Harvard:SysBio 204/2015

Course overview

• A course focusing on the rational design, construction, and applications of nucleic acid and protein-based synthetic molecular and cellular machinery and systems. Students are mentored to produce substantial term projects.
• Intended for graduate students in Systems Biology, Biophysics, Engineering, Biology and related disciplines. No formal prerequisites. Projects are tailored to each student's strengths and interests.
• Website: http://sb204.net
• Poster: http://openwetware.org/images/e/e0/Sb204.2015.pdf

Midterm and Final

• There will be two midterms and one final project for this class
  • Policy: strict submission deadline, we encourage you to submit your work the night before
  • Midterm #1 due: 12pm Monday Oct. 5th (slides, video), and 12pm Monday Oct. 12th (report, sequences, caDNAno file)
  • Midterm #2 due: 12pm Monday Nov. 2nd (slides, video), and 12pm Monday Nov. 9th (report, sequences)
  • Final project due: 12pm Monday Nov. 30th (slides, video), and 12pm Monday Dec. 7th (report, other files)
  • Method of submission: email slides and presentations to TA and submit them to Dropbox folder shared by TF
• Midterm and Final Projects (to be updated with due dates)

Logistics

• Instructors: George Church, William Shih, Pamela Silver, Peng Yin
• Teaching Fellow: Josie Kishi (jkishi@g.harvard.edu)
• Meeting time: 2:30 - 4:00 PM, Mon/Wed, Fall 2015
• Location: Room 521, Wyss Institute, 3 Blackfan circle, Boston, 02115
• First class on Wednesday Sep 2nd.
• No exams
• Prerequisites: none
• Grading
  • 20% Participation
  • 40% Midterm projects
  • 40% Final project
• Harvard course site

Example topics for final design project

• miRNA pattern recognition in eukaryotic cells
• Directed evolution of chemical sensors
• Nano-breadboards for probing electron transport in proteins
• Altered genetic codes and amino acid alphabets
• Modification of proteins for function in harsh environments
• Automatable assembly of large synthetic genes and circuits
• Synthetic biology of stem cells and epigenetic reprogramming pathways
• Structural re-engineering of adenoviruses
• Artificial chemotactic swimmers
• Nonequilibrium networks of nano-machines mimicking dynamic instability in the cytoskeleton
• Recombinase-based multi-state memory in bacteria
• Exosome manufacturing
• Self-assembled solar energy harvester based on bio-inorganic nano-antennae for uv-vis
• Systematic debugging of DNA labeling chemistries by atomic-resolution TEM imaging of DNA origami
• Transcriptional activation and repression through rational molecular design
• Tissue engineering scaffold nano-materials
• Programmable multistep chemical synthesis by templating on catalytic nanostructures
• Ultra-sensitive signal processing for synthetic biology
• Antibody 2.0
• Synthetic nanostructure - virus conjugates
• Replication of information in synthetic crystals
• Cheap large-scale production of protein or DNA-based materials
• Etc. Etc. Etc.

Background Info and previous class projects

• BPH242r 2008-2009 http://openwetware.org/wiki/Biophysics_242r/2009 (Synthetic Biology)
• BPH242r 2010-2011 http://openwetware.org/wiki/Harvard:Biophysics_242r/2011 (Biologically Inspired Molecular Engineering)
• SB204 2011-2012 http://openwetware.org/wiki/Harvard:SysBio_204/2011
  • Harvard Course Site
• SB204 2012-2013 http://openwetware.org/wiki/Harvard:SysBio_204/2012
  • Harvard Course Site
• SB204 2013-2014 http://openwetware.org/wiki/Harvard:SysBio_204/2013
  • Harvard Course Site
• SB204 2013-2014 http://openwetware.org/wiki/Harvard:SysBio_204/2014
  • Harvard Course Site