Rutgers School of Environmental and Biological Sciences [Biotechnology Undergraduate Program]

Biotechnology Course Synopses

Available courses:


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.

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

Normally Offered:

Spring, by Profs. Dawn Brasaemle & Michael Lawton (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

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.

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:

  • 70% 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% Weekly take-home assignments/class activities. The format will vary from week-to-week: sometimes it will involving answering short questions, other times performing research on a more general question that will be discussed first thing in the next week's class.
  • 15% Group Activities and 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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    11:126:121. Biotechnology Scholars Seminar (1)

    Normally Offered:

    Fall Semester

    Pre-requisites and other registration restrictions:

    None

    Description:

    The Biotechnology Scholars Program is being developed with funds from an NSF S-STEM grant. The grant provides scholarships to talented and financially needy students who are majors in biotechnology at the School of Environmental and Biological Sciences. The program will include a one-credit class, in seminar/workshop format, offered to the two cohorts of biotechnology scholars (one incoming freshmen and the other sophomores). The course will focus on tools for students to do their best in college. They will learn effective study strategies; time and stress management; exercises to encourage effective collaboration and teamwork; how to balance work and play; how to improve library research, leadership, and oral communication skills; and confidence building. In addition, the students will participate in a field trip to a pharmaceutical or biotechnology company to acquaint them with opportunities in the field of biotechnology.

    The students will be evaluated based on their active participation in the course, two writing assignments, and one oral presentation.

    Topics

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                            11:126:401. Seminar in Biotechnology (1)

                            Normally Offered:

                            Fall by Professors Faith Belanger, Elisabetta Bini and Barbara Zilinskas

                            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.

                            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 (since 2003) 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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                            11:126:405. Microbial Technology (3)

                            Normally Offered:

                            Fall, by Professors Dr. Max Häggblom and Douglas Eveleigh

                            Format:

                            Two 80-minute lectures

                            Pre-requisites and other registration restrictions:

                            11:680:390, 11:680:394 or 11:126:394 or 11:126:491 or 11:680:491.

                            Description:

                            The objective is to assess Microbial Biotechnology in a discusive manner. The general outline includes - The history of microbial biotechnology; microbial biodiversity, production of proteins by bacteria; fuel alcohol, beer, wine; and of amino acids, vitamins, alkaloids;,biomass transformation and microbiology of pulp and paper; polymer synthesis; bioremediation using microbes; patents and regulations in biotechnology.

                            Topics

                                  Examinations

                                  Two examinations - The exams are comprised of multiple choice, short answers plus an essay question. The second exam is not cumulative. Each exam will count for 45% of the final course grade.

                                  Other requirements:

                                • Grading

                                  Integrated within the lectures are student presentations. Each student will make a class presentation of a current research paper/ sphere (15-20 minutes) and will be assessed 10% of the final grade.

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                                  11:126:406. Plant Gene Transfer (4)

                                  Normally Offered:

                                  Spring, by Dr. Chee-kok Chin

                                  Pre-requisites and other registration restrictions:

                                  01:447:380 or 11:776:305.

                                  Format

                                  Lecture and Laboratory. Meet once a week for an 80-minute lecture period and a 160-minute lab. In addition to the normal lab schedule, some of the will require students to come to the lab briefly at flexible time to complete lab work.

                                  Description:

                                  Principles and experimental techniques of nonsexual gene transfer in plants. The course outline is as follows:

                                  Topics

                                  1. Introduction:

                                  2. Overview of sexual and parasexual gene transfer
                                  3. Plant cell and tissue culture
                                    1. General techniques
                                    2. Organogenesis
                                    3. Somatic embryogenesis
                                    4. Protoplast technology
                                  4. Agrobacterium-mediated gene transfer
                                    1. General characteristics of crown gall disease
                                    2. Colonization and attachment
                                    3. Ti plasmids
                                      1. Organization of functions of genes in T-region
                                      2. Organization of functions of genes in Vir-region
                                      3. Other genes on Ti plasmid
                                    4. Chromosomal virulence genes
                                      1. Host range and specificity
                                      2. Plant roles in transformation
                                    5. Regulation of vir genes expression
                                    6. T-DNA transfer
                                      1. Proteins involved in gene transfer
                                      2. T-DNA transfer process
                                    7. Nuclear targeting of DNA
                                    8. Integration of T-DNA into plant genome
                                    9. Expression of transgene
                                    10. Silencing of transgenes
                                    11. Inheritance of transferred genes
                                    12. Various methodologies
                                  5. Direct gene transfer
                                    1. Biolistic bombardment
                                    2. Electroporation
                                    3. Microinjection including Liposome encapsulation
                                    4. Ultrasound mediated DNA transfer

                                  Examinations

                                  Other requirements:

                                • Grading

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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

                                  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.

                                  Grading

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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.

                                  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

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

                                  Normally Offered:

                                  Spring in even numbered years by Professors Randall Kerstetter, 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 in Recombinant DNA Technology (4)

                                  Normally Offered:

                                  Fall by Professors Barbara Zilinskas 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 is an upper level course, required of all biotechnology majors. This course is designed to introduce you to the many techniques used in molecular biology, all of which rely on advances possible through recombinant DNA technology. While you will learn through hands-on experience many of the techniques in laboratory sessions, time does not permit an all-inclusive presentation. Therefore, we shall use lectures (Tuesdays) to acquaint you with a broad range of methods and the applications of the methodology. In addition, you will be assigned reading to help round-out this laboratory experience.

                                  The first laboratory experiment will serve to acquaint you with the use of restriction enzymes, the very reagents that gave birth to the field of recombinant DNA technology. It will let you "get your feet wet" and be a warm-up exercise. The remaining sessions are designed to teach you fundamentals of the technology, while "telling you a story". You will isolate a cDNA clone from an phage cDNA expression library of Arabidopsis using antibodies raised against a protein unknown to you. You will proceed to analyze this clone, eventually identifying it by nucleotide sequence analysis. In collaboration with your classmates, you will also design experiments to find out whether this gene is differentially expressed. Is it expressed only in certain tissues, or only at certain times in development, or only under certain environmental conditions? You will analyze expression by northern blot, quantitative RT-PCR, and western blot analysis. Hopefully, through all these experiments, in addition to learning the techniques commonly used in recombinant DNA technology, you will experience first-hand how one goes about the isolation and analysis of eukaryotic genes.

                                  Topics

                                                                Examinations

                                                                There are two exams each worth 20% of the final grade.

                                                                Other requirements:

                                                                A laboratory report will be required for Experiment 1, worth 15% of the final grade. Another writing assignment (5% of your final grade), will be a research proposal describing your gene expression experiment. You and your lab partners will be expected to describe and analyze data obtained in your group projects in formal PowerPoint presentation (15% of final grade). There will be two unannounced quizzes, each worth 5% of the final grade. Finally, 5% of the grade will be subjective in nature. Reflected in this will be: a) attendance and promptness; b) preparedness for laboratory; and c) general competence in the laboratory (e.g., ability to follow instructions, care in doing experiments, thoroughness of data recording in each laboratory session, and notebook keeping ability).

                                                                Grading

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                                                                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.

                                                                Topics

                                                                                              Examinations

                                                                                              2 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

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                                                                                              11:126:482. Molecular Genetics Laboratory (3)

                                                                                              Normally Offered:

                                                                                              Spring semester by Professors Don Kobayashi 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.

                                                                                              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

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                                                                                                                            11:126:483. Nucleotide Sequence Analysis (3)

                                                                                                                            Normally Offered:

                                                                                                                            Fall and winter terms by Dr. Gerben J. Zylstra

                                                                                                                            Pre-requisites and other registration restrictions:

                                                                                                                            The prerequisite for Nucleotide Sequence Analysis is one of the following courses:

                                                                                                                          • 11:115:403,404 General Biochemistry
                                                                                                                          • 11:126:481 Molecular Genetics
                                                                                                                          • 11:126:427 Methods in Recombinant DNA
                                                                                                                          • Students must be familiar with DNA structure, restriction enzymes, general cloning technology, DNA sequencing, transcription and translation, and general gene and operon structure. Students should have a working knowledge of PC computers.

                                                                                                                            Format:

                                                                                                                            One three-period computer laboratory per week. Fridays 8:10 to 12:50 in the Biotechnology, Animal Science, and Chang Library Computer Teaching Laboratory, 124 Foran Hall.

                                                                                                                            Description:

                                                                                                                            This is a computer laboratory course that utilizes various PC and web-based programs for the analysis of nucleotide and amino acid sequences. The course serves as an advanced elective in both the Biotechnology and Biochemistry majors and satisfies the general computer competence requirement. The course is highly recommended for students interested in a career in biotechnology, biochemistry, or molecular biology.

                                                                                                                            The course introduces students to the methods of analyzing DNA sequences and the use of sequence information available in international databases. The course 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, identifying genes and proteins by database searches, determining which database searching method to use (blastN, blastP, blastX, etc.), motif searches to identify amino acid signature sequences, searching for and downloading sequences from the GenBank database, importing and interconversion of sequences, aligning sequences, calculating and drawing phylogenetic trees, and genome analysis.

                                                                                                                            Special emphasis is placed on the application of computer programs to answering questions about nucleotide and amino acid sequences. Each week of the course will introduce a new method of sequence analysis through a laboratory exercise. A series of practical problems will then be solved. Each week builds on information learned in previous exercises.

                                                                                                                            Topics

                                                                                                                                                          Examinations

                                                                                                                                                          Two 2-hour examinations are given during the laboratory period at one-third and two-thirds the way through the course. The exams are open book/notes, problem-solving, timed tests. A final written project report is due at the end of the term in place of a final exam.

                                                                                                                                                          Other requirements:

                                                                                                                                                          Many of the required readings and other course materials are available only on-line or in the help files of the computer programs. Students are encouraged to purchase a zip disk to store the data for the lab exercises.

                                                                                                                                                          Grading

                                                                                                                                                          30% each exam, 30% final projects, 10% attendance and assignments.

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                                                                                                                                                          11:126:484. Biotechnology Robotics (3)

                                                                                                                                                          Normally Offered:

                                                                                                                                                          Pre-requisites and other registration restrictions:

                                                                                                                                                          11:115:403, 11:115:313 or 413, 11:680:390.

                                                                                                                                                          Format:

                                                                                                                                                          One 80-minute lecture; 4.5 hour lab.

                                                                                                                                                          Description:

                                                                                                                                                          Application and use of robotic equipment in the analysis of large numbers of samples; assay and protocol design; data collating, analysis and interpretation; applications in various life science industries.

                                                                                                                                                          Topics

                                                                                                                                                                                        Examinations

                                                                                                                                                                                        Other requirements:

                                                                                                                                                                                      • Grading

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                                                                                                                                                                                        11:126:486. Analytical Methods in Microbiology (3)

                                                                                                                                                                                        Normally Offered:

                                                                                                                                                                                        Fall semester in odd numbered years only; Dr. Max Häggblom and Dr. Diane Davis

                                                                                                                                                                                        Pre-requisites and other registration restrictions:

                                                                                                                                                                                        11:680:390 and 11:126:394 or 11:680:394

                                                                                                                                                                                        Format:

                                                                                                                                                                                        One 80 minute lecture per week, one 4 - hour lab

                                                                                                                                                                                        Description:

                                                                                                                                                                                        The course "Analytical Microbiology" is intended to provide hands-on training in the use of analytical instrumentation in microbiological research and applications. Research in all areas of microbiology relies heavily on analytical instrumentation; whether it is the analysis of microbial fermentation products, biotransformations, biodegradation of biocides and other recalcitrant chemicals, or the analysis of chemical markers for use in identification and taxonomy of microorganisms. The course will combine lectures and laboratory experiments with training in the use of analytical instrumentation, including gas chromatography, GC-mass spectrometry, liquid chromatography (HPLC), ion chromatography, and PCR methods. Laboratory experiments will include analytical applications in 1) biotransformations and fermentations, 2) biodegradation of environmental pollutants and 3) rapid-high throughput methods for identification of bacteria and fungi. This course will serve as an introduction to chromatographic analysis, basic principles of mass spectrometry, and review different choices of methods and instruments. This includes familiarization with different analytical software and methods of data analysis and interpretation.

                                                                                                                                                                                        The course is targeted at students in their junior/senior year majoring in biotechnology, and is intended to provide them with analytical skills needed in independent research projects that they may be pursuing in their senior year. The analytical laboratory will also be used for the training of graduate students and post-doctoral associates.

                                                                                                                                                                                        Topics

                                                                                                                                                                                                                      Examinations

                                                                                                                                                                                                                      Other requirements:

                                                                                                                                                                                                                    • Grading

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                                                                                                                                                                                                                      11:126:494. Bioinformatics (3)

                                                                                                                                                                                                                      Normally Offered:

                                                                                                                                                                                                                      Spring Semester, beginning in 2009.

                                                                                                                                                                                                                      Pre-requisites and other registration restrictions:

                                                                                                                                                                                                                      11:126:483 or permission of instructor

                                                                                                                                                                                                                      Description:

                                                                                                                                                                                                                      This course is designed to introduce biologists to utilizing UNIX, perl and R in bioinformatics. The concepts, principles and tools of bioinformatics will be introduced in the framework of basic shell scripting. Students will learn how to script, install programs and navigate in the UNIX shell. Students will learn how to setup and use command line BLAST. Students will learn basic perl scripting and handling of large datasets. Finally, students will be introduced to the statistical package R, and learn basic functions such as file handling, analysis and graphing.

                                                                                                                                                                                                                      Syllabus

                                                                                                                                                                                                                        Introduction to bioinformatics, real world problems
                                                                                                                                                                                                                        Introduction to bioinformatics, real world solutions
                                                                                                                                                                                                                        The Unix Shell, installation
                                                                                                                                                                                                                        Shell commands
                                                                                                                                                                                                                        BLAST, installation
                                                                                                                                                                                                                        BLAST your favorite protein
                                                                                                                                                                                                                        Identifying protein domains
                                                                                                                                                                                                                        Phylogenetics in the shell
                                                                                                                                                                                                                        Protein alignment real world problems
                                                                                                                                                                                                                        Class project, find genes between species using command blast
                                                                                                                                                                                                                        Introduction to perl
                                                                                                                                                                                                                        Perl commands, regular expression
                                                                                                                                                                                                                        Basic concepts in scripting, common to all languages
                                                                                                                                                                                                                        Scripting vs. algorithms
                                                                                                                                                                                                                        Handling DNA and protein
                                                                                                                                                                                                                        Motif searching
                                                                                                                                                                                                                        Parsing
                                                                                                                                                                                                                        File handling, FASTA
                                                                                                                                                                                                                        Bioinformatic algorithms
                                                                                                                                                                                                                        Advanced scripting, an introduction
                                                                                                                                                                                                                        Perl, real world problem
                                                                                                                                                                                                                        Class project, find real world solutions
                                                                                                                                                                                                                        Introduction to R, bioinformatics and statistics
                                                                                                                                                                                                                        Scripting in R
                                                                                                                                                                                                                        Basic analysis in R
                                                                                                                                                                                                                        Graphing in R
                                                                                                                                                                                                                        R, real world problems
                                                                                                                                                                                                                        R, scripting on the move, future of bioinformatics

                                                                                                                                                                                                                      Examinations

                                                                                                                                                                                                                      Other requirements:

                                                                                                                                                                                                                    • Grading

                                                                                                                                                                                                                      The class will be held in the Foran Hall computer lab, and the students’ work will be monitored in real time. Each class period will include a practical scripting assignment, and students will be directly evaluated in the output and speed of their script (70%). Two larger projects will require multi-functional scripts that will be evaluated for midterm and final grades (30%). Three classmates and the professor will evaluate each scripting project for functionality, speed, and script documentation.

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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 or Robert Wood Johnson Medical School who does research in biotechnology, biochemistry, molecular biology or genetics may supervise student research projects.

                                                                                                                                                                                                                      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 Curriculum Coordinator 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.

                                                                                                                                                                                                                      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 Curriculum Coordinator.

                                                                                                                                                                                                                      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:

                                                                                                                                                                                                                      If you desire additional information, speak with the Biotechnology Curriculum Coordinator.

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