Course Descriptions

This course is open first to declared Genetics (447) majors. If space is available, the course will be open to second year students who intend to be Genetics majors and have completed the prerequisites courses. Special Permission Numbers are required. Contact Prof. Vershon by E-mail  for a special permission number. In your e-mail please include your name, RUID, class year, major and preferred section.  

Offered:  Spring Lecture: T3 (Tues 12:00-1:20 PM) Waksman Auditorium, Workshop: H3* (Thurs. 12:15-1:10 PM) Waksman Auditorium, 
       Lab Section 01 T45 (Tues 1:40-4:40 PM) Waksman Rm 019
       Lab Section 02 W45 (Wed 1:40-4:40 PM) Waksman Rm 019.

Credits:  3  (Credit not given for both this course and 01:447:315, 694:215 or 694:214.)

Prerequisites:  General Biology 01:119:116, 117 and General Chemistry 01:160:162  or 01:160:-164.
       Lab Section H1 is for SAS Honors Program or SAS Honors College students only

Course Description

Learning Goals: The purpose of this course is to train students in many of the techniques used in modern molecular biology and biochemistry by giving them as much "hands on" experience as possible. In designing this course, we wanted to avoid the problems of lab courses in which the experimental outcome is already known and the aim of the laboratory exercises is to simply reproduce the expected results as closely as possible. We have therefore developed a course in which students will carry out a research project for which the results are unknown.

The project: After some initial training in techniques commonly used in molecular biology, students will start to work on their main research project. The project involves sequencing random clones from a cDNA library. The sequences derived from these experiments will be used to query a database for sequence similarity using the appropriate computer software. When matches are found, students will then search the scientific literature for information on the genes that they have identified. Students have the potential of identifying novel genes. 

Tentative Lecture and Lab Schedule

WeekTopic (Download lecture and lab notes and figures from the Sakai site)
1 Lecture: Introduction, Project, Ch. 1-The Central Dogma
  Lab: Lab Introduction and Rules
2 Lecture: Ch. 2 - Cloning Vectors, DNA libraries 
  Lab: Pipeting 
3 Lecture: Ch. 3- Analyzing DNA - Restriction enzymes & PCR, 
  Lab: Basic Techniques: Dilutions, DNA concentration by comparison, Plating Library
4 Lecture: Ch. 4 & 5 -Sequencing DNA, Crop and edit DNA sequences 
  Lab: DNA concentration by OD, Colony streakouts 
5 Lecture: Ch. 6- Bioinformatics Analysis Part I: BLASTN, 
  Lab: Set up bacterial cultures
6 Lecture: Ch. 7 - Bioinformatics Analysis Part II: BLASTX 
  Lab: Plasmid DNA Minipreps
7 Lecture: In Class Exam (Lectures & Labs for weeks 1-6) 
  Lab: Restriction Digests & PCR, DNA sequence analysis
8 Lecture: Ch. 7- Bioinformatics Analysis Part III: ORF, BLASTP 
  Lab: Gel Electrophoresis, Choose clones to sequence, DNA Sequence Analysis of Practice Clones,
9 No Class or labs - Spring Break
10 Lecture: Ch. 8- Bioinformatics Analysis Part IV: Determining the function of the protein-Literature and database searches 
  Lab: Set up cultures II, DNA Sequence Analysis of PCs
11 Lecture: Ch. 9 - Clustal, Protein structure and modeling 
  Lab: Plasmid DNA Minipreps II, PCR II, Restriction Digests II, DNA Sequence Analysis Due: Analysis of Practice Clones 1-3 completed 
12 Lecture: Ch. 10 - Tools of Molecular Biology 
  Lab: Gel Electrophoresis II, Choose clones to sequence, Sequence Analysis of Unknown Clones 
13 Lecture: Ch. 11 - Tools of Molecular Biology (cont)
  Lab: Sequence Analysis of Unknown Clones 
14 Lecture: Ch. 12 - RNAi and CRIPR, 
  Lab: Sequence analysis  
15 Lecture: Careers in Biomedical Sciences, Choice of Majors Help Sessions.  
  Lab: Sequence analysis, Analysis of ALL clones must be completed 
16 Final Exam (Please bring a computer if you have one)

Course satisfies the following MBB Dept. Learning Goals:

1. Students should demonstrate an understanding of the knowledge that is needed to begin biomedical research and that is required for post-graduate exams and studies.
2. Students should demonstrate the ability to find and evaluate information about specific biological systems or problems.
3. Students should demonstrate the ability to design experiments and critically analyze data.
4. Students should demonstrate the ability to communicate their research and findings orally through seminar and poster presentations and through written research papers.

Core Curriculum Learning Goals met by this course:
NS e. Understand and apply basic principles and concepts in the physical or biological sciences.
NS f. Explain and be able to assess the relationship among assumptions, method, evidence, arguments, and theory in scientific analysis.
IRT y. Employ current technologies to access information, to conduct research, and to communicate findings.
IRT z. Analyze and critically assess information from traditional and emergent technologies.

1. Exams (40%): The in-class mid-term and the final exam will focus on the material covered in the lectures, labs, and assigned reading. 

2. Quizzes (30%): Brief, unannounced quizzes will be given during lectures and/or workshops to test student understanding of the lecture material covered in the previous week and the lab exercises planned for the upcoming week.  No quizzes will be dropped and there will be no make-ups unless there are extreme circumstances.

3. Lab Reports (20%):  During the semester, students will be expected to turn a series of Lab Reports in which they will report about the data they collected.  Students will be expected to mock up their data and answer questions about their conclusions from the analysis of their data.  These reports will be submitted through the Assignments page on the course‚Äôs Sakai site.  

To simplify and better organize the analysis of your DNA sequences we have developed an online tool, the DNA Sequence Analysis Program (DSAP), to help guide students in the analysis of their DNA sequences and record their data.  During the course, each student will analyze a series of practice DNA sequences, called PCs for practice clones, as well as their own unknown clones.  At various points during the semester, students will need to submit this analysis for review by the staff.  If the analysis is not correct, the students will be notified what needs to be changed to correctly complete the analysis.  Although students will not be penalized if the answers are incorrect, the submission and completion of the analysis on time will be graded.

 4. Assignments (5%)  Workshops in the course will be used to review material that was covered in the lectures and labs, as well as discuss specific aspects of the material more in depth.  Attendance at the workshops is mandatory and there may be quizzes and clicker questions administered during these periods.  To help instructors to know what material to review for the worshops, each student must submit a question on the material that was covered in the lecture or lab that week.  These questions are due by 5:00 AM the day of the workshop and are submitted through the Sakai Assignment page.  Submission of a question each week will be calculated into the grade. Although the questions themselves are not graded, it is hoped that the students put thought into these and ask things that are unclear or confusing.  However, questions that are clear examples of no thought process (i.e. What is DNA?) will not get full credit.  Other homework, problem sets and work sheets may also be assigned and graded. 

5. Clickers (5%):  Several times during each lecture and workshop there will be questions that the students will respond to using the I-clicker response systems.  Many of these responses will be graded and will count for 5% of the total grade for the course. Correct answers will account for 2 points while wrong answers will account for 1 point.  It is your responsibility to bring your clicker to each class and keep it in working order.  No days will be dropped from the final score.

Course Materials:  A laboratory and lecture manual is posted on the course Sakai site. 

iClicker: Publisher: W H Freeman & Co:   ISBN-10: 0716779390 or ISBN-13: 9780716779391

Course Closed?  
To register for the course you must obtain a special permission number from Prof. Andrew Vershon (This email address is being protected from spambots. You need JavaScript enabled to view it.) . In your e-mail please include your name, RUID, class year and major.


Dr. Bryce Nickels
Waksman Institute, Room 335
phone: 445-6852
Email:  This email address is being protected from spambots. You need JavaScript enabled to view it.

Dr. Andrew Vershon
Waksman Institute, Rm 233
Phone: 445-2905
Email:  This email address is being protected from spambots. You need JavaScript enabled to view it.

Laboratory Coordinator:
Dr. Janet Mead
Waksman Institute, Rm 231
Phone: 445-3901
Email: This email address is being protected from spambots. You need JavaScript enabled to view it.

Office Hours: This course is designed to provide students with a unique, specialized laboratory experience. Thus, course participants are likely to require individualized attention at irregular and unpredictable intervals. In order to accommodate this unusual situation, the instructors have arranged to be as accessible as possible. Faculty are present during the entire laboratory period to answer questions.  

** All information is subject to change at the discretion of the course coordinator.