Call For Ideas

Winning Statements

• Fermentation of Gaseous Carbon Feedstocks
  Anonymous

  Fermentation of Gaseous Carbon Feedstocks

  However, if the goal is meaningful displacement of petroleum, the continued focus on crop-based sugar may be misdirecteFermentation of gaseous carbon feedstocks could be the catalyst to sustainability that has so far eluded sugar-based fermentation. In particular, the environmental thesis of microbial synthetic biology has revolved largely around the up-conversion of carbon-sequestering plant starch. d. Its vastly lower abundance vs. petroleum, inherent conflict with the food supply, and questionable benefit (once petroleum-derived fertilizers and total energy use are considered) are among the well-documented critiques. An alternative that, in fact, exists on the scale of fossil carbon and directly mitigates atmospheric carbon is that of CO2, CO, and CH4 emissions themselves. Capture and upgrading of otherwise released emissions from anaerobic digestion (e.g., municipal solid waste) and industrial production (e.g., steel, cement, bioethanol) would decarbonize over 20% of the US carbon footprint. As important, the ability to utilize gaseous feedstocks would provide a long-sought, and easily scalable, pathway for mobilizing the 1–1.5B tons of potentially available lignocellulosic biomass. Despite the prospects of displacing almost 50% of US petroleum consumption, lignocellulose (e.g., energy crops, forestry and agricultural residues) remains largely untapped due to deconstruction challenges. Pretreatment and hydrolysis into monosaccharides are still sufficiently complex such that agricultural sugar continues to be the more competitive option. In contrast, gasification of biomass into syngas (CO2/CO/H2) is a mature technology that could, for example, be added to existing thermal plants at a reasonable cost of $400–600/kW. However, other than the biotech LanzaTech (syngas-to-ethanol), few others have invested in tools and methods for commercial-scale gas fermentation. Moreover, their technology remains proprietary. Therefore, greater — and publicly available — resources for engineering autotrophic and methanotrophic organisms (e.g., Clostridium, Methylocystis), as well as efforts to advance continuous gas bioreactor systems, are critical to enable the next generation of highly carbon negative chemicals.

• Selection Phase Fermentation Strategy
  Piyush Nanda

  Selection Phase Fermentation Strategy

  “The dream of every cell is to become two cells”
  -François Jacob

  Problem

  Mitigating climate change requires a rapid switch to biomanufacturing. Scalable biomanufacturing poses a dual challenge: i) effectively driving metabolic fluxes towards the formation of the product of interest (a metabolic engineering challenge) and ii) maintaining the engineered strains in their optimal bioproduction state during fermentation (a bioprocessing challenge). Natural selection complicates an engineer’s bioproduction objectives by favoring strains that grow faster throughout fermentation. Such growth dynamics lead to the enrichment of non-producing strains-fast dividing cheaters in the bioreactor, especially in a continuous reactor system (Rugbjerg et al. 2019, Nat. Biotech.). Addressing this challenge requires a new, innovative strategy.

  Several strategies are proposed, including deep DNA sequencing for actively monitoring the rise of such mutants. Moreover, recent studies have proposed coaxing strains towards bioproduction by driving an essential gene’s expression proportionately to the product generated – a strategy that will penalize non-producing strains (Rugbjerg et al. 2020). Despite years of research, we have yet to develop an easier-to-implement but scalable strategy. I propose a simple approach to counter-select fast-growing mutants by transiently changing from a ‘production mode’ to a ‘selection mode’.

  A risk-benefit tradeoff shapes growth rates. A cell can either allocate resources to reproduction-filling its cytosol with ribosomes and metabolic machinery to grow fast, or allocate a part of the resources towards accumulating proteins it might need during periods of starvation (Basan et al. 2020, Nature; Wu et al. 2022, PNAS). Studying the behavior of microbes in fluctuating environments has established tradeoffs between growth during feast and preparation for famine. Naturally occurring wild isolates of model yeast, Saccharomyces cerevisiae, show significant variations in the growth rate ( Chiara et al, 2022, Nat. Eco. and Evol.). Different strains were likely subjected to varying forms of environmental fluctuations. The presence of abundant glucose, like in a bioreactor, preferentially selects for populations with high growth rates. Meanwhile, periods of feasts followed by prolonged famines select strains that grow slowly but can survive well during famine.

  Solution

  I propose a new kind of fermentation strategy: Fluctuostat. This involves switching between a production phase (fermentation) and a selection phase (artificial famine induced by stressors). Fast-growing mutants will rise during the fermentation phase but will face a survival challenge during the selection phase, where slower-growing cell factories will get an evolutionary advantage. Of course, the selection phase won’t generate any bioproducts. Therefore, it is essential to estimate the duration of the selection phase so that effective productivity is maximized.

  Current studies (Rugbjerg et al. 2019, Nat. Biotech.; Figure 1) reveal a pressing issue: within just 60-70 generations of growth from a single colony to a 200 m3 bioreactor, a significant fraction, i.e. 40% of the population, is overtaken by non-producing strains-a substantial productivity cost to the industry. Determining which stressors will be best suited for the existing biomanufacturing infrastructure is crucial. This strategy presents an unexplored approach to improving productivity by subjecting a population of microbial cell factories to a fluctuating environment.

• Modular Bioreactor Systems
  Kweku Opoku-Agyemang

  Modular Bioreactor Systems

  Concept
  Modular Bioreactor Systems for Scalable Synthetic Biology.

  The Problem
  Current fermentation systems are often designed for large-scale, single-product processes, which limits flexibility and adaptability. This one-size-fits-all approach hinders the scalability of synthetic biology applications that require customized conditions for different organisms and products.

  A Proposed Solution
  Develop a modular bioreactor system that can be easily reconfigured for different synthetic biology applications. Each module would be designed to cater to the specific needs of different organisms, allowing for optimal growth conditions and product yields. The system would include:

  Interchangeable Vessels: Different vessel designs that can be swapped out depending on the organism and product, ranging from micro-bioreactors for small-scale experiments to larger vessels for commercial production.
  Adaptive Control Systems: Smart control systems that can adjust parameters such as temperature, pH, and nutrient flow in real-time based on feedback from sensors monitoring the organisms’ growth and product formation.
  Scalable Architecture: A design that allows for the addition of more modules to increase production without the need for entirely new systems, thus reducing costs and increasing efficiency.
  Integrated Data Analysis: Software that can analyze data from the bioreactors to optimize conditions and predict outcomes, leading to faster iteration and improvement of synbio processes.

  This modular approach would allow manufacturers to scale their synthetic biology solutions more effectively, adapting quickly to new organisms and products without significant downtime or capital expenditure. It would also facilitate a more rapid transition from R&D to production, accelerating the path to market for new synbio innovations.

  Potential for Lifting All Boats:
  By providing a flexible and adaptable platform, this idea could serve a wide range of synthetic biology applications, from pharmaceuticals to biofuels, making it easier for the entire field to scale and meet the growing demand for sustainable and eco-friendly products.

  This concept aligns with Astera’s objectives by offering a tangible innovation that could be further explored in workshops and residencies, potentially attracting interest and investment from various stakeholders in the synthetic biology community.

• Integrating Microcarriers
  Kenza Samlali

  Integrating Microcarriers

  Scaling mammalian cell culture for cell therapies is challenging for many reasons, including the cells’ preference for the physiological conditions of their natural environment, leading to low throughput and high costs. To address this, microcarriers—100-300 um beads—are becoming a popular solution to increase production capacity by enhancing the surface area of bioreactors. Similarly, in large scale fermentation of micro-organisms, solid state fermentation is an often used method. However, transitioning from screening into scaling still remains challenging as current high throughput screening methods are not capable of screening strains or cell lines for their ability to thrive in such environments. A proposed solution is to integrate microcarriers into screening steps using droplet microfluidics.

  TL;DR – Use microcarriers in screening steps early on, offering a means to increase yield and reduce strain failure during scaling from screening to large-scale fermentation.

• Open-Source Library of Cell Lines
  Eye's Hand

  Open-Source Library of Cell Lines

  My general idea is to create an open-source library of cell lines with protein expression or other revolutionizing capabilities. The library could be a relatively modest collection of a specific cell type e.g. Chinese Hamster Ovary (CHO) cell lines, which are commonly used to produce therapeutic antibodies in the oncology / immunology space. In the case of CHO cell production, one of the industry bottlenecks is the use of antibiotics at large-scale. The over-use of antibiotics across the fields of human health, agriculture and livestock is of grave concern, with the potential to generate antibiotic-resistant pathogens. Therefore, the use of antibiotics in large-scale bioreactors is limited, if not prohibited. A library of metabolic knock-out (auxotrophic) CHO cell lines would allow selective growth of protein-producing cells by simple addition of the necessary metabolite to the growth media, with the advantage over today’s technology of complete elimination of the use of antibiotics in the process.

  On the other hand, the library of cell lines could be more extensive to include other mammalian cell types e.g. Human Embryonic Kidney (HEK) cells, which are often used for vaccine production among other industry uses. The library could go even further to include various metabolomic knock-out strains of Saccharomyces cerevisiae (baker’s yeast), which are much more amendable to genetic manipulation than the previously mentioned mammalian cell lines. Baker’s yeast could theoretically be engineered to metabolize environmental hazards (such as oil spills by utilizing petroleum as a carbon source) or produce an industrial product that is otherwise too costly or complex to make. The library could take one step further by incorporating various strains of (non-pathogenic) E. coli or other bacteria that are commonly used for protein production, with much quicker turnaround times due to their faster growth.

  Overall, I would love to see someone take this idea and run with it. Currently, the vast majority of CHO and other cell lines are only available through cost-prohibitive licensing / royalty agreements, such that only large corporations have access to the best protein-producing cells. Even then, production of the protein of interest is often linked to the use of antibiotics in the growth media, creating scale-up challenges as well as contributing to the environmental crisis that the global community is beginning to realize. Creation of an open-source library of metabolomic knock-out CHO cell lines would eliminate one bottleneck in the scale-up of therapeutic protein production that is currently used to treat patients who suffer from cancer and various immunological diseases.