Bio Sci M118L-Microbiology laboratory

Syllabus
COURSE Microbiology laboratory
NAME:
COURSE #: Bio Sci M118L
QUARTER: Summer Session II 2019
MEETING AM: TTh – 8 – 11:50 am; F 12-12:50 pm
TIMES: PM: TTh – 1 - 4:50 pm: F 1-1:50 pm

FINAL EXAM None.

INSTRUCTOR

NAME Dr. Cathie Overstreet

OFFICE LOCATION SH - 237
CONTACT INFO coverstr@uci.edu
OFFICE HOURS ½ hour before class and ½ hour after class

REQUIRED COURSE MATERIALS:

 M118L Laboratory manual (Summer 2019 only!)
 Additional reading materials (journal articles) will be posted on CANVAS.
 The Virtual Interactive Bacteriology Laboratory by Dr. Cindy Grove Arvidson, Ph.D., Michigan
State University.

COURSE DESCRIPTION:
The goal of this course is for you to gain a hands-on understanding of microbiology. We will isolate
bacteria from soil and a bacteria from your body. Isolated bacteria will be identified using biochemistry
testing and/or molecular biology techniques. This lab is discovery based, which means we don’t know
what microorganism you will identify thus, you will be given organisms of known genus and species for
you to use to fine tune your skills. You will be working with novel samples just as a real researcher! Not
only will you learn how to perform several techniques, you will gain an understanding of how to think
like a scientist. Throughout the summer, you will learn what it is like to work, think, and learn in an
actual laboratory setting.

CONTENT LEARNING OUTCOMES:

By the end of this course, you will be able to…

 Properly prepare and view specimens for examination using microscopy
 Use pure culture and selective techniques to enrich for and isolate microorganisms.
 Use appropriate methods to identify microorganisms (media-based, molecular)
 Use appropriate microbiological and molecular lab equipment and methods
 Practice safe microbiology, using appropriate protective and emergency procedures.
 Document and report on experimental protocols, results and conclusions.

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 Explain the principle of the various microbiology techniques we will use in the lab.
 Analyze and interpret results from a variety of microbiological methods
 Identify credible scientific sources and interpret and evaluate the information therein.
 Demonstrate an ability to formulate hypotheses and design experiments based on the scientific method.
You will accomplish these in numerous ways:
 You will perform classic and modern microbiology techniques in lab experiments and become proficient
in numerous lab skills. You will present your results in the form of laboratory reports. Your reading,
writing and proficiency in lab will be assessed by reading quizzes, lab reports, and Professional points.
Note: This class fulfills part of the writing component for your major.
 We will discuss a few microbiology techniques and experiments and important microbiology concepts
during lectures. Your reading and participation in class will be assessed by reading quizzes.
 You will then apply these core concepts to solve microbiology problems (assigned in class, lab and
quizzes). This part of your learning will be assessed by in class participation and by your performance in
quizzes and the final exam.
 You will read various journal articles, answering and discussing high-level cognitive questions about the
author’s findings. These articles will present you with examples on how biochemistry concepts can be
applied to research and human health. Real life applications will help you make broader connections in
the field. Your reading and participation in these activities will be assessed by article discussion handouts
and paper quiz.
SCIENTIFIC SKILLS LEARNING OUTCOMES:
By the end of this course, you will be able to…
1)Effectively communicate microbiology through discussions of research articles and written exams and
lab reports.
2)Interpret and evaluate results from lab experiments and primary research articles
3)Gain critical thinking and analytical skills through working in class activities, problems and analysis of
research articles.

ASSESSMENTS & GRADES:

Lab Quizzes (6 x 20 points each – drop 1) 100 points
Annotated Pre Lab (3 pts x 11 – drop 1) 30 points
Lab Notebook Maintenance 45 points
Scientific Paper Quiz (1) 35 points
Lab reports (2) 150 points
Scientific Paper Assignments (2 x 20 pts) 40 points
Professionalism Points 50 points
Lab Practicum 50 points
Total: 500 points

Quizzes will be held at the beginning of class (please see the course schedule). The quizzes will cover
specifics concerning the experimental protocols you perform during the lab, especially principles and
applications of those lab protocols. There is no need to memorize protocols. You will, however, be

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responsible for understanding the principle of the techniques you run in lab to answer application and
understanding quiz questions. These quizzes are cumulative.

Scientific Paper assessments

An important part of your college and laboratory experience is being able to read and understand
primary scientific literature. We will cover 2 papers that will be posted on CANVAS. You will have brief
handouts to work at home (Scientific paper Assignments) and we will discuss them as time allows. The
3nd paper will be the subject of a quiz (Scientific Paper Quiz). The paper quiz will be held during lecture
(please see the course schedule).

Lab reports
Lab reports are to be formatted like a scientific paper, with a title, introduction, results section and
discussion (no material and methods section required). This will teach you to organize your thoughts
and data in a way that can be used to teach others about what you accomplished in the lab. You should
get familiar with Lab projects 1-2 (lab manual). More detailed lab report information can be found on
our website. Please note that you will be required to follow the requested formatting and sections for
your lab report. This is all detailed in the Lab report information on our website. Penalties will be added
to reports that do not follow the rules.
Late report policy: Lab reports that are turned in late (either the hard copy or online copy) will be
subject to a late penalty. This consists of a 15% deduction (off of the total points possible) for one day
late, 30% for two days, and so on. I highly recommend that you turn in your report on time. Taking extra
time to polish your report does not guarantee more points, but turning it in late does guarantee a loss of
points. Please remember that this class fulfills the writing requirement for your major, and, as such, we
will be using rubrics that follow general writing rules for all Biology majors. All rubrics will be posted on
CANVAS.
TurnItIn.com
Various assignments will be submitted to TurnItIn.com. For lab reports, an identical paper copy must be
submitted in lab. You will be automatically enrolled in the course account through your UCI email
address.
Annotated (providing a drawing as well as a written checklist) Pre-Labs:
It is very important you come to lab/discussion prepared. I have found if students visualize what they
will be doing in lab, before they arrive in lab, they are more focused and less likely to make errors. I
require you submit a detailed checklist of what needs to be done for each of your experiments,
accompanied by a drawing of what you will be doing. If you cannot visualize what you are going to be
doing in lab, you need to ask questions before lab starts!

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COURSE POLICIES & INSTRUCTOR EXPECTATIONS:

 Arrive on time.
 Attendance: Attendance to laboratory and discussion classes is mandatory. If you miss more than one
lab or discussion class without an excused absence (original doctor’s note), you will receive an F in the
class. In the case of a true emergency, please contact me within 48 hours.
 Exam attendance: There are no make-up quizzes, no make-ups of any kind. In the case of a true
emergency (I will only consider immediate medical emergency with hospital documentation) you must
notify me within 48 hours of the assessment time and provide proper documentation (which will be
verified by our Department personnel). For VERIFIED emergencies, the other quizzes/assessments will
carry a greater weight to compensate for the missed assessment/quiz or you will take the assessment as
an oral communication (decided on case by case basis).
 Participation in lab and lectures: you will be tested on your reading of that day’s lab experiments as
well as any appropriate material from past labs or lectures. You are EXPECTED to read the lab material
before coming to class to ensure that not only can you participate actively but also to maximize your
time in lab. Important: You should have a plan of action before stepping into the lab (see Pre-Lab
requirements above).
 Lab Manual: You must bring your lab manual and a lined lab notebook of some kind to all labs. Older
manuals will not be allowed nor will sharing a lab manual with your lab partner. Each student must have
their own lab manual. All materials published in the laboratory manual are protected by Copyright laws.
Therefore, you are not allowed to photocopy other students’ materials. All M118L lab manuals are
printed at cost. Therefore, the copyright laws are not meant to protect monetary gains (no royalty
associated to M118L lab manual). The laws are meant to protect our protocols and figures. Please help
us protect our work.
 Lab safety: During lab you are required to wear long pants, close-toed shoes a full-length lab coat (lab
aprons not acceptable) and goggles when asked. The UCI bookstore carries a stock of appropriate lab
attire for M118L. In lab, safety is of the utmost importance, so please be aware of your surroundings and
let us know if anything appears to be wrong. Additional safety rules are listed in your lab manual.
 Technology Policy: you will be asked to turn your cell phones off during class unless otherwise stated.
Please note we have a strict policy on use of phones and tablets during lab. All phones and tablets will
be kept in a basket in front of the class to avoid distractions (enforced at the instructors discretion). No
exceptions! Points will be deducted for electronics misuse in lab.
 E-mail Policies: if you have questions related to due dates, class schedule, lab protocols: please refer to
our web site and lab manual. All schedules, assignments and protocols will be posted online. It is YOUR
responsibility to read and know where to find this information. For all other reasons you may email me
and I will try to help you. Put M118L in the subject line so I will know the email is from you and may give
it the priority attention it deserves.

 Academic Honesty/Principles of Community: Students are responsible for turning in their own work,
citing material properly, and conducting themselves in a civil and ethical manner. Students are also
responsible for abiding by the University Academic Honesty policy and the Principles of Community

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(http://www.editor.uci.edu/11-12/appx/appx.2.htm). We will be taking academic integrity VERY

seriously and report all cases.
 Violations of academic honesty include plagiarizing from published or unpublished work, such as
utilizing lab reports from past students or other students in your group. If it is published, be sure to cite
your source to avoid this problem. In this instance, it is still necessary to paraphrase the contents. While
accepted in some non-science courses, you may NOT use QUOTATIONS of another authors words. YOU
MUST PARAPHRASE and then cite appropriately. You cannot write your reports in groups. All your lab
report writing work as well as annotating figures and making graphs must be your INDEPENDENT effort.
Plagiarizing from your lab partner is still plagiarism. It is also worth noting that intent to cheat is still
cheating, regardless of whether you follow through. Feel free to talk to me if you are unsure of whether
something constitutes cheating. Failure to comply with this policy will result in disciplinary action which
may include a failing grade in the class, suspension or expulsion from the university. In the case of
copying a past report, the owner of the old paper will also be subject to disciplinary action.
 Accommodation Policies: For students with learning disabilities recognized by the university, please let
me know in advance so I can set up the necessary accommodations. Review the policies on
accommodation at: http://disability.uci.edu/ . Your accommodation letter must state all
accommodations granted to you.

How to succeed in this (or any) class?

 Be prepared for lecture/lab – review the class schedule often, read the material before coming to
class.
 Don’t underestimate the amount of time required to complete assignments– allocate plenty time
to work on lab reports and lab notebooks.
 Use the lab report and quiz feedback to improve your academic skills
 You are a vital part of any experiment you perform. The role of the scientist (you) in an
experiment is to plan the experiment well, make careful observations, record those observations
accurately, and interpret the results thoughtfully. Be mindful in lab.
 Lab protocols are a little bit like cooking. Most people can follow cooking recipes, but only chefs
can create recipes or know the reason behind every single step necessary to make a delicious dish. In
lab, you want to be the chef, not the recipe follower.
 Be patient with papers. Papers are documents that present original data that (at least partially)
answer a scientific question in a field, with enough details to replicate the experiments. Thus, papers
are usually written in a “from experts to experts” fashion, with a lot of field-specific jargon and
technical vocabulary. It is absolutely normal to find the content a little difficult at the beginning. But
once you see past the jargon, it gets easier. Think of it as learning to play a complicated board or video
game. Once you learn the rules and right approach for it, playing becomes naturally easier. So, be
patient and don’t give up! Remember: papers will give you direct access to the SOURCE of scientific
knowledge. How cool is that?

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