Projects
Final projects:
- ABSTRACT Zea Mays, or the common maize plant has been cultivated for feeding purposes for roughly over 9 ‘000 years, since when humans domesticated it, and now is a true symbol for agriculture and farming. Modern monocultures have hugely impacted the way plants are grown, introducing the practice of efficient, yet harmful chemical usage. By genetically engineering corn to overproduce specific volatile compounds, its defence against pests could heavily be enhanced; leading to more stable yields, and slower pathogen adaptation. Green leaf volatiles (GLVs) and terpenes play a significant role in moderating plant response to biotic and abiotic stress, furthermore, being also used as signaling molecules for plant intercommunication. The advantage of their mix stands in the synergy that could theoretically be taken advantage of and the increased diversity of compounds pests have to adapt to, which will certainly take longer as not only are they chemically different, but also pose different effects upon herbivory. Neither impacts the environment or surrounding beneficial fauna at the aimed concentrations, as opposed to industrially used harmful pesticides.
- Additional Information and resources Proposal and presentation slides Proposal Modern crop growing techniques mainly revolve around monoculturing and industrial-scale usage of different chemical compounds, ranging from synthetic fertilisers to pesticides. Because regulating exact pest attacks on crops like corn is rather inefficient, farmers tend to have tons of pesticides sprayed atop of their cultures, more than often resulting in undesired pollution and other ecosystematic side effects which the present genetic engineering plan aims to diminish. Genetically modified plants such as MON810 (BT-corn) defend themselves by using specific compounds; specifically a protein expressed in Bacillus thuringiensis; similar alternatives are considerably better than reckless spraying of harmful insecticides, fungicides etc, however they still have to confront the problem of adapting pests.
- Find a group of ~3–4 students Read through the Phage Reading material listed under “Reading & Resources” below. Review the Bacteriophage Final Project Goals for engineering the L Protein: Increased stability (easiest) Higher titers (medium) Higher toxicity of lysis protein (hard) Brainstorm Session Choose one or two main goals from the list that you think you can address computationally (e.g., “We’ll try to stabilize the lysis protein,” or “We’ll attempt to disrupt its interaction with E. coli DnaJ.”). Write a 1-page proposal (bullet points or short paragraphs) describing: Which tools/approaches from recitation you propose using (e.g., “Use Protein Language Models to do in silico mutagenesis, then AlphaFold-Multimer to check complexes.”). Why do you think those tools might help solve your chosen sub-problem? Name one or two potential pitfalls (e.g., “We lack enough training data on phage–bacteria interactions.”). Include a schematic of your pipeline. This resource may be useful: HTGAA Protein Engineering Tools Each individually put your plan on your HTGAA website Include your group’s short plan for engineering a bacteriophage High level summary: The objective of this assignment is to improve the stability and auto-folding of the lysis protein of a MS2-phage. This mechanism is key to the understanding of how phages can potentially solve antibiotic-resistance.