1
|
Torres-Acosta MA, Olivares-Molina A, Kent R, Leitão N, Gershater M, Parker B, Lye GJ, Dikicioglu D. Practical deployment of automation to expedite aqueous two-phase extraction. J Biotechnol 2024; 387:32-43. [PMID: 38555021 DOI: 10.1016/j.jbiotec.2024.03.013] [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: 01/25/2024] [Revised: 03/15/2024] [Accepted: 03/26/2024] [Indexed: 04/02/2024]
Abstract
The feasibility of bioprocess development relies heavily on the successful application of primary recovery and purification techniques. Aqueous two-phase extraction (ATPE) disrupts the definition of "unit operation" by serving as an integrative and intensive technique that combines different objectives such as the removal of biomass and integrated recovery and purification of the product of interest. The relative simplicity of processing large samples renders this technique an attractive alternative for industrial bioprocessing applications. However, process development is hindered by the lack of easily predictable partition behaviours, the elucidation of which necessitates a large number of experiments to be conducted. Liquid handling devices can assist to address this problem; however, they are configured to operate using low viscosity fluids such as water and water-based solutions as opposed to highly viscous polymeric solutions, which are typically required in ATPE. In this work, an automated high throughput ATPE process development framework is presented by constructing phase diagrams and identifying the binodal curves for PEG6000, PEG3000, and PEG2000. Models were built to determine viscosity- and volume-independent transfer parameters. The framework provided an appropriate strategy to develop a very precise and accurate operation by exploiting the relationship between different liquid transfer parameters and process error. Process accuracy, measured by mean absolute error, and device precision, evaluated by the coefficient of variation, were both shown to be affected by the mechanical properties, particularly viscosity, of the fluids employed. For PEG6000, the mean absolute error improved by six-fold (from 4.82% to 0.75%) and the coefficient of variation improved by three-fold (from 0.027 to 0.008) upon optimisation of the liquid transfer parameters accounting for the viscosity effect on the PEG-salt buffer utilising ATPE operations. As demonstrated here, automated liquid handling devices can serve to streamline process development for APTE enabling wide adoption of this technique in large scale bioprocess applications.
Collapse
Affiliation(s)
- Mario A Torres-Acosta
- The Advanced Centre for Biochemical Engineering, Department of Biochemical Engineering, University College London, London WC1E 6BT, United Kingdom; Tecnologico de Monterrey, School of Engineering and Science, Av. Eugenio Garza Sada 2501 Sur, Monterrey, N.L. 64849, México
| | - Alex Olivares-Molina
- The Advanced Centre for Biochemical Engineering, Department of Biochemical Engineering, University College London, London WC1E 6BT, United Kingdom
| | - Ross Kent
- Synthace Ltd., The Westworks 4th Floor, 195 Wood Lane, W12 7FQ, United Kingdom
| | - Nuno Leitão
- Synthace Ltd., The Westworks 4th Floor, 195 Wood Lane, W12 7FQ, United Kingdom
| | - Markus Gershater
- Synthace Ltd., The Westworks 4th Floor, 195 Wood Lane, W12 7FQ, United Kingdom
| | - Brenda Parker
- The Advanced Centre for Biochemical Engineering, Department of Biochemical Engineering, University College London, London WC1E 6BT, United Kingdom
| | - Gary J Lye
- The Advanced Centre for Biochemical Engineering, Department of Biochemical Engineering, University College London, London WC1E 6BT, United Kingdom
| | - Duygu Dikicioglu
- The Advanced Centre for Biochemical Engineering, Department of Biochemical Engineering, University College London, London WC1E 6BT, United Kingdom.
| |
Collapse
|
2
|
Dufour N, Delattre R, Debarbieux L. High-Throughput Bacteriophage Testing with Potency Determination: Validation of an Automated Pipetting and Phage Drop-Off Method. Biomedicines 2024; 12:466. [PMID: 38398068 PMCID: PMC10886619 DOI: 10.3390/biomedicines12020466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 02/15/2024] [Accepted: 02/16/2024] [Indexed: 02/25/2024] Open
Abstract
The development of bacteriophages (phages) as active pharmaceutical ingredients for the treatment of patients is on its way and regulatory agencies are calling for reliable methods to assess phage potency. As the number of phage banks is increasing, so is the number of phages that need to be tested to identify therapeutic candidates. Currently, assessment of phage potency on a semi-solid medium to observe plaque-forming units is unavoidable and proves to be labor intensive when considering dozens of phage candidates. Here, we present a method based on automated pipetting and phage drop-off performed by a liquid-handling robot, allowing high-throughput testing and phage potency determination (based on phage titer and efficiency of plaquing). Ten phages were tested, individually and assembled into one cocktail, against 126 Escherichia coli strains. This automated method was compared to the reference one (manual assay) and validated in terms of reproducibility and concordance (ratio of results according to the Bland and Altman method: 0.99; Lin's concordance correlation coefficient: 0.86). We found that coefficients of variation were lower with automated pipetting (mean CV: 13.3% vs. 24.5%). Beyond speeding up the process of phage screening, this method could be used to standardize phage potency evaluation.
Collapse
Affiliation(s)
- Nicolas Dufour
- Réanimation Médico-Chirurgicale, Hôpital NOVO—Site de Pontoise, 95300 Pontoise, France
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Bacteriophage Bacterium Host, 75015 Paris, France (L.D.)
- IAME, Université de Paris, INSERM U1137, Université Sorbonne Paris Nord, 75018 Paris, France
| | - Raphaëlle Delattre
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Bacteriophage Bacterium Host, 75015 Paris, France (L.D.)
- IAME, Université de Paris, INSERM U1137, Université Sorbonne Paris Nord, 75018 Paris, France
- Réanimation, Centre Hospitalier de Digne-les-Bains, 04000 Digne-les-Bains, France
| | - Laurent Debarbieux
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Bacteriophage Bacterium Host, 75015 Paris, France (L.D.)
| |
Collapse
|
3
|
Rimmer MA, Twarog NR, Li Y, Shelat AA, Rankovic Z, Yang L. A high-throughput quality control method for assessing the serial dilution performance of dose-response plates with acoustic ejection mass spectrometry. SLAS Technol 2024; 29:100115. [PMID: 37925158 DOI: 10.1016/j.slast.2023.10.007] [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: 07/26/2023] [Revised: 09/26/2023] [Accepted: 10/31/2023] [Indexed: 11/06/2023]
Abstract
This study aimed to develop a streamlined method for evaluating the dilution ratio of drug dose-response plates created by automated liquid handlers in the early stages of drug discovery. The quantitative techniques commonly used for this purpose have restrictions due to their limited linear dynamic range and inaccuracies in assessing serial dilution performance. To address this challenge, we describe a method based on acoustic ejection mass spectrometry (AEMS). The method involves using standard compounds and an internal standard to evaluate each dilution point in quality control (QC) plates. The samples are transferred to a chromatography-free tandem mass spectrometry system through an acoustic source, enabling the analysis of one sample per three seconds from a microtiter plate. This approach provides precise, accurate, label-free, and rapid data acquisition to support high-throughput screening efforts.
Collapse
Affiliation(s)
- Mary Ashley Rimmer
- Analytical Technologies Center, Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Nathaniel R Twarog
- Lead Discovery Informatics, Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Yong Li
- Analytical Technologies Center, Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Anang A Shelat
- Lead Discovery Informatics, Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Zoran Rankovic
- Analytical Technologies Center, Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, United States.
| | - Lei Yang
- Analytical Technologies Center, Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, United States.
| |
Collapse
|
4
|
Zhang H, He X, Wang S, Wu F, Zhi Y, Li Y, Wang X, Ma Y, Meng F, Wang C. Research on accurate pipetting complementation model for high-throughput molecular detection platform. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2024; 95:024702. [PMID: 38376384 DOI: 10.1063/5.0159016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 01/18/2024] [Indexed: 02/21/2024]
Abstract
The incidence of infectious diseases has risen in recent years, leading to a significant surge in the demand for medical molecular detection. High-throughput molecular detection platforms play a crucial role in facilitating rapid and efficient molecular detection. Among the various techniques employed in high-throughput molecular detection, microliquid transfer stands out as one of the most frequently utilized methods. However, ensuring the accuracy of liquid transfer poses a challenge due to variations in the physical and chemical properties of different samples and reagents. In this study, a pipetting complementation model was developed specifically for the serum, paraffin oil, and throat swabs. The aim was to enhance the transfer accuracy of diverse liquids in the context of high-throughput molecular detection, ultimately ensuring detection reliability and stability. The experimental findings revealed notable improvements in pipetting accuracy after compensating for the three liquids. In particular, the pipetting error rates decreased by 52.5, 96, and 71.4% for serum, paraffin oil, and throat swabs, respectively. These results underscore the model's effectiveness in providing reliable support for the precise transfer of liquids on the high-throughput molecular detection platform.
Collapse
Affiliation(s)
- Haotian Zhang
- Department of Biomedical Engineering, School of Biomedical Engineering and Informatics, Nanjing Medical University, Longmian Avenue 101, Jiangning District, Nanjing 211166, People's Republic of China
| | - Xinyi He
- Department of Biomedical Engineering, School of Biomedical Engineering and Informatics, Nanjing Medical University, Longmian Avenue 101, Jiangning District, Nanjing 211166, People's Republic of China
| | - Shaochen Wang
- Department of Biomedical Engineering, School of Biomedical Engineering and Informatics, Nanjing Medical University, Longmian Avenue 101, Jiangning District, Nanjing 211166, People's Republic of China
| | - Fengxue Wu
- Department of Biomedical Engineering, School of Biomedical Engineering and Informatics, Nanjing Medical University, Longmian Avenue 101, Jiangning District, Nanjing 211166, People's Republic of China
| | - Yinjie Zhi
- Department of Biomedical Engineering, School of Biomedical Engineering and Informatics, Nanjing Medical University, Longmian Avenue 101, Jiangning District, Nanjing 211166, People's Republic of China
| | - Yanfeng Li
- Department of Biomedical Engineering, School of Biomedical Engineering and Informatics, Nanjing Medical University, Longmian Avenue 101, Jiangning District, Nanjing 211166, People's Republic of China
| | - Xiaonan Wang
- Department of Biomedical Engineering, School of Biomedical Engineering and Informatics, Nanjing Medical University, Longmian Avenue 101, Jiangning District, Nanjing 211166, People's Republic of China
| | - Yuxuan Ma
- Department of Biomedical Engineering, School of Biomedical Engineering and Informatics, Nanjing Medical University, Longmian Avenue 101, Jiangning District, Nanjing 211166, People's Republic of China
| | - Fan Meng
- Department of Anesthesiology, Sir Run Run Hospital Affiliated to Nanjing Medical University, Longmian Avenue 109, Jiangning District, Nanjing 211166, People's Republic of China
| | - Chao Wang
- Department of Biomedical Engineering, School of Biomedical Engineering and Informatics, Nanjing Medical University, Longmian Avenue 101, Jiangning District, Nanjing 211166, People's Republic of China
| |
Collapse
|
5
|
Matsumura Y, Nakazaki T, Kitamori K, Kure E, Shinohara K, Tsuchido Y, Yukawa S, Noguchi T, Yamamoto M, Nagao M. Development and evaluation of the automated multipurpose molecular testing system PCRpack for high-throughput SARS-CoV-2 testing. Microbiol Spectr 2023; 11:e0271623. [PMID: 37943047 PMCID: PMC10715159 DOI: 10.1128/spectrum.02716-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 10/03/2023] [Indexed: 11/10/2023] Open
Abstract
IMPORTANCE Accurate and fast molecular testing is important for the diagnosis and control of COVID-19. During patient surges in the COVID-19 pandemic, laboratories were challenged by a higher demand for molecular testing under skilled staff shortages. We developed an automated multipurpose molecular testing system, named PCRpack, for the rapid, high-throughput testing of infectious pathogens, including SARS-CoV-2. The system is provided in an all-in-one package, including a liquid handling instrument, a laboratory information management system, and other materials needed for testing operation; is highly customizable; and is easily implemented. PCRpack showed robust liquid handling performance, high clinical diagnostic performance, a shorter turn-around time with minimal hands-on time, and a high testing capacity. These features contribute to the rapid implementation of the high-performance and high-throughput molecular testing environment at any phase of the pandemic caused by SARS-CoV-2 or future emerging pathogens.
Collapse
Affiliation(s)
- Yasufumi Matsumura
- Department of Clinical Laboratory Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | | | - Kanako Kitamori
- Department of Clinical Laboratory Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
- Nippon Control System, Yokohama, Japan
| | - Eiki Kure
- Department of Clinical Laboratory Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
- Faculty of Pharmacy, Kyoto Pharmaceutical University, Kyoto, Japan
| | - Koh Shinohara
- Department of Clinical Laboratory Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Yasuhiro Tsuchido
- Department of Clinical Laboratory Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Satomi Yukawa
- Department of Clinical Laboratory Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Taro Noguchi
- Department of Clinical Laboratory Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Masaki Yamamoto
- Department of Clinical Laboratory Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Miki Nagao
- Department of Clinical Laboratory Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| |
Collapse
|
6
|
Pokrovskaya MS, Borisova AL, Kondratskaya VA, Efimova IA, Ershova AI, Drapkina OM. Approaches to automation of the preanalytical phase of large-scale research in the biobank of the National Medical Research Center for Therapy and Preventive Medicine of the Ministry of Health of Russia. КАРДИОВАСКУЛЯРНАЯ ТЕРАПИЯ И ПРОФИЛАКТИКА 2022. [DOI: 10.15829/1728-8800-2022-3404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Aim. To create and validate an algorithm for automatic aliquoting of serum and plasma samples for biobanking as part of a large-scale study.Material and methods. Biobank of the National Medical Research Center for Therapy and Preventive Medicine is equipped with a Tecan automated aliquoting system. When compiling the aliquoting program (script), the following parameters were selected: the time spent on spotting one complete cryobox, with a capacity of 96 cryotubes, the optimal number of vacutainers and tips for a single loading of the device. The program was created to receive 12 aliquots of 0,5 ml of blood serum, plasma with ethylenediaminetetraacetic acid and plasma with sodium citrate in cryotubes per 1 ml from eight participants in total from each in one cycle of device loading. Automatic and manual spotting was assessed in terms of the time spent on sample preparation and the quality of the aliquots obtained.Results. A methodology for conducting the preanalytical phase of a large-scale study based on the automation of biosample aliquoting has been developed and validated. We created scripts for aliquoting serum and blood plasma at the automated Tecan Freedom EVO system. An experiment conducted on biomaterial from 64 participants showed, that with an expected flow of 32 participants per day, it took more than 2 hours for manual aliquoting, and for automatic aliquoting (4 launches of the aliquot robot for 24 vacutainers from 8 participants) — less than 1,5 hours with the complete exclusion of human errors.Conclusion. Automated aliquoting has a following number of advantages in comparison with manual: it allows to guarantee standardization and efficiency of sample preparation, reduce the time and increase the accuracy of aliquoting of biomaterial, save space in long-term storage freezers due to the use of smaller cryotubes. The developed algorithm for creating aliquoting programs and calculating the optimal use of consumables can be used in other projects.
Collapse
Affiliation(s)
- M. S. Pokrovskaya
- National Medical Research Center for Therapy and Preventive Medicine
| | - A. L. Borisova
- National Medical Research Center for Therapy and Preventive Medicine
| | | | - I. A. Efimova
- National Medical Research Center for Therapy and Preventive Medicine
| | - A. I. Ershova
- National Medical Research Center for Therapy and Preventive Medicine
| | - O. M. Drapkina
- National Medical Research Center for Therapy and Preventive Medicine
| |
Collapse
|
7
|
Dudman J, Ferreira AM, Gentile P, Wang X, Dalgarno K. Microvalve Bioprinting of MSC-Chondrocyte Co-Cultures. Cells 2021; 10:cells10123329. [PMID: 34943837 PMCID: PMC8699323 DOI: 10.3390/cells10123329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/28/2021] [Accepted: 11/23/2021] [Indexed: 12/05/2022] Open
Abstract
Recent improvements within the fields of high-throughput screening and 3D tissue culture have provided the possibility of developing in vitro micro-tissue models that can be used to study diseases and screen potential new therapies. This paper reports a proof-of-concept study on the use of microvalve-based bioprinting to create laminar MSC-chondrocyte co-cultures to investigate whether the use of MSCs in ACI procedures would stimulate enhanced ECM production by chondrocytes. Microvalve-based bioprinting uses small-scale solenoid valves (microvalves) to deposit cells suspended in media in a consistent and repeatable manner. In this case, MSCs and chondrocytes have been sequentially printed into an insert-based transwell system in order to create a laminar co-culture, with variations in the ratios of the cell types used to investigate the potential for MSCs to stimulate ECM production. Histological and indirect immunofluorescence staining revealed the formation of dense tissue structures within the chondrocyte and MSC-chondrocyte cell co-cultures, alongside the establishment of a proliferative region at the base of the tissue. No stimulatory or inhibitory effect in terms of ECM production was observed through the introduction of MSCs, although the potential for an immunomodulatory benefit remains. This study, therefore, provides a novel method to enable the scalable production of therapeutically relevant micro-tissue models that can be used for in vitro research to optimise ACI procedures.
Collapse
Affiliation(s)
- Joseph Dudman
- School of Engineering, Newcastle University, Newcastle upon Tyne NE3 1PS, UK; (J.D.); (A.M.F.); (P.G.)
| | - Ana Marina Ferreira
- School of Engineering, Newcastle University, Newcastle upon Tyne NE3 1PS, UK; (J.D.); (A.M.F.); (P.G.)
| | - Piergiorgio Gentile
- School of Engineering, Newcastle University, Newcastle upon Tyne NE3 1PS, UK; (J.D.); (A.M.F.); (P.G.)
| | - Xiao Wang
- Translational and Clinical Research Institute, Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK;
| | - Kenneth Dalgarno
- School of Engineering, Newcastle University, Newcastle upon Tyne NE3 1PS, UK; (J.D.); (A.M.F.); (P.G.)
- Correspondence:
| |
Collapse
|
8
|
Raj K, Venayak N, Diep P, Golla SA, Yakunin AF, Mahadevan R. Automation assisted anaerobic phenotyping for metabolic engineering. Microb Cell Fact 2021; 20:184. [PMID: 34556155 PMCID: PMC8461876 DOI: 10.1186/s12934-021-01675-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 09/10/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Microorganisms can be metabolically engineered to produce a wide range of commercially important chemicals. Advancements in computational strategies for strain design and synthetic biological techniques to construct the designed strains have facilitated the generation of large libraries of potential candidates for chemical production. Consequently, there is a need for high-throughput laboratory scale techniques to characterize and screen these candidates to select strains for further investigation in large scale fermentation processes. Several small-scale fermentation techniques, in conjunction with laboratory automation have enhanced the throughput of enzyme and strain phenotyping experiments. However, such high throughput experimentation typically entails large operational costs and generate massive amounts of laboratory plastic waste. RESULTS In this work, we develop an eco-friendly automation workflow that effectively calibrates and decontaminates fixed-tip liquid handling systems to reduce tip waste. We also investigate inexpensive methods to establish anaerobic conditions in microplates for high-throughput anaerobic phenotyping. To validate our phenotyping platform, we perform two case studies-an anaerobic enzyme screen, and a microbial phenotypic screen. We used our automation platform to investigate conditions under which several strains of E. coli exhibit the same phenotypes in 0.5 L bioreactors and in our scaled-down fermentation platform. We also propose the use of dimensionality reduction through t-distributed stochastic neighbours embedding (t-SNE) in conjunction with our phenotyping platform to effectively cluster similarly performing strains at the bioreactor scale. CONCLUSIONS Fixed-tip liquid handling systems can significantly reduce the amount of plastic waste generated in biological laboratories and our decontamination and calibration protocols could facilitate the widespread adoption of such systems. Further, the use of t-SNE in conjunction with our automation platform could serve as an effective scale-down model for bioreactor fermentations. Finally, by integrating an in-house data-analysis pipeline, we were able to accelerate the 'test' phase of the design-build-test-learn cycle of metabolic engineering.
Collapse
Affiliation(s)
- Kaushik Raj
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, M5S 3E5 Canada
| | - Naveen Venayak
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, M5S 3E5 Canada
| | - Patrick Diep
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, M5S 3E5 Canada
| | - Sai Akhil Golla
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, M5S 3E5 Canada
| | - Alexander F. Yakunin
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, M5S 3E5 Canada
- School of Natural Sciences, Bangor University, Bangor, LL57 2DG UK
| | - Radhakrishnan Mahadevan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, M5S 3E5 Canada
- Institute of Biomedical Engineering, University of Toronto, 164 College Street, Toronto, M5S 3G9 Canada
| |
Collapse
|
9
|
Young R, Haines M, Storch M, Freemont PS. Combinatorial metabolic pathway assembly approaches and toolkits for modular assembly. Metab Eng 2020; 63:81-101. [PMID: 33301873 DOI: 10.1016/j.ymben.2020.12.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 11/16/2020] [Accepted: 12/03/2020] [Indexed: 12/18/2022]
Abstract
Synthetic Biology is a rapidly growing interdisciplinary field that is primarily built upon foundational advances in molecular biology combined with engineering design principles such as modularity and interoperability. The field considers living systems as programmable at the genetic level and has been defined by the development of new platform technologies and methodological advances. A key concept driving the field is the Design-Build-Test-Learn cycle which provides a systematic framework for building new biological systems. One major application area for synthetic biology is biosynthetic pathway engineering that requires the modular assembly of different genetic regulatory elements and biosynthetic enzymes. In this review we provide an overview of modular DNA assembly and describe and compare the plethora of in vitro and in vivo assembly methods for combinatorial pathway engineering. Considerations for part design and methods for enzyme balancing are also presented, and we briefly discuss alternatives to intracellular pathway assembly including microbial consortia and cell-free systems for biosynthesis. Finally, we describe computational tools and automation for pathway design and assembly and argue that a deeper understanding of the many different variables of genetic design, pathway regulation and cellular metabolism will allow more predictive pathway design and engineering.
Collapse
Affiliation(s)
- Rosanna Young
- Department of Infectious Disease, Sir Alexander Fleming Building, South Kensington Campus, Imperial College London, SW7 2AZ, UK
| | - Matthew Haines
- Department of Infectious Disease, Sir Alexander Fleming Building, South Kensington Campus, Imperial College London, SW7 2AZ, UK
| | - Marko Storch
- Department of Infectious Disease, Sir Alexander Fleming Building, South Kensington Campus, Imperial College London, SW7 2AZ, UK; London Biofoundry, Imperial College Translation & Innovation Hub, London, W12 0BZ, UK
| | - Paul S Freemont
- Department of Infectious Disease, Sir Alexander Fleming Building, South Kensington Campus, Imperial College London, SW7 2AZ, UK; London Biofoundry, Imperial College Translation & Innovation Hub, London, W12 0BZ, UK; UK DRI Care Research and Technology Centre, Imperial College London, Hammersmith Campus, Du Cane Road, London, W12 0NN, UK.
| |
Collapse
|
10
|
Wang L, Dalglish G, Ouyang Z, David-Brown DG, Chiriac C, Duo J, Kozhich A, Ji QC, Peterson JE. Integration of Acoustic Liquid Handling into Quantitative Analysis of Biological Matrix Samples. SLAS Technol 2020; 25:463-473. [PMID: 32351162 DOI: 10.1177/2472630320915844] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Acoustic liquid handlers deliver small volumes (nL-µL) of multiple fluid types with accuracy and dynamic viscosity profiling. They are widely used in the pharmaceutical industry with applications extending from high-throughput screening in compound management to gene expression sequencing, genomic and epigenetic assays, and cell-based assays. The capability of the Echo to transfer small volumes of multiple types of fluids could benefit bioanalysis assays by minimization of sample volume and by simplifying dilution procedures by direct dilution. In this study, we evaluated the Labcyte Echo 525 liquid handler for its ability to deliver small volumes of sample preparations in biological matrix (plasma and serum) and to assess the feasibility of integration of the Echo with three types of bioanalytical assay platforms: microplate enzyme-linked immunosorbent assay, Gyrolab immunoassay, and liquid chromatography with tandem mass spectrometry. The results demonstrated acceptable consistency of dispensed plasma samples from multiple lots and species by the Echo. Equivalent assay performance demonstrated between the Echo and manual liquid procedures indicated great potential for the integration of the Echo with the bioanalytical assay, which allows the successful implementation of microsampling strategies in drug discovery and development.
Collapse
Affiliation(s)
- Linna Wang
- Bioanalytical Sciences, Translational Medicine, Bristol-Myers Squibb, Princeton, NJ, USA
| | - Gerard Dalglish
- Bioanalytical Sciences, Translational Medicine, Bristol-Myers Squibb, Princeton, NJ, USA
| | - Zheng Ouyang
- Bioanalytical Sciences, Translational Medicine, Bristol-Myers Squibb, Princeton, NJ, USA
| | | | - Camelia Chiriac
- Bioanalytical Sciences, Translational Medicine, Bristol-Myers Squibb, Princeton, NJ, USA
| | - Jia Duo
- Bioanalytical Sciences, Translational Medicine, Bristol-Myers Squibb, Princeton, NJ, USA
| | - Alexander Kozhich
- Bioanalytical Sciences, Translational Medicine, Bristol-Myers Squibb, Princeton, NJ, USA
| | - Qin C Ji
- Bioanalytical Sciences, Translational Medicine, Bristol-Myers Squibb, Princeton, NJ, USA
| | - Jon E Peterson
- Bioanalytical Sciences, Translational Medicine, Bristol-Myers Squibb, Princeton, NJ, USA
| |
Collapse
|
11
|
Coppola L, Smaldone G, Cianflone A, Baselice S, Mirabelli P, Salvatore M. Purification of viable peripheral blood mononuclear cells for biobanking using a robotized liquid handling workstation. J Transl Med 2019; 17:371. [PMID: 31718655 PMCID: PMC6852781 DOI: 10.1186/s12967-019-2125-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 11/01/2019] [Indexed: 12/16/2022] Open
Abstract
Background The purification of peripheral blood mononuclear cells (PBMCs) by means of density gradient (1.07 g/mL) centrifugation is one of the most commonly used methods in diagnostics and research laboratories as well as in biobanks. Here, we evaluated whether it was possible to set up an automated protocol for PBMC purification using a programmable liquid handling robotized workstation (Tecan, Freedom EVO 150). We selected a population composed of 30 subjects for whom it was possible to dispose of two ethylenediaminetetraacetic acid (EDTA) vacutainer tubes containing unfractionated peripheral blood. The purification of PBMCs was performed in parallel using automated and manual workflows. Results An automated workflow using the Freedom EVO 150 liquid handling workstation was generated for the isolation of PBMCs. This protocol allowed blood dilution in Dulbecco’s phosphate-buffered saline (DPBS), stratification onto the density gradient, and the collection of PBMC rings after centrifugation. The comparison between the automated and manual methods revealed no significant differences after separation in terms of total mononuclear cell enrichment, red blood cell contamination, or leucocyte formula, including the percentage of lymphoid subpopulations as B, T and natural killer (NK) lymphocytes. Conclusions Our results show that it is possible to set up an automated protocol for the isolation of PBMCs using a robotized liquid handling workstation. This automated protocol provided comparable results to the routinely used manual method. This automatic method could be of interest for those working in biobanking or industries involved in diagnostics and therapeutics field, to avoid operator-dependent errors as well as procedures standardization.
Collapse
Affiliation(s)
- Luigi Coppola
- IRCCS SDN, Naples Via Emanuele Gianturco, 113, 80143, Naples, Italy
| | | | | | - Simona Baselice
- IRCCS SDN, Naples Via Emanuele Gianturco, 113, 80143, Naples, Italy
| | - Peppino Mirabelli
- IRCCS SDN, Naples Via Emanuele Gianturco, 113, 80143, Naples, Italy.
| | - Marco Salvatore
- IRCCS SDN, Naples Via Emanuele Gianturco, 113, 80143, Naples, Italy
| |
Collapse
|
12
|
Wang G, Das C, Ledden B, Sun Q, Nguyen C, Kumar S. Evaluation of disposable microfluidic chip design for automated and fast Immunoassays. BIOMICROFLUIDICS 2017; 11:014115. [PMID: 28344726 PMCID: PMC5325810 DOI: 10.1063/1.4977198] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 02/10/2017] [Indexed: 05/08/2023]
Abstract
We report here, the design and development of a disposable immunoassay chip for protein biomarker detection within ∼1 h. The unique design allows for real-time dynamic calibration of immunoassay for multiple biomarker detections on the chip. The limit of detection achieved for this test chip is 10 pg/ml for IL6, and 50 pg/ml for GFAP with a detection time of 1 h. The prototype instrument used for flowing the reagents through the chip can be easily assembled from off-the-shelf components with the final chemiluminescent detection carried out in a commercial plate reader. Optimization of different aspects of chip design, fabrication, and assay development is discussed in detail.
Collapse
Affiliation(s)
- Guochun Wang
- SFC Fluidics, Inc. , Fayetteville, Arkansas 72701, USA
| | - Champak Das
- SFC Fluidics, Inc. , Fayetteville, Arkansas 72701, USA
| | | | - Qian Sun
- SFC Fluidics, Inc. , Fayetteville, Arkansas 72701, USA
| | - Chien Nguyen
- SFC Fluidics, Inc. , Fayetteville, Arkansas 72701, USA
| | - Sai Kumar
- Diligent CXO , Norcross, Georgia 30071, USA
| |
Collapse
|
13
|
Das C, Wang G, Nguyen C. A Low-Cost, Accurate, and High-Precision Fluid Dispensing System for Microscale Application. SLAS Technol 2016; 22:144-152. [PMID: 27811326 DOI: 10.1177/2211068216676082] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
We present here the development of a low-cost, accurate, and precise fluid dispensing system. It can be used with peristaltic or any other pump to improve the flow characteristics. The dispensing system has a range of 1 to 100 µL with accuracy of ~99.5% and standard deviation at ~150 nL over the entire range. The system developed does not depend on the accuracy or precision of the driving pump; therefore, any positive displacement pump can be used to get similar accuracy and precision, which gives an opportunity to reduce the cost of the system. The dispensing system does not require periodic calibration and can also be miniaturized for microfluidic application. Although primarily designed for aqueous liquid, it can be extended for different nonconductive liquids as well with modifications. The unit is further used for near real-time measurement of lactate from microdialysate. The individual components can easily be made disposable or sterilized for use in biomedical applications.
Collapse
|