Brian's blog: https://tanet.mit.edu/
  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
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