1. choose a problem
2. explore the problem
   1. state of the art
   2. who are stakeholders
   3. requirements for a "good" solution
   4. safety and regulatory concerns
   the point:
   have a completely authentic research experience, do the best science we can
3. choose an approach
4. Designing DNA/experiments
5. Order DNA -> construction

6. Make data

    

   First half of semester:

• Small groups focused around specific potential projects

• Developing a problem

• Interacting with the primary literature (3 hours with a medical dictionary)

• reporting- journal clubs by the summer

• stakeholders (don't forget to talk about funding!)
  

   

Skills

• TC

• Cloning (PCR)
• Genious
• Data analysis (Modelling) not just trial and error, get computers involved! Model protein structure and dynamics, biomaterials and metabolic engineering. iGEM judges like this. 

Ideas

• Kyle: Mammalian metabolic engineering
  • glycosilation: many proteins are amino acids decorated with sugars by the golgi body. It's how immune system tells self from not-self. Produce anti bodies with mammalian cells so the immune system doesn't destroy them
  • heparin?
  • synthetic meat- to please our steak-holders. VEGAN MEAT!
    • tissues by design
• Jesse:
  • fighting resistant strains. let's make crispa that targets bad plasmids (done and published)
  • By phages: already done b4y the Lu lab. 
  • Prevent horizontal gene transfer (by conjugation or other methods)
• Marjorie:
  • bacterial beauty products
  • microbiome: gut, skin? 
    • damage repair
    • secretory: replace proteins
    • bacteria tattoo
• brain measurements, optogenetics. delivery issues?
  • deep tissue imaging is hard
  • live animals
  • high spacial/temporal resolution needed
  • grow george church's brain in a dish and get a sensor to detect neural circuitry
• Autoimmune diseases
  • immunology is a deep and complex field, we don't know much about it?
  • cell-cell communications
  • specificity
  • use integrins to mediate whether immune cells get to inflammatory sites
  • design antibodies
  • dynamics of response. think about the way things operate in time 
  • cell movement- things crossing epithelial barriers
• Randomise collagen structure
  • as people age more collagen builds up, and when people are wounded collagen displaces natural cells creating scar tissue and increasing in size. 
  • collagen forms neat rows and is hard to break down. inducing a more random structure could help dissolve scar tissue and lessen stiffness
  • collagenases
  • A cream that makes scars disappear?
  • liver fibrosis
• Biofilms
  • can lead to resistance and diseases 
  • give biofilms cancer!
  • what makes a prokaryote "multicellular"?
  • use slime molds to clean surfaces
• Sickle cell anemia
  • classic monogenic disease -> genome editing
  • hematopoetic
  • RED BLOOD CELLS DON'T HAVE GENOMES! engineered RBCs
• Biological sunflower
  • ask how vibrio does it? vibrio fischeri
  • luciferase
  • couple energy input to luciferin production and light sensing module coupled to luciferase
  • marchantia = synthetic biology for plants platform
• Yeast Soylent: macronutrient composition of soylent is a bit of fat from soybeans and some long chain sugars, protein is rice powder. Could we engineer a yeast strain that made macronutrients at a biologically compelte level?
  • engineer yeast to enrich bread
  • research cost of inputs
  • Good Manufacturing Practices
  • first do proof of concept, then try moving it to a larger scale in a GMP lab. make a yeast strain that produces proteins, carbs and fat at levels that, supplimented with appropriate micronutrients, you could live on for the rest of your life
  • People modified yeast to make bioengineered beer (banana, wintergreen flavoured...) -> you can modify yeast to produce flavour components!
• Biofilm 3D printing. 
  • last year: 3D printing with light
  • program cells to make interesting structures using cell-cell communication. use light sensor with multiple colours
  • mammalian cells: to calcify things (directed tissue formation)
  • interesting model organism: modify silica shell walls of a diatom. control over silica wall deposition
  • produce mother of pearl