Course Synopses/Descriptions

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 synopses 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.

COURSE DESCRIPTIONS:

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11:126:110. Concepts and Issues in Biotechnology (1.5)

Normally Offered:

Spring, by Profs. Dawn Brasaemle & 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:

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

  1. To gain familiarity with basic approaches to biotechnology research and development, and the wide range of biotechnology applications
  2. To understand ethics and societal issues relevant to controversial applications of biotechnology
  3. To gain oral and written communications skills

Assessment Measures

  1. Weekly readings on basic biotechnology applications are assessed by weekly quizzes.
  2. 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.
  3. Class participation in group discussions is recorded and assessed as 5% of the student grade.
  4. A final term paper project assesses student ability to write about one current aspect of biotechnology and the societal issues surrounding it.

Topics

    Bioethics
    Gene Therapy
    Plant Biotechnology
    Marine Biotechnology
    Bioinformatics & the Pharmaceutical Industry
    Vaccine Development
    Animal Biotechnology
    Intellectual Property & Career Choices
    Risk Perception of Biotechnology
    Biotechnology and the Developing World
    Environmental Impact of Biotechnology
    Gene Screening & Pharmacogenomics
    Stem Cell Biology
    Microbial Biotechnology

Examinations

There are no end-of-course examinations in this course. There will be occasional class tests.

Other requirements:

Students will work in small groups to examine a specialized topic in biotechnology. The topic will be determined in conjunction with the instructor. Each group will present the topic to the class.

Each student will develop an individual project on a topical issue in biotechnology. Course instructors will provide students with details of topics and format for this project. Grading is principally by individual, with a smaller component awarded for the group project.


Grading

Grades: Grades will be based on the following distribution for 100 points total:

40% quizzes (9 to 10) during most weeks, based on reading of the associated textbook.

40% Individual written project. The project will be chosen from a set of themes/questions that will be provided. Further details of projects will be given out in week 3.

15% Group Activities and 5% Class Participation. You will sometimes work in groups, for example when we discuss case-studies in class. Groups will also make a class presentation during the semester.

Attendance will be taken during each class period. Perfect attendance will be awarded 3 bonus points towards the final grade. 1 or 2 unexcused absences are allowed without penalty. 3 unexcused absences will be penalized by subtracting 3 points from the final grade based on 100 points. Each successive absence will result in the loss of 3 additional points.

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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

1. Critically analyze nucleotide and amino acid sequences; and find homologous sequences.
2. Examine and extract gene, protein & disease information available at various biological databases.
3. Utilize computational methods to design genetic manipulation experiments in wet-laboratory.
4. Understand & analyze primary sequence data obtained from DNA sequencing projects.
5. 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.

 

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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

  1. To read critically, understand thoroughly and discuss primary journal articles from high impact scientific journals
  2. To develop and improve oral communication skills
  3. 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
  4. To present effective and interesting seminars
  5. To evaluate the quality of seminar presentations

Assessment Measures

  1. Each student chooses two journal articles that will present in two formal, 30 minute seminars.
  2. Each presentation is evaluated by the student's peers and the instructor in written format.
  3. 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.


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11:126:407. Comparative Virology (3)

Course Webpage:

http://www.rci.rutgers.edu/~bhillman/comparative_virology/

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

    Introduction to virology
    Virus composition & structure, and classification
    RNA viruses - positive strand
    RNA viruses - negative strand, ambisense, and double strand
    Reverse transcribing viruses
    DNA viruses
    Satellites, viroids, defective nucleic acids, and prions
    Antivirals and genetic engineering to protect against virus infection
    Use of viruses in biotechnology

Learning Goals

  1. Understand the differences between viruses and other microbes.
  2. Understand the methods used to study viruses at physico-chemical, molecular, and population levels and how viruses are used in biotechnology and gene therapy.
  3. To learn about similarities and differences among viruses that infect different kinds of prokaryotic and eukaryotic hosts.
  4. To learn about similarities and differences in genome composition, organization, replication, and gene expression strategies of viruses.
  5. To learn details of some major virus diseases.
  6. To learn about host mechanisms used for defense against virus infection.
  7. To learn about current topics in virology through classroom presentations and discussion.

Assessment Measures

  1. Exams covering lecture and reading material (long answer, short answer, multiple choice, true-false).
  2. Group presentation on topic of current interest.
  3. Reference-based paper summarizing and expanding on group presentation.
  4. 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.

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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:

  1. Employ the general of mass and energy conservation principles to problems not previously seen.
  2. Formulate models for quantitative understanding of biological growth and metabolism
  3. Perform data analysis and parameter estimation for algebraic models, including nonlinear models
  4. Know how to build flux analysis models from genomic-derived pathway data
  5. Analyze journal papers that employ conservation models and flux analysis in biological systems
  6. Summarize the major unit operations used downstream in bioprocess systems
  7. Diagram a process flow sheet for large-scale industrial synthesis of biological products

Topics

    Presentation and Analysis of Data; Linear Models; Nonlinear Models
    Mass Balances; Species mass; Continuous, Transient; Recycle
    Microbial and Cellular Growth Stoichiometry
    Product Formation, Reductance Balance; Yield; Maintenance
    Energy Balance; Enthalpy
    Unsteady State Mass and Energy Balances
    Reaction Kinetics and Biological Systems
    Chemostats, Batch Fermentors, Fed-Batch Fermentations
    Immobilized Enzymes and Cells; Heterogeneous Reactions
    Mass Transfer; Oxygen Transfer Rate
    Unit Operations; Downstream Processing
    Filtration, Centrifugation, Chromatography
    Bioprocess Synthesis

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%)

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11:126:413. Plant Molecular Biology (3)

Normally Offered:

Spring in even-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

    The plant gene; Transcription
    Chromatin
    mRNA maturation, stability and turnover
    Regulation by small RNAs: RNAi, and microRNAs
    Translation
    Subcellular protein targeting
    Protein stability and turnover
    Plastid genes and regulation of gene expression
    Mitochondrial genes and regulation of gene expression
    Agrobacterium biology and plant transformation
    Genome sequencing - Arabidopsis and rice
    Genome annotation
    Proteomics: 2D gels, mass spectrometry, databases
    Cytoskeleton
    Cell wall
    Cell cycle
    Plant cell death
    Intercellular communication: plasmodesmata, pistil-pollen incompatibility
    Light signaling
    Circadian rhythms
    Meristem development
    Flower development
    Root development
    Plant hormones
      Auxin
      Cytokinins
      GA
      Brassinosteroids

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).

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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

  1. 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
  2. To understand the underlying principals of molecular biology techniques and their applications
    Assessment: Exams and laboratory notebook
  3. To learn proper experimental design with appropriate controls
    Assessment: Group research proposal and oral presentation
  4. 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
  5. To learn how to document, record, and interpret scientific data
    Assessment: Laboratory notebook and oral presentation
  6. To develop effective oral and written communication skills
    Assessment: Short essay component of exams, group research proposal, oral presentation
  7. To build skills required to work as a member of a team
    Assessment: Group research proposal and oral presentation
  8. To develop critical thinking skills needed for 21st century science
    Assessment: Exams and group research proposal

Specific Measures of Assessment

  1. Two exams (short essay, multiple choice, true/false)
  2. 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.
  3. Oral Powerpoint Presentation of Group Project
  4. Subjective Evaluation of Laboratory Performance
  5. Laboratory Notebook (to be recorded in weekly)
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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

  1. Learning goals -
  2. 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
  3. Assessment tools

    All goals will be assessed by:

    1. Satisfactory completion of class and take-home assignments
    2. Participation in group activities - in-class discussion and presentations
    3. Performance in midterm and final exams
    4. Completion of an individual or group project that designs a delivery solution to a specific problem.

    Grading:

    1. Attendance/Class Participation 10%
    2. Midterm and Final Exams 30%
    3. Homework/Quizzes 30%
    4. Individual/Group project(s) 30%
    5. Topics

      • Natural cellular delivery/communication strategies versus man-made
      • Large versus small molecule delivery issues
      • Types of nanoscale constructs
      • Vesicular versus solid particles; lipid-based vs. polymers
      • Characterizing particles; analysis of the physical parameters of particles; assessing biological compatibility and suitability.
      • Biological responses to particles

      - various types of immune and non-immune responses
      - uptake mechanisms; endocytosis, pinocytosis, etc.
      - non-specific mechanisms of biological degradation of delivery particles
      - clearance mechanisms

      • The relative importance of physical versus biological parameters in delivery
      • Methods of targeting delivery - Antibodies, ligands, randomly-generated binding molecules
      • Delivery using synthetic biology - the potential role of engineered extracellular vesicles
      • Design of multifunctional delivery particles
      • Monitoring delivery in tissues - (where did my molecule go? Is it bioavailable?)
      • Biopharmaceutical applications
      • Agricultural applications of formulation and nanotechnology

    11:126:444. Advanced Technologies in Biosciences (3)

    Normally Offered:

    Spring, by Dr. Nilgun Tumer, co-instructors 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

    1. 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
    2. 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
    3. 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
    4. After completing the course students will understand the importance of attending events to which they have made a commitment. Assessment: Class attendance
    5. Specific assessment tools

      1. Three quizzes on lecture material and material covered in the group presentations. The quizzes will consist of 60% of the grade.
      2. 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 groups 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
      3. Class attendance and participation will consist of 20% of the grade.
      4. Student performance on three quizzes

      Topics

      1. Quantitative reverse transcription PCR (qRT-PCR)
      2. Laser scanning confocal microscopy
      3. Genotyping
      4. Surface plasmon resonance label-free detection (Biacore)
      5. Mass spectroscopy
      6. Flow cytometry and cell sorting (FACS)
      7. TNO intestinal models (TIM)
      8. Next generation sequencing (NextGen)

      11:126:481. Molecular Genetics (3)

      Course Webpage:

      http://aesop.rutgers.edu/~molgen/

      Normally Offered:

      Fall Semester by Professor Thomas Leustek

      Pre-requisites and other registration restrictions:

      01:447:380 Genetics (with grad of C or better); Organic Chemistry

      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

      1. To learn about the methods used to study genomes including
        1. The concept of omics
        2. Molecular techniques
        3. DNA sequencing
        4. Innovations leading to modern high throughput DNA sequencing
        5. Methods for identifying genes
        6. Methods for studying how genomes function
      2. To learn about the anatomy of genomes
        1. Eukaryotic genomes
        2. Prokaryotic genomes
        3. Viral genomes
      3. To learn how genomes function
        1. Central dogma
        2. Chromatin structure
        3. Transcription-transcriptome
        4. Translation-proteome
        5. Regulation of genome activity
        6. Genome replication

      Assessment Measures

      1. Three hourly exams are given that test fact memorization, knowledge integration, and problem solving.
      2. 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.
      3. Three out-of-class reading/writing assignments are required for which students read an assigned paper from the primary literature and write a summary.
      4. 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.
      5. Use of iClicker to gain real time information about student satisfaction with the class format, teaching strategies, course content, and fairness of their evaluations.
      6. 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

      1. 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
      2. 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
      3. Development of skills related to effective teamwork
        Assessment of lab performance of the entire team and individual members of the team
      4. Development of effective communication skills
        Assessment of writing skills by short answer/essay questions on exams, lab reports and speaking skills by oral presentations
      5. Mastery of the operation of standard equipment used in molecular biology laboratories
        Assessment by evaluation of lab performance and lab reports
      6. Ability to analyze data and present results effectively
        Assessment by specific questions on exams, lab quizzes, lab reports and oral presentations
      7. 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
      8. Understanding the use of formulas for quantitative purposes in experimental procedures
        Assessment by quizzes, exams and evaluations of lab performance during experimental procedures
      9. 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 to 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:

      1. To obtain the ability to critically examine biological meta- databases.
      2. To be proficient in bioinformatic methods of DNA, RNA and protein analysis at small & large scale.
      3. To understand methods and application of structural bioinformatics.
      4. To utilize computational methods to design and explore drug like candidates.
      5. To be able to interpret experimental datasets that form basis of bioinformatic analysis.

      6. 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

    1. Introduce students to current bioinformatics algorithms/concepts, principles, and techniques within the framework of basic shell scripting and web-based databases/tools.
    2. 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.
    3. 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.
    4. Prepare students for more advanced bioinformatics courses involving method development.
    5. 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:

    1. 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.
    2. 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.
    3. 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.
    4. 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

    1. Introduction to Bioinformatics / Intro to Linux
    2. Gene finding / Sequencing, databases & intro to EMBOSS
    3. Sequence alignment:  / EMBOSS Water and Needle 
    4. BLAST  / Sequence alignment & BLAST 101
    5. Sequence signatures and motifs / Sequence signature databases & InterPro
    6. Protein function prediction and protein-protein interactions / STRING, GO, etc.
    7. Phylogenetics /  Phylogenetics MSA, MAFFT lab
    8. Midterm exam week 
    9. Variation and molecular level natural selection / HIV Ka/Ks
    10. Structural bioinformatics   / Structural bioinformatics, Chimera, PyMol
    11. Whole genome annotations | Whole genome comparisons
    12. Disease gene prioritization | Data mining

    Examinations

    Other requirements

  • Grading

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    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

    1. Proficiency in the tools and scientific approaches used in biotechnology and how they are applied to answering specific scientific problems
    2. Integration of knowledge from coursework and applying it to research
    3. 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

    1. Observation of the technical and intellectual proficiency of the student in research setting
    2. Evaluation of the student's ability to formulate a hypothesis from available literature, design well-controlled experiments, and analyze and interpret data
    3. 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:
    1) the list of biotech faculty mentors in the documentRESEARCH IN BIOTECHNOLOGY1.pdf (for faculty on this campus) and
    2) 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.