Course BIT 150
Title Applied Bioinformatics
Instructor Dubcovsky, Neale
Units 4
Quarter Offered Fall
Prerequisites Engineering: Computer Science 10 or 15 or Agricultural Management and Rangeland Resources 21 (formerly Agricultural Systems and Environment 21). Biological Sciences 101 and 104. Agricultural Management and Rangeland Resources 120 or Statistics 13 or Statistics 100.
Catalog Description Concepts and programs needed to apply bioinformatics in biotechnology research. Sequence analysis and annotation and use of plant and animal databases for students in biological and agricultural sciences. Two units credit for students who have completed Engineering: Computer Science 124.
Summary Engineering: Computer Science 10 or 15 or Agricultural Management and Rangeland Resources 21 (formerly Agricultural Systems and Environment 21). Biological Sciences 101 and 104. Agricultural Management and Rangeland Resources 120 or Statistics 13 or Statistics 100.
Course   BIT 160
Title Principles of Plant Biotechnology
Instructor Dandekar
Units 3
Quarter Offered Winter
Prerequisites Principles of Plant Biotechnology
Catalog Description Principles and concepts of plant biotechnology including recombinant DNA technology, molecular biology, genomics, cell and tissue culture, gene transfer and crop improvement strategies using transgenic crops.
Summary Gene Transfer in Plants
Plant Biotechnology to Genetics: evolution of the revolution
Agrobacterium, the crown gall bacteria
The mechanism of plant transformation
Other methods of gene transfer
Vectors and foreign genes
Plant Molecular Biology and Tissue Culture
Regulation of transgene expression
Mechanisms of plant gene expression
Gene Discovery: Current Approaches
Protein targeting in plant cells
Protein trafficking in plant cells
Plant tissue culture
Plant regeneration
Plant Genomics
Structural genomics
Functional genomics
Case Histories: Plant Protection
Bacterial frost tolerance
Herbicide tolerance
Pest Resistance: insecticidal proteins
Resistance to insect pests via Bt: insecticidal crystal proteins
Resistance to plant viruses
Host plant defense response to pathogens
Systemic acquired resistance
Case Histories: Plants as Factories Applications of plant cell cuture
Production of biopharmaceuticals, bioplastics and biofuels
Case Histories: Improving Quality and Productivity
Antisense control of fruit ripening
Modification: lipid metabolism
Commercialization, regulatory, social and ethical issues
Course   BIT 161A
Title Genetics and Biotechnology Laboratory
Instructor Beckles
Units 6
Quarter Offered Winter, Summer
Prerequisites Plant Sciences 152 or Biological Sciences 101
Catalog Description Techniques of genetic analysis at the molecular level including recombinant DNA, gene mapping and basic computational biology.
Summary Course Organization
* Lab safety
* Basic laboratory practices
* Lab notebook and record keeping
* Introduction to pipetting techniques
Recombinant DNA
* Plasmid DNA isolation (mini prep)
* Restriction digest plasmid DNA
* Agarose gel electrophoresis
* Restriction mapping
* DNA fragment isolation
PCR-Cloning of DNA fragments and ligation
* DNA ligation
* Transformation of E. coli
* Blue/white lac system
* Flurescence selection
* Restriction analysis
* Miniprep screen of transformants
Basic bacterial culture techniques
* Growth
* Genetic selection
* Pure culture isolation and cryo-storage
* Inoculation broth and plates
DNA Sequencing and Analysis
* Analysis of DNA chromatograms
* Sequencing manipulation tools
* DNA sequence homology analysis and searching
* SNP discovery
* Protein structure-function analysis
* Vector NTI and Genetool programs for sequence analysis
RFLP (Genome Mapping)
* DNA purification
* DNA quantification and analysis (fluorometer)
* Restriction digests of genomic DNA
* Agarose gel electrophoresis
* Southern blot
* Labeling of probe
* Prehybridization and hybridization of blot
* Autoradiography
PCR markers
* Microsatellite detection by PCR
* Mapping molecular markers
Course   BIT 161B
Title Plant Genetics and Biotechnology Laboratory
Instructor Bennett, Blumwald
Units 6
Quarter Offered Spring
Prerequisites Plant Sciences 152 or Biological Sciences 101
Catalog Description Advanced techniques of genetic analysis at the molecular and organismal levels, including transformation, gene expression, analysis of transgenic plants and QTL analysis.
Summary 1. Safety, lab books, sterile technique, seed sterilization and planting. Micropropagation, Agrobacterium culture and leaf-disk innoculation.
2. Cocultivation and genetic selection. Regeneration, GUS analysis.
3. Preparation of SDS-PAGE for seed proteins. Preparation of seed samples for protein extraction. Running PAGE, counting and weighing of 50 seed samples.
4. Data analysis and interpretation of SDS-PAGE variability. Isolation of RNA.
5. Determination of RNA concentration and RT-PCR. Formaldehyde gels and northern blots. Analysis of gene expression: RNA.
6. Gel electrophoresis of RT-PCR products, stain RNA blots and prepare DNA probe. Prehybridization/hybridization of RNA blots, prepare RNA slot blots.
7. Hybridize slot blots. Protein analysis, isolation of proteins.
8. SDS-PAGE, Coomassie-stained gels, western transfer. Develop western blots.
9. Gene transfer via particle gun. Transient expression, quantitative GUS analysis.
10. DNA isolation and PCR analysis from transformed tissue.
Course BIT 171
Title Professionalism and Ethics in Genomics and Biotechnology
Instructor Yoder, Bradford
Units 3
Quarter Offered Fall, Winter, Spring
Prerequisites Upper division standing in a natural science major
Catalog Description Real and hypothetical case studies to illustrate ethical issues in genomics and biotechnology. Training and practice in difficult ethical situations and evaluating personal and social consequences.
Summary 1) Genomics and new biology
2) Moral reasoning and making moral arguments
3) Personal values, priorities and goals
4) Careers in genomics and biotechnology
5) Genetic markers and pre-symptomatic disease screening
6) Behavior genomics
7) Research ethics and peer review
8) Intellectual property
9) Conflicts of interest
10) Ethics in the classroom
Course   BIT 188
Title Undergraduate Research Proposal
Instructor Kliebenstein
Units 3
Quarter Offered Spring
Prerequisites Upper division standing
Catalog Description Preparation and review of a scientific proposal. Problem definition, identification of objectives, literature survey, hypothesis generation, design of experiments, data analysis planning, proposal outline and preparation.
Summary In the lecture component of the course students will gain a clear understanding of the scientific process, its strengths and limitations. In the group discussions, they will develop a research proposal, present their ideas in a clear and logical manner, give and receive criticism, and learn how to revise scholarly work. Students will be matched individually with faculty mentors having expertise in the student’s chosen topic. In some cases the student will have participated in research with the faculty mentor, in other cases the mentor will be selected from the faculty participating in their major (Plant Sciences or Biotechnology). The completed proposal will be in the form appropriate for submission to a granting agency and will be the basis for research conducted in the companion course PLS 189L or BIT 189L.

1. Scientific communication: grants, manuscripts and seminars
2. The basis of the scientific method, deduction, induction, and hypothesis testing
3. Putting your best foot forward: how to prepare a curriculum vitae and biographical sketches
4. Components of a research proposal
5. Library research and background information
6. What are controls and how do you analyze results?
7. How to develop the appropriate experimental procedure
8. Defining a project rationale
9. Outlining and preparing a draft proposal
10. The role of peer review in scientific communication