Instructor:   Dr. David Gondek

164 Ctr for Natural Sciences

dgondek@ithaca.edu
274-3979


Class material is on Sakai.
Lecture Schedule

      BIOL-45200  Microbiology
(Biology Elective)
Spring 2012

Class: MWF, CNS-119  R, CNS115

Lab: WR – CNS107

M,W,F   11-11:50am  /  R 1-4pm


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Course Description:

This course examines the structure, physiology, and genetics of microorganisms. An emphasis is placed on understanding microbial growth, ecology, use of microorganisms in research and commerce, how these organisms affect food and water quality, and the human immune response to pathogens. Microbiological laboratory procedures include sterile technique, microscopy, identification, enrichment, isolation, and preservation.  Molecular Biology techniques include genome purification, PCR, cloning, RDP-analysis, and phylogeny construction.

 

At the conclusion of this course, students will be able to:


Grading System:
The acceptable grades and corresponding points for GPA calculations are as follows. 


 
Grade Points:  A 4.00 (excellent) A- 3.70 B+ 3.30 B 3.00 (good) B- 2.70 C+ 2.30 C 2.00 (satisfactory) C- 1.70 D+ 1.30 D 1.00 D- 0.70 F 0

 Exams
   2 exams 100 pts each
   1 final exam 100 pts
Quizzes/Participation 100 pts (5/per)
 Concept maps 100 pts (10/per)
 Lab final report 100pts
 Lab Questions/skills 100pts
 Total pts awarded = 700


Course details:


Active classroom learning: 
The course will employ a variety of active learning techniques which provide the student with an opportunity for self reflection, evaluation, and questioning.


Quiz
zes/Participation: 


Attendance (see below) is expected but not enforced.  However, short quizzes will be announced in class and due the following class period.  Participation grades will be given for in class activities.


Extra Credit:

Students can earn up to 30pts of extra credit throughout the term.  Extra credit can be earned by submitting unique APQ questions generated by the individual.  In addition to the question, the student must provide a typed answer key/explanation for the question.  Extra credit questions should be based on the assigned reading and are due PRIOR to that days lecture.  Each days submission is worth 2pts.  If the question is used as part of an exam, the student earns an additional 3pts.  More than one question can be submitted per day, increasing your chances of being selected for an exam question.

 

Missed quizzes/participation/concept map assignments:  

The lowest 20% of quiz/participation grades will be dropped.  There are no make-ups.

 

Missed Exams:  

In accordance with New York State law, students who miss class due to their religious beliefs shall be excused from class or examinations on that day. The faculty member is responsible for providing the student with an equivalent opportunity to make up any examination, study, or work requirement that the student may have missed. It is suggested that students notify their course instructors at least one week before any anticipated absence so that proper arrangements may be made to make up any missed work or examination. Any such work is to be completed within a reasonable time frame, as determined by the faculty member.

Any student, who missed class due to a verifiable family or individual health emergency, or to a required appearance in a court of law, shall be excused. The student or a family member/legal guardian may report the absence to the Office of Student Affairs and Campus Life, (340 Egbert Hall or via email at studentabsence@ithaca.edu or by phone at 607-274-3374) which will notify the student’s dean’s office, as well as residential life if the student lives on campus. The dean’s office will disseminate the information to the appropriate faculty. Follow-up by the student with his or her professors is imperative. Students may need to consider a leave of absence, medical leave of absence, selected course withdrawals, and so on, if they have missed a significant portion of class work.

 

Laboratory:  The lab is scheduled as a very open ended endeavor.  Three major outcomes must be generated but the conclusion of the semester.

  1. A hypothesis selected
  2. A minimum of 8 quality DNA samples submitted for sequencing / lab pair
  3. A summary report and presentation of the data collected
                

The lab is not a cook-book lab.  There is no right or wrong answer.  Much like the real world, the outcome of the work is a product formed by a team.  Should something not work and need to be repeated, this may need to happen on the individuals own time.  Lab supplies will be always available for completing additional experiments.  HOWEVER, a budget must be maintained and YOU MAY NOT EXCEED THE BUDGET FOR THE TERM.  Additional details provided in the lab section.

 



Group grading:  

Peer evaluations will be used to determine the level of work put in by the individual as part of the team.  As such you must grade each other’s performance in the group on a 1-4 scale.  You must include yourself in the grading, and a number can only be used once (ie. someone must get a 4, and someone must get a 1).  Grades for the final lab report will be weighted based on these peerevaluations. (You cannot lose more than 1 letter grade, however, you can exceed 100pts for the final project)

 

Academic honesty:  

Honesty is a cornerstone of the mission of the College. Unless it is otherwise stipulated, students may submit for evaluation only that work that is their own. For more information see Student Handbook 7.1.4 

 

Attendance: 

Attendance is expected for all classes, and students are responsible for work missed during any absence from class. Students should notify their instructors as soon as possible of any anticipated absences

 

Online Course Evaluations: 

Student input is highly valued and is important to maintain high quality instruction. Course evaluations are mandatory and must be completed online the last week of classes

 

Incompletes: 

Incompletes are given only when a student is doing satisfactory work but cannot complete the course for a reason not related to academic performance (i.e., medical, family emergency). Terms for completion will be determined by instructor and are due no later than the end of the following semester. If no complete grade is received by the due date, a grade of F is recorded on the transcript. 

 

Policy on Grade Disputes: 

Grade disputes will be resolved directly between the course instructor and the student. As a general principle, the authority to change a grade rests with the faculty member.  See Students' Right to Petition 

 

Accommodations:  

Academic accommodations are available to students with documented disabilities. To access services, students must self-identify and provide appropriate documentation to the Office of Academic Support Services. For further information, please contact the Office of Academic Support Services at 274-1257.

 

Disclaimer: 

This syllabus is intended to give the student guidance in what may be covered during the semester and will be followed as closely as possible. However, the professor reserves the right to modify, supplement and make changes as the course needs arise.


 

Lecture Schedule - Subject to change if required 


 

Section

Date

 

Type

Chapter Reading

Topic

Other:

1

Intro/History

23-Jan

M

Class

 

Discussion of syllabus - Outcomes of course

 

 

2

 

25-Jan

W

Class

1.1-1.10, 

History - Intro to microbiology

 

 

3

 

26-Jan

R

LAB-3

 

Compost collection: Discussion of project for term/Budget/"grant"

 

  PAPER: 1

Lab book 2.2

Q:8-16

4

Structure / Function

27-Jan

F

Class

2.5-2.7, 3.1/2, 3.6-3.8

Continued: History - Intro to microbiology 

Bacterial cell: Structure Function 1

 

 CM-History 

5

 

30-Jan

M

Class

3.9-3.15

Bacterial cell: Structure Function 2

 

 

6

Microbial Growth

1-Feb

W

Class

4.2/3, 5.1-5.4, 22.1,2

Media and Microbial growth (fts/mreB)

 

PAPER:1, 2

Other: 1, 2

CM- struc/func 

7

 

2-Feb

R

LAB-3

1.2/3/4, 2.1, 5.1

Soil pH,H20, Enrichment 1,  (Practice gram staining)

Genomic isolation (practice GS)

 

8

 

3-Feb

F

Class

5.5-5.18

Microbial growth (measurement and control)

 

 

9

Metabolism

6-Feb

M

Class

4.8-4.16

Nutrition- Anabolism/Catabolism

 

 CM- Micro growth

10

 

8-Feb

W

LAB-1

1.3, 2.2, 5.2

Enrichment 2, 

PCR 16s

 

11

 

9-Feb

R

LAB-2

2.2, 4.1/2/3

Enrichment 2, Gram Staining

Gram stain

 

11.5

 

9-Feb

R

Class

13.1-9

Phototrophy, chemolithotrophy

 

 

12

 

10-Feb

F

Class

13.10-13.15

Nitrogen fixation and nitrification

 

 

13

 

13-Feb

M

Class

14.1/2, 14.5-11

Fermentation and Anaerobic respiration

 

 

14

 

15-Feb

W

LAB-1

2.3, 5.4

Isolation, 

PCR gel clean-up

 

15

Genetics

16-Feb

R

LAB-2

2.4, 3.1, 5.5/6

Cryo-preserve isolates, Genomic DNA isolation

OD DNA/Topo-clone

 

15.5

 

16-Feb

R

Class

(Review chap7) 8.1-6

Central dogma, regulation of gene expression, lac operon

 

 CM - metabolism

16

 

17-Feb

F

Class

8.7-8.13

Sensing and signal transduction

 

 

17

 

20-Feb

M

Class

8.14-16

RNA based regulation, defense, trp operon

 

PAPER:1,2

18

 

22-Feb

W

LAB-1

3.2, 5.2

Pcr 16S

Isolate colonies, "dirty"

 











 

 

 

 

 

 

 

 

PCR

 

19

 

23-Feb

R

LAB-2

5.8

restriction digest

restriction digest

 

19.5

 

23-Feb

R

Class

10.6-10.13

Horizontal gene transfer

 

 

20

Virology

24-Feb

F

Class

9.1-9.10, 21.6

virology overview: Virus of procaryotes

 

 CM - Genetics

21

 

27-Feb

M

Class

9.11/12, 21.8-11, 

Virus of euckaryotes 

Flu - 33.8, pg923  HIV -33.14 32.6

 

News:

Other:1

 

22

 

EXAM 1

 

29-Feb

 

W

 

Class/review

 

 CM - Virology

 

23

 

 

1-Mar

 

R

 

***Exam 1***

 

 

24

Microbial Disease

2-Mar

F

Class

27.1-27.13

Microbial interactions with humans

 

 

25

 

5-Mar

M

Class

33.1-33.7

airborne strep/TB

 

News:1,2,3

26

 

7-Mar

W

LAB-1

 

gel analysis (isolate more colonies if needed)

 

 

27

 

8-Mar

R

LAB-2

5.7

SAME

minipreps/OD

 

27.5

 

8-Mar

R

Class

33.9-13

contact/std Staph/chlamydia

 

News:1,2

28

 

9-Mar

F

Class

34.3-7

Vector Lyme/plague

 

News: 1,2

 

XX

 

 

 

 

Spring break

 

 

29

 

19-Mar

M

Class

31.1-31.4, 36.8-12

Food - Salmonella/e.coli

 

News:1,2,3,4

30

 

21-Mar

W

LAB-1

Handouts

Bacteria of Medical importance (gram stain)

SAME

 

31

 

22-Mar

R

LAB-2

Handouts

Medical bacteria - Phenotypic assays(restart soil clones)

SAME

 

31.5

 

22-Mar

R

Class

35.4-8

Water - cholera/legionella

 

News: 1

32

Immunology

23-Mar

F

Class

28.1-6, 29.1-4, 30.1-4

Immunology - Innate vs Adaptive - TLR

 

 

CM – Micro disease

 Other: 1, 

33

 

26-Mar

M

Class

29.5/6, 30.7-10

T cells

 

 Other: 1

34

 

28-Mar

W

LAB-1

4.4/5

Assess - Medical unknowns / phenotypic tests of soil clones

SAME

 

35

 

29-Mar

R

LAB-2

3.6, 5.9

Unknowns - phenotypic assays (send out samples for Sequencing)

SAME

 

35.5

 

29-Mar

R

Class

29.7-9 30.5

B-cells

 

 Other: 1

36

 

30-Mar

F

Class

32.1-12, 28.7-10

Epidemiology, Vaccines/Autism, auto-immunity/hygiene hypothesis

 

 PAPER: 1,2

37

 

2-Apr

M

Class

26.1-13

Microbial control: Antibiotics/anti-

 

News: 1, 2, 3

















 

 

 

 

 

 

 

virals

 

Other: 1, 2

 

38

 

EXAM 2

 

4-Apr

 

W

 

Class/review

 

 CM - Immunology

 

39

 

 

5-Apr

 

R

 

***Exam 2***

 

 

40

Evolution/ Systematics

6-Apr

F

Class

16.1/2

Microbial evolution

 

 

41

 

9-Apr

M

Class

22.3-10

Methods in microbial ecology

 

 

42

 

11-Apr

W

class

16.5-13

Systematics

 

PAPER:1,2,3

43

 

12-Apr

R

LAB-3

6.2/3

 Begin RDP analysis

SAME

 

44

Ecology

13-Apr

F

Class

23.1-5

ecology - biofilms And freshwater ecosystems

 

 CM-evolution/sys

45

 

16-Apr

M

Class

23.6-12

ecology2 - soil and marine ecosystems

 

 

46

 

18-Apr

W

class

24.1-10

ecology 3 - nutrient cycles/bio remediation

 

 

47

 

19-Apr

R

LAB-3

7.1/2 

Phylogeny and tree construction

SAME

 

48

Symbiosis

20-Apr

F

Class

16.3, 20.2-20.5

microbial symbiosis. Mito-chloro

 

 CM - Ecology

49

 

23-Apr

M

Class

25.1-5

symbiosis - plants

 

 

50

 

25-Apr

W

class

25.6-14

symbiosis - animals

 

 

51

 

26-Apr

R

LAB-3

 

Group work time/ 

OPTIONAL Practical exam final

SAME

 

52

Using microbiology

27-Apr

F

Class

15.1-9

Commerical microbiology

 

 CM - symbiosis

53

 

30-Apr

M

Class

15.10-18

Biotechnology/genetic engineering/synthetic biology

 

 

54

Fungi/ protists/ algae

2-May

W

Class

20.6-20

What did we forget: fungi/protists/algae

 

 CM - Biotech

55

 

3-May

R

LAB-3

 

Presentations (submit report, poster, and all data on flash drive)

SAME

 

 

56

 

 

 

4-May

 

F

 

Class/review

 

 CM-Fungi/protist













 

 FINAL EXAM: Friday  May 11  10:30 am 1 pm 

 

 




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