BIOL412-GENERAL BACTERIOLOGY

Laboratory FALL 2007

Lecture Instructor:

Dr. Jianmin Zhong (Dr. Z)

E-mail: jz15 Phone: (707) 826-5554

Office: SciB-324E

Office hours: MW 5:00-6:00 PM, TR 2:00-3:00 PM or by appointment

Tues / Thurs 2-5 Laboratory Instructor:

Dr. Mark S. Wilson (Mark)

E-mail: msw13 Phone: (707) 826-5557

Office: SciB-222

Office hours: TR 5-6 PM, W 10-noon or by appointment

LAB LOCATION: SciB 228

LAB MANUAL: Microbiology: A Laboratory Manual. 8^th edition by Cappuccino and Sherman (ISBN: 0-8053-2578-6)

COURSE OVERVIEW: The Biol412 is an upper division course that is designed for Biology majors who want to expand their knowledge of the microscopic world. The lecture section is designed as an overview of the world of the microorganisms, such as prokaryotes and viruses. The overall themes of this course will cover different aspects of microbes such as their morphology, classification, structure, metabolism, growth, evolution, and genetics. We also will learn how microbes cause disease in humans and about our immune response to microbial infections.

The laboratory section provides hands-on training experience on how to work with bacteria. In the first two weeks we will review basic microbiological laboratory techniques such as laboratory safety, bright field and phase-contrast microscopies, staining methods, aseptic techniques, and cultivation of bacteria. There will be two modules in the rest of the semester that reinforce the microbiological techniques you have learned. The first module focuses on how to isolate and identify of unknown bacterial organisms from environment, such as in a pond or from your nose. The second module focuses on environmental factors that affect bacterial growth. In each of modules you will first learn relevant microbiological techniques and then carry out independent researches.

COURSE OBJECTIVES

The lecture is designed to:

· Provide a survey of different microbial forms, their structure, taxonomy and importance

· Develop an appreciation for the ubiquity, longevity and importance of microorganisms.

· Sharpen critical thinking skills.

· Awaken your interest in this field. For those of you who will not take upper division courses related to microbiology, this course should provide a basic knowledge of the characteristics of bacteria and viruses. For those who will follow a path related to microbiology, this course should provide with a solid foundation for the future stages of your career.

The lab is designed for students:

· To learn and practice microbiological laboratory techniques such as laboratory safety, aseptic technique, microscopy, identification methods (staining/culturing), and quantitative techniques (pipetting and population counts)

· To promote analytical reasoning skills such as maintaining a lab notebook and analyzing data

· To develop communication skills in oral presentations, such as poster and powerpoint presentations

· To express ideas clearly in writing through the composition of scientific articles

· To work effectively in groups to design, perform, and report research work

PREPEQUISITES: The prerequisite for this course is BIOL 340 with a grade of C- or higher. If you have not completed the course, you should register in the prerequisite and drop this course. I reserve the right to check your records and drop anyone without the appropriate prerequisite.

GRADING: The final grade for the course will take into account your grades in the lab and the lecture. Since dates of exams and quizzes are listed on my syllabus, students should put things in order to insure presence in class on exam day. No make-up exams will be given unless arrangements are made prior to the exam. In the case of an emergency, notify me by email or in person. Any illness must be appropriately documented by a medical professional. Known conflicts with exams must be approved prior to the exam date. I ask that you adhere to this policy in order to be fairness to all students and to yourself.

I believe that “No student has ever passed microbiology while having poor attendance”. Although attendance is not required, I strongly recommend you to attend the lectures. Of course, missing one or more lectures cannot be used as an excuse for anything.

LETTER GRADE PERCENTAGE

A =93% A- =89%

B+ =86% B =83% B- =80%

C+ =76% C =73% C- =70%

D+ =66% D =63% D- =60%

F <57%

Note that a Grade of D or below will not meet the requirement for elective credit.

GRADING DETAILS:

The grade breakdown for the course is as follows:

Lecture Midterm exams (2; 100 points each) 200pnt

Lecture Assignments (2; 20 and 30 points) 50pnt

Lecture Quizzes (3; 10 points each) 30pnt

Lecture Final exam (1; 150 points) 150pnt

Lab midterms (3; 30 pnts each) 90pnts

Lab quizzes (3; not graded)

Lab Unknown Identifications (2; 15 and 10 pnts) 25pnts

Lab skill tests (5) 30pnts

1. Streak Plate (5 pnts)

2. Spread Plate (5 pnts)

3. Gram stain (5 pnts)

4. Phase-contrast microscope (5 pnts)

5. Dilution Problems (10 pnts)

Lab Notebook (3; 25pnts each) 75pnts

Lab Group projects

1. Poster presentation 25pnts

2. PowerPoint presentation 25pnts

3. Written report 25pnts

4. Effectiveness as a team member 5pnts

Attendance/participation/attitude 30pnts

(Lab attendance is mandatory)

Total possible points: 760 points

Extra bonus points: 10 points

LECTURE GRADING SPECIFICS:

Midterm and Final exams: There will be two midterms and a final exam for the lecture section. The midterms will not be comprehensive but the final will (The final contains 15% part I:15% part II:70% part III). All exams can be in true-and-false, multiple-choice, and short-answer questions.

Assignments: There will also be 2 research paper based assignments. The first one is a classification assignment that asks you to compare and contrast the prokaryotic & eukaryotic cells, and bacteria and archaea. The second one is an assignment for bacterial cell growth. There are two parts for the second assignment. The part 1 is to calculate growth rate and doubling time using a semilog graph paper; and part 2 is to predict the effect of changing conditions on the growth rate.

Quizzes: There will be 3 in-class quizzes in the form of multiple-choice and/or true-and-false. The dates of these quizzes are listed on the syllabus. However, these quizzes will not be graded. Short quizzes will push you to retain many of the new information you are reading. The questions will be based on materials that we have already covered in the lectures. You are responsible for reading the textbook and preparing for the quizzes before class.

Bonus points: You may earn bonus points by writing your feedbacks on lectures and/or labs (5 points). In addition, I will give you 5 points for attending the HMMI annual conference that will be held at HSU on August 24, 2007.

LAB GRADING SPECIFIECS:

Lab Midterm Exams: Although we don’t have final exam for the lab part, there will be three lab midterms. All lab exams will have either true-or-false or short-answer questions format.

Quizzes: There will be 3 quizzes in the lab over the course of the semester. The format of the course is true-and-false and short-answer question. The dates of these quizzes are listed on the syllabus, so it is best that you be prepared to take one every time. The questions will be based on the experimental methods and/or techniques that we have already covered. You are responsible for reading the lab manual and preparing for lab before class.

Skill tests: They are designed as open-book tests. Since all of our BacT experiments are carried out in groups, the skill tests will show if you are capable of doing right BacT experiments by your own. The date of the skill tests will be usually 3 weeks after the particular experiment is done.

Unknowns: Unknown 1 is to create a dichotomous key to differentiate between a given list of 13 organisms in a mixed culture (15 points). Unknown 2 is a PCR simulation (10 points). Additional information regarding these assignments will be given later on. Homework must be submitted at the beginning of the designated lab period.

Lab Notebook: Prior to each lab session, you should enter the date, title, and objectives for that day’s activities. Do not write the protocol ahead of time. It is important to do this as you work so that you have an accurate record of what you did. The notebook needs to be kept up to date. The notebook will be collected three times and evaluated for completeness, accuracy, and format.

Group activities: There will be a poster presentation, an oral (power point) presentation, and a written report submitted in the form of a journal article. The presentations will be given in groups of 2. Drafts of the final report will be submitted for me to review. All reports must be typed. More detailed information on how to format the report and what to include will be given later.

ACADEMIC INTEGRITY: Academic Integrity is a requirement of this course and of the University. Academic honesty applies both to your performance on exams and on written assignments.

• Plagiarism is the unacknowledged used of another's words or ideas as your own. Use your own words when writing. Use quotation marks and cite the source of any phrase that you "borrow". Changing one or two words in a sentence is still plagiarism!

• Cheating is the use of another's work as your own. Copying another student's homework, looking at another student's exam, or using information from another student to enhance your performance on a task are all examples of cheating.

Students who violate university standards of academic integrity are subject to disciplinary sanctions, including failure in the course and suspension from the university. University policies are strictly enforced in this course. Please familiarize yourself with the academic integrity guidelines found in the current student handbook.

REQUIRED MATERIALS in the lab:

You will be assigned a lab drawer for the duration of the semester. However, I do not recommend leaving personal belongings of importance in your drawer. You may need to have each of the following items:

Required: Recommended:

- Lab notebook - Straight edge ruler

- Lab coat - Calculator

- Waterproof marker

(a fine point sharpie in a dark color is best)

- Masking tape

GENERAL LAB RULES:

1. NO EATING OR DRINKING OF ANY KIND IS PERMITTED IN THE LAB.

2. All students must wear closed-toed shoes.

3. All culture tubes are to be stored in racks. Never lay tubes on the bench top.

4. Keep long hair away from open flames.

5. At the beginning and end of each lab period, all benchtops are to be wiped down with disinfectant.

6. WASH YOUR HANDS after working with live organisms and before you leave the laboratory.

7. At the end of the lab period put all materials away in their place, clean all ink off of glassware, place materials for disposal in the proper containers, wipe down all bench tops

You are required to wear a lab coat and close-toed shoes at all times. Points will be subtracted from the subjective portion of your grade for wearing sandals. This is for your own personal safety; some of these organisms are hazards to human health, so please respect them and use common sense when handling them. When in doubt, please ask me first!!!

Attendance counts: Lab attendance is MANDATORY. You are allowed 2 excused absences. These require prior approval from the instructor or written documentation that must be submitted by the next lab period. For each additional absence, 10% will be deducted from the student’s lab grade.

Punctuality counts: If you arrive late 10 mins you will not be permitted to take the quiz, and any assignment due for that day will be considered late. Late assignments will lose 10% per day. You will receive two warnings for late arrivals. Each additional “offense” will result in 5% of the lab grade deducted (unless there is a good, instructor approved, excuse).

Laboratory etiquette is expected: After one warning, 5% of your total lab grade will be deducted if you fail to clean the microscope, leave a Bunsen burner on, or fail to correctly dispose of live cultures or any other behavior that could harm yourself or others. A note on cell phone usage: Cell phones need to be on silent or vibrate during class. You are not permitted to answer them during the lecture/discussion portion of the class. If, during the lab activities, you need to answer a call, make sure you are at a point in your work where you can stop or pause safely and then go outside in the hall. If you frequently and/or disruptively continue to leave class to use the phone, you will be given one verbal warning. After that points will be subtracted from your subjective grade.

LAB SAFETY:

There are several precautions that must be taken to avoid problems, especially when working with live and potentially harmful organisms. Please read the section in your lab manual thoroughly. If you have any questions, do not hesitate to ask me.

Accommodations for special needs: Students with documented learning disabilities should make me aware of the need for accommodations. I will work with you to ensure that you have the best possible learning experience.

TETATIVE CLASS SYLLABUS

The following is a tentative class syllabus. If there are modifications to the schedule, they will be announced in class. The chapters are just a guide. The specific pages for reading will be included in my powerpoint slides. Further, the course is not a mere reading of the book. Extra material will be provided that you will not find in the book and some materials in the book will not be part of the course. Therefore, I recommend you again to attend the lectures or at least make sure of what has been discussed in class. Important: In class it will be assumed that you have a basic knowledge of the molecules of life (proteins, nucleic acids, carbohydrates).

Lecture	DATE	LECTURE TOPICS	READINGS
1	Aug. 20	Introduction Prokaryotes and eukaryotes	Chapter 2, 11
2	Aug. 22	Prokaryotes and eukaryotes	Chapter 2, 11
3	Aug. 27	Microbial evolution and taxonomy I	2, 11
4	Aug. 29	Microbial evolution and taxonomy II	2, 11
	Sep. 3	Campus closed
5	Sep. 5	Prokaryotic cell structure I	4, 8
6	Sep. 10	Prokaryotic cell structure II	4, 8
7	Sep. 12	Lecture quiz #1 Prokaryotic cell structure III	4, 8
8	Sep. 17	Prokaryotic cell structure IV	8, 12
9	Sep. 19	Biofilms and Quorum sensing	19
10	Sep. 24	Microbial nutrition	5
	Sep. 25	Lecture Midterm I (Lecture 1-9)
11	Sep. 26	Microbial growth I	6
12	Oct. 1	Microbial growth II	6
13	Oct. 3	Control of microbial growth I	20
14	Oct. 8	Control of microbial growth II	20
15	Oct. 10	Microbial metabolism I	4, 5, 13
16	Oct. 15	Microbial metabolism II	4, 5, 13
17	Oct. 17	Lecture quiz #2 Microbial metabolism III	4, 5, 13
18	Oct. 22	Gene structure and regulation I	7
19	Oct. 24	Gene structure and regulation II	7
20	Oct. 29	Gene structure and regulation III	7
	Oct. 30	Lecture Midterm II (Lecture 10-19)
21	Oct. 31	Microbial genomics	15
22	Nov. 5	Virus general properties I	9
23	Nov. 7	Virus general properties II	9
24	Nov. 12	Microbial genetics I	10
25	Nov. 14	Microbial genetics II	10
	11/19-11/21	Fall recess
26	Nov. 26	Pathogenicity I	21
27	Nov. 28	Pathogenicity II	21
28	Dec. 3	Lecture quiz #3 Pathogenicity III	21
29	Dec. 5	Immune response	22
30	Dec. 10	3:00-6:00 PM FINAL EXAM (Lec. 1-29)

LAB COURSE SCHEDULE:

Date	Activities	Pages/Exp.
Aug. 21	1) Review appropriate protocols and safety procedures for working in a microbiology lab 2) Where things are in the lab? 3) Discussion: a proper lab notebook 4) Basic laboratory techniques 5) Exp.: Bacteria are everywhere 6) Exp: How to culture bacteria using aseptic techniques?	Pg. xv – xviii Handout Pg. 1-6 Handout Exp. #1
Aug. 23	1) Use and care of the bright field microscope 2) Pure bacterial culture isolation (Streaking, spreading, pouring) 3) Review pipetting procedures	Exp. 4 Exp. 2 PowerPoint
Aug. 28	1) Preparation of Smears and simple stain 2) Structural stains: Capsule staining 3) Spore stain	Exp. 8, 9 Exp. 13 Exp. 13
Aug. 30	Lab quiz #1 (open-booked) 1) Gram staining 2) Dilution technique 3) Sterilization procedures overview	Exp. 11 Pg. 539-540 Exp. 41
MODULE 1: Isolation and identification of unknown bacteria from environment
Sept. 4	How to grow bacteria? 1) Media overview: different kinds and their usefulness 2) Anaerobic culture techniques	Exp. 14, 15 Exp. 18, 19
Sept. 6	Lab Midterm I (Aug. 21 – Aug. 30) What can the microscope show? 1) Motility 2) Direct count (next lab) Lab notebooks #1 due after class (Aug. 21-Aug. 30)	Exp. 5
Sept. 11	How to count bacteria? 1) Direct count 2) Serial dilution/Pour-plate analysis 3) Spectrophotometric analysis	Exp. 20 Exp. 20 Exp. 14
Sept. 13	How to identify bacteria? 1) Microbial metabolism: Biochemical activities of microbes	Exp. 23, 24, 25,
Sept. 18	1) How to identify bacteria? A) Biochemical activities of microbes continue B) Bacterial motility 2) Unknown 1: making a flow chart for identification 3) Investigation of an environmental sample - Bring your sample	Exp. 22, 26,27, 29,30,31,32
Sept. 20	1) Continue environmental sample ---Preparation of stock and working cultures of isolated bacterium from environment 2) How to make a table 3) How to graph research data	Handout Handout
Sept. 25	Lecture Midterm I Continue environmental sample
Sept. 27	Lab quiz #2 (open-booked) Continue environmental sample 1) Identification of enteric microorganisms using multiple test/rapid test systems	Exp. 68
Oct. 2	Continue environmental sample
Oct. 4	Lab Midterm II (Sept. 4-Sept. 25) Continue environmental sample Lab notebooks #2 due after class (Sept. 4-Sept. 25)
Oct. 9	Complete investigation of unknown 3; prepare poster
Oct. 11	Group poster presentations
	MODULE 2: Effects of environmental factors on the microbial growth
Oct. 16	1) How to measure dynamics of the microbial growth? – the growth curve 2) Unknown 2: PCR simulation with genetic analysis http://www.hhmi.org/biointeractive/vlabs/index.htm	Exp. 21 Handout
Oct. 18	1) What factors affect microbial growth? – the role of temperature, pH, and oxygen 2) Protocol design of the group project	Exp. 16,17 Handout
Oct. 23	Control of microbial growth 1) Sterilization procedures overview (Aug. 30) 2) Chemical agents of control: chemotherapeutic agents 3) Development of hypothesis and experimental design – group project	Exp. 41 Exp. 44 Handout
Oct. 25	Control of microbial growth continues 1) Determination of penicillin activity (MIC) 2) Group study hypotheses due	Exp. 45
Oct. 30	Lecture Midterm II
Nov. 1	1) Exp.: Bacteria transformation 2) Perform experiments – group project 3) Reference search due	Exp. 60
Nov. 6	Lab quiz #3 (open-booked) 1) Perform experiments – group project 2) Draft of introduction due
Nov. 8	1) Perform experiments – group project 2) Draft of methods due
Nov. 13	Lab Midterm III (Sept. 27-Nov. 8) Perform experiments – group project Lab notebooks #3 due after class (Sept. 27-Nov.8)
Nov. 15	1) Perform experiments – group project 2) Draft of results due
Nov. 20	No Class – Thanksgiving
Nov. 22	No Class – Thanksgiving
Nov. 27	1) Plaque counts 2) Perform experiments – group project 3) Draft of discussion due	Exp. 39
Nov. 29	1) Completion of the group project 2) Writing the powerpoint
Dec. 4	PowerPoint Presentations
Dec. 6	No labs Final written paper due 5 pm by email