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

From biotechnology to pharmaceuticals to food, a plethora of industries are in-part fueled by the ability to manipulate and manufacture DNA efficiently and precisely. This need from the industry in turn makes a process called DNA cloning an essential tool for research and innovation across fields. DNA cloning is - like the name entails - the process of ligasing shorter sequences of DNA together into the desired longer vector plasmid in order to replicate the targeted vector in E. coli cells. How can supply meet demand in an exponentially developing industry with ever-growing need? Endonuclease cloning has been a viable method for cloning DNA sequences since the late 1990s, such as the Golden Gate Assembly method which is well-regarded for its ability to prevent “scarring” when recognition sequences are removed and the focus of our project. However, the process of pipetting all the various components of the assembly process can be overwhelmingly tedious, time-consuming and inefficient with even small projects when done by hand. For that reason, BIOME decided to automate the Golden Gate Assembly molecular cloning process with the use of an OT-2 robot to augment efficiency and boost cost-effectiveness. We, however, extended our goal to potentially completely automate the DNA cloning process. Through our programs, a user could simply offer the DNA sequence of their desired vector plasmid and allow automation to do the rest. From segmenting the DNA into workable strands to order (as well as providing price estimates) to pipetting for Golden Gate Assembly, to performing the transformation of your complete DNA into E. coli cells and giving them a much-needed “water bath”, our project should make it as easy and precise as clicking a button to clone your vector plasmids. Additionally, our program intends to develop a protocol for assembling much larger and complex chains of DNA segments than what is conventional for Golden Gate Assembly - the typical limit (10+) for the number of segments that can be joined without a significant hit to the efficiency of Golden Gate Assembly.

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.