MCB 301
Experimental Microbiology
School of Molecular and Cellular Biology
University of Illinois at Urbana-Champaign
course home pagecourse contactUniversity of Illinois

 
MCB 301 Syllabus: Fall 2017 (Downloadable PDF)

Course Web Site: http://www.life.uiuc.edu/mcb/301

Course Instructor:
Dr. Jack Ikeda
175A Burrill Hall
244-8732
jikeda@illinois.edu
Laboratory Coordinator:
Renee L. Alt
232A Burrill Hall
333-4306 (Office)
rlalt@illinois.edu
Dr. Ikeda
Office Hours

MW: 1:00 2:00 pm
(or by appointment)
Ms. Alt
Office Hours

By appointment only

Course Description: Laboratory emphasizing the fundamentals of microbiology. Topics include growth, isolation, and identification of bacteria; antibiotic resistance; ELISA; conjugation and transposon mutagenesis.

Credit:3 credit hours. Students must register for one lab-discussion and one lecture section.

Prerequisite: Students are expected to have taken MCB 250 and MCB 251 or course equivalents prior to enrolling in MCB 301. Students should also have credit or concurrent registraton in MCB 300, or consent of instructor.

Required Course Materials:

  1. “Experimental Microbiology: Laboratory Exercises for MCB 301, Fall 2017 ”.  Gail K. Grabner, Jack Ikeda and Renee L. Alt.
  2. “Biology Laboratory Notebook” Carbonless with duplicate, numbered pages
  3. Ruler and non-graphing Scientific Calculator, required at every lab and exam

Course Policies:
All students are assumed to have read and understood the “Student Code 2016-2017” University of Illinois, and will be expected to act accordingly.
The Code is available online at: http://www.admin.uiuc.edu/policy/code/index.html

Contacting MCB Course Personnel:

  • MCB course personnel are more than happy to assist students.
  • Emails to instructors, TAs, or course coordinators will only be answered if they come from an @illinois.edu account. We will only use this account in order to protect your educational information and profile. As a student, please remember that when you email a staff member, it is important to include all pertinent information so that we can assist you in the most efficient and effective manner possible. This information includes:
    • The course rubric in the subject line
    • Your full first and last name
    • Your NetID (the first part of your illinois.edu email account)
    • Your UIN (9 digit number that can be found on your ICard)
    • The course that you are concerned about (the course personnel often work with multiple courses)
    • Your section letter/number
    • The previous email "thread" or previous communicated information pertinent to the situation
  • Your cooperation will help us respond much more quickly to your concerns.
Social Media Use
  1. Use of any social or electronic media to share course information, request course information or make confidential course information public is prohibited. Any use of this type may earn you a zero or a more extreme penalty at the discretion of the instructor on an assignment or exam.

  2. Any social media sites created in relation to MCB courses must grant access to course personnel upon request. Failure to provide access will result in a failing grade in the course for the group/site's administrator(s).
Course Recordings
  1. Students are welcome and encouraged to make audio recordings of course lectures.

  2. The material recorded is intellectual and copyrighted property of the University of Illinois Board of Trustees and may be made for personal use only.

  3. Video recordings of any kind are strictly prohibited.

  4. Posting of audio recordings or transcriptions on social or electronic media platforms is strictly prohibited.

Religious Observances and Practices:

  • Students are required to submit the Request for Accommodation for Religious Observances Form (which can be found at www.odos.illinois.edu/.../Religious_Observance_Accommodation_Request_ Form.docx) to their instructors and the Office of the Dean of Students requesting accommodation by the end of the second week of the course. Requests that are not submitted within this time frame may not be granted.

DRES Accommodations:

  • If a student has DRES (Disability Resources and Educational Services) accommodations, documentation must be submitted to course personnel by the end of the second week of class.
  • If a student believes that they need DRES accommodations, they should contact DRES at disability@illinois.edu.

Course Syllabus
Laboratory Schedule   Lecture Schedule   Assignment Schedule


Laboratory Schedule

An experiment highlighted in bold type indicates a pre-lab is due for that exercise prior to the lab period

Date (pt total) Experiment Lab Manual Pages
Day 1
Mon Aug 28
Tu Aug 29
Course introduction
1: Streak Plate
2: Luminescent bacteria
I-XXXII
1-9
10-13
Day 2
Wed Aug 30
Th Aug 31
1, 2: Evaluations
3: Spread plate
4: Simple stain
8, 13
14-17
18.29

Mon Sept 4
Tu Sept 5

Holiday-No Labs  
Day 3
Wed Sept 6
Th Sept 7
3: Evaluations
5: Gram stain
17
30-32
Day 4 (12)
Mon Sept 11
Tu Sept 12
6: Wet mount, Darkfield
7a-d: Enzymes and adaptation, 1
33-42
43-53
Day 5 (33)
Wed Sept 13
Thu Sept 14
7a-d: Enzymes and adaptation, 2
8a: Lactic acid bacteria enrichment

43-54
55-63

Day 6 (22)
Mon Sept 18
Tue Sept 19
8b: Lactic acid bacteria isolation
9: Antibiotic producing bacteria, drying soil
63-64
66-71
Day 7 (42)
Wed Sept 20
Th Sept 21

8c: Lactic acid bacteria observation
9a: Antibiotic producing bacteria, enrichment
10a-b: Environmental effects, 1

64-65
72
83-90
Day 8 (20)
Mon Sept 25
Tue Sept 26
9b: Antibiotic producing bacteria purification, 2
10a-b: Environmental effects, 2
10c-d: Environmental effects, 1
72
89-90
93-96
Day 9 (32)
Wed Sept 27
Thu Sept 28
10c-d: Environmental effects, 2
11a: Sporeformers enrichment
93-98
99-110
Day 10 (12)
Mon Oct 2
Tue Oct 3
11b: Sporeformers isolation, 1
9b: Antibiotic producing bacteria purification, 2
111-112
72
Day 11 (13)
Wed Oct 4
Thu Oct 5
9b: Antibiotic producing bacteria purification, 3
11b: Sporeformers isolation, 2
72
113-114
Day 12 (13)
Mon Oct 9
Tue Oct 10
11c: Sporeformers post-enrichment, 1
9b: Antibiotic producing bacteria purification, 4
115-116
72
Day 13 (20)
Wed Oct 11
Thu Oct 12
11c: Sporeformers post-enrichment, 2
9b: Antibiotic producing bacteria: isolation, 1
13a-b: MIC determination, 1

116-119

72

131-136

Day 14 (6)
Mon Oct 16
Tue Oct 17
9c: Antibiotic producing bacteria: determination of antimicrobial spectrum, 1
9d: Antibiotic producing bacteria: Preparing frozen stock
9e: Antibiotic producing bacteria: preparing DNA
13a-b: MIC determination, 2

73

74

75

135-138

Day 15 (29)
Wed Oct 18
Thu Oct 19
9c: Antibiotic producing bacteria: determination of antimicrobial spectrum, 2
9e: Antibiotic producing bacteria: DNA isolation, 1

73

76

Day 16 (34)
Mon Oct 23
Tue Oct 24
9d: Antibiotic producing bacteria: DNA isolation, 2
9e: Antibiotic producing bacteria: PCR

77

78-79

Day 17 (13)
Wed Oct 25
Thu Oct 26
9c: Antibiotic producing bacteria: determination of antimicrobial spectrum, 3
9g: Antibiotic producing bacteria: PCR cleanup, prepare samples for sequencing

73

79

Day 18 (25)
Mon Oct 30
Tue Oct 31
9h: Antibiotic producing bacteria: gel eletrophoresis
14a: Identification isolation
80
139-147
Day 19 (24)
Wed Nov 1
Thu Nov 2
14b: Identification purification, 1
15a-c: Biochemical tests, 1
148-149
153-184
Thurs Nov 2 OPEN HOURS BEGIN
SEE SCHEDULE
 
Day 20 (13)
Mon Nov 6
Tue Nov 7
9h: Antibiotic producing bacteria: analyzing DNA sequences
14b: Identification purification, 2
15a-c: Biochemical tests, 2
81-82
148-149
158-185
Day 21 (33)
Wed Nov 8
Thu Nov 9
14c: Identification dichotomous keys; inoculate tests, 1
16a: Transposon mutagenesis conjugation

150-152
186-190
Day 22 (21)
Mon Nov 13
Tue Nov 14
14c: Identification; inoculate tests, 2
16c: Transposon mutagenesis selection, 1
150-152
191
Day 23 (20)
Wed Nov 15
Thu Nov 16
14c: Identification; inoculate tests, 3
16c: Transposon mutagenesis selection, 2
150-152
192
Th Nov 16 OPEN HOURS END  
Sat Nov 18 to Sun Nov 26
Fall Break  
Day 24 (12)
Mon Nov 27
Tue Nov 28
16c: Transposon mutagenesis characterization, 1
193-197
Day 25 (12)
Wed Nov 29
Thu Nov 30
16c: Transposon mutagenesis characterization, 2
17a: ELISA fluid exchange
17a: ELISA analysis

193-198

199-207

207-212

Day 26
Mon Dec 4
Tue Dec 5
Lab Practical Review and Practice
Lab clean up & drawer inventory
TA ICES forms
 
Day 27 (42)
Wed Dec 6
Thu Dec 7
Lab Practical Exam, Part I
Dilution problem calculation, Gram stain, Brightfield microscopy, streak plate
Day 28 (58)
Mon Dec 11
Tue Dec 12
Lab Practical Exam, Part II
Dilutions & spread plate, wet mount & phase contrast, biochemical tests, dichotomous key

Lecture Schedule

Date Topic(s)
September 1
Lecture 1

Basic microbiology techniques (aseptic technique, pure culture, plating); Luminescent bacteria; Microscopy; Staining (cell wall structure)

September 8
Lecture 2

Microscopy; Enzymes and adaptation

September 15
Lecture 3
Enzymes and adaptation; Lactic acid bacteria
September 22
Exam 1
Basic microbiology techniques; Microscopy; Staining; Luminescent bacteria; Enzymes and adaptation
September 29
Lecture 4
Lactic acid bacteria; Environmental effects
October 6
Lecture 5
Bacterial growth; Sporeformers
October 13
Lecture 6
Sporeformers; MIC
October 20

Exam 2
Lactic acid bacteria; Bacterial growth; Environmental effects;

DROP DEADLINE

October 27
Lecture 7

Sporeformers; Antibiotic producing bacteria

November 3
Lecture 8
Biochemical tests
November 10
Lecture 9
Identification; Transposon mutagenesis
November 17
Exam 3
Sporeformers; MIC; Biochemical tests
November 24
Fall Break
December 1
Lecture 10
Transposon mutagenesis; ELISA/Agglutination; Dilution problem
December 8
Lecture 11
TBA

Finals Week

Final Exam
Transposon mutagenesis; Identification; ELISA/Agglutination; Antibiotic producing bacteria

Assignment Schedule

Date Assignment Due
Point Total
Day 1
Mon Aug 28
Tu Aug 29
Nothing Due
Day 2
Wed Aug 30
Th Aug 31
Nothing Due
Day 3
Wed Sept 6
Th Sept 7
Pre-lab 1-6: Basic Technique
10 points
Day 4
Mon Sept 11
Tu Sept 12

Pre-lab 7: Enzymes & adaptation

10 points

Day 5
Wed Sept 13
Thu Sept 14

Pre-lab 8: Lactic acid bacteria

Post-lab 1-6: Basic Technique

10 points

10 points

Day 6
Mon Sept 18
Tues Sept 19
Pre-lab 9: Antibiotic producing bacteria
Post-lab 7: Enzymes & adaptation

10 points

10 points

Day 7
Wed Sept 20
Thu Sept 21

7: Enzymes & adaptation Lab Report

Pre-lab 10: Enviornmental effects

24 points

10 points

Fri Sept 22
Exam 1
Basic microbiology techniques; Microscopy; Staining; Luminescent bacteria; Enzymes and adaptation
50 points
Day 8
Mon Sept 25
Tue Sept 26

Post-lab 8: Lactics

10 points
Day 9
Wed Sept 27
Thu Sept 28

Pre-lab 11: Sporeforming bacteria

8: Lactic acid bacteria lab report

10 points

65 points

Day 10
Mon Oct 2
Tue Oct 3
Post-lab 10: Environmental effects
10 points
Day 11
Wed Oct 4
Thu Oct 5
10: Environmental effects Lab Report
60 points
Fri Oct 6

12: Growth Curve opens in LON-CAPA at 2pm

Day 12
Mon Oct 9
Tue Oct 10

Nothing Due

 

Day 13
Wed Oct 11
Thu Oct 12
Pre-lab 13: MIC determination

10 points

Day 14
Mon Oct 16
Tue Oct 17

12: Growth Curve exercise on LON-CAPA

Post-lab 11: Sporeforming bacteria

41 points

10 points

Day 15
Wed Oct 18
Thu Oct 19

11: Sporeforming bacteria lab report

Post-lab 13: MIC determination

63 points

10 points

Fri Oct 20
Exam 2
Lactic acid bacteria; Bacterial growth; Environmental effects
50 points
Day 16
Mon Oct 23
Tu Oct 24

13: MIC Lab Report

24 points

Day 17
Wed Oct 25
Thu Oct 26

Nothing Due

 

Day 18
Mon Oct 30
Tue Oct 31

Pre-lab 15: Identification

10 points

Day 19
Wed Nov 1
Thu Nov 2

Pre-lab 16: Biochemical tests

10 points

Day 20
Mon Nov 6
Tue Nov 7

Nothing Due

Day 21
Wed Nov 8
Thu Nov 9

Pre-lab 17: Transposon mutagenesis

Post-lab 9: Antibiotic producing bacteria

Post-lab 16: Biochemical tests

10 points

10 points

10 points

Day 22
Mon Nov 13
Tue Nov 14

16: Biochemical tests Lab Report

43 points

Day 23
Wed Nov 15
Thu Nov 16
9: Antibiotic producing bacteria Lab Report
65 points

Fri Nov 17

Exam 3
Sporeformers; MIC; Biochemical tests
50 points
Sat Nov 18 to
Sun Nov 26
Spring Break
Day 24
Mon Nov 27
Tue Nov 28

Post-lab 15: Identification

10 points

Day 25
Wed Nov 29
Thu Nov 30

Pre-lab 17: ELISA

15: Identification Lab Report

10 points

47 points

Day 26
Mon Dec 4
Tue Dec 5

16: Transposon mutagenesis Lab Report (NO LATE LAB REPORTS ACCEPTED)

17: ELISA Lab Report (NO LATE LAB REPORTS ACCEPTED)

Post-lab 16: Transposon mutagenesis

Post-lab 17: ELISA


62 points

 

26 points

 

10 points

10 points

Day 27
Wed Dec 6
Thu Dec 7
Lab Practical Exam, Part I
Dilution problem calculation, Gram stain, Brightfield microscopy, streak plate
Parts 1 and 2 worth a total of 100 points
Day 28
Mon Dec 11
Tue Dec 12
Lab Practical Exam, Part II
Dilutions & spread plate, wet mount & phase contrast, biochemical tests, dichotomous key

Finals Week

Final Exam
Transposon mutagenesis; Identification; ELISA/Agglutination; Antibiotic producing bacteria
50 points

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