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Bourdat AG, den Dulk R, Serrano B, Boizot F, Clarebout G, Mermet X, Charles R, Porcherot J, Keiser A, Alessio M, Laurent P, Sarrut N, Cubizolles M. An integrated microfluidic platform for on-site qPCR analysis: food allergen detection from sample to result. LAB ON A CHIP 2024. [PMID: 39397566 DOI: 10.1039/d4lc00570h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/15/2024]
Abstract
Improving food safety is crucial in the context of a "One Health" approach. To guarantee product quality and safety, the food industry, which has a very high turnover rate, needs short time-to-result analyses. Therefore, user-friendly systems at the point-of-need are necessary, presenting relevant analytical information and fulfilling the current regulations. To answer these challenges, a microfluidic platform integrating sample preparation and subsequent multiplex qPCR detection has been developed for on-site testing. The system consists of a fully automated instrument driving a microfluidic cartridge dedicated to the detection of multiple allergens in complex food matrices. The first part of the microfluidic cartridge contains pumps, reservoirs, valves and a filter to achieve DNA extraction, concentration and purification. Multiplex qPCR detection is carried out in the second part of the cartridge including a negative control chamber and five chambers for target analyte detection. The in-house developed instrument contains all functions to autonomously drive the microfluidic cartridge: pneumatic control for fluid actuation, thermal control for qPCR amplification and an optical system using three fluorescent wavelengths for multiplex detection of the target analytes and controls. We demonstrate the simultaneous detection of four different allergens - gluten, sesame, soy and hazelnut - from various complex food matrices. The turn-around-time from sample to result is close to two hours and controls in place validate the obtained results. For gluten, a direct comparison with ELISA shows that the regulatory threshold of 20 ppm is comfortably fulfilled. Moreover, all results are in agreement with external laboratory analyses performed in parallel on the same samples. Our findings confirm that the system can be used safely on-site without the risk of cross contamination between the various samples being analysed. In conclusion, our microfluidic platform offers a robust method for on-site allergen management.
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Affiliation(s)
| | - Remco den Dulk
- Univ. Grenoble Alpes, CEA Leti, F-38000 Grenoble, France.
| | | | | | | | - Xavier Mermet
- Univ. Grenoble Alpes, CEA Leti, F-38000 Grenoble, France.
| | | | - Jean Porcherot
- Univ. Grenoble Alpes, CEA Leti, F-38000 Grenoble, France.
| | - Armelle Keiser
- Univ. Grenoble Alpes, CEA Leti, F-38000 Grenoble, France.
| | - Manuel Alessio
- Univ. Grenoble Alpes, CEA Leti, F-38000 Grenoble, France.
| | | | - Nicolas Sarrut
- Univ. Grenoble Alpes, CEA Leti, F-38000 Grenoble, France.
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Steinbach MK, Leipert J, Matzanke T, Tholey A. Digital Microfluidics for Sample Preparation in Low-Input Proteomics. SMALL METHODS 2024:e2400495. [PMID: 39205538 DOI: 10.1002/smtd.202400495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 08/16/2024] [Indexed: 09/04/2024]
Abstract
Low-input proteomics, also referred to as micro- or nanoproteomics, has become increasingly popular as it allows one to elucidate molecular processes in rare biological materials. A major prerequisite for the analytics of minute protein amounts, e.g., derived from low cell numbers, down to single cells, is the availability of efficient sample preparation methods. Digital microfluidics (DMF), a technology allowing the handling and manipulation of low liquid volumes, has recently been shown to be a powerful and versatile tool to address the challenges in low-input proteomics. Here, an overview is provided on recent advances in proteomics sample preparation using DMF. In particular, the capability of DMF to isolate proteomes from cells and small model organisms, and to perform all necessary chemical sample preparation steps, such as protein denaturation and proteolytic digestion on-chip, are highlighted. Additionally, major prerequisites to making these steps compatible with follow-up analytical methods such as liquid chromatography-mass spectrometry will be discussed.
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Affiliation(s)
- Max K Steinbach
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, 24105, Kiel, Germany
| | - Jan Leipert
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, 24105, Kiel, Germany
| | - Theo Matzanke
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, 24105, Kiel, Germany
| | - Andreas Tholey
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, 24105, Kiel, Germany
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Rodoplu Solovchuk D. Advances in AI-assisted biochip technology for biomedicine. Biomed Pharmacother 2024; 177:116997. [PMID: 38943990 DOI: 10.1016/j.biopha.2024.116997] [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: 04/24/2024] [Revised: 06/13/2024] [Accepted: 06/15/2024] [Indexed: 07/01/2024] Open
Abstract
The integration of biochips with AI opened up new possibilities and is expected to revolutionize smart healthcare tools within the next five years. The combination of miniaturized, multi-functional, rapid, high-throughput sample processing and sensing capabilities of biochips, with the computational data processing and predictive power of AI, allows medical professionals to collect and analyze vast amounts of data quickly and efficiently, leading to more accurate and timely diagnoses and prognostic evaluations. Biochips, as smart healthcare devices, offer continuous monitoring of patient symptoms. Integrated virtual assistants have the potential to send predictive feedback to users and healthcare practitioners, paving the way for personalized and predictive medicine. This review explores the current state-of-the-art biochip technologies including gene-chips, organ-on-a-chips, and neural implants, and the diagnostic and therapeutic utility of AI-assisted biochips in medical practices such as cancer, diabetes, infectious diseases, and neurological disorders. Choosing the appropriate AI model for a specific biomedical application, and possible solutions to the current challenges are explored. Surveying advances in machine learning models for biochip functionality, this paper offers a review of biochips for the future of biomedicine, an essential guide for keeping up with trends in healthcare, while inspiring cross-disciplinary collaboration among biomedical engineering, medicine, and machine learning fields.
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Affiliation(s)
- Didem Rodoplu Solovchuk
- Institute of Biomedical Engineering and Nanomedicine, National Health Research Institutes, Zhunan, Miaoli 35053, Taiwan.
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Picard B, Cougoul A, Couvreur S, Bonnet M. Relationships between the abundance of 29 proteins and several meat or carcass quality traits in two bovine muscles revealed by a combination of univariate and multivariate analyses. J Proteomics 2023; 273:104792. [PMID: 36535620 DOI: 10.1016/j.jprot.2022.104792] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 12/05/2022] [Accepted: 12/06/2022] [Indexed: 12/23/2022]
Abstract
We aimed to evaluate the relationships between meat or carcass properties and the abundance of 29 proteins quantified in two muscles, Longissimus thoracis and Rectus abdominis, of Rouge des Prés cows. The relative abundance of the proteins was evaluated using a high throughput immunological method: the Reverse Phase Protein array. A combination of univariate and multivariate analyses has shown that small HSPs (CRYAB, HSPB6), fast glycolytic metabolic and structural proteins (MYH1, ENO3, ENO1, TPI1) when assayed both in RA and LT, were related to meat tenderness, marbling, ultimate pH, as well as carcass fat-to-lean ratio or conformation score. In addition to some small HSP, ALDH1A1 and TRIM72 contributed to the molecular signature of muscular and carcass adiposity. MYH1 and HSPA1A were among the top proteins related to carcass traits. We thus shortened the list to 10 putative biomarkers to be considered in future tools to manage both meat and carcass properties. SIGNIFICANCE: In three aspects this manuscript is notable. First, this is the first proteomics study that aims to evaluate putative biomarkers of both meat and carcass qualities that are of economic importance for the beef industry. Second, the relationship between the abundance of proteins and the carcass or meat traits were evaluated by a combination of univariate and multivariate analyses on 48 cows that are representative of the biological variability of the traits. Third, we provide a short list of ten proteins to be tested in a larger population to feed the pipeline of biomarker discovery.
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Affiliation(s)
- Brigitte Picard
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, F-63122 Saint-Genès-Champanelle, France
| | - Arnaud Cougoul
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, F-63122 Saint-Genès-Champanelle, France
| | - Sébastien Couvreur
- École Supérieure d'Agricultures, USC ESA-INRAE 1481 Systèmes d'Elevage, 55 rue Rabelais - BP 30748 - 49007 Angers Cedex 01, France
| | - Muriel Bonnet
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, F-63122 Saint-Genès-Champanelle, France.
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Aubry G, Lee HJ, Lu H. Advances in Microfluidics: Technical Innovations and Applications in Diagnostics and Therapeutics. Anal Chem 2023; 95:444-467. [PMID: 36625114 DOI: 10.1021/acs.analchem.2c04562] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Guillaume Aubry
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Hyun Jee Lee
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Hang Lu
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States.,Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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Dupuy A, Ju LA, Chiu J, Passam FH. Mechano-Redox Control of Integrins in Thromboinflammation. Antioxid Redox Signal 2022; 37:1072-1093. [PMID: 35044225 DOI: 10.1089/ars.2021.0265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Significance: How mechanical forces and biochemical cues are coupled remains a miracle for many biological processes. Integrins, well-known adhesion receptors, sense changes in mechanical forces and reduction-oxidation reactions (redox) in their environment to mediate their adhesive function. The coupling of mechanical and redox function is a new area of investigation. Disturbance of normal mechanical forces and the redox balance occurs in thromboinflammatory conditions; atherosclerotic plaques create changes to the mechanical forces in the circulation. Diabetes induces redox changes in the circulation by the production of reactive oxygen species and vascular inflammation. Recent Advances: Integrins sense changes in the blood flow shear stress at the level of focal adhesions and respond to flow and traction forces by increased signaling. Talin, the integrin-actin linker, is a traction force sensor and adaptor. Oxidation and reduction of integrin disulfide bonds regulate their adhesion. A conserved disulfide bond in integrin αlpha IIb beta 3 (αIIbβ3) is directly reduced by the thiol oxidoreductase endoplasmic reticulum protein 5 (ERp5) under shear stress. Critical Issues: The coordination of mechano-redox events between the extracellular and intracellular compartments is an active area of investigation. Another fundamental issue is to determine the spatiotemporal arrangement of key regulators of integrins' mechanical and redox interactions. How thromboinflammatory conditions lead to mechanoredox uncoupling is relatively unexplored. Future Directions: Integrated approaches, involving disulfide bond biochemistry, microfluidic assays, and dynamic force spectroscopy, will aid in showing that cell adhesion constitutes a crossroad of mechano- and redox biology, within the same molecule, the integrin. Antioxid. Redox Signal. 37, 1072-1093.
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Affiliation(s)
- Alexander Dupuy
- Central Clinical School, Faculty of Medicine and Health, The University of Sydney, Camperdown, Australia.,Charles Perkins Centre, The University of Sydney, Camperdown, Australia.,Heart Research Institute, Newtown, Australia
| | - Lining Arnold Ju
- Charles Perkins Centre, The University of Sydney, Camperdown, Australia.,Heart Research Institute, Newtown, Australia.,School of Biomedical Engineering, Faculty of Engineering, The University of Sydney, Darlington, Australia
| | - Joyce Chiu
- Charles Perkins Centre, The University of Sydney, Camperdown, Australia.,ACRF Centenary Cancer Research Centre, The Centenary Institute, Camperdown, Australia
| | - Freda H Passam
- Central Clinical School, Faculty of Medicine and Health, The University of Sydney, Camperdown, Australia.,Charles Perkins Centre, The University of Sydney, Camperdown, Australia.,Heart Research Institute, Newtown, Australia
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Deutsch EW, Omenn GS, Sun Z, Maes M, Pernemalm M, Palaniappan KK, Letunica N, Vandenbrouck Y, Brun V, Tao SC, Yu X, Geyer PE, Ignjatovic V, Moritz RL, Schwenk JM. Advances and Utility of the Human Plasma Proteome. J Proteome Res 2021; 20:5241-5263. [PMID: 34672606 PMCID: PMC9469506 DOI: 10.1021/acs.jproteome.1c00657] [Citation(s) in RCA: 91] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The study of proteins circulating in blood offers tremendous opportunities to diagnose, stratify, or possibly prevent diseases. With recent technological advances and the urgent need to understand the effects of COVID-19, the proteomic analysis of blood-derived serum and plasma has become even more important for studying human biology and pathophysiology. Here we provide views and perspectives about technological developments and possible clinical applications that use mass-spectrometry(MS)- or affinity-based methods. We discuss examples where plasma proteomics contributed valuable insights into SARS-CoV-2 infections, aging, and hemostasis and the opportunities offered by combining proteomics with genetic data. As a contribution to the Human Proteome Organization (HUPO) Human Plasma Proteome Project (HPPP), we present the Human Plasma PeptideAtlas build 2021-07 that comprises 4395 canonical and 1482 additional nonredundant human proteins detected in 240 MS-based experiments. In addition, we report the new Human Extracellular Vesicle PeptideAtlas 2021-06, which comprises five studies and 2757 canonical proteins detected in extracellular vesicles circulating in blood, of which 74% (2047) are in common with the plasma PeptideAtlas. Our overview summarizes the recent advances, impactful applications, and ongoing challenges for translating plasma proteomics into utility for precision medicine.
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Affiliation(s)
- Eric W Deutsch
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Gilbert S Omenn
- Institute for Systems Biology, Seattle, Washington 98109, United States.,Departments of Computational Medicine & Bioinformatics, Internal Medicine, and Human Genetics and School of Public Health, University of Michigan, Ann Arbor, Michigan 48109-2218, United States
| | - Zhi Sun
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Michal Maes
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Maria Pernemalm
- Department of Oncology and Pathology/Science for Life Laboratory, Karolinska Institutet, 171 65 Stockholm, Sweden
| | | | - Natasha Letunica
- Murdoch Children's Research Institute, 50 Flemington Road, Parkville 3052, Victoria, Australia
| | - Yves Vandenbrouck
- Université Grenoble Alpes, CEA, Inserm U1292, Grenoble 38000, France
| | - Virginie Brun
- Université Grenoble Alpes, CEA, Inserm U1292, Grenoble 38000, France
| | - Sheng-Ce Tao
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, B207 SCSB Building, 800 Dongchuan Road, Shanghai 200240, China
| | - Xiaobo Yu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Philipp E Geyer
- OmicEra Diagnostics GmbH, Behringstr. 6, 82152 Planegg, Germany
| | - Vera Ignjatovic
- Murdoch Children's Research Institute, 50 Flemington Road, Parkville 3052, Victoria, Australia.,Department of Paediatrics, The University of Melbourne, 50 Flemington Road, Parkville 3052, Victoria, Australia
| | - Robert L Moritz
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Jochen M Schwenk
- Affinity Proteomics, Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Tomtebodavägen 23, SE-171 65 Solna, Sweden
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