Information Processing Track
Information Processing in iGEM covers a diverse range of projects. Like the Foundational Advance track, Information Processing teams are not trying to solve a real world problem with practical applications, but tackling an interesting problem that might otherwise not attract attention. Teams enter this track if they are attempting projects such as building elements of a biological computer, creating a game using biology or working on a signal processing challenges.
Engineering ways to make biological systems perform computation is one of the core goals of synthetic biology. We generally work at the DNA level, engineering systems to function using BioBricks. In most biological systems, protein-protein interactions are where the majority of processing takes place. Being able to design proteins to accomplish computation would allow for systems to function on a much faster timescale than the current transcription-translation paradigm. These are some of the challenges that face teams entering projects into the Information Processing track in iGEM.
You will find images and abstracts of the winning Information Processing track teams from 2015 and 2016 in the page below.
CryptoGERM: Encode it, keep it
The world’s silicon supply won’t be able to cover the demand for data storage by 2040. However, nature has been encoding enormous amounts of information in DNA for billions of years. By introducing a sequence into DNA of bacterial spores, one of the most resistant-to-harsh-conditions forms of life, “CryptoGERM” tries to combine storing information and transferring it in a safe way. The goal is to safely send a key and an encrypted message in two separate spore systems of Bacillus subtilis. Digital and biological protection layers will prevent this information from being captured by unauthorized parties. The message is protected by computational encryption, while the sensitive key can only be accessed from the spores with the right growing conditions. For example, light-switchable antibiotics have to be activated by the correct frequency of light. If the recipient fails, the sequence will be destroyed and the message is lost forever.
Intelligent design is becoming ever more important in the world of biology. Designing cells to match researchers' needs exactly has important therapeutic and diagnostic applications. To be able to conveniently harness this technology, new and straightforward tools are required. In light of this, our project aims to develop an innovative CRISPR-dCas9 system in yeasts, capable of regulating genetic transcription and creating robust synthetic circuits. Our model is based around a scaffold guide RNA. This scaffold allows us to recruit transcriptional activators, repressors, and dCas9, as well as direct the complex to a given locus in the genome. In addition, the presence of both activators and repressors in our system would permit a modularity previously unseen in CRISPR-dCas9 based systems. Furthermore, we aspire to improve on Cello, a software that takes a user-given circuit and predicts a plasmid that could recreate it in vivo.
Talk Alpha to Me
Cellular communities exhibit both asocial and social behaviors through sensing and secreting the same extracellular molecule, eliciting population-wide behaviors such as quorum sensing, cell differentiation, and averaging. Drawing inspiration from collective behaviors and cellular decision-making in biological systems, our team aims to engineer a synthetic model to understand the factors that play into reshaping community phenotypes. We have engineered novel sense-and-secrete circuits in yeast by repurposing the endogenous mating pathway and using fluorescent reporters to read out individual and community responses to a stimulus. We aspire to understand how intercellular signaling can shepherd noisy individual responses into robust community level behaviors. Particularly, we hope that by tuning parameters such as receptor level, secretion rate, signal degradation, and spatial retention, we will be able to customize communication to model natural systems and elicit distinct community phenotypes.
We want to replay the Prisoner’s Dilemma, a well-known game analysed in game theory, by using E. coli. This game involves dilemma between cooperation and defection. Although each prisoner knows both player's cooperation mutually benefits each other, one will always defect when the individual is pursuing his or her own benefit. We will express this dilemma by using a genetic circuit centering in quorum sensing. We will also provide various strategies and aim to determine the best strategy in this game. By combining the idea with synthetic biology, we demonstrated this game among students. We also made our own pay-off matrix. In our project we will focus on the prisoners’ emotions as well. The metaphoric usage of cherry blossoms appears in countless Haikus and Tankas, and expresses the heart of the Japanese. Therefore, we will express the prisoners’ emotions using E. coli, which will mimic the characteristics of cherry blossoms.