Team:Calgary/Appendix



SYNBIO EDUCATION PACKAGE

An undergraduate-level course

Click on the following links below to view the different components of our educational package that we implemented as part of an introductory synthetic biology course in our university:
Lectures

  • Dry Lab
    1. Data science in iGEM
    2. Web Development
    3. Human Practices, Outreach, Entrepreneurship
    4. Neural Networks
    5. Evolutionary Genetic Algorithms
    6. Principal Component Analysis
    7. Effective Meeting Practices
    8. Git
    9. Protein Modelling
    10. iGEM for dry lab
  • Wet lab: content part 1
    1. Welcome to iGEM
    2. Basics of synbio
    3. The central dogma
    4. Genetic circuits I
  • Wet lab: content part 2
    1. Genetic Circuits II
    2. Genetic Circuits III
    3. Genetic Circuits IV
    4. Interactions and Characterizations
    5. Refresher Slides
  • Wet lab: labs
    1. Introduction to wet lab
    2. Digestions and Ligations
    3. Transformations
    4. Colony PCR
    5. Gel Electrophoresis
    6. Plasmid Miniprep
    7. SDS-PAGE Gel
Assignments/Worksheets
  1. Wet lab: Restriction Enzyme exercise
  2. Wet lab: Midterm assignment
  3. Final Group Assignment Guidelines
  4. Final Group Assignment Example
Guides & Tools
  1. Benchling Guide
  2. BLAST Guide
  3. Mendeley Guide
  4. NCBI Guide
  5. OligoAnalyzer Tool Guide
  6. How to create a primer
  7. Genetic Construct Design Tips


PART COLLECTION GIBSON PLASMIDS

Plasmids made from modular Gibson Assembly

Our part collection was designed so different gene cassettes could be assembled using Gibson Assembly using the different Gibson homology sequences built-in each part. The nourseothricin expression construct (BBa_K3629015), when cloned into a plasmid, acts as the destination vector for all the other expression constructs. Download the tables below to see the unique plasmids that can be made and how they can be made.

*The following plasmids can be made ONLY if the nourseothricin expression construct (BBa_K3629015), is in a plasmid without XhoI, NcoI, BamHI, BbsI, SalI, SmaI, EcoRV, or HpaI restriction sites.

Table 1 outlines the plasmids that can be made in a single Gibson reaction (i.e. no prior plasmid has to be made). Each part must be individually digested by the corresponding restriction enzyme, after which the digestion products can be placed together for Gibson Assembly

Download table 1 here.

Table 2 outlines the plasmids that can be made in a sequential Gibson reaction (i.e a plasmid from table 1 has to be made first), as this can increase the assembly efficiency in some cases. Each part and plasmid must be individually digested by the corresponding restriction enzyme, after which the digestion products can be placed together for Gibson Assembled

Download table 2 here.


GLUCOSE STANDARD

We conducted a number of DNS assays that relied on glucose standard below to quantify the production of glucose by cellulase.

Figure 1. DNS Assay glucose standard produced from glucose concentrations of 0.4, 0.8, 1.2, 1.6, and 2.0mg/mL. The trend line equation is y=1.542x - 0.2514.


Y. LIPOLYTICA GROWTH ON CELLULOSE

Extra graphs from Y. lipolytica cellulose growth experiments

Our main analysis on our Cellulase Integration page was to compare the Y. lipolytica growth on different cellulose substrates: pure 1% w/v cellulose, straw, and chickpea shells. However, we also tested growth on these substrates with different concentrations of cellulase

Figure 2. OD600 over time of Yarrowia lipolytica cultivated with 1% w/v cellulose solution and incubated with different concentrations of pure cellulase.

Figure 3. OD600 over time of Yarrowia lipolytica cultivated with boiled lemongrass straw (Cymbopogon citratus) and incubated with different concentrations of pure cellulase.

Figure 3. OD600 over time of Yarrowia lipolytica cultivated on boiled chickpea (Cicer arietinum) seed pod and incubated with different concentrations of pure cellulase.