Biology Microbiology with Lab - Spring 2019

Transcription

1 Biology Microbiology with Lab - Spring 2019 Lectures: Monday and Wednesday, 1:30-2:45, Anderson 211 Labs: Tuesdays, 1:20-4:20pm or 6:00-9:00pm, SEC Room 027a Instructor: Dr. Benjamin Wolfe, benjamin.wolfe@tufts.edu Office hour: Tuesday, 4:30-5:30pm, SEC Room 027a Teaching assistants: Elizabeth Landis, elizabeth.landis@tufts.edu Esther Miller, esther.miller@tufts.edu Course description: As an introduction to microbiology, this lecture and lab course surveys the forms and functions of microbes, including bacteria, archaea, viruses, and some eukaryotic microbes. Laboratory work will teach students fundamental techniques used to isolate, identify, and manipulate microbes. Course objectives: After taking this course, you should be able to: - Describe and organize diversity of microbial life, including both prokaryotic and eukaryotic microbes - Understand how microbiology has developed as a field and how it fits within the larger context of the natural sciences - Employ culture-dependent and culture-independent to isolate, identify, quantify, and characterize microbes - Describe the structure and function of prokaryotic and eukaryotic microbial cells, both as monocultures in the lab and as multispecies communities in nature - Explain ecological and evolutionary processes that determine how microbial communities (microbiomes) assemble - Give examples of the positive and negative impacts of microbes in relation to human health, agriculture, industry, and the environment - Be able to read, comprehend, and constructively critique primary literature in microbiology - Give a presentation that explores a microbial species, microbial community, or microbial process that has a direct impact on your daily activities Class meetings: I expect every student to attend all lectures and labs. Your participation grade depends on you being present in class and participating in class by asking questions and engaging with fellow students. -1 -

2 Textbook: Microbiology: An Evolving Science, 4th edition, J.L. Slonczewski & J.W. Foster, It is OK to purchase the 3rd edition of this text. The content has generally not changed between the 3rd and 4th editions. Most of the figures in the lecture slides will be from the 3rd edition. The 2nd edition it too old and should not be purchased. There is a code to access extra materials that comes with the textbook, but may not be available if you purchase a used copy. This access code is not required. Additional Readings from the Primary Literature: To learn about some of the exciting new advances in microbiology, we ll be reading and discussing three scientific papers throughout the semester. These papers will be posted on Canvas and due dates for reading and responding to these papers will be announced in class. Reading responses (2-page essays) will be counted in the class participation grade. Resources: See Canvas for course information and updates, to find lecture slides, and for other materials related to the course. Grading Policy: Your final grade in the course will be based on the following breakdown: Highest scoring exams 35% Lowest scoring exam 15% Class participation* 10% Lab** 40% *Class participation grade will be based on lecture attendance, participation in class discussions, and completion of 3 reading responses (see Additional Readings from the Primary Literature above and RR#1-RR#3 in schedule below) **The lab component of the grade is composed of 4 major assignments/exercises: 1) a lab practical, 2) a 10-page lab report due at the end of the semester, 3) a microbial diversity presentation, and 4) quizzes at the start of each lab session that evaluate your understanding of the lab guide. Each of these components of the lab section is equally weighted (counts towards 10% of total course gra de). Academic Integrity: Science is not done in isolation; scientists collaborate and communicate their findings. I expect you to work together with your fellow students to communicate your findings in the lab or share your excitement for microbes. But when it comes time for exams or assignments, please only express your own original ideas or answers. Any type of cheating or plagiarism in the course will be punished as harshly as possible as described in the Tufts Academic Integrity Handbook. Please be familiar with the policies described in this handbook. We may use TurnItIn to examine potential causes of plagiarism. Student needs: Students who may need specific assistance with taking this course should inform the instructor at the beginning of the semester. -2 -

3 LECTURE SCHEDULE: Date Lecture # Lecture Topic Reading/Assignment Due 16-Jan 1 Our Microbial World & History of Microbiology Chapter 1, 2 21-Jan NO CLASS (MLK Day) 23-Jan 2 Bacterial Cell Structure & Function ( Weds.=Mon. ) Chapter 3 28-Jan 3 Bacterial Culture, Growth, & Development Chapter 4 & 5 30-Jan 4 Viral Structure and Function Chapter 6 4-Feb 5 Genes & Genomes Chapters Feb 6 Genes & Genomes II Chapter 9 11-Feb 7 Molecular Regulation Chapter 10 & RR* #1 13-Feb 8 Viral Molecular Biology I Chapter Feb NO CLASS (Presidents Day) 20-Feb 9 Viral Molecular Biology II Chapter Feb 10 Catabolism & Biosynthesis ( Thurs.=Mon. ) Chapter Feb EXAM 1 (covers lectures 1-9) 27-Feb 11 Origins & Evolution Chapter 17 4-Mar 12 Archaeal Diversity Chapter 19 6-Mar 13 Bacterial Diversity I Chapter Mar 14 Bacterial Diversity II Chapter 18 & RR #2 13-Mar 15 Bacterial Diversity III Chapter Mar SPRING RECESS 20-Mar SPRING RECESS 25-Mar 16 Eukaryotic Microbial Diversity II Chapter Mar 17 Microbial Ecology I Chapter 21 1-Apr EXAM 2 (covers lectures 10-16) 3-Apr 18 Microbial Ecology II Chapter 22 8-Apr 19 The Human Microbiome I Chapter 23 & RR #3 10-Apr 20 The Human Microbiome II Chapter Apr NO CLASS (Patriots Day) 17-Apr 21 Microbes in Industry, Ag, & Food Systems Chapter Apr 22 Microbial Pathogenesis & Disease I Chapter Apr 23 Microbial Pathogenesis & Disease II Chapter Apr Course synthesis * RR= Reading response. Papers from primary literature will be posted on Canvas. Students will respond to questions FINAL EXAM: Monday May 6th, 12:00-2:00pm (G block) Note: We ll do our best to stick to the schedule of the syllabus for both lectures and labs, but we may veer off slightly as we progress through the semester or due to cancellation of classes due to snow. Please pay attention at beginning of lectures for announcements about schedule changes. -3 -

4 Microbiology Lab Overview: The laboratory component of Bio 106 is intended to familiarize you with both traditional culture-based approaches used to identify microbes, but also more recently developed culture-independent (DNA/RNA sequencing) approaches. We will spend considerable time developing excellent microscopy skills, because the microscope remains one of the most important tools in a microbiology lab. Research Project and Lab Report: At the beginning of the semester you will adopt a set of sourdough samples for the term. As we move through the semester from one lab exercise to the next, you will isolate, identify, and characterize a variety of traits for each unique microbe in your sourdough samples. A 10-page lab report due at the end of the semester will summarize your findings from throughout the semester. Please keep in mind that as you complete each lab exercise, you are collecting data that you will need for this report at the end of the semester. Pre-Lab Assignments: For each lab session, please complete the Pre-Lab before the start of the lab section. These short exercises are part of your laboratory grade and are designed to help you come to each lab section with a good understanding of the techniques that will be used. Pre-labs should be printed out on paper and handed in to your lab TA before the lab begins. Late or ed pre-labs will not be accepted. Lab Guides: For each lab, a guide will be posted on Canvas that provides background on each activity, specific details on procedures, and space to record data or observations. These guides will only cover a small subset of microbiological techniques that are used in microbiology research labs. If you are interested in learning more about other microbiology lab techniques that we won t have time to use in this course, I recommend the following text: Microbiology: Laboratory Theory & Application, M. J. Leboffe & B.E. Pierce, This text is not required for the course. Important note about opportunistic pathogens: The microbes that we will be working with throughout the semester are not virulent. But some, such as Staphylococcus species, can be opportunistic pathogens. If you have a compromised immune system or are taking drugs that might suppress your immune system, please consult your physician about taking this course. -4 -

5 LAB SCHEDULE: Week # Date Exercise Reading and Assignments Due (see Canvas) 1 1/22 - Safety in a microbiology lab - Light microscopy - Cell morphology - Quadrant streaking 2 1/29 - Quantification of microbial populations: serial dilutions of spoiled milk - Introduction to kombucha or sauerkraut microbiomes - Plating out kombucha or sauerkraut microbiomes samples 3 2/5 - Gram staining - Growth curve of Vibrio natriegens 4 2/12 - Describing colony morphotypes - Isolating pure cultures from kombucha or sauerkraut mixed community 5 2/19 - DNA isolation and 16S/ITS PCR of kombucha or sauerkraut community isolates 6 2/26 - Sanger sequencing, alignments, and phylogenies using MEGA - Quantifying viruses using the plaque assay 7 3/5 - Characterizing growth and physiology of kombucha or sauerkraut isolates - Count plaque assay from last week -Lab #1 Guide -Lab #2 Guide -Background reading on kombucha or sauerkraut -Lab #3 Guide -Lab #4 Guide - Growth curve data from 2/5 -Lab #5 Guide -Lab #6 Guide -Lab #7 Guide 8 3/12 - LAB PRACTICAL - Review and analyze growth and physiology data from last week 3/19 Spring Break 9 3/26 - Diversity of eukaryotic microbes: mushrooms, molds, protists, and algae - Fluorescence microscopy 10 4/2 - Microbial symbiosis: lichens, mycorrhizal fungi, kombucha, termites - Species interactions: measuring microbial interactions using kombucha or sauerkraut isolates 11 4/9 - Assembling/annotating bacterial genomes; comparative genomics of microbial genomes using KBase - Disinfectants and antiseptics - Kirby-Bauer and antibiotic resistance -Lab #8 Guide -Pre-lab #8 -Lab #9 Guide -Pre-lab #9 -Lab #10 Guide - Answers to KBase exercise from last week 12 4/16 - Industrial and food microbiology -Lab #11 Guide - 10-page Lab Report Due 13 4/23 Microbial diversity presentations Submit Microbial Diversity Presentation by noon on 4/22-5 -