1
|
Hoffmann A, Timm A, Johnson C, Rupp S, Grumaz C. Automation of customizable library preparation for next-generation sequencing into an open microfluidic platform. Sci Rep 2024; 14:17150. [PMID: 39060329 PMCID: PMC11282295 DOI: 10.1038/s41598-024-67950-6] [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: 12/12/2023] [Accepted: 07/17/2024] [Indexed: 07/28/2024] Open
Abstract
Next-generation sequencing (NGS) is becoming more relevant for medical diagnostics, especially for using cell-free DNA to monitor response to therapy in cancer management, as high sensitivity of NGS enables detection of rare events. Sequencing Library preparation is a time-consuming and complex process, and large-scale liquid handlers are often used for automation. However, for smaller labs and low-to-medium throughput samples, these liquid handlers are expensive and need experts for handling. This work presents a proof-of-concept for library preparation on a commercially available and open lab-on-a-chip platform, which provides an alternative automation for low-to-medium throughput requirements. It covers common library preparation steps optimized to a microfluidic environment that include customizable PCR for target enrichment, end-repair, adapter ligation, nucleic acid purification via magnetic beads, and an integrated quantification step. The functionality of the cartridge is demonstrated with reference cfDNA containing different allelic frequencies of seven known mutations. Processing the samples in the cartridge reveals highly comparable results to manual processing (Pearson r = 0.94) based on amplicon sequencing. Summarized, the proposed automated lab-on-a-chip workflow for customizable library preparation could further pave the way for NGS to evolve from a technology used for research purposes to one that is applied in routine cancer management.
Collapse
Affiliation(s)
- Anne Hoffmann
- Institute of Interfacial Process Engineering and Plasma Technology, University of Stuttgart, Nobelstraße 12, 70569, Stuttgart, Germany
- Corporate Sector Research and Advance Engineering, Robert Bosch GmbH, Robert-Bosch-Campus 1, 71272, Renningen, Germany
| | - Anke Timm
- Corporate Sector Research and Advance Engineering, Robert Bosch GmbH, Robert-Bosch-Campus 1, 71272, Renningen, Germany
| | - Christopher Johnson
- Robert Bosch Research & Technology Center, Robert Bosch LLC, 384 Santa Trinita Avenue, Sunnyvale, CA, 94085, USA
| | - Steffen Rupp
- Institute of Interfacial Process Engineering and Plasma Technology, University of Stuttgart, Nobelstraße 12, 70569, Stuttgart, Germany
- Fraunhofer Institute for Interfacial Engineering and Biotechnology, Nobelstr. 12, 70569, Stuttgart, Germany
| | - Christian Grumaz
- Corporate Sector Research and Advance Engineering, Robert Bosch GmbH, Robert-Bosch-Campus 1, 71272, Renningen, Germany.
| |
Collapse
|
2
|
Hess JF, Kotrová M, Fricke B, Songia S, Rigamonti S, Cavagna R, Tosi M, Paust N, Langerak AW, Spinelli O, Cazzaniga G, Brüggemann M, Hutzenlaub T. Clinical pilot study on microfluidic automation of IGH-VJ library preparation for next generation sequencing. Clin Chem Lab Med 2024; 62:e164-e167. [PMID: 38153095 DOI: 10.1515/cclm-2023-1346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 12/18/2023] [Indexed: 12/29/2023]
Affiliation(s)
- Jacob F Hess
- Hahn-Schickard, Freiburg, Germany
- Laboratory for MEMS Applications, IMTEK - Department of Microsystems Engineering, University of Freiburg, Freiburg, Germany
| | - Michaela Kotrová
- Unit for Hematological Diagnostics, II. Medical Department, University Medical Center Schleswig Holstein, Kiel, Germany
| | - Birgit Fricke
- Unit for Hematological Diagnostics, II. Medical Department, University Medical Center Schleswig Holstein, Kiel, Germany
| | - Simona Songia
- Centro Tettamanti, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
| | - Silvia Rigamonti
- Centro Tettamanti, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
| | - Roberta Cavagna
- Struttura Complessa Ematologia, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Manuela Tosi
- Struttura Complessa Ematologia, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Nils Paust
- Hahn-Schickard, Freiburg, Germany
- Laboratory for MEMS Applications, IMTEK - Department of Microsystems Engineering, University of Freiburg, Freiburg, Germany
| | - Anton W Langerak
- Department of Immunology, Laboratory Medical Immunology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Orietta Spinelli
- Struttura Complessa Ematologia, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Giovanni Cazzaniga
- Centro Tettamanti, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
- School of Medicine and Surgery, University of Milan-Bicocca, Monza, Italy
| | - Monika Brüggemann
- Unit for Hematological Diagnostics, II. Medical Department, University Medical Center Schleswig Holstein, Kiel, Germany
| | - Tobias Hutzenlaub
- Hahn-Schickard, Freiburg, Germany
- Laboratory for MEMS Applications, IMTEK - Department of Microsystems Engineering, University of Freiburg, Freiburg, Germany
| |
Collapse
|
3
|
Ott O, Tolppi S, Figueroa-Cruz J, Myagmar K, Unurbuyan K, Tripathi A. Leveraging the fundamentals of heat transfer and fluid mechanics in microscale geometries for automated next-generation sequencing library preparation. Sci Rep 2024; 14:12564. [PMID: 38822053 DOI: 10.1038/s41598-024-63014-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 05/23/2024] [Indexed: 06/02/2024] Open
Abstract
Next-generation sequencing (NGS) is emerging as a powerful tool for molecular diagnostics but remains limited by cumbersome and inefficient sample preparation. We present an innovative automated NGS library preparation system with a simplified mechanical design that exploits both macro- and microfluidic properties for optimizing heat transfer, reaction kinetics, mass transfer, fluid mechanics, adsorption-desorption rates, and molecular thermodynamics. Our approach introduces a unique two-cannula cylindrical capillary system connected to a programmable syringe pump and a Peltier heating element able to execute all steps with high efficiency. Automatic reagent movement, mixing, and magnetic bead-based washing with capillary-based thermal cycling (capillary-PCR) are completely integrated into a single platform. The manual 3-h library preparation process is reduced to less than 15 min of hands-on time via optimally pre-plated reagent plates, followed by less than 6 h of instrument run time during which no user interaction is required. We applied this method to two library preparation assays with different DNA fragmentation requirements (mechanical vs. enzymatic fragmentation), sufficiently limiting consumable use to one cartridge and one 384 well-plate per run. Our platform successfully prepared eight libraries in parallel, generating sequencing data for both human and Escherichia coli DNA libraries with negligible coverage bias compared to positive controls. All sequencing data from our libraries attained Phred (Q) scores > 30, mapping to reference genomes at 99% confidence. The method achieved final library concentrations and size distributions comparable with the conventional manual approach, demonstrating compatibility with downstream sequencing and subsequent data analysis. Our engineering design offers repeatability and consistency in the quality of sequence-able libraries, asserting the importance of mechanical design considerations that employ and optimize fundamental fluid mechanics and heat transfer properties. Furthermore in this work, we provide unique insights into the mechanisms of sample loss within NGS library preparation assays compared with automated adaptations and pinpoint areas in which the principles of thermodynamics, fluid mechanics, and heat transfer can improve future mechanical design iterations.
Collapse
Affiliation(s)
- Olivia Ott
- Center for Biomedical Engineering, School of Engineering, Brown University, Providence, RI, USA
| | - Sabrina Tolppi
- Center for Biomedical Engineering, School of Engineering, Brown University, Providence, RI, USA
| | - Jennifer Figueroa-Cruz
- Center for Biomedical Engineering, School of Engineering, Brown University, Providence, RI, USA
| | - Khaliun Myagmar
- Center for Biomedical Engineering, School of Engineering, Brown University, Providence, RI, USA
| | - Khulan Unurbuyan
- Center for Biomedical Engineering, School of Engineering, Brown University, Providence, RI, USA
| | - Anubhav Tripathi
- Center for Biomedical Engineering, School of Engineering, Brown University, Providence, RI, USA.
| |
Collapse
|
4
|
Guo J, Brassard D, Adam N, Verster AJ, Shay JA, Miville-Godin C, Janta-Polczynski M, Ferreira J, Mounier M, Pilar AV, Tapp K, Classen A, Shiu M, Charlebois D, Petronella N, Weedmark K, Corneau N, Veres T. Automated centrifugal microfluidic system for the preparation of adaptor-ligated sequencing libraries. LAB ON A CHIP 2024; 24:182-196. [PMID: 38044704 DOI: 10.1039/d3lc00781b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
The intensive workload associated with the preparation of high-quality DNA libraries remains a key obstacle toward widespread deployment of sequencing technologies in remote and resource-limited areas. We describe the development of single-use microfluidic devices driven by an advanced pneumatic centrifugal microfluidic platform, the PowerBlade, to automate the preparation of Illumina-compatible libraries based on adaptor ligation methodology. The developed on-chip workflow includes enzymatic DNA fragmentation coupled to end-repair, adaptor ligation, first DNA cleanup, PCR amplification, and second DNA cleanup. This complex workflow was successfully integrated into simple thermoplastic microfluidic devices that are amenable to mass production with injection molding. The system was validated by preparing, on chip, libraries from a mixture of genomic DNA extracted from three common foodborne pathogens (Listeria monocytogenes, Escherichia coli and Salmonella enterica serovar Typhimurium) and comparing them with libraries made via a manual procedure. The two types of libraries were found to exhibit similar quality control metrics (including genome coverage, assembly, and relative abundances) and led to nearly uniform coverage independent of GC content. This microfluidic technology offers a time-saving and cost-effective alternative to manual procedures and robotic-based automation, making it suitable for deployment in remote environments where technical expertise and resources might be scarce. Specifically, it facilitates field practices that involve mid- to low-throughput sequencing, such as tasks related to foodborne pathogen detection, characterization, and microbial profiling.
Collapse
Affiliation(s)
- Jimin Guo
- Medical Devices Research Center, Life Sciences Division, National Research Council of Canada, 75 de Mortagne Boulevard, Boucherville, QC, J4B 6Y4, Canada.
| | - Daniel Brassard
- Medical Devices Research Center, Life Sciences Division, National Research Council of Canada, 75 de Mortagne Boulevard, Boucherville, QC, J4B 6Y4, Canada.
| | - Nadine Adam
- Bureau of Microbial Hazards, Microbiology Research Division, Health Canada, 251 Sir Frederick Banting Driveway, Ottawa, ON, K1A 0K9, Canada.
| | - Adrian J Verster
- Bureau of Food Surveillance and Science Integration, Bioinformatics High-Capacity Computing Laboratory, Health Canada, 251 Sir Frederick Banting Driveway, Ottawa, ON, K1A 0K9, Canada
| | - Julie A Shay
- Bureau of Food Surveillance and Science Integration, Bioinformatics High-Capacity Computing Laboratory, Health Canada, 251 Sir Frederick Banting Driveway, Ottawa, ON, K1A 0K9, Canada
| | - Caroline Miville-Godin
- Medical Devices Research Center, Life Sciences Division, National Research Council of Canada, 75 de Mortagne Boulevard, Boucherville, QC, J4B 6Y4, Canada.
| | - Mojra Janta-Polczynski
- Medical Devices Research Center, Life Sciences Division, National Research Council of Canada, 75 de Mortagne Boulevard, Boucherville, QC, J4B 6Y4, Canada.
| | - Jason Ferreira
- Medical Devices Research Center, Life Sciences Division, National Research Council of Canada, 75 de Mortagne Boulevard, Boucherville, QC, J4B 6Y4, Canada.
| | - Maxence Mounier
- Medical Devices Research Center, Life Sciences Division, National Research Council of Canada, 75 de Mortagne Boulevard, Boucherville, QC, J4B 6Y4, Canada.
| | - Ana V Pilar
- Bureau of Microbial Hazards, Microbiology Research Division, Health Canada, 251 Sir Frederick Banting Driveway, Ottawa, ON, K1A 0K9, Canada.
| | - Kyle Tapp
- Bureau of Microbial Hazards, Microbiology Research Division, Health Canada, 251 Sir Frederick Banting Driveway, Ottawa, ON, K1A 0K9, Canada.
| | - Adam Classen
- Bureau of Microbial Hazards, Microbiology Research Division, Health Canada, 251 Sir Frederick Banting Driveway, Ottawa, ON, K1A 0K9, Canada.
| | - Matthew Shiu
- Medical Devices Research Center, Life Sciences Division, National Research Council of Canada, 75 de Mortagne Boulevard, Boucherville, QC, J4B 6Y4, Canada.
| | - Denis Charlebois
- Canadian Space Agency, 6767 Route de l'Aéroport, Saint-Hubert, QC J3Y 8Y9, Canada
| | - Nicholas Petronella
- Bureau of Food Surveillance and Science Integration, Bioinformatics High-Capacity Computing Laboratory, Health Canada, 251 Sir Frederick Banting Driveway, Ottawa, ON, K1A 0K9, Canada
| | - Kelly Weedmark
- Bureau of Microbial Hazards, Microbiology Research Division, Health Canada, 251 Sir Frederick Banting Driveway, Ottawa, ON, K1A 0K9, Canada.
| | - Nathalie Corneau
- Bureau of Microbial Hazards, Microbiology Research Division, Health Canada, 251 Sir Frederick Banting Driveway, Ottawa, ON, K1A 0K9, Canada.
| | - Teodor Veres
- Medical Devices Research Center, Life Sciences Division, National Research Council of Canada, 75 de Mortagne Boulevard, Boucherville, QC, J4B 6Y4, Canada.
| |
Collapse
|
5
|
Coelho BJ, Neto JP, Sieira B, Moura AT, Fortunato E, Martins R, Baptista PV, Igreja R, Águas H. Hybrid Digital-Droplet Microfluidic Chip for Applications in Droplet Digital Nucleic Acid Amplification: Design, Fabrication and Characterization. SENSORS (BASEL, SWITZERLAND) 2023; 23:4927. [PMID: 37430841 DOI: 10.3390/s23104927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 05/05/2023] [Accepted: 05/17/2023] [Indexed: 07/12/2023]
Abstract
Microfluidic-based platforms have become a hallmark for chemical and biological assays, empowering micro- and nano-reaction vessels. The fusion of microfluidic technologies (digital microfluidics, continuous-flow microfluidics, and droplet microfluidics, just to name a few) presents great potential for overcoming the inherent limitations of each approach, while also elevating their respective strengths. This work exploits the combination of digital microfluidics (DMF) and droplet microfluidics (DrMF) on a single substrate, where DMF enables droplet mixing and further acts as a controlled liquid supplier for a high-throughput nano-liter droplet generator. Droplet generation is performed at a flow-focusing region, operating on dual pressure: negative pressure applied to the aqueous phase and positive pressure applied to the oil phase. We evaluate the droplets produced with our hybrid DMF-DrMF devices in terms of droplet volume, speed, and production frequency and further compare them with standalone DrMF devices. Both types of devices enable customizable droplet production (various volumes and circulation speeds), yet hybrid DMF-DrMF devices yield more controlled droplet production while achieving throughputs that are similar to standalone DrMF devices. These hybrid devices enable the production of up to four droplets per second, which reach a maximum circulation speed close to 1540 µm/s and volumes as low as 0.5 nL.
Collapse
Affiliation(s)
- Beatriz J Coelho
- CENIMAT|i3N, Department of Materials Science, NOVA School of Science and Technology, Campus de Caparica, NOVA University of Lisbon and CEMOP/UNINOVA, 2829-516 Caparica, Portugal
- UCIBIO, I4HB, Department of Life Sciences, NOVA School of Science and Technology, Campus de Caparica, NOVA University of Lisbon, 2829-516 Caparica, Portugal
| | - Joana P Neto
- CENIMAT|i3N, Department of Materials Science, NOVA School of Science and Technology, Campus de Caparica, NOVA University of Lisbon and CEMOP/UNINOVA, 2829-516 Caparica, Portugal
| | - Bárbara Sieira
- CENIMAT|i3N, Department of Materials Science, NOVA School of Science and Technology, Campus de Caparica, NOVA University of Lisbon and CEMOP/UNINOVA, 2829-516 Caparica, Portugal
| | - André T Moura
- CENIMAT|i3N, Department of Materials Science, NOVA School of Science and Technology, Campus de Caparica, NOVA University of Lisbon and CEMOP/UNINOVA, 2829-516 Caparica, Portugal
| | - Elvira Fortunato
- CENIMAT|i3N, Department of Materials Science, NOVA School of Science and Technology, Campus de Caparica, NOVA University of Lisbon and CEMOP/UNINOVA, 2829-516 Caparica, Portugal
| | - Rodrigo Martins
- CENIMAT|i3N, Department of Materials Science, NOVA School of Science and Technology, Campus de Caparica, NOVA University of Lisbon and CEMOP/UNINOVA, 2829-516 Caparica, Portugal
| | - Pedro V Baptista
- UCIBIO, I4HB, Department of Life Sciences, NOVA School of Science and Technology, Campus de Caparica, NOVA University of Lisbon, 2829-516 Caparica, Portugal
| | - Rui Igreja
- CENIMAT|i3N, Department of Materials Science, NOVA School of Science and Technology, Campus de Caparica, NOVA University of Lisbon and CEMOP/UNINOVA, 2829-516 Caparica, Portugal
| | - Hugo Águas
- CENIMAT|i3N, Department of Materials Science, NOVA School of Science and Technology, Campus de Caparica, NOVA University of Lisbon and CEMOP/UNINOVA, 2829-516 Caparica, Portugal
| |
Collapse
|
6
|
Luo Y, Cao Z, Liu Y, Zhang R, Yang S, Wang N, Shi Q, Li J, Dong S, Fan C, Zhao J. The emerging landscape of microfluidic applications in DNA data storage. LAB ON A CHIP 2023; 23:1981-2004. [PMID: 36946437 DOI: 10.1039/d2lc00972b] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
DNA has been considered a promising alternative to the current solid-state devices for digital information storage. The past decade has witnessed tremendous progress in the field of DNA data storage contributed by researchers from various disciplines. However, the current development status of DNA storage is still far from practical use, mainly due to its high material cost and time consumption for data reading/writing, as well as the lack of a comprehensive, automated, and integrated system. Microfluidics, being capable of handling and processing micro-scale fluid samples in a massively paralleled and highly integrated manner, has gradually been recognized as a promising candidate for addressing the aforementioned issues. In this review, we provide a discussion on recent efforts of applying microfluidics to advance the development of DNA data storage. Moreover, to showcase the tremendous potential that microfluidics can contribute to this field, we will further highlight the recent advancements of applying microfluidics to the key functional modules within the DNA data storage workflow. Finally, we share our perspectives on future directions for how to continue the infusion of microfluidics with DNA data storage and how to advance toward a truly integrated system and reach real-life applications.
Collapse
Affiliation(s)
- Yuan Luo
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 200050, China.
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhen Cao
- College of Information Science and Electronic Engineering, Zhejiang University, Hangzhou 310027, China.
- International Joint Innovation Center, Zhejiang University, Haining 314400, China
| | - Yifan Liu
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
- Shanghai Clinical Research and Trial Center, Shanghai, 201210, China
| | - Rong Zhang
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
| | - Shijia Yang
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 200050, China.
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ning Wang
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 200050, China.
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qingyuan Shi
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
| | - Jie Li
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
| | - Shurong Dong
- College of Information Science and Electronic Engineering, Zhejiang University, Hangzhou 310027, China.
- International Joint Innovation Center, Zhejiang University, Haining 314400, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jianlong Zhao
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 200050, China.
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, P.R. China
| |
Collapse
|
7
|
Xu X, Cai L, Liang S, Zhang Q, Lin S, Li M, Yang Q, Li C, Han Z, Yang C. Digital microfluidics for biological analysis and applications. LAB ON A CHIP 2023; 23:1169-1191. [PMID: 36644972 DOI: 10.1039/d2lc00756h] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Digital microfluidics (DMF) is an emerging liquid-handling technology based on arrays of microelectrodes for the precise manipulation of discrete droplets. DMF offers the benefits of automation, addressability, integration and dynamic configuration ability, and provides enclosed picoliter-to-microliter reaction space, making it suitable for lab-on-a-chip biological analysis and applications that require high integration and intricate processes. A review of DMF bioassays with a special emphasis on those actuated by electrowetting on dielectric (EWOD) force is presented here. Firstly, a brief introduction is presented on both the theory of EWOD actuation and the types of droplet motion. Subsequently, a comprehensive overview of DMF-based biological analysis and applications, including nucleic acid, protein, immunoreaction and cell assays, is provided. Finally, a discussion on the strengths, challenges, and potential applications and perspectives in this field is presented.
Collapse
Affiliation(s)
- Xing Xu
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, The Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, Department of Chemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China.
| | - Linfeng Cai
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, The Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, Department of Chemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China.
| | - Shanshan Liang
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, The Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, Department of Chemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China.
| | - Qiannan Zhang
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, The Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, Department of Chemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China.
| | - Shiyan Lin
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, The Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, Department of Chemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China.
| | - Mingying Li
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, The Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, Department of Chemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China.
| | - Qizheng Yang
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, The Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, Department of Chemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China.
| | - Chong Li
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, The Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, Department of Chemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China.
| | - Ziyan Han
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, The Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, Department of Chemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China.
| | - Chaoyong Yang
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, The Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, Department of Chemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China.
- Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| |
Collapse
|
8
|
Nemr CR, Sklavounos AA, Wheeler AR, Kelley SO. Digital microfluidics as an emerging tool for bacterial protocols. SLAS Technol 2023; 28:2-15. [PMID: 36323389 DOI: 10.1016/j.slast.2022.10.001] [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: 06/20/2022] [Revised: 09/30/2022] [Accepted: 10/25/2022] [Indexed: 11/05/2022]
Abstract
Bacteria are widely studied in various research areas, including synthetic biology, sequencing and diagnostic testing. Protocols involving bacteria are often multistep, cumbersome and require access to a long list of instruments to perform experiments. In order to streamline these processes, the fluid handling technique digital microfluidics (DMF) has provided a miniaturized platform to perform various steps of bacterial protocols from sample preparation to analysis. DMF devices can be paired/interfaced with instrumentation such as microscopes, plate readers, and incubators, demonstrating their versatility with existing research tools. Alternatively, DMF instruments can be integrated into all-in-one packages with on-chip magnetic separation for sample preparation, heating/cooling modules to perform assay steps and cameras for absorbance and/or fluorescence measurements. This perspective outlines the beneficial features DMF offers to bacterial protocols, highlights limitations of current work and proposes future directions for this tool's expansion in the field.
Collapse
Affiliation(s)
- Carine R Nemr
- Department of Chemistry, Harvey Mudd College, 301 Platt Boulevard, Claremont, CA, 91711, USA; Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario, M5S 3H6, Canada.
| | - Alexandros A Sklavounos
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario, M5S 3H6, Canada; Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario, M5S 3G9, Canada
| | - Aaron R Wheeler
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario, M5S 3H6, Canada; Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario, M5S 3G9, Canada; Institute of Biomedical Engineering, University of Toronto, 164 College Street, Toronto, Ontario, M5S 3G9, Canada
| | - Shana O Kelley
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario, M5S 3H6, Canada; Institute of Biomedical Engineering, University of Toronto, 164 College Street, Toronto, Ontario, M5S 3G9, Canada; Department of Pharmaceutical Science, University of Toronto, 144 College Street, Toronto, Ontario, M5S 3E5, Canada; Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA; Department of Biomedical Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA
| |
Collapse
|
9
|
Chantipmanee N, Xu Y. Toward nanofluidics‐based mass spectrometry for exploring the unknown complex and heterogenous subcellular worlds. VIEW 2022. [DOI: 10.1002/viw.20220036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Affiliation(s)
- Nattapong Chantipmanee
- Department of Chemical Engineering Graduate School of Engineering Osaka Metropolitan University Sakai Japan
| | - Yan Xu
- Department of Chemical Engineering Graduate School of Engineering Osaka Metropolitan University Sakai Japan
- Japan Science and Technology Agency (JST) PRESTO Kawaguchi Japan
- Japan Science and Technology Agency (JST) CREST Kawaguchi Japan
| |
Collapse
|
10
|
Schneider L, Usherwood T, Tripathi A. A microfluidic platform for high-purity cell free DNA extraction from plasma for non-invasive prenatal testing. Prenat Diagn 2022; 42:240-253. [PMID: 35032044 DOI: 10.1002/pd.6092] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 12/22/2021] [Accepted: 01/10/2022] [Indexed: 12/15/2022]
Abstract
OBJECTIVES Increase the yield and purity of cell-free DNA (cfDNA) extracted from plasma for non-invasive prenatal testing (NIPT) as inefficiencies in this extraction and purification can dramatically affect the sensitivity and specificity of the test. METHODS This work integrates cfDNA extraction from plasma with a microfluidic chip platform by combining magnetic bead-based extraction and electroosmotic flow on the microfluidic chip. Various wash buffers and voltage conditions were simulated using COMSOL Multiphysics Modeling and tested experimentally. RESULTS When performing the first wash step of this assay on the microfluidic chip with 300 V applied across the channel there was a six-fold increase in the A260 /A230 ratio showing a significant improvement (p value 0.0005) in the purity of the extracted sample all while maintaining a yield of 68.19%. These values are critical as a high yield results in more sample to analyze and an increase in A260 /A230 ratio corresponds to a decrease in salt contaminants such as guanidinium thiocyanate which can interfere with downstream processes during DNA library preparation and potentially hinder the NIPT screening results. CONCLUSIONS This technique has the potential to improve NIPT outcomes and other clinically relevant workflows that use cfDNA as an analyte such as cancer detection.
Collapse
Affiliation(s)
- Lindsay Schneider
- Center for Biomedical Engineering, Brown University, Providence, Rhode Island, USA
| | - Thomas Usherwood
- Center for Biomedical Engineering, Brown University, Providence, Rhode Island, USA
| | - Anubhav Tripathi
- Center for Biomedical Engineering, Brown University, Providence, Rhode Island, USA
| |
Collapse
|
11
|
Hess JF, Hess ME, Zengerle R, Paust N, Boerries M, Hutzenlaub T. Automated library preparation for whole genome sequencing by centrifugal microfluidics. Anal Chim Acta 2021; 1182:338954. [PMID: 34602197 DOI: 10.1016/j.aca.2021.338954] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 07/19/2021] [Accepted: 08/02/2021] [Indexed: 11/18/2022]
Abstract
Next generation sequencing is evolving from a research tool into a method applied in diagnostic routine. The complete sequencing workflow includes sample pre-processing, library preparation, sequencing and bioinformatics. High quality in each of these steps is necessary to obtain excellent sequencing results. The tedious and error-prone library preparation poses a significant challenge for smaller laboratories, where high throughput pipetting robots are not cost-effective. Here we present an automated library preparation for whole genome sequencing using centrifugal microfluidics. Two samples can be run per cartridge. Precise metering of reagents allows the required liquid volumes to be reduced by 40% and the amount of sample used by 60%. The functionality of the cartridge is demonstrated with bacteria and DNA extracted from a human FFPE sample. For the bacterial sample, mean sequencing depths from 140 to 183 reads and a coverage of 99.8% of the reference genome were detected. For the human DNA, mean sequencing depths of 4.4-5.7 reads and a coverage of 78.2% of the effective reference genome were observed.
Collapse
Affiliation(s)
- Jacob Friedrich Hess
- Laboratory for MEMS Applications, IMTEK, University of Freiburg, Georges-Koehler-Allee 103, 79110, Freiburg, Germany; Hahn-Schickard, Georges-Koehler-Allee 103, 79110, Freiburg, Germany.
| | - Maria Elena Hess
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Breisacherstr. 153, 79110, Freiburg, Germany; Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Roland Zengerle
- Laboratory for MEMS Applications, IMTEK, University of Freiburg, Georges-Koehler-Allee 103, 79110, Freiburg, Germany; Hahn-Schickard, Georges-Koehler-Allee 103, 79110, Freiburg, Germany
| | - Nils Paust
- Laboratory for MEMS Applications, IMTEK, University of Freiburg, Georges-Koehler-Allee 103, 79110, Freiburg, Germany; Hahn-Schickard, Georges-Koehler-Allee 103, 79110, Freiburg, Germany
| | - Melanie Boerries
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Breisacherstr. 153, 79110, Freiburg, Germany; German Cancer Consortium (DKTK), Partner Site Freiburg and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Tobias Hutzenlaub
- Laboratory for MEMS Applications, IMTEK, University of Freiburg, Georges-Koehler-Allee 103, 79110, Freiburg, Germany; Hahn-Schickard, Georges-Koehler-Allee 103, 79110, Freiburg, Germany
| |
Collapse
|
12
|
Ha NS, de Raad M, Han LZ, Golini A, Petzold CJ, Northen TR. Faster, better, and cheaper: harnessing microfluidics and mass spectrometry for biotechnology. RSC Chem Biol 2021; 2:1331-1351. [PMID: 34704041 PMCID: PMC8496484 DOI: 10.1039/d1cb00112d] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 07/01/2021] [Indexed: 12/14/2022] Open
Abstract
High-throughput screening technologies are widely used for elucidating biological activities. These typically require trade-offs in assay specificity and sensitivity to achieve higher throughput. Microfluidic approaches enable rapid manipulation of small volumes and have found a wide range of applications in biotechnology providing improved control of reaction conditions, faster assays, and reduced reagent consumption. The integration of mass spectrometry with microfluidics has the potential to create high-throughput, sensitivity, and specificity assays. This review introduces the widely-used mass spectrometry ionization techniques that have been successfully integrated with microfluidics approaches such as continuous-flow system, microchip electrophoresis, droplet microfluidics, digital microfluidics, centrifugal microfluidics, and paper microfluidics. In addition, we discuss recent applications of microfluidics integrated with mass spectrometry in single-cell analysis, compound screening, and the study of microorganisms. Lastly, we provide future outlooks towards online coupling, improving the sensitivity and integration of multi-omics into a single platform.
Collapse
Affiliation(s)
- Noel S Ha
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory Berkeley CA USA
- US Department of Energy Joint BioEnergy Institute Emeryville CA USA
| | - Markus de Raad
- Environmental Genomics and Systems Biology, Biosciences, Lawrence Berkeley National Laboratory Berkeley CA USA
| | - La Zhen Han
- Environmental Genomics and Systems Biology, Biosciences, Lawrence Berkeley National Laboratory Berkeley CA USA
- US Department of Energy Joint Genome Institute Berkeley CA USA
| | - Amber Golini
- Environmental Genomics and Systems Biology, Biosciences, Lawrence Berkeley National Laboratory Berkeley CA USA
- US Department of Energy Joint Genome Institute Berkeley CA USA
| | - Christopher J Petzold
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory Berkeley CA USA
- US Department of Energy Joint BioEnergy Institute Emeryville CA USA
| | - Trent R Northen
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory Berkeley CA USA
- US Department of Energy Joint BioEnergy Institute Emeryville CA USA
- Environmental Genomics and Systems Biology, Biosciences, Lawrence Berkeley National Laboratory Berkeley CA USA
- US Department of Energy Joint Genome Institute Berkeley CA USA
| |
Collapse
|
13
|
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
|
14
|
Paul S, Moon H. Drop-to-drop liquid-liquid extraction of DNA in an electrowetting-on-dielectric digital microfluidics. BIOMICROFLUIDICS 2021; 15:034110. [PMID: 34136060 PMCID: PMC8189723 DOI: 10.1063/5.0054003] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 05/25/2021] [Indexed: 05/11/2023]
Abstract
Recent advancements in microfluidics and lab-on-a-chip technologies enabled miniaturization and automation of many downstream nucleic acid analysis steps such as PCR. However, DNA extraction/isolation protocol remains a stand-alone sample preparation step. For a quick sample-to-result solution, downstream protocols and sample preparation protocols need to be seamlessly integrated into a single lab-on-a-chip platform. As a step toward such integration, this paper introduces microfluidic DNA isolation using the liquid-liquid extraction (LLE) method in the drop-to-drop (DTD) format. The electrowetting-on-dielectric digital microfluidic platform is capable of handling a two-phase liquid system easily, which enables DTD LLE. In this study, the extraction of plasmid DNA (pDNA) from an aqueous sample to an ionic liquid is demonstrated. Prior to pDNA extraction study, the DTD LLE protocol was developed and optimized using organic dyes as solutes. The selective extraction of pDNA in the presence of proteins as interfering molecules is also demonstrated. This work implies that DTD LLE can substitute for magnetic beads steps in standard DNA isolation protocols.
Collapse
Affiliation(s)
| | - Hyejin Moon
- Author to whom correspondence should be addressed:
| |
Collapse
|
15
|
Schneider L, Fraser M, Tripathi A. Integrated magneto-electrophoresis microfluidic chip purification on library preparation device for preimplantation genetic testing for aneuploidy detection. RSC Adv 2021; 11:14459-14474. [PMID: 35423999 PMCID: PMC8697746 DOI: 10.1039/d1ra01732b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 04/06/2021] [Indexed: 12/14/2022] Open
Abstract
Next generation sequencing (NGS) technology has revolutionized the field of personalized medicine through providing patient specific diagnostic information on a nucleic acid level. A key bottleneck in the NGS workflow is the preparation of nucleic acids for sequencing, or library preparation. One approach to overcoming this bottleneck on time and resources is through automating library preparation as much as possible from the stage of DNA extraction to a sequence-ready sample. Here, we have integrated microscale purification and macroscale PCR amplification to create an automated platform to replace manual DNA library preparation and magnetic bead-based cleanup steps. This microfluidic chip integrates magnetic bead transport and electrokinetic flow to remove unbound adapter dimers and other impurities from samples. We incorporate this method to develop an automated NGS DNA library preparation device that also includes macro- and microfluidic reagent movement and mixing and a thermoelectric cooler for controlled capillary heating and cooling. We greatly reduce the hands-on time, amount of pipetting required, and volumes of reagents needed as we test the feasibility of the platform on the clinically important diagnostic field of preimplantation genetic testing for aneuploidy (PGT-A). We prepared euploid and aneuploid five cell samples for sequencing and found our results were accurate for the cell samples with a sequencing quality equivalent to the standard of the DNA libraries prepared manually. Our device platform utilizes concepts such as: magneto-electrophoresis, integrated capillary PCR, and automated sample loading and unloading onto a microfluidic chip.
Collapse
Affiliation(s)
- Lindsay Schneider
- Center for Biomedical Engineering, School of Engineering, Brown University 182 Hope Street Providence RI 02912 USA
| | - Michelle Fraser
- PerkinElmer Health Sciences (Australia) Thebarton South Australia 5031 Australia
| | - Anubhav Tripathi
- Center for Biomedical Engineering, School of Engineering, Brown University 182 Hope Street Providence RI 02912 USA
| |
Collapse
|
16
|
Advantages and Limitations of 16S rRNA Next-Generation Sequencing for Pathogen Identification in the Diagnostic Microbiology Laboratory: Perspectives from a Middle-Income Country. Diagnostics (Basel) 2020; 10:diagnostics10100816. [PMID: 33066371 PMCID: PMC7602188 DOI: 10.3390/diagnostics10100816] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 09/18/2020] [Accepted: 10/11/2020] [Indexed: 12/19/2022] Open
Abstract
Bacterial culture and biochemical testing (CBtest) have been the cornerstone of pathogen identification in the diagnostic microbiology laboratory. With the advent of Sanger sequencing and later, next-generation sequencing, 16S rRNA next-generation sequencing (16SNGS) has been proposed to be a plausible platform for this purpose. Nevertheless, usage of the 16SNGS platform has both advantages and limitations. In addition, transition from the traditional methods of CBtest to 16SNGS requires procurement of costly equipment, timely and sustainable maintenance of these platforms, specific facility infrastructure and technical expertise. All these factors pose a challenge for middle-income countries, more so for countries in the lower middle-income range. In this review, we describe the basis for CBtest and 16SNGS, and discuss the limitations, challenges, advantages and future potential of using 16SNGS for bacterial pathogen identification in diagnostic microbiology laboratories of middle-income countries.
Collapse
|
17
|
Hess JF, Kotrová M, Calabrese S, Darzentas N, Hutzenlaub T, Zengerle R, Brüggemann M, Paust N. Automation of Amplicon-Based Library Preparation for Next-Generation Sequencing by Centrifugal Microfluidics. Anal Chem 2020; 92:12833-12841. [DOI: 10.1021/acs.analchem.0c01202] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Jacob Friedrich Hess
- Laboratory for MEMS Applications, IMTEK-Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
| | - Michaela Kotrová
- Unit for Hematological Diagnostics, II. Medical Department, University Medical Center Schleswig Holstein, Langer Segen 8-10, 24105 Kiel, Germany
| | - Silvia Calabrese
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
| | - Nikos Darzentas
- Unit for Hematological Diagnostics, II. Medical Department, University Medical Center Schleswig Holstein, Langer Segen 8-10, 24105 Kiel, Germany
| | - Tobias Hutzenlaub
- Laboratory for MEMS Applications, IMTEK-Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
| | - Roland Zengerle
- Laboratory for MEMS Applications, IMTEK-Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
| | - Monika Brüggemann
- Unit for Hematological Diagnostics, II. Medical Department, University Medical Center Schleswig Holstein, Langer Segen 8-10, 24105 Kiel, Germany
| | - Nils Paust
- Laboratory for MEMS Applications, IMTEK-Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
| |
Collapse
|
18
|
Hess J, Kohl T, Kotrová M, Rönsch K, Paprotka T, Mohr V, Hutzenlaub T, Brüggemann M, Zengerle R, Niemann S, Paust N. Library preparation for next generation sequencing: A review of automation strategies. Biotechnol Adv 2020; 41:107537. [DOI: 10.1016/j.biotechadv.2020.107537] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 02/27/2020] [Accepted: 03/16/2020] [Indexed: 01/08/2023]
|
19
|
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
|
20
|
Xu Z, Qiao Y, Tu J. Microfluidic Technologies for cfDNA Isolation and Analysis. MICROMACHINES 2019; 10:mi10100672. [PMID: 31623361 PMCID: PMC6843514 DOI: 10.3390/mi10100672] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 09/27/2019] [Accepted: 09/29/2019] [Indexed: 12/18/2022]
Abstract
Cell-free DNA (cfDNA), which promotes precision oncology, has received extensive concern because of its abilities to inform genomic mutations, tumor burden and drug resistance. The absolute quantification of cfDNA concentration has been proved as an independent prognostic biomarker of overall survival. However, the properties of low abundance and high fragmentation hinder the isolation and further analysis of cfDNA. Microfluidic technologies and lab-on-a-chip (LOC) devices provide an opportunity to deal with cfDNA sample at a micrometer scale, which reduces required sample volume and makes rapid isolation possible. Microfluidic platform also allow for high degree of automation and high-throughput screening without liquid transfer, where rapid and precise examination and quantification could be performed at the same time. Microfluidic technologies applied in cfDNA isolation and analysis are limited and remains to be further explored. This paper reviewed the existing and potential applications of microfluidic technologies in collection and enrichment of cfDNA, quantification, mutation detection and sequencing library construction, followed by discussion of future perspectives.
Collapse
Affiliation(s)
- Zheyun Xu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.
| | - Yi Qiao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.
| | - Jing Tu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.
| |
Collapse
|
21
|
Moazami E, Perry JM, Soffer G, Husser MC, Shih SCC. Integration of World-to-Chip Interfaces with Digital Microfluidics for Bacterial Transformation and Enzymatic Assays. Anal Chem 2019; 91:5159-5168. [DOI: 10.1021/acs.analchem.8b05754] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Ehsan Moazami
- Department of Electrical and Computer Engineering, Concordia University, Montréal, Québec H3G1M8, Canada
- Centre for Applied Synthetic Biology, Concordia University, Montréal, Québec H4B1R6, Canada
| | - James M. Perry
- Centre for Applied Synthetic Biology, Concordia University, Montréal, Québec H4B1R6, Canada
- Department of Biology, Concordia University, Montréal, Québec H4B1R6, Canada
| | - Guy Soffer
- Department of Electrical and Computer Engineering, Concordia University, Montréal, Québec H3G1M8, Canada
- Centre for Applied Synthetic Biology, Concordia University, Montréal, Québec H4B1R6, Canada
| | - Mathieu C. Husser
- Centre for Applied Synthetic Biology, Concordia University, Montréal, Québec H4B1R6, Canada
- Department of Biology, Concordia University, Montréal, Québec H4B1R6, Canada
| | - Steve C. C. Shih
- Department of Electrical and Computer Engineering, Concordia University, Montréal, Québec H3G1M8, Canada
- Centre for Applied Synthetic Biology, Concordia University, Montréal, Québec H4B1R6, Canada
- Department of Biology, Concordia University, Montréal, Québec H4B1R6, Canada
| |
Collapse
|
22
|
Razu ME, Kim J. Digital microfluidics using a differentially polarized interface (DPI) to enhance translational force. LAB ON A CHIP 2018; 18:3293-3302. [PMID: 30264074 DOI: 10.1039/c8lc00652k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Direct current (DC)-digital microfluidics (DMF) enables the manipulation of droplets to revolutionize medical diagnostics, environmental assays, and fundamental biology. However, DC-DMF requires high voltages to generate droplet motion, which often breaks dielectric layers at the micro/nano scale, causing electrolysis. To minimize these issues, oil-fillers are commonly used to decrease the voltage requirement by reducing the surface tension of the droplet to the surrounding fluid. However, these oil-fillers increase DC-DMF complexity and decrease versatility. In this study, by adapting a differentially polarized interface (DPI) to generate an effective electromechanical force, the voltage required to manipulate a droplet was reduced from 600 V to 85 V without an oil-filler or special dielectric materials. By analyzing the temporal profiles of the contact angles during droplet motion under this DPI condition, this study, for the first time, distinguished the contributions of electrowetting and electromechanical forces to the translational movement of droplets. Dominant contribution of electrowetting is observed at the initial stage of the droplet translation with 52.8% reduction in the advancing contact angle and 20% reduction in the receding contact angle. However, after saturation in the temporal change of the contact angle, the effect of electrowetting contribution gradually decreases and electromechanical forces predominate. DPI-based digital microfluidics reduces the overall cost and complexity of stand-alone DC-DMF platforms, enabling filler-less and low-voltage applications for manipulating a wide range of liquid samples.
Collapse
Affiliation(s)
- Md Enayet Razu
- Department of Mechanical Engineering, Texas Tech University, Lubbock, Texas 79409, USA.
| | | |
Collapse
|
23
|
Snider A, Nilsson M, Dupal M, Toloue M, Tripathi A. A Microfluidics Workflow for Sample Preparation for Next-Generation DNA Sequencing. SLAS Technol 2018; 24:196-208. [PMID: 30142015 DOI: 10.1177/2472630318796133] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Next-generation sequencing technology requires amplified, short DNA fragments with known end sequences. Samples must undergo processing steps, including extraction and purification of genomic DNA (gDNA), fragmentation, end repair, adapter ligation, and amplification, to prepare a sequencing library. The process of sample preparation requires careful control of temperature and buffer conditions, as well as the stringent removal of contaminants. As a result, library preparation methods are often plagued by sample loss, long protocol times, numerous manual steps, and high cost. We attempt to understand and optimize each step of sample preparation on a microfluidic platform using magnetic bead motion through channels containing immiscible phases. Our platform integrates all steps associated with library preparation with no buffer exchanges and utilizes just 30-60 µL of reagents. Our chip shows a sixfold improvement in yield compared with an affinity spin column when capturing gDNA from samples of ~50 ± 4 MCF-7 cells. Finally, we show whole-genome shotgun sequencing results from 660 pg of human gDNA, in which >93 ± 1% of reads map to a reference genome at or above 99.9% confidence, matching a commercially available sample preparation kit optimized for low-cell-count samples.
Collapse
Affiliation(s)
- Adam Snider
- 1 Center for Biomedical Engineering, School of Engineering, Brown University, Providence, RI, USA
| | | | | | | | - Anubhav Tripathi
- 1 Center for Biomedical Engineering, School of Engineering, Brown University, Providence, RI, USA
| |
Collapse
|
24
|
Serra M, Ferraro D, Pereiro I, Viovy JL, Descroix S. The power of solid supports in multiphase and droplet-based microfluidics: towards clinical applications. LAB ON A CHIP 2017; 17:3979-3999. [PMID: 28948991 DOI: 10.1039/c7lc00582b] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Multiphase and droplet microfluidic systems are growing in relevance in bioanalytical-related fields, especially due to the increased sensitivity, faster reaction times and lower sample/reagent consumption of many of its derived bioassays. Often applied to homogeneous (liquid/liquid) reactions, innovative strategies for the implementation of heterogeneous (typically solid/liquid) processes have recently been proposed. These involve, for example, the extraction and purification of target analytes from complex matrices or the implementation of multi-step protocols requiring efficient washing steps. To achieve this, solid supports such as functionalized particles (micro or nanometric) presenting different physical properties (e.g. magnetic, optical or others) are used for the binding of specific entities. The manipulation of such supports with different microfluidic principles has both led to the miniaturization of existing biomedical protocols and the development of completely new strategies for diagnostics and research. In this review, multiphase and droplet-based microfluidic systems using solid suspensions are presented and discussed with a particular focus on: i) working principles and technological developments of the manipulation strategies and ii) applications, critically discussing the level of maturity of these systems, which can range from initial proofs of concept to real clinical validations.
Collapse
Affiliation(s)
- M Serra
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, CNRS UMR168, Paris, France.
| | | | | | | | | |
Collapse
|
25
|
Printed droplet microfluidics for on demand dispensing of picoliter droplets and cells. Proc Natl Acad Sci U S A 2017; 114:8728-8733. [PMID: 28760972 DOI: 10.1073/pnas.1704020114] [Citation(s) in RCA: 118] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Although the elementary unit of biology is the cell, high-throughput methods for the microscale manipulation of cells and reagents are limited. The existing options either are slow, lack single-cell specificity, or use fluid volumes out of scale with those of cells. Here we present printed droplet microfluidics, a technology to dispense picoliter droplets and cells with deterministic control. The core technology is a fluorescence-activated droplet sorter coupled to a specialized substrate that together act as a picoliter droplet and single-cell printer, enabling high-throughput generation of intricate arrays of droplets, cells, and microparticles. Printed droplet microfluidics provides a programmable and robust technology to construct arrays of defined cell and reagent combinations and to integrate multiple measurement modalities together in a single assay.
Collapse
|
26
|
Digital Microfluidics for Nucleic Acid Amplification. SENSORS 2017; 17:s17071495. [PMID: 28672827 PMCID: PMC5539496 DOI: 10.3390/s17071495] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2017] [Revised: 06/17/2017] [Accepted: 06/22/2017] [Indexed: 01/08/2023]
Abstract
Digital Microfluidics (DMF) has emerged as a disruptive methodology for the control and manipulation of low volume droplets. In DMF, each droplet acts as a single reactor, which allows for extensive multiparallelization of biological and chemical reactions at a much smaller scale. DMF devices open entirely new and promising pathways for multiplex analysis and reaction occurring in a miniaturized format, thus allowing for healthcare decentralization from major laboratories to point-of-care with accurate, robust and inexpensive molecular diagnostics. Here, we shall focus on DMF platforms specifically designed for nucleic acid amplification, which is key for molecular diagnostics of several diseases and conditions, from pathogen identification to cancer mutations detection. Particular attention will be given to the device architecture, materials and nucleic acid amplification applications in validated settings.
Collapse
|
27
|
Ma S, Murphy TW, Lu C. Microfluidics for genome-wide studies involving next generation sequencing. BIOMICROFLUIDICS 2017; 11:021501. [PMID: 28396707 PMCID: PMC5346105 DOI: 10.1063/1.4978426] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 02/16/2017] [Indexed: 05/11/2023]
Abstract
Next-generation sequencing (NGS) has revolutionized how molecular biology studies are conducted. Its decreasing cost and increasing throughput permit profiling of genomic, transcriptomic, and epigenomic features for a wide range of applications. Microfluidics has been proven to be highly complementary to NGS technology with its unique capabilities for handling small volumes of samples and providing platforms for automation, integration, and multiplexing. In this article, we review recent progress on applying microfluidics to facilitate genome-wide studies. We emphasize on several technical aspects of NGS and how they benefit from coupling with microfluidic technology. We also summarize recent efforts on developing microfluidic technology for genomic, transcriptomic, and epigenomic studies, with emphasis on single cell analysis. We envision rapid growth in these directions, driven by the needs for testing scarce primary cell samples from patients in the context of precision medicine.
Collapse
Affiliation(s)
- Sai Ma
- Department of Biomedical Engineering and Mechanics, Virginia Tech , Blacksburg, Virginia 24061, USA
| | - Travis W Murphy
- Department of Chemical Engineering, Virginia Tech , Blacksburg, Virginia 24061, USA
| | - Chang Lu
- Department of Chemical Engineering, Virginia Tech , Blacksburg, Virginia 24061, USA
| |
Collapse
|
28
|
Kim S, De Jonghe J, Kulesa AB, Feldman D, Vatanen T, Bhattacharyya RP, Berdy B, Gomez J, Nolan J, Epstein S, Blainey PC. High-throughput automated microfluidic sample preparation for accurate microbial genomics. Nat Commun 2017; 8:13919. [PMID: 28128213 PMCID: PMC5290157 DOI: 10.1038/ncomms13919] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 11/11/2016] [Indexed: 12/30/2022] Open
Abstract
Low-cost shotgun DNA sequencing is transforming the microbial sciences. Sequencing instruments are so effective that sample preparation is now the key limiting factor. Here, we introduce a microfluidic sample preparation platform that integrates the key steps in cells to sequence library sample preparation for up to 96 samples and reduces DNA input requirements 100-fold while maintaining or improving data quality. The general-purpose microarchitecture we demonstrate supports workflows with arbitrary numbers of reaction and clean-up or capture steps. By reducing the sample quantity requirements, we enabled low-input (∼10,000 cells) whole-genome shotgun (WGS) sequencing of Mycobacterium tuberculosis and soil micro-colonies with superior results. We also leveraged the enhanced throughput to sequence ∼400 clinical Pseudomonas aeruginosa libraries and demonstrate excellent single-nucleotide polymorphism detection performance that explained phenotypically observed antibiotic resistance. Fully-integrated lab-on-chip sample preparation overcomes technical barriers to enable broader deployment of genomics across many basic research and translational applications. Shotgun DNA sequencing experiments for microbial genomic analysis are often impractical due to minimum sample input requirements. Here the authors develop a microfluidic sample preparation platform that reduces sample input requirements 100-fold and enables high throughput sequencing from low numbers of cells.
Collapse
Affiliation(s)
- Soohong Kim
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Joachim De Jonghe
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - Anthony B Kulesa
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - David Feldman
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Tommi Vatanen
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Department of Computer Science, Aalto University School of Science, Espoo 02150, Finland
| | - Roby P Bhattacharyya
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - Brittany Berdy
- Department of Biology, Northeastern University, Boston, Massachusetts 02115, USA
| | - James Gomez
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Jill Nolan
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Slava Epstein
- Department of Biology, Northeastern University, Boston, Massachusetts 02115, USA
| | - Paul C Blainey
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| |
Collapse
|
29
|
Dirks RAM, Stunnenberg HG, Marks H. Genome-wide epigenomic profiling for biomarker discovery. Clin Epigenetics 2016; 8:122. [PMID: 27895806 PMCID: PMC5117701 DOI: 10.1186/s13148-016-0284-4] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Accepted: 11/02/2016] [Indexed: 12/24/2022] Open
Abstract
A myriad of diseases is caused or characterized by alteration of epigenetic patterns, including changes in DNA methylation, post-translational histone modifications, or chromatin structure. These changes of the epigenome represent a highly interesting layer of information for disease stratification and for personalized medicine. Traditionally, epigenomic profiling required large amounts of cells, which are rarely available with clinical samples. Also, the cellular heterogeneity complicates analysis when profiling clinical samples for unbiased genome-wide biomarker discovery. Recent years saw great progress in miniaturization of genome-wide epigenomic profiling, enabling large-scale epigenetic biomarker screens for disease diagnosis, prognosis, and stratification on patient-derived samples. All main genome-wide profiling technologies have now been scaled down and/or are compatible with single-cell readout, including: (i) Bisulfite sequencing to determine DNA methylation at base-pair resolution, (ii) ChIP-Seq to identify protein binding sites on the genome, (iii) DNaseI-Seq/ATAC-Seq to profile open chromatin, and (iv) 4C-Seq and HiC-Seq to determine the spatial organization of chromosomes. In this review we provide an overview of current genome-wide epigenomic profiling technologies and main technological advances that allowed miniaturization of these assays down to single-cell level. For each of these technologies we evaluate their application for future biomarker discovery. We will focus on (i) compatibility of these technologies with methods used for clinical sample preservation, including methods used by biobanks that store large numbers of patient samples, and (ii) automation of these technologies for robust sample preparation and increased throughput.
Collapse
Affiliation(s)
- René A M Dirks
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, 6500HB Nijmegen, The Netherlands
| | - Hendrik G Stunnenberg
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, 6500HB Nijmegen, The Netherlands
| | - Hendrik Marks
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, 6500HB Nijmegen, The Netherlands
| |
Collapse
|
30
|
Ha D, Hong J, Shin H, Kim T. Unconventional micro-/nanofabrication technologies for hybrid-scale lab-on-a-chip. LAB ON A CHIP 2016; 16:4296-4312. [PMID: 27761529 DOI: 10.1039/c6lc01058j] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Micro-/nanofabrication-based lab-on-a-chip (LOC) technologies have recently been substantially advanced and have become widely used in various inter-/multidisciplinary research fields, including biological, (bio-)chemical, and biomedical fields. However, such hybrid-scale LOC devices are typically fabricated using microfabrication and nanofabrication processes in series, resulting in increased cost and time and low throughput issues. In this review, after briefly introducing the conventional micro-/nanofabrication technologies, we focus on unconventional micro-/nanofabrication technologies that allow us to produce either in situ micro-/nanoscale structures or master molds for additional replication processes to easily and conveniently create novel LOC devices with micro- or nanofluidic channel networks. In particular, microfabrication methods based on crack-assisted photolithography and carbon-microelectromechanical systems (C-MEMS) are described in detail because of their superior features from the viewpoint of the throughput, batch fabrication process, and mixed-scale channels/structures. In parallel with previously reported articles on conventional micro-/nanofabrication technologies, our review of unconventional micro-/nanofabrication technologies will provide a useful and practical fabrication guideline for future hybrid-scale LOC devices.
Collapse
Affiliation(s)
- Dogyeong Ha
- Department of Mechanical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea.
| | - Jisoo Hong
- Department of Mechanical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea.
| | - Heungjoo Shin
- Department of Mechanical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea.
| | - Taesung Kim
- Department of Mechanical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea.
| |
Collapse
|
31
|
Stark A, Shin DJ, Pisanic T, Hsieh K, Wang TH. A parallelized microfluidic DNA bisulfite conversion module for streamlined methylation analysis. Biomed Microdevices 2016; 18:5. [PMID: 26759004 DOI: 10.1007/s10544-015-0029-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Aberrant methylation of DNA has been identified as an epigenetic biomarker for numerous cancer types. The vast majority of techniques aimed at detecting methylation require bisulfite conversion of the DNA sample prior to analysis, which until now has been a benchtop process. Although microfluidics has potential benefits of simplified operation, sample and reagent economy, and scalability, bisulfite conversion has yet to be implemented in this format. Here, we present a novel droplet microfluidic design that facilitates rapid bisulfite conversion by reducing the necessary processing steps while retaining comparable performance to existing methods. This new format has a reduced overall processing time and is readily scalable for use in high throughput DNA methylation analysis.
Collapse
Affiliation(s)
- Alejandro Stark
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Dong Jin Shin
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Thomas Pisanic
- Johns Hopkins Institute for NanoBioTechnology, Baltimore, MD, 21218, USA
| | - Kuangwen Hsieh
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Tza-Huei Wang
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA. .,Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA. .,Johns Hopkins Institute for NanoBioTechnology, Baltimore, MD, 21218, USA.
| |
Collapse
|
32
|
Coissac E, Hollingsworth PM, Lavergne S, Taberlet P. From barcodes to genomes: extending the concept of DNA barcoding. Mol Ecol 2016; 25:1423-8. [DOI: 10.1111/mec.13549] [Citation(s) in RCA: 233] [Impact Index Per Article: 29.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 12/28/2015] [Accepted: 01/19/2016] [Indexed: 12/20/2022]
Affiliation(s)
- Eric Coissac
- CNRS; LECA; F-38000 Grenoble France
- Univ. Grenoble Alpes; LECA; F-38000 Grenoble France
| | | | - Sébastien Lavergne
- CNRS; LECA; F-38000 Grenoble France
- Univ. Grenoble Alpes; LECA; F-38000 Grenoble France
| | - Pierre Taberlet
- CNRS; LECA; F-38000 Grenoble France
- Univ. Grenoble Alpes; LECA; F-38000 Grenoble France
| |
Collapse
|
33
|
Li Y, Li H, Baker RJ. A Low-Cost and High-Resolution Droplet Position Detector for an Intelligent Electrowetting on Dielectric Device. ACTA ACUST UNITED AC 2015; 20:663-9. [DOI: 10.1177/2211068214566940] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Indexed: 11/16/2022]
|
34
|
Gorbatsova J, Jaanus M, Vaher M, Kaljurand M. Digital microfluidics platform for interfacing solid-liquid extraction column with portable capillary electropherograph for analysis of soil amino acids. Electrophoresis 2015; 37:472-5. [DOI: 10.1002/elps.201500284] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2015] [Revised: 09/18/2015] [Accepted: 09/18/2015] [Indexed: 11/09/2022]
Affiliation(s)
- Jelena Gorbatsova
- Department of Chemistry, Faculty of Science; Tallinn University of Technology; Tallinn Estonia
| | - Martin Jaanus
- Department of Computer Control, Faculty of Information Technology; Tallinn University of Technology; Tallinn Estonia
| | - Merike Vaher
- Department of Chemistry, Faculty of Science; Tallinn University of Technology; Tallinn Estonia
| | - Mihkel Kaljurand
- Department of Chemistry, Faculty of Science; Tallinn University of Technology; Tallinn Estonia
| |
Collapse
|
35
|
Ultra-Portable Smartphone Controlled Integrated Digital Microfluidic System in a 3D-Printed Modular Assembly. MICROMACHINES 2015. [DOI: 10.3390/mi6091289] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
|
36
|
Building bio-assays with magnetic particles on a digital microfluidic platform. N Biotechnol 2015; 32:485-503. [DOI: 10.1016/j.nbt.2015.03.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 02/16/2015] [Accepted: 03/13/2015] [Indexed: 12/16/2022]
|
37
|
Bartsch MS, Edwards HS, Lee D, Moseley CE, Tew KE, Renzi RF, Van de Vreugde JL, Kim H, Knight DL, Sinha A, Branda SS, Patel KD. The rotary zone thermal cycler: a low-power system enabling automated rapid PCR. PLoS One 2015; 10:e0118182. [PMID: 25826708 PMCID: PMC4380418 DOI: 10.1371/journal.pone.0118182] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 01/09/2015] [Indexed: 12/17/2022] Open
Abstract
Advances in molecular biology, microfluidics, and laboratory automation continue to expand the accessibility and applicability of these methods beyond the confines of conventional, centralized laboratory facilities and into point of use roles in clinical, military, forensic, and field-deployed applications. As a result, there is a growing need to adapt the unit operations of molecular biology (e.g., aliquoting, centrifuging, mixing, and thermal cycling) to compact, portable, low-power, and automation-ready formats. Here we present one such adaptation, the rotary zone thermal cycler (RZTC), a novel wheel-based device capable of cycling up to four different fixed-temperature blocks into contact with a stationary 4-microliter capillary-bound sample to realize 1-3 second transitions with steady state heater power of less than 10 W. We demonstrate the utility of the RZTC for DNA amplification as part of a highly integrated rotary zone PCR (rzPCR) system that uses low-volume valves and syringe-based fluid handling to automate sample loading and unloading, thermal cycling, and between-run cleaning functionalities in a compact, modular form factor. In addition to characterizing the performance of the RZTC and the efficacy of different online cleaning protocols, we present preliminary results for rapid single-plex PCR, multiplex short tandem repeat (STR) amplification, and second strand cDNA synthesis.
Collapse
Affiliation(s)
- Michael S. Bartsch
- Sandia National Laboratories, Livermore, CA, United States of America
- * E-mail:
| | | | - Daniel Lee
- Sandia National Laboratories, Livermore, CA, United States of America
| | | | - Karen E. Tew
- Sandia National Laboratories, Livermore, CA, United States of America
| | - Ronald F. Renzi
- Sandia National Laboratories, Livermore, CA, United States of America
| | | | - Hanyoup Kim
- Sandia National Laboratories, Livermore, CA, United States of America
| | | | - Anupama Sinha
- Sandia National Laboratories, Livermore, CA, United States of America
| | - Steven S. Branda
- Sandia National Laboratories, Livermore, CA, United States of America
| | - Kamlesh D. Patel
- Sandia National Laboratories, Livermore, CA, United States of America
| |
Collapse
|
38
|
Jebrail MJ, Renzi RF, Sinha A, Van De Vreugde J, Gondhalekar C, Ambriz C, Meagher RJ, Branda SS. A solvent replenishment solution for managing evaporation of biochemical reactions in air-matrix digital microfluidics devices. LAB ON A CHIP 2015; 15:151-158. [PMID: 25325619 DOI: 10.1039/c4lc00703d] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Digital microfluidics (DMF) is a powerful technique for sample preparation and analysis for a broad range of biological and chemical applications. In many cases, it is desirable to carry out DMF on an open surface, such that the matrix surrounding the droplets is ambient air. However, the utility of the air-matrix DMF format has been severely limited by problems with droplet evaporation, especially when the droplet-based biochemical reactions require high temperatures for long periods of time. We present a simple solution for managing evaporation in air-matrix DMF: just-in-time replenishment of the reaction volume using droplets of solvent. We demonstrate that this solution enables DMF-mediated execution of several different biochemical reactions (RNA fragmentation, first-strand cDNA synthesis, and PCR) over a range of temperatures (4-95 °C) and incubation times (up to 1 h or more) without use of oil, humidifying chambers, or off-chip heating modules. Reaction volumes and temperatures were maintained roughly constant over the course of each experiment, such that the reaction kinetics and products generated by the air-matrix DMF device were comparable to those of conventional benchscale reactions. This simple yet effective solution for evaporation management is an important advance in developing air-matrix DMF for a wide variety of new, high-impact applications, particularly in the biomedical sciences.
Collapse
Affiliation(s)
- Mais J Jebrail
- Biotechnology and Bioengineering, Sandia National Laboratories, Livermore, CA, USA.
| | | | | | | | | | | | | | | |
Collapse
|
39
|
Shih SCC, Gach PC, Sustarich J, Simmons BA, Adams PD, Singh S, Singh AK. A droplet-to-digital (D2D) microfluidic device for single cell assays. LAB ON A CHIP 2015; 15:225-36. [PMID: 25354549 DOI: 10.1039/c4lc00794h] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
We have developed a new hybrid droplet-to-digital microfluidic platform (D2D) that integrates droplet-in-channel microfluidics with digital microfluidics (DMF) for performing multi-step assays. This D2D platform combines the strengths of the two formats-droplets-in-channel for facile generation of droplets containing single cells, and DMF for on-demand manipulation of droplets including control of different droplet volumes (pL-μL), creation of a dilution series of ionic liquid (IL), and parallel single cell culturing and analysis for IL toxicity screening. This D2D device also allows for automated analysis that includes a feedback-controlled system for merging and splitting of droplets to add reagents, an integrated Peltier element for parallel cell culture at optimum temperature, and an impedance sensing mechanism to control the flow rate for droplet generation and preventing droplet evaporation. Droplet-in-channel is well-suited for encapsulation of single cells as it allows the careful manipulation of flow rates of aqueous phase containing cells and oil to optimize encapsulation. Once single cell containing droplets are generated, they are transferred to a DMF chip via a capillary where they are merged with droplets containing IL and cultured at 30 °C. The DMF chip, in addition to permitting cell culture and reagent (ionic liquid/salt) addition, also allows recovery of individual droplets for off-chip analysis such as further culturing and measurement of ethanol production. The D2D chip was used to evaluate the effect of IL/salt type (four types: NaOAc, NaCl, [C2mim] [OAc], [C2mim] [Cl]) and concentration (four concentrations: 0, 37.5, 75, 150 mM) on the growth kinetics and ethanol production of yeast and as expected, increasing IL concentration led to lower biomass and ethanol production. Specifically, [C2mim] [OAc] had inhibitory effects on yeast growth at concentrations 75 and 150 mM and significantly reduced their ethanol production compared to cells grown in other ILs/salts. The growth curve trends obtained by D2D matched conventional yeast culturing in microtiter wells, validating the D2D platform. We believe that our approach represents a generic platform for multi-step biochemical assays such as drug screening, digital PCR, enzyme assays, immunoassays and cell-based assays.
Collapse
Affiliation(s)
- Steve C C Shih
- Sandia National Laboratories, 7011 East Ave, Livermore, CA, USA.
| | | | | | | | | | | | | |
Collapse
|
40
|
Lapierre F, Harnois M, Coffinier Y, Boukherroub R, Thomy V. Split and flow: reconfigurable capillary connection for digital microfluidic devices. LAB ON A CHIP 2014; 14:3589-3593. [PMID: 25058858 DOI: 10.1039/c4lc00650j] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Supplying liquid to droplet-based microfluidic microsystems remains a delicate task facing the problems of coupling continuous to digital or macro- to microfluidic systems. Here, we take advantage of superhydrophobic microgrids to address this problem. Insertion of a capillary tube inside a microgrid aperture leads to a simple and reconfigurable droplet generation setup.
Collapse
Affiliation(s)
- Florian Lapierre
- Institute of Electronics, Microelectronics and Nanotechnology (IEMN), UMR CNRS 8520, University Lille 1, F-59652 Villeneuve d'Ascq, France.
| | | | | | | | | |
Collapse
|
41
|
Automated long-term monitoring of parallel microfluidic operations applying a machine vision-assisted positioning method. ScientificWorldJournal 2014; 2014:608184. [PMID: 25133248 PMCID: PMC4124227 DOI: 10.1155/2014/608184] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2014] [Accepted: 06/25/2014] [Indexed: 01/13/2023] Open
Abstract
As microfluidics has been applied extensively in many cell and biochemical applications, monitoring the related processes is an important requirement. In this work, we design and fabricate a high-throughput microfluidic device which contains 32 microchambers to perform automated parallel microfluidic operations and monitoring on an automated stage of a microscope. Images are captured at multiple spots on the device during the operations for monitoring samples in microchambers in parallel; yet the device positions may vary at different time points throughout operations as the device moves back and forth on a motorized microscopic stage. Here, we report an image-based positioning strategy to realign the chamber position before every recording of microscopic image. We fabricate alignment marks at defined locations next to the chambers in the microfluidic device as reference positions. We also develop image processing algorithms to recognize the chamber positions in real-time, followed by realigning the chambers to their preset positions in the captured images. We perform experiments to validate and characterize the device functionality and the automated realignment operation. Together, this microfluidic realignment strategy can be a platform technology to achieve precise positioning of multiple chambers for general microfluidic applications requiring long-term parallel monitoring of cell and biochemical activities.
Collapse
|
42
|
Resistance determinants and mobile genetic elements of an NDM-1-encoding Klebsiella pneumoniae strain. PLoS One 2014; 9:e99209. [PMID: 24905728 PMCID: PMC4048246 DOI: 10.1371/journal.pone.0099209] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Accepted: 05/12/2014] [Indexed: 01/12/2023] Open
Abstract
Multidrug-resistant Enterobacteriaceae are emerging as a serious infectious disease challenge. These strains can accumulate many antibiotic resistance genes though horizontal transfer of genetic elements, those for β-lactamases being of particular concern. Some β-lactamases are active on a broad spectrum of β-lactams including the last-resort carbapenems. The gene for the broad-spectrum and carbapenem-active metallo-β-lactamase NDM-1 is rapidly spreading. We present the complete genome of Klebsiella pneumoniae ATCC BAA-2146, the first U.S. isolate found to encode NDM-1, and describe its repertoire of antibiotic-resistance genes and mutations, including genes for eight β-lactamases and 15 additional antibiotic-resistance enzymes. To elucidate the evolution of this rich repertoire, the mobile elements of the genome were characterized, including four plasmids with varying degrees of conservation and mosaicism and eleven chromosomal genomic islands. One island was identified by a novel phylogenomic approach, that further indicated the cps-lps polysaccharide synthesis locus, where operon translocation and fusion was noted. Unique plasmid segments and mosaic junctions were identified. Plasmid-borne blaCTX-M-15 was transposed recently to the chromosome by ISEcp1. None of the eleven full copies of IS26, the most frequent IS element in the genome, had the expected 8-bp direct repeat of the integration target sequence, suggesting that each copy underwent homologous recombination subsequent to its last transposition event. Comparative analysis likewise indicates IS26 as a frequent recombinational junction between plasmid ancestors, and also indicates a resolvase site. In one novel use of high-throughput sequencing, homologously recombinant subpopulations of the bacterial culture were detected. In a second novel use, circular transposition intermediates were detected for the novel insertion sequence ISKpn21 of the ISNCY family, suggesting that it uses the two-step transposition mechanism of IS3. Robust genome-based phylogeny showed that a unified Klebsiella cluster contains Enterobacter aerogenes and Raoultella, suggesting the latter genus should be abandoned.
Collapse
|
43
|
Mudrik JM, Dryden MD, Lafrenière NM, Wheeler AR. Strong and small: strong cation-exchange solid-phase extractions using porous polymer monoliths on a digital microfluidic platform. CAN J CHEM 2014. [DOI: 10.1139/cjc-2013-0506] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
We present the first method for digital microfluidics-based strong cation-exchange solid-phase extractions. Digital microfluidics is a microscale fluid handling technique in which liquid droplets are actuated over an array of electrodes by electrodynamic forces. Strong cation exchange has gained considerable importance in the field of proteomics as a separation mode for protein and peptide extractions. The marriage of these two techniques is achieved by incorporating sulphonate-functionalised porous polymer monolith discs onto digital microfluidic chips. By manipulating sample and solvent droplets onto and off of these porous polymer monoliths, proteins and peptides are extracted by controlling solution pH and ionic strength. This novel microscale extraction method has efficiency comparable to commercially available strong cation-exchange ZipTips and is highly effective for sample cleanup. We anticipate that this digital microfluidic strong cation-exchange extraction technique will prove useful for microscale proteomic analyses and other applications requiring separation of cationic compounds.
Collapse
Affiliation(s)
- Jared M. Mudrik
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S 3H6, Canada
| | - Michael D.M. Dryden
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S 3H6, Canada
| | - Nelson M. Lafrenière
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S 3H6, Canada
| | - Aaron R. Wheeler
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S 3H6, Canada
- Institute for Biomaterials and Biomedical Engineering, University of Toronto, 164 College Street, Toronto, ON M5S 3G9, Canada
- Donnelly Centre for Cellular and Biomolecular Research, 160 College Street, Toronto, ON M5S 3E1, Canada
| |
Collapse
|
44
|
Jebrail MJ, Sinha A, Vellucci S, Renzi RF, Ambriz C, Gondhalekar C, Schoeniger JS, Patel KD, Branda SS. World-to-Digital-Microfluidic Interface Enabling Extraction and Purification of RNA from Human Whole Blood. Anal Chem 2014; 86:3856-62. [DOI: 10.1021/ac404085p] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Mais J. Jebrail
- Departments of Biotechnology and Bioengineering, ‡Systems Biology, and §Advanced Systems Engineering and
Deployment, Sandia National Laboratories, Livermore, California, United States
| | - Anupama Sinha
- Departments of Biotechnology and Bioengineering, ‡Systems Biology, and §Advanced Systems Engineering and
Deployment, Sandia National Laboratories, Livermore, California, United States
| | - Samantha Vellucci
- Departments of Biotechnology and Bioengineering, ‡Systems Biology, and §Advanced Systems Engineering and
Deployment, Sandia National Laboratories, Livermore, California, United States
| | - Ronald F. Renzi
- Departments of Biotechnology and Bioengineering, ‡Systems Biology, and §Advanced Systems Engineering and
Deployment, Sandia National Laboratories, Livermore, California, United States
| | - Cesar Ambriz
- Departments of Biotechnology and Bioengineering, ‡Systems Biology, and §Advanced Systems Engineering and
Deployment, Sandia National Laboratories, Livermore, California, United States
| | - Carmen Gondhalekar
- Departments of Biotechnology and Bioengineering, ‡Systems Biology, and §Advanced Systems Engineering and
Deployment, Sandia National Laboratories, Livermore, California, United States
| | - Joseph S. Schoeniger
- Departments of Biotechnology and Bioengineering, ‡Systems Biology, and §Advanced Systems Engineering and
Deployment, Sandia National Laboratories, Livermore, California, United States
| | - Kamlesh D. Patel
- Departments of Biotechnology and Bioengineering, ‡Systems Biology, and §Advanced Systems Engineering and
Deployment, Sandia National Laboratories, Livermore, California, United States
| | - Steven S. Branda
- Departments of Biotechnology and Bioengineering, ‡Systems Biology, and §Advanced Systems Engineering and
Deployment, Sandia National Laboratories, Livermore, California, United States
| |
Collapse
|