NCBS Bangalore 2006

From 2006.igem.org

Contents 1 The Living Networks Wiki 1.1 The team 1.2 The projects 1.3 Lab notes

The Living Networks Wiki

December 13, 2024

The NCBS iGEM team grew out of an interdisciplinary workshop which ran through the spring of 2006. Participants included students, faculty, and industry researchers; physicists, biologists, computer scientists, and engineers; lawyers, educators, and entrepreneurs. Our discussions on genetic networks, synthetic biology, open-source ideas, and industrial applications, are documented on the workshop [http://www.ncbs.res.in/~faculty/ssb website].

The team

Please feel free to change your titles. We'll order new business cards every week.

• Mukund: Chief Mentor and Brainstormer (thattai@ncbs.res.in)

• Adil: Chief Critic and Voice of Reason (adil@ncbs.res.in)

• Aparna: Chief Mind-Mapping Officer (aparna@ncbs.res.in)

• Ashesh: Head of Getting-Things-To-Work Department (ashesh@ncbs.res.in)

• Dhanya: Wild Ideas Consultant (dhanya@ncbs.res.in)

• Krithiga: Team Whip and Strategist (krithiga@ncbs.res.in)

• Ruchi: Head of Enthusiasm Department (mallik@ncbs.res.in)

• Sugat: Chief Technical Officer and Head of Big-Picture Department (sugat@ncbs.res.in)

The projects

1. X-Y regulation of bacterial chemotaxis
2. Synchronization of bacterial cell cycle
3. Monitoring long-term effects of UV exposure

Lab notes

Feb 4, 2006

What should we work on?

• Group I:
  • Develop a system by which Ecoli can sense two different colours. Red detection already exists, how can we pick up green independently? Can the two sensors be used to drive two different outputs? Try to couple these to X-Y chemotaxis. Problems: where can we quickly find a green sensor?
  • Bacterial Fourier transform. Deliver some stimulus, e.g. light, in square pulses of a certain frequency. The output is the level of a reporter which can be correlated to frequency. Problems: how to make the amplitute of the output independent of the amplitute of the input signal, dependent only on the frequency?
  • Bacterial signaling on wires and other patterns. Use a lawn of bacteria and some kind of template (e.g. a pattern of light) to activate certain cells. These cells can then talk to each other, transmitting a signal in defined patterns. Problems: for signalling around a ring, how to establish the initial asymmetry that makes transmission uni-directional?

• Group II:
  • Using localized plasmids to detect the activity of a DNA-binding protein. (This is a research project in MT’s lab.) Introduce binding sites for CRP onto pole-localized plasmids; make a CRP-CFP fusion. When CRP is active, it will be pole localized; when it is inactive, it will be cytoplasmic. Problems: which pole-localized plasmid? How to ensure that additional binding sites and fusion proteins don’t perturb cell function?
  • X-Y chemotaxis. We would like +/- control on two independent axes. This would require 4 different chemical gradients, two in each orthogonal direction. Suggestion: we could have default taxis in the ‘-' orientation, and active taxis in the ‘+’ orientation. Problems: how to make the cell ‘stand still’ in this configuration? Active feedback?
  • Bacterial log book. If we have a single cell moving around a plate, can we reproduce its path? We would have to use DNA sequence rather than proteins, because the latter limits us to a few points. Use lambda insertion or transposon insertion; kill cells that return to the same point twice. Problems: The insertion mechanism is completely undefined.
  • Synchronizing cell cycles. Use a cell cycle-dependent promoter (e.g. cya in Ecoli) to drive a cell-cell signal. Use the signal to modulate cell cycle in the receiver cell. This should allow synchronization of the population. Problems: How to modulate the cell cycle?

• Group III:
  • Magnetic paintbox. Combine magnetotaxis with 3 colour detection to make a colour pattern generator. Problems: cannot reconstitute magnetotaxis in Ecoli.
  • Synchronizing repressilators. This is based on a suggestion by Strogatz and Elowitz. Problems: the repressilator is an unreliable oscillator.
  • An early warning chemotaxis system for UV damage. (This was suggested by Mrinalini Puranik.) A beam of UV light slowly moves over a bacterial lawn. Cells under UV suffer DNA damage and upregulate their repair mechanisms. Some of these cells actively move away from the light toward other parts of the plate, and trigger the repair response in neighboring cells. Problems: can we get unidirectional motion? How to sense UV damage? What pathways should we upregulate in receiver cells?
  • Bacterial segregation by attractant/repellent strategy. Two populations of cells will be mixed. One synthesizes an attractant for its own kind; another synthesizes a repellent for the first kind. Together, this would cause cells to segregate, leading to Turing-like patterns. Suggestion: make use of molecules which can behave both as attractants and repellents depending on concentration (e.g. L-Lysine). Problems: we can make sure that different populations have distinct attractants, but we do not have control over repellents. Is a universal repellent sufficient to achieve the desired effect?