Molecular Biology and Biochemistry Courses
01:694:230 Analytical Methods in Biology
- This course is for students interested in learning numerical techniques for biology applications. Matlab will be used as a programming tool. All the methods and ideas presented will be developed using concrete examples of how they apply to actual biological phenomena.
- Semester Offered: Spring
- Credits: 3
- Course URL: canvas
01:694:230 ANALYTICAL METHODS IN BIOLOGY
This course may also be used to fulfill the elective requirements of the Biological Sciences and MBB majors.
Offered
Spring T/H4 (Tues/Thurs 5:40 - 7:00 PM) Tillet 207 Livingston
Credits
3
Prerequisites:
General Biology (01:119:116) AND Calculus I (01:640:135 or 01:640:151)
Course Description
This course is for students interested in learning numerical techniques for biology applications. Matlab will be used as a programming tool. All the methods and ideas presented will be developed using concrete examples of how they apply to actual biological phenomena.
Course Topics:
- Probability Theory, Theory of Distributions and Moments, Central Limit Theorem,
- Linear and non-Linear Regression,
- Parametric and Non-Parametric Tests of Significance and Analysis of Variance (ANOVA).
- Hardy Weinberg Theory, Mathematics of Mutations, Drift, Recombination and Selection.
- Sequence Alignment and Phylogenetic Analysis
- Clustering Methods: k-means clustering, Principle Component Analysis (PCA), t-SNE and non-negative matrix factorization.
- Analysis of high throughput RNA and DNA sequencing data
- Monte Carlo Simulations
- Modeling the Covid-19 pandemic
- Neural Networks
- Evolutionary Game Theory
Lecture notes will be distributed in advance of lectures and students are expected to have read these notes before class. For each topic, there will be one formal lecture and an in-class worksheet which we will work through in class. The students must complete the worksheet on their own after class and uploaded their solutions on Canvas by Sunday 11:59 PM of the week of the class. These worksheets will count for 30% of the grade. In addition, homework on the material covered will be posted on Canvas and will be due approximately one week later. Homework will also count for 30% of the grade. There will be two mid-terms (15% of grade each) but no final. Students will be required to read a book they choose from a list provided by the instructor and will present a formal summary of this book in class at the end of the semester. This will count for 10% of the grade.
Course Schedule:
Week 1-4
- Introduction to the class and Matlab Tutorial
- Introduction to Probability Theory, Bayes Theorem, Random Variables; Expected Value and Variance.
- Distribution Theory - Binomial, Poisson, Bernoulli & Geometric Distributions
- Demonstration of Central Limit Theorem.
- Parametric Tests of Significance based on the Central Limit Theorem (t-test, F-test, ANOVA)
- Non-parametric tests of significance
Week 5-9
- Bio Intro, The Genetic Code, Mutation and Drift, Hardy Weinberg Theory
- Analytical methods to understand Recombination and Selection.
- Sequence Alignment and Phylogenetics.
- Clustering Methods: k-means clustering, PCA, t-SNE and non-negative matrix factorization methods.
- Mid-term and assignment of term paper topics after week 6.
Week 9-14
- Analysis of Genetic and Genomic data using the techniques learned.
- Introduction to Viruses - FLU, HIV, SARS, MERS and Zoonotic diseases
- Analytical Modeling – The SIR Model of Pandemics - Modeling Covid-19 data
- Monte Carlo Simulations
- Neural Networks
- Evolutionary Game Theory
- Mid-Term 2
- Class book presentations
Course URL:
Canvas
Course Satisfies Learning Goals
MBB Departmental Learning Goals: 1, 2,and 3
Course Learning Goals: The overall goal of this course is to give the students the mathematical tools and programming skills necessary to analyze and interpret biological and biomedical data correctly and with confidence.
Course Materials
Matlab: Students should download and install Matlab on their laptops and always bring your laptops with Matlab installed to class. To download and install Matlab, start from the following link: https://www.mathworks.com/academia/tah-portal/rutgers-university-354167.html
Course Closed?
Enrollment is limited to 50 students.
Faculty
Course Coordinator:
Email:
Phone: 848-391-7508
Office Hours: There will be two 1-hour long online office hours. The timing of these will be arranged by discussion in class with students.
Academic Integrity:
Students are expected to maintain the highest level of academic integrity. You should be familiar with the university policy on academic integrity: http://academicintegrity.rutgers.edu/academic-integrity-policy/ Violations will be reported and enforced according to this policy.
Use of external sources to obtain solutions to homework assignments or exams is cheating and a violation of the University Academic Integrity policy. Cheating in the course may result in penalties ranging from a zero on an assignment to an F for the course, or expulsion from the University. Posting of homework assignments, exams, recorded lectures, or other lecture materials to external sites without the permission of the instructor is a violation of copyright and constitutes a facilitation of dishonesty, which may result in the same penalties as explicit cheating.
Not only does the use of such sites violate the University’s policy on Academic Integrity, using such sites interferes with your achievement of the learning you are paying tuition for. Assignments, quizzes, and exams are given not simply to assign grades, but to promote the active learning that occurs through completing assignments on your own. Getting the right answer is much less important than learning how to get the right answer. This learning is critical to your success in subsequent courses and your careers.
01:694:316 Honors Introduction to Research in Molecular Biology
- The main goal of this course is to encourage undergraduate students to conduct independent projects in biomedical research laboratories at Rutgers and RWJMS. The course is designed to introduce students to many of the modern techniques used in genetics, molecular biology, and biochemistry that they may use in research by giving them as much "hands on" experience as possible. Students will carry out a research project for which the results are unknown. The topics covered in this course will provide students with a very good foundation for taking upper level genetics and biochemistry courses in subsequent years.
- Semester Offered: Fall
- Credits: 4
- Course URL: canvas
Prerequisites
Registration will only be allowed to second or third year Honors MBB or Genetics students. Registration is by SPN only. Contact
Course Description
The main goal of this course is to encourage undergraduate students to conduct independent projects in biomedical research laboratories at Rutgers and RWJMS. The course is designed to introduce students to many of the modern techniques used in genetics, molecular biology, and biochemistry that they may use in research by giving them as much "hands on" experience as possible. Students will carry out a research project for which the results are unknown. The topics covered in this course will provide students with a very good foundation for taking upper level genetics and biochemistry courses in subsequent years.
The Project
After some initial training in techniques commonly used in biomedical research labs, students will work on their main research project. The project involves analyzing mutants in a transcriptional regulatory protein in yeast. Students will analyze the data from different assays to determine how the mutations affect transcriptional silencing and repression of genes in yeast. The DNA sequences of the mutants will be determined and the students will derive the predicted change in the protein sequence. Students will then map their mutation on a model of the protein structure and hypothesize how it will affect the protein's activity. There will also be discussions about finding a research lab to do independent research projects as an undergraduate at Rutgers.
Week Topic
1 Introduction; Why is transcription important for biology and human diseases? Review of the general process of gene expression.
2 Why do we work in yeast? Review of yeast biology and genetics.
3 Eukaryotic chromatin structure and the role of Sir2 in transcriptional silencing
4 Vectors and plasmid DNA purification
5 Analyzing DNA - Restriction enzymes, PCR, and gel electrophoresis
6 DNA sequencing and analysis
7 Exam
8 Genetic and biochemical analysis of transcriptional regulatory sites
9 Genetic and biochemical analysis of transcriptional regulatory proteins
10 Silencing vs repression, PCR Mutagenesis and genetic screens for mutants
11 Principals of protein structure
12 Protein structure modeling using jMo,l Results, problems and interpretations
13 Finding a Lab, Careers in Biomedical Sciences
14 Exam
In Fall 2022 the course will be given in a "flipped" manner. All of the content will be posted in videos and lecture notes on the course Canvas. Students will be expected to work through the chapters and take review quizzes on their own. There will be at least two 80 minute discussion periods each week where we will quickly review the content and then work through problems.
Course URL
Canvas site
Learning Goals
This course satisfies learning goals 1, 2, 3, and 4 of the MBB Department.
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.
Exams, Assignments, and Grading Policy
Exams: 30%
Quizzes: 40%
Assignments: 30%
Exams will be timed asynchronous over a 10 hr period and will account for 30% of the grade. The exams will focus on the material covered in the lectures, data analysis, and assigned reading. There will be a midterm and a final (cumulative).
Quizzes
There will be three forms of quizzes:
- Chapter Review Quizzes: After watching the video or reading the lecture notes on a chapter student will take quizzes posted on Canvas on the material. These will be used for the students to gauge their basic understanding of the material. These will be self-paced, but must be completed before the topics are discussed in the on-line meetings. These will represent 10% of the grade.
- Analysis Quizzes will be given over a 10 hr period to gauge the understanding of the material that was presented in the lecture notes and videos and then covered in the online discussion sections in the previous week. These quizzes will account for 20% of your grade.
- Lab Quizzes: After watching the video and reading the protocol notes on a lab students will take quizzes posted on Canvas on the material. These are mainly used to ensure that students are prepared to conduct the lab procedures. The purpose it to avoid mistakes and to allow students to complete the lab more efficiently. These will be due before the lab. These will represent 10% of the grade.
Assignments: Assignments and lab reports will be given out through the semester. These are all posted in the Assignments section on Canvas. These include submitting weekly questions on material that was covered in class and homework assignments such as the Yeast Gene Search and Restriction Mapping Problem set (see Canvas assignments). Lab reports will contain the data (plate and gel figures, sequence alignments and a picture of the structure) that were previously generated during this course and your interpretation of the results. The Assignments & Lab Reports will count for 30% of the grade.
Course Materials: A laboratory and lecture manual is provided on-line with the class. All course materials will be posted on the course Canvas site.
Course Closed? This course is primarily for second year Honors students intending to major in the MBB. Non-Honors MBB or Genetics students interested in this course should contact Dr. Vershon for an SPN or should enroll in 694:214 or 694:315, which will be held in the spring semester.
Faculty: Course Coordinator:
Office Hours: Dr. Vershon’s official hours are 7:00 AM to 10:00 AM (East Coast time) Tuesdays using the meeting software in Canvas. However, since the best time to ask questions and get help is in the laboratory section of the class. Students may also email or call us to make an appointment if you have problems or questions.
** All information is subject to change at the discretion of the course coordinator.
01:694:492 Gene Regulation in Cancer & Development
- 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. There are no textbooks. Material taught in this course is based on understanding general concepts, in-depth analysis of selected primary research articles and enhancing critical thinking skills. Topics include, gene therapy, inherited diseases, circadian rhythms, metabolic disorders, microbiome, COVID/vaccines, immunity and cancer resistant animals.
- Semester 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. There are no textbooks. Material taught in this course is based on understanding general concepts, in-depth analysis of selected primary research articles and enhancing critical thinking skills. Topics include, gene therapy, inherited diseases, circadian rhythms, metabolic disorders, microbiome, COVID/vaccines, immunity and cancer resistant animals.
Syllabus:
Course Satisfies Learning Goals
- 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.
- Students should demonstrate the ability to find and evaluate information about specific biological systems or problems.
Exams, Assignments, and Grading Policy
PowerPoint lecture material and readings for each class will be posted on the relevant Canvas site for this course. 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, critiques, 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 course coordinator concerning special permission numbers.
Faculty
The course will be taught by two faculty members from the Department of Molecular Biology and Biochemistry, Drs. Annika Barber and Isaac Edery.
Course Coordinator:
** All information is subject to change at the discretion of the course coordinator.
01:694:484 Seminar in Molecular Biology and Biochemistry
- 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.
- Semester Offered: Spring
- Credits: 1
Prerequisites: 0
1:694:408
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
- 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.
- Students should demonstrate the ability to find and evaluate information about specific biological systems or problems.
- Students should demonstrate the ability to design experiments and critically analyze data.
- 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 are presenting
3) Your timely hand-in of abstracts and revised abstracts
4) Grades will be curved based on end-of-semester distribution
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, or provide a doctor’s note for emergency medical absences) no points to minus one point as per instructors’ discretion. But we will still keep track to prevent abuse
Course Materials: All course materials are posted on the course's Canvas site
Course Closed?
If this course is closed please contact the course instructor concerning special permission numbers.
Faculty
Course Coordinator:
Annika Barber
Rm 238 Waksman Institute
Participating Faculty:
Kevin Monahan
A128 Nelson lab,
Jia Fei
A128 Nelson lab,
Ruth Steward
Waksman Institute, Busch Campus
** All information is subject to change at the discretion of the course coordinator.
01:694:412 Proteomics and Functional Genomics
- 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.
- Semester Offered: Spring
- Credits: 3
- Course URL: canvas
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
Canvas
Course Satisfies Learning Goals
- 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.
- 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, CALL 848-445-2075. If the course is closed, please use the following link: Wait List Sign Up for Spring 2023 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
Dr. Jia Fei
E-mail:
Dr. Stephen Anderson
CABM305
E-mail:
** All information is subject to change at the discretion of the course coordinator.
