Importance Notice for All Biotechnology Majors
Please be aware of grade requirements as prerequisites for core biotechnology courses:
Students not meeting grade requirement(s) will not be allowed to register for these courses.
Available Courses
CURRENT COURSE SYLLABI ARE PROVIDED AS LINKS NEXT TO EACH SPECIFIC COURSE; GENERAL COURSE DESCRIPTIONS ARE BELOW
Note
These course synopsis are being provided to give you a general idea of the course structure. Specific details may change from semester to semester and will be provided by the instructors in the first week of the semester. Links to syllabi are above.
COURSE DESCRIPTIONS
11:126:110. Concepts and Issues in Biotechnology (1.5)
Normally Offered
As equivalency course
Pre-requisites and Other Registration Restrictions
The course has no prerequisites; it is a required course for Biotechnology majors but is open to transfer students as an equivalency course.
Format
1 80 minute lecture
Description
The purpose of this course is to survey the methods and applications of biotechnology and to examine the consequences of developments in this area. This is an area of great public interest with a pressing need for informed debate. The course is organized by topic and covers many aspects of biotechnology, including those that relate to animals, microbes, human health, agriculture and the environment. A specialist guest lecturer will introduce each topic and lead the subsequent class discussion.
Learning Goals
- To gain familiarity with basic approaches to biotechnology research and development, and the wide range of biotechnology applications
- To understand ethics and societal issues relevant to controversial applications of biotechnology
- To gain oral and written communications skills
Assessment Measures
- Weekly readings on basic biotechnology applications are assessed by weekly quizzes.
- Students give oral presentations on ethical and societal aspects of biotechnology in small group format (3-4 students per group); oral presentations comprise 15% of the grade for the course.
- Class participation in group discussions is recorded and assessed as 5% of the student grade.
- A final term paper project assesses student ability to write about one current aspect of biotechnology and the societal issues surrounding it.
11:126:111: Ethical and Scientific Challenges in Biotechnology (3)
.jpg)
NS and CCO-2
Normally Offered
Spring, by Prof Paul Meers (2 sections)
Pre-requisites and other registration restrictions
The course has no prerequisites; it is a required course for Biotechnology majors but is open to any student interested in biotechnology, its applications and social and ethical consequences.
Format
2 80 minute lecture/discussion/student presentations
Description
The purpose of this course is to survey the methods and applications of biotechnology and to examine the consequences of developments in this area. This is an area of great public interest with a pressing need for informed debate. The course is organized by topic and covers many aspects of biotechnology, including those that relate to animals, plants, microbes, human health, agriculture, medicine and the environment. A specialist guest lecturer will introduce each topic with a lecture and lead the subsequent class discussion. Students learn about the scientific basics from the textbook Introduction to Biotechnology and will also investigate and present viewpoints on ethical issues in various fields of biotechnology.
Learning Goals
Course learning goals: Upon training in this course students will:
- have knowledge of the basic approaches to biotechnology research and development, and the wide range of biotechnology applications, including a basic knowledge of the scientific method.
- be able to address ethical and societal issues relevant to controversial applications of biotechnology.
- have gained basic oral and written communications skills in the sciences.
This course addresses the following Biotechnology program learning goals:
As a Biotechnology Major, each student will:
- be able to describe the basic molecular concepts essential for understanding the field of biotechnology and the applications of biotechnology.
- be able to find and read published scientific research in biotechnology and summarize and communicate that research effectively and critically.
- acquire knowledge of ethical aspects of biotechnology and be able to analyze alternate viewpoints.
Topics
Assessment Measures
- Weekly readings on basic biotechnology applications are assessed by weekly quizzes.
- Students give oral presentations on ethical and societal aspects of biotechnology in small group format (3–4 students per group); oral presentations comprise 20% of the grade for the course. The topic will be determined in conjunction with the instructor. Each group will present the topic to the class.
- Class participation in group discussions is recorded and assessed as 5% of the student grade.
- A final term paper project assesses student ability to write about one current aspect of biotechnology and the societal issues surrounding it.
11:126:383: Nucleotide Sequence Analysis (3)
Normally Offered
Fall and Spring semesters by Dr. Sonia Arora
Pre-requisites
01:160:308 Organic Chemistry and 01:447:380 Genetics
Format
One period lecture followed by two- period computer laboratory per week.Course Description
This is a mixture of lecture & dry laboratory based course. It is aimed at examining the basic tools that form the foundation of bioinformatics. The course introduces students to DNA, RNA & amino acid sequence analysis using publically available and web based tools such as Blast, Clustal etc. The course also covers biological databases; and identification of genes & proteins in these databases. The students obtain mastery of analyzing information on NCBI, Genbank and OMIM databases. In addition, the course familiarizes students with techniques of genetic manipulation, recombinant DNA technology & restriction mapping. The students learn how to use programs like NEBcutter, Net Primer and Primer 3Plus. The course also covers analysis of primary data obtained from DNA sequencers, assembly of raw data into a contiguous sequence, finding open reading frames, translating nucleotide sequences into amino acid sequences, determining protein and DNA characteristics using computer program like CLC Bio Main Workbench.
Student Learning Goals
Upon completion of the course, students should be able to
- Critically analyze nucleotide and amino acid sequences; and find homologous sequences.
- Examine and extract gene, protein & disease information available at various biological databases.
- Utilize computational methods to design genetic manipulation experiments in wet-laboratory.
- Understand & analyze primary sequence data obtained from DNA sequencing projects.
- To understand how computational methods aid in answering various research questions.
Assessment Measures
Learning Goals 1, 2, 3 & 4 assess applied knowledge of the students. These are measured by two closed book closed notes examinations. The exams involve written as well as practical portions. Each exam is graded on a 100 point scale.Learning Goal 5 assesses holistic knowledge of the students and is measured using final term project. Students use dry lab techniques taught in the class to identify a gene & its encoded product. They decipher its known or predicted structure of the protein, clinical relevance in a disease process and evolutionary conservation across various organisms. They discuss their results in a written project report that is graded on a 100 point scale.
Examinations & Grading
(A) In Class Dry Lab Exercises (40% of grade)
Each lecture class is followed by computational dry lab exercises. These exercises give opportunity for students to gain hands on experience on various tools and techniques described in the class. Exercises make 40% of the grade.
(B) Examinations (40% of grade)
There are two closed book closed notes examinations (100 points each). The exams involve written as well as practical portions. Written exam may contain questions ranging from multiple choice questions; labeling diagrams, and short answer questions. Practical exam will involve mini dry lab exercises similar to the one done during the classes. Examinations make 40% of grade.
(C) Sequence Analysis Term Project (20% of grade)
Students use dry lab techniques taught in the class to identify a gene & its encoded product. They also try to decipher known or predicted structure of the protein, clinical relevance of the protein in a disease and evolutionary process. The results of the project are discussed in a written project report, which accounts for 20% of the grade.
11:126:401. Seminar in Biotechnology (1.5)
Normally Offered
Fall by Professors Faith Belanger, Sonia Arora and Paul Meers
Pre-requisites and Other Registration Restrictions
Open only to seniors majoring in biotechnology.
Format
One 80-min seminar and discussion session.
Description
Development of communication skills needed by professionals in the field of biotechnology through student oral presentations and facilitated discussion. Topics include current scientific advances in biotechnology and the social impact of biotechnology.
Biotechnology is a rapidly expanding field in which new information, discoveries and applications are reported each and every day. As with many areas of science, the most current information can only be found in journals or presented at scientific conferences and meetings; by the time textbooks are written, edited and published, much of the cutting edge information may be outdated. This seminar course is designed to give you practice in the critical reading of research articles from scientific journals, and in the oral and visual presentation of scientific information to your colleagues. Because the use of genetically-engineered organisms in modern biotechnology has given rise to social, ethical and legal considerations, we will examine these issues as well.
Learning Goals
- To read critically, understand thoroughly and discuss primary journal articles from high impact scientific journals
- To develop and improve oral communication skills
- To understand key components of an effective seminar, including structure of the seminar, technical aspects of effective slide production and data presentation, and spoken delivery
- To present effective and interesting seminars
- To evaluate the quality of seminar presentations
Assessment Measures
- Each student chooses two journal articles that will present in two formal, 30 minute seminars.
- Each presentation is evaluated by the student's peers and the instructor in written format.
- Each student must attend two outside seminars within the field of biotechnology, and s/he writes summaries of the seminar content, as well as detailed evaluations of the seminar speaker's presentation.
Topics
Examinations
None
Other Requirements
Students are required to give two 30 minute presentations during the course of the semester. At least one presentation will be on a recently published paper from a scientific journal, on a topic of your choice in the area of biotechnology. It should be a "primary" journal article, containing original data, and not a review article. You must provide your course instructor with a copy of the paper you have chosen one week before the scheduled presentation, so that she can review the selection for appropriateness.
The other presentation will take either one of two possible formats. If you are involved in research or a co-op project this semester (or were over the past summer), you may choose to describe your research project. If you are not involved in a research project, or if you prefer, your second presentation will focus on one of the social, economic, ethical, and/or legal aspects of biotechnology. Students are encouraged to make PowerPoint presentations.
It is often helpful to learn how to give seminars by attending presentations of other speakers who are more experienced than you might be. Each student should attend at least two "outside seminar" presentations during the semester. Notices are posted on bulletin boards alerting you to time, place and topic. Each week, we shall devote a few minutes to discussion of these outside seminars.
Grading
Grading: Grades will be based on participation in class discussions as well as your presentations. Some of you have never given this type of presentation before, so improvement from the first to the second presentation will be monitored in particular. Students will (anonymously) critique each other. You are expected to attend all classes and to be an active participant in class discussion. If not, your grade will reflect this. One third of your grade will be based on class participation and the other two-thirds will be based on your presentations.
11:126:407. Comparative Virology (3)
Normally Offered
Fall, every other year (odd numbered years) by Profs. Bradley Hillman and Nilgun Tumer
Pre-requisites and Other Registration Restrictions
Two semesters of (01:119:101-102) general biology are required, and organic chemistry is required. Exposure to cellular processes in a course such as Genetics, Microbiology, Molecular Genetics, or Biochemistry is recommended.
Format
Two 80-minute lectures.
Description
This course may be appropriate for students from several curricula, for example: biotechnology, biology (including pre-med), biochemistry and microbiology, plant science, or animal science.
This course is intended to introduce students to a broad variety of viruses that infect members of all kingdoms. The emphasis is on the viruses themselves, not on clinical aspects. Emphasis at the end of the course is on the use of viruses in biotechnology, and the impact of biotechnology on virology and virus diseases. An overall outline of the course is as follows:
Topics
Learning Goals
- Understand the differences between viruses and other microbes.
- Understand the methods used to study viruses at physico-chemical, molecular, and population levels and how viruses are used in biotechnology and gene therapy.
- To learn about similarities and differences among viruses that infect different kinds of prokaryotic and eukaryotic hosts.
- To learn about similarities and differences in genome composition, organization, replication, and gene expression strategies of viruses.
- To learn details of some major virus diseases.
- To learn about host mechanisms used for defense against virus infection.
- To learn about current topics in virology through classroom presentations and discussion.
Assessment Measures
- Exams covering lecture and reading material (long answer, short answer, multiple choice, true-false).
- Group presentation on topic of current interest.
- Reference-based paper summarizing and expanding on group presentation.
- Participation in classroom discussions.
Examinations
Two midterm exams are given during the lecture periods. The final exam given during the final exam week is comprehensive, but emphasizes the last section of the course.
Other Requirements
Students are required to participate in a small group project/presentation during the second half of the semester.
11:126:410. Process Biotechnology (3)
Normally Offered
Spring (every other year) by Professor Henrik Pedersen
Pre-requisites and Other Registration Restrictions
11:680:390 or 01:447:390; one term of biochemistry. Intended for junior or senior year students in biotechnology. A basic background in microbiology and mathematics through ordinary differential equations.
Format
Lecture twice a week in an 80-minute class period.
Description
This course satisfies elective requirements in the biotechnology curriculum and is typically offered every other year. Participants are typically juniors or seniors, but it is also open to graduate students. It is not intended for those students with a biochemical engineering background.
This course introduces quantitative methods used in biochemical engineering practice to students with a biological sciences background. The basic principles of mass and energy balances are discussed and their application to a variety of biological systems from molecules to production facilities are presented. Students will acquire tools that allow them to describe biological phenomena in useful model formats. They will also acquire the communication jargon needed for effective interaction with their engineering counterparts in the pharmaceutical industry. A basic background in microbiology is assumed and some knowledge of elementary differential equations is expected.
Learning Goals
Students will learn to:
- Employ the general of mass and energy conservation principles to problems not previously seen.
- Formulate models for quantitative understanding of biological growth and metabolism
- Perform data analysis and parameter estimation for algebraic models, including nonlinear models
- Know how to build flux analysis models from genomic-derived pathway data
- Analyze journal papers that employ conservation models and flux analysis in biological systems
- Summarize the major unit operations used downstream in bioprocess systems
- Diagram a process flow sheet for large-scale industrial synthesis of biological products
Topics
Examinations
2 hourly exams given in the lecture period.
Other Requirements
A text is utilized for the class that contains numerous solved examples. Handouts will supplement the text. Homeworks will be assigned throughout the semester (about 8) and solutions will be available for all material.
Grading/Assesment
Homeworks (40%), exams (50%), class participation (10%)
11:126:413. Plant Molecular Biology (3)
Normally Offered
Fall in odd-numbered years by Professors Michael Lawton, and Pal Maliga
Pre-requisites and Other Registration Restrictions
Taking one of the following courses - 01:447:380 (General Genetics); 11:126:481 (Molecular Genetics) or 11:115:404 or 01:694:408 (Biochemistry) or 11:776:305 (Plant Genetics)
Format
Two 80-minute lectures/week
Description
Fundamental and applied aspects of plant molecular biology; structure, expression and isolation of plant nuclear genes; molecular biology of plant development, plant organelles, and plant-microbe interactions; and plant biotechnology.
Topics
Examinations
There are three 80-minute exams each worth 1/3 of the final grade. These exams are in short essay format.
Other Requirements
Grading
There will be three hourly exams, each worth one third of the final grade. The Final Exam will cover lectures during the entire semester (40% lectures in last Section, 30% each covered in Exams 1 and 2).
11:126:427 Methods and Applications in Molecular Biology (4)
Normally Offered
Fall by Professors Rong Di and Wendie Cohick
Pre-requisites and Other Registration Restrictions
Organic Chemistry and 01:447:380 and completion of 11:126:481 and 482 (with grades of C or better).
Format
Lecture, laboratory and follow-up laboratory (recitation). All sections meet together once a week for lecture in an 80-minute class period. Individual sections meet each week for one three-period laboratory (4hr 40 min) combined with an 80-minute follow-up laboratory/recitation the following day.
Description
This course is designed to introduce you to general techniques used in molecular biology. Monday lectures will be used to orient you to the upcoming laboratory, teach the theory behind the techniques you will be using, and acquaint you with additional methodologies and their applications that we don't have time to cover in lab. You will be assigned reading to help enrich this laboratory experience.
Over the course of the semester you will learn fundamentals such as cloning and DNA sequencing. With your lab partners, you will design and conduct your own experiment to study the regulation of heat shock protein 70 (HSP70) in a mammalian cell line. You will determine how your experimental treatments regulate HSP70 mRNA and protein levels using quantitative RT-PCR and western immunoblotting, respectively. In the last laboratory session of the semester, each lab group will present their results to their classmates using a PowerPoint presentation.
Learning Goals and Measures of Assessment
- To master basic laboratory techniques and the use of standard equipment used in molecular biology studies
Assessment: Exams and evaluation of weekly performance in the laboratory - To understand the underlying principals of molecular biology techniques and their applications
Assessment: Exams and laboratory notebook - To learn proper experimental design with appropriate controls
Assessment: Group research proposal and oral presentation - To learn how to formulate and test a scientific hypothesis, i.e., how to conduct hypothesis-driven research
Assessment: Group research proposal and oral presentation - To learn how to document, record, and interpret scientific data
Assessment: Laboratory notebook and oral presentation - To develop effective oral and written communication skills
Assessment: Short essay component of exams, group research proposal, oral presentation - To build skills required to work as a member of a team
Assessment: Group research proposal and oral presentation - To develop critical thinking skills needed for 21st century science
Assessment: Exams and group research proposal
Specific Measures of Assessment
- Two exams (short essay, multiple choice, true/false)
- Group Research Proposal: Students work in groups to design an experimental approach which tests how a specific factor of their choosing regulates expression of a given gene in mammalian cells. The group's written proposal states a specific hypothesis and objectives, gives the rationale behind the hypothesis based on current scientific knowledge, and describes the general methods to be used to test the hypothesis. The draft proposal will be evaluated and feedback given by the instructors on how to improve the proposal for the final version. The hypothesis will be tested by experimentation in the laboratory over the course of the semester.
- Oral Powerpoint Presentation of Group Project
- Subjective Evaluation of Laboratory Performance
- Laboratory Notebook (to be recorded in weekly)
11:126:434. Molecular Delivery Applications in Biotechnology (3)
Normally Offered
Spring, by Dr. Paul Meers
Pre-requisites and Other Registration Restrictions
Organic Chemistry (01:160:308), General Microbiology (11:680:390)
Highly recommended - General Biochemistry (11:115:403) or Molecular Biology and Biochemistry (01:694:407)
Format
Each week will typically involve one 80 minute lecture and one 80 minute period of lecture/discussion/student presentations
Description
Both man and nature produce delivery systems for biomolecules. An increasing number of biotechnological innovations are being aided by packaging into various supramolecular or particulate delivery systems, often on the nano scale. This strategy has already evolved within a number of natural biological species as well. In this course, the applications and mechanisms-of-action of formulated and natural biological delivery systems are explored, such as liposomes, carbon-based nanostructures, polymeric complexes, dendrimers, viruses, extracellular vesicles, etc. A broad range of applications will be addressed, from agricultural to pharmaceutical.
Learning Goals and Assessments
Learning Goals
Upon completion of this course, students will be able to:
- Understand the choice of delivery systems for specific purposes or specific active molecules
- Understand the current experimental methods used to generate appropriate delivery systems
- Predict potential biological challenges to specific types of delivery
- Design experiments to test the bioavailability and efficacy of formulation
- Know how to design/develop targeting technologies
- Understand how to test for innate immune responses
- Understand how to choose analytical tools for physical characterization of delivery particle
Assessment tools
All goals will be assessed by:
- Satisfactory completion of class and take-home assignments
- Participation in group activities - in-class discussion and presentations
- Performance in midterm and final exams
- Completion of an individual or group project that designs a delivery solution to a specific problem.
Grading
- Attendance/Class Participation 10%
- Midterm and Final Exams 30%
- Homework/Quizzes 30%
- Individual/Group project(s) 30%
Topics
11:126:444. Advanced Technologies in Biosciences (3)
Normally Offered
Spring, by Dr. Michael Pierce
Pre-requisites and Other Registration Restrictions
General Biochemistry (11:115:403) or Molecular Biology and Biochemistry (01:694:407) Molecular Genetics (11:126:481)
Format
Two 80 minute Lectures
Description
This course will provide an overview of technologies in molecular biosciences. It will cover the basic principles of these technologies and discuss various applications to biotechnology. The course is designed for students with some understanding of molecular biology who wish to be familiar with the latest technologies. The course will consist of a lecture and demonstration format with two 80 minute lecture periods per week. The course is separated into six modules each providing a general introduction and explanation of the technical theory behind a specific biotechnology technique. Unique features and limitations of each modality along with advantages and disadvantages of each are explored. The lecture periods include demonstration of each instrument, detailed description of data analysis and interpretation of results. Application of these techniques to relevant research is highlighted using current primary literature that will be used for class presentation and discussion.
Learning Goals and Assessments
- After completing the course students will have a clear understanding of the underlying principles of each technology.
Assessment: Student performance on quizzes and evaluation of performance in the classroom - After completing the course students will understand the unique role each technique has in basic and applied research and understand the limits of each.
Assessment: Student performance on quizzes and performance on the group independent project and presentation - After completing the course students will have used current literature examples to understand how each technology is applied to address a biological question, why the particular technology is chosen and how the results are interpreted.
Assessment: Student performance on the group independent project and group presentation - After completing the course students will understand the importance of attending events to which they have made a commitment.
Assessment: Class attendance
Specific assessment tools
- Three quizzes on lecture material and material covered in the group presentations. The quizzes will consist of 60% of the grade.
- One group presentation. Students will read an assigned paper covering the particular technology discussed in the
lecture and present it in class. Group presentations will be made in roups of 2-3 students each and will focus on a current research paper assigned by the instructor covering that technology in class. The presentation will consist of 20% of the grade.
The presentation will cover:
a) Hypothesis, the objective of the research
b) Why the particular technology is chosen to address this hypothesis
c) How the particular technology addresses the hypothesis
d) What are the results obtained with the particular technology
e) How are these results interpreted - Class attendance and participation will consist of 20% of the grade.
- Student performance on three quizzes
Topics
- Quantitative reverse transcription PCR (qRT-PCR)
- Laser scanning confocal microscopy
- Genotyping
- Surface plasmon resonance label-free detection (Biacore)
- Mass spectroscopy
- Flow cytometry and cell sorting (FACS)
- TNO intestinal models (TIM)
- Next generation sequencing (NextGen)
11:126:481. Molecular Genetics (3)
Normally Offered
Fall Semester by Professor Thomas Leustek
Pre-requisites and Other Registration Restrictions
01:447:380 Genetics (with grad of C or better)
Format
Lecture, two 80-minute class periods per week.
Description
Molecular Genetics is a challenging lecture course that covers a range of basic topics including the concept of the gene, transcription, translation, regulation of gene expression and replication. The course focuses primarily on prokaryotic systems as a paradigm for processes in eukaryotes. It takes a historical and methodological approach with the aim of providing insight into how understanding was obtained through experimentation and discovery. The course delves extensively into the intricacies of bacterial virus (bacteriophage) molecular genetics and into eukaryotic chromosome structure. The course also covers topics in genome analysis, a field that is currently driving the rapid advancement of knowledge in the area of molecular genetics.
Learning Goals
- To learn about the methods used to study genomes including
- The concept of omics
- Molecular techniques
- DNA sequencing
- Innovations leading to modern high throughput DNA sequencing
- Methods for identifying genes
- Methods for studying how genomes function
- To learn about the anatomy of genomes
- Eukaryotic genomes
- Prokaryotic genomes
- Viral genomes
- To learn how genomes function
- Central dogma
- Chromatin structure
- Transcription-transcriptome
- Translation-proteome
- Regulation of genome activity
- Genome replication
Assessment Measures
- Three hourly exams are given that test fact memorization, knowledge integration, and problem solving.
- Test analysis software available for the Scantron grader in Martin Hall is used to assess question quality, which is used to fine-tune the writing of future tests.
- Three out-of-class reading/writing assignments are required for which students read an assigned paper from the primary literature and write a summary.
- Use of the iClicker to record class participation, assess concept understanding in real-time, and to make corrections to the lectures in real-time. Class participation is 15% of the grade calculation.
- Use of iClicker to gain real time information about student satisfaction with the class format, teaching strategies, course content, and fairness of their evaluations.
- An optional, extra credit term paper is offered to students to improve their final grade. The students who choose the extra credit paper research a topic from the primary literature and write a report on their research.
Examinations
Two common hourly exams each valued at 30% of the final grade, 1 comprehensive final exam valued at 30% of the final grade, 2 surprise quizzes each valued at 5% of the final grade. Surprise quizzes will test on recent lecture information.
Other Requirements
The textbook GENES VII (Benjamin Lewin) is required. Detailed course description, lecture notes, supplementary readings and practice exams are provided on the web page.
Grading
11:126:482. Molecular Genetics Laboratory (4)
Normally Offered
Spring semester by Professors Don Kobayashi, Ning Zhang and Faith Belanger
Pre-requisites and Other Registration Restrictions
General Microbiology (11:680:390) AND Molecular Genetics (11:126:481) with grades C or better are prerequisites.
Format
Lecture, laboratory and follow-up laboratory (recitation). All sections meet once a week for one 80-minute lecture period. Sections are comprised of one three-period laboratory (4 hr 40 min) combined with a follow-up laboratory (recitation period of 55 min) the next day.
Description
This is an upper level laboratory course for juniors and seniors and is a requirement of all Biotechnology majors.
In this course, students are introduced to both chemical and transposon mutagenesis as approaches to gene identification in bacteria. Students also investigate gene identification in bacteria by direct cloning for phenotype expression in heterologous hosts. Advantages and disadvantages of the various approaches are discussed.
This course also uses yeast as a model system to provide an introduction to laboratory methods used to investigate the genetics of eucaryotic organisms. The labs illustrate: 1) the use of genetic crosses to create individuals with particular genetic characteristics; 2) cloning a gene by complementation; and 3) deletion of a gene from the yeast chromosome.
Learning Goals & Assessment Measures
- Mastery of basic methods and applications for molecular genetic studies, and comparing and contrasting these methods and applications between prokaryotic and eukaryotic systems
Assessment through exams, quizzes, oral presentations, and evaluation of lab performance - Understanding the purpose of appropriate and adequate controls and knowing how to establish these controls when designing experiments
Assessment through exams, quizzes, oral presentations and lab reports - Development of skills related to effective teamwork
Assessment of lab performance of the entire team and individual members of the team - Development of effective communication skills
Assessment of writing skills by short answer/essay questions on exams, lab reports and speaking skills by oral presentations - Mastery of the operation of standard equipment used in molecular biology laboratories
Assessment by evaluation of lab performance and lab reports - Ability to analyze data and present results effectively
Assessment by specific questions on exams, lab quizzes, lab reports and oral presentations - Development of organizational skills
Assessment by weekly review of flow charts written in lab notebooks, data entry in lab notebooks and evaluation of ability to conduct weekly experiments in a timely manner - Understanding the use of formulas for quantitative purposes in experimental procedures
Assessment by quizzes, exams and evaluations of lab performance during experimental procedures - Understanding hypothesis-driven experimentation
Assessment by exams, quizzes, lab reports, oral presentations, inspection of data recorded in lab notebook, and evaluation of lab performance
Topics
Examinations
One midterm and one non-comprehensive final.
Other Requirements
In addition to exams, grading is based on written lab reports on all laboratory experiments conducted in class, 4-6 quizzes, and a group, oral presentation given on a selected lab at the end of the semester. Attendance, active participation in labs and an organized lab notebook are also required.
Grading
11:126:484 Tools for Bioinformatic Analysis (3)
Normally Offered
Spring semester by Dr. Sonia Arora
Format
One 80-min lecture, one 180 min.dry laboatory
Pre-requisites and Other Registration Restrictions
Molecular Genetics 11:126:481 OR Genetic Analysis II 01:447:385 OR Molecular Biology and Biochemistry 01:694:408 OR Biochemistry 11:115:404 OR Permission of Instructor
Description
This is a mixture of lecture & dry laboratory based course. It is aimed at examining various bioinformatics tools to study biological data. The course introduces t o the students
(a) various biological meta-databases such as NCBI, Ensembl, UCSC-Genome browser, TAIR etc.
(b) methods of DNA sequencing and sequence analysis
(c) methods of RNA expression analysis: microarrays and RNA Seq
(d) protein families, domains & Motifs
(e) protein structure prediction and three dimensional structure of proteins
(f) significance of mutations, single nucleotide polymorphisms & biomarkers in disease characterization
(g) in silico drug design & discovery.
While the course focuses on human health and pharmaceutical research, the approaches taught in this course are generally applicable to many areas in biology, including the agricultural, natural and environmental sciences.
Learning Goals
Upon completion of the course, students should be able:
- To obtain the ability to critically examine biological meta- databases.
- To be proficient in bioinformatic methods of DNA, RNA and protein analysis at small & large scale.
- To understand methods and application of structural bioinformatics.
- To utilize computational methods to design and explore drug like candidates.
- To be able to interpret experimental datasets that form basis of bioinformatic analysis.
- To recognize interdisciplinary approach to biological discovery process.
Assessment Measures
Learning Goals 1, 2 & 3 assess broad applied knowledge of the students. These are measured by weekly dry laboratory exercises and a closed book exam. Each weekly lecture is followed by in class computational dry laboratory exercise. The exercises are graded on a 100 point scale. The exam involves written as well as practical portions. Exam is graded on a 100 point scale.
Learning goal 4 assesses applied knowledge in a subfield of structural bioinformatics and is measured by final term project. Students use dry lab techniques taught in the class to do a computer aided drug discovery project. They discuss their results in a written project report that is graded on a 100 point scale.
Learning Goals 5 & 6 assess holistic knowledge of the students. These are measured using journal club model. Journal Clubs included discussion and presentation of original research papers focused on various bioinformatic tools and their applications. Students formed small groups and work together to present assigned papers in power-point format. Journal clubs presentations and participation is scored on 100 point scale.
Topics
Biological Information & History of Bioinformatics
Biological Meta Databases
Tools for DNA Analysis, ORFs
Variation in Gene sequences
Next Generation Sequencing, Contig Assembly
Tools for RNA Sequences & Motifs, microRNAs
RNA Seq, RNA prediction servers
Exploring Protein Function & Disease
Protein Families & Domains
Protein Structure
X-Ray Crystallography
Computer Aided Drug Design & Discovery
In Silico Drug Databases
Virtual Screening
Molecular Docking
Drug-Target Interactions
Examinations/Grading
(A) In Class Dry Lab Exercises (25 % of total grade)
Each weekly lecture is followed by in class dry lab exercises. Dry lab exercises give students opportunities to have hands on practice on various bioinformatic analysis tools.
(B) Examination (25% of total grade)
There is one closed book exam that involve written as well as practical section. Written exam may contain questions ranging from multiple choice questions; labeling diagrams, and short answer questions. Practical exam involve mini dry lab exercises similar to the one done during the classes.
(C) Journal Club Presentation, Report & Participation (25% of total grade)
Journal Clubs include discussion and presentation of original research papers focused on various tools for genomic & proteomic studies. Students form small groups and work together to present assigned papers in power-point format. In addition to the oral presentation, all the students are expected to read the article, submit a one page summary report and participate in discussion.
(D) Structural Genomics Project (25% of total grade) Students use dry lab techniques taught in the class to complete a structural genomics drug discovery project and discuss their results in a written project report.
11:126:485. Bioinformatics (3)
Normally Offered
Fall Semester
Pre-requisites and Other Registration Restrictions
01:447:380 and 01:198:111
Description
Bioinformatics as a field attempts to build computational models of the biological systems and mechanisms. More specifically, bioinformatics involves creating algorithms, databases, systems, and web applications to solve problems in molecular biology. Many bioinformatics tools use artificial intelligence, some rely on cloud computing, others borrow concepts from signal processing and circuit theory and all are necessary to deal with the inordinate amounts of data that are produced by modern high-throughput experimental techniques. Due to the drop in sequencing costs, we are awash in DNA, RNA, and protein sequences. Massive genomics and metagenomics efforts are opening new horizons in variation analysis. The past few years of structural genomics efforts have produced a crystal structure representative of almost every protein family. Microarray technologies allow simultaneous studies of expression of thousands of genes on a single chip. The improvements keep on coming more information, higher resolution. Yet the unintended result of improved experimental techniques is a flood data that we have yet to make sense of. What does our genome encode? Can we decipher the mechanisms of disease? How are we different from other organisms? How are we different from each other? Bioinformatics attempts to answer all these questions and give the statistical significance.
Learning Goals
- Introduce students to current bioinformatics algorithms/concepts, principles, and techniques within the framework of basic shell scripting and web-based databases/tools.
- Introduce students to the basics of working in a Linux environment, GridEngine submissions for parallel computing, Perl scripting, and automating applications for use with large data sets.
- Teach students to cast a molecular biology problem as a bioinformatic problem, provide them with the skills necessary to independently select relevant tools, optimize their settings, and build pipelines to solve the set problem.
- Prepare students for more advanced bioinformatics courses involving method development.
- Teach students a sufficient bioinformatics skill set, including an informed vocabulary and knowledge of basic script development, for productive collaboration within a multi-disciplined research team.
Assessment
- Attendance / Class Participation. Regular, on-time, attendance is expected of all students. Asking questions and/or participating in class discussions is also expected and reflected in the grade.
- Homework / Quizzes. Homework (scripts and written assignments) will be assigned every week. Announced and unannounced written or coding (or both) quizzes covering lab and/or lecture material will be given at the discretion of the lab instructor.
- Midterm / Final. The midterm will be a take-home programming project based on material covered in lecture AND lab. The final will be a multi-tool workflow/pipeline exercise and will focus on all techniques learned throughout class. The grade for the final project will be based on three components: (1) computational implementation, (2) selection of appropriate methods, and (3) written component describing the pipeline.
- Journal Club (Graduate Component Only). Graduate students in the class will be required to attend journal club meetings (time is TBA). In the span of the semester each student will be required to read, analyze, and present two bioinformatics papers of your choice. The presentations will be graded on a pass/fail basis. Undergraduates are encouraged to attend the journal club, read the papers, and potentially present. Note, however, that this will NOT count as extra credit.
Topics
Lecture /LAB
- Introduction to Bioinformatics / Intro to Linux
- Gene finding / Sequencing, databases & intro to EMBOSS
- Sequence alignment: / EMBOSS Water and Needle
- BLAST / Sequence alignment & BLAST 101
- Sequence signatures and motifs / Sequence signature databases & InterPro
- Protein function prediction and protein-protein interactions / STRING, GO, etc.
- Phylogenetics / Phylogenetics MSA, MAFFT lab
- Midterm exam week
- Variation and molecular level natural selection / HIV Ka/Ks
- Structural bioinformatics / Structural bioinformatics, Chimera, PyMol
- Whole genome annotations | Whole genome comparisons
- Disease gene prioritization | Data mining
Examinations
Other Requirements
Grading
11:126:486. Functional Genomics for Research (3)
Normally Offered
Spring by Professor Dana Price
Pre-requisites and Other Registration Restrictions
01:119:116 and (11:216:251/486 OR 01:447:380 OR 11:115:301/403 OR 01:694:315/407)
Format
One 80-min seminar and one 80 minute dry lab period.
Description
This course will focus on execution of tools and protocols used to elucidate the biology, ecology and life histories of organisms through analysis of their genomes. Using genome research projects recently completed by the instructor and collaborators as templates, students will carry out each step of the research pipeline (unique to that project) in depth - from taxon selection, bioinformatic analysis of next-generation sequencing data, genome assembly, gene prediction/functional annotation, and finally how these data answer a functional biological hypothesis or question about the target organism. As new topics are introduced, they will be framed in the context of their applicability to the current project. At the end of the course, students will be able to select the appropriate protocols and analysis pipelines to complete the majority of today’s genome research. Each topic (or introduced research project) will consist of one or more lectures with background discussion, tool and material review, and a second hands-on computer (or dry) lab period during which students will apply the concepts and tools to complete a phase the genomic analysis. This course illustrates evolutionary concepts current tools in a hands-on manner within the confines of a goal or results-oriented genome research project.
Learning Goals
Upon completion of course requirements, students will be able to:
- Apply knowledge of genome sequencing and bioinformatics analyses to test hypotheses regarding organismal biology and evolution.
- Communicate effectively how various bioinformatic analyses are impacted by similarities and differences in eukaryote genomes.
- Apply appropriate bioinformatic tools and analysis protocols for individual genome sequencing projects.
- Analyze and report on recent published research in the field of genomics.
Assessments Measures
- Specific questions on exams; final project.
- Specific essay/long-answer questions on exams; paper discussion; final project.
- Final project; exam questions; class participation.
- Paper discussion; presentation and class participation.
Topics
- Introduction / Next-gen sequencing
- Basics I: Genome/transcriptome assembly; Gene prediction and annotation
- Basics II: Homology search and public databases / Phylogenetics
- The algal tree of life and origins of photosynthesis – The Cyanophora paradoxa genome project
- Horizontal and Endosymbiotic gene transfer
- RNAseq / Differential expression
- Homology and function
- Gene Ontologies
- Eukaryotic HGT and EGT revisited: The Porphyridium purpureum genome
- Orthologous gene families / Protein evolution and selection
- Paulinella and the role of HGT in endosymbiosis
- Paulinella and the role of HGT in endosymbiosis II
- Metabolic pathways, KEGG maps and dinoflagellate metabolism
- Lab exercises – Differential expression, PhySortR and branch-site selection
- Transcriptional regulation / CRISPR-Cas9 and RNAi
- Single-cell genomics
- Protein-DNA interactions / ChIP-seq, ATAC
- Metagenomics
- Presentations
11:126:497/498 Research in Biotechnology (1–6 by arrangement)
Normally Offered
Fall Term (as 11:126:497) and Spring Term and Summer (as 11:126:498). Any faculty member at Rutgers University, Robert Wood Johnson Medical School, or the Cancer Institute of New Jersey who does research in biotechnology, biochemistry, molecular biology or genetics may supervise student research projects (see below for links to find relevant laboratories). Students working in internships at outside biotechnology-related companies can also gain credit throught the SPIN internship program.
Pre-requisites and Other Registration Restrictions
Open to biotechnology and life science majors by special permission from the Biotechnology Curriculum Coordinator. Requires approval of the faculty member who will supervise the research project. Once approval is acquired, a special permission number may be obtained from the Biotechnology Undergraduate Program Director located in Foran Hall.
Format
The student carries out an independent research project under the supervision of the research advisor. A minimum of 3 hrs/wk per credit in the laboratory is expected.
Description
The student, under the guidance of a faculty member, carries out a research project. Most often, a faculty member may engage the student in some aspect of a research project that the faculty member is pursuing. However, the student may also identify her/his own project in consultation with the research advisor.
Learning Goals
- Proficiency in the tools and scientific approaches used in biotechnology and how they are applied to answering specific scientific problems
- Integration of knowledge from coursework and applying it to research
- Ability to survey public literature, define an original problem for inquiry, formulate a testable hypothesis, design and execute experiments to test this problem, analyze data, and present the research in written form and orally
Assessment Measures
- Observation of the technical and intellectual proficiency of the student in research setting
- Evaluation of the student's ability to formulate a hypothesis from available literature, design well-controlled experiments, and analyze and interpret data
- Evaluation of the student's written and oral presentations on the research conducted
Examinations
None
Other Requirements
All students are expected to write a paper describing the research project at the end of the semester in journal article format. Copies are submitted to the research advisor and the Biotechnology Undergraduate Program Director.
Grading
The research advisor is responsible for grading the student and reporting the grade to the Curriculum Coordinator. The grade reflects overall performance in the laboratory, including the final report.
Additional Information
To find a lab:
Look at two sources:
- the list of biotech faculty mentors in the document RESEARCH IN BIOTECHNOLOGY (for faculty on this campus) and
- http://lifesci.rutgers.edu/~molbiosci/faculty (for faculty who do research in "biotech" at Rutgers and UMDNJ and affiliated hospitals.
Then make a short list (~10) of faculty that most interest you. After doing a little more searching on the web about the research conducted in each of these faculty labs, carefully compose a brief email that 1) tells the prospective mentor about yourself (major,year, college, interests, etc.); 2) states why the you are interested in the research of the faculty mentor; and 3) asking for an appointment to meet the faculty member to talk about the research and possibly working in that faculty member's lab in the coming (semester).
To get credit, enroll in Research in Biotechnology 11:126:497 when you have enough time in your schedule to do three credits (minimum of nine hr/wk in the lab for the entire semester). If you have less time, you should volunteer (or get their feet wet by working with a grad student) until they can enroll for three credits. The program coordinator gives special permission numbers for Research in Biotech after the student has a mentor.
In terms of paid internships, you should visit the SPIN Office in Martin Hall. They should also visit the Career Services Office with help to prepare a resume.
If you desire additional information, speak with the Biotechnology Undergraduate Program Director.