BIOL 4630 Molecular Biology II / BIOL 6690 Advanced Molecular Biology
BIOL 4630: 4 credit hours                               BIOL 6690: 3 credit hours
Meets:             Mon/ Thurs 8:00am-9:50am in Science Center 2C25
Prerequisite/ Co-requisite: BIOL 4620 and BIOL 4760 or equivalent

INSTRUCTOR: Dr. Donna E. Crone Lecturer
Office location: Science Center 3C11
Office telephone number: 276-3299
Office hours: Mon 1:30-2:30 or by appointment
e-mail address: croned@rpi.edu

Course Description: . Students use a variety of tools (textbooks, scientific journals and internet resources including molecular databases and data mining tools) to increase understanding of genes, their expression, their products and their inter-relatedness.

Student Learning Outcomes
At the end of the course a successful student will be able to:

Required Textbook: 

Electronic options (ebook purchase, rental or purchase of individual chapters) http://www.garlandscience.com/product/isbn/9780815341499

Grading criteria


HW Assignments

30%

Weekly – due Thursdays at 8am unless otherwise indicated

Exams (3)

30%

in class: open book/ open laptop/ independently done

ENCODE project

5%

Short presentation on assigned topic

Final Project

25%

presentation and paper weighted evenly

Class Participation

15%

The class participation grade will be based on prompt and regular attendance, appropriate participation in in-class exercises, and participation in class discussions.

Students granted extra time for exams: Please provide a copy of the letter from ALAC requesting extra time to take the exams. This must be done at least one week prior to the first exam, so we can make arrangements for the extended exam time.

Student grades are posted in RPILMS where students can view assignments due and grades assigned.

BIOL 4630

Grading

 

 

 

BIOL6690

93-100%

A

90-92%

A-

87-89%

B+

Same grading however lowest passing grade for graduate students is C-

83-86%

B

80-82%

B-

77-79%

C+

73-76%

C

70-72%

C-

67-69%

D+

60-66%

D

Below 60%

F

 

 

 

ATTENDENCE POLICY:  Students registered in this class should make every effort to attend class regularly and to use class time appropriately.  Class participation is 15% of final grade.
Please be considerate to yourself and the others in class – do not come to class if you have flu symptoms.  If you miss class, you must notify me by phone or email by 5pm on the day missed (preferably before class) to be excused.
Class participation is scored on scale of 0-3
            3 on time and attentive
            2.5 excused absence (missed assignments must be completed before next class period)
2 inattentive (e.g. using computer for other than class activities –other HW, social acitivities, inappropriate/disruptive conversation) or significantly late
            1 persistently inattentive or late and inattentive
            0 unexcused absence
Absences excused by Dean’s letter (serious illness, family emergency) will be evaluated individually following discussion between student and instructor.
Laptop is required for participation in in-class activities.

Assignments are posted in LMS and are due at 8am.  Unless otherwise instructed, assignments should be submitted electronically via RPILMS as .doc, .docx, .ppt or .pptx (as appropriate).  Assignments that are submitted in any other form (eg pdf), will not be graded unless I receive an accompanying hard copy.  In the case of LMS issues, you may send to my email; however, you must send via your RPI email address – not gmail or yahoo.  Please do not send email via Blackberry or similar device; it is likely to go to Respite (which I do not check regularly).
Late assignments will be accepted and a late penalty will be assessed.  Assignment score is reduced 10% for each day that it is late (weekend counts as one day)

ACADEMIC INTEGRITY:
Student-teacher relationships are built on trust. For example, students must trust that teachers have made appropriate decisions about the structure and content of the courses they teach, and teachers must trust that the assignments that students turn in are their own. Acts, which violate this trust, undermine the educational process. The Rensselaer Handbook of Student Rights and Responsibilities defines various forms of Academic Dishonesty and you should make yourself familiar with these. In this class, all assignments that are turned in for a grade must represent the student’s own work. In cases where help was received, a notation on the assignment should indicate your collaboration. When working within a group for the final project, the contributions of each member of the group should be explicitly stated orally at the end of the presentation and in writing in the acknowledgement section of the paper.  References should be properly cited.  Copy and paste of material from any source without the use of quotes AND proper reference is PLAGARISM and a violation of academic integrity. If you do not know how to paraphrase, ask for help before submitting assignment. Submission of any assignment that is in violation of this policy will result in a penalty of grade of F for assignment for first instance and grade of F in the course for subsequent violation  If you have any question concerning this policy before submitting an assignment, please ask for clarification.
Molecular Biology II Fall 2011 Course calendar:
 “This is a tentative schedule and subject to change depending upon the progress of the class”    
HW and supplemental material are accessible at course site in RPI-LMS. https://rpilms.rpi.edu/webct/logon/199326894001

Date

topic

Read before class
HMG4 = Human Molecular Genetics text

Assignment

Mon 8/29

Genes, Genomes and Genome projects

Human Genome Project
What is a Gene?
HMG4 p276  (ch9)

HW1 due 9/1

Thurs 9/1

Genome sequencing

HMG4 p 217-235 (ch8)
NextGen_Review

HW2 due 9/8

Mon 9/5

Labor Day No Class

 

 

Thurs 9/8

Data search and pairwise analysis

Krane and Raymer (pdf)

 

Mon 9/12

Genome annotation – gene finding

HMG4 p 235-238, p 265-273  and 308-313 (ch8,9,10)

HW3 due 9/15

Thurs 9/15

Genome annotation- Comparative genomics

HMG4 p 297-312 and 384-388 (ch 10,12)

 

Mon 9/19

Non coding annotation

HMG4 p 274-288 (ch9)

I

Thurs 9/22

In class exam 1

 

 

Mon 9/26

Nucleic acid hybridization

HMG4 p 191-211 (ch7)

 

Thurs 9/29

Basic gene expression analysis

HMG4 p 239-253 (ch8)-

 

Mon 10/3

Microarray- data clustering

 

 

Thurs 10/6

Next Gen: ChIP Seq/RNA Seq

 

 

Mon 10/10

Columbus Day No Class

 

 

Tues 10/11
Mon sched

Functional genomics - RNAi

HMG4 389-393 and Table 12.4 (ch12)

 

Thurs 10/13

Analysis of the Genome
ENCODE/modENCODE

HMG4 362-364 and 393-403  (ch11,12)
Fly_wormENCODE (new2009)

 

Mon 10/17

Analysis of the Genome
ENCODE/modENCODE

 

Thurs 10/20

Analysis of the Genome
ENCODE/modENCODE

 

Mon 10/24

In class exam 2

 

 

Thurs 10/27

Phylogeny

HMG4 p 326—341 (ch 10)

 

Mon 10/31

Genome variation

HMG4 p405-410 (ch13)

 

Thurs 11/3

Student presentations

 

 

Mon 11/7

SNPs / Linkage Disequilbrium
Human pathogenic DNA variants

HMG4 p416-427 (ch13)

 

Thurs 11/10

Student presentations

 

 

Mon 11/14

SNPs/ GWAS

HMG4 (ch15)

 

Thurs 11/17

Student presentations

 

 

Mon 11/21

Genomes in the news

 

 

Thurs 11/24

Thanksgiving

No Class

 

Mon 11/28

Genomic identification/ pharmacogenomics

HMG4 (ch 16)

 

Thurs 12/1

Student presentations

 

 

Mon 12/5

Review/ Wrap Up

 

 

Thurs 12/8

Student presentations

 

 

Finals week

Exam 3 (scheduled by registrar)