Accelerating the engineering of biological systems - Geoff Baldwin (Department of Life Sciences, Imperial College London)

In this lecture, I will present our work combining optogenetic experiments, automated image analysis and mathematical modeling to understand which elements on a mammalian promoter play a role in decoding TF dynamics. I will first describe LINuS, a light-inducible nuclear localization system developed by us, then show how, by imposing various TF dynamics with blue light and reading out the response from a library of synthetic promoters built with well-studied and defined elements, we find that sustained and pulsatile activation are distinguishable provided the coupling between TF binding and transcription pre-initiation complex formation is inefficient. Additionally, we show that the efficiency of translation initiation affects the ability of the promoter to sense TF dynamics. Using the knowledge acquired, we built a synthetic circuit that allows us to obtain two gene expression programs (proteins A and B both highly expressed versus protein A highly expressed and protein B only very weakly expressed) depending solely on TF dynamics. Taken together, these results help elucidate how gene expression is regulated in mammalian cells and open up the possibility to build synthetic circuits that respond better to determined TF dynamics.

Cellular innovation by rational design and evolution - Prof Ahmad (Mo) Khalil (Boston University)

Dr. Khalil seeks to understand the design principles of living systems by creating and analyzing synthetic ones in the laboratory. His team has pioneered synthetic biology approaches to rationally construct and dissect the molecular circuits that control gene regulation in eukaryotes, work that has resulted in fundamental discoveries on transcription regulation and epigenetic memory and led to platforms for creating programmable cellular therapies. In addition, his team has developed powerful automation technologies, such as the eVOLVER, that enable researchers to perform laboratory evolution at unprecedented scale. His team is applying these technologies to recreate the evolutionary histories of biological systems in the laboratory and to harness the power of evolution to generate biomolecules with new and improved functions for a variety of applications.

Dr. Khalil’s research has been recognized by numerous awards, including the Presidential Early Career Award for Scientists and Engineers (PECASE), DoD Vannevar Bush Faculty Fellowship, NIH New Innovator Award, NSF CAREER Award, DARPA Young Faculty Award, Hartwell Foundation Biomedical Research Award, and election to the AIMBE College of Fellows. He has also received numerous awards for teaching excellence at both the Department and College levels. Khalil was an HHMI Postdoctoral Fellow with Dr. James Collins at Boston University. He obtained his Ph.D. with Dr. Angela Belcher at MIT, and his B.S. (Phi Beta Kappa) from Stanford University.

Recoding regulation - Synthetic Expansions of Plant Metabolism  - Dr Nicola Patron (Earlham Institute)

To survive in environments that they cannot simply walk away from, plants have evolved arsenals of novel chemical compounds and complex regulatory networks to fine-tune their metabolism and growth. In our lab, we aim to understand the genetic basis of these abilities and to develop technologies that enable us to rationally engineer them.

One focus of our work is to use computational design and rebuilding approaches to understand the intrinsic properties of plant regulatory sequences, examining how functional elements and their relative arrangements contribute to overall regulatory function. This enables us to build synthetic promoters of predictable strengths and to elucidate complex gene regulatory networks, providing insights into how plant phenotypes emerge from network functions and identifying genetic targets for engineering complex and quantitative crop traits.

A second focus is to discover, understand, and utilise bioactive metabolites. We use multiomics approaches to elucidate the genetic basis of bioactive molecules and to understand the evolution of novel chemodiversity. We then aim to produce molecules of interest to agriculture and medicine, utilizing our synthetic regulatory elements to build synthetic circuits that enable expression in photosynthetic chassis, which we optimise for bioproduction.

Biomining and Electromicrobial Production  - Prof Buz Barstow (Cornell University)

Creation of a new sustainable energy infrastructure means that the demand for metals is increasingly rapidly, but traditional mining technology won't be able to keep up with demand. Rare earth elements (REE) are essential ingredients in high field magnets for wind turbines and electric vehicles, solid state lighting and superconductors; nickel is essential for catalysts; cobalt for batteries; platinum group elements for electrical contacts and H2-producing catalysts; and magnesium could be essential for carbon mineralization. Demand for REE is projected to increase 7× between now and 2040; the demand for Mg could go up 6,000× by the end of the century. Traditional mining processes can be highly environmentally damaging, and traditional deposits of many metals won't be sufficient to meet the needs of the energy transition. 

Biomining could replace traditional mining with environmentally-friendly bioprocesses. My lab has used our Knockout Sudoku technology to characterize the genome of the mineral-dissolving microbe Gluconobacter oxydans and discover the genetic systems that enable it to mine rare earth elements. We have used this new knowledge to create a roadmap for engineering G. oxydans that has already improved biomining of REE by 73%.

Data-Driven Methods for Designing Biosensors and Identifying Genetic Targets for Biological Control in Non-Model Microbes  - Prof Enoch Yeung (UC Santa Barbara)

I present the development and experimental validation of two, novel data-driven methods for identifying critical genetic targets for synthetic biosensing and control applications. First, my laboratory has developed a data-driven, transcriptome-wide approach to rank perturbation-inducible genes from time-series RNA sequencing data for the discovery of analyte-responsive promoters. This provides a set of biomarkers that act as a proxy for the transcriptional state referred to as the cell state. We construct low-dimensional models of gene expression dynamics and rank genes by their ability to capture the perturbation-specific cell state using the method of observability analysis.

We show it is possible to extract 15 analyte-responsive promoters for a novel, previously untested organophosphate compound, from over 4000 genes, in the underutilized host organism Pseudomonas fluorescens SBW25. Furthermore, we enhance malathion reporting through the aggregation of the response of individual reporters with a synthetic consortium approach, and we exemplify the library’s ability to be useful outside the lab by detecting malathion in the environment.

Next, we use deep learning and dynamic mode decomposition to downselect and identify 15 genetic targets out of 5,564 genes in Pseudomonas putida KT2440 to modulate cell biomass in a soil simulant media. We use CRISPRi to repress expression of 15 endogenous, genomic targets and experimentally show that 90% of the predicted gene targets have the potential to control dynamic cell biomass.

Current biotechnology is typically based on sugar-based substrates, which production competes with food production and can further threaten biodiversity. As alternative, formate and methanol can be produced from CO₂ and renewable electricity, making them promising microbial feedstocks for sustainable bioproduction. However, we lack attractive biotechnological hosts that can convert these one-carbon feedstocks to products in an efficient way. Available, genetically accessible organisms can either not grow on these feedstocks, or they use inefficient metabolic pathways for one-carbon assimilation. Hence, in our research we are focusing on the engineering of efficient, 'synthetic' one-carbon assimilation pathways in genetically accessible hosts, such as Cupriavidus necator and Escherichia coli. In my talk I will highlight some of our recent work in this area. I will discuss how we can utilize modular engineering, growth-coupled selection, rational enigneering and adaptive laboratory evolution to realize new synthetic pathways.

Artificial nucleic acid backbones for Synthetic Biology  - Prof Tom Brown (Oxford University)

Chemical ligation of DNA strands can be used to produce artificial DNA backbones which have potential for use in therapeutics and synthetic biology.1-6 I will discuss recent developments from our laboratory7, 8 and present data on the effects of various DNA backbone analogues on duplex stability. In addition, I will discuss results from next-generation sequencing analysis of modified DNA templates that can be read through and copied accurately by DNA polymerases. These results provide insights into the design of biocompatible backbone mimics that could be used in the assembly of large modified DNA constructs and used in various applications9 including Crispr gene editing.10 Preliminary work on the use of artificial DNA backbones in therapeutic oligonucleotides will also be presented.

Interrogating and programming microbiomes with next-generation synthetic biology

Microbes that live in soil are responsible for a variety of key decomposition and remediation activities in the biosphere. Microbes that colonize the gastrointestinal tract play important roles in host metabolism, immunity, and homeostasis. Better tools to study and alter these microbiomes are essential for unlocking their vast potential to improve human health and the environment. This talk will describe our recent efforts to develop next-generation tools to study and modify microbial communities. Specifically, I will discuss new platforms for automated microbial culturomics, techniques to genetically engineer complex microbial consortia and methods for biocontainment. These emerging capabilities provide a foundation to accelerate the development of microbiome-based products and therapies.