Office of Undergraduate Instruction

 

This course is intended for Life Science majors or those with a strong background in the Biological Sciences.

This course may be used to fulfill the elective requirements of the Biological Sciences major.


Offered

Spring

Credits

3

Prerequisites

General Biology 01:119:115-116, 117 or 01:119:101-102 and Organic Chemistry 01:160:307 or 160:315 and Physics I  01: 50:203 or 01:750:201 or 01:750:194; and Calculus I  01: 640:151 or 01:640:135.

Course Description

This course covers strategies invented by nature to absorb and convert solar energy into other forms for storage or work (force generation). A quantitative accounting of solar energy utilization and losses in biology and analogous man-made solar devices will be provided along with basic aspects of biological energy conversion in general (energy metabolism). Current topical interest will focus on natural photosynthesis and how efficiently it can harness solar energy by conversion to chemical precursors that produce molecular hydrogen and biofuels, or photoelectric cells (bio-fuel cells). Emerging knowledge will be presented on the development of the synthetic “artificial leaf.“

Both Chemistry and Biochemistry majors, or students in related curricula who have met the course requirements, will be provided with a fundamental understanding of biolog- ical energy conversion, work and entropy (equilibrium thermodynamics) through applications in metabolism, photosynthesis, and emerging solar energy technologies. Students will be introduced to energy related research strategies necessary to meet the daunting 21st century energy challenge. 

Course URL

Sakai

Course Satisfies 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. Both Chemistry and Biochemistry majors, or students in related curricula who have met the course requirements, will be provided with a fundamental understanding of biological energy conversion, work and entropy (equilibrium thermodynamics) through applications in metabolism, photosynthesis, and emerging solar energy technologies.

5.Students will be introduced to energy related research strategies neceessary to meet the daunting 21st century energy challenge.

Schedule

#

Date/ Lecturer

Topic

Learning Goals

 

1

1/20 RAN,

Photosynthesis and solar energy as alternative energy sources

Background on light reactions. applications

 

2

1/25 “

Renewable world energy resources

Recognition of energy crisis and solutions

 

3

1/27 “

Harnessing solar energy for production of biofuels (ESF)

Basis for biomass and other alternative fuels

 

4

2/1 “

Coal and natural gas power a warming world

Basis for anthropomorphic global warming --

 

5

2/3 “

Anoxygenic photosynthetic life

Applicatictions of metabolism, bioenergetics

 

6

2/8 ”

Oxygenic photosynthesis

Applicatictions of metabolism, bioenergetics

 

7

2/10 “

Biological strategies for CO2 capture and reduction

Metabolism, anabolic mechanisms

 

8

2/15 “

Anoxygenic photosystem based biohybrid solar cells

Application of basic photophysical principles

 

9

2/17 “

 

Application of basic photophysical principles

 
 

2/22

Exam 1

   

10

2/24 RCP

An industry perspective on photobiological energy production and usage

Industrial perspective

 

11

2/29 “

 

12

3/2 GCD

The biochemical logic of metabolic pathways

Applicatictions of metabolism, bioenergetics

 

13

3/7 “

Oxygenic photosynthetic life: Kinetics and thermodynamics of PSII and H2O oxidation

Energy conversion, thermodynamics

 

14

3/9 “

Artificial photosynthetic life: Bioinspired catalysts for H2O oxid- ation and H2 evolution

Biomimetic catalysis

 
 

3/12--3/20

Spring break

   

15

3/21 RAN

PSII and PSI based biohybrid solar cells

Applicatictions of metabolism

 

16

3/23 “

Biofuels from algae Biomass to solar types and conversion?

Metabolism, anabolic mechanisms

 

17

3/28 “

Artificial photosynthesis: protein maquettes as solar energy converters

In silico biomimetic approaches and aplications

 
 

3/30

Exam 2

   

18

4/4 “

Biological hydrogen via hydrogenase and nitrogenase

Applicatictions of metabolism, bioenergetics

 

19

4/6 “

Evaluation of biofuels

 

20

4/11 JM

Sorghum as an alternative biofuel

Genetic studies

 

21

4/13 JM

Duckweed as an alternative biofuel

Genetic studies

 

22

4/18 VN

Toward an artificial photosynthesis

In silico biomimetic approaches, aplications

 

23

4/20 RAN

Starch and cellulosic biofuels

Applicatictions of metabolism

 

24

4/25 “

Engineering metabolic systems for production of advanced fuels

 

25

4/27 “

Harvesting wind energy

Application of basic physical principles

 
 

5/2

Exam 3

   
         

Exams, Assignments, and Grading Policy
Each topic will be followed by a discussion session with an assigned discussion leader. This will be of prime importance in achieving learning goals and academic potential; participation in the discussions will count for 20% of the final grade. For the rest of the grade, the three exam grades will be weighted equally. Review sessions will be scheduled before each exam. 

Course Materials

Text (as background for lectures on Biochemical topics) Principles of Biochemistry (2012) Lehninger, A.L. Nelson, D.L. and Cox, M.M. 6th Edition. New York, W. H. Freeman and Co. and relevant outside readings.

Course Closed? 

Please contact This email address is being protected from spambots. You need JavaScript enabled to view it. for special permission.

Faculty

Dr. R. Niederman and Dr. G. C. Dismukes


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

 

 

This course may be used to fulfill the elective requirements of the Biological Sciences major.


Offered

 Spring

Credits

 3

Pre- or Corequisites

01:694:407-408 or 01:447:384-385 or 11:115:403-404 or 11:126:481

Course Description

Gene Regulation in Cancer and Development (01:694:492) is a course for advanced undergraduate students majoring in the Life Sciences. Molecular biology is an experimental science, and a major goal of this course is to explain not just what molecular biologists know, but how they know it. Thus, while covering selected topics in gene regulation, development, and cancer, we will emphasize the methods, experimental design, history, and deductive reasoning that has led to the current state of understanding of these topics.

Syllabus (subject to revision):

1                         Irvine            Course Introduction & Review of some fundamental concepts in Molecular Biology

2                         Steward        Drosophila as a model system:  genetics and development

3                         Steward        Induction of mutations and analysis of mutant phenotypes      

4                         Steward        Genomics and micro RNAs            

5                         Steward        Control of gene expression in development:  activated and repressed promoters

6                         Edery            Circadian rhythms: overview and principles

7                         Edery            Clock Mechanisms I

8                         Edery            Clock Mechanisms II

9                         Edery            Circadian rhythms and connection to cancer and other diseases I

10                       Edery            Exam 1 (covers lectures 1-9 & readings)

11                       Steward        Prenatal diagnosis/ Inherited diseases in humans

12                       Steward        Gene therapy

13                       Steward        Personalized genomics

14                       Steward        TBD

15                       Edery            Circadian rhythms and connection to cancer and other diseases II

16                       Edery            Signaling to and from the clock I

17                       Edery            Signaling to and from the clock II

18                       Edery            TBD                

19                       Steward        Exam 2  (covers lectures 11-18 & readings)  

20                       Irvine            Introduction to signal transduction and Wnt signaling

21                       Irvine            Genetic approaches toward identifying & ordering genes in a pathway                                            

22                       Irvine            Extracellular Regulation of Wnt Signaling

23                       Irvine            Biochemical & Cell biological analysis of cytoplasmic & nuclear events in Wnt Signaling I

24                       Irvine            Biochemical & Cell biological analysis of cytoplasmic & nuclear events in Wnt Signaling II

                                                Irvine Take Home handed Out

25                       Irvine            Downstream of Wnt Signaling:  Transcriptional responses & Cellular Outcomes                                              

26                       Irvine            Wnts, Stem cells, and Cancer Irvine Take Home Due                                           

27                       Irvine            Wnts & PCP

28                       Irvine            Hallmarks of Cancer & Review

29                       Irvine            Exam 3  (covers lectures 20-28 & readings)

Course Satisfies 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.

Exams, Assignments, and Grading Policy

There will be three exams over the semester that will cover the material presented in class; there will not be a cumulative final exam. Each exam will count for 25% of the grade. In addition, there will be problem sets, in class quizzes, and/or other assignments that together will count for the remaining 25% of the grade. Absence from exams will be excused only in the case of serious illness or family emergency, and only when backed up by appropriate documentation. Requests for regrades must be submitted within 72 hours of return of the exam.

Course Materials

Because we are focusing on current topics, there is no textbook, but there will be assigned readings and literature research from the primary literature, and where appropriate, background reference material will be recommended by the instructors.

Course Closed?

If this course is closed please contact the This email address is being protected from spambots. You need JavaScript enabled to view it.concerning special permission numbers.

Faculty

The course will be taught by three faculty members from the Department of Molecular Biology and Biochemistry, Drs. Isaac Edery, Ken Irvine and Ruth Steward, plus some guest lecturers.

Course Coordinator: This email address is being protected from spambots. You need JavaScript enabled to view it.


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

 

 

This course is intended for undergraduate Molecular Biology and Biochemistry (MBB) majors or those with a strong background in the Biological Sciences. It may be used to fulfill the elective requirements of Biological Sciences or MBB majors.


Offered: Spring

Credits:  3

Prerequisites: Molecular Biology and Biochemistry 01:694:407 and Genetics 01:447:380

Course Description

This course is a survey of modern techniques of protein biochemistry, bioinformatics, proteomics, and functional genomics. It will include a discussion of basic concepts of protein structure and function, protein characterization and purification, enzyme kinetics, nmr and x-ray crystallography, mass spectrometry, and various techniques of functional and structural genomics.

1          Course introduction and overview of genomics & proteomics           

2          New strategies and technologies for DNA sequencing                      

3          DNA sequencing – current technologies & applications                    

4            Applications of new DNA sequencing technologies (con’d)             

5          Amino acids and proteins                                                                   

6          Conformational properties of proteins                                    

7          Blast and dynamic programming algorithm                            

8          Sequence-based bioinformatics                                                          

9          Analytical and preparative protein chemistry                                      

10        Preparative protein chemistry (cont’d)                                    

11        Protein domains and folds                                                                  

Take-home Exam I handed out

12        Structural Bioinformatics                                                                   

13        Protein folding in vitro                                                                       

Take-home Exam I due

14        Protein folding in vivo                                                                        

15        Protein NMR and structure analysis                                                  

16        Protein X-ray crystallography                                                            

17        Protein Mass Spectrometry and Proteomics                                       

18        Cryo Electron Microscopy.  Homology Modeling                             

19        Protein-protein interactions I                                                              

20        Protein-protein interactions II                                                             

21        Enzyme kinetics                                                                                 

22        Enzyme kinetics / Protein dynamics                                                   

Take-home Exam II handed out

23        Student Presentations                                                                         

24        Student Presentations                                                                         

Take-home Exam II due

25        Student Presentations                                                                         

26        Student Presentations                                                                         

27        Student Presentations                                                                         

28        Student Presentations                                                                                     

Take-home Exam III

 

Course URL: All course materials will be posted on Sakai

Course satisfies Learning Goals

1. Students should demonstrate an understanding of the knowledge that is needed to begin biomedical research in the areas of proteomics, functional genomics, and/or bioinformatics. They will learn the theory and practice of key methods needed for postgraduate studies in these fields. .

2. Students should demonstrate the ability to work independently to find and evaluate information about specific biological systems or problems.

 Exams, Assignments, and Grading Policy

Take-home Exams I & II will each count for 30% of your grade.  The Student Presentation counts for 25% of your grade.  Take-home Exam III counts for 15% of your grade.  We also take into account class participation, especially in the Student Presentation part of the course.  There will be no final exam.

Course Materials:  Readings provided by instructors.

Course Closed?

This course is by special permission only, with priority given to MBB majors. The majority of the class will be juniors and seniors. To obtain a special permission number or to get on the waiting list if you are not an MBB major, please use the following link:Wait List Sign Up for Spring 2018 Courses If you have any questions, please contact the Division of Life Sciences - Office of Undergraduate Instruction at 848-445-2075 or visit our office at Nelson Biological Laboratories B112, Busch Campus.

Faculty

Prof. Gaetano Montelione
E-mail: This email address is being protected from spambots. You need JavaScript enabled to view it.

Prof. Stephen Anderson
E-mail: This email address is being protected from spambots. You need JavaScript enabled to view it.


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

 

Course is only for Seniors majoring in Molecular Biology and Biochemistry


Offered:  Spring W2 (Wed 10:35-11:30 AM) Waksman Rm 1001

Credits: 3

Prerequisites: 01:694:408

Course Description:  The course is designed to give students a chance to present their research projects in front of an audience or their peers.

The course will break up into smaller sections each taught and graded by one of the section instructors. These smaller sections will serve as a forum for the oral presentation of student research or literature reports pertinent to the student's research project, regardless of whether the student is following the Laboratory or Non-Laboratory Options in the MBB major. Students will give two 20 minute oral presentation related to their research activities: one in the first half of the semester and one in the second half. Students should also plan for 5 minutes of discussion/questions for a total of 25 minutes. Note: students should target their presentation for a scientific audience, therefore this is not a "Newsweek Magazine Level" or "New York Times Journalistic Level" type of presentation. Thus the introduction, results, conclusions of the talk should match the level of the audience, which means students should assume everyone has a B.S. degree in molecular biology and biochemistry. One week prior to the talk students must email an abstract (~1 page) to their section instructor. We will critique it and very likely we will ask for students to submit a revised abstract. We will then distribute the revised abstract by email to the students in the section. Students who are presenting are expected to invite their P.I. (or Grad. student or Postdoc) from your lab to sit in on the presentation.

Students will present a poster on their research at the MBB Poster session near the end of the semester.

Course satisfies 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 demonstrate the ability to communicate their research and findings orally through seminar and poster presentations and through written research papers.

Exams, Assignments, and Grading Policy

MBB 484 Guidelines for Grading

 

strong A

A/B+

B+

B

C

60% presentation

excellent 

good 

OK

poor 

bad

20% participation + discussant

often 

often to sometimes 

sometimes 

rare 

never

20% attendance

<1 point

1-1.5

1.5-2.5

2.5-3

>3.5

Explanation of Grading

Presentations are based on several criteria:

1) the instructors' critique sheet, (not the students)

2) how well you prepared, your organization, enthusiasm, interest in your subject, understanding and ability to discuss what you presenting

Participation and Discussant:

Your role as a "Discussant" contributes to only part of the "Participation" grade. The remainder of this grade is based on how active you are in asking questions during the other 12 weeks of the course when you are not a participant.

Attendance Point System

Unexcused absence (no prior notification) is minus one point.

Late is minus 0.5 points.

Excused absence (inform us before the class) no points to minus one point as per instructors discretion. But we will still keep track to prevent abuse. Also if you are sick and provide us with a Doctor's note that would help.

Course Materials: All course materials are posted on the course's Sakai site

Course Closed?  If this course is closed please contact the course instructor concerning special permission numbers.

Faculty

Samuel Gunderson
A322 Nelson lab, 445-1016
This email address is being protected from spambots. You need JavaScript enabled to view it.
Office hours by appointment only

Additional MBB faculty will work with sections of the course.


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

 

 

This course is open first to declared Molecular Biology and Biochemistry (694) majors.This course is also open to second year students who intend to be Molecular Biology and Biochemistry majors and have completed the prerequisites courses. If there is space the course is open to non-MBB majors.  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.

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

Week Topic (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’s 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.

Faculty

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.

 

Contact Us

Nelson Biological Laboratories

Nelson Biological Laboratories
604 Allison Rd
Piscataway, NJ 08854


p. (848) 445-2075
f.  (732) 445-5870