Drosophilia melanogaster juvenile hormone acid O-methytransferase (DmJHAMT) is an insect enzyme that natively methylates juvenile hormone acids, but also works on fatty acid substrates, such as lauric acid to produce fatty acid methyl esters (FAMEs), a form of biodiesel, both in vitro and in vivo. Production of biodiesel in bacteria using DmJHAMT is comparable to the most currently effective pathway for doing so and uses fewer enzymes, making it a promising candidate for further pathway optimization. Our goal is to express DmJHAMT in a lauric-acid secreting strain of cyanobacteria to produce an organism that can produce biodiesel directly from carbon dioxide. Although it is effective at producing biodiesel from a fatty acid substrate, DmJHAMT does so with poor kinetics. With the MSKC’s help, we plan to crystallize DmJHAMT and determine its structure so that we can tune its substrate selectivity and increase its kinetics to produce higher FAME titers at a lower cost to the cell.

In order to survive, cells must sense stimuli and respond accordingly. Responding "accordingly" requires some form of computation on the part of the cell - and because of evolution, this computation is done in a wide variety of ways and a variety of levels. Thus, rational engineering of a gene circuit that can take in multiple stimuli (scalable) and is designable (standardizable) by a human engineer is difficult. We are attempting to develop a platform for transcriptional regulation that addresses both of these challenges by using a recombinase-dCas9 fusion protein to act as an invertase to "flip" a region of DNA. The state of the DNA - flipped or unflipped - can be represented as either a 0 or 1, i.e. manipulated to perform logical operations. Current work is focused on testing the recCas9 fusion protein from Chaikind et al. 2016 to see if it can excise DNA in E. coli. We then hope to test its invertase activity and, if successful, use the protein to build an architecture for standardized, scalable logic gates.

If working with a robot became as easy as working with an assistant, how would our relationship with lab automation change? This summer, we built a prototype of an inexpensive, real-time lab automation platform using the open-source Opentrons OT-1 robot. This platform removes the need for lengthy calibrations and is a first step towards accessible, effortless automation. A $40 camera and a 3D printed camera mount are used for the video feed. Real-time item calibration uses TensorFlow's Object Detection API and OpenCV. The frontend is built using React. Packaged code and hardware specs will be posted at https://github.com/EndyLab

LabFlow is a digital platform designed to enhance the precision and efficiency of laboratory workflows. It provides tools for managing and standardizing experimental protocols, ensuring consistency and reproducibility across experiments. The platform features real-time error detection, reducing the likelihood of mistakes during complex experimental processes, and integrates collaborative tools to enable seamless communication and sharing of protocols and results among researchers. By centralizing workflow management and incorporating data-driven insights, LabFlow supports reliable research practices and promotes the efficient execution of scientific experiments.

In this project we will build the Personal Food Computer, an open source grow chamber managed by the Open Agriculture project at the MIT Media Lab. The personal food computer is a controllable environment, made entirely of easily accessible parts, that can sit on your desktop. It allows users to monitor plant growth under controlled lighting, temperature, and humidity. The personal food computer has a community of growers, hackers, and bio enthusiasts supporting it. We hope to use this project to connect with the bio hacker community. We believe that low-cost, open source, modular research equipment is badly needed in the world today, and we want to use this build as an attempt to both learn what already exists in the space and evaluate where we might be able to contribute to the community going forward. More information about the MIT OpenAg Personal Food Computer 3.0 that we are going to build can be found here: https://wiki.openag.media.mit.edu/pfc_edu_3.0

The creation of a synthetic, understandable cell would mark a great leap forward for humanity’s understanding of the necessary components to create and sustain life and facilitate the eventual construction of designer organisms adept at performing specialized tasks. Self-replication not only fulfills a vital function for synthetic cells, but also is a prerequisite for evolution - which can be harnessed to optimize the functioning of other modules needed to sustain life (e.g. transcription, translation, energy generation). Therefore, we view genome self-replication as a necessary stepping stone to build a synthetic cell.