Core-Shell Droplet-Based Microfluidic Screening System for Filamentous Fungi

A comprehensive understanding on droplets

Droplets are ubiquitous and necessary in natural phenomena, daily life, and industrial processes, which play a crucial role in many fields. So, the manipulation of droplets has been extensively investigated for meeting widespread applications, consequently, a great deal of progresses have been achieved across multiple disciplines ranging from chemistry to physics, material, biological, and energy science. For example, microdroplets have been utilized as reactors, colorimetric or electrochemical sensors, drug-delivery carriers, and energy harvesters. Moreover, droplet manipulation is the basis in both fundamental researches and practical applications, especially the combination of smart materials and external fields for achieving multifunctional applications of droplets. In view of this background, this review initiates discussion of the manipulation strategies of droplets including Laplace pressure, wettability gradients, electric field, magnetic force, light and temperature. Thereafter, based on their manipulation strategies, this review mainly summarizes the applications of droplets in the fields of robot, green energy, sensors, biomedical treatments, microreactors and chemical reactions. Application related basic concepts, theories, principles and progresses also have been introduced. Finally, this review addresses the challenges of manipulation and applications of droplets and provides the potential directions for their future development. By presenting these results, we aim to provide a comprehensive overview of water droplets and establish a unified framework that guides the development of droplets in various fields.

Characterization of Aspergillus oryzae mutant and its application in heterologous lipase expression

The Aspergillus oryzae expression system has been developed into a chassis for the production of heterologous lipases, attributed to its strong capabilities in protein production and secretion, robust post-translational modifications, and favourable safety profile. However, the system's relatively low expression levels remain a challenge, hindering its ability to meet the increasing demands of large-scale production. Strain C19, screened by high-throughput methods combining droplet microfluidics and flow cytometry, was demonstrated to be a potential chassis cell based on fermentation kinetic analysis and transcriptome sequencing. By leveraging the endogenous α-amylase's expression elements and integration sites, a combination of random and site-directed integration strategies was employed to enhance the expression of heterologous lipases in strain C19. As a result, lipase production in shake-flask fermentation reached a titer of 113.6 U/L. The study further demonstrated that the different α-amylase gene loci could serve as effective integration sites for the multi-copy expression of heterologous proteins because the lipase activity of the 3-amylase site integrated strain C19#1-ABC was 3.3 times higher than that of C19#1. Furthermore, fermentation results in a 5-L bioreactor indicated that optimization of fermentation processes and facilities had the potential to further increase heterologous protein expression levels. These findings offered valuable insights into the advancement of A. oryzae expression systems and the potential for scaling engineered strains for industrial applications.

Advanced droplet microfluidic platform for high-throughput screening of industrial fungi

Industrial fungi are pivotal candidates for the production of a diverse array of bioproducts. To enhance their productivity, these strains are frequently subjected to genetic modifications. Following transformation, the selection of optimal production strains is critical; however, traditional screening methods often suffer from limitations in throughput and sensitivity. This article explores the transformative potential of Droplet Microfluidic Technology (DMFS) for high-throughput screening of industrial fungi. DMFS enables real-time monitoring and precise single-cell analysis by encapsulating individual fungal spores or cells within droplets, ranging from picoliters to nanoliters, functioning as isolated microreactors. This technology effectively addresses the challenges posed by conventional methods, such as agar plate assays and fluorescence-activated cell sorting. Key advancements discussed include microfluidic chip fabrication, droplet generation and regulation techniques, and multimodal signal detection methods-encompassing fluorescence, Raman spectroscopy, and mass spectrometry. Notably, strategies to mitigate droplet breakage in filamentous fungi, including physical constraints, bionic core-shell hydrogels, and genetic engineering approaches, are analyzed to prolong stable culture times. Future developments will likely emphasize interdisciplinary applications, including automation driven by artificial intelligence and label-free detection methods. We anticipate that this review will catalyze further research into high-quality industrial fungi, thereby promoting sustainable biomanufacturing through enhanced throughput, cost-effectiveness, and scalability.

Droplet Microfluidics for High-Throughput Screening and Directed Evolution of Biomolecules

Directed evolution is a powerful technique for creating biomolecules such as proteins and nucleic acids with tailor-made properties for therapeutic and industrial applications by mimicking the natural evolution processes in the laboratory. Droplet microfluidics improved classical directed evolution by enabling time-consuming and laborious steps in this iterative process to be performed within monodispersed droplets in a highly controlled and automated manner. Droplet microfluidic chips can generate, manipulate, and sort individual droplets at kilohertz rates in a user-defined microchannel geometry, allowing new strategies for high-throughput screening and evolution of biomolecules. In this review, we discuss directed evolution studies in which droplet-based microfluidic systems were used to screen and improve the functional properties of biomolecules. We provide a systematic overview of basic on-chip fluidic operations, including reagent mixing by merging continuous fluid streams and droplet pairs, reagent addition by picoinjection, droplet generation, droplet incubation in delay lines, chambers and hydrodynamic traps, and droplet sorting techniques. Various microfluidic strategies for directed evolution using single and multiple emulsions and biomimetic materials (giant lipid vesicles, microgels, and microcapsules) are highlighted. Completely cell-free microfluidic-assisted in vitro compartmentalization methods that eliminate the need to clone DNA into cells after each round of mutagenesis are also presented.

Integrating microfluidics and synthetic biology: advancements and diverse applications across organisms

Synthetic biology is the design and modification of biological systems for specific functions, integrating several disciplines like engineering, genetics, and computer science. The field of synthetic biology is to understand biological processes within host organisms through the manipulation and regulation of their genetic pathways and the addition of biocontrol circuits to enhance their production capabilities. This pursuit serves to address global challenges spanning diverse domains that are difficult to tackle through conventional routes of production. Despite its impact, achieving precise, dynamic, and high-throughput manipulation of biological processes is still challenging. Microfluidics offers a solution to those challenges, enabling controlled fluid handling at the microscale, offering lower reagent consumption, faster analysis of biochemical reactions, automation, and high throughput screening. In this review, we diverge from conventional focus on automating the synthetic biology design-build-test-learn cycle, and instead, focus on microfluidic platforms and their role in advancing synthetic biology through its integration with host organisms - bacterial cells, yeast, fungi, animal cells - and cell-free systems. The review illustrates how microfluidic devices have been instrumental in understanding biological systems by showcasing microfluidics as an essential tool to create synthetic genetic circuits, pathways, and organisms within controlled environments. In conclusion, we show how microfluidics expedite synthetic biology applications across diverse domains including but not limited to personalized medicine, bioenergy, and agriculture.

High-throughput droplet microfluidics screening and genome sequencing analysis for improved amylase-producing Aspergillus oryzae

BACKGROUND

The exceptional protein secretion capacity, intricate post-translational modification processes, and inherent safety features of A. oryzae make it a promising expression system. However, heterologous protein expression levels of existing A. oryzae species cannot meet the requirement for industrial-scale production. Therefore, establishing an efficient screening technology is significant for the development of the A. oryzae expression system.

RESULTS

In this work, a high-throughput screening method suitable for A. oryzae has been established by combining the microfluidic system and flow cytometry. Its screening efficiency can reach 350 droplets per minute. The diameter of the microdroplet was enlarged to 290 µm to adapt to the polar growth of A. oryzae hyphae. Through enrichment and screening from approximately 450,000 droplets within 2 weeks, a high-producing strain with α-amylase increased by 6.6 times was successfully obtained. Furthermore, 29 mutated genes were identified by genome resequencing of high-yield strains, with 15 genes subjected to editing and validation. Two genes may individually influence α-amylase expression in A. oryzae by affecting membrane-associated multicellular processes and regulating the transcription of related genes.

CONCLUSIONS

The developed high-throughput screening strategy provides a reference for other filamentous fungi and Streptomyces. Besides, the strains with different excellent characteristics obtained by efficient screening can also provide materials for the analysis of genetic and regulatory mechanisms in the A. oryzae expression system.