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Bio 311 Microbiology Spring 2019

Mon/Wed 11:45 am - 1:00 pm Payson-Smith 303 Dr. Rachel Larsen rachel.larsen@maine.edu Office: 477 Science Building Phone: 207-780-4263 Office hours: Mondays 10:00 – 11:00 am or by appointment Recommended Text: Microbiology, An Evolving Science, 4th edition. Slonczewski and Foster 2017. (older editions are also fine, but the chapters may not match the schedule below) Other reading assignments: Other required reading will be posted on Blackboard when assigned. Course Objectives: This course is aimed at biology and biochemistry majors with the assumption that you already have a strong background in both biology and chemistry. Your objectives for this class include (but are not limited to): - Gain an understanding of the ubiquity and variability of microbes - Gain an understanding of the basic functioning and metabolism of a microbial cell - Learn how these basic functions are relevant to the lifestyle of a microbe (including how some cause

disease) - Gain an understanding of the ways in which microbes interact with each other and their environment,

including both positive and negative interactions with a human host - Communicate science to classmates and to non-scientists Grading Criteria: Exams (3) 70% Quizzes (3) 15% Community and poster projects 8% Worksheets/Discussions 5% One-minute presentation 2% Grading Scale: Final grades will be awarded on a typical scale. 93-100 = A, 90-92 = A-, 87-89 = B+, 83-86 = B, 80-82 = B-, 77-79 = C+, 73-76 = C, 70-72 = C-, 67-69 = D+, 63-66 = D, 60-62 = D-, <60 = F Exams: There will be three exams, each consisting of both multiple-choice and short answer questions. The third exam will be during final exam week and is not cumulative, but the expectation is that you have learned concepts throughout the semester and continue to apply these ideas. (Exam 1 = 20%, Exam 2 = 25%, Exam 3 = 25%) Make a note of these dates (included in the schedule below) because make-up exams will only be offered in cases where extreme, justifiable excuses can be provided. You must contact me before or during the exam if are going to miss class and need to take a make-up exam. If you fail to get in touch with me before or during the exam, then you may NOT take a make-up exam.

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Past students have found it very useful to study by drawing, teaching each other, making concept maps, and other active methods. Simply making flashcards and/or reading the book/notes is NOT the best way to study for this class! I am more than happy to meet with you to guide you towards the best study techniques. Quizzes: There will be three quizzes throughout the semester, each given at the beginning of class on the dates noted in the schedule below. Quizzes cover material we have discussed since the previous quiz or exam, and the purpose of these is to assess your level of understanding between exams and to give you an additional way to earn examination points. You must contact me before or during the quiz if you are going to miss class and need to take a make-up quiz. If you fail to get in touch with me before or during the quiz, then you may NOT take a make-up. Worksheets/Discussions: Worksheets/problems will be used to support and expand upon the lecture material throughout the semester. These are designed to help you think more deeply about the lecture topics and better prepare for the exams. Topics from these worksheets or discussions will be on the exams unless announced otherwise. Communicating science: Throughout the semester we will engage in several types of activities that focus on communicating scientific information. Detailed instructions about these will be provided separately.

I. “One-minute current event presentation The purpose of this assignment is to encourage you to pay attention to microbiology in the news (it is in the news every day!) and to practice speaking in front of the class. One time during the semester, on the class day of your choice, you will give a very short (~1 minute) presentation about recent research into microbiology, accompanied by one slide as a visual aide. The best sources of information are website like Science Daily or Eurekalert, which summarize recent publications in the scientific literature. I encourage you to find research that has been published recently (within the past ~6 months) but certain older studies are acceptable as well. Do not read directly from your source word for word. You may have notes for yourself, but we want to hear your summary of the article you read. Sign up for one of the available slots listed on Blackboard and include the title of your article to ensure that stories are not repeated. If you wait too long and all remaining slots are filled (a maximum of 5 per class day) then you will receive a “0” for this assignment. No exceptions. II. Community outreach project This assignment is to: 1) provide you the benefit of learning to take a topic from this class and teach it to members of the community and 2) benefit the community through an exciting and educational visit from USM students. Most of you will do this with a partner (or two) and collaborate with a local secondary school classroom (grades ~3-12), but there are other options as well. The date designated in the schedule below is the deadline to submit a plan for your “curriculum”, but the project may be completed at any point in the semester. A separate handout will describe the project in detail. You will also have the option to earn extra credit through a number of different efforts, many of which are associated with extra effort in a community service capacity. This will also be described on the handout. III. Human microbiome poster session The last project will be an exploration of recent research into the exciting world of the human microbiome, which we now know plays a huge role in our health and wellness. Because much of this research is new, it is useful to go beyond the textbook and study recent reports in the literature. On the date indicated in the syllabus, you and a partner (or you individually) will bring a poster (of your own design) describing research on a specific topic related to the human microbiome, and you will share these with each other through an informal meeting-style poster session.

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Blackboard: Blackboard will be used as our course website. I will post the syllabus, handouts, announcements, lecture notes, supplemental reading, exam grades, etc. It is your responsibility to check this website regularly and locate information for classes that you may have missed. Electronic devices and other distractions: Electronic devices (cell phones, tablets, laptops, etc.) are distracting and often a disturbance to the class as a whole. Unless you have some kind of extreme and justifiable reason for looking at your phone or if you can prove you are taking notes on your table, these devices must be out of sight for the duration of the class. Likewise, unnecessary conversations with your neighbor during class are disruptive and disrespectful to both me and your classmates. If you are the cause of any type of class disruption, you may be asked to leave. Academic Integrity: You are expected to understand and follow the guidelines laid out by the Student Academic Integrity Policy for the University of Southern Maine. Cheating during quizzes and exams (including deliberately providing answers to another student) is unacceptable and will be dealt with appropriately. In addition, any evidence of plagiarism on the writing assignment will not be tolerated. If you have any questions about what constitutes cheating or plagiarism, please review the university policies or come talk to me. Here is a link to the university policy: http://usm.maine.edu/deanofstudents/student-academic-integrity-policy-0 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 experience difficulty in courses for a variety of reasons. The following are resources on campus for students.

• 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

• The USM learning commons has launched a website called AGILE (academic gains thrugh improved learning effectiveness). The learning tools described on this website are highly recommended. https://usm.maine.edu/agile

• 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

The University of Southern Maine shall not discriminate on the grounds of race, color, religion, sex, sexual orientation, national origin or citizenship status, age, disability or veteran's status in education, employment, and all other areas of the University. Discrimination inquiries should be directed to Betsy Stivers, Director, Equal Opportunity Center of Excellence. She can be reached at 780-4709 or elizabeth.stivers@maine.edu

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Tentative Schedule Note: This schedule is very likely to change if we spend more or less time on any given topic! Any changes that are made will be announced and updated schedules will be posted on Blackboard when necessary. There are many interesting topics that we will not have time to cover but if you see something in the book or elsewhere that sounds particularly interesting feel free to put in a request!

Date Topic Readings

1/21 M NO CLASS – MLK Jr Holiday

1/23 W What is a microbe and how are they studied? definitions, relationships, microscopy, culturing Ch. 1, 2, 17, (4.3)

1/28 M What are the external features of a bacterial cell? membranes, cell walls Ch. 3, (4), 25.3

1/30 W What are the external features of a bacterial cell? flagella, pili, capsule Ch. 3, (4), 25.3

2/4 M Quiz 1 How do bacteria grow and divide? cell division, growth

Ch. 3, 4, 5

2/6 W How do bacteria grow and divide? growth, environmental factors Ch. 3, 4, 5

2/11 M How do bacteria grow and differentiate? biofilms, endospore forming bacteria Ch. 4.6, 4.7 (18.3)

2/13 W EXAM 1

2/18 M No class – President’s Day

2/20 W How does a bacterial cell get energy? catabolism (transport), phototropy, respiration Ch. 13, 14 (18)

2/25 M How does a bacterial cell get energy? respiration, fermentation Ch. 14, 15, 16

2/27 W How does a bacterial cell get energy? lithotrophy, methanogenesis Ch. 13, 14, 15, (18)

3/4 M Building a cell biosynthesis, Calvin cycle, nitrogen fixation Ch. 15

3/6 W Quiz 2 How do we control the growth of bacteria?

physical and chemical methods, antibiotics Ch. 5, (8), 16, 27

3/11 M How do bacteria resist being killed? antibiotic resistance Ch. 27

3/13 W Who are the "non-living" microbes? viruses

Ch. 6, 11 (26, 27) Community project update due

3/18 M No class – Spring break

3/20 W No class – Spring break

3/25 M Class discussion about the origins and evolution of viruses

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3/27 W EXAM 2

4/1 M What is the "instruction manual" of the cell? genomes, plasmids, DNA transfer, CRISPR Ch. 7, 8, 9

4/3 W How is the “instruction manual” interpreted? replication, sigma factors Ch. 7, 8, 9, 10

4/8 M How is the "instruction manual" interpreted? gene expression, quorum sensing Ch. 10

4/10 W Manipulating bacterial cells techniques used to study bacterial cells Ch. 12

4/15 M Quiz 3 The good guys who live with us human microbiome

Ch. 23

4/17 W The good guys who live with us human microbiome Ch. 23

4/22 M Microbiome poster session today

4/24 W A few dangerous species pathogens Ch. 25, 26

4/29 M The few dangerous species pathogens, epidemiology, vaccinations Ch. 25, 26

5/1 W The few dangerous species pathogens Ch. 25, 26

5/8 W EXAM 3 – 10:45 – 12:45 pm

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