As part of the Boston University Biological Design Center, our wetlab team conducts research into the design and construction of synthetic biological systems, with particular focus on the development of tools for engineering novel biological devices in E. coli.
Wetlab researchers also work closely with programmers and engineers to test and evaluate our design automation tools. These real-world applications are essential to making our software effective and relevant to creating new workflows for biological engineering, making this feedback an integral part of our development process.
Modular Part Optimization and Library Development
One of the major tenets of synthetic biology is the ability to assemble genetic devices from standardized biological parts. While new formats and methodologies for DNA assembly are emerging rapidly, the availability of well-characterized component parts that conform to these formats is low, leading many researchers to use less efficient methods that offer a wider selection of pre-existing parts.
MoClo is a relatively new assembly method utilizing Type IIs restriction enzymes that allows the ligation of up to six DNA fragments together at one time using small, oligo-derived fusion sites. Our wetlab team has adapted the MoClo methodology to reduce thermocycler reaction time and reaction volume, thereby lowering labor and reagent costs. Using this modified protocol, we have constructed a library of well-characterized, reliable MoClo parts for use in the assembly of biological devices in E. coli. This library includes many part types that are essential to the construction of basic genetic circuits, including promoters, ribosome binding sites, reporter genes, and transcriptional terminators.
The CIDAR MoClo Library is the first bacterial DNA part library compatible with a multipart assembly standard. CIDAR MoClo allows for the rapid assembly of interchangeable DNA parts. While many DNA assembly standards have been published in recent years, only the Modular Cloning standard, or MoClo, has the advantage of providing publicly available part libraries for use in plant, yeast, mammalian systems, and now E. coli.
This library is publicly available as part of the Hummingbird project and is intended to facilitate the adoption of the MoClo format as a viable alternative to both the BioBrick standard and less-modular scarless assembly methods, such as Gibson Assembly.
In synthetic biology, there exists a significant demand for designing and constructing functional, complex genetic circuits in a high-throughput, cost-efficient, reproducible, and rational manner. This project is developing an improved and modular Cello library of parts and devices compatible with a multipart assembly standard for the construction of a new generation of Cello constructs (e.g., sequential logic circuits) in a fast and reproducible manner in E. coli.
In this project, we aim to engineer multiple modular gates and S/R latches in live E. coli cells. The development of intricate circuit designs, such as those of sequential logic circuits, can be achieved from simpler abstractions of such DNA circuits using CAD tools, e.g., Cello. In a multi-lab effort, we are developing workflows for the fully automated construction and testing of sequential logic circuits. Once proven functional, the new Cello library will be publicly available in SBOL file format on the Living Computing Project's SynBioHub webpage to ease access and implementation of Cello designs.
This study help address the question "How generalizable are the concepts and "design rules" which can be learned from studying biological systems?" which is part of the goals established by the Living Computing Project. The work has been conducted in collaboration with the DAMP lab for fast DNA assembly of parts.
There is an extensive collection of genetic parts and devices for building genetic circuits that can perform computation functions. Monoclonal microbial species have been extensively studied and have been reliably used to create synthetic systems with bio-computation features. This has been achieved by implementing well-characterized intracellular components and the help of signal-matching algorithms for the selection of logic gates in different layers, in software tools such as Cello. The computation capacity of such large genetic circuits can be limited by overwhelming metabolic load and the limited number of orthogonal genetic parts. A solution for this problem, with much higher potential for computation, is the partitioning of such systems into smaller sub-circuits, located in different cell-types, with the ability to communicate and coordinate the desired function among each other, such as synthetic consortia.
Consortia-level computation has the potential for the division of labor and the re-usability of well-characterized components in different cells. A significant effort in implementing synthetic consortia has been the characterization of the new components able to coordinate the communication among cells in co-cultures. In this context, we are developing microfluidic platforms that enable the study and characterization of cell-cell communication mechanisms (e.g., bacterial quorum sensing) for bio-computation applications.
Overall, this project addresses the question, “What communication mechanisms are available to biology, what are their limits, and how do they perform?”, which is part of the goals established by the Living Computing Project. This work has been conducted in collaboration with Prof. Lauren Andrews from the University of Massachusetts, Amherst.
Computational Synthetic Biology for Engineers (ENG EC552) presents the field of computational synthetic biology through the lens of four distinct activities: Specification, Design, Assembly, and Test. Engineering students of all backgrounds are provided an introduction to synthetic biology and then exposed to core challenges and approaches in each of these four areas. Homework assignments are provided which allow the students to use existing computational software to explore each of these themes. In addition, advanced concepts are presented around data management, design algorithms, standardization, and simulation challenges in the field.
The course culminates in a group project in which the students apply computational design methods to an experimentally created system (working with graduate students in the Biological Design Center).
Find the Course Website here: https://www.compsynbioclass.org/