Outline

1. Introduction – Shinjini
   1. What problems synthetic biology has addressed
   2. Inspiration for synthetic biology (computers, etc.)
   3. Sensing, processing, actuation
      1. Sensing = receive input
      2. Processing = tune input, connect to output
      3. Actuation = output
2. Biology background – Lyla
   1. What is a gene?
      1. Gene = piece of DNA
      2. DNA to mRNA to protein
      3. Protein is responsible for phenotype (fluorescent proteins, eye color, etc.)
   2. What is a promoter?
      1. Promoter controls when genes are expressed
      2. Constitutive vs. repressible/inducible
         1. Activator (must be present for expression)
         2. Repressor (keeps expression from happening)
   3. What is a miRNA?
      1. Represses a gene on the transcriptional level
      2. Binds mRNA and targets it for degradation
      3. Like repressor, but further "down-stream"
      4. Normally present in cells - different profiles in different cell types
3. Interchangeable parts - Kathryn
   1. What is a plasmid?
   2. Connections between sensing/processing/actuation are proteins, miRNAs, etc.
   3. Can change out gene/promoter pairs
      1. Tuning circuit - get better output for different inputs
         1. "Digital" - input reaches threshold, then output on
         2. "Analog" - output varies with level of input
      2. Connecting different sensors to different actuations
         1. Produce fluorescent color outputs for diverse sensors
         2. Sense one state and produce different outputs (like diagnosis vs. treatment)
4. Alzheimer's circuit - does an individual have Alzheimer's disease?
   How can we treat the disease using a patient's own neurons? - Shinjini
   1. What is Alzheimer's disease?
      1. Affects cognition, etc.
      2. Molecular pathology
         1. Beta-amyloid plaques
         2. (Tau neurofibrillary tangles)
   2.  How do we sense that an individual has Alzheimer's disease?
      1. Receptor-mediated sensing
         1. Extracellular input to intracellular output
         2. Output transcription factor via Tango system
      2. miRNA sensing
         1. Alzheimer's cells have different miRNA profile
         2. Use an AND gate
   3. Processing = transcription factor
   4. How do we treat Alzheimer's disease?
      1. Introduce BACE2
         1. Degrade beta-amyloid
         2. Under control of inducible promoter (to connect to sensing)
      2. Down-regulate BACE1
         1. BACE1 makes beta-amyloid
         2. Use miRNA because down-regulating endogenous BACE1
5. Computation/experiments - Gary
   1. What it's like to actually be in the lab
      1. iGEM is mostly novices
         1. We know a lot of biology
         2. We don't have a lot of lab experience
      2. Everything starts with a protocol
         1. Optimizing protocols once you know what you're doing
      3. Failures happen and that's okay
   2. How computation can aid biologists
      1. Predictive models
         1. Preventative measure from wasting resources on experiments that won't work
         2. Ex. MATLAB, BioCompiler, Python, Java
      2. Data analysis
         1. Machine learning algorithms can better analyze data
      3. Robotics
         
         1. Automated machines are stupid
6. Activity:  What can you do with synthetic biology?