Concepts in Biotechnology and Genomics
Concepts in Biotechnology and Genomics focuses on recent developments in biotechnology and genomics with a particular emphasis on technologies that promise to have a transformative effect on science, human health and the environment. It will illustrate these technologies through specific applications in medicine, agriculture, microbiology and the environmental sciences. The course combines formal presentations with group learning projects, class presentations by students, site visits, and guest lecturers from industry, business and academia.
Concepts in Biotechnology and Genomics integrates recent developments in the technology underpinning biotechnology and genomics with specific applications and case studies in medicine, agriculture, microbiology and the environmental sciences. The course outlines recent technologies and developments in the following areas: manipulating genes and gene expression, transformation of genes into organisms and cells, structural and functional genomics, proteomics, metabolomics, metagenomics, epigenetic regulation of genes, phenomics, protein-protein interactions and networks, signal transduction and receptors, structural techniques (crystallography, NMR, AFM), data mining and bioinformatics, systems biology and synthetic biology, the use of in vivo imaging methods.
The course illustrates these approaches through applications in basic and applied research. Some examples of applications are: development of Next-Gen DNA and protein sequencing methods; whole genome engineering of microbes for biofuels; development of in vivo molecular sensors; developing ultra-high throughput screens for identifying drug targets; gene therapy using RNAi and peptide-based drugs; regenerative medicine and stem cell biology; developing personalized medicines; using whole genome association methods in medicine and agriculture; novel methods for delivering drugs and biologicals.
On completion of this course students will have acquired a basic understanding of science and business important to the biotechnology industry and to related industries that make use of genomic technologies, i.e.,
1) a comprehensive overview of the major innovations in biotechnology and genomics; 2) an understanding of existing and potential applications of these technologies, including the limitations and advantages of competing approaches; 3) an understanding of the problems and opportunities associated with scale-up and deployment of genome-wide approaches; 4) the ability to work in teams to identify potential new applications of biotechnology and genomics; 5) an understanding of the economic, social and ethical constraints that application of these technologies but also spur innovation; 6) the necessary written and oral communications skills needed to work within a team and communicate the team project objectives and plan to the rest of the class.
- Introduction, Assignments, History of Biotechnology & Genomics
- Microbial Biotechnology: Antibiotic Discovery & Production, Biotransformation, Bioremediation
- DNA Manipulation and Gene Expression: Heterologous Gene Expression: examples of Insulin, rBST, hGH, Herceptin
- Gene Delivery and Transformation: Getting DNA into Cells: Human Gene Therapy, Transgenic Plants
- DNA Sequencing I –principals and methods: How NextGen DNA sequencers have transformed R&D; Using NextGen DNA seq for de novo research & discovery
- DNA Sequencing II –competing approaches: Evolutionary & Comparative Genomics, Metagenomics in Medicine and the Environmental Sciences
- Structural Genomics: Genome Annotation, Whole Genome Association Studies, Applications in Congenital Disease and Sugarcane
- Functional Genomics I:Transcriptomics,ESTs,, SAGE, Microarrays, Transcriptome Profiling, Applications in Cancer Research; Phenomics
- Functional Genomics II: Manipulating Gene Expression: Using RNAi to discover gene function ; Indicible Protein Degradation Systems; Zinc-Protease-Mediated DNA Cleavage; Epigenetic Methods to Control Genes: Using RNAi to discover gene function ; Indicible Protein Degradation Systems; Zinc-Protease-Mediated DNA Cleavage; Epigenetic Methods to Control Genes
- Proteomics I: Uses of Mass Spectrometry, Stable Isotope Labeling, 2-Hybrid Assay, Pull-Down IP Assay, Building Interactomes
- Proteomics II: Crystallography, NMR, AFM, Structural Biology, High Throughput Approaches, Structure/Function Approaches
- Synthetic Biology: Whole Genome Mutant Collections, Minimal Genomes, Whole Genome Engineering, Applications in Bioenergy
- Metabolomics: Ultra High Throughput Methods, MS/MS etc. Integrating metabolomics with genomic and proteomic data
- Imaging and Microscopy: In vivo imaging methods; GFPs and Protein Tagging; Imaging Protein-Protein Interactions in vivo, Confocal, AFM, Real Time Imaging
- Data Mining and Bioinformatics: Storage and Handling Large Data Sets; Methods for Displaying Data; Using Data to Form Hypotheses.
- Drug Design: Genome Wide Screens for drug targets, Rational-Based Drug Design, Directed Evolution, Combinatorial Libraries,
- Regenerative Medicine & Stem Cells: Embryonic Stem Cells, Adult Stem Cells, Developmental Reprogramming; in vivo vs. in vitro approaches, tissue rejection, organ and tissue engineering. Other approaches for preventing degenerative diseases.
- Nanotechnology and Biosensors: Encapsulation, Nanospheres, Drug Delivery and Clearance, Modifications for targeting specific diseases, tissues (Cancer, Brain). Constructing biosensors and their applications.
Course Pedagogy: These technologies will be introduced to students through presentations made by the course coordinator or by guest lecturers from industry and academia who are specialists in these fields. Each class will consist of a first period in which each topic is reviewed, followed by a second period in which students have time to work as teams on their individual projects. The second period for first half of the course will be given over to teams identifying and working on their projects, along with class activities that focus on non-scientific topics relevant for developing and marketing a product (identifying novel applications of a technology, understanding the economics of R&D, estimating market size, identifying competing approaches, developing a plan to bring a product to market, understanding regulatory aspects, making a business plan, obtaining financial support, constructing a presentation, building consumer awareness). The second period for the second half of the course will involve students making their presentations to the class, coupled with discussions of the student presentations. Students’ knowledge of the subject matter and their ability to integrate this knowledge will be assessed and graded through a combination of exams and the team project presentation.
This class includes a trip to the Commercialization Center for innovative Technologies, a biotech incubator in North Brunswick, NJ.