BIOLOGY 384 MOLECULAR BIOLOGY SPRING 2004 SCHEDULE

(DRAFTŠ specific readings will change: see the website)

 

Class

Day

Date

Topics

Read

Problems

Other

 

 

 

 

 

 

 

1

Tues

Feb 8

Defining Genomes

Ch 1

1-2,3-4,6,9,12, 13-14,17

 

2

Thur

Feb 10

Defining Genomes

1+ Cole

22-3,31-2, 35-8

 

3

Tues

Feb 15

Defining Genomes

Ch1.2

 

 

4

Thur

Feb 17

Analyzing Genomes

Ch 2

7,9-10,12-13,22-26

 

5

Tues

Feb 22

Analyzing Genomes

Ch 2

 

 

6

Thur

Feb 24

Microarrays-Basics

Ch 4

2,3,5,7,9,11,12,17-19

Read PPE paper for next week

7

Tues

Mar 1

Microarrays-Basics

Ch 4

 

 

8

Thur

Mar 3

Microarrays-Basics

Ch 4

 

 

9

Tues

Mar 8

Microarrays-Applied

Ch 5

 

 

10

Thur

Mar 10

 

 

 

Discuss topics with Rutherford

11

Tues

Mar 15

Genomic Variability

Ch 3

 

 

12

Thur

Mar 17

Midterm Exam

 

 

Midterm Exam

13

Tues

Mar 22

Spring Break

 

 

 

14

Thur

Mar 24

Spring Break

 

 

 

15

Tues

Mar 29

 

 

 

 

16

Thur

Mar 31

Proteomics

Ch 6

 

 

17

Tues

Apr 5

Genome Circuits

7.1

 

Outline and works cited due

18

Thur

Apr 7

Genome Circuits

7.2

 

 

19

Tues

Apr 12

Integrated Genomic Circuits

8.1

 

 

20

Thur

Apr 14

Whole Genome Circuits

9

 

 

21

Tues

Apr 19

Whole Gen. Circuits

 

 

 

22

Thur

Apr 21

 

 

 

Background Due

23

Tues

Apr 26

No Class, meetings

 

 

Meet with Rutherford

24

Thur

Apr 28

No Class, meetings

 

 

Meetings

25

Tues

May 5

Student Proposal Presentations

 

 

Presentations

26

Thurs

May 7

Student Proposal Presentations

 

 

Presentations

27

Tues

May 10-12

Topics

 

 

Proposal Due

 

Wed

May 18

Poster Session 2-4:30

 

 

 

 

Course Syllabus

 

 Instructor Office Hours

                 

Professor Rob Rutherford, SC228, robruth@stolaf.edu,

 

My standing office hours are immediately after class, each Wednesday 11-12pm or other time Iım in my office with the door open.   You can also check my availability for appointments online and can email me with open time that works for you and the amount of time you would like.  If you drop by outside of office hours, I may be good to meet, but sometimes am in the middle of projects between office hours.   In this case, I'm always glad to arrange a better time for us to meet.

 

Texts

1)         Cambell and Heyer Discovering Genomics, Proteomics and Bioinformatics.  Benjamin Cummings CSHL.  A bit out of date but the best thing out there.

2)         A booklet of Primary Research Articles. 

 

Assessment

                 

Credit Breakdown

 

 

Midterm Exam

20%

Problems

15%

In class Paper Discussion(s)

10%

 

 

Poster (with your lab partner)

20%

Lab Notebook

5%

 

 

Proposed Plan of Research- Talk

10%

Proposed Plan of Research- Paper

20% in parts

 

Grading Scale (Roughly)

 

 

94%

A

90-94%

A-

87-90%

B+

83-87%

B

80-83%

B-

77-80%

C+

73-77%

C

70-73%

C-

67-70%

D+

63-67%

D

60-63%

D-

 

 

Professionalism

                 

Professionalism being the best scientist you can be; working in a focused and earnest way and pursing scientific and personal excellence.  Most of you do this already as second nature, and this means that this is an easy way for you to boost your grade just for being who you are.  

 

Examples of professional behavior:

 

 

Being a good professional doesn't mean being perfect: good professionals are not afraid to ask "dumb" questions, and they all get sick, drop glassware, and can't remember what that important question we dropped by to ask from time to time.    

 

While professionalism isn't perfectionism, it IS very important.  Whatever your vocation, other people will depend on your professionalism for their livelihoods.   In science, people's very lives will often depend on it.    

 

Attendance

                 

Attendance in lecture is encouraged, but if you need to be gone occasionally, I do not need to know.  In fact, you should be able to find some of the lecture content online on this very page. Unfortunately, this flexibility does not extend to labs or exams.

Timely attendance at exams and laboratory is mandatory.  

 

This is why:

 

·                                               We share space with another course and most of the labs involve the use of living organisms and/or health hazards, and cannot be "made-up" in a way which allows us to move forward as a class.  

·                                               In lab in particular, it is critical that you do everything you can to be on time: we will often discuss important issues, including safety issues, in the first 10 minutes of lab.   

·                                               Your lab partner(s) will be counting on you.

 

In fairness to the rest of the class and to allow me to return material promptly, exams will be given only as scheduled.  Makeups will NOT be given except under the most extraordinary circumstances.   If you have a conflict ahead of time, the most professional course of action is to discuss it with me in the first week or two of class.    If you have a last minute crisis, the best course of action is to let me know before the exam or to bring me a note documenting it from the Dean of Students as soon as you return.

 

Special Needs

                 

If you have a documented disability that will impair your work in this class, please contact me to discuss your needs.  Additionally, you will need to register with Student Disability Services located in the Academic Support Center in Room 1 of the Old Main Annex. All such discussions will be confidential.

 

PROPOSED PLAN OF RESEARCH

(Think of this as your lecture final, although you will be working on it all semester)

 

 

General

 

Should reflect your own thinking and work

Should demonstrate your understanding of research principles

Must contain a clear plan and clear hypothesis

 

Topic

 

You and I choose this together.   You bring me two options you are excited about and we meet sometime between now and March 10th..  You can choose topics in light of your destination after St. Olaf, a current or future specific research interest or tangentially related to your laboratory project in this class.  If you do this right, you will be able to plug it right into an NSF application for a graduate research fellowship.

 

Structure

 

A) Specific Aim(s)- A concise 1-2 page description of what you intend to do.

                        Include at the end a list of 1-3 specific aims.

B) Background- Why is the work important and what has already been done? Review of the primary literature in light of your goal (2-4 pages, including figures, probably including )

C) Research Design and Method- How are you going to do the work? 

       You should also address alternative approaches and hazards.

        (2-6 pages, including figures)

D)  Works Cited- In numbered, Cambridge Scientific Abstracts format.

 

Format

Arial 12 point, with margins of no less than 1 inch margins all around.