BTC 505 Advanced Cell and Molecular Biology: This course will review aspects of DNA replication and protein synthesis in eukaryotes and prokaryotes, with an emphasis on the regulation or control of gene expression via post-transcriptional and post-translational processes. It will explore in great depth the currently used tools for genetic modification, editing and cloning, ranging from traditional restriction enzymes and zinc finger nucleases to TALENs and CRISPR-Cas-based systems, and their applications in research, agriculture, and medicine. Finally, it will cover aspects of eukaryotic cell structure and function. Specific topics from this will include the assembly, maintenance, and composition of membranes, the mitochondria and its involved in cellular processes such as apoptosis and autophagy, ribosome assembly and function, the cytoskeleton and its roles in cell division, motility, and intracellular transport, cell signaling pathways, cell differentiation and development, and experimental techniques in cell biology.
Recommended Books:
Bruce Alberts. 2014. Molecular Biology of the Cell (6th Edition). Garland Science
Harvey Lodish, Arnold Berk, S. Lawrence Zipursky, Paul Matsudaira, David Baltimore, and James Darnell. 2007. Molecular Cell Biology (6th Edition). W.H. Freeman
BTC 510 Principles of Immunology: This course will cover aspects of adaptive and innate immunity, including recognition of microbe-associated molecular patterns, inflammation, the interferon response, antigen presentation, lymphocyte development, VDJ recombination, somatic hypermutation, clonal expansion, antibody-antigen interactions, and immunological assays.
Recommended Book:
Kenneth Murphy. 2014. Janeway’s Immunobiology (8th Edition). Garland Science
BTC 515 Advanced Biochemistry: This course is centered on biochemical pathways that are important to metabolism. To that end, specific topics will include biological macromolecules, enzyme structure and function, the action of hormones, metabolic disorders, and canonical pathways and reactions such as glycolysis, Krebs cycle, oxidative phosphorylation, nucleic acid synthesis, and fatty acid metabolism.
Recommended Book:
Michael Cox, David Nelson. 2012. Lehninger Principles of Biochemistry (6th Edition). W.H. Freeman
BTC 520 Bioethics and Biosafety in Biotechnology: This course will cover the central tenets and aims of bioethics and aspects of biosafety in research. Specific topics include core ethical issues in clinical care, public health, science and research, the Cartegena protocol on biosafety, identifying risks and hazards, molecular analyses for predicting gene flow and its consequences, agrobiodiversity, conservation, health impacts, legal and economic aspects, containment and monitoring of hazardous biological agents, and cost-benefit assessment of GMO agroecosystems.
Recommended Books:
Ruth Mackenzie, Alfonso Ascencio. 2003. An Explanatory Guide to the Cartagena Protocol on Biosafety. IUCN
Timothy Murphy. 2004. Case Studies in Biomedical Research Ethics (1st Edition). MIT Press
BTC 525 Introduction to Bioinformatics: This course will introduce the student to the scope and content of the field of bioinformatics. It will be conducted in a computer laboratory setting to enhance practical skills. Students will learn about sources and databases online for data mining. Specific topics include finding homologous protein and DNA sequences and multiple alignment, gene prediction, protein sequence analysis and structure prediction, and basic analysis using Biopython and Bioconductor (on R).
Recommended Books:
Jonathan Pevsner. 2015. Bioinformatics and Functional Genomics (3rd Edition). Wiley-Blackwell Publishers
Arthur Lesk. 2012. Introduction to Bioinformatics (2nd Edition). Oxford University Press, USA
BTC 530 Methods in Biostatistics: This course is designed to introduce students to biostatistical concepts that are necessary for the design, analysis, and presentation of biomedical research. Specific topics will include study design, randomization, control of bias, variability, confounding factors and interactions, description statistics, hypothesis testing, regression models, analysis of variance, and statistical distributions. Students will learn to apply this knowledge to real datasets on the statistical program Stata.
Recommended Books:
Marcelo Pagano, Kimberlee Gauyreau. Principles of Biostatistics (2nd Edition). Cengage Learning.
BTC 535 Advanced Molecular Biology Laboratory: Most, if not all, applications of biotechnology require a deep understanding of the techniques of molecular biology. This course is designed to familiar students with the standard repertoire of techniques for manipulating DNA. Specific laboratory modules include plasmid and genomic DNA extractions, molecular cloning using restriction enzymes and ligase, site-directed mutagenesis using homologous recombination, detection of polymorphisms by PCR and sequencing, RNA extraction, and measurement of gene expression by qRT-PCR.
No textbook. Laboratory manual provided.
BTC 540 Protein Bioinformatics: This course will begin by building familiarity with protein visualization tools such as Pymol and Chimera. Through these, students will learn about protein databases, examining intra-molecular bonds, and exploring protein-protein interactions. They will then learn about prediction of secondary structures, and inference of the thermodynamic properties of proteins.
The relationship between the primary sequence of a protein and the structure it folds into is still being explored through the development of various computational approaches to predict protein 3D structures from amino acid sequences. The final module of the course will focus on developing an understanding of various prediction methods such as homology modeling and threading.
Recommended Book:
M. Michael Gromiha. 2010. Protein Bioinformatics: From Sequence to Function (1st Edition). Academic Press
BTC 545 Plant Biotechnology: Modern plant biotechnology promises to bring on another green revolution in agriculture and eliminate world hunger. This course is designed to introduce students to the techniques of plant biotechnology, and their enormous potential. Specific topics will include selection of high-yielding or climate-resilient wild varieties of plants, isolation and cloning of responsible genes, transformation, plant tissue culture, somatic embryogenesis, and hybridization.
Recommended Book:
C. Neal Stewart Jr. 2008. Plant Biotechnology and Genetics: Principles, Techniques, and Applications. Wiley-Interscience Publishers.
BTC 550 Pharmaceutical Biotechnology: This course will serve as a comprehensive introduction to diverse applications of biological agents and molecules in the pharmaceutical industry. Specific topics will include traditional techniques such as fermentation and bioprocessing; discovery and production of antimicrobial compounds; recombinant protein drugs; monoclonal antibodies for therapeutics; probiotic therapies; and vaccine production.
Recommended Book:
Daan Crommelin, Robert Sindelar, Bernd Meibohm. 2007. Pharmaceutical Biotechnology: Fundamentals and Applications (3rd Edition).CRC Press.
BTC 555 Molecular Phylogenetics: This course will introduce students to the inference of phylogenies from gene or genome sequences, and subsequent analyses. Students will learn about different methods of deriving phylogenetic trees, namely distance-based methods, parsimony, maximum likelihood, and Bayesian. They will apply several computational tools, including PAUP, MEGA, the PHYLIP package, the PAML package, and more, to perform various kinds of analyses, such as selection analysis and ancestral sequence prediction, from molecular sequences. They will learn to date specific divergence events using molecular clock models. Whenever necessary, the conceptual and statistical bases of different approaches and tests will be elaborated on to ascertain application of phylogenetic tools in proper contexts.
Recommended Book:
Barry Hall. 2011. Phylogenetic Trees Made Easy: A How To Manual (4th Edition). Sinauer Associates
BTC 560 Vaccine Development: This course will focus on research and development of vaccines against viruses, bacteria, parasites, and cancer. Students will learn about all the steps involved in the development and ultimate commercial production of a vaccine through examining several historical cases, such as the polio vaccines, the MMR vaccine, and Gardasil. Main areas of focus include safety and effectiveness regulations, clinical trials, evaluation of protective immunity, biological basis of protection induced by various vaccines (relative roles of antibody-mediated or killer T cell-mediated immunity), and novel or recent strategies in vaccine development such as DNA vaccines and chimeric vaccines.
No textbook. Journal articles describing vaccine development and vaccine efficacy studies and trials.
BTC 565 Entrepreneurship in Biotechnology: This course is designed for students who are interested in starting up and managing a biotechnology company. Topics include market assessment of innovative technology, patents and licensing, corporate law, preparing a business plan, raising money from angels and venture capitalists, government grants, strategic alliances, sales and marketing, real estate, human resources, and regulatory affairs.
Recommended Book:
Craig Shimasaki. 2014. Biotechnology Entrepreneurship: Starting, Managing, and Leading Biotech Companies (1st Edition). Academic Press
BTC 570 Diagnostics and Screening: This course will focus on various approaches for developing biological assays for research, screening, and diagnostics. Students will learn how to identify current needs in the rapid, economical, and specific diagnostics of infectious diseases and physiological markers of diseases such as cancer and diabetes, and how to design high-throughput screening assays, assay systems such as immunological assays, quenching assays, and cell-based assays. They will finally be introduced to biosensors and microfluidics, and their current and future applications in medicine and research.
No textbook. Journal articles describing the development and application of bioassays and diagnostic tests.
BTC 575 Computer-Aided Drug Design: Traditional methods of drug discovery are laborious and inefficient, needing to screen hundreds of candidate drugs for binding and activity. Advances in computational modeling now allow us to narrow down candidate drugs to the most likely few by predicting the extent of binding between the drug and the target protein. In this computer laboratory-based course, students will learn about this initial discovery process, and to similarly use computational tools to design and modify drugs, evaluate binding, examine non-bonding interactions, study molecular dynamics, and predict possible activity.
No textbook. Laboratory manual provided.
BTC 580 Introduction to Programming for Bioinformatics: This course is designed for students with a life sciences background with little to no experience in programming. Students will learn to develop basic analytical tools with Python. In addition, they will get familiarized with the UNIX operating system, and learn about structured programming, and object-oriented programming.
Recommended Book:
Mitchell Model. 2009. Bioinformatics Programming Using Python: Practical Programming for Biological Data (1st Edition). O’Reilly Media.
BTC 585 Genomics: This course is designed to focus on the study of genomes, from acquiring the sequence of a genome to its analysis. To that end, the course will explore in detail traditional and next-generation sequencing methods, genome assembly from shorter reads, and genome annotation, which includes the assigning of exon boundaries (in eukaryotes only), regulatory regions, repeat regions, and other genomic regions. Students will learn to analyze transcriptome or gene expression data to determine coding regions of a gene from mRNA sequences. Finally, students will learn about tools and applications of comparative genomics, such as the identification of specific from genome-wide association studies.
Recommended Book:
Jonathan Pevsner. 2015. Bioinformatics and Functional Genomics (3rd Edition). Wiley-Blackwell Publishers
BTC 590 Master’s Thesis: Comprises original laboratory-based research in the School of Life Sciences laboratory, research using computational tools, or both. The student will be supervised by a faculty member within the department. Requirements include lab and/or bioinformatics work, thesis submission, and oral presentation.