1
|
Wippold JA, Chu M, Renberg R, Li Y, Adams B, Han A. XPORT ENTRAP: A droplet microfluidic platform for enhanced DNA transfer between microbial species. N Biotechnol 2024; 81:10-19. [PMID: 38408724 DOI: 10.1016/j.nbt.2024.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 02/20/2024] [Accepted: 02/20/2024] [Indexed: 02/28/2024]
Abstract
A significant hurdle for the widespread implementation and use of synthetic biology is the challenge of highly efficient introduction of DNA into microorganisms. This is especially a barrier for the utilization of non-model organisms and/or novel chassis species for a variety of applications, ranging from molecular biology to biotechnology and biomanufacturing applications. Common approaches to episomal and chromosomal gene editing, which employ techniques such as chemical competence and electroporation, are typically only amenable to a small subset of microbial species while leaving the vast majority of microorganisms in nature genetically inaccessible. To address this challenge, we have employed the previously described B. subtilis broad-host conjugation strain, XPORT, which was modularly designed for loading DNA cargo and conjugating such DNA into recalcitrant microbes. In this current work, we have leveraged and adapted the XPORT strain for use in a droplet microfluidic platform to enable increased efficiency of conjugation-based DNA transfer. The system named DNA ENTRAP (DNA ENhanced TRAnsfer Platform) utilizes cell-encapsulated water-in-oil emulsion droplets as pico-liter-volume bioreactors that allows controlled contacts between the donor and receiver cells within the emulsion bioreactor. This allowed enhanced XPORT-mediated genetic transfer over the current benchtop XPORT process, demonstrated using two different Bacillus subtilis strains (donor and receiver), as well as increased throughput (e.g., number of successfully conjugated cells) due to the automated assay steps inherent to microfluidic lab-on-a-chip systems. DNA ENTRAP paves the way for a streamlined automation of culturing and XPORT-mediated genetic transfer processes as well as future high-throughput cell engineering and screening applications.
Collapse
Affiliation(s)
- Jose A Wippold
- United States Combat Capabilities Development Command Army Research Laboratory - DEVCOM ARL, Adelphi, MD, USA
| | - Monica Chu
- United States Combat Capabilities Development Command Army Research Laboratory - DEVCOM ARL, Adelphi, MD, USA
| | - Rebecca Renberg
- United States Combat Capabilities Development Command Army Research Laboratory - DEVCOM ARL, Adelphi, MD, USA
| | - Yuwen Li
- Department of Electrical and Computer Engineering, USA
| | - Bryn Adams
- United States Combat Capabilities Development Command Army Research Laboratory - DEVCOM ARL, Adelphi, MD, USA.
| | - Arum Han
- Department of Electrical and Computer Engineering, USA; Department of Biomedical Engineering, USA; Department of Chemical Engineering, Texas A&M University, College Station, TX, USA.
| |
Collapse
|
2
|
Wells KCDH, Kharma N, Jaunky BB, Nie K, Aguiar-Tawil G, Berry D. BioCloneBot: A versatile, low-cost, and open-source automated liquid handler. HARDWAREX 2024; 18:e00516. [PMID: 38524156 PMCID: PMC10955647 DOI: 10.1016/j.ohx.2024.e00516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 02/03/2024] [Accepted: 02/25/2024] [Indexed: 03/26/2024]
Abstract
Liquid handler systems can provide significant benefits to researchers by automating laboratory work, however, their unaffordable price provides a steep barrier to entry. Therefore, we provide the BioCloneBot, a versatile, low-cost, and open-source automated liquid handler. This system can be easily built with 3D-printed parts and readily available commercial components. The BioCloneBot is highly adaptive to user needs and facilitates various liquid handling tasks in research and diagnostics. Its user-friendly interface and programmable nature make it suitable for a wide range of applications, from small-scale experiments to larger laboratory setups. By utilizing BioCloneBot, researchers and scientists can streamline their liquid handling processes without the financial constraints posed by traditional systems. In this paper, we detail the design, construction, and validation of BioCloneBot, showcasing its precise control, accuracy, and repeatability in various liquid handling tasks. The open-source nature of the system encourages collaboration and customization, enabling researchers to contribute and adapt the technology to specific experimental requirements.
Collapse
Affiliation(s)
- Ke’Koa CDH Wells
- Department of Electrical and Computer Engineering, Concordia University, Montréal, Québec, Canada
| | - Nawwaf Kharma
- Department of Electrical and Computer Engineering, Concordia University, Montréal, Québec, Canada
- Department of Biology, Concordia University, Montréal, Québec, Canada
| | - Brandon B. Jaunky
- Department of Biology, Concordia University, Montréal, Québec, Canada
| | - Kaiyu Nie
- Department of Electrical and Computer Engineering, Concordia University, Montréal, Québec, Canada
| | | | - Daniel Berry
- Department of Mechanical, Industrial and Aerospace Engineering, Concordia University, Montréal, Québec, Canada
| |
Collapse
|
3
|
Leal-Alves C, Deng Z, Kermeci N, Shih SCC. Integrating microfluidics and synthetic biology: advancements and diverse applications across organisms. LAB ON A CHIP 2024; 24:2834-2860. [PMID: 38712893 DOI: 10.1039/d3lc01090b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
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.
Collapse
Affiliation(s)
- Chiara Leal-Alves
- Centre for Applied Synthetic Biology, Concordia University, 7141 Sherbrooke St. W, Montréal, QC, H4B1R6 Canada.
- Department of Electrical and Computer Engineering, Concordia University, 1515 Ste-Catherine St. W, Montréal, QC, H3G1M8 Canada
| | - Zhiyang Deng
- Centre for Applied Synthetic Biology, Concordia University, 7141 Sherbrooke St. W, Montréal, QC, H4B1R6 Canada.
- Department of Electrical and Computer Engineering, Concordia University, 1515 Ste-Catherine St. W, Montréal, QC, H3G1M8 Canada
| | - Natalia Kermeci
- Centre for Applied Synthetic Biology, Concordia University, 7141 Sherbrooke St. W, Montréal, QC, H4B1R6 Canada.
- Department of Biology, Concordia University, 7141 Sherbrooke St. W, Montréal, QC, H4B1R6 Canada
| | - Steve C C Shih
- Centre for Applied Synthetic Biology, Concordia University, 7141 Sherbrooke St. W, Montréal, QC, H4B1R6 Canada.
- Department of Electrical and Computer Engineering, Concordia University, 1515 Ste-Catherine St. W, Montréal, QC, H3G1M8 Canada
- Department of Biology, Concordia University, 7141 Sherbrooke St. W, Montréal, QC, H4B1R6 Canada
| |
Collapse
|
4
|
Fasciano S, Wang S. Recent advances of droplet-based microfluidics for engineering artificial cells. SLAS Technol 2024; 29:100090. [PMID: 37245659 DOI: 10.1016/j.slast.2023.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 05/09/2023] [Accepted: 05/24/2023] [Indexed: 05/30/2023]
Abstract
Artificial cells, synthetic cells, or minimal cells are microengineered cell-like structures that mimic the biological functions of cells. Artificial cells are typically biological or polymeric membranes where biologically active components, including proteins, genes, and enzymes, are encapsulated. The goal of engineering artificial cells is to build a living cell with the least amount of parts and complexity. Artificial cells hold great potential for several applications, including membrane protein interactions, gene expression, biomaterials, and drug development. It is critical to generate robust, stable artificial cells using high throughput, easy-to-control, and flexible techniques. Recently, droplet-based microfluidic techniques have shown great potential for the synthesis of vesicles and artificial cells. Here, we summarized the recent advances in droplet-based microfluidic techniques for the fabrication of vesicles and artificial cells. We first reviewed the different types of droplet-based microfluidic devices, including flow-focusing, T-junction, and coflowing. Next, we discussed the formation of multi-compartmental vesicles and artificial cells based on droplet-based microfluidics. The applications of artificial cells for studying gene expression dynamics, artificial cell-cell communications, and mechanobiology are highlighted and discussed. Finally, the current challenges and future outlook of droplet-based microfluidic methods for engineering artificial cells are discussed. This review will provide insights into scientific research in synthetic biology, microfluidic devices, membrane interactions, and mechanobiology.
Collapse
Affiliation(s)
- Samantha Fasciano
- Department of Cellular and Molecular Biology, University of New Haven, West Haven, CT, USA
| | - Shue Wang
- Department of Chemistry, Chemical and Biomedical Engineering, University of New Haven, West Haven, CT, USA.
| |
Collapse
|
5
|
Lehnert T, Gijs MAM. Microfluidic systems for infectious disease diagnostics. LAB ON A CHIP 2024; 24:1441-1493. [PMID: 38372324 DOI: 10.1039/d4lc00117f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Microorganisms, encompassing both uni- and multicellular entities, exhibit remarkable diversity as omnipresent life forms in nature. They play a pivotal role by supplying essential components for sustaining biological processes across diverse ecosystems, including higher host organisms. The complex interactions within the human gut microbiota are crucial for metabolic functions, immune responses, and biochemical signalling, particularly through the gut-brain axis. Viruses also play important roles in biological processes, for example by increasing genetic diversity through horizontal gene transfer when replicating inside living cells. On the other hand, infection of the human body by microbiological agents may lead to severe physiological disorders and diseases. Infectious diseases pose a significant burden on global healthcare systems, characterized by substantial variations in the epidemiological landscape. Fast spreading antibiotic resistance or uncontrolled outbreaks of communicable diseases are major challenges at present. Furthermore, delivering field-proven point-of-care diagnostic tools to the most severely affected populations in low-resource settings is particularly important and challenging. New paradigms and technological approaches enabling rapid and informed disease management need to be implemented. In this respect, infectious disease diagnostics taking advantage of microfluidic systems combined with integrated biosensor-based pathogen detection offers a host of innovative and promising solutions. In this review, we aim to outline recent activities and progress in the development of microfluidic diagnostic tools. Our literature research mainly covers the last 5 years. We will follow a classification scheme based on the human body systems primarily involved at the clinical level or on specific pathogen transmission modes. Important diseases, such as tuberculosis and malaria, will be addressed more extensively.
Collapse
Affiliation(s)
- Thomas Lehnert
- Laboratory of Microsystems, École Polytechnique Fédérale de Lausanne, Lausanne, CH-1015, Switzerland.
| | - Martin A M Gijs
- Laboratory of Microsystems, École Polytechnique Fédérale de Lausanne, Lausanne, CH-1015, Switzerland.
| |
Collapse
|
6
|
McIntyre D, Lashkaripour A, Arguijo D, Fordyce P, Densmore D. Versatility and stability optimization of flow-focusing droplet generators via quality metric-driven design automation. LAB ON A CHIP 2023; 23:4997-5008. [PMID: 37909215 PMCID: PMC10694034 DOI: 10.1039/d3lc00189j] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Droplet generation is a fundamental component of droplet microfluidics, compartmentalizing biological or chemical systems within a water-in-oil emulsion. As adoption of droplet microfluidics expands beyond expert labs or integrated devices, quality metrics are needed to contextualize the performance capabilities, improving the reproducibility and efficiency of operation. Here, we present two quality metrics for droplet generation: performance versatility, the operating range of a single device, and stability, the distance of a single operating point from a regime change. Both metrics were characterized in silico and validated experimentally using machine learning and rapid prototyping. These metrics were integrated into a design automation workflow, DAFD 2.0, which provides users with droplet generators of a desired performance that are versatile or flow stable. Versatile droplet generators with stable operating points accelerate the development of sophisticated devices by facilitating integration of other microfluidic components and improving the accuracy of design automation tools.
Collapse
Affiliation(s)
- David McIntyre
- Biomedical Engineering Department, Boston University, MA, USA.
- Biological Design Center, Boston University, Boston, MA, USA
| | - Ali Lashkaripour
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Diana Arguijo
- Biomedical Engineering Department, Boston University, MA, USA.
- Biological Design Center, Boston University, Boston, MA, USA
| | - Polly Fordyce
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
- Chan-Zuckerberg Biohub, San Francisco, CA, USA
| | - Douglas Densmore
- Biological Design Center, Boston University, Boston, MA, USA
- Electrical & Computer Engineering Department, Boston University, Boston, MA, USA
| |
Collapse
|
7
|
Isenmann M, Stoddart MJ, Schmelzeisen R, Gross C, Della Bella E, Rothweiler RM. Basic Principles of RNA Interference: Nucleic Acid Types and In Vitro Intracellular Delivery Methods. MICROMACHINES 2023; 14:1321. [PMID: 37512632 PMCID: PMC10383872 DOI: 10.3390/mi14071321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 06/23/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023]
Abstract
Since its discovery in 1989, RNA interference (RNAi) has become a widely used tool for the in vitro downregulation of specific gene expression in molecular biological research. This basically involves a complementary RNA that binds a target sequence to affect its transcription or translation process. Currently, various small RNAs, such as small interfering RNA (siRNA), micro RNA (miRNA), small hairpin RNA (shRNA), and PIWI interacting RNA (piRNA), are available for application on in vitro cell culture, to regulate the cells' gene expression by mimicking the endogenous RNAi-machinery. In addition, several biochemical, physical, and viral methods have been established to deliver these RNAs into the cell or nucleus. Since each RNA and each delivery method entail different off-target effects, limitations, and compatibilities, it is crucial to understand their basic mode of action. This review is intended to provide an overview of different nucleic acids and delivery methods for planning, interpreting, and troubleshooting of RNAi experiments.
Collapse
Affiliation(s)
- Marie Isenmann
- Department of Oral and Maxillofacial Surgery, Faculty of Medicine, University of Freiburg, Hugstetterstrasse 55, 79106 Freiburg, Germany
- AO Research Institute Davos, Clavadelerstrasse 8, 7270 Davos, Switzerland
| | - Martin James Stoddart
- Department of Oral and Maxillofacial Surgery, Faculty of Medicine, University of Freiburg, Hugstetterstrasse 55, 79106 Freiburg, Germany
- AO Research Institute Davos, Clavadelerstrasse 8, 7270 Davos, Switzerland
| | - Rainer Schmelzeisen
- Department of Oral and Maxillofacial Surgery, Faculty of Medicine, University of Freiburg, Hugstetterstrasse 55, 79106 Freiburg, Germany
| | - Christian Gross
- Department of Oral and Maxillofacial Surgery, Faculty of Medicine, University of Freiburg, Hugstetterstrasse 55, 79106 Freiburg, Germany
| | - Elena Della Bella
- AO Research Institute Davos, Clavadelerstrasse 8, 7270 Davos, Switzerland
| | - René Marcel Rothweiler
- Department of Oral and Maxillofacial Surgery, Faculty of Medicine, University of Freiburg, Hugstetterstrasse 55, 79106 Freiburg, Germany
- AO Research Institute Davos, Clavadelerstrasse 8, 7270 Davos, Switzerland
| |
Collapse
|
8
|
Campelo SN, Huang PH, Buie CR, Davalos RV. Recent Advancements in Electroporation Technologies: From Bench to Clinic. Annu Rev Biomed Eng 2023; 25:77-100. [PMID: 36854260 DOI: 10.1146/annurev-bioeng-110220-023800] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
Over the past decade, the increased adoption of electroporation-based technologies has led to an expansion of clinical research initiatives. Electroporation has been utilized in molecular biology for mammalian and bacterial transfection; for food sanitation; and in therapeutic settings to increase drug uptake, for gene therapy, and to eliminate cancerous tissues. We begin this article by discussing the biophysics required for understanding the concepts behind the cell permeation phenomenon that is electroporation. We then review nano- and microscale single-cell electroporation technologies before scaling up to emerging in vivo applications.
Collapse
Affiliation(s)
- Sabrina N Campelo
- Department of Biomedical Engineering and Mechanics, Virginia Tech-Wake Forest School of Biomedical Engineering and Sciences, Virginia Tech, Blacksburg, Virginia, USA;
| | - Po-Hsun Huang
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Cullen R Buie
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Rafael V Davalos
- Department of Biomedical Engineering and Mechanics, Virginia Tech-Wake Forest School of Biomedical Engineering and Sciences, Virginia Tech, Blacksburg, Virginia, USA;
| |
Collapse
|
9
|
Sun G, Qu L, Azi F, Liu Y, Li J, Lv X, Du G, Chen J, Chen CH, Liu L. Recent progress in high-throughput droplet screening and sorting for bioanalysis. Biosens Bioelectron 2023; 225:115107. [PMID: 36731396 DOI: 10.1016/j.bios.2023.115107] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 01/09/2023] [Accepted: 01/25/2023] [Indexed: 01/31/2023]
Abstract
Owing to its ability to isolate single cells and perform high-throughput sorting, droplet sorting has been widely applied in several research fields. Compared with flow cytometry, droplet allows the encapsulation of single cells for cell secretion or lysate analysis. With the rapid development of this technology in the past decade, various droplet sorting devices with high throughput and accuracy have been developed. A droplet sorter with the highest sorting throughput of 30,000 droplets per second was developed in 2015. Since then, increased attention has been paid to expanding the possibilities of droplet sorting technology and strengthening its advantages over flow cytometry. This review aimed to summarize the recent progress in droplet sorting technology from the perspectives of device design, detection signal, actuating force, and applications. Technical details for improving droplet sorting through various approaches are introduced and discussed. Finally, we discuss the current limitations of droplet sorting for single-cell studies along with the existing gap between the laboratory and industry and provide our insights for future development of droplet sorters.
Collapse
Affiliation(s)
- Guoyun Sun
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China; Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Lisha Qu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Fidelis Azi
- Department of Chemical Engineering, Guangdong Technion-Israel Institute of Technology GTIIT, Shantou, Guangdong, 515063, China
| | - Yanfeng Liu
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China; Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Jianghua Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Xueqin Lv
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China; Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Guocheng Du
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China; Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Jian Chen
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China; Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Chia-Hung Chen
- Department of Biomedical Engineering, College of Engineering, City University of Hong Kong, Hong Kong, China.
| | - Long Liu
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China; Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China.
| |
Collapse
|
10
|
Jiang Z, Shi H, Tang X, Qin J. Recent advances in droplet microfluidics for single-cell analysis. Trends Analyt Chem 2023. [DOI: 10.1016/j.trac.2023.116932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
|
11
|
Sun G, Wu Y, Huang Z, Liu Y, Li J, Du G, Lv X, Liu L. Directed evolution of diacetylchitobiose deacetylase via high-throughput droplet sorting with a novel, bacteria-based biosensor. Biosens Bioelectron 2023; 219:114818. [PMID: 36327560 DOI: 10.1016/j.bios.2022.114818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 10/02/2022] [Accepted: 10/12/2022] [Indexed: 11/19/2022]
Abstract
Numerous biological disciplines rely on high-throughput cell sorting. Flow cytometry, the current gold standard, is capable of ultrahigh-throughput cell sorting, but measurements are primarily limited to cell size and surface marker. Droplet sorting technology is gaining increasing attention with the ability to provide an individual environment for the analysis of single-cell secretion. Although various droplet detecting methods, such as fluorescence, absorbance, mass spectrum, imaging analysis, have been developed for droplet sorting, it remains challenging to establish high-throughput sorting methods for numerous analytes. We aim to develop a high-throughput sorting system based on the glucosamine (GlcN) measurement for the directed evolution of diacetylchitobiose deacetylase (Dac), the key enzyme for GlcN production. To overcome the limitation that no high-throughput sorting system existed for GlcN, we designed a novel bacteria-based biosensor capable of converting GlcN to a positively correlated fluorescence signal. Through characterization and optimization, it was possible to detect GlcN in droplets for high-throughput droplet sorting. We recovered the best Dac mutant S60I/R157T/F168S after sorting ∼0.2 million Dac mutants; its activity was 48.6 ± 1.5 U/mL, which was 1.8-times that of our previously discovered Dac mutant R157T (27.2 ± 1.8 U/mL). This result successfully demonstrated the combination of high-throughput droplet sorting technology and a bacteria-based biosensor, which could facilitate the industrial production of GlcN and serve as a model for similar droplet sorting applications.
Collapse
Affiliation(s)
- Guoyun Sun
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
| | - Yaokang Wu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
| | - Ziyang Huang
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
| | - Yanfeng Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
| | - Jianghua Li
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
| | - Guocheng Du
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
| | - Xueqin Lv
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
| | - Long Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China.
| |
Collapse
|
12
|
Flexible on-chip droplet generation, switching and splitting via controllable hydrodynamics. Anal Chim Acta 2022; 1229:340363. [PMID: 36156234 DOI: 10.1016/j.aca.2022.340363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 08/27/2022] [Accepted: 09/03/2022] [Indexed: 11/23/2022]
Abstract
Flexible droplet preparation and manipulation are significant for lots applications such as immunoreaction and monocellular culture. Herein, we present a novel method for effective on-chip droplet generation, splitting and switching via controllable hydrodynamics. The microchannel of the designed chip has 6 inlets and 3 three outlets. The water solution is injected from a specific inlet (inlet d), and the other 5 inlets are used to inject oil fluids. Under the shearing effect of immiscible oils, the water phase breaks into dispersed droplets first, and the generated droplets can be further split into daughter drops or switched into side outlets from the middle outlet. To investigate the hydrodynamic droplet manipulation behaviors, a two-dimensional simulation model based on phase-field method is established. Utilizing the computational model, we systematically analyze the influences of the flow rates of continuous and dispersed fluids and the manipulation modes on droplet generation, splitting and switching. The numerical results indicate that the droplets can be generated with controlled sizes. For instance, at Qd = 5 μL/min and Qc1,2 = 5 μL/min, the droplet diameter decreases from 89.2 μm to 49.2 μm as Qs1,2 gradually rises from 15 μL/min to 40 μL/min. Moreover, the prepared droplets can realize on-demand splitting and switching. When Qd, Qc1,2, and Qs1,2 are fixed at 5 μL/min, 5 μL/min and 25 μL/min, respectively, the generated droplet is split into different proportional daughter drops with the rising of Qs3 (or Qs4) at first, and finally it is switched into the side-outlets when Qs3 (or Qs4) is higher than 80 μL/min. Therefore, this proposed droplet manipulation approach will be promising for various applications, and the numerical simulations can provide useful guidelines on the design and operation of droplet-based microfluidic systems.
Collapse
|
13
|
Oliveira SMD, Densmore D. Hardware, Software, and Wetware Codesign Environment for Synthetic Biology. BIODESIGN RESEARCH 2022; 2022:9794510. [PMID: 37850136 PMCID: PMC10521664 DOI: 10.34133/2022/9794510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 08/10/2022] [Indexed: 10/19/2023] Open
Abstract
Synthetic biology is the process of forward engineering living systems. These systems can be used to produce biobased materials, agriculture, medicine, and energy. One approach to designing these systems is to employ techniques from the design of embedded electronics. These techniques include abstraction, standards, modularity, automated design, and formal semantic models of computation. Together, these elements form the foundation of "biodesign automation," where software, robotics, and microfluidic devices combine to create exciting biological systems of the future. This paper describes a "hardware, software, wetware" codesign vision where software tools can be made to act as "genetic compilers" that transform high-level specifications into engineered "genetic circuits" (wetware). This is followed by a process where automation equipment, well-defined experimental workflows, and microfluidic devices are explicitly designed to house, execute, and test these circuits (hardware). These systems can be used as either massively parallel experimental platforms or distributed bioremediation and biosensing devices. Next, scheduling and control algorithms (software) manage these systems' actual execution and data analysis tasks. A distinguishing feature of this approach is how all three of these aspects (hardware, software, and wetware) may be derived from the same basic specification in parallel and generated to fulfill specific cost, performance, and structural requirements.
Collapse
Affiliation(s)
- Samuel M. D. Oliveira
- Department of Electrical and Computer Engineering, Boston University, MA 02215, USA
- Biological Design Center, Boston University, MA 02215, USA
| | - Douglas Densmore
- Department of Electrical and Computer Engineering, Boston University, MA 02215, USA
- Biological Design Center, Boston University, MA 02215, USA
| |
Collapse
|
14
|
Sierra AMR, Arold ST, Grünberg R. Efficient multi-gene expression in cell-free droplet microreactors. PLoS One 2022; 17:e0260420. [PMID: 35312702 PMCID: PMC8936439 DOI: 10.1371/journal.pone.0260420] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Accepted: 02/28/2022] [Indexed: 11/19/2022] Open
Abstract
Cell-free transcription and translation systems promise to accelerate and simplify the engineering of proteins, biological circuits and metabolic pathways. Their encapsulation on microfluidic platforms can generate millions of cell-free reactions in picoliter volume droplets. However, current methods struggle to create DNA diversity between droplets while also reaching sufficient protein expression levels. In particular, efficient multi-gene expression has remained elusive. We here demonstrate that co-encapsulation of DNA-coated beads with a defined cell-free system allows high protein expression while also supporting genetic diversity between individual droplets. We optimize DNA loading on commercially available microbeads through direct binding as well as through the sequential coupling of up to three genes via a solid-phase Golden Gate assembly or BxB1 integrase-based recombineering. Encapsulation with an off-the-shelf microfluidics device allows for single or multiple protein expression from a single DNA-coated bead per 14 pL droplet. We envision that this approach will help to scale up and parallelize the rapid prototyping of more complex biological systems.
Collapse
Affiliation(s)
- Ana Maria Restrepo Sierra
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
- KAUST Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
- Bionanoscience Department/Applied Sciences, Technische Universiteit Delft, Delft, The Netherlands
| | - Stefan T. Arold
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
- KAUST Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
- Centre de Biologie Structurale (CBS)/CNRS/INSERM, Université Montpellier, Montpellier, France
| | - Raik Grünberg
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
- KAUST Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
- * E-mail:
| |
Collapse
|
15
|
Iwai K, Wehrs M, Garber M, Sustarich J, Washburn L, Costello Z, Kim PW, Ando D, Gaillard WR, Hillson NJ, Adams PD, Mukhopadhyay A, Garcia Martin H, Singh AK. Scalable and automated CRISPR-based strain engineering using droplet microfluidics. MICROSYSTEMS & NANOENGINEERING 2022; 8:31. [PMID: 35359611 PMCID: PMC8924257 DOI: 10.1038/s41378-022-00357-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 09/21/2021] [Accepted: 10/18/2021] [Indexed: 06/14/2023]
Abstract
We present a droplet-based microfluidic system that enables CRISPR-based gene editing and high-throughput screening on a chip. The microfluidic device contains a 10 × 10 element array, and each element contains sets of electrodes for two electric field-actuated operations: electrowetting for merging droplets to mix reagents and electroporation for transformation. This device can perform up to 100 genetic modification reactions in parallel, providing a scalable platform for generating the large number of engineered strains required for the combinatorial optimization of genetic pathways and predictable bioengineering. We demonstrate the system's capabilities through the CRISPR-based engineering of two test cases: (1) disruption of the function of the enzyme galactokinase (galK) in E. coli and (2) targeted engineering of the glutamine synthetase gene (glnA) and the blue-pigment synthetase gene (bpsA) to improve indigoidine production in E. coli.
Collapse
Affiliation(s)
- Kosuke Iwai
- Technology Division, DOE Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Biotechnology and Bioengineering Department, Sandia National Laboratories, Livermore, CA 94550 USA
| | - Maren Wehrs
- Biofuels and Bioproducts Division, DOE Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Megan Garber
- Biofuels and Bioproducts Division, DOE Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Jess Sustarich
- Technology Division, DOE Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Biotechnology and Bioengineering Department, Sandia National Laboratories, Livermore, CA 94550 USA
| | - Lauren Washburn
- Technology Division, DOE Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Biotechnology and Bioengineering Department, Sandia National Laboratories, Livermore, CA 94550 USA
| | - Zachary Costello
- Biofuels and Bioproducts Division, DOE Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Peter W. Kim
- Technology Division, DOE Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Biotechnology and Bioengineering Department, Sandia National Laboratories, Livermore, CA 94550 USA
| | - David Ando
- Biofuels and Bioproducts Division, DOE Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - William R. Gaillard
- Technology Division, DOE Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Biotechnology and Bioengineering Department, Sandia National Laboratories, Livermore, CA 94550 USA
| | - Nathan J. Hillson
- Technology Division, DOE Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Paul D. Adams
- Technology Division, DOE Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
- Department of Bioengineering, University of California, Berkeley, CA 94720 USA
| | - Aindrila Mukhopadhyay
- Biofuels and Bioproducts Division, DOE Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Hector Garcia Martin
- Biofuels and Bioproducts Division, DOE Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
- BCAM, Basque Center for Applied Mathematics, Bilbao, 48009 Spain
| | - Anup K. Singh
- Technology Division, DOE Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Biotechnology and Bioengineering Department, Sandia National Laboratories, Livermore, CA 94550 USA
| |
Collapse
|
16
|
Lin H, Liu Y, Yang C, Zhao G, Song J, Zhang T, Huang X. Microfluidic artificial photosynthetic system for continuous NADH regeneration and l-glutamate synthesis. Catal Sci Technol 2022. [DOI: 10.1039/d2cy00466f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Artificial photosynthesis coenzyme regeneration and photoenzymatic synthesis of l-glutamate by glutamate dehydrogenase.
Collapse
Affiliation(s)
- Huichao Lin
- State Key Laboratory of Biobased Material and Green Papermaking, Department of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250300, China
| | - Yang Liu
- State Key Laboratory of Biobased Material and Green Papermaking, Department of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250300, China
| | - Chonghui Yang
- State Key Laboratory of Biobased Material and Green Papermaking, Department of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250300, China
| | - Gaozhen Zhao
- State Key Laboratory of Biobased Material and Green Papermaking, Department of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250300, China
| | - Jiaao Song
- State Key Laboratory of Biobased Material and Green Papermaking, Department of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250300, China
| | - Taiyi Zhang
- State Key Laboratory of Biobased Material and Green Papermaking, Department of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250300, China
| | - Xiaowen Huang
- State Key Laboratory of Biobased Material and Green Papermaking, Department of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250300, China
| |
Collapse
|
17
|
Gerlt MS, Ruppen P, Leuthner M, Panke S, Dual J. Acoustofluidic medium exchange for preparation of electrocompetent bacteria using channel wall trapping. LAB ON A CHIP 2021; 21:4487-4497. [PMID: 34668506 PMCID: PMC8577197 DOI: 10.1039/d1lc00406a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 10/13/2021] [Indexed: 06/02/2023]
Abstract
Comprehensive integration of process steps into a miniaturised version of synthetic biology workflows remains a crucial task in automating the design of biosystems. However, each of these process steps has specific demands with respect to the environmental conditions, including in particular the composition of the surrounding fluid, which makes integration cumbersome. As a case in point, transformation, i.e. reprogramming of bacteria by delivering exogenous genetic material (such as DNA) into the cytoplasm, is a key process in molecular engineering and modern biotechnology in general. Transformation is often performed by electroporation, i.e. creating pores in the membrane using electric shocks in a low conductivity environment. However, cell preparation for electroporation can be cumbersome as it requires the exchange of growth medium (high-conductivity) for low-conductivity medium, typically performed via multiple time-intensive centrifugation steps. To simplify and miniaturise this step, we developed an acoustofluidic device capable of trapping the bacterium Escherichia coli non-invasively for subsequent exchange of medium, which is challenging in acoustofluidic devices due to detrimental acoustic streaming effects. With an improved etching process, we were able to produce a thin wall between two microfluidic channels, which, upon excitation, can generate streaming fields that complement the acoustic radiation force and therefore can be utilised for trapping of bacteria. Our novel design robustly traps Escherichia coli at a flow rate of 10 μL min-1 and has a cell recovery performance of 47 ± 3% after washing the trapped cells. To verify that the performance of the medium exchange device is sufficient, we tested the electrocompetence of the recovered cells in a standard transformation procedure and found a transformation efficiency of 8 × 105 CFU per μg of plasmid DNA. Our device is a low-volume alternative to centrifugation-based methods and opens the door for miniaturisation of a plethora of microbiological and molecular engineering protocols.
Collapse
Affiliation(s)
- M S Gerlt
- Mechanics and Experimental Dynamics, Department of Mechanical and Process Engineering, Swiss Federal Institute of Technology (ETH Zurich), Tannenstrasse 3, CH-8092 Zurich, Switzerland.
| | - P Ruppen
- Bioprocess Laboratory, Department of Biosystems Science and Engineering, Swiss Federal Institute of Technology (ETH Zurich), Mattenstrasse 26, CH-4058 Basel, Switzerland.
- NCCR Molecular Systems Engineering, BPR 1095, Mattenstrasse 24a, CH-4058 Basel, Switzerland
| | - M Leuthner
- Mechanics and Experimental Dynamics, Department of Mechanical and Process Engineering, Swiss Federal Institute of Technology (ETH Zurich), Tannenstrasse 3, CH-8092 Zurich, Switzerland.
| | - S Panke
- Bioprocess Laboratory, Department of Biosystems Science and Engineering, Swiss Federal Institute of Technology (ETH Zurich), Mattenstrasse 26, CH-4058 Basel, Switzerland.
- NCCR Molecular Systems Engineering, BPR 1095, Mattenstrasse 24a, CH-4058 Basel, Switzerland
| | - J Dual
- Mechanics and Experimental Dynamics, Department of Mechanical and Process Engineering, Swiss Federal Institute of Technology (ETH Zurich), Tannenstrasse 3, CH-8092 Zurich, Switzerland.
| |
Collapse
|
18
|
Liu Y, Huang Y, Lu R, Xin F, Liu G. Synthetic biology applications of the yeast mating signal pathway. Trends Biotechnol 2021; 40:620-631. [PMID: 34666896 DOI: 10.1016/j.tibtech.2021.09.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/17/2021] [Accepted: 09/17/2021] [Indexed: 12/18/2022]
Abstract
Cell fusion is a fundamental biological process that is involved in the development of most eukaryotic organisms. During the fusion process in Saccharomyces cerevisiae, cells respond to pheromones to trigger the MAPK (mitogen-activated protein kinase) cascade to initiate mating, followed by polarization, cell-wall remodeling, membrane fusion, and karyogamy. We highlight the applications of the yeast mating signal pathway in promoter engineering for tuning the expression of output genes, as well as in metabolic engineering for decoupling growth and metabolism, biosensors for sensitive detection and signal amplification, genetic circuits for programmable biological functionalities, and artificial consortia for cell-cell communication. Strategies such as exploiting rational engineering of modular circuits and optimizing the reproductive pathway to precisely maneuver physiological events have implications for scientific research and industrial development.
Collapse
Affiliation(s)
- Ying Liu
- College of Biological and Pharmaceutical Engineering, Nanjing Tech University, Jiangsu Province, China
| | - Yuxin Huang
- College of Biological and Pharmaceutical Engineering, Nanjing Tech University, Jiangsu Province, China
| | - Ran Lu
- College of Biological and Pharmaceutical Engineering, Nanjing Tech University, Jiangsu Province, China
| | - Fengxue Xin
- College of Biological and Pharmaceutical Engineering, Nanjing Tech University, Jiangsu Province, China
| | - Guannan Liu
- College of Biological and Pharmaceutical Engineering, Nanjing Tech University, Jiangsu Province, China; Jiangsu Synergetic Innovation Center for Advanced Bio-Manufacture, Nanjing Tech University, Jiangsu Province, China.
| |
Collapse
|
19
|
Ottonelli I, Duskey JT, Rinaldi A, Grazioli MV, Parmeggiani I, Vandelli MA, Wang LZ, Prud’homme RK, Tosi G, Ruozi B. Microfluidic Technology for the Production of Hybrid Nanomedicines. Pharmaceutics 2021; 13:1495. [PMID: 34575571 PMCID: PMC8465086 DOI: 10.3390/pharmaceutics13091495] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 09/06/2021] [Accepted: 09/13/2021] [Indexed: 12/15/2022] Open
Abstract
Microfluidic technologies have recently been applied as innovative methods for the production of a variety of nanomedicines (NMeds), demonstrating their potential on a global scale. The capacity to precisely control variables, such as the flow rate ratio, temperature, total flow rate, etc., allows for greater tunability of the NMed systems that are more standardized and automated than the ones obtained by well-known benchtop protocols. However, it is a crucial aspect to be able to obtain NMeds with the same characteristics of the previously optimized ones. In this study, we focused on the transfer of a production protocol for hybrid NMeds (H-NMeds) consisting of PLGA, Cholesterol, and Pluronic® F68 from a benchtop nanoprecipitation method to a microfluidic device. For this aim, we modified parameters such as the flow rate ratio, the concentration of core materials in the organic phase, and the ratio between PLGA and Cholesterol in the feeding organic phase. Outputs analysed were the chemico-physical properties, such as size, PDI, and surface charge, the composition in terms of %Cholesterol and residual %Pluronic® F68, their stability to lyophilization, and the morphology via atomic force and electron microscopy. On the basis of the results, even if microfluidic technology is one of the unique procedures to obtain industrial production of NMeds, we demonstrated that the translation from a benchtop method to a microfluidic one is not a simple transfer of already established parameters, with several variables to be taken into account and to be optimized.
Collapse
Affiliation(s)
- Ilaria Ottonelli
- Nanotech Lab, Te. Far.T.I., Department Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy; (I.O.); (J.T.D.); (A.R.); (M.V.G.); (I.P.); (M.A.V.); (B.R.)
- Clinical and Experimental Medicine Ph.D. Program, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Jason Thomas Duskey
- Nanotech Lab, Te. Far.T.I., Department Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy; (I.O.); (J.T.D.); (A.R.); (M.V.G.); (I.P.); (M.A.V.); (B.R.)
| | - Arianna Rinaldi
- Nanotech Lab, Te. Far.T.I., Department Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy; (I.O.); (J.T.D.); (A.R.); (M.V.G.); (I.P.); (M.A.V.); (B.R.)
- Clinical and Experimental Medicine Ph.D. Program, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Maria Vittoria Grazioli
- Nanotech Lab, Te. Far.T.I., Department Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy; (I.O.); (J.T.D.); (A.R.); (M.V.G.); (I.P.); (M.A.V.); (B.R.)
| | - Irene Parmeggiani
- Nanotech Lab, Te. Far.T.I., Department Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy; (I.O.); (J.T.D.); (A.R.); (M.V.G.); (I.P.); (M.A.V.); (B.R.)
| | - Maria Angela Vandelli
- Nanotech Lab, Te. Far.T.I., Department Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy; (I.O.); (J.T.D.); (A.R.); (M.V.G.); (I.P.); (M.A.V.); (B.R.)
| | - Leon Z. Wang
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA; (L.Z.W.); (R.K.P.)
| | - Robert K. Prud’homme
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA; (L.Z.W.); (R.K.P.)
| | - Giovanni Tosi
- Nanotech Lab, Te. Far.T.I., Department Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy; (I.O.); (J.T.D.); (A.R.); (M.V.G.); (I.P.); (M.A.V.); (B.R.)
| | - Barbara Ruozi
- Nanotech Lab, Te. Far.T.I., Department Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy; (I.O.); (J.T.D.); (A.R.); (M.V.G.); (I.P.); (M.A.V.); (B.R.)
| |
Collapse
|
20
|
Orsi E, Claassens NJ, Nikel PI, Lindner SN. Growth-coupled selection of synthetic modules to accelerate cell factory development. Nat Commun 2021; 12:5295. [PMID: 34489458 PMCID: PMC8421431 DOI: 10.1038/s41467-021-25665-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Accepted: 08/23/2021] [Indexed: 11/18/2022] Open
Abstract
Synthetic biology has brought about a conceptual shift in our ability to redesign microbial metabolic networks. Combining metabolic pathway-modularization with growth-coupled selection schemes is a powerful tool that enables deep rewiring of the cell factories’ biochemistry for rational bioproduction.
Collapse
Affiliation(s)
- Enrico Orsi
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Nico J Claassens
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Steffen N Lindner
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany.
| |
Collapse
|
21
|
Shi N, Mohibullah M, Easley CJ. Active Flow Control and Dynamic Analysis in Droplet Microfluidics. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2021; 14:133-153. [PMID: 33979546 PMCID: PMC8956363 DOI: 10.1146/annurev-anchem-122120-042627] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Droplet-based microfluidics has emerged as an important subfield within the microfluidic and general analytical communities. Indeed, several unique applications such as digital assay readout and single-cell sequencing now have commercial systems based on droplet microfluidics. Yet there remains room for this research area to grow. To date, most analytical readouts are optical in nature, relatively few studies have integrated sample preparation, and passive means for droplet formation and manipulation have dominated the field. Analytical scientists continue to expand capabilities by developing droplet-compatible method adaptations, for example, by interfacing to mass spectrometers or automating droplet sampling for temporally resolved analysis. In this review, we highlight recently developed fluidic control techniques and unique integrations of analytical methodology with droplet microfluidics-focusing on automation and the connections to analog/digital domains-and we conclude by offering a perspective on current challenges and future applications.
Collapse
Affiliation(s)
- Nan Shi
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, USA;
| | - Md Mohibullah
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, USA;
| | - Christopher J Easley
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, USA;
| |
Collapse
|
22
|
Kojabad AA, Farzanehpour M, Galeh HEG, Dorostkar R, Jafarpour A, Bolandian M, Nodooshan MM. Droplet digital PCR of viral DNA/RNA, current progress, challenges, and future perspectives. J Med Virol 2021; 93:4182-4197. [PMID: 33538349 PMCID: PMC8013307 DOI: 10.1002/jmv.26846] [Citation(s) in RCA: 96] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 02/01/2021] [Indexed: 12/18/2022]
Abstract
High-throughput droplet-based digital PCR (ddPCR) is a refinement of the conventional polymerase chain reaction (PCR) methods. In ddPCR, DNA/RNA is encapsulated stochastically inside the microdroplets as reaction chambers. A small percentage of the reaction chamber contains one or fewer copies of the DNA or RNA. After PCR amplification, concentrations are determined based on the proportion of nonfluorescent partitions through the Poisson distribution. Some of the main features of ddPCR include high sensitivity and specificity, absolute quantification without a standard curve, high reproducibility, good tolerance to PCR inhibitor, and high efficacy compared to conventional molecular methods. These advantages make ddPCR a valuable addition to the virologist's toolbox. The following review outlines the recent technological advances in ddPCR methods and their applications in viral identification.
Collapse
Affiliation(s)
- Amir Asri Kojabad
- Applied Virology Research CenterBaqiyatallah University of Medical SciencesTehranIran
| | - Mahdieh Farzanehpour
- Applied Virology Research CenterBaqiyatallah University of Medical SciencesTehranIran
| | | | - Ruhollah Dorostkar
- Applied Virology Research CenterBaqiyatallah University of Medical SciencesTehranIran
| | - Ali Jafarpour
- Research Center for Clinical VirologyTehran University of Medical SciencesTehranIran
| | - Masoumeh Bolandian
- Applied Virology Research CenterBaqiyatallah University of Medical SciencesTehranIran
| | | |
Collapse
|
23
|
Xing Y, Liu Y, Chen R, Li Y, Zhang C, Jiang Y, Lu Y, Lin B, Chen P, Tian R, Liu X, Cheng X. A robust and scalable active-matrix driven digital microfluidic platform based on printed-circuit board technology. LAB ON A CHIP 2021; 21:1886-1896. [PMID: 34008645 DOI: 10.1039/d1lc00101a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Two-dimensional digital microfluidic platforms, on which droplets are actuated by electrowetting on dielectrics, have merits such as dynamic reconfigurability and ease for automation. However, concerns for digital microfluidic platforms based on low-cost printed circuit boards, such as the scalability of the electrode array and the reliability of the device operation, should be addressed before high throughput and fully automatic applications can be realized. In this work we report the progress in addressing those issues by using active-matrix circuitry to automatically drive a large electrode array with enhanced device reliability. We describe the design and the fabrication of a robust and scalable active-matrix driven digital microfluidic platform based on printed-circuit board technology. Reliable actuation of aqueous and organic droplets is achieved using a free-standing double-layer hydrophobic membrane. To demonstrate the versatility of the digital microfluidic platform, a pentapeptide is synthesized on the device within 30 minutes. With these improvements, a fully automatic, scalable, robust, reusable, and low-cost digital microfluidic platform capable of parallel manipulation of a large number of droplets can find numerous applications in chemical engineering, bioengineering and biomedical engineering.
Collapse
Affiliation(s)
- Yaru Xing
- Harbin Institute of Technology, Harbin 150001, China and Department of Materials Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China.
| | - Yu Liu
- Department of Materials Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China.
| | - Rifei Chen
- Department of Materials Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China.
| | - Yuyan Li
- Department of Electrical and Electronic Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Chengzhi Zhang
- Department of Materials Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China.
| | - Youwei Jiang
- Department of Materials Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China. and SUSTech Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yao Lu
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
| | - Bingcheng Lin
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
| | - Peizhong Chen
- Department of Chemistry, Southern University of Science and Technology, Shenzhen 518055, China
| | - Ruijun Tian
- Department of Chemistry, Southern University of Science and Technology, Shenzhen 518055, China
| | - Xianming Liu
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
| | - Xing Cheng
- Department of Materials Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China.
| |
Collapse
|
24
|
Wagner HJ, Weber W, Fussenegger M. Synthetic Biology: Emerging Concepts to Design and Advance Adeno-Associated Viral Vectors for Gene Therapy. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:2004018. [PMID: 33977059 PMCID: PMC8097373 DOI: 10.1002/advs.202004018] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 12/18/2020] [Indexed: 05/28/2023]
Abstract
Three recent approvals and over 100 ongoing clinical trials make adeno-associated virus (AAV)-based vectors the leading gene delivery vehicles in gene therapy. Pharmaceutical companies are investing in this small and nonpathogenic gene shuttle to increase the therapeutic portfolios within the coming years. This prospect of marking a new era in gene therapy has fostered both investigations of the fundamental AAV biology as well as engineering studies to enhance delivery vehicles. Driven by the high clinical potential, a new generation of synthetic-biologically engineered AAV vectors is on the rise. Concepts from synthetic biology enable the control and fine-tuning of vector function at different stages of cellular transduction and gene expression. It is anticipated that the emerging field of synthetic-biologically engineered AAV vectors can shape future gene therapeutic approaches and thus the design of tomorrow's gene delivery vectors. This review describes and discusses the recent trends in capsid and vector genome engineering, with particular emphasis on synthetic-biological approaches.
Collapse
Affiliation(s)
- Hanna J. Wagner
- Department of Biosystems Science and EngineeringETH ZurichMattenstrasse 26Basel4058Switzerland
- Faculty of BiologyUniversity of FreiburgSchänzlestraße 1Freiburg79104Germany
- Signalling Research Centres BIOSS and CIBSSUniversity of FreiburgSchänzlestraße 18Freiburg79104Germany
| | - Wilfried Weber
- Faculty of BiologyUniversity of FreiburgSchänzlestraße 1Freiburg79104Germany
- Signalling Research Centres BIOSS and CIBSSUniversity of FreiburgSchänzlestraße 18Freiburg79104Germany
| | - Martin Fussenegger
- Department of Biosystems Science and EngineeringETH ZurichMattenstrasse 26Basel4058Switzerland
- Faculty of ScienceUniversity of BaselKlingelbergstrasse 50Basel4056Switzerland
| |
Collapse
|
25
|
David F, Davis AM, Gossing M, Hayes MA, Romero E, Scott LH, Wigglesworth MJ. A Perspective on Synthetic Biology in Drug Discovery and Development-Current Impact and Future Opportunities. SLAS DISCOVERY 2021; 26:581-603. [PMID: 33834873 DOI: 10.1177/24725552211000669] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The global impact of synthetic biology has been accelerating, because of the plummeting cost of DNA synthesis, advances in genetic engineering, growing understanding of genome organization, and explosion in data science. However, much of the discipline's application in the pharmaceutical industry remains enigmatic. In this review, we highlight recent examples of the impact of synthetic biology on target validation, assay development, hit finding, lead optimization, and chemical synthesis, through to the development of cellular therapeutics. We also highlight the availability of tools and technologies driving the discipline. Synthetic biology is certainly impacting all stages of drug discovery and development, and the recognition of the discipline's contribution can further enhance the opportunities for the drug discovery and development value chain.
Collapse
Affiliation(s)
- Florian David
- Department of Biology and Biological Engineering, Division of Systems and Synthetic Biology, Chalmers University of Technology, Gothenburg, Sweden
| | - Andrew M Davis
- Discovery Sciences, Biopharmaceutical R&D, AstraZeneca, Cambridge, UK
| | - Michael Gossing
- Discovery Sciences, Biopharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Martin A Hayes
- Discovery Sciences, Biopharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Elvira Romero
- Discovery Sciences, Biopharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Louis H Scott
- Discovery Sciences, Biopharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | | |
Collapse
|
26
|
Destgeer G, Ouyang M, Di Carlo D. Engineering Design of Concentric Amphiphilic Microparticles for Spontaneous Formation of Picoliter to Nanoliter Droplet Volumes. Anal Chem 2021; 93:2317-2326. [DOI: 10.1021/acs.analchem.0c04184] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Ghulam Destgeer
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Mengxing Ouyang
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Dino Di Carlo
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, California 90095, United States
- Department of Mechanical and Aerospace Engineering, University of California, Los Angeles, Los Angeles, California 90095, United States
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, California 90095, United States
| |
Collapse
|
27
|
Setting Up an Automated Biomanufacturing Laboratory. Methods Mol Biol 2021; 2229:137-155. [PMID: 33405219 DOI: 10.1007/978-1-0716-1032-9_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
Laboratory automation is a key enabling technology for genetic engineering that can lead to higher throughput, more efficient and accurate experiments, better data management and analysis, decrease in the DBT (Design, Build, and Test) cycle turnaround, increase of reproducibility, and savings in lab resources. Choosing the correct framework among so many options available in terms of software, hardware, and skills needed to operate them is crucial for the success of any automation project. This chapter explores the multiple aspects to be considered for the solid development of a biofoundry project including available software and hardware tools, resources, strategies, partnerships, and collaborations in the field needed to speed up the translation of research results to solve important society problems.
Collapse
|
28
|
Zhang F, Sun Y, Luo C. Microfluidic approaches for synthetic gene circuits’ construction and analysis. QUANTITATIVE BIOLOGY 2021. [DOI: 10.15302/j-qb-021-0235] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
29
|
Lawson CE, Martí JM, Radivojevic T, Jonnalagadda SVR, Gentz R, Hillson NJ, Peisert S, Kim J, Simmons BA, Petzold CJ, Singer SW, Mukhopadhyay A, Tanjore D, Dunn JG, Garcia Martin H. Machine learning for metabolic engineering: A review. Metab Eng 2020; 63:34-60. [PMID: 33221420 DOI: 10.1016/j.ymben.2020.10.005] [Citation(s) in RCA: 86] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 10/22/2020] [Accepted: 10/31/2020] [Indexed: 12/14/2022]
Abstract
Machine learning provides researchers a unique opportunity to make metabolic engineering more predictable. In this review, we offer an introduction to this discipline in terms that are relatable to metabolic engineers, as well as providing in-depth illustrative examples leveraging omics data and improving production. We also include practical advice for the practitioner in terms of data management, algorithm libraries, computational resources, and important non-technical issues. A variety of applications ranging from pathway construction and optimization, to genetic editing optimization, cell factory testing, and production scale-up are discussed. Moreover, the promising relationship between machine learning and mechanistic models is thoroughly reviewed. Finally, the future perspectives and most promising directions for this combination of disciplines are examined.
Collapse
Affiliation(s)
- Christopher E Lawson
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Joint BioEnergy Institute, Emeryville, CA, 94608, USA
| | - Jose Manuel Martí
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Joint BioEnergy Institute, Emeryville, CA, 94608, USA; DOE Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Tijana Radivojevic
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Joint BioEnergy Institute, Emeryville, CA, 94608, USA; DOE Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Sai Vamshi R Jonnalagadda
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Joint BioEnergy Institute, Emeryville, CA, 94608, USA; DOE Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Reinhard Gentz
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Joint BioEnergy Institute, Emeryville, CA, 94608, USA; Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Nathan J Hillson
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Joint BioEnergy Institute, Emeryville, CA, 94608, USA; DOE Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Sean Peisert
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; University of California Davis, Davis, CA, 95616, USA
| | - Joonhoon Kim
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA; Pacific Northwest National Laboratory, Richland, 99354, WA, USA
| | - Blake A Simmons
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Joint BioEnergy Institute, Emeryville, CA, 94608, USA; DOE Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Christopher J Petzold
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Joint BioEnergy Institute, Emeryville, CA, 94608, USA; DOE Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Steven W Singer
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Joint BioEnergy Institute, Emeryville, CA, 94608, USA
| | - Aindrila Mukhopadhyay
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Joint BioEnergy Institute, Emeryville, CA, 94608, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, USA
| | - Deepti Tanjore
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Advanced Biofuels and Bioproducts Process Development Unit, Emeryville, CA, 94608, USA
| | | | - Hector Garcia Martin
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Joint BioEnergy Institute, Emeryville, CA, 94608, USA; DOE Agile BioFoundry, Emeryville, CA, 94608, USA; Basque Center for Applied Mathematics, 48009, Bilbao, Spain; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, USA.
| |
Collapse
|
30
|
McIntyre D, Lashkaripour A, Densmore D. Rapid and inexpensive microfluidic electrode integration with conductive ink. LAB ON A CHIP 2020; 20:3690-3695. [PMID: 32895672 DOI: 10.1039/d0lc00763c] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Electrode integration significantly increases the versatility of droplet microfluidics, enabling label-free sensing and manipulation at a single-droplet (single-cell) resolution. However, common fabrication techniques for integrating electronics into microfluidics are expensive, time-consuming, and can require cleanroom facilities. Here, we present a simple and cost-effective method for integrating electrodes into thermoplastic microfluidic chips using an off-the-shelf conductive ink. The developed conductive ink electrodes cost less than $10 for an entire chip, have been shown here in channel geometries as small as 75 μm by 50 μm, and can go from fabrication to testing within a day without a cleanroom. The geometric fabrication limits of this technique were explored over time, and proof-of-concept microfluidic devices for capacitance sensing, droplet merging, and droplet sorting were developed. This novel method complements existing rapid prototyping systems for microfluidics such as micromilling, laser cutting, and 3D printing, enabling their wider use and application.
Collapse
Affiliation(s)
- David McIntyre
- Boston University Biomedical Engineering Department, 44 Cummington Mall, Boston, USA and Biological Design Center, 610 Commonwealth Ave, Boston, USA
| | - Ali Lashkaripour
- Boston University Biomedical Engineering Department, 44 Cummington Mall, Boston, USA and Biological Design Center, 610 Commonwealth Ave, Boston, USA
| | - Douglas Densmore
- Biological Design Center, 610 Commonwealth Ave, Boston, USA and Boston University Electrical and Computer Engineering Department, 8 Saint Mary's St., Boston, USA.
| |
Collapse
|
31
|
Köpke M, Simpson SD. Pollution to products: recycling of ‘above ground’ carbon by gas fermentation. Curr Opin Biotechnol 2020; 65:180-189. [DOI: 10.1016/j.copbio.2020.02.017] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 02/21/2020] [Accepted: 02/26/2020] [Indexed: 02/01/2023]
|
32
|
Tarn MD, Sikora SNF, Porter GCE, Wyld BV, Alayof M, Reicher N, Harrison AD, Rudich Y, Shim JU, Murray BJ. On-chip analysis of atmospheric ice-nucleating particles in continuous flow. LAB ON A CHIP 2020; 20:2889-2910. [PMID: 32661539 DOI: 10.1039/d0lc00251h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Ice-nucleating particles (INPs) are of atmospheric importance because they catalyse the freezing of supercooled cloud droplets, strongly affecting the lifetime and radiative properties of clouds. There is a need to improve our knowledge of the global distribution of INPs, their seasonal cycles and long-term trends, but our capability to make these measurements is limited. Atmospheric INP concentrations are often determined using assays involving arrays of droplets on a cold stage, but such assays are frequently limited by the number of droplets that can be analysed per experiment, often involve manual processing (e.g. pipetting of droplets), and can be susceptible to contamination. Here, we present a microfluidic platform, the LOC-NIPI (Lab-on-a-Chip Nucleation by Immersed Particle Instrument), for the generation of water-in-oil droplets and their freezing in continuous flow as they pass over a cold plate for atmospheric INP analysis. LOC-NIPI allows the user to define the number of droplets analysed by simply running the platform for as long as required. The use of small (∼100 μm diameter) droplets minimises the probability of contamination in any one droplet and therefore allows supercooling all the way down to homogeneous freezing (around -36 °C), while a temperature probe in a proxy channel provides an accurate measure of temperature without the need for temperature modelling. The platform was validated using samples of pollen extract and Snomax®, with hundreds of droplets analysed per temperature step and thousands of droplets being measured per experiment. Homogeneous freezing of purified water was studied using >10 000 droplets with temperature increments of 0.1 °C. The results were reproducible, independent of flow rate in the ranges tested, and the data compared well to conventional instrumentation and literature data. The LOC-NIPI was further benchmarked in a field campaign in the Eastern Mediterranean against other well-characterised instrumentation. The continuous flow nature of the system provides a route, with future development, to the automated monitoring of atmospheric INP at field sites around the globe.
Collapse
Affiliation(s)
- Mark D Tarn
- School of Earth and Environment, University of Leeds, Leeds, LS2 9JT, UK. and School of Physics and Astronomy, University of Leeds, Leeds, LS2 9JT, UK.
| | | | - Grace C E Porter
- School of Earth and Environment, University of Leeds, Leeds, LS2 9JT, UK. and School of Physics and Astronomy, University of Leeds, Leeds, LS2 9JT, UK.
| | - Bethany V Wyld
- School of Earth and Environment, University of Leeds, Leeds, LS2 9JT, UK.
| | - Matan Alayof
- Department of Earth and Planetary Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Naama Reicher
- Department of Earth and Planetary Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | | | - Yinon Rudich
- Department of Earth and Planetary Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Jung-Uk Shim
- School of Physics and Astronomy, University of Leeds, Leeds, LS2 9JT, UK.
| | - Benjamin J Murray
- School of Earth and Environment, University of Leeds, Leeds, LS2 9JT, UK.
| |
Collapse
|
33
|
Kothamachu VB, Zaini S, Muffatto F. Role of Digital Microfluidics in Enabling Access to Laboratory Automation and Making Biology Programmable. SLAS Technol 2020; 25:411-426. [PMID: 32584152 DOI: 10.1177/2472630320931794] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Digital microfluidics (DMF) is a liquid handling technique that has been demonstrated to automate biological experimentation in a low-cost, rapid, and programmable manner. This review discusses the role of DMF as a "digital bioconverter"-a tool to connect the digital aspects of the design-build-learn cycle with the physical execution of experiments. Several applications are reviewed to demonstrate the utility of DMF as a digital bioconverter, namely, genetic engineering, sample preparation for sequencing and mass spectrometry, and enzyme-, immuno-, and cell-based screening assays. These applications show that DMF has great potential in the role of a centralized execution platform in a fully integrated pipeline for the production of novel organisms and biomolecules. In this paper, we discuss how the function of a DMF device within such a pipeline is highly dependent on integration with different sensing techniques and methodologies from machine learning and big data. In addition to that, we examine how the capacity of DMF can in some cases be limited by known technical and operational challenges and how consolidated efforts in overcoming these challenges will be key to the development of DMF as a major enabling technology in the computer-aided biology framework.
Collapse
|
34
|
Arjun A, Ajith RR, Kumar Ranjith S. Mixing characterization of binary-coalesced droplets in microchannels using deep neural network. BIOMICROFLUIDICS 2020; 14:034111. [PMID: 32549924 PMCID: PMC7274813 DOI: 10.1063/5.0008461] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 05/21/2020] [Indexed: 05/16/2023]
Abstract
Real-time object identification and classification are essential in many microfluidic applications especially in the droplet microfluidics. This paper discusses the application of convolutional neural networks to detect the merged microdroplet in the flow field and classify them in an on-the-go manner based on the extent of mixing. The droplets are generated in PMMA microfluidic devices employing flow-focusing and cross-flow configurations. The visualization of binary coalescence of droplets is performed by a CCD camera attached to a microscope, and the sequence of images is recorded. Different real-time object localization and classification networks such as You Only Look Once and Singleshot Multibox Detector are deployed for droplet detection and characterization. A custom dataset to train these deep neural networks to detect and classify is created from the captured images and labeled manually. The merged droplets are segregated based on the degree of mixing into three categories: low mixing, intermediate mixing, and high mixing. The trained model is tested against images taken at different ambient conditions, droplet shapes, droplet sizes, and binary-fluid combinations, which indeed exhibited high accuracy and precision in predictions. In addition, it is demonstrated that these schemes are efficient in localization of coalesced binary droplets from the recorded video or image and classify them based on grade of mixing irrespective of experimental conditions in real time.
Collapse
Affiliation(s)
- A Arjun
- Micro/nanofluidics Research Laboratory, Department of Mechanical Engineering, College of Engineering Trivandrum, Thiruvananathapuram 695016, Kerala, India
| | - R R Ajith
- Micro/nanofluidics Research Laboratory, Department of Mechanical Engineering, College of Engineering Trivandrum, Thiruvananathapuram 695016, Kerala, India
| | - S Kumar Ranjith
- Micro/nanofluidics Research Laboratory, Department of Mechanical Engineering, College of Engineering Trivandrum, Thiruvananathapuram 695016, Kerala, India
| |
Collapse
|
35
|
Flow Chemistry in Contemporary Chemical Sciences: A Real Variety of Its Applications. Molecules 2020; 25:molecules25061434. [PMID: 32245225 PMCID: PMC7146634 DOI: 10.3390/molecules25061434] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 03/14/2020] [Accepted: 03/16/2020] [Indexed: 12/15/2022] Open
Abstract
Flow chemistry is an area of contemporary chemistry exploiting the hydrodynamic conditions of flowing liquids to provide particular environments for chemical reactions. These particular conditions of enhanced and strictly regulated transport of reagents, improved interface contacts, intensification of heat transfer, and safe operation with hazardous chemicals can be utilized in chemical synthesis, both for mechanization and automation of analytical procedures, and for the investigation of the kinetics of ultrafast reactions. Such methods are developed for more than half a century. In the field of chemical synthesis, they are used mostly in pharmaceutical chemistry for efficient syntheses of small amounts of active substances. In analytical chemistry, flow measuring systems are designed for environmental applications and industrial monitoring, as well as medical and pharmaceutical analysis, providing essential enhancement of the yield of analyses and precision of analytical determinations. The main concept of this review is to show the overlapping of development trends in the design of instrumentation and various ways of the utilization of specificity of chemical operations under flow conditions, especially for synthetic and analytical purposes, with a simultaneous presentation of the still rather limited correspondence between these two main areas of flow chemistry.
Collapse
|
36
|
Shimizu H, Takeda S, Mawatari K, Kitamori T. Ultrasensitive detection of nonlabelled bovine serum albumin using photothermal optical phase shift detection with UV excitation. Analyst 2020; 145:2580-2585. [PMID: 32195506 DOI: 10.1039/d0an00037j] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Ultrasensitive detection of nonlabelled bovine serum albumin is performed in micro/nanofluidic chips using a photothermal optical phase shift (POPS) detection system. Currently, micro- and nanofluidics allow the analysis of various single cells, and their targets of interest are shifting from nucleic acids to proteins. Previously, our group developed photothermal detection techniques for the sensitive detection of nonfluorescent molecules. For example, we developed a thermal lens microscope (TLM) with ultrahigh sensitivity at the single-molecule level and a POPS detector that is applicable to nanochannels smaller than the wavelength of light. The POPS detector also realized the detection of nonlabelled proteins in nanochannels, although its detection sensitivity is less than that of the TLM in microchannels due to insufficient background light reduction. To overcome this problem, we developed a new POPS detector using relay optics for further reduction of the background light. In addition, heat transfer from the sample solution to the nanochannel wall was thoroughly investigated to achieve ultrahigh sensitivity. The limit of detection (LOD) obtained with the new POPS detector is 30 molecules in 1.0 fL. Considering this LOD, the performance of the new POPS detector is comparable with that of the TLM. Owing to the applicability of the POPS detector for sensitive detection even in nanochannels or single-μm channels, which cannot be realized with the TLM, combinations of the POPS detector and separation techniques employing unique nanochannel properties will contribute to advances in single-cell proteomics in the future.
Collapse
Affiliation(s)
- Hisashi Shimizu
- International Research Center for Neurointelligence, The University of Tokyo, 7-3-1, Hongo, Bunkyo, Tokyo 113-0033, Japan.
| | | | | | | |
Collapse
|
37
|
Hengoju S, Wohlfeil S, Munser AS, Boehme S, Beckert E, Shvydkiv O, Tovar M, Roth M, Rosenbaum MA. Optofluidic detection setup for multi-parametric analysis of microbiological samples in droplets. BIOMICROFLUIDICS 2020; 14:024109. [PMID: 32547676 PMCID: PMC7148121 DOI: 10.1063/1.5139603] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 03/27/2020] [Indexed: 05/03/2023]
Abstract
High-throughput microbiological experimentation using droplet microfluidics is limited due to the complexity and restricted versatility of the available detection techniques. Current detection setups are bulky, complicated, expensive, and require tedious optical alignment procedures while still mostly limited to fluorescence. In this work, we demonstrate an optofluidic detection setup for multi-parametric analyses of droplet samples by easily integrating micro-lenses and embedding optical fibers for guiding light in and out of the microfluidic chip. The optofluidic setup was validated for detection of absorbance, fluorescence, and scattered light. The developed platform was used for simultaneous detection of multiple parameters in different microbiological applications like cell density determination, growth kinetics, and antibiotic inhibition assays. Combining the high-throughput potential of droplet microfluidics with the ease, flexibility, and simplicity of optical fibers results in a powerful platform for microbiological experiments.
Collapse
Affiliation(s)
| | - S. Wohlfeil
- Fraunhofer Institute for Applied Optics and Precision Engineering IOF, Albert-Einstein-Str. 7, 07745 Jena, Germany
| | - A. S. Munser
- Fraunhofer Institute for Applied Optics and Precision Engineering IOF, Albert-Einstein-Str. 7, 07745 Jena, Germany
| | - S. Boehme
- Fraunhofer Institute for Applied Optics and Precision Engineering IOF, Albert-Einstein-Str. 7, 07745 Jena, Germany
| | - E. Beckert
- Fraunhofer Institute for Applied Optics and Precision Engineering IOF, Albert-Einstein-Str. 7, 07745 Jena, Germany
| | - O. Shvydkiv
- Leibniz Institute for Natural Product Research and Infection Biology, Hans Knoell Institute, Beutenbergstr. 11a, 07745 Jena, Germany
| | - M. Tovar
- Leibniz Institute for Natural Product Research and Infection Biology, Hans Knoell Institute, Beutenbergstr. 11a, 07745 Jena, Germany
| | - M. Roth
- Leibniz Institute for Natural Product Research and Infection Biology, Hans Knoell Institute, Beutenbergstr. 11a, 07745 Jena, Germany
| | | |
Collapse
|
38
|
Gioiello A, Piccinno A, Lozza AM, Cerra B. The Medicinal Chemistry in the Era of Machines and Automation: Recent Advances in Continuous Flow Technology. J Med Chem 2020; 63:6624-6647. [PMID: 32049517 PMCID: PMC7997576 DOI: 10.1021/acs.jmedchem.9b01956] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
![]()
Medicinal
chemistry plays a fundamental and underlying role in
chemical biology, pharmacology, and medicine to discover safe and
efficacious drugs. Small molecule medicinal chemistry relies on iterative
learning cycles composed of compound design, synthesis, testing, and
data analysis to provide new chemical probes and lead compounds for
novel and druggable targets. Using traditional approaches, the time
from hypothesis to obtaining the results can be protracted, thus limiting
the number of compounds that can be advanced into clinical studies.
This challenge can be tackled with the recourse of enabling technologies
that are showing great potential in improving the drug discovery process.
In this Perspective, we highlight recent developments toward innovative
medicinal chemistry strategies based on continuous flow systems coupled
with automation and bioassays. After a discussion of the aims and
concepts, we describe equipment and representative examples of automated
flow systems and end-to-end prototypes realized to expedite medicinal
chemistry discovery cycles.
Collapse
Affiliation(s)
- Antimo Gioiello
- Laboratory of Medicinal and Advanced Synthetic Chemistry (Lab MASC), Department of Pharmaceutical Sciences, University of Perugia, Via del Liceo 1, 06123 Perugia, Italy
| | - Alessandro Piccinno
- Laboratory of Medicinal and Advanced Synthetic Chemistry (Lab MASC), Department of Pharmaceutical Sciences, University of Perugia, Via del Liceo 1, 06123 Perugia, Italy
| | - Anna Maria Lozza
- Laboratory of Medicinal and Advanced Synthetic Chemistry (Lab MASC), Department of Pharmaceutical Sciences, University of Perugia, Via del Liceo 1, 06123 Perugia, Italy
| | - Bruno Cerra
- Laboratory of Medicinal and Advanced Synthetic Chemistry (Lab MASC), Department of Pharmaceutical Sciences, University of Perugia, Via del Liceo 1, 06123 Perugia, Italy
| |
Collapse
|
39
|
Zhang R, Ye Z, Gao M, Gao C, Zhang X, Li L, Gui L. Liquid metal electrode-enabled flexible microdroplet sensor. LAB ON A CHIP 2020; 20:496-504. [PMID: 31840725 DOI: 10.1039/c9lc00995g] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
This study presented a flexible liquid metal-based microdroplet capacitive sensor that would simply and accurately measure the speed and length of droplets flowing in microchannels. A pair of coplanar U-shaped electrodes was used to form a capacitance through droplet microchannels. Liquid metal was injected into polydimethylsiloxane (PDMS) channels to form the U-shaped electrodes. The sensor would generate a multi-plateau capacitance waveform as a droplet passes through the sensing area, and each plateau period corresponds to the droplet position in the sensing area. The droplet speed and length would be directly calculated from the multi-plateau capacitance waveform. The errors for the capacitive result relative to the real value were <7.2% for length and <2.8% for speed. Moreover, the sensor still maintained excellent performance for droplet length and speed measurement even though the microfluidic chip was bent to 96°. We have demonstrated that the capacitive sensor would be used for sweat rate monitoring.
Collapse
Affiliation(s)
- Renchang Zhang
- Key Laboratory of Cryogenics, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, 29 Zhongguancun East Road, Haidu District, Beijing 10019, China. and University of Chinese Academy of Sciences, 19 Yuquan road, Shijingshan District, Beijing 100039, China
| | - Zi Ye
- Key Laboratory of Cryogenics, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, 29 Zhongguancun East Road, Haidu District, Beijing 10019, China. and University of Chinese Academy of Sciences, 19 Yuquan road, Shijingshan District, Beijing 100039, China
| | - Meng Gao
- Key Laboratory of Cryogenics, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, 29 Zhongguancun East Road, Haidu District, Beijing 10019, China.
| | - Chang Gao
- Key Laboratory of Cryogenics, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, 29 Zhongguancun East Road, Haidu District, Beijing 10019, China. and University of Chinese Academy of Sciences, 19 Yuquan road, Shijingshan District, Beijing 100039, China
| | - Xudong Zhang
- Key Laboratory of Cryogenics, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, 29 Zhongguancun East Road, Haidu District, Beijing 10019, China. and University of Chinese Academy of Sciences, 19 Yuquan road, Shijingshan District, Beijing 100039, China
| | - Lei Li
- Key Laboratory of Cryogenics, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, 29 Zhongguancun East Road, Haidu District, Beijing 10019, China.
| | - Lin Gui
- Key Laboratory of Cryogenics, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, 29 Zhongguancun East Road, Haidu District, Beijing 10019, China. and University of Chinese Academy of Sciences, 19 Yuquan road, Shijingshan District, Beijing 100039, China
| |
Collapse
|
40
|
Swiner DJ, Jackson S, Burris BJ, Badu-Tawiah AK. Applications of Mass Spectrometry for Clinical Diagnostics: The Influence of Turnaround Time. Anal Chem 2020; 92:183-202. [PMID: 31671262 PMCID: PMC7896279 DOI: 10.1021/acs.analchem.9b04901] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
This critical review discusses how the need for reduced clinical turnaround times has influenced chemical instrumentation. We focus on the development of modern mass spectrometry (MS) and its application in clinical diagnosis. With increased functionality that takes advantage of novel front-end modifications and computational capabilities, MS can now be used for non-traditional clinical analyses, including applications in clinical microbiology for bacteria differentiation and in surgical operation rooms. We summarize here recent developments in the field that have enabled such capabilities, which include miniaturization for point-of-care testing, direct complex mixture analysis via ambient ionization, chemical imaging and profiling, and systems integration.
Collapse
Affiliation(s)
- Devin J. Swiner
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210
| | - Sierra Jackson
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210
| | - Benjamin J. Burris
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210
| | - Abraham K. Badu-Tawiah
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210
| |
Collapse
|
41
|
Snyder JE, Walsh D, Carr PA, Rothschild LJ. A Makerspace for Life Support Systems in Space. Trends Biotechnol 2019; 37:1164-1174. [DOI: 10.1016/j.tibtech.2019.05.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 05/03/2019] [Accepted: 05/06/2019] [Indexed: 12/12/2022]
|
42
|
Dahabieh MS, Thevelein JM, Gibson B. Multimodal Microorganism Development: Integrating Top-Down Biological Engineering with Bottom-Up Rational Design. Trends Biotechnol 2019; 38:241-253. [PMID: 31653446 DOI: 10.1016/j.tibtech.2019.09.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 09/28/2019] [Accepted: 09/30/2019] [Indexed: 12/12/2022]
Abstract
Biological engineering has unprecedented potential to solve society's most pressing challenges. Engineering approaches must consider complex technical, economic, and social factors. This requires methods that confer gene/pathway-level functionality and organism-level robustness in rapid and cost-effective ways. This article compares foundational engineering approaches - bottom-up, gene-targeted engineering, and top-down, whole-genome engineering - and identifies significant complementarity between them. Cases drawn from engineering Saccharomyces cerevisiae exemplify the synergy of a combined approach. Indeed, multimodal engineering streamlines strain development by leveraging the complementarity of whole-genome and gene-targeted engineering to overcome the gap in design knowledge that restricts rational design. As biological engineers target more complex systems, this dual-track approach is poised to become an increasingly important tool to realize the promise of synthetic biology.
Collapse
Affiliation(s)
- Matthew S Dahabieh
- Renaissance BioScience, 410-2389 Health Sciences Mall, Vancouver, BC V6T1Z3, Canada
| | - Johan M Thevelein
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, Katholieke Universiteit (KU) Leuven, Leuven, Belgium; Center for Microbiology, Vlaams Instituut voor Biotechnologie (VIB), Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
| | - Brian Gibson
- VTT Technical Research Centre of Finland, Tietotie 2, VTT, PO Box 1000, FI-02044 Espoo, Finland.
| |
Collapse
|
43
|
Han W, Chen X. New insights into generation of highly controllable monodisperse high-throughput microdroplets in a T-junction microchannel with step structure. J DISPER SCI TECHNOL 2019. [DOI: 10.1080/01932691.2019.1679643] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Wenbo Han
- Faculty of Mechanical Engineering and Automation, Liaoning University of Technology, Jinzhou, China
| | - Xueye Chen
- Faculty of Mechanical Engineering and Automation, Liaoning University of Technology, Jinzhou, China
| |
Collapse
|
44
|
Grösche M, Korvink JG, Rabe KS, Niemeyer CM. Comparison of Storage Methods for Microfluidically Produced Water‐in‐Oil Droplets. Chem Eng Technol 2019. [DOI: 10.1002/ceat.201900075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Maximilian Grösche
- Karlsruhe Institute of Technology (KIT)Institute for Biological Interfaces (IBG 1) Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Germany
| | - Jan G. Korvink
- Karlsruhe Institute of Technology (KIT)Institute of Microstructure Technology (IMT) Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Germany
| | - Kersten S. Rabe
- Karlsruhe Institute of Technology (KIT)Institute for Biological Interfaces (IBG 1) Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Germany
| | - Christof M. Niemeyer
- Karlsruhe Institute of Technology (KIT)Institute for Biological Interfaces (IBG 1) Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Germany
| |
Collapse
|
45
|
Sun M, Li Z, Wang S, Maryu G, Yang Q. Building Dynamic Cellular Machineries in Droplet-Based Artificial Cells with Single-Droplet Tracking and Analysis. Anal Chem 2019; 91:9813-9818. [PMID: 31284720 PMCID: PMC7260773 DOI: 10.1021/acs.analchem.9b01481] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Although the application of droplet microfluidics has grown exponentially in chemistry and biology over the past decades, robust universal platforms for the routine generation and comprehensive analysis of droplet-based artificial cells are still rare. Here we report using microfluidic droplets to reproduce a variety of types of cellular machinery in in vitro artificial cells. In combination with a unique image-based analysis method, the system enables full automation in tracking single droplets with high accuracy, high throughput, and high sensitivity. These powerful performances allow broad applicability evident in three representative droplet-based analytical prototypes that we develop for (i) droplet digital detection, (ii) in vitro transcription and translation reactions, and (iii) spatiotemporal dynamics of cell-cycle oscillations. The capacities of this platform to generate, incubate, track, and analyze individual microdroplets via real-time, long-term imaging unleash its great potential in accelerating cell-free synthetic biology. Moreover, the wide scope covering from digital to analog to morphological detections makes this droplet analysis technique adaptable for many other divergent types of droplet-based chemical and biological assays.
Collapse
Affiliation(s)
- Meng Sun
- Department of Biophysics, University of Michigan, 930 N. University Avenue, Ann Arbor, Michigan 48109, United States
| | - Zhengda Li
- Department of Biophysics, University of Michigan, 930 N. University Avenue, Ann Arbor, Michigan 48109, United States
| | - Shiyuan Wang
- Department of Biophysics, University of Michigan, 930 N. University Avenue, Ann Arbor, Michigan 48109, United States
| | - Gembu Maryu
- Department of Biophysics, University of Michigan, 930 N. University Avenue, Ann Arbor, Michigan 48109, United States
| | - Qiong Yang
- Department of Biophysics, University of Michigan, 930 N. University Avenue, Ann Arbor, Michigan 48109, United States
| |
Collapse
|
46
|
Geng H, Cho SK. Antifouling digital microfluidics using lubricant infused porous film. LAB ON A CHIP 2019; 19:2275-2283. [PMID: 31184676 DOI: 10.1039/c9lc00289h] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Electrowetting-driven digital (droplet-based) microfluidics has a tremendous impact on lab-on-a-chip applications. However, the biofouling problem impedes the real applications of such digital microfluidics. Here we report antifouling digital microfluidics by introducing lubricant infused porous film to electrowetting (more exactly, electrowetting on dielectric or EWOD). Such film minimizes direct contact between droplets and the solid surface but provides liquid-liquid contact between droplets and the lubricant liquid, which thus prevents unspecific adsorption of biomolecules to the solid surface. We demonstrate the compatibility of the lubricant infused film with EWOD to transport bio droplets. This configuration shows robust and high performance even for long cyclic operations without fouling in a wide range of concentrations of protein solutions. In addition, a variety of conductive droplets, including deionized (DI) water, saline, protein solution, DNA solution, sheep blood, milk, ionic liquid and honey, are examined, similarly showing high performance in cyclic transportations. In addition, using the same electrode patterns used in EWOD, transportations of dielectric (non-conductive) droplets including light crude oil, propylene carbonate and alcohol are also achieved. Such capability of droplet handling without fouling will certainly benefit the practical applications of digital microfluidics in droplet handling, sampling, reaction, diagnosis in clinic medicine, biotechnology and chemistry fields.
Collapse
Affiliation(s)
- Hongyao Geng
- Department of Mechanical Engineering and Materials Science, University of Pittsburgh, PA 15261, USA.
| | | |
Collapse
|
47
|
Göpfrich K, Haller B, Staufer O, Dreher Y, Mersdorf U, Platzman I, Spatz JP. One-Pot Assembly of Complex Giant Unilamellar Vesicle-Based Synthetic Cells. ACS Synth Biol 2019; 8:937-947. [PMID: 31042361 PMCID: PMC6528161 DOI: 10.1021/acssynbio.9b00034] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
![]()
Here, we introduce
a one-pot method for the bottom-up assembly
of complex single- and multicompartment synthetic cells. Cellular
components are enclosed within giant unilamellar vesicles (GUVs),
produced at the milliliter scale directly from small unilamellar vesicles
(SUVs) or proteoliposomes with only basic laboratory equipment within
minutes. Toward this end, we layer an aqueous solution, containing
SUVs and all biocomponents, on top of an oil–surfactant mix.
Manual shaking induces the spontaneous formation of surfactant-stabilized
water-in-oil droplets with a spherical supported lipid bilayer at
their periphery. Finally, to release GUV-based synthetic cells from
the oil and the surfactant shell into the physiological environment,
we add an aqueous buffer and a droplet-destabilizing agent. We prove
that the obtained GUVs are unilamellar by reconstituting the pore-forming
membrane protein α-hemolysin and assess the membrane quality
with cryotransmission electron microscopy (cryoTEM), fluorescence
recovery after photobleaching (FRAP), and zeta-potential measurements
as well as confocal fluorescence imaging. We further demonstrate that
our GUV formation method overcomes key challenges of standard techniques,
offering high volumes, a flexible choice of lipid compositions and
buffer conditions, straightforward coreconstitution of proteins, and
a high encapsulation efficiency of biomolecules and even large cargo
including cells. We thereby provide a simple, robust, and broadly
applicable strategy to mass-produce complex multicomponent GUVs for
high-throughput testing in synthetic biology and biomedicine, which
can directly be implemented in laboratories around the world.
Collapse
Affiliation(s)
- Kerstin Göpfrich
- Max Planck Institute for Medical Research, Department of Cellular Biophysics, Jahnstraße 29, D 69120, Heidelberg, Germany
- Department of Biophysical Chemistry, University of Heidelberg, Im Neuenheimer Feld 253, D 69120 Heidelberg, Germany
| | - Barbara Haller
- Max Planck Institute for Medical Research, Department of Cellular Biophysics, Jahnstraße 29, D 69120, Heidelberg, Germany
- Department of Biophysical Chemistry, University of Heidelberg, Im Neuenheimer Feld 253, D 69120 Heidelberg, Germany
| | - Oskar Staufer
- Max Planck Institute for Medical Research, Department of Cellular Biophysics, Jahnstraße 29, D 69120, Heidelberg, Germany
- Department of Biophysical Chemistry, University of Heidelberg, Im Neuenheimer Feld 253, D 69120 Heidelberg, Germany
| | - Yannik Dreher
- Max Planck Institute for Medical Research, Department of Cellular Biophysics, Jahnstraße 29, D 69120, Heidelberg, Germany
- Department of Biophysical Chemistry, University of Heidelberg, Im Neuenheimer Feld 253, D 69120 Heidelberg, Germany
| | - Ulrike Mersdorf
- Max Planck Institute for Medical Research, Department of Biomolecular Mechanisms, Jahnstraße 29, D 69120, Heidelberg, Germany
| | - Ilia Platzman
- Max Planck Institute for Medical Research, Department of Cellular Biophysics, Jahnstraße 29, D 69120, Heidelberg, Germany
- Department of Biophysical Chemistry, University of Heidelberg, Im Neuenheimer Feld 253, D 69120 Heidelberg, Germany
| | - Joachim P. Spatz
- Max Planck Institute for Medical Research, Department of Cellular Biophysics, Jahnstraße 29, D 69120, Heidelberg, Germany
- Department of Biophysical Chemistry, University of Heidelberg, Im Neuenheimer Feld 253, D 69120 Heidelberg, Germany
| |
Collapse
|
48
|
Eilenberger C, Spitz S, Bachmann BEM, Ehmoser EK, Ertl P, Rothbauer M. The Usual Suspects 2019: of Chips, Droplets, Synthesis, and Artificial Cells. MICROMACHINES 2019; 10:E285. [PMID: 31035574 PMCID: PMC6562886 DOI: 10.3390/mi10050285] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 04/24/2019] [Accepted: 04/26/2019] [Indexed: 12/03/2022]
Abstract
Synthetic biology aims to understand fundamental biological processes in more detail than possible for actual living cells. Synthetic biology can combat decomposition and build-up of artificial experimental models under precisely controlled and defined environmental and biochemical conditions. Microfluidic systems can provide the tools to improve and refine existing synthetic systems because they allow control and manipulation of liquids on a micro- and nanoscale. In addition, chip-based approaches are predisposed for synthetic biology applications since they present an opportune technological toolkit capable of fully automated high throughput and content screening under low reagent consumption. This review critically highlights the latest updates in microfluidic cell-free and cell-based protein synthesis as well as the progress on chip-based artificial cells. Even though progress is slow for microfluidic synthetic biology, microfluidic systems are valuable tools for synthetic biology and may one day help to give answers to long asked questions of fundamental cell biology and life itself.
Collapse
Affiliation(s)
- Christoph Eilenberger
- Institute of Applied Synthetic Chemistry, Institute of Chemical Technologies and Analytics, Faculty of Technical Chemistry, Vienna University of Technology, A-1060 Vienna, Austria.
| | - Sarah Spitz
- Institute of Applied Synthetic Chemistry, Institute of Chemical Technologies and Analytics, Faculty of Technical Chemistry, Vienna University of Technology, A-1060 Vienna, Austria.
| | - Barbara Eva Maria Bachmann
- Austrian Cluster for Tissue Regeneration, Vienna, Austria; Ludwig Boltzmann Institute for Experimental and Clinical Traumatology, Allgemeine Unfallversicherungsanstalt (AUVA) Research Centre, A-1200 Vienna, Austria.
| | - Eva Kathrin Ehmoser
- Institute of Synthetic Bioarchitectures, Department of Nanobiotechnology, University of Natural Resources and Life Sciences Vienna, A-1190 Vienna, Austria.
| | - Peter Ertl
- Institute of Applied Synthetic Chemistry, Institute of Chemical Technologies and Analytics, Faculty of Technical Chemistry, Vienna University of Technology, A-1060 Vienna, Austria.
| | - Mario Rothbauer
- Institute of Applied Synthetic Chemistry, Institute of Chemical Technologies and Analytics, Faculty of Technical Chemistry, Vienna University of Technology, A-1060 Vienna, Austria.
| |
Collapse
|
49
|
Gorter de Vries AR, Koster CC, Weening SM, Luttik MAH, Kuijpers NGA, Geertman JMA, Pronk JT, Daran JMG. Phenotype-Independent Isolation of Interspecies Saccharomyces Hybrids by Dual-Dye Fluorescent Staining and Fluorescence-Activated Cell Sorting. Front Microbiol 2019; 10:871. [PMID: 31105669 PMCID: PMC6498416 DOI: 10.3389/fmicb.2019.00871] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 04/04/2019] [Indexed: 11/13/2022] Open
Abstract
Interspecies hybrids of Saccharomyces species are found in a variety of industrial environments and often outperform their parental strains in industrial fermentation processes. Interspecies hybridization is therefore increasingly considered as an approach for improvement and diversification of yeast strains for industrial application. However, current hybridization methods are limited by their reliance on pre-existing or introduced selectable phenotypes. This study presents a high-throughput phenotype-independent method for isolation of interspecies Saccharomyces hybrids based on dual dye-staining and subsequent mating of two strains, followed by enrichment of double-stained hybrid cells from a mating population by fluorescence-activated cell sorting (FACS). Pilot experiments on intra-species mating of heterothallic haploid S. cerevisiae strains showed that 80% of sorted double-stained cells were hybrids. The protocol was further optimized by mating an S. cerevisiae haploid with homothallic S. eubayanus spores with complementary selectable phenotypes. In crosses without selectable phenotype, using S. cerevisiae and S. eubayanus haploids derived from laboratory as well as industrial strains, 10 to 15% of double-stained cells isolated by FACS were hybrids. When applied to rare mating, sorting of double-stained cells consistently resulted in about 600-fold enrichment of hybrid cells. Mating of dual-stained cells and FACS-based selection allows efficient enrichment of interspecies Saccharomyces hybrids within a matter of days and without requiring selectable hybrid phenotypes, both for homothallic and heterothallic strains. This strategy should accelerate the isolation of laboratory-made hybrids, facilitate research into hybrid heterosis and offer new opportunities for non-GM industrial strain improvement and diversification.
Collapse
Affiliation(s)
| | - Charlotte C Koster
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Susan M Weening
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Marijke A H Luttik
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Niels G A Kuijpers
- Global Innovation and Research, HEINEKEN Supply Chain B.V., Zoeterwoude, Netherlands
| | | | - Jack T Pronk
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Jean-Marc G Daran
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| |
Collapse
|
50
|
Hürtgen D, Vogel SK, Schwille P. Cytoskeletal and Actin-Based Polymerization Motors and Their Role in Minimal Cell Design. ACTA ACUST UNITED AC 2019; 3:e1800311. [PMID: 32648711 DOI: 10.1002/adbi.201800311] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 02/28/2019] [Indexed: 01/28/2023]
Abstract
Life implies motion. In cells, protein-based active molecular machines drive cell locomotion and intracellular transport, control cell shape, segregate genetic material, and split a cell in two parts. Key players among molecular machines driving these various cell functions are the cytoskeleton and motor proteins that convert chemical bound energy into mechanical work. Findings over the last decades in the field of in vitro reconstitutions of cytoskeletal and motor proteins have elucidated mechanistic details of these active protein systems. For example, a complex spatial and temporal interplay between the cytoskeleton and motor proteins is responsible for the translation of chemically bound energy into (directed) movement and force generation, which eventually governs the emergence of complex cellular functions. Understanding these mechanisms and the design principles of the cytoskeleton and motor proteins builds the basis for mimicking fundamental life processes. Here, a brief overview of actin, prokaryotic actin analogs, and motor proteins and their potential role in the design of a minimal cell from the bottom-up is provided.
Collapse
Affiliation(s)
- Daniel Hürtgen
- Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiology & LOEWE Center for Synthetic Microbiology (Synmikro), D-35043, Marburg, Germany
| | - Sven Kenjiro Vogel
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry , Am Klopferspitz 18, D-82152, Martinsried, Germany
| | - Petra Schwille
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry , Am Klopferspitz 18, D-82152, Martinsried, Germany
| |
Collapse
|