Week 1 HW: Principles and Practices

First, describe a biological engineering application or tool you want to develop and why Bioengineered watercress salad plants with nanoparticles enhancing conductivity and emitting light (phluorescence or phosphorecence). Along with Venus flytrap plant which naturally performs electrophysiological reactions closer to those in animals these research objects will be studied at Open BioArt Lab course on bioart practices related with plant electrophysiology. The course will be based on collaboration of Art&Science Center and Hybrid nanophotonics lab at ITMO University (Russia).

2. Governance/policy goals

• Safety and security: the course will be oriented on non-professionals in Biology and take place in the public university with some access limitation. So, prior to final student’s list announcing, there should be Lab safety training (written test? video course? in-person at lab?). I also will suggest some introductory courses on some biological concepts to potential participants in case it will improve their experience.
• Accessibility and impact for community: the main goal of the course is to open-up the curtain of research world and engage people to participate in creative, even artistic, practices, which could contribute to modern scientific and philisophical discourse either. Another aim is in promoting more ethic and compassionate attitude towards plants in line with “plant turn” tendency. Hence, from open call announcement till the classes themselves this philosophy should be clearly stated.
• Interaction with other nodes of bioart, bio-hack, open-bio etc. communities for mutual enrichment our discourse and practices
• Ethics and non-harmfulness: ensure that nanoparticles injections won’t harm plants and cause unnecessary molecular and cellular responses. Propper ways are either via stomata or root system.
• Interaction with the faculty administration for coordination and presentation of key course goals and ideas which correspond to the University’s goals. It will increase chances for financial support and dealing with all the concerns for their approval.

• Purpose: education + art + bioengineering. Accuiring new skills allong with proposing new ideas and their implementation
• Design: collaboration of biologists, nanochimists, and bioartists as teachers with approval of University administration and support of bio-enthusiasts’ community. Participation of St. petersburg bio- and bioart-interested community as listeners and contributors. Potential funding sources: University, federal grants, and industrial partnership (non-profit organisations functioning is down-regulated in this jurisdiction)
• Assumptions: acc. to my experience, heterogenity of potential listeners could either improve experience of all the participants or over-complicate the working process
• Failure: complicated interaction with University, failure in experiments, troubles with finding and decrease in quality of research and the course.
• Success: impact to University public appearance, some course projects can be developed as student thesis or art projects, new collaborations, impact to more ethic and emphatic attitude towards plants

Professor Jacobson

1. What is the error rate of polymerase? 1:10⁶ How does this compare to the length of the human genome? Human genome is 3-3.2*10⁹ bp, hence, 3000 bp of human genome could be wrong How does biology deal with that discrepancy? There are DNA repare systems: MutS, MutH, and MutL among prokaryotes, MSH and MLH in eukaryotes
2. How many different ways are there to code (DNA nucleotide code) for an average human protein? Average human protein consists of 300-400 AA. There are 20 types of proteinogenic AA which are coded by 61 codons in total. Considering code degeneracy, there could be up to 6 synonymous substitutions per some AA. Considering this, there could be up to 10²⁰⁰ theoretical sequences. In practice what are some of the reasons that all of these different codes don’t work to code for the protein of interest? There are conservative domains providing mRNA and/or folding stability, some functional patterns, zones marking exons/introns, start/termination of translation etc. So some sequences won’t give chemically stable, functioning or translation apropriate proteins.

Dr. LeProust

1. What’s the most commonly used method for oligo synthesis currently? Next Generation (Chip Based) Oligo Nucleotide Synthesis
2. Why is it difficult to make oligos longer than 200nt via direct synthesis? Yield decrease with further synthesis steps, lower fidelity + error accumulation, hairpin / dimers / cloggs formation
3. Why can’t you make a 2000bp gene via direct oligo synthesis? Direct oligo synthesis is step-by-step base addition to the chain. With this technology, the yield of the full-length product decreases exponentially with each added base. Even if synthesize exact 2000 bp oligo, it would be hard to purify from, for instance, 1990 bp oligo by gel electrophoresis.

George Church

1. What are the 10 essential amino acids in all animals and how does this affect your view of the “Lysine Contingency”? There is 9 essential amino acids: histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, valine. There is pyrrolysine also, wich occurs only in some organisms, so it could be considered as 10th essential one. Lysine Contigency in “Jurassic Park” movie was presented as “engineered” lack of dinosaurs’ ability to produce lysine amed to tie them to the park therritory where they could get needed supplements. As we can see, almost all vertebrates share this disability, so the movie creators should’ve used alanine, for instance

Week 1 Lab: Pipetting

Individual Final Project

Group Final Project