1
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Beck S, Shin D, Kim SJ, Hedde PN, Zhao W. Digital Protein Detection in Bulk Solutions. ACS OMEGA 2022; 7:37714-37723. [PMID: 36312374 PMCID: PMC9608401 DOI: 10.1021/acsomega.2c04666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 09/21/2022] [Indexed: 06/16/2023]
Abstract
Quick and accurate molecular diagnostics in protein detection can greatly benefit medicine in disease diagnosis and lead to positive patient outcomes. However, specialized equipment used in clinical laboratories often comes with trade-offs between operation and function serving a single role for very specific needs. For example, to achieve high analytical sensitivity and specificity, instruments such as high-performance liquid chromatography and/or liquid chromatography-mass spectrometry use a complex instrument design and require thorough training of the users. On the other hand, simple tests such as protein detection in urinary tract infection using dip-stick assays provide very quick results but suffer from poor analytical sensitivity. Here, we present an application study for the 3D particle counter technology, which is based on optical confocal detection in order to scan large sample volumes (0.5-3 mL) in glass cuvettes, that aims to close the gap between analytical sensitivity and turnover assay time and simplify protein detection by adopting bead-based immunoassays. Combining the 3D particle counter technology with bead-based immunoassays, a subpicomolar limit of detection-ranging from 119 to 346 fM-was achieved within 3.5-hour assay time for recombinant mouse interleukin 6 detection. As an alternative instrument to a flow cytometer, the 3D particle counter takes advantages of bead-based immunoassays and provides unique accessibility and flexibility for users.
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Affiliation(s)
- Sungjun Beck
- Department
of Biological Chemistry, University of California,
Irvine, Irvine, California 92697, United States
| | - Donghae Shin
- Department
of Biological Chemistry, University of California,
Irvine, Irvine, California 92697, United States
| | - Sun Jin Kim
- Department
of Pharmaceutical Sciences, University of
California, Irvine, Irvine, California 92697, United States
| | - Per Niklas Hedde
- Department
of Pharmaceutical Sciences, University of
California, Irvine, Irvine, California 92697, United States
- Laboratory
for Fluorescence Dynamics, University of
California, Irvine, Irvine, California 92697, United States
- Beckman
Laser Institute & Medical Clinic, University
of California, Irvine, Irvine, California 92697, United States
| | - Weian Zhao
- Department
of Biological Chemistry, University of California,
Irvine, Irvine, California 92697, United States
- Department
of Pharmaceutical Sciences, University of
California, Irvine, Irvine, California 92697, United States
- Institute
for Immunology, University of California,
Irvine, Irvine, California 92697, United States
- Sue and Bill
Gross Stem Cell Research Center, University
of California, Irvine, Irvine, California 92697, United States
- Chao
Family Comprehensive Cancer Center, University
of California, Irvine, Irvine, California 92697, United States
- Edwards
Life Sciences Center for Advanced Cardiovascular Technology, University of California, Irvine, Irvine, California 92697, United States
- Department
of Biomedical Engineering, University of
California, Irvine, Irvine, California 92697, United States
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2
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Rodríguez-Sevilla P, Thompson SA, Jaque D. Multichannel Fluorescence Microscopy: Advantages of Going beyond a Single Emission. ADVANCED NANOBIOMED RESEARCH 2022. [DOI: 10.1002/anbr.202100084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Paloma Rodríguez-Sevilla
- Nanomaterials for Bioimaging Group (NanoBIG) Departamento de Física de Materiales Universidad Autónoma de Madrid C/Francisco Tomás y Valiente 7 Madrid 28049 Spain
| | - Sebastian A. Thompson
- Madrid Institute for Advanced Studies in Nanoscience (IMDEA Nanociencia) C/Faraday 9 Madrid 28049 Spain
- Nanobiotechnology Unit Associated to the National Center for Biotechnology (CNB-CSIC-IMDEA) Madrid 28049 Spain
| | - Daniel Jaque
- Nanomaterials for Bioimaging Group (NanoBIG) Departamento de Física de Materiales Universidad Autónoma de Madrid C/Francisco Tomás y Valiente 7 Madrid 28049 Spain
- Instituto Ramón y Cajal de Investigación Sanitaria Hospital Ramón y Cajal Ctra. Colmenar km. 9,100 Madrid 28034 Spain
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3
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Nicolai E, Pieri M, Gratton E, Motolese G, Bernardini S. Bacterial Infection Diagnosis and Antibiotic Prescription in 3 h as an Answer to Antibiotic Resistance: The Case of Urinary Tract Infections. Antibiotics (Basel) 2021; 10:antibiotics10101168. [PMID: 34680749 PMCID: PMC8532666 DOI: 10.3390/antibiotics10101168] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 09/18/2021] [Accepted: 09/23/2021] [Indexed: 11/30/2022] Open
Abstract
Current methods for the diagnosis of urinary tract infections with antimicrobial susceptibility testing take 2–3 days and require a clinical laboratory. The lack of a rapid, point-of-care antibiotic susceptibility test (AST) has contributed to the misuse of antibiotics when treating urinary tract infections (UTIs) and consequently to the rise of multi-drug-resistant organisms. The current clinical approach has led to reduced treatment options and increased costs of diagnosis and therapy. To address this issue, novel diagnostics are needed for the timely determination of antimicrobial susceptibility. We present a rapid, point-of-care, phenotypic AST device that can report the antibiotic susceptibility/resistance of a uropathogen to a panel of antibiotics in as few as 3 h by utilizing fluorescent-labelling chemistry and a highly sensitive particle-counting instrument. We analysed 744 urine samples from the outpatients and inpatients of two Italian hospitals. The 130 UTI-positive patient urine samples we found were measured using a panel of six common UTI antibiotics plus a growth control. By comparing our results to hospital laboratory urine cultures, we obtained an overall sensitivity = 81%, a specificity = 83%, an SPV (sensitivity predicted value) = 95%, and an RPV (resistance predicted value) = 54%. According to our preliminary data, the sensitivity predicted value for a single antibiotic agent was 95%, thus allowing (in the vast majority of cases) an early (within 3 h) recognition of an effective agent for a single patient.
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Affiliation(s)
- Eleonora Nicolai
- Department of Experimental Medicine, University of Rome Tor Vergata, Via Montpellier 1, 00133 Rome, Italy; (M.P.); (S.B.)
- Correspondence:
| | - Massimo Pieri
- Department of Experimental Medicine, University of Rome Tor Vergata, Via Montpellier 1, 00133 Rome, Italy; (M.P.); (S.B.)
| | - Enrico Gratton
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California-Irvine, Irvine, CA 92697, USA;
| | | | - Sergio Bernardini
- Department of Experimental Medicine, University of Rome Tor Vergata, Via Montpellier 1, 00133 Rome, Italy; (M.P.); (S.B.)
- IFCC Emerging Technologies Divison, Via Carlo Farini 81, 20159 Milan, Italy
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4
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Hanami T, Tanabe T, Hanashi T, Yamaguchi M, Nakata H, Mitani Y, Kimura Y, Soma T, Usui K, Isobe M, Ogawa T, Itoh M, Hayashizaki Y, Kondo S. Scanning single-molecule counting system for Eprobe with highly simple and effective approach. PLoS One 2020; 15:e0243319. [PMID: 33320908 PMCID: PMC7737986 DOI: 10.1371/journal.pone.0243319] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 11/18/2020] [Indexed: 02/07/2023] Open
Abstract
Here, we report a rapid and ultra-sensitive detection technique for fluorescent molecules called scanning single molecular counting (SSMC). The method uses a fluorescence-based digital measurement system to count single molecules in a solution. In this technique, noise is reduced by conforming the signal shape to the intensity distribution of the excitation light via a circular scan of the confocal region. This simple technique allows the fluorescent molecules to freely diffuse into the solution through the confocal region and be counted one by one and does not require statistical analysis. Using this technique, 28 to 62 aM fluorescent dye was detected through measurement for 600 s. Furthermore, we achieved a good signal-to-noise ratio (S/N = 2326) under the condition of 100 pM target nucleic acid by only mixing a hybridization-sensitive fluorescent probe, called Eprobe, into the target oligonucleotide solution. Combination of SSMC and Eprobe provides a simple, rapid, amplification-free, and high-sensitive target nucleic acid detection system. This method is promising for future applications to detect particularly difficult to design primers for amplification as miRNAs and other short oligo nucleotide biomarkers by only hybridization with high sensitivity.
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Affiliation(s)
- Takeshi Hanami
- Genetic Diagnosis Technology Unit, RIKEN Center for Integrative Medical Science, Yokohama, Kanagawa, Japan.,RIKEN Innovation Center, Wako, Saitama, Japan
| | - Tetsuya Tanabe
- Genetic Diagnosis Technology Unit, RIKEN Center for Integrative Medical Science, Yokohama, Kanagawa, Japan.,RIKEN Innovation Center, Wako, Saitama, Japan.,Advanced Analysis Technology Dept., Medical Technology R&D Division, Olympus Corporation, Hachioji, Tokyo, Japan
| | - Takuya Hanashi
- Genetic Diagnosis Technology Unit, RIKEN Center for Integrative Medical Science, Yokohama, Kanagawa, Japan.,RIKEN Innovation Center, Wako, Saitama, Japan.,Advanced Analysis Technology Dept., Medical Technology R&D Division, Olympus Corporation, Hachioji, Tokyo, Japan
| | - Mitsushiro Yamaguchi
- Genetic Diagnosis Technology Unit, RIKEN Center for Integrative Medical Science, Yokohama, Kanagawa, Japan.,RIKEN Innovation Center, Wako, Saitama, Japan.,Advanced Analysis Technology Dept., Medical Technology R&D Division, Olympus Corporation, Hachioji, Tokyo, Japan
| | - Hidetaka Nakata
- RIKEN Innovation Center, Wako, Saitama, Japan.,Advanced Analysis Technology Dept., Medical Technology R&D Division, Olympus Corporation, Hachioji, Tokyo, Japan
| | | | | | - Takahiro Soma
- Genetic Diagnosis Technology Unit, RIKEN Center for Integrative Medical Science, Yokohama, Kanagawa, Japan
| | - Kengo Usui
- Genetic Diagnosis Technology Unit, RIKEN Center for Integrative Medical Science, Yokohama, Kanagawa, Japan
| | | | | | - Masayoshi Itoh
- Genetic Diagnosis Technology Unit, RIKEN Center for Integrative Medical Science, Yokohama, Kanagawa, Japan.,RIKEN Innovation Center, Wako, Saitama, Japan.,RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Saitama, Japan
| | | | - Seiji Kondo
- RIKEN Innovation Center, Wako, Saitama, Japan.,Advanced Analysis Technology Dept., Medical Technology R&D Division, Olympus Corporation, Hachioji, Tokyo, Japan
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Rapid Detection of β-Lactamase-Producing Bacteria Using the Integrated Comprehensive Droplet Digital Detection (IC 3D) System. SENSORS 2020; 20:s20174667. [PMID: 32824984 PMCID: PMC7506896 DOI: 10.3390/s20174667] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 08/15/2020] [Accepted: 08/17/2020] [Indexed: 12/22/2022]
Abstract
Antibiotic-resistant bacteria have emerged as an imminent global threat. The lack of rapid and sensitive diagnostic techniques leaves health care providers with inadequate resources for guiding therapy and risks the lives of patients. The traditional plate culturing methods for identifying antibiotic-resistant bacteria is laborious and time-consuming. Bulk PCR (Polymerase Chain Reaction) and qPCR are limited by poor detection sensitivity, which is critical for the early-stage detection of bloodstream infections. In this study, we introduce a technique for detecting β-lactamase-producing bacteria at single-cell sensitivity based on a commercial β-lactamase sensor (Fluorocillin), droplet microfluidics, and a custom 3D particle counter. Bacteria-containing samples were encapsulated within picoliter-sized droplets at the single-cell level and cultured within water-in-oil droplets containing antibiotics and the Fluorocillin sensor. Then, fluorescent droplets were digitally quantified with the 3D particle counter, which is capable of analyzing milliliter-scale volumes of collected droplets within 10 min. The fluorescence signal from single-colony droplets was detectable in less than 5 h, and the 3D scanning was performed in less than 10 min, which was significantly faster than conventional culture-based methods. In this approach, the limit of detection achieved was about 10 bacterial cells per mL of sample, and the turnaround time from sample to result was less than 6 h. This study demonstrates a promising strategy for the detection of β-lactamase-producing bacteria using the recently developed IC 3D system.
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6
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Hedde PN, Bouzin M, Abram TJ, Chen X, Toosky MN, Vu T, Li Y, Zhao W, Gratton E. Rapid isolation of rare targets from large fluid volumes. Sci Rep 2020; 10:12458. [PMID: 32719382 PMCID: PMC7385493 DOI: 10.1038/s41598-020-69315-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 06/26/2020] [Indexed: 11/24/2022] Open
Abstract
Rapidly isolating rare targets from larger, clinically relevant fluid volumes remains an unresolved problem in biomedicine and diagnosis. Here, we describe how 3D particle sorting can enrich targets at ultralow concentrations over 100-fold within minutes not possible with conventional approaches. Current clinical devices based on biochemical extraction and microfluidic solutions typically require high concentrations and/or can only process sub-milliliter volumes in time. In a proof-of-concept application, we isolated bacteria from whole blood as demanded for rapid sepsis diagnosis where minimal numbers of bacteria need to be found in a 1–10 mL blood sample. After sample encapsulation in droplets and target enrichment with the 3D particle sorter within a few minutes, downstream analyses were able to identify bacteria and test for antibiotic susceptibility, information which is critical for successful treatment of bloodstream infections.
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Affiliation(s)
- Per Niklas Hedde
- Department of Biomedical Engineering, University of California, Irvine, CA, USA. .,Department of Biochemistry, University of Hawaii at Manoa, Manoa, HI, USA.
| | - Margaux Bouzin
- Department of Biomedical Engineering, University of California, Irvine, CA, USA.,Physics Department, Università degli Studi di Milano-Bicocca, Milan, Italy
| | | | - Xiaoming Chen
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, USA
| | | | - Tam Vu
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, USA
| | - Yiyan Li
- Department of Physics and Engineering, Fort Lewis College, Durango, CO, USA
| | - Weian Zhao
- Department of Biomedical Engineering, University of California, Irvine, CA, USA.,Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, USA.,Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA, USA.,Chao Family Comprehensive Cancer Center, University of California, Irvine, Irvine, CA, USA.,Edwards Life Sciences Center for Advanced Cardiovascular Technology, University of California, Irvine, Irvine, CA, USA.,Department of Biological Chemistry, University of California, Irvine, Irvine, CA, USA
| | - Enrico Gratton
- Department of Biomedical Engineering, University of California, Irvine, CA, USA
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7
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Zhang K, Qin S, Wu S, Liang Y, Li J. Microfluidic systems for rapid antibiotic susceptibility tests (ASTs) at the single-cell level. Chem Sci 2020; 11:6352-6361. [PMID: 34094102 PMCID: PMC8159419 DOI: 10.1039/d0sc01353f] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 04/01/2020] [Indexed: 12/21/2022] Open
Abstract
Infectious diseases caused by multidrug resistant (MDR) bacterial pathogens are impending threats to global health. Since delays in identifying drug resistance would significantly increase mortality, fast and accurate antibiotic susceptibility tests (ASTs) are critical for addressing the antibiotic resistance issue. However, the conventional methods for ASTs are always labor-intensive, imprecise, complex and slow (taking 2-3 days). To address these issues, some advanced microfluidic systems have been designed for rapid phenotypic and genotypic analysis of antibiotic resistance. This review highlights the recent development of microfluidics-based ASTs at the single-cell or single-molecule level for guiding antibiotic treatment decisions and predicting therapeutic outcomes.
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Affiliation(s)
- Kaixiang Zhang
- School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Zhengzhou University Zhengzhou 450001 China
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University Beijing 100084 China
| | - Shangshang Qin
- School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Zhengzhou University Zhengzhou 450001 China
| | - Sixuan Wu
- School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Zhengzhou University Zhengzhou 450001 China
| | - Yan Liang
- School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Zhengzhou University Zhengzhou 450001 China
| | - Jinghong Li
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University Beijing 100084 China
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8
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Toosky MN, Grunwald JT, Pala D, Shen B, Zhao W, D’Agostini C, Coghe F, Angioni G, Motolese G, Abram TJ, Nicolai E. A rapid, point-of-care antibiotic susceptibility test for urinary tract infections. J Med Microbiol 2020; 69:52-62. [PMID: 31846419 PMCID: PMC7440674 DOI: 10.1099/jmm.0.001119] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 11/12/2019] [Indexed: 11/18/2022] Open
Abstract
Introduction. The alarming rise in urinary tract infection (UTI) antimicrobial resistance has resulted from a combination of high prevalence, low specificity and the lack of a rapid, point-of-care (POC) antibiotic susceptibility test (AST), which has led to the overuse/inappropriate use of antibiotics.Aim. This study aimed to evaluate the performance of a rapid POC phenotypic AST device in reporting susceptibility information within 2 h.Methodology. Instrument calibration was performed with model bacteria and fluorescent microbeads to determine the dynamic range and limit of detection for quantifying concentrations of bacteria and demonstrate the ability to rapidly differentiate susceptible and resistant model bacteria. We then evaluated 30 presumptive UTI-positive patient urine samples in a clinical pilot study using a panel of 5 common UTI antibiotics plus a growth control and compared our results to the hospital standard of care AST.Results. Our device was able to robustly detect and quantify bacteria concentrations from 50 to 105 colony-forming units (c.f.u.) ml-1. The high sensitivity of this measurement technique enabled the device to differentiate between susceptible and resistant model bacteria with 100 % specificity over a 2 h growth period. In the clinical pilot study, an overall categorical agreement (CA) of 90.7 % was observed (sensitivity=91.4 %, specificity=88.9 %, n=97) with performance for individual drugs ranging from 85 % CA (ceftazidime) to 100 % (nitrofurantoin).Conclusions. By reducing the typical timeframe for susceptibility testing from 2-3 days to 2 h, our POC phenotypic AST can provide critical information to clinicians prior to the administration of antibiotic therapy.
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Affiliation(s)
| | | | - Daniela Pala
- Apparecchiature Scientifiche Innovative, S.r.l., Milan, Italy
| | | | - Weian Zhao
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, CA, USA
- Department of Pharmaceutical Sciences, University of California, Irvine, CA, USA
- Department of Biomedical Engineering, University of California, Irvine, CA, USA
- Chao Family Comprehensive Cancer Center, University of California, Irvine, CA, USA
- Edwards Life Sciences Center for Advanced Cardiovascular Technology, University of California, Irvine, CA, USA
- Department of Biological Chemistry, University of California, Irvine, CA, USA
| | - Cartesio D’Agostini
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Ferdinando Coghe
- Laboratory Clinical Chemical Analysis and Microbiology, University Hospital of Cagliari, Cagliari, Italy
| | - Giancarlo Angioni
- Laboratory Clinical Chemical Analysis and Microbiology, AOBrotzu, Cagliari, Italy
| | - Guido Motolese
- Apparecchiature Scientifiche Innovative, S.r.l., Milan, Italy
| | | | - Eleonora Nicolai
- Apparecchiature Scientifiche Innovative, S.r.l., Milan, Italy
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
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9
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Sahoo B, Sil TB, Karmakar B, Garai K. A Fluorescence Correlation Spectrometer for Measurements in Cuvettes. Biophys J 2019; 115:455-466. [PMID: 30089243 DOI: 10.1016/j.bpj.2018.05.038] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 05/27/2018] [Accepted: 05/29/2018] [Indexed: 12/13/2022] Open
Abstract
We have developed a fluorescence correlation spectroscopy (FCS) setup for performing single-molecule measurements on samples inside regular cuvettes. The cuvette FCS uses a horizontally mounted extra-long working distance, 0.7 NA, air objective with a working distance of >1.8 mm instead of a high NA water or oil immersion objective. The performance of the cuvette FCS is found to be highly sensitive to the quality and alignment of the cuvette. The radial resolution and effective observation volume obtained using the optimized setup are ∼340 nm and 1.8 fL, respectively. The highest molecular brightness and the signal/noise ratio in the autocorrelation data achieved using an aqueous solution of rhodamine B are greater than 44 kHz and 110, respectively. Here, we demonstrate two major advantages of cuvette FCS. For example, the cuvette FCS can be used for measurements over a wide range of temperatures that is beyond the range permitted in the microscope-based FCS. Furthermore, cuvette FCS can be coupled to automatic titrators to study urea-dependent unfolding of proteins with unprecedented accuracy. The ease of use and compatibility with various accessories will enable applications of cuvette FCS in the experiments that are regularly performed in spectrofluorometers but are generally avoided in microscope-based FCS.
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Affiliation(s)
- Bankanidhi Sahoo
- Tata Institute of Fundamental Research, Serilingampally, Hyderabad, India
| | - Timir Baran Sil
- Tata Institute of Fundamental Research, Serilingampally, Hyderabad, India
| | | | - Kanchan Garai
- Tata Institute of Fundamental Research, Serilingampally, Hyderabad, India.
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10
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Hedde PN, Abram T, Vu T, Zhao W, Gratton E. Fluorescence lifetime detection with particle counting devices. BIOMEDICAL OPTICS EXPRESS 2019; 10:1223-1233. [PMID: 30891341 PMCID: PMC6420272 DOI: 10.1364/boe.10.001223] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 01/27/2019] [Accepted: 01/27/2019] [Indexed: 05/30/2023]
Abstract
Fluorescence-based single particle counting devices have become very powerful tools for human health-related applications such as the detection of blood-borne pathogens. Instead of passing the sample fluid through a thin tube or microfluidic chip, as it is commonly practiced in flow cytometers and sorter devices, single particle counters scan the fluid volume by rotation and translation of the sample container. Hence, single particle counters are not limited by the fluid flow friction and can scan a large volume in a short timeframe while maintaining high sensitivity. A single particle can be detected in a milliliter of the fluid sample within minutes, and diagnostics are being developed using this principle. Until now, signal detection with particle counters has been based on signal intensity and signal separation into multiple wavelength bands coupled with multiple detectors, which limits the number of species that can be resolved. In this paper, we applied fluorescence lifetime detection to single particle counting to increase specificity and enable multiplexing with a single detector. We demonstrate how this principle can be used for diagnostic assays based on fluorescence quenching.
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Affiliation(s)
- Per Niklas Hedde
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California Irvine, Irvine, CA, USA
| | - Tim Abram
- Velox Biosystems, 5 Mason St, Ste 160, Irvine, CA 92618, USA
| | - Tam Vu
- Sue and Bill Gross Stem Cell Research Center, Chao Family Comprehensive Cancer Center, Edwards Life Sciences Center for Advanced Cardiovascular Technology, Department of Biomedical Engineering, Department of Biological Chemistry, Department of Pharmaceutical Sciences, University of California Irvine, Irvine, CA, USA
| | - Weian Zhao
- Sue and Bill Gross Stem Cell Research Center, Chao Family Comprehensive Cancer Center, Edwards Life Sciences Center for Advanced Cardiovascular Technology, Department of Biomedical Engineering, Department of Biological Chemistry, Department of Pharmaceutical Sciences, University of California Irvine, Irvine, CA, USA
| | - Enrico Gratton
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California Irvine, Irvine, CA, USA
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11
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Building, Characterization, and Applications of Cuvette-FCS in Denaturant-Induced Expansion of Globular and Disordered Proteins. Methods Enzymol 2018. [PMID: 30471694 DOI: 10.1016/bs.mie.2018.08.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Fluorescence correlation spectroscopy (FCS) is a single-molecule sensitive technique with widespread applications in biophysics. However, conventional microscope-based FCS setups have limitations in performing certain experiments such as those requiring agitations such as stirring or heating, and those involving measurements in solvents with the mismatch of refractive indices. We have recently developed an FCS setup that is suitable for performing measurements inside regular cuvettes. The cuvette-FCS is suitable for performing single-molecule measurements in experiments that are regularly performed in spectrofluorometers but are generally avoided in microscope-based FCS. Here we describe building and characterization of the performance of the cuvette-FCS setup in detail. Finally, we have used a natively folded protein and an intrinsically disordered protein to demonstrate and describe how cuvette-FCS can be applied conveniently to measure urea-dependent expansion of hydrodynamic size of proteins.
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12
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Back to the Future: Fluorescence Correlation Spectroscopy Moves Back in the Cuvette. Biophys J 2018; 115:427-428. [DOI: 10.1016/j.bpj.2018.06.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 06/11/2018] [Indexed: 11/22/2022] Open
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13
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Sinha M, Jupe J, Mack H, Coleman TP, Lawrence SM, Fraley SI. Emerging Technologies for Molecular Diagnosis of Sepsis. Clin Microbiol Rev 2018; 31:e00089-17. [PMID: 29490932 PMCID: PMC5967692 DOI: 10.1128/cmr.00089-17] [Citation(s) in RCA: 181] [Impact Index Per Article: 30.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Rapid and accurate profiling of infection-causing pathogens remains a significant challenge in modern health care. Despite advances in molecular diagnostic techniques, blood culture analysis remains the gold standard for diagnosing sepsis. However, this method is too slow and cumbersome to significantly influence the initial management of patients. The swift initiation of precise and targeted antibiotic therapies depends on the ability of a sepsis diagnostic test to capture clinically relevant organisms along with antimicrobial resistance within 1 to 3 h. The administration of appropriate, narrow-spectrum antibiotics demands that such a test be extremely sensitive with a high negative predictive value. In addition, it should utilize small sample volumes and detect polymicrobial infections and contaminants. All of this must be accomplished with a platform that is easily integrated into the clinical workflow. In this review, we outline the limitations of routine blood culture testing and discuss how emerging sepsis technologies are converging on the characteristics of the ideal sepsis diagnostic test. We include seven molecular technologies that have been validated on clinical blood specimens or mock samples using human blood. In addition, we discuss advances in machine learning technologies that use electronic medical record data to provide contextual evaluation support for clinical decision-making.
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Affiliation(s)
- Mridu Sinha
- Bioengineering Department, University of California, San Diego, San Diego, California, USA
| | - Julietta Jupe
- Donald Danforth Plant Science Center, Saint Louis, Missouri, USA
| | - Hannah Mack
- Bioengineering Department, University of California, San Diego, San Diego, California, USA
| | - Todd P Coleman
- Bioengineering Department, University of California, San Diego, San Diego, California, USA
- Center for Microbiome Innovation, University of California, San Diego, San Diego, California, USA
| | - Shelley M Lawrence
- Department of Pediatrics, Division of Neonatal-Perinatal Medicine, University of California, San Diego, San Diego, California, USA
- Rady Children's Hospital of San Diego, San Diego, California, USA
- Clinical Translational Research Institute, University of California, San Diego, San Diego, California, USA
- Center for Microbiome Innovation, University of California, San Diego, San Diego, California, USA
| | - Stephanie I Fraley
- Bioengineering Department, University of California, San Diego, San Diego, California, USA
- Clinical Translational Research Institute, University of California, San Diego, San Diego, California, USA
- Center for Microbiome Innovation, University of California, San Diego, San Diego, California, USA
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14
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Abstract
A digital assay is one in which the sample is partitioned into many containers such that each partition contains a discrete number of biological entities (0, 1, 2, 3, . . .). A powerful technique in the biologist’s toolkit, digital assays bring a new level of precision in quantifying nucleic acids, measuring proteins and their enzymatic activity, and probing single-cell genotype and phenotype. Where part I of this review focused on the fundamentals of partitioning and digital PCR, part II turns its attention to digital protein and cell assays. Digital enzyme assays measure the kinetics of single proteins with enzymatic activity. Digital enzyme-linked immunoassays (ELISAs) quantify antigenic proteins with 2 to 3 log lower detection limit than conventional ELISA, making them well suited for low-abundance biomarkers. Digital cell assays probe single-cell genotype and phenotype, including gene expression, intracellular and surface proteins, metabolic activity, cytotoxicity, and transcriptomes (scRNA-seq). These methods exploit partitioning to 1) isolate single cells or proteins, 2) detect their activity via enzymatic amplification, and 3) tag them individually by coencapsulating them with molecular barcodes. When scaled, digital assays reveal stochastic differences between proteins or cells within a population, a key to understanding biological heterogeneity. This review is intended to give a broad perspective to scientists interested in adopting digital assays into their workflows.
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Affiliation(s)
- Amar S. Basu
- Department of Electrical and Computer Engineering, and Department of Biomedical Engineering, Wayne State University, Detroit, MI, USA
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15
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Zhang K, Kang DK, Ali MM, Liu L, Labanieh L, Lu M, Riazifar H, Nguyen TN, Zell JA, Digman MA, Gratton E, Li J, Zhao W. Digital quantification of miRNA directly in plasma using integrated comprehensive droplet digital detection. LAB ON A CHIP 2015; 15:4217-26. [PMID: 26387763 PMCID: PMC4631652 DOI: 10.1039/c5lc00650c] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Quantification of miRNAs in blood can be potentially used for early disease detection, surveillance monitoring and drug response evaluation. However, quantitative and robust measurement of miRNAs in blood is still a major challenge in large part due to their low concentration and complicated sample preparation processes typically required in conventional assays. Here, we present the 'Integrated Comprehensive Droplet Digital Detection' (IC 3D) system where the plasma sample containing target miRNAs is encapsulated into microdroplets, enzymatically amplified and digitally counted using a novel, high-throughput 3D particle counter. Using Let-7a as a target, we demonstrate that IC 3D can specifically quantify target miRNA directly from blood plasma at extremely low concentrations ranging from 10s to 10 000 copies per mL in ≤3 hours without the need for sample processing such as RNA extraction. Using this new tool, we demonstrate that target miRNA content in colon cancer patient blood is significantly higher than that in healthy donor samples. Our IC 3D system has the potential to introduce a new paradigm for rapid, sensitive and specific detection of low-abundance biomarkers in biological samples with minimal sample processing.
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Affiliation(s)
- Kaixiang Zhang
- Department of Chemistry, Beijing Key Laboratory for Analytical Methods and Instrumentation, Tsinghua University, Beijing, 100084, China
- Department of pharmaceutical Sciences, Department of Biomedical Engineering, Sue and Bill Gross Stem Cell Research Center, Chao Family Comprehensive Cancer Center, Edwards Life Sciences Center for Advanced Cardiovascular Technology, University of California, Irvine, Irvine, CA, 92697, USA
| | - Dong-Ku Kang
- Department of pharmaceutical Sciences, Department of Biomedical Engineering, Sue and Bill Gross Stem Cell Research Center, Chao Family Comprehensive Cancer Center, Edwards Life Sciences Center for Advanced Cardiovascular Technology, University of California, Irvine, Irvine, CA, 92697, USA
| | - M. Monsur Ali
- Department of pharmaceutical Sciences, Department of Biomedical Engineering, Sue and Bill Gross Stem Cell Research Center, Chao Family Comprehensive Cancer Center, Edwards Life Sciences Center for Advanced Cardiovascular Technology, University of California, Irvine, Irvine, CA, 92697, USA
| | - Linan Liu
- Department of pharmaceutical Sciences, Department of Biomedical Engineering, Sue and Bill Gross Stem Cell Research Center, Chao Family Comprehensive Cancer Center, Edwards Life Sciences Center for Advanced Cardiovascular Technology, University of California, Irvine, Irvine, CA, 92697, USA
| | - Louai Labanieh
- Department of pharmaceutical Sciences, Department of Biomedical Engineering, Sue and Bill Gross Stem Cell Research Center, Chao Family Comprehensive Cancer Center, Edwards Life Sciences Center for Advanced Cardiovascular Technology, University of California, Irvine, Irvine, CA, 92697, USA
| | - Mengrou Lu
- Department of pharmaceutical Sciences, Department of Biomedical Engineering, Sue and Bill Gross Stem Cell Research Center, Chao Family Comprehensive Cancer Center, Edwards Life Sciences Center for Advanced Cardiovascular Technology, University of California, Irvine, Irvine, CA, 92697, USA
| | - Hamidreza Riazifar
- Department of pharmaceutical Sciences, Department of Biomedical Engineering, Sue and Bill Gross Stem Cell Research Center, Chao Family Comprehensive Cancer Center, Edwards Life Sciences Center for Advanced Cardiovascular Technology, University of California, Irvine, Irvine, CA, 92697, USA
| | - Thi N. Nguyen
- Department of pharmaceutical Sciences, Department of Biomedical Engineering, Sue and Bill Gross Stem Cell Research Center, Chao Family Comprehensive Cancer Center, Edwards Life Sciences Center for Advanced Cardiovascular Technology, University of California, Irvine, Irvine, CA, 92697, USA
| | - Jason A. Zell
- Division of Hematology/Oncology, University of California Irvine Medical Center, Orange, CA 92868, USA
| | - Michelle A. Digman
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, CA, 92697, USA
- Centre for Bioactive Discovery in Health and Ageing, School of Science & Technology, University of New England, Armidale, Australia
| | - Enrico Gratton
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, CA, 92697, USA
| | - Jinghong Li
- Department of Chemistry, Beijing Key Laboratory for Analytical Methods and Instrumentation, Tsinghua University, Beijing, 100084, China
| | - Weian Zhao
- Department of pharmaceutical Sciences, Department of Biomedical Engineering, Sue and Bill Gross Stem Cell Research Center, Chao Family Comprehensive Cancer Center, Edwards Life Sciences Center for Advanced Cardiovascular Technology, University of California, Irvine, Irvine, CA, 92697, USA
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16
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Kang DK, Ali MM, Zhang K, Huang SS, Peterson E, Digman MA, Gratton E, Zhao W. Rapid detection of single bacteria in unprocessed blood using Integrated Comprehensive Droplet Digital Detection. Nat Commun 2014; 5:5427. [PMID: 25391809 PMCID: PMC4243214 DOI: 10.1038/ncomms6427] [Citation(s) in RCA: 221] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Accepted: 09/30/2014] [Indexed: 01/08/2023] Open
Abstract
Blood stream infection or sepsis is a major health problem worldwide, with extremely high mortality, which is partly due to the inability to rapidly detect and identify bacteria in the early stages of infection. Here we present a new technology termed 'Integrated Comprehensive Droplet Digital Detection' (IC 3D) that can selectively detect bacteria directly from milliliters of diluted blood at single-cell sensitivity in a one-step, culture- and amplification-free process within 1.5-4 h. The IC 3D integrates real-time, DNAzyme-based sensors, droplet microencapsulation and a high-throughput 3D particle counter system. Using Escherichia coli as a target, we demonstrate that the IC 3D can provide absolute quantification of both stock and clinical isolates of E. coli in spiked blood within a broad range of extremely low concentration from 1 to 10,000 bacteria per ml with exceptional robustness and limit of detection in the single digit regime.
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Affiliation(s)
- Dong-Ku Kang
- Department of Pharmaceutical Sciences, University of California–Irvine, 845 Health Sciences Road, Irvine, California 92697, USA
- Sue and Bill Gross Stem Cell Research Center, University of California–Irvine, 845 Health Sciences Road, Irvine, California 92697, USA
- Chao Family Comprehensive Cancer Center, University of California–Irvine, 845 Health Sciences Road, Irvine, California 92697, USA
- Edwards Lifesciences Center for Advanced Cardiovascular Technology, University of California–Irvine, 845 Health Sciences Road, Irvine, California 92697, USA
- Department of Biomedical Engineering, University of California–Irvine, 845 Health Sciences Road, Irvine, California 92697, USA
| | - M. Monsur Ali
- Department of Pharmaceutical Sciences, University of California–Irvine, 845 Health Sciences Road, Irvine, California 92697, USA
- Sue and Bill Gross Stem Cell Research Center, University of California–Irvine, 845 Health Sciences Road, Irvine, California 92697, USA
- Chao Family Comprehensive Cancer Center, University of California–Irvine, 845 Health Sciences Road, Irvine, California 92697, USA
- Edwards Lifesciences Center for Advanced Cardiovascular Technology, University of California–Irvine, 845 Health Sciences Road, Irvine, California 92697, USA
- Department of Biomedical Engineering, University of California–Irvine, 845 Health Sciences Road, Irvine, California 92697, USA
| | - Kaixiang Zhang
- Department of Pharmaceutical Sciences, University of California–Irvine, 845 Health Sciences Road, Irvine, California 92697, USA
- Sue and Bill Gross Stem Cell Research Center, University of California–Irvine, 845 Health Sciences Road, Irvine, California 92697, USA
- Chao Family Comprehensive Cancer Center, University of California–Irvine, 845 Health Sciences Road, Irvine, California 92697, USA
- Edwards Lifesciences Center for Advanced Cardiovascular Technology, University of California–Irvine, 845 Health Sciences Road, Irvine, California 92697, USA
- Department of Biomedical Engineering, University of California–Irvine, 845 Health Sciences Road, Irvine, California 92697, USA
- Department of Chemistry, Beijing Key Laboratory for Analytical Methods and Instrumentation, Tsinghua University, Beijing 100084, China
| | - Susan S. Huang
- Division of Infectious Diseases and Health Policy Research Institute, School of Medicine, University of California–Irvine, Irvine, California 92697, USA
| | - Ellena Peterson
- Department of Pathology and Laboratory Medicine, University of California, Irvine, California 92697, USA
| | - Michelle A. Digman
- Department of Biomedical Engineering, University of California–Irvine, 845 Health Sciences Road, Irvine, California 92697, USA
- Laboratory for Fluorescence Dynamics, University of California, Irvine, California 92697, USA
- Centre for Bioactive Discovery in Health and Ageing, School of Science and Technology, University of New England, Armidale, New South Wales 2351, Australia
| | - Enrico Gratton
- Department of Biomedical Engineering, University of California–Irvine, 845 Health Sciences Road, Irvine, California 92697, USA
- Laboratory for Fluorescence Dynamics, University of California, Irvine, California 92697, USA
| | - Weian Zhao
- Department of Pharmaceutical Sciences, University of California–Irvine, 845 Health Sciences Road, Irvine, California 92697, USA
- Sue and Bill Gross Stem Cell Research Center, University of California–Irvine, 845 Health Sciences Road, Irvine, California 92697, USA
- Chao Family Comprehensive Cancer Center, University of California–Irvine, 845 Health Sciences Road, Irvine, California 92697, USA
- Edwards Lifesciences Center for Advanced Cardiovascular Technology, University of California–Irvine, 845 Health Sciences Road, Irvine, California 92697, USA
- Department of Biomedical Engineering, University of California–Irvine, 845 Health Sciences Road, Irvine, California 92697, USA
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17
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Skinner JP, Swift KM, Ruan Q, Perfetto S, Gratton E, Tetin SY. Simplified confocal microscope for counting particles at low concentrations. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2013; 84:074301. [PMID: 23902088 PMCID: PMC3724729 DOI: 10.1063/1.4812782] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
We describe a compact scanning confocal fluorescence microscope capable of detecting particles concentrations less than 100 particles∕ml in ~15 min. The system mechanically moves a cuvette containing ~3 ml of sample. A relatively large confocal volume is observed within the cuvette using a 1 mm pinhole in front of a detection PMT. Due to the motion of the sample, particles traverse the confocal volume quickly, and analysis by pattern recognition qualifies spikes in the emission intensity data and counts them as events. We show linearity of detection as a function of concentration and also characterize statistical behavior of the instrument. We calculate a detection sensitivity of the system using 3 μm fluorescent microspheres to be 5 particles/ml. Furthermore, to demonstrate biological application, we performed a dilution series to quantify stained E. coli and yeast cells. We counted E. coli cells at a concentration as low as 30 cells∕ml in 10 min/sample.
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Affiliation(s)
- Joseph P Skinner
- Diagnostics Research, Abbott Diagnostics Division, Abbott Park, Illinois 60064, USA
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