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Bio 282: Microbiology Laboratory Fall 2019

Science Building 405

Dr. Rachel Larsen rachel.larsen@maine.edu Office: 477 Science Building Office hours: Scheduled time to be determined; or by appointment

Required materials 1. Bio 282 Lab Manual, Custom manual published by Cognella (available to order directly from Cognella

or through eCampus)2. A spiral notebook (any type is fine but needs to be dedicated to this class this semester)3. Safety glasses (available at the bookstore or local hardware stores)4. Lab coat

Course Objectives This lab course is a companion to both BIO 281 and BIO 311 Microbiology lecture courses, which should be taken 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 it is 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! If you 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.

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.

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Copyright 2019 Dr. Rachel Larsen

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Assessments Lab reports (3) 65% Presentations (3) 12% Assignments/Worksheets 10% Lab notebooks 8% Performance and participation 5% Assignments/Worksheets Assignments and worksheets will either be assigned ahead of time or completed in class. All assignments/worksheets must be turned in on time (or sent via email if you are absent) otherwise you will receive “0” points. Due dates (some tentative) are noted in the schedule below. Notebooks Laboratory notebooks are an essential way to document the scientific process, and keeping thorough notes will make it much easier to write your lab reports. Several times throughout the semester, without warning, notebooks will be checked or collected and this score is a significant percentage of your final course grade. 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. - Details, details, details! Lab reports You will write and submit three lab reports (due dates listed in the schedule below), each designed to give you experience explaining your data and understanding how scientific data should be presented. These will generally be written in the format of a primary scientific article. Detailed instructions will be provided for each paper. (Point distribution will likely be 20%, 20%, and 25%, but this is subject to change.) You typically work 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, a report to the Dean of Students Office, and/or possible failure in the course.

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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 At the end of each of the three major experiments, 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 supported with a well-prepared slide show (Google slides). 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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Copyright 2019 Dr. Rachel Larsen

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FALL 2019 Date Experiment(s) Chapters Reminders 9-2/9-3 Mon/Tues

No lab – Labor Day

9-4/9-5 Wed/Thurs

Safety Microbes in the Environment Sample yourself and environment

1 6

Safety quiz

9-9/9-10 Mon/Tues

Microbes in the environment Observe and discuss Plate Count Discuss and plan Discuss dilutions

6 11 Appendix V

Bibliography due Dilution problems

9-11/9-12 Wed/Thurs

Plate Count Set up experiment

11 Bring samples to test

9-16/9-17 Mon/Tues

Plate Count Observe and analyze Plan second experiment

11

[Draft of introduction due]

9-18/9-19 Wed/Thurs

Plate Count Set up second experiment Discuss scientific paper format

11 Graph due Worksheet (tentative)

9-23/9-24 Mon/Tues

Plate Count Observe and analyze Outline reports and presentations

11

9-25/9-26 Wed/Thurs

Plate Count Presentations and Discussion

Plate Count report due Saturday 9/28 by midnight

9-30/10-1 Mon/Tues

Microscopy Introduction Prepared slides Size measurements

4-1,-2,-3 4-4

Microscopy worksheet

10-2/10-3 Wed/Thurs

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

4-5 8-1 3-2

10-7/10-8 Mon/Tues

Unknown Microbe/ Microscopy Wet mount and simple stain Gram stain [Motility deep]

5-4 5-6 8-3

10-9/10-10 Wed/Thurs

Unknown microbe (set up) Phenol Red (sugar fermentation) Blood agar Unknown microbe (do today) Catalase, Oxidase KOH test

8-8 8-24 8-6, -7 5-7

10-14/10-15 Mon/Tues

No Lab – Columbus Day

10-16/10-17 Wed/Thurs

Unknown microbe Analyze results

10-21/10-22 Mon/Tues

Unknown microbe (set up) Motility Starch/DNA/(other)

8-3 8-19, -23

10-23/10-24 Wed/Thurs

Unknown microbe Analyze results Flagella stain

5-9

Worksheet (project progress)

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10-28/10-29 Mon/Tues

Unknown microbe Biolog test – set up

10

Biolog Worksheet

10-30/10-31 Wed/Thurs

Unknown microbe Biolog test – analyze

10

11-4/11-5 Mon/Tues

Unknown microbe Antibiotic resistance – set up Set up additional tests as assigned

9

11-6/11-7 Wed/Thurs

Unknown microbe Antibiotic resistance – observe Observe additional tests Outline reports and presentations

9

11-11/11-12 Mon/Tues

No Lab – Veterans Day

11-13/11-14 Wed/Thurs

Unknown microbe Presentations DNA Sequencing Analysis Plan

Unknown microbe lab report due Saturday 11/16 at midnight

11-18/11-19 Mon/Tues

DNA Sequencing Analysis Spread plates

3 Bring samples (if relevant)

11-20/11-21 Wed/Thurs

DNA Sequencing Analysis Microscopy and second isolation streak

3.4.5 Bibliography due

11-25/11-26 Mon/Tues

DNA Sequencing Analysis PCR

12-2

PCR worksheet

11-27/11-28 Wed/Thurs

No Lab – Thanksgiving

12-2/12-3 Mon/Tues

DNA Sequencing Analysis Gel electrophoresis and Purification

12-3, 12-4

(Send DNA samples for sequencing)

12-4/12-5 Wed/Thurs

DNA Sequencing Analysis Discussion of sequence analysis

10-6

12-9/12-10 Mon/Tues

DNA Sequencing Analysis Sequence analysis Outline reports and presentations

12-5

12-11/12-12 Wed/Thurs

DNA Sequencing Analysis Presentations Lab Clean up

DNA lab report due Saturday 12/15 by midnight

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Copyright 2019 Dr. Rachel Larsen