1
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McElvania E, Mindel S, Lemstra J, Brands K, Patel P, Good CE, Morel D, Orny C, Volle JM, Desjardins M, Rhoads D. Automated detection of methicillin-resistant Staphylococcus aureus with the MRSA CHROM imaging application on BD Kiestra Total Lab Automation System. J Clin Microbiol 2024; 62:e0144523. [PMID: 38557148 DOI: 10.1128/jcm.01445-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Accepted: 03/08/2024] [Indexed: 04/04/2024] Open
Abstract
The virulence of methicillin-resistant Staphylococcus aureus (MRSA) and its potentially fatal outcome necessitate rapid and accurate detection of patients colonized with MRSA in healthcare settings. Using the BD Kiestra Total Lab Automation (TLA) System in conjunction with the MRSA Application (MRSA App), an imaging application that uses artificial intelligence to interpret colorimetric information (mauve-colored colonies) indicative of MRSA pathogen presence on CHROMagar chromogenic media, anterior nares specimens from three sites were evaluated for the presence of mauve-colored colonies. Results obtained with the MRSA App were compared to manual reading of agar plate images by proficient laboratory technologists. Of 1,593 specimens evaluated, 1,545 (96.98%) were concordant between MRSA App and laboratory technologist reading for the detection of MRSA growth [sensitivity 98.15% (95% CI, 96.03, 99.32) and specificity 96.69% (95% CI, 95.55, 97.60)]. This multi-site study is the first evaluation of the MRSA App in conjunction with the BD Kiestra TLA System. Using the MRSA App, our results showed 98.15% sensitivity and 96.69% specificity for the detection of MRSA from anterior nares specimens. The MRSA App, used in conjunction with laboratory automation, provides an opportunity to improve laboratory efficiency by reducing laboratory technologists' labor associated with the review and interpretation of cultures.
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Affiliation(s)
- Erin McElvania
- Northshore University Health System, Evanston, Illinois, USA
| | - Susan Mindel
- Becton, Dickinson and Company- Integrated Diagnostic Solutions, Sparks, Maryland, USA
| | | | | | - Parul Patel
- Northshore University Health System, Evanston, Illinois, USA
| | - Caryn E Good
- University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA
| | - Didier Morel
- Becton, Dickinson and Company - HEOR & RWE Data Science, Eybens Isere, France
| | - Cedrick Orny
- Becton, Dickinson and Company - Innovation Software Engineering, Eybens Isere, France
| | - Jean-Marc Volle
- Becton, Dickinson and Company - Innovation Software Engineering, Eybens Isere, France
| | - Marc Desjardins
- Eastern Ontario Regional Laboratory Association, Ottawa, Ontario, Canada
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2
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Wang Y, Troutman MC, Hofmann C, Gonzalez A, Song L, Levin R, Pixley HY, Kearns K, DePhillips P, Loughney JW. Fully automated high-throughput immuno-µPlaque assay for live-attenuated tetravalent dengue vaccine development. Front Immunol 2024; 15:1356600. [PMID: 38410513 PMCID: PMC10895029 DOI: 10.3389/fimmu.2024.1356600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 01/29/2024] [Indexed: 02/28/2024] Open
Abstract
Dengue fever has remained a continuing global medical threat that impacts half of the world's population. Developing a highly effective dengue vaccine, with live-attenuated tetravalent vaccines as leading candidates, remains essential in preventing this disease. For the development of live virus vaccines (LVVs), potency measurements play a vital role in quantifying the active components of vaccine drug substance as well as drug product during various stages of research, development, and post-licensure evaluations. Traditional plaque-based assays are one of the most common potency test methods, but they generally take up to weeks to complete. Less labor and time-intensive potency assays are thus called for to aid in the acceleration of vaccine development, especially for multivalent LVVs. Here, we introduce a fully automated, 96-well format µPlaque assay that has been optimized as a high-throughput tool to evaluate process and formulation development of a live-attenuated tetravalent dengue vaccine. To the best of our knowledge, this is the first report of a miniaturized viral plaque method for dengue with full automation via an integrated robotic system. Compared to the traditional manual plaque assay, this newly developed method substantially reduces testing time by approximately half and allows for the evaluation of over ten times more samples per run. The fully automated workflow, from cell culture to plaque counting, significantly minimizes analyst hands-on time and improves assay repeatability. The study presents a pioneering solution for the rapid measurement of LVV viral titers, offering promising prospects for advancing vaccine development through high-throughput analytics.
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Affiliation(s)
- Yi Wang
- Analytical Research & Development, Merck & Co., Inc., Rahway, NJ, United States
| | - Matthew C. Troutman
- Analytical Research & Development, Merck & Co., Inc., Rahway, NJ, United States
| | - Carl Hofmann
- Analytical Research & Development, Merck & Co., Inc., Rahway, NJ, United States
| | - Ariel Gonzalez
- Analytical Research & Development, Merck & Co., Inc., Rahway, NJ, United States
| | - Liping Song
- Biostatistics, Merck & Co., Inc., Rahway, NJ, United States
| | - Robert Levin
- Vaccine Drug Product Development, Merck & Co., Inc, Rahway, NJ, United States
| | - Heidi Yoder Pixley
- Vaccine Drug Product Development, Merck & Co., Inc, Rahway, NJ, United States
| | - Kristine Kearns
- Analytical Research & Development, Merck & Co., Inc., Rahway, NJ, United States
| | - Pete DePhillips
- Analytical Research & Development, Merck & Co., Inc., Rahway, NJ, United States
| | - John W. Loughney
- Analytical Research & Development, Merck & Co., Inc., Rahway, NJ, United States
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3
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Sarker NH, Hakim ZA, Dabouei A, Uddin MR, Freyberg Z, MacWilliams A, Kangas J, Xu M. Detecting anomalies from liquid transfer videos in automated laboratory setting. Front Mol Biosci 2023; 10:1147514. [PMID: 37214339 PMCID: PMC10192699 DOI: 10.3389/fmolb.2023.1147514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 04/17/2023] [Indexed: 05/24/2023] Open
Abstract
In this work, we address the problem of detecting anomalies in a certain laboratory automation setting. At first, we collect video images of liquid transfer in automated laboratory experiments. We mimic the real-world challenges of developing an anomaly detection model by considering two points. First, the size of the collected dataset is set to be relatively small compared to large-scale video datasets. Second, the dataset has a class imbalance problem where the majority of the collected videos are from abnormal events. Consequently, the existing learning-based video anomaly detection methods do not perform well. To this end, we develop a practical human-engineered feature extraction method to detect anomalies from the liquid transfer video images. Our simple yet effective method outperforms state-of-the-art anomaly detection methods with a notable margin. In particular, the proposed method provides 19% and 76% average improvement in AUC and Equal Error Rate, respectively. Our method also quantifies the anomalies and provides significant benefits for deployment in the real-world experimental setting.
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Affiliation(s)
- Najibul Haque Sarker
- Computer Science and Engineering Department, Bangladesh University of Engineering and Technology, Dhaka, Bangladesh
| | - Zaber Abdul Hakim
- Computer Science and Engineering Department, Bangladesh University of Engineering and Technology, Dhaka, Bangladesh
| | - Ali Dabouei
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, United States
| | - Mostofa Rafid Uddin
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, United States
| | - Zachary Freyberg
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, United States
| | - Andy MacWilliams
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, United States
| | - Joshua Kangas
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, United States
| | - Min Xu
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, United States
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4
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Ko SC, Cho M, Lee HJ, Woo HM. Biofoundry Palette: Planning-Assistant Software for Liquid Handler-Based Experimentation and Operation in the Biofoundry Workflow. ACS Synth Biol 2022; 11:3538-3543. [PMID: 36173735 DOI: 10.1021/acssynbio.2c00390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Lab automation has facilitated synthetic biology applications in an automated workflow, and biofoundry facilities have enabled automated high-throughput experiments of gene cloning and genome engineering to be conducted following a precise experimental design and protocol. However, before-experiment procedures in biofoundry applications have been underdetermined. We aimed to develop a Python-based planning-assistant software, namely Biofoundry Palette, for liquid handler-based experimentation and operation in the biofoundry workflow. Depending on the synthetic biology project, variable information and content information may vary; the Biofoundry Palette provides precise information for the before-experiment units for each process module in the biofoundry workflow. As a demonstration, more than 200 unique information sets, generated by Biofoundry Palette, were used in automated gene cloning or pathway construction. The information on planning and management can potentially help the operator faithfully execute the biofoundry workflow after securing the before-experiment unit, thereby lowering the risk of human errors and performing successful biofoundry operations for synthetic biology applications.
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Affiliation(s)
- Sung Cheon Ko
- Department of Food Science and Biotechnology, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea.,Biofoundry Research Center, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
| | - Mingu Cho
- Department of Food Science and Biotechnology, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
| | - Hyun Jeong Lee
- Department of Food Science and Biotechnology, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea.,Biofoundry Research Center, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
| | - Han Min Woo
- Department of Food Science and Biotechnology, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea.,Biofoundry Research Center, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
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5
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Ouyang W, Bowman RW, Wang H, Bumke KE, Collins JT, Spjuth O, Carreras-Puigvert J, Diederich B. An Open-Source Modular Framework for Automated Pipetting and Imaging Applications. Adv Biol (Weinh) 2022; 6:e2101063. [PMID: 34693668 DOI: 10.1002/adbi.202101063] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 09/14/2021] [Indexed: 01/27/2023]
Abstract
The number of samples in biological experiments is continuously increasing, but complex protocols and human error in many cases lead to suboptimal data quality and hence difficulties in reproducing scientific findings. Laboratory automation can alleviate many of these problems by precisely reproducing machine-readable protocols. These instruments generally require high up-front investments, and due to the lack of open application programming interfaces (APIs), they are notoriously difficult for scientists to customize and control outside of the vendor-supplied software. Here, automated, high-throughput experiments are demonstrated for interdisciplinary research in life science that can be replicated on a modest budget, using open tools to ensure reproducibility by combining the tools OpenFlexure, Opentrons, ImJoy, and UC2. This automated sample preparation and imaging pipeline can easily be replicated and established in many laboratories as well as in educational contexts through easy-to-understand algorithms and easy-to-build microscopes. Additionally, the creation of feedback loops, with later pipetting or imaging steps depending on the analysis of previously acquired images, enables the realization of fully autonomous "smart" microscopy experiments. All documents and source files are publicly available to prove the concept of smart lab automation using inexpensive, open tools. It is believed this democratizes access to the power and repeatability of automated experiments.
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Affiliation(s)
- Wei Ouyang
- W. Ouyang, Science for Life Laboratory School of Engineering Sciences in Chemistry, Biotechnology and Health KTH - Royal Institute of Technology, Stockholm, 114 28, Sweden
| | - Richard W Bowman
- R. W. Bowman, K. E. Bumke, J. T. Collins, Department of Physics, University of Bath, Bath, BA2 7AY, UK
| | - Haoran Wang
- H. Wang, B. Diederich, Leibniz Institute for Photonic Technology, Albert-Einstein-Str. 9, 07749, Jena, Germany.,H. Wang, B. Diederich, Institute of Physical Chemistry, Friedrich-Schiller-Universität Jena, Helmholtzweg 4, 07743, Jena, Germany
| | - Kaspar E Bumke
- R. W. Bowman, K. E. Bumke, J. T. Collins, Department of Physics, University of Bath, Bath, BA2 7AY, UK
| | - Joel T Collins
- R. W. Bowman, K. E. Bumke, J. T. Collins, Department of Physics, University of Bath, Bath, BA2 7AY, UK
| | - Ola Spjuth
- O. Spjuth, J. Carreras-Puigvert, Department of Pharmaceutical Biosciences and Science for Life Laboratory, Uppsala University, Box 591, Uppsala, SE-75124, Sweden
| | - Jordi Carreras-Puigvert
- O. Spjuth, J. Carreras-Puigvert, Department of Pharmaceutical Biosciences and Science for Life Laboratory, Uppsala University, Box 591, Uppsala, SE-75124, Sweden
| | - Benedict Diederich
- H. Wang, B. Diederich, Leibniz Institute for Photonic Technology, Albert-Einstein-Str. 9, 07749, Jena, Germany.,H. Wang, B. Diederich, Institute of Physical Chemistry, Friedrich-Schiller-Universität Jena, Helmholtzweg 4, 07743, Jena, Germany
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6
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Abstract
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Surface-enhanced
Raman spectroscopy (SERS) is considered an attractive
candidate for quantitative and multiplexed molecular sensing of analytes
whose chemical composition is not fully known. In principle, molecules
can be identified through their fingerprint spectrum when binding
inside plasmonic hotspots. However, competitive binding experiments
between methyl viologen (MV2+) and its deuterated isomer
(d8-MV2+) here show that determining
individual concentrations by extracting peak intensities from spectra
is not possible. This is because analytes bind to different binding
sites inside and outside of hotspots with different affinities. Only
by knowing all binding constants and geometry-related factors, can
a model revealing accurate concentrations be constructed. To collect
sufficiently reproducible data for such a sensitive experiment, we
fully automate measurements using a high-throughput SERS optical system
integrated with a liquid handling robot (the SERSbot). This now allows
us to accurately deconvolute analyte mixtures through independent
component analysis (ICA) and to quantitatively map out the competitive
binding of analytes in nanogaps. Its success demonstrates the feasibility
of automated SERS in a wide variety of experiments and applications.
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Affiliation(s)
- David-Benjamin Grys
- Department of Physics, NanoPhotonics Centre, Cavendish Laboratory, JJ Thompson Avenue University of Cambridge, Cambridge CB3 0HE, United Kingdom
| | - Bart de Nijs
- Department of Physics, NanoPhotonics Centre, Cavendish Laboratory, JJ Thompson Avenue University of Cambridge, Cambridge CB3 0HE, United Kingdom
| | - Junyang Huang
- Department of Physics, NanoPhotonics Centre, Cavendish Laboratory, JJ Thompson Avenue University of Cambridge, Cambridge CB3 0HE, United Kingdom
| | - Oren A. Scherman
- Melville Laboratory for Polymer Synthesis, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Jeremy J. Baumberg
- Department of Physics, NanoPhotonics Centre, Cavendish Laboratory, JJ Thompson Avenue University of Cambridge, Cambridge CB3 0HE, United Kingdom
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7
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Furtmann N, Schneider M, Spindler N, Steinmann B, Li Z, Focken I, Meyer J, Dimova D, Kroll K, Leuschner WD, Debeaumont A, Mathieu M, Lange C, Dittrich W, Kruip J, Schmidt T, Birkenfeld J. An end-to-end automated platform process for high-throughput engineering of next-generation multi-specific antibody therapeutics. MAbs 2021; 13:1955433. [PMID: 34382900 PMCID: PMC8366542 DOI: 10.1080/19420862.2021.1955433] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Next-generation multi-specific antibody therapeutics (MSATs) are engineered to combine several functional activities into one molecule to provide higher efficacy compared to conventional, mono-specific antibody therapeutics. However, highly engineered MSATs frequently display poor yields and less favorable drug-like properties (DLPs), which can adversely affect their development. Systematic screening of a large panel of MSAT variants in very high throughput (HT) is thus critical to identify potent molecule candidates with good yield and DLPs early in the discovery process. Here we report on the establishment of a novel, format-agnostic platform process for the fast generation and multiparametric screening of tens of thousands of MSAT variants. To this end, we have introduced full automation across the entire value chain for MSAT engineering. Specifically, we have automated the in-silico design of very large MSAT panels such that it reflects precisely the wet-lab processes for MSAT DNA library generation. This includes mass saturation mutagenesis or bulk modular cloning technologies while, concomitantly, enabling library deconvolution approaches using HT Sanger DNA sequencing. These DNA workflows are tightly linked to fully automated downstream processes for compartmentalized mammalian cell transfection expression, and screening of multiple parameters. All sub-processes are seamlessly integrated with tailored workflow supporting bioinformatics. As described here, we used this platform to perform multifactor optimization of a next-generation bispecific, cross-over dual variable domain-Ig (CODV-Ig). Screening of more than 25,000 individual protein variants in mono- and bispecific format led to the identification of CODV-Ig variants with over 1,000-fold increased potency and significantly optimized production titers, demonstrating the power and versatility of the platform.
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Affiliation(s)
- Norbert Furtmann
- R&D Large Molecules Research Platform Germany, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, Frankfurt Am Main, Germany
| | - Marion Schneider
- R&D Large Molecules Research Platform Germany, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, Frankfurt Am Main, Germany
| | - Nadja Spindler
- R&D Large Molecules Research Platform Germany, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, Frankfurt Am Main, Germany
| | - Bjoern Steinmann
- R&D Large Molecules Research Platform Germany, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, Frankfurt Am Main, Germany
| | - Ziyu Li
- R&D Integrated Drug Discovery Germany, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, Frankfurt Am Main, Germany
| | - Ingo Focken
- R&D Large Molecules Research Platform Germany, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, Frankfurt Am Main, Germany
| | - Joachim Meyer
- Digital R&D, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, Frankfurt Am Main, Germany
| | - Dilyana Dimova
- R&D Large Molecules Research Platform Germany, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, Frankfurt Am Main, Germany
| | - Katja Kroll
- R&D Large Molecules Research Platform Germany, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, Frankfurt Am Main, Germany
| | - Wulf Dirk Leuschner
- R&D Large Molecules Research Platform Germany, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, Frankfurt Am Main, Germany
| | - Audrey Debeaumont
- R&D Large Molecules Research Platform Germany, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, Frankfurt Am Main, Germany
| | - Magali Mathieu
- R&D Integrated Drug Discovery France, Sanofi, Vitry Sur Seine Cedex, France
| | - Christian Lange
- R&D Large Molecules Research Platform Germany, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, Frankfurt Am Main, Germany
| | - Werner Dittrich
- R&D Large Molecules Research Platform Germany, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, Frankfurt Am Main, Germany
| | - Jochen Kruip
- IA Specialty Care Digital Innovation Biologics, Sanofi-Aventis Deutschland GmbH, Frankfurt Am Main, Germany
| | - Thorsten Schmidt
- R&D Large Molecules Research Platform Germany, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, Frankfurt Am Main, Germany
| | - Joerg Birkenfeld
- R&D Large Molecules Research Platform Germany, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, Frankfurt Am Main, Germany
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8
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Zucchelli P, Horak G, Skinner N. Highly Versatile Cloud-Based Automation Solution for the Remote Design and Execution of Experiment Protocols during the COVID-19 Pandemic. SLAS Technol 2020; 26:127-139. [PMID: 33210978 PMCID: PMC7684276 DOI: 10.1177/2472630320971218] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
There is an urgent need to accelerate the development and validation of both diagnostics and vaccines for COVID-19. These priorities are challenging both public and private sector research groups around the world and have shone a spotlight on both existing bottlenecks in the research workflows involved as well as on the implications of having to do much of this work remotely because of enforced social distancing and lockdown measures. The ability to respond quickly to rapidly evolving events, coupled with an emerging understanding of the disease and its pathology, as well as different mutations of the virus, necessitates a highly flexible liquid-handling automation solution that is amenable to rapid switching between different assay workflows and processes to be exploited tactically as needed. In addition, the use of cloud-based software imparts a unique benefit in enabling multiple research groups and remote technical staff around the world to have ready access to the same protocols in real-time without delays, down to the required level of detail, sharing methods and data (for example, in faster clinical trials). Informed by a recent use case, this article explores these issues alongside the recent development and deployment of an automation solution, whose unique approach in terms of both its cloud-native software and its highly modular hardware aligns especially well with achieving the challenge set by this new frontier in the bioanalytical laboratory.
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9
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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.
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10
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Li J, Tu Y, Liu R, Lu Y, Zhu X. Toward "On-Demand" Materials Synthesis and Scientific Discovery through Intelligent Robots. Adv Sci (Weinh) 2020; 7:1901957. [PMID: 32274293 PMCID: PMC7141037 DOI: 10.1002/advs.201901957] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 01/08/2020] [Indexed: 05/07/2023]
Abstract
A Materials Acceleration Operation System (MAOS) is designed, with unique language and compiler architecture. MAOS integrates with virtual reality (VR), collaborative robots, and a reinforcement learning (RL) scheme for autonomous materials synthesis, properties investigations, and self-optimized quality assurance. After training through VR, MAOS can work independently for labor and intensively reduces the time cost. Under the RL framework, MAOS also inspires the improved nucleation theory, and feedback for the optimal strategy, which can satisfy the demand on both of the CdSe quantum dots (QDs) emission wavelength and size distribution quality. Moreover, it can work well for extensive coverages of inorganic nanomaterials. MAOS frees the experimental researchers out of the tedious labor as well as the extensive exploration of optimal reaction conditions. This work provides a walking example for the "On-Demand" materials synthesis system, and demonstrates how artificial intelligence technology can reshape traditional materials science research in the future.
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Affiliation(s)
- Jiagen Li
- Shenzhen Institute of Artificial Intelligence and Robotics for Society (AIRS)The Chinese University of Hong KongShenzhenGuangdong518172China
| | - Yuxiao Tu
- Shenzhen Institute of Artificial Intelligence and Robotics for Society (AIRS)The Chinese University of Hong KongShenzhenGuangdong518172China
| | - Rulin Liu
- Shenzhen Institute of Artificial Intelligence and Robotics for Society (AIRS)The Chinese University of Hong KongShenzhenGuangdong518172China
| | - Yihua Lu
- Shenzhen Institute of Artificial Intelligence and Robotics for Society (AIRS)The Chinese University of Hong KongShenzhenGuangdong518172China
| | - Xi Zhu
- Shenzhen Institute of Artificial Intelligence and Robotics for Society (AIRS)The Chinese University of Hong KongShenzhenGuangdong518172China
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11
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Shapira M, Boico O, Cohen A, Sagi R, Aharon A, Navon R, Kronenfeld G, Maler K, Pri-Or E, Stein M, Klein A, Eden E, Oved K. Automating a new host-protein assay for differentiating bacterial from viral infection to reduce operator hands-on time. Biotechniques 2018; 65:93-5. [PMID: 30091387 DOI: 10.2144/btn-2018-0028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Distinguishing bacterial from viral infections is often challenging, leading to antibiotic misuse, and detrimental ramifications for the patient, the healthcare system and society. A novel ELISA-based assay that integrates the circulating levels of three host-response proteins (TRAIL, IP-10 and CRP) was developed to assist in differentiation between bacterial and viral etiologies. We developed a new protocol for measuring the host-based assay biomarkers using an automated ELISA workstation. The automated protocol was validated and was able to reduce technician hands-on time by 76%, while maintaining high analytical performance. Following automation, the assay has been incorporated into the routine workflow at a pediatric department, and is performed daily on admitted and emergency department patients. The automation protocol reduces the overall burden on the hospital laboratory performing the assay. This benefit has potential to promote adoption of the host-based assay, facilitating timely triage of febrile patients and prudent use of antibiotics.
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12
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Hemmerich J, Tenhaef N, Steffens C, Kappelmann J, Weiske M, Reich SJ, Wiechert W, Oldiges M, Noack S. Less Sacrifice, More Insight: Repeated Low-Volume Sampling of Microbioreactor Cultivations Enables Accelerated Deep Phenotyping of Microbial Strain Libraries. Biotechnol J 2018; 14:e1800428. [PMID: 30318833 DOI: 10.1002/biot.201800428] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 09/26/2018] [Indexed: 12/18/2022]
Abstract
With modern genetic engineering tools, high number of potentially improved production strains can be created in a short time. This results in a bottleneck in the succeeding step of bioprocess development, which can be handled by accelerating quantitative microbial phenotyping. Miniaturization and automation are key technologies to achieve this goal. In this study, a novel workflow for repeated low-volume sampling of BioLector-based cultivation setups is presented. Six samples of 20 μL each can be taken automatically from shaken 48-well microtiter plates without disturbing cell population growth. The volume is sufficient for quantification of substrate and product concentrations by spectrophotometric-based enzyme assays. From transient concentration data and replicate cultures, valid performance indicators (titers, rates, yields) are determined through process modeling and random error propagation analysis. Practical relevance of the workflow is demonstrated with a set of five genome-reduced Corynebacterium glutamicum strains that are engineered for Sec-mediated heterologous cutinase secretion. Quantitative phenotyping of this strain library led to the identification of a strain with a 1.6-fold increase in cutinase yield. The prophage-free strain carries combinatorial deletions of three gene clusters (Δ3102-3111, Δ3263-3301, and Δ3324-3345) of which the last two likely contain novel target genes to foster rational engineering of heterologous cutinase secretion in C. glutamicum.
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Affiliation(s)
- Johannes Hemmerich
- Institute of Bio-und Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany.,Bioeconomy Science Center (BioSC), c/o Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Niklas Tenhaef
- Institute of Bio-und Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Carmen Steffens
- Institute of Bio-und Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Jannick Kappelmann
- Institute of Bio-und Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Marc Weiske
- Institute of Bio-und Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Sebastian J Reich
- Institute of Bio-und Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Wolfgang Wiechert
- Institute of Bio-und Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany.,Computational Systems Biotechnology (AVT.CSB), RWTH Aachen, 52062 Aachen, Germany.,Bioeconomy Science Center (BioSC), c/o Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Marco Oldiges
- Institute of Bio-und Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany.,Institute for Biotechnology, RWTH Aachen, 52062 Aachen, Germany.,Bioeconomy Science Center (BioSC), c/o Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Stephan Noack
- Institute of Bio-und Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany.,Bioeconomy Science Center (BioSC), c/o Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
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13
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Hemmerich J, Noack S, Wiechert W, Oldiges M. Microbioreactor Systems for Accelerated Bioprocess Development. Biotechnol J 2018; 13:e1700141. [PMID: 29283217 DOI: 10.1002/biot.201700141] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 12/15/2017] [Indexed: 12/14/2022]
Abstract
In recent years, microbioreactor (MBR) systems have evolved towards versatile bioprocess engineering tools. They provide a unique solution to combine higher experimental throughput with extensive bioprocess monitoring and control, which is indispensable to develop economically and ecologically competitive bioproduction processes. MBR systems are based either on down-scaled stirred tank reactors or on advanced shaken microtiter plate cultivation devices. Importantly, MBR systems make use of optical measurements for non-invasive, online monitoring of important process variables like biomass concentration, dissolved oxygen, pH, and fluorescence. The application range of MBR systems can be further increased by integration into liquid handling robots, enabling automatization and, thus standardization, of various handling and operation procedures. Finally, the tight integration of quantitative strain phenotyping with bioprocess development under industrially relevant conditions greatly increases the probability of finding the right combination of producer strain and bioprocess control strategy. This review will discuss the current state of the art in the field of MBR systems and we can readily conclude that their importance for industrial biotechnology will further increase in the near future.
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Affiliation(s)
- Johannes Hemmerich
- Forschungszentrum Jülich, Institute of Bio- and Geosciences - Biotechnology (IBG-1), Wilhelm-Johnen Straße 1, 52425, Jülich, Germany.,Bioeconomy Science Center (BioSC), c/o Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Stephan Noack
- Forschungszentrum Jülich, Institute of Bio- and Geosciences - Biotechnology (IBG-1), Wilhelm-Johnen Straße 1, 52425, Jülich, Germany.,Bioeconomy Science Center (BioSC), c/o Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Wolfgang Wiechert
- RWTH Aachen University, Computational Systems Biotechnology (AVT.CSB), Forckenbeckstraße 51, 52074 Aachen, Germany.,Bioeconomy Science Center (BioSC), c/o Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Marco Oldiges
- Forschungszentrum Jülich, Institute of Bio- and Geosciences - Biotechnology (IBG-1), Wilhelm-Johnen Straße 1, 52425, Jülich, Germany.,RWTH Aachen University, Institute of Biotechnology, Worringer Weg 3, 52074 Aachen, Germany.,Bioeconomy Science Center (BioSC), c/o Forschungszentrum Jülich, 52425 Jülich, Germany
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14
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Abstract
The methods to execute biological experiments are evolving. Affordable fluid handling robots and on-demand biology enterprises are making automating entire experiments a reality. Automation offers the benefit of high-throughput experimentation, rapid prototyping, and improved reproducibility of results. However, learning to automate and codify experiments is a difficult task as it requires programming expertise. Here, we present a web-based visual development environment called BioBlocks for describing experimental protocols in biology. It is based on Google's Blockly and Scratch, and requires little or no experience in computer programming to automate the execution of experiments. The experiments can be specified, saved, modified, and shared between multiple users in an easy manner. BioBlocks is open-source and can be customized to execute protocols on local robotic platforms or remotely, that is, in the cloud. It aims to serve as a de facto open standard for programming protocols in Biology.
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Affiliation(s)
- Vishal Gupta
- Departamento de Inteligencia
Artificial, Universidad Politécnica de Madrid. Campus de Montegancedo, Boadilla del Monte
(Madrid), 28660, Spain
| | - Jesús Irimia
- Departamento de Inteligencia
Artificial, Universidad Politécnica de Madrid. Campus de Montegancedo, Boadilla del Monte
(Madrid), 28660, Spain
| | - Iván Pau
- Departamento de Inteligencia
Artificial, Universidad Politécnica de Madrid. Campus de Montegancedo, Boadilla del Monte
(Madrid), 28660, Spain
| | - Alfonso Rodríguez-Patón
- Departamento de Inteligencia
Artificial, Universidad Politécnica de Madrid. Campus de Montegancedo, Boadilla del Monte
(Madrid), 28660, Spain
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15
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Abstract
Enzyme-linked immunosorbent assay (ELISA) automation for routine operation in a small research environment would be very attractive. A portable fully automated low-cost immunoassay system was designed, developed, and evaluated with several protein analytes. It features disposable capillary columns as the reaction sites and uses real-time calibration for improved accuracy. It reduces the overall assay time to less than 75 min with the ability of easy adaptation of new testing targets. The running cost is extremely low due to the nature of automation, as well as reduced material requirements. Details about system configuration, components selection, disposable fabrication, system assembly, and operation are reported. The performance of the system was initially established with a rabbit immunoglobulin G (IgG) assay, and an example of assay adaptation with an interleukin 6 (IL6) assay is shown. This system is ideal for research use, but could work for broader testing applications with further optimization.
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Affiliation(s)
| | | | | | - Qian Sun
- 1 SFC Fluidics, Inc., Fayetteville, AR, USA
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16
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Klimeš P, Mazura P, Turek D, Brzobohatý B. An automated method to evaluate the enzyme kinetics of β-glucosidases. Protein Sci 2016; 26:382-388. [PMID: 27862518 DOI: 10.1002/pro.3078] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 10/27/2016] [Accepted: 11/02/2016] [Indexed: 11/05/2022]
Abstract
Enzyme kinetic measurements are important for the characterization and engineering of biocatalysts, with applications in a wide range of research fields. The measurement of initial reaction velocity is usually slow and laborious, which motivated us to explore the possibilities for automating this process. Our model enzyme is the maize β-glucosidase Zm-p60.1. Zm-p60.1 plays a significant role in plant growth and development by regulating levels of the active plant hormone cytokinin. Zm-p60.1 belongs to a wide group of hydrolytic enzymes. Members of this group hydrolyze several different types of glucosides, releasing glucose as a secondary product. Enzyme kinetic measurements using artificial substrates are well established, but burdensome and time-consuming. Thus, they are a suitable target for process automation. Simple optical methods for enzyme kinetic measurements using natural substrates are often impossible given the optical properties of the enzymatic reaction products. However, we have developed an automated method based on glucose detection, as glucose is released from all substrates of glucosidase reactions. The presented method can obtain 24 data points from up to 15 substrate concentrations to precisely describe the enzyme kinetics. The combination of an automated liquid handling process with assays that have been optimized for measuring the initial hydrolysis velocity of β-glucosidases yields two distinct methods that are faster, cheaper, and more accurate than the established protocols.
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Affiliation(s)
- Pavel Klimeš
- Department of Molecular Biology and Radiobiology, Laboratory of Plant Molecular Biology, Institute of Biophysics AS CR, v.v.i. and CEITEC-Central European Institute of Technology, Mendel University in Brno, Zemědělská 1, Brno, CZ-613 00, Czech Republic
| | - Pavel Mazura
- Department of Molecular Biology and Radiobiology, Laboratory of Plant Molecular Biology, Institute of Biophysics AS CR, v.v.i. and CEITEC-Central European Institute of Technology, Mendel University in Brno, Zemědělská 1, Brno, CZ-613 00, Czech Republic
| | - Dušan Turek
- Department of Molecular Biology and Radiobiology, Laboratory of Plant Molecular Biology, Institute of Biophysics AS CR, v.v.i. and CEITEC-Central European Institute of Technology, Mendel University in Brno, Zemědělská 1, Brno, CZ-613 00, Czech Republic
| | - Břetislav Brzobohatý
- Department of Molecular Biology and Radiobiology, Laboratory of Plant Molecular Biology, Institute of Biophysics AS CR, v.v.i. and CEITEC-Central European Institute of Technology, Mendel University in Brno, Zemědělská 1, Brno, CZ-613 00, Czech Republic
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17
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Abstract
Although developments in liquid dispensers have made the use of 1536-well plates for high-throughput screening (HTS) standard, there is still a gap in dispenser technology for performing matrix experiments with several components. Experiments such as those performed during assay development and enzymological studies are therefore still performed by manual pipetting in lower-density plates. We have evaluated a new dispenser, the Certus liquid dispenser (Gyger Fluidics GmbH, Switzerland), that is capable of flexible dispensing in 1536-well format, with a dead volume of less than 200 µL. Taking advantage of the precision of the dispenser for volumes down to 50 nL, we have created concentration gradients on plates by dispensing different volumes of reagent and then backfilling with buffer. Using this method and the flexibility of the dispenser software, we have performed several multidimensional experiments varying two to three components, including an assay development for an HTS, a mode of inhibition study, and a cofactor optimization, in which we determined 32 KM values. Overall, the flexibility of the plate layout for multiple components, the accuracy to dispense volumes ranging 2 log orders, and minimal reagent usage enable this dispenser for complex biochemical experiments.
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