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Bio 282: Microbiology Laboratory Fall 2018

Science Building 405

Dr. Rachel Larsen rachel.larsen@maine.edu Office: 477 Science Building Office hours: After lab or by appointment

Required materials 1. Bio 282 Lab Manual, Custom manual published by University Readers and available at the bookstore2. A dedicated notebook (any type of notebook is fine, but must be used solely for this class this semester)3. Safety glasses (available at the bookstore or local hardware stores)4. Lab coat (some are available to borrow, but not enough for everyone)

Course Objectives This lab course is a companion to both BIO 281 and BIO 311 Microbiology lecture courses, which should betaken either concurrently or prior to this lab. The experiments will not always be coordinated with the lecture,but the topics will enhance what you are learning in the lecture, and vice versa.

Throughout the semester you will: - Learn a variety of skills used to study microorganisms- Understand how to properly document your efforts in a lab notebook- Learn how to read about research and plan an experiment- Consider ways to troubleshoot when experiments do not go as planned- Learn how to analyze data- Become skilled at explaining your results both verbally and in written form

Attendance Attendance is required! The laboratory experience is all about hands-on participation and experimentation so itis difficult to make up the work if you miss a class. If you have a valid and reasonable excuse for missing class,then it is important to let me know as soon as possible. Sending a text to your lab partner is NOT sufficient! Ifyou miss a lab, the following are appropriate options for making up the work:

1. Attend another section. (this is the best option)2. Make up the work outside of class at a time that is convenient for an instructor or a tutor, which may or

may not be possible depending on the experiment and the schedule.3. Make up the appropriate amount of hands-on work along with a written assignment to be determined by

the instructor.Make every effort to arrive on time to class and stay until the end of the session. We start class with an explanation of the work for the day and a demonstration of the techniques you need to learn, so if you are late, you will be unprepared for the day. Being late is also disrespectful to your lab partner(s). Points will be deducted from your participation score if you repeatedly arrive late or leave early without explanation.

If you miss a lab and do not make up the work satisfactorily, your course grade will be lowered appropriately. Three or more unexcused absences with missed work will result in an F in the class.

Additionally, it is unsafe to work in the laboratory if you are under the influence of drugs or alcohol. If you come to class under the influence, you will be sent home and will receive an unexcused absence for that day.

Copyright 2018 Dr. Rachel Larsen

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Assessments Lab reports (3) 65% Pre-labs, readings & assignments 5% Lab notebooks 10% Presentations (2) 10% Performance and participation 10% Assignments Assignments will either be in preparation for that lab day or assigned on the day indicated in the schedule. Assignments must be turned in on time (or emailed to me if you are absent) otherwise you will receive “0” points. No exceptions. Additional assignments, including worksheets to complete during lab or at home, are noted in the schedule below. Readings for each experiment and lab day are indicated in the schedule below. The more prepared you are when you come to the lab, the more smoothly your experiments will go! Notebooks Laboratory notebooks are essential to documenting the scientific process and thorough notes will make writing your reports much easier. Several times throughout the semester, without warning, I will be checking to see that you have your notebook with you in lab and are using it appropriately. Additionally, notebooks will be collected and graded several times during the semester. Notebook guidelines:

1. Maintain a table of contents on the first page(s) and fill this in as you go. If your notebook does not have page numbers, number the pages as you go.

2. Each lab day, write the date (mm/dd/yy), a brief title describing your work, and a brief purpose describing what you intend to learn from that experiment(s). If an experiment spans more than one day, use the same title on each page (this helps you keep track of the experiment).

3. Outline or draw your plan for the day (some experiments will require more planning than others). 4. If you are following published instructions (like your lab manual or a handout) write down the page

numbers and/or chapter titles. 5. There is no need to re-copy step-by-step instructions from your manual (assuming you make note of the

page numbers), but you should write down anything you did differently from the published protocol or anything you varied as part of your experiment, including any mistakes that you made.

6. Write out calculations (culture labels, weights, dilutions, etc.) 7. Clearly describe your observations and results for each experiment or measurement made. 8. Provide a summary or conclusion at the end of every experiment. Include your thoughts about the

results. Other things to remember about keeping a notebook: - Maintain the notebook chronologically. Do not leave pages blank so you can return to fill them in later. - Keep your notebook legible and organized so we can both read it. - However, do not spend time rewriting your notes just to make them neater. If you rewrite, you might copy

incorrectly and introduce incorrect information. - Sometimes experiments go for several days or overlap with other experiments. Thus, it is important to use

the brief title each time you are referring to different aspects of the same experiment at a later date. - Details, details, details! Lab reports You will write and submit three papers (due dates listed in the schedule below), each designed to give you experience explaining your data and understanding how scientific data should be presented. Detailed instructions will be provided for each paper.

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You will typically be working with a partner in the lab, however, all written work should be completed independently. It is very important that you understand what constitutes plagiarism by reading through the academic integrity guidelines laid out by the university (http://usm.maine.edu/deanofstudents/student-academic-integrity-policy-0). Any evidence of copying or plagiarism will result in a “0” for that assignment and will likely be reported to the Dean of Students Office. Late reports will be penalized with a 10% deduction per day for each day (24 hours) they are submitted beyond the deadline. However, you have four floating “grace days” (a total of four days for the semester) that you may use to turn in reports late without penalty. For example, you may turn in the first report four days late and the remaining two must be on time, or you may turn in one report two days late and each of the remaining reports one day late, etc. Because you have this flexibility, no other late excuses (with the exception of those most extreme and dire) will be accepted. Presentations Twice during the semester, as indicated on the schedule, you and your lab partner(s) will present your results to the class. Your presentation will be short (~5 minutes per person) but should be well organized and clearly supported with a slide show (via Google slides). In addition, you will each present about one of the metabolic methods associated with the Unknown Microbe lab. Detailed instructions will be provided. Performance and Participation Because this class is heavily based on your active participation, you will receive a score for the effort you put forth in the class and your level of participation. If you are working carefully and trying your best, then failed experiments will not count against you. If poor results are due to inattention and sloppiness then deductions will be made. Because this type of score is very subjective, you are welcome to talk to me at any point during the semester to find out how you are doing. Blackboard The course Blackboard web site is accessible directly from the USM homepage under “QuickLinks”. Here you will find all pertinent information including lab report instructions, presentation instructions, pre-lab questions, protocols, etc. It is your responsibility to find the information for any classes you may have missed. Use of electronics in lab Because we will be working with live microbes in the lab, you may not use cell phones or computers in lab. If you need to use your cell phone as a camera or as a calculator, it must be protected in a zip-lock bag. When there is a lab session for which laptop computers are helpful, this will be announced. Any non-educational activities including talking or texting on cell phones, chatting, web-surfing, and game-playing in lab is not allowed in the lab. Accommodations At any point in the semester, if you encounter difficulty with the course or feel that you could be performing at a higher level, consult with me. Students may experience difficulty with coursework for a variety of reasons. The following are campus resources that can be helpful.

• For writing skills or time management, you can make an appointment to see a student tutor at the Learning Commons located in both the Portland and Gorham libraries. For more information, visit http://www.usm.maine.edu/learningcommons. The Writing Center at LAC is also available to all USM students and is a great option for students living in the greater Lewiston/Auburn area. For more information, please visit http://usm.maine.edu/writingcenter.

• If you need accommodations due to a disability, please contact the Disability Services Center for confidential assistance and accommodation authorization. Timely notification of accommodations is essential. For more information, visit http://usm.maine.edu/dsc.

• University Health and Counseling Services is a student resource that promotes the health and well-being of the USM community. More information can be found at www.usm.maine.edu/uhcs.

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Schedule: (Subject to change, if necessary) Date Experiment(s) Chapters Reminders 9-3/9-4 Mon/Tues

No lab – Labor Day

9-5/9-6 Wed/Thurs

Safety Microbes in the Environment Sample yourself and environment

1 6

Safety quiz

9-10/9-11 Mon/Tues

Microbes in the environment Observe and discuss Water Testing Discuss and plan

6 7

Bibliography due

9-12/9-13 Wed/Thurs

Water Testing Set up experiment Outline introduction section of paper

7 Bring water samples to class

9-17/9-18 Mon/Tues

Water Testing Observe and analyze Discuss scientific paper format

7

9-19/9-20 Wed/Thurs

Microscopy Introduction Prepared slides Size measurements

4 4-4

Microscopy worksheet

9-24/9-25 Mon/Tues

Microscopy View live cells (wet mounts) Unknown Microbe First isolation streak

4-5 8-1 3-2

Water testing report due Saturday by midnight

9-26/9-27 Wed/Thurs

Unknown Microbe/ Microscopy Wet mount and simple stain Gram stain

5-4 5-6

10-1/10-2 Mon/Tues

Unknown Microbe (set up) OF media or Thioglycollate Phenol Red (fermentation), MR-VP Mannitol Salt, Blood agar SIM (Continue Gram stain, if necessary)

8-4,8-5 8-8,8-9 8-11,8-24 8-14

10-3/10-4 Wed/Thurs

Unknown microbe Analyze results from Mon/Tues Catalase, Oxidase KOH test

8-6. 8-7 5-7

10-8/10-9 Mon/Tues

No Lab – Columbus Day

10-10/10-11 Wed/Thurs

Unknown microbe (set up) Lysine decarboxylase Nitrate, Urea Starch, Casein, Gelatin, (Lipid), DNA Endospores, Citrate (optional)

8-17 8-15, 8-16 8-19 – 8-23 8-25, 8-26

Worksheet (part 1) due

10-15/10-16 Mon/Tues

Unknown microbe Analyze results from Wed/Thurs Set up Motility deep

8-3

10-17/10-18 Wed/Thurs

Unknown microbe Flagella stain Set up any additional tests

5-9 8-27

Worksheet (part 2) due

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10-22/10-23 Mon/Tues

Unknown microbe Antibiotic resistance – set up Any additional testing [UV mutagenesis]

9

10-24/10-25 Wed/Thurs

Unknown microbe Antibiotic resistance – observe [Observe UV mutants] Plan presentation

9

10-29/10-30 Mon/Tues

Unknown microbe Presentations

Unknown microbe lab report due Saturday at midnight

10-31/11-1 Wed/Thurs

Microbes in Food Plan Discuss dilutions

10 Appendix V

Worksheet/planning assignment

11-5/11-6 Mon/Tues

Microbes in Food Set up experiment

10-2

Bring food samples to class

11-7/11-8 Wed/Thurs

Microbes in Food Observe plates; record data Plan second experiment

10-2

Dilution problems set due

11-12/11-13 Mon/Tues

No Lab – Veterans Day

11-14/11-15 Wed/Thurs

Microbes in Food Set up second experiment Discuss data and graphs

10-2

Bring food samples to class

11-19/11-20 Mon/Tues

Microbes in Food Observe plates; record data Isolation streak of chosen colonies

10 Graph of 1st expt data due

11-21/11-22 Wed/Thurs

No Lab – Thanksgiving

11-26/11-27 Mon/Tues

Microbes in Food Microscopy and second isolation streak Discuss data and graphs

10

11-28/11-29 Wed/Thurs

Microbes in Food PCR

10-3

PCR worksheet

12-3/12-4 Mon/Tues

Microbes in Food Gel electrophoresis and Purification

10-4, 10-5

Graph of 2nd expt data due (Send DNA samples for sequencing)

12-5/12-6 Wed/Thurs

Microbes in Food Discussion of sequence analysis

10-6

12-10/12-11 Mon/Tues

Microbes in Food Sequence analysis Organize presentations

10-6

12-12/12-13 Wed/Thurs

Microbes in Food Presentations Lab Clean up

Food lab report due Saturday by midnight

Copyright 2018 Dr. Rachel Larsen