Download BE755 Molecular Systems and Synthetic Biology Laboratory

BE755
Molecular Systems and Synthetic Biology Laboratory
This is an elective advanced laboratory course for the bioengineering of nucleic acids, genetic circuits
and genome. This is the first wet laboratory-based course in BME that covers advanced molecular and synthetic
biology technology and will complement existing lecture/dry-lab based courses in molecular and systems biology
track in the department. In the nucleic acids engineering portion, focus will be on the use, modification, and
amplification of DNA/RNA for diagnostic purposes. In the genetic engineering and genome editing portion,
students will learn some of latest DNA assembly technologies, such as the gene recombineering and Gibson
cloning as well as genome editing using the CRISPR/Cas system and discuss ethics in genome engineering.
Students will also be exposed to single cell gene expression analysis and the concept of heterogeneity and
stochasticity in gene expression. In the functional genomic portion, we will provide the theory and practice of
transcriptome analysis.
The course is a superposition of a traditional lecture course, lab sessions and a modified “journal club.”
Proposed Syllabus
Theme 1:
Nucleic Acids Detection and Amplification
Module 1: Engineering with nucleic acids analogs, application for
diagnostics and genotyping
Duration: 1 week, 2 lab sessions
Discussion: Artificial DNA, PNA and LNA. PD-loops, DNA labeling,
sequencing, molecular beacons, aptamers
Lab 1: Allele genotyping using molecular beacons and DNA for cystic
fibrosis samples
Module 2: Isothermal methods of DNA/RNA amplification and quantification
Duration: 2 weeks, 4 lab sessions
Discussion: RCA, LAMP, loop mediated isothermal amplification; HDA,
helicase dependent amplification, development of nucleic acid-based
diagnostics
Lab 2: Microbial detection through PNA opening, RCA amplification and
nucleic acids analysis
Theme 2:
Genetic and genome engineering
Module 3: DNA assembly
Duration: 3 weeks, 6 lab sessions
Discussion: In depth discussion on DNA preparation, and the principles on
cell lysis, and DNA precipitation. DNA assembly techniques such as
Gibson cloning and recombineering. Ethics of genome assembly
Lab 4-6: Cloning genetic tools, or circuits, or library that can potentially be
publishable. Each student will produce different constructs. Gene
expression quantified through single cell analysis techniques (e.g. flow
cytometry) with comparison to classical techniques (e.g. Western blot).
Module 4: Genome editing
Duration: 3 weeks, 6 lab sessions
Discussion: Compare genome editing technologies in prokaryotes and
eukaryotes. Discuss the pros and cons of various programmable
nuclease technologies (e.g. Zinc-finger, TALEN, CRISPR/Cas). Discuss
the ethical concerns of genome engineering in the context of human
health and ecology.
Lab 7-9: Genome editing in eukaryotic cells (starting with yeast first, may
eventually move to human T cells).
Module 5: Transcriptome sequencing
Duration: 3 weeks, 6 lab sessions
Discussion: transcription of coding and non-coding RNA, RNA interference
Lab 10-12: RNA isolation from cells from knockout and wild type (ideally
related to the genome editing module). RNA-seq or microarray analysis.