your unknown and for public health project...................................16
DNA lims – to retrieve your 16s DNA sequence...................................................................16
BLAST – for sequence alignment..........................................................................................16
Food Safety First – for growth curve simulation..................................................................16
Optional software and database..........................................................................................16
EndnoteWeb Reference management program..................................................................16
HealthMap...........................................................................................................................16
Microbiology Videos...................................................................................................16
Microbiology intro...............................................................................................................17
Lab Safety Rules...................................................................................................................17
Daily Routines......................................................................................................................17
Aseptic Techniques..............................................................................................................17
Basic Methods.....................................................................................................................17
Art of Microscopy.................................................................................................................17
Basic Anatomy of a Microscope...........................................................................................17
Wet Mount...........................................................................................................................17
Streak for isolation...............................................................................................................17
Pipetting...............................................................................................................................17
Computer Tutorials..............................................................................................................17
Graphing with Excel.............................................................................................................17
Growth curve and growth rate calculation..........................................................................18
Visualizing Microbes............................................................................................................18
Gram Stain...........................................................................................................................18
Negative Stain......................................................................................................................18
Capsule Stain........................................................................................................................18

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 Flagella Stain........................................................................................................................18
Traditional Diagnostic Methods...........................................................................................18
SIM.......................................................................................................................................18
Phenol Red Broth.................................................................................................................18
Blood Agar............................................................................................................................18
Mannitol Salt Agar...............................................................................................................18
MacConkey agar...................................................................................................................18
DNAse Agar..........................................................................................................................18
Citrate Agar..........................................................................................................................18
Catalase Test........................................................................................................................18
Anaerobe Jar........................................................................................................................19
Molecular Diagnostic test....................................................................................................19
PCR 1....................................................................................................................................19
PCR 2....................................................................................................................................19
PCR 3....................................................................................................................................19
Bioinformatics.....................................................................................................................19
Sequence retrieval and Blast................................................................................................19
Blast tutorial and phylogenetic tree.....................................................................................19
Basic Bioinformatics Tutorial...............................................................................................19
Diagnostic tests...................................................................................................................19
ELISA....................................................................................................................................19
Parasites..............................................................................................................................19
Fecal float.............................................................................................................................19
Other Software....................................................................................................................19
Endnote reference management.........................................................................................19
Virtual Field Trips.................................................................................................................20
Diagnostic lab UF Vet School................................................................................................20
Documentaries – student projects.......................................................................................20
Lyme documentary..............................................................................................................20
Cholera outbreak in Haiti (public health).............................................................................20
Cool Stuff.............................................................................................................................20
Microbes did you know……..................................................................................................20
Why microbiology?..............................................................................................................20
Meet the MCS faculty..........................................................................................................20
Microbiology @ UF Lab Terminology: Quizlet Vocabulary Sets...................................20
Modules...............................................................................................................................20
Mini modules.......................................................................................................................22
Meet the microbes..............................................................................................................22
Other sets............................................................................................................................22

Welcome!
Welcome to the Microbiology Laboratory. In this course, you will learn techniques used in
(micro)biology labs and you will realize how microbes affect all aspects of our lives, every day.
Many of you will be familiar with some of the topics covered in the lab exercises, but hands-on

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experience is invaluable to really understand many of the techniques taught. Your TAs and I will
work closely with you to ensure that you have a good grasp of the topics and methods covered.
We have incorporated a number of projects and student initiated activities in to the syllabus as
well as student presentations to provide you with a variety of learning experiences. Our ultimate
goal is for you to complete the semester with the feeling that microbes are important in every
aspect of our lives – and with the notion that you have learned something you can use for the
rest of your life and not just to get an A!
I would like to emphasize that we are here to help you. Your TAs and I hope to see you all during
open lab or our office hours (or by appointment), especially if you have questions or need
assistance.  

Course Overview
This is an undergraduate laboratory course to learn and explore a variety of microbiological
techniques, skills and concepts. Topics that will be covered include visualization and
enumeration of microbes, traditional, molecular and immunological diagnostic techniques, basic
techniques used in parasitology, virology and mycology. Students will generate, analyze and
interpret data, design and conduct a small research project and gain experience in technical
writing and presentation skills. You will gain awareness about the ubiquity and diversity of
microbes and the good and bad roles they play in your every day life.

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What you will know at the end of the course
A student successfully completing basic microbiology lab course will demonstrate ability to use,
explain and practice…..

Laboratory Safety
1. Microbiological procedure, including, proper lab etiquette (hand washing, disinfecting lab
benches and equipment), follow methods for aseptic transfer, reporting all spills, understanding
OSHA’s Blood borne Pathogen Standard, proper disposal of different types of waste, following
good lab practice, including returning materials to proper locations, proper care and handling of
equipment
2. Protective procedures, Including tying long hair back, wearing personal protective equipment
(lab coats, gloves when needed, closed toed shoes); No eating or drinking in the laboratory
3. Emergency procedures, including, locating and properly using emergency
equipment, reporting all injuries immediately to the instructor

Laboratory Skills
1. Use a bright field light microscope to view and interpret slides, properly prepare slides and
various stains to visualize microbes. Use standard microbiology laboratory equipment correctly
(including, incubators, centrifuges, vortex, spectrophotometer, PCR machine, imaging system)
and follow experimental protocols
2. Use micropipettes and understand the correct volume and pipette tips to use for each
experiment, comprehend accuracy and precision to have a good pipetting technique
3. Properly use aseptic techniques, to obtain and maintain a pure culture
4. Identify unknown organisms by using appropriate microbiological media and test systems,
and molecular methods
5. Estimate the number of microbes using dilution techniques, spectrophotometer and a
hemocytometer; predict how various growth conditions affect the number of life cells
6. Perform and interpret a disk diffusion assay and understand how to test for the effectiveness
of a variety antimicrobial agents
7. Perform and interpret an ELISA assay and know techniques how to determine antibody
prevalence in a patients immune response to pathogens;
8. Be able to describe the problem of global water contamination, and understand the
prevalence of global occurrence of parasites, perform and interpret a fecal float and conduct
water purification methods to prevent water born infections
9. Get a taste how microbes contribute to the production of various foods and drinks and be
aware of the importance of a healthy microbiome

Laboratory Thinking Skills

1. Understand and apply the scientific method, including formulation of a clear, answerable
question and hypothesis; research of peer reviewed scientific literature, conduct and execute
appropriate experiments with correct controls, evaluate, analyze and interpret results
2. Analytical skills, including collection and organizing data in a spreadsheet, analyze and
presenting data in an appropriate from (graphs, tables, figures, or descriptive paragraphs),

5
assessing the validity of the data (means, standard deviation, significance) and drawing
appropriate conclusions based on the results
3. Communication skills, including preparation of presentations of current topics in
microbiology, developing educational materials and presenting lab results or findings to your
peers
4. “Big picture” skills, including understanding how microbes play a beneficial and detrimental
role in our loves and the environment. Students should be able to read and interpret current
news and popular literature relating to microbiology and evaluate the scientific merit of the
information presented. All students should comprehend that science is not “black and white”
and that new scientific findings may alter the interpretation of older dogmas. Finally students
should get a glimpse of how microbes have always shaped history and affect our every day life in
a myriad of ways.

Textbooks and Required reading

NO LABMANUAL is required. All information will be posted in CANVAS

Vimeo Video Channel

Over the years we created numerous videos in house that will help you significantly to perform
the techniques you are learning in the lab. The UF Microbiology channel is a collection of
tutorials, visual aids and educational videos to help spark the interest in microbiology and to
teach students the basic skills. All videos were produced in house and are copy-written by Dr.
Monika Oli, faculty at UF.
The videos are used to teach MCB2000L, 3020L and 3023L in the Department of Microbiology
and Cell Science at UF.
https://vimeo.com/channels/859405

Quizlet Flash Cards

To help you learn this new language of “microbiology” we created a Quizlet for each
module.
https://quizlet.com/join/4SDKvWjQn
https://quizlet.com/class/2282683/
You will be prompted for each set of definitions in the different modules. We hope that
helps you learn!

Books and references

You may find these references interesting or they can be a good refresher if you need more
help.

Getting started
Course Correspondence as well as lab exercises, assignments and exams will be available via
eLearning Canvas Website http://lss.at.ufl.edu/. If you need any help with the eLearning system

6
please visit the eLearning Help page at https://lss.at.ufl.edu/help.shtml. You may also contact
the UF help desk at 352-392-HELP, Option 2.

Your section specific site is maintained and administered by your TAs. You are responsible for
the material posted in your section. I do not check email in the individual sections!
Furthermore:
1.     All students should sign up for “Science Daily – Infectious Disease” (automatic email
update)  http://www.sciencedaily.com/news/health_medicine/infectious_diseases/  Some class
discussions will be based on current news and you can use the topics for your public health
projects
2.     Like the UF Microbiology and Cell Science & ASM Gators @UFMicrobiology
page for interesting news and current updates; the postings can be part of the class material!
http://www.facebook.com/UFMicrobiology
you can use the topics for your public health projects
3.     Please Remember to check the Announcements and Mail each day in Canvas. “I did not
know about the assignment, deadline…” is NOT an accepted excuse. For this course there are
two Canvas sites for the course. Your instructor will have his/her own Canvas webpage where
section specific information will be posted.
4.     Please bring your labtop computer or tablet to each lab. We often will do computer based
exercises. Bring a camera, cell phone or tablet to take pictures of your lab results.
5.     Throughout the Semester there will be Open Lab sessions to provide you with extra hands
on time and an opportunity to ask questions and get more experience with the techniques
discussed in class. Information regarding open lab will be emailed as schedules are finalized.
6.     All assignments, projects and reports are expected to be submitted electronically through
Canvas. Each assignment is processed through Turnitin.com and as such is checked for
plagiarism.
7.     Attendance is mandatory. Each day new techniques are taught and it is easy to fall behind!
Arriving late and not coming to class without an excused absence will affect your attendance
and participation and lab etiquette grade (up to 10%)
8.     Got a Question? Please come see us - we are here to help!

Expectations of the students

 Read the Syllabus to know your deadlines and exam schedules. Your TA however will
announce specific days for your own section so PAY ATTENTION!
 As student, you are expected to fully engage yourself in all aspects of the class
 You are expected to COME PREPARED to class and have read the assigned reading material
and especially watched the introductory videos.
 You are expected to FOLLOW OUR LAB ETIQUETTE at all times (see next chapter). You have
to respect the potential pathogens we are working with.
 Most importantly: ENJOY THE LAB!

Student evaluation 
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Student grades are composed through a multitude of
activities, including quizzes, exams, presentations, projects,
Items Graded % Value
attendance and participation. FOLLOWING INSTRUCTIONS IS
A MUST as well as CREATIVITY WILL BE REWARDED. Participation,
5
Attendance
Attendance and Participation (5%) Lab etiquette 5
Attendance to all laboratory sessions is mandatory and
Quizzes 20
your instructor will record attendance. Should a conflict
arise, notify your lab instructor in advance if possible and Midterm Exam 25
find arrangements to make up the missed material and
quizzes. Unexcused absences will result in a zero for that Final Exam/project 25
day’s attendance. You must e-mail your instructor within Projects, talks 10
24h before/after the missed lab to qualify for makeup
opportunity and provide valid written excuse. ELN 10
No cheating and plagiarism is allowed. You will receive an Total 100
automatic 0 without warning if caught for a particular
assignment, project or exam. You will be reported to the Extra credit 5
Dean of Student office (DSO) for cheating!

Lab Etiquette (5%)

Lab etiquette is a class based grade. All the students
together are responsible to leave the lab clean and to
use the equipment with care – EVERY WEEK. Points will be taken off from EVERYONE in
the class if a class is observed to not follow the lab etiquette rules – regardless if one
student messes up or the whole class.
This includes, but is not restricted to:
· Emptying your benchtop trash container (without throwing away the bag)
· Cleaning bench before and after lab
· Making sure all items are in your lab bin when you arrive and when you leave
o No broken, damaged or stained pipettes
o 3 pipettes per pair of students
o No strikers in the bin….
· Making sure that all items on your bench are present and in order
· Maintain the microscope: Wiping oil of the 100X oil lens, put cover on the scope,
secure he cable
· Obtain refill tip boxes and eppendorf tubes, microscope slides and cover slips from
TAs when you are out
· Putting the trash in the appropriate and correct container (regular trash, biohazard
trash)
 check with your TA for details

Quizzes (10%)
Quizzes will either be given in the lab or assigned to be completed in Canvas. This will be up to
your individual TAs. Quizzes will contain material from the upcoming lab and from any previous

8
module. Quizzes can also contain the videos to be watched before class and the vocabulary and
definitions in Quizlet. Quizzes can include material from required readings and student
presentations and the following week’s material. All quizzes are cumulative. The lowest quiz
grade will be dropped.

Midterm Exam (25%)

Exams are designed to test your knowledge of practical skills learned in class and also determine
comprehension of the learned material.
Practical component: a large part of the midterm is comprised of a practical exam where you
have to perform the skills and techniques learned over the first weeks of class. Final exam could
be a take home or practical exam. Details for each examination will be explained and discussed
by your TA.  Cheating will automatically result in 0 points without warning and may lead to a
report to the Dean of Students Office (DSO).
A typical midterm will test you on: microscopy (parts and how to use it), wet mount,
identification of organisms, streak for isolation, Gram stain (and other stains), pipetting,
graphing (mean+STDEV), growth curve/calculations, enumeration, lab math, identification of
microbes using GIDEON and molecular techniques (bioinformatics - BLAST). Make sure you
UNDERSTAND the techniques, the instruments (+microscope), the purpose and the importance
of each module.
Be prepared, this is a challenging and hard exam, make sure you know how to do each
teachnique and labmath, EVERYTHING you have learned up to that point

Final Exam (10%)

Your final exam is determined by your TA

Projects, talks (10%)

Your TA will assign various projects. Please follow the instructions of your TA exactly. Projects
can include public health projects with role play, presentations, diagnostic project, etc.

Electronic lab notebook (10%)

You will keep an electronic lab notebook (ELN), which contains all your results, answers to
questions, projects, observations, etc. This will help you to understand the material better. You
can add any information into the ELN. This semester you will NOT be allowed to use your ELN
for the exam but you can make your own “cheat sheet” to help you with procedures etc.
Depending on your TA you may be asked to comply with a particular format. In general your ELN
should include the following.
·      Detailed explanation of the concepts being learned that day
·      Key terms/Vocabulary
·      A proper protocol
·      Data in the form of pictures, graphs, tables, etc
·      Results
·      Conclusion
·      Answer to end of chapter questions and other material as directed by your TA

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Make sure you also know the definitions and terminology as well as answering the end of
module questions!!!!
Student Initiated Research Project (20%)
Each student has the opportunity to work on an independent research project as part of the
class. You can work in groups and the project has to be approved by your TA. Your approach has
to follow the principles of scientific method. You have to submit a small research proposal and
include current papers from the literature as well as a budget for your research. It is possible to
conduct a bioinformatics study using existing databases. The final project will be presented as a
poster during the last week of class.
Project submissions
1.     Submissions after the deadline will be treated as late submissions, and 10% of the total
assignment points will be deducted for each day after the deadline for 5 days; submission will
not be accepted after that.
2.     If you experience any problem with e-Learning system or while uploading assignments,
contact the helpdesk immediately (352) 392-4357 (select option 2) or e-mail: learning-
support@ufl.edu. Retain your e-mail or helpdesk ticket number as
documentation of your problem. A 92
Extra credit (no more than 5%) A- 90
With the discression of your TA you may get some extra credit which
can include B+ 87
· Participation in online discussion B 82
· Bringing/sharing environmental samples for wet mount examination
· Bringing/sharing fecal samples with potential parasite eggs for the fecal B- 80
float (parasitology) lab C+ 77
· Bringing/sharing fermented food products for the food lab
· Sharing interesting news and articles about microbiology with your class C 72
Extra Credit Opportunities will be available throughout the semester at the C- 70
discretion of your TA. Such Extra Credit Opportunities may include: Attending
Open Lab, Presentation of current topic in class and posting it to Wiki, Wiki D+ 67
postings, contribution to discussion board
D+ 62
Grading and final grades D- 60
We don’t curve and the grading scale will not be adjusted based on class
performance. After ISIS allows you to view your final grade. You have 2 weeks E <60
to challenge your grade and request a change of grade by contacting Dr. Oli
(moli@ufl.edu)

Makeup Policy
We will work with you if you provide us with a UF accepted excuse for your absence
during labs or the exam. https://catalog.ufl.edu/ugrad/current/regulations/info
/attendance.aspx.
We do accept school and career interviews and tests (MCAT, GRE, DAT) as excused
absence - as long as you provide a written note or invitation to BEFORE your absence.
You will work with your TA to make up missed work. Remember: open lab is NOT

10
intended for makeup as there will be no actual instructor. Do NOT miss your midterm
exam.

Seating and Locker assignment

Please take the same seat in each class period. We will make notice of your location in the room
and a seating chart will be handed out the fist day of class.
You will be assigned a personal or shared locker for the period of the class or semester to leave
your lab coats and backpack during lab and between lab periods. Please bring a lock for security.

Biosafety in the Microbiology Laboratory

We are regulated and inspected annually by the UF Environmental Health and Safety
Department. We follow their guidelines - and you follow our instructions - to prevent any
accidents and problems with contaminations. For more information about the regulations go to:
http://www.ehs.ufl.edu/Lab/EHSintro.htm
To comply with the University of Florida biosafety requirements closed toed shoes are
mandatory in the laboratory. You can leave a pair in your locker so you don’t forget. Disposable
lab coats will be provided to you on the first day of class. It is mandatory to wear them at all
times. Write your names on your coats and keep them in your lockers. Do not take them home.
Do not take anyone else's’ coat. Lab coats will be autoclaved and disposed according to UF
regulations on the last day of the semester.

Underlying medical conditions

If you have any underlying medical conditions which can affect your immune system or make
you more susceptible to infectious disease, you must inform your TA and consult with your
physician before working in the microbiology laboratory.
For students and TAs with preexisting conditions, including pregnancy, taking
immunosuppressive drugs, or who have other medical conditions (e.g., diabetes, immune
system disorder) that might necessitate special precautions and it is recommended that they get
medical clearance from the infirmary.
http://shcc.ufl.edu/
If you notice any unusual symptoms or of any spills or accidents occur, contact your TA
immediately.
Please come and see Dr. Oli if you have any concerns (moli@ufl.edu)

Future teaching assistants for micro labs and Letter of recommendation

You may request a letter of recommendation only if you attend the section I am teaching. I will
also write recommendation letters for most students who sign up to be TA the microbiology
laboratories. To sign up to TA after you have taken the class, fill out the information in the online
app http://microcell.ufl.edu/TA_app/ . The spots for TAs are limited and will be filled on a first
come first served basis.

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Other UF policies
Academic Honesty
In 1995 the UF student body enacted an honor code and voluntarily committed itself to the
highest standards of honesty and integrity. When students enroll at the university, they commit
themselves to the standard drafted and enacted by students.
The Honor Pledge: We, the members of the University of Florida community, pledge to hold
ourselves and our peers to the highest standards of honesty and integrity.
On all work submitted for credit by students at the university, the following pledge is either
required or implied: "On my honor, I have neither given nor received unauthorized aid in doing
this assignment."
Students should report any condition that facilitates dishonesty to the instructor, department
chair, college dean, Student Honor Council, or Student Conduct and Conflict Resolution in the
Dean of Students Office. It is assumed all work will be completed independently unless the
assignment is defined as a group project, in writing by the instructor. This policy will be
vigorously upheld at all times in this course.
http://www.dso.ufl.edu/sccr/honorcodes/honorcode.php
 (Source: 2011-2012 Undergraduate Catalog)

Software Use
All faculty, staff and students of the university are required and expected to obey the laws and
legal agreements governing software use. Failure to do so can lead to monetary damages and/or
criminal penalties for the individual violator. Because such violations are also against university
policies and rules, disciplinary action will be taken as appropriate.
We require for each students to have MS Office (Mac or PC) installed on their/a computers.
Similar graphing programs are available for iPads and tablets
Microsoft Software for UF students
http://www.software.ufl.edu/
The Office of Information Technology has great news for University of Florida students! If you
want to upgrade your operating system or need Microsoft Office Suite, this media will be
available in the Spring 2011 semester.  The different media available are: Windows 7 operating
system Upgrade, Microsoft Office Professional Plus 2010 (32-bit/64-bit) for PC or Microsoft
Office for Mac 2011. Software is free for UF students.
To check for availability of the media and technical requirements, contact the UF Computing
Help Desk at (352)392-HELP(4357). Once the media is available, you can get it at the UF
Computing Help Desk or at the UF Bookstore .
Other software training opportunities are available. For examples through Lynda.com
http://www.lynda.com/member.aspx

Campus Helping Resources

Students experiencing crises or personal problems that interfere with their general well-being
are encouraged to utilize the university’s counseling resources. The Counseling & Wellness
Center provides confidential counseling services at no cost for currently enrolled students.
Resources are available on campus for students having personal problems or lacking clear career
or academic goals, which interfere with their academic performance.

12
University Counseling & Wellness Center, 3190 Radio Road, 352-392-1575,
www.counseling.ufl.edu/cwc/
Career Resource Center, First Floor JWRU, 392-1601, www.crc.ufl.edu/

Services for Students with Disabilities

Please come and talk to your TA at the beginning of the semester about any accommodations
required. We will make sure that the student’s needs are met to the best of our abilities in the
laboratory setting.
The Disability Resource Center coordinates the needed accommodations of students with
disabilities. This includes registering disabilities, recommending academic accommodations
within the classroom, accessing special adaptive computer equipment, providing interpretation
services and mediating faculty-student disability related issues.
0001 Reid Hall, 352-392-8565, www.dso.ufl.edu/drcStudents with Disabilities
www.dso.ufl.edu/drc/
Students requesting classroom accommodation must first register with the Dean of Students
Office in Peabody hall. The Dean of Student Office will provide documentation to the student
who must then provide this documentation to the Instructor when requesting accommodation
at the beginning of the semester.

We take your wellbeing VERY serious, so please don’t hesitate to meet with your TA or see me
(Dr. Oli moli@ufl.edu) any time with problems or difficulties you may encounter during your
time at UF.

13
Generic weekly schedule

Module Exercises

Intro - syllabus, canvas, lab safety, art of microscopy,

Welcome,
life in a drop of water, taxonomy/phylogeny, eukaryote
Intro & 1 - prokaryote

Introduction to your unknown project, Microorganisms

Bioterroris
in the environment and on you, gram stain, simple
m&2 stain, negative stain, aseptic technique, pipetting

Introduction to Labmath, Streak for isolation, scientific

method, enumeration of bacterial populations CFU/ml,
Labmath & 3
growth curve, isolation of colonies from a mixed
culture,

Microbes in Chose & present your public health topic; Diagnostic

the News & mirobiology - selective and differential media,
4 biochemical tests, growth characteristics.

Gideon database, DNA isolation,

5
16s RNA PCR & gel elctrophoresis

Bioinformatics & review,

6
Student research project proposals

Midterm practical and visual exam

Antibiotic disk diffusion susceptibility test & the post

7 antibiotic aera, disinfectants and other antimicrobials,
ELISA, MRSA screen

14
8 Fecal float and water lab

9 Microbe art, mycology

Fermented + rotten foods prebiotics, probiotics , food

10
sample,

Finish student projects & Presentations

15
Databases you will use
Virtual pond dip – for wet mount identification
http://www.microscopy-uk.org.uk/index.html?http://www.microscopy-uk.org.uk/ponddip/

NCBI Taxonomy (no password)

http://www.ncbi.nlm.nih.gov/taxonomy

Gideon – to determine your unknown and for public health project

http://web.GIDEONonline.com/loginx.php?user=ufmicro (no password)
If you are not on campus you have to use VPN to connect to the database
http://www.uflib.ufl.edu/ufproxy.html

DNA lims – to retrieve your 16s DNA sequence

http://dnalims.dnatools.com/cgi-bin/dna/password.cgi
login: monikaoli
password: microbiology

BLAST – for sequence alignment

http://blast.ncbi.nlm.nih.gov/Blast.cgi

Food Safety First – for growth curve simulation

http://www.foodsafetyfirst.org/fsf_mgsp.html

Optional software and database

EndnoteWeb Reference management program
http://web.uflib.ufl.edu/endnoteweb.html

HealthMap
http://healthmap.org/en/

Microbiology Videos
Your TA will let you know when you have to watch each video for which module! You
may have quizzes about the content of the videos

Check out the UF MICROBIOLOGY video channel in Vimeo

https://vimeo.com/channels/859405

16
Please note all of the videos are produced at the Department of Microbiology and Cell
Science and many of them were actually made as part of the independent student
project!!!! Thanks to all our amazing students!

Thanks to some of our amazing students we have two new tutorials, one for using
Endnote reference management
https://vimeo.com/114244854

and a great overview of bioinformatics!

https://vimeo.com/116163972

Microbiology intro
Lab Safety Rules
https://vimeo.com/46094533

Daily Routines
https://vimeo.com/46094085

Aseptic Techniques
https://vimeo.com/41315162

Basic Methods
Art of Microscopy
https://vimeo.com/166713949

Basic Anatomy of a Microscope

https://vimeo.com/44820192

Wet Mount
https://vimeo.com/48160779

Streak for isolation

https://vimeo.com/48162797

Pipetting
https://vimeo.com/44820191

Computer Tutorials
Graphing with Excel
https://vimeo.com/49518570

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 Growth curve and growth rate calculation
https://vimeo.com/52150245

Visualizing Microbes
Gram Stain
https://vimeo.com/44820193

Negative Stain
https://vimeo.com/73670001

Capsule Stain
https://vimeo.com/73672899

Flagella Stain
https://vimeo.com/73666368

Traditional Diagnostic Methods

SIM
https://vimeo.com/73671768

Phenol Red Broth

https://vimeo.com/73671112

Blood Agar
https://vimeo.com/73656591

Mannitol Salt Agar

https://vimeo.com/73668944

MacConkey agar
https://vimeo.com/73668126

DNAse Agar
https://vimeo.com/73662034

Citrate Agar
https://vimeo.com/73661148

Catalase Test
https://vimeo.com/73659734

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 Anaerobe Jar
https://vimeo.com/73655513

Molecular Diagnostic test

PCR 1
https://vimeo.com/49327264

PCR 2
https://vimeo.com/49520521

PCR 3
https://vimeo.com/49520034

Bioinformatics
Sequence retrieval and Blast
https://vimeo.com/50079545

Blast tutorial and phylogenetic tree

https://vimeo.com/51947843

Basic Bioinformatics Tutorial

https://vimeo.com/116163972

Diagnostic tests
ELISA
https://vimeo.com/73662873

Parasites
Fecal float
https://vimeo.com/73664907

Other Software
Endnote reference management
https://vimeo.com/114244854
http://web.uflib.ufl.edu/endnoteweb.html

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Virtual Field Trips
Diagnostic lab UF Vet School
https://vimeo.com/41315011

Documentaries – student projects

Lyme documentary
https://vimeo.com/54990581

Cholera outbreak in Haiti (public health)

https://vimeo.com/48172281

Cool Stuff
Microbes did you know…….
https://vimeo.com/51246086
https://vimeo.com/63859256

Why microbiology?
https://vimeo.com/41315163

Meet the MCS faculty

https://vimeo.com/41315161

Microbiology @ UF Lab Terminology:

Quizlet Vocabulary Sets
All study sets
https://quizlet.com/class/2282683/

Modules

Biosafety
https://quizlet.com/118956260/biosafety-flash-cards/

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Microscopy
https://quizlet.com/118956966/microscopy-flash-cards/

Life in a drop of water

https://quizlet.com/118960595/life-in-a-drop-of-water-flash-cards/

Microbiome
https://quizlet.com/145781826/microbiome-flash-cards/

Bioterrorism
https://quizlet.com/121416442/bioterrorism-flash-cards/

Visualizing bacteria
https://quizlet.com/118964990/visualizing-bacteria-flash-cards/

Isolation of microbes
https://quizlet.com/118974444/isolation-of-microbes-flash-cards/

Pipetting
https://quizlet.com/118965384/pipetting-flash-cards/

Labmath and Graphing

https://quizlet.com/118963031/labmath-and-graphing-flash-cards/

Enumeration of microbes
https://quizlet.com/118975469/enumeration-of-microbes-flash-cards/

Growing microbes
https://quizlet.com/118971694/growing-microbes-flash-cards/

Traditional diagnostics
https://quizlet.com/118969630/traditional-diagnostics-flash-cards/

Molecular diagnostics
https://quizlet.com/118977597/molecular-diagnostics-flash-cards/

Combating microbes
https://quizlet.com/118985037/combatting-microbes-flash-cards/

Antibiogram and Antibiotics

https://quizlet.com/112849756/antibiogram-and-antibiotics-flash-cards/

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MRSA screen
https://quizlet.com/118986660/mrsa-screen-flash-cards/

Immunological methods & STDs

https://quizlet.com/118982561/immunological-methods-stds-flash-cards/

Global Traveler – water crisis

https://quizlet.com/118987142/global-traveler-water-crisis-flash-cards/

Fungi
https://quizlet.com/112850493/fungi-flash-cards/

Microbes, food and fermentation

https://quizlet.com/118990517/microbes-food-and-fermentation-flash-cards/

Mini modules
https://quizlet.com/118981521/biofilm-flash-cards/

Meet the microbes

Pathogens - Bacteria
https://quizlet.com/112850007/pathogens-bacteria-flash-cards/

Pathogens – Parasites
https://quizlet.com/112848889/pathogens-parasites-flash-cards/

Other sets
Definitions MO (summary of key terms)
https://quizlet.com/110252546/definitions-mo-flash-cards/

Etymology – word origins

https://quizlet.com/110251306/etymology-word-origins-flash-cards/

Famous microbiologists
https://quizlet.com/112845093/famous-microbiologists-flash-cards/

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