Harvard:SysBio 204/2014

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

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: October 3rd at noon
  • Midterm #2 due: October 24th at noon
  • Final project due: November 28
  • Method of submission: email TA your slides and presentations
• Midterm and Final Projects (2013, to be updated)

Logistics

• Instructors: George Church, William Shih, Pamela Silver, Peng Yin
• Teaching Fellow: Evan Daugharthy
• Meeting time: 2:30 - 4:00 PM, Mon/Wed, Fall 2014
• Location: Room 521, Wyss Institute, 3 Blackfan circle, Boston, 02115
• First class on Wednesday Sep 3rd.
• Location: CLSB521
• No exams
• Prerequisites: none
• Grading
  • 20% Participation
  • 40% Midterm projects
  • 40% Final project
• Harvard course site

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

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.

Recent changes

19 July 2018

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UA Biophysics:Protocols: Multilamellar Vesicles‎ (diff | hist) . . (+440)‎ . . Elizabeth Suesca (talk | contribs) (Created page with "'''Multilamellar Vesicles''' The dried lipid, prepared as described in "liposome stock", is hydrated using a hydration buffer. #Preheat the buffer at a temperature approxima...")

		14:20	(Upload log)‎ . . [Juan David Orjuela Zuniga‎; Wjshearon‎]
			14:20 . . Juan David Orjuela Zuniga (talk | contribs) uploaded a new version of File:409421 4812568067637 569998243 n.jpg ‎
			10:17 . . Wjshearon (talk | contribs) uploaded File:Hrsdayheadshot18.jpeg ‎

09:42

McClean: Working with the LoxP/Cre System in S. cerevisiae‎ (diff | hist) . . (+153)‎ . . Jidapas An-Adirekkun (talk | contribs) (→‎Using loxP/Cre in vivo with Yeast)

		N    09:06	UA Biophysics:Protocols: Lipid stock‎‎ (2 changes | history) . . (+870)‎ . . [Elizabeth Suesca‎ (2×)]
			09:06 (cur | prev) . . (+53)‎ . . Elizabeth Suesca (talk | contribs)
		N	09:03 (cur | prev) . . (+817)‎ . . Elizabeth Suesca (talk | contribs) (Created page with "'''Lipid stock''' #Lipids from the company are stored to -80°C for ensure stability #Prior to weighting, lipids should be brought to room temperature in a container containin...")

08:13

UA Biophysics:Protocols: LUV‎ (diff | hist) . . (-896)‎ . . Elizabeth Suesca (talk | contribs) (Replaced content with "'''Preparation of LUV''' Return to Protocols<br>") (Tag: Replaced)

08:07

UA Biophysics:Protocols:Transformation of Competent Cells‎ (diff | hist) . . (-81)‎ . . Elizabeth Suesca (talk | contribs)

18 July 2018

		N    17:18	User:Joncalles‎‎ (3 changes | history) . . (+718)‎ . . [Joncalles‎ (3×)]
			17:18 (cur | prev) . . (-1)‎ . . Joncalles (talk | contribs)
			17:17 (cur | prev) . . (+685)‎ . . Joncalles (talk | contribs)
		N	17:13 (cur | prev) . . (+34)‎ . . Joncalles (talk | contribs) (Created page with "I now have a page, but it is empty")

13:40

UA Biophysics:Protocols:Lymphocytes immunostaining with anti-AlphaTubulin‎ (diff | hist) . . (+53)‎ . . Elizabeth Suesca (talk | contribs)

• Collaboration Policy added to Midterm and Final Page (8/27/14)