Identification and monitoring of cell heterogeneity from plasmid recombination during limonene production.

Detecting alterations in plasmid structures is often performed using conventional molecular biology. However, these methods are laborious and time-consuming for studying the conditions inducing these mutations, which prevent real-time access to cell heterogeneity during bioproduction. In this work, we propose combining both flow cytometry and fluorescence-activated cell sorting, integrated with mechanistic modelling to study conditions that lead to plasmid recombination using a limonene-producing microbial system as a case study.

Optimizing HMG-CoA Synthase Expression for Enhanced Limonene Production in through Temporal Transcription Modulation Using Optogenetics.

Overexpression of a single enzyme in a multigene heterologous pathway may be out of balance with the other enzymes in the pathway, leading to accumulated toxic intermediates, imbalanced carbon flux, reduced productivity of the pathway, or an inhibited growth phenotype. Therefore, optimal, balanced, and synchronized expression levels of enzymes in a particular metabolic pathway is critical to maximize production of desired compounds while maintaining cell fitness in a growing culture. Furthermore, the optimal intracellular concentration of an enzyme is determined by the expression strength, specific timing/duration, and degradation rate of the enzyme.

Graphene oxide aptasensor droplet assay for detection of metabolites secreted by single cells applied to synthetic biology.

Synthetic biology harnesses the power of natural microbes by re-engineering metabolic pathways to manufacture desired compounds. Droplet technology has emerged as a high-throughput tool to screen single cells for synthetic biology, while the challenges in sensitive flexible single-cell secretion assay for bioproduction of high-value chemicals remained. Here, a novel droplet modifiable graphene oxide (GO) aptasensor was developed, enabling sensitive flexible detection of different target compounds secreted from single cells.

A biological camera that captures and stores images directly into DNA.

The increasing integration between biological and digital interfaces has led to heightened interest in utilizing biological materials to store digital data, with the most promising one involving the storage of data within defined sequences of DNA that are created by de novo DNA synthesis. However, there is a lack of methods that can obviate the need for de novo DNA synthesis, which tends to be costly and inefficient. Here, in this work, we detail a method of capturing 2-dimensional light patterns into DNA, by utilizing optogenetic circuits to record light exposure into DNA, encoding spatial locations with barcoding, and retrieving stored images via high-throughput next-generation sequencing.

Modelling, Characterization of Data-Dependent and Process-Dependent Errors in DNA Data Storage.

Using DNA as the medium to store information has recently been recognized as a promising solution for long-term data storage. While several system prototypes have been demonstrated, the error characteristics in DNA data storage are discussed with limited content. Due to the data and process variations from experiment to experiment, the error variation and its effect on data recovery remain to be uncovered.

Designing a Model-Driven Approach Towards Rational Experimental Design in Bioprocess Optimization.

To enable a more rational optimization approach to drive the transition from lab-scale to large industrial bioprocesses, a systematic framework coupling both experimental design and integrated modeling was established to guide the workflow executed from small flask scale to bioreactor scale. The integrated model relies on the coupling of biotic cell factory kinetics to the abiotic bioreactor hydrodynamics to offer a rational means for an in-depth understanding of two-way spatiotemporal interactions between cell behaviors and environmental variations. This model could serve as a promising tool to inform experimental work with reduced efforts via full-factorial in silico predictions.

BMSS2: A Unified Database-Driven Modeling Tool for Systematic Biomodel Selection.

Modeling in synthetic biology constitutes a powerful means in our continuous search for improved performance with a rational Design-Build-Test-Learn approach. Particularly, kinetic models unravel system dynamics and enable system analysis for guiding experimental design. However, a systematic yet modular pipeline that allows one to identify the appropriate model and guide the experimental designs while tracing the entire model development and analysis is still lacking.

Engineered Nucleotide Chemicapacitive Microsensor Array Augmented with Physics-Guided Machine Learning for High-Throughput Screening of Cannabidiol.

The recent legalization of cannabidiol (CBD) to treat neurological conditions such as epilepsy has sparked rising interest across global pharmaceuticals and synthetic biology industries to engineer microbes for sustainable synthetic production of medicinal CBD. Since the process involves screening large amounts of samples, the main challenge is often associated with the conventional screening platform that is time consuming, and laborious with high operating costs. Here, a portable, high-throughput Aptamer-based BioSenSing System (ABS ) is introduced for label-free, low-cost, fully automated, and highly accurate CBD concentrations' classification in a complex biological environment.

Toward Multiplexed Optogenetic Circuits.

Owing to its ubiquity and easy availability in nature, light has been widely employed to control complex cellular behaviors. Light-sensitive proteins are the foundation to such diverse and multilevel adaptive regulations in a large range of organisms. Due to their remarkable properties and potential applications in engineered systems, exploration and engineering of natural light-sensitive proteins have significantly contributed to expand optogenetic toolboxes with tailor-made performances in synthetic genetic circuits.

Thermogenetics: Applications come of age.

Temperature is a ubiquitous physical cue that is non-invasive, penetrative and easy to apply. In the growing field of thermogenetics, through beneficial repurposing of natural thermosensing mechanisms, synthetic biology is bringing new opportunities to design and build robust temperature-sensitive (TS) sensors which forms a thermogenetic toolbox of well characterised biological parts. Recent advancements in technological platforms available have expedited the discovery of novel or de novo thermosensors which are increasingly deployed in many practical temperature-dependent biomedical, industrial and biosafety applications.

Future trends in synthetic biology in Asia.

Synthetic biology research and technology translation has garnered increasing interest from the governments and private investors in Asia, where the technology has great potential in driving a sustainable bio-based economy. This Perspective reviews the latest developments in the key enabling technologies of synthetic biology and its application in bio-manufacturing, medicine, food and agriculture in Asia. Asia-centric strengths in synthetic biology to grow the bio-based economy, such as advances in genome editing and the presence of biofoundries combined with the availability of natural resources and vast markets, are also highlighted.

Novel Modalities in DNA Data Storage.

The field of storing information in DNA has expanded exponentially. Most common modalities involve encoding information from bits into synthesized nucleotides, storage in liquid or dry media, and decoding via sequencing. However, limitations to this paradigm include the cost of DNA synthesis and sequencing, along with low throughput.

A model-driven approach towards rational microbial bioprocess optimization.

Due to sustainability concerns, bio-based production capitalizing on microbes as cell factories is in demand to synthesize valuable products. Nevertheless, the nonhomogenous variations of the extracellular environment in bioprocesses often challenge the biomass growth and the bioproduction yield. To enable a more rational bioprocess optimization, we have established a model-driven approach that systematically integrates experiments with modeling, executed from flask to bioreactor scale, and using ferulic acid to vanillin bioconversion as a case study.

Capturing Multicellular System Designs Using Synthetic Biology Open Language (SBOL).

Synthetic biology aims to develop novel biological systems and increase their reproducibility using engineering principles such as standardization and modularization. It is important that these systems can be represented and shared in a standard way to ensure they can be easily understood, reproduced, and utilized by other researchers. The Synthetic Biology Open Language (SBOL) is a data standard for sharing biological designs and information about their implementation and characterization.

Blue Light-Directed Cell Migration, Aggregation, and Patterning.

Bacterial motility is related to many cellular activities, such as cell migration, aggregation, and biofilm formations. The ability to control motility and direct the bacteria to certain location could be used to guide the bacteria in applications such as seeking for and killing pathogen, forming various population-level patterns, and delivering of drugs and vaccines. Currently, bacteria motility is mainly controlled by chemotaxis (prescribed chemical stimuli), which needs physical contact with the chemical inducer.

High capacity DNA data storage with variable-length Oligonucleotides using repeat accumulate code and hybrid mapping.

Background: With the inherent high density and durable preservation, DNA has been recently recognized as a distinguished medium to store enormous data over millennia. To overcome the limitations existing in a recently reported high-capacity DNA data storage while achieving a competitive information capacity, we are inspired to explore a new coding system that facilitates the practical implementation of DNA data storage with high capacity.

Result: In this work, we devised and implemented a DNA data storage scheme with variable-length oligonucleotides (oligos), where a hybrid DNA mapping scheme that converts digital data to DNA records is introduced.

Oligo Design with Single Primer Binding Site for High Capacity DNA-Based Data Storage.

DNA has become an attractive medium for long-term data archiving due to its extremely high storage density and longevity. Short single-stranded DNAs, called oligonucleotides (oligos), have been designed and synthesized to store digital data. Previous works designed the oligos with a pair of primer binding sites (PBSs) (each with a length of around 200) attached at the two ends of each basic readable data block.

Author Correction: Building a global alliance of biofoundries.

The original version of this Comment contained errors in the legend of Figure 2, in which the locations of the fifteenth and sixteenth GBA members were incorrectly given as '(15) Australian Genome Foundry, Macquarie University; (16) Australian Foundry for Advanced Biomanufacturing, University of Queensland.'. The correct version replaces this with '(15) Australian Foundry for Advanced Biomanufacturing (AusFAB), University of Queensland and (16) Australian Genome Foundry, Macquarie University'.

An Automated Biomodel Selection System (BMSS) for Gene Circuit Designs.

Constructing a complex functional gene circuit composed of different modular biological parts to achieve the desired performance remains challenging without a proper understanding of how the individual module behaves. To address this, mathematical models serve as an important tool toward better interpretation by quantifying the performance of the overall gene circuit, providing insights, and guiding the experimental designs. As different gene circuits might require exclusively different mathematical representations in the form of ordinary differential equations to capture their transient dynamic behaviors, a recurring challenge in model development is the selection of the appropriate model.

Programming the Dynamic Control of Bacterial Gene Expression with a Chimeric Ligand- and Light-Based Promoter System.

To program cells in a dynamic manner, synthetic biologists require precise control over the threshold levels and timing of gene expression. However, in practice, modulating gene expression is widely carried out using prototypical ligand-inducible promoters, which have limited tunability and spatiotemporal resolution. Here, we built two dual-input hybrid promoters, each retaining the function of the ligand-inducible promoter while being enhanced with a blue-light-switchable tuning knob.

Regulating exopolysaccharide gene wcaF allows control of Escherichia coli biofilm formation.

While biofilms are known to cause problems in many areas of human health and the industry, biofilms are important in a number of engineering applications including wastewater management, bioremediation, and bioproduction of valuable chemicals. However, excessive biofilm growth remains a key challenge in the use of biofilms in these applications. As certain amount of biofilm growth is required for efficient use of biofilms, the ability to control and maintain biofilms at desired thickness is vital.