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Kobeissy F, Goli M, Yadikar H, Shakkour Z, Kurup M, Haidar MA, Alroumi S, Mondello S, Wang KK, Mechref Y. Advances in neuroproteomics for neurotrauma: unraveling insights for personalized medicine and future prospects. Front Neurol 2023; 14:1288740. [PMID: 38073638 PMCID: PMC10703396 DOI: 10.3389/fneur.2023.1288740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 11/01/2023] [Indexed: 02/12/2024] Open
Abstract
Neuroproteomics, an emerging field at the intersection of neuroscience and proteomics, has garnered significant attention in the context of neurotrauma research. Neuroproteomics involves the quantitative and qualitative analysis of nervous system components, essential for understanding the dynamic events involved in the vast areas of neuroscience, including, but not limited to, neuropsychiatric disorders, neurodegenerative disorders, mental illness, traumatic brain injury, chronic traumatic encephalopathy, and other neurodegenerative diseases. With advancements in mass spectrometry coupled with bioinformatics and systems biology, neuroproteomics has led to the development of innovative techniques such as microproteomics, single-cell proteomics, and imaging mass spectrometry, which have significantly impacted neuronal biomarker research. By analyzing the complex protein interactions and alterations that occur in the injured brain, neuroproteomics provides valuable insights into the pathophysiological mechanisms underlying neurotrauma. This review explores how such insights can be harnessed to advance personalized medicine (PM) approaches, tailoring treatments based on individual patient profiles. Additionally, we highlight the potential future prospects of neuroproteomics, such as identifying novel biomarkers and developing targeted therapies by employing artificial intelligence (AI) and machine learning (ML). By shedding light on neurotrauma's current state and future directions, this review aims to stimulate further research and collaboration in this promising and transformative field.
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Affiliation(s)
- Firas Kobeissy
- Department of Neurobiology, School of Medicine, Neuroscience Institute, Atlanta, GA, United States
| | - Mona Goli
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, United States
| | - Hamad Yadikar
- Department of Biological Sciences Faculty of Science, Kuwait University, Safat, Kuwait
| | - Zaynab Shakkour
- Department of Pathology and Anatomical Sciences, University of Missouri School of Medicine, Columbia, MO, United States
| | - Milin Kurup
- Alabama College of Osteopathic Medicine, Dothan, AL, United States
| | | | - Shahad Alroumi
- Department of Biological Sciences Faculty of Science, Kuwait University, Safat, Kuwait
| | - Stefania Mondello
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Messina, Italy
| | - Kevin K. Wang
- Department of Neurobiology, School of Medicine, Neuroscience Institute, Atlanta, GA, United States
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, United States
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Tarim EA, Anil Inevi M, Ozkan I, Kecili S, Bilgi E, Baslar MS, Ozcivici E, Oksel Karakus C, Tekin HC. Microfluidic-based technologies for diagnosis, prevention, and treatment of COVID-19: recent advances and future directions. Biomed Microdevices 2023; 25:10. [PMID: 36913137 PMCID: PMC10009869 DOI: 10.1007/s10544-023-00649-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/21/2023] [Indexed: 03/14/2023]
Abstract
The COVID-19 pandemic has posed significant challenges to existing healthcare systems around the world. The urgent need for the development of diagnostic and therapeutic strategies for COVID-19 has boomed the demand for new technologies that can improve current healthcare approaches, moving towards more advanced, digitalized, personalized, and patient-oriented systems. Microfluidic-based technologies involve the miniaturization of large-scale devices and laboratory-based procedures, enabling complex chemical and biological operations that are conventionally performed at the macro-scale to be carried out on the microscale or less. The advantages microfluidic systems offer such as rapid, low-cost, accurate, and on-site solutions make these tools extremely useful and effective in the fight against COVID-19. In particular, microfluidic-assisted systems are of great interest in different COVID-19-related domains, varying from direct and indirect detection of COVID-19 infections to drug and vaccine discovery and their targeted delivery. Here, we review recent advances in the use of microfluidic platforms to diagnose, treat or prevent COVID-19. We start by summarizing recent microfluidic-based diagnostic solutions applicable to COVID-19. We then highlight the key roles microfluidics play in developing COVID-19 vaccines and testing how vaccine candidates perform, with a focus on RNA-delivery technologies and nano-carriers. Next, microfluidic-based efforts devoted to assessing the efficacy of potential COVID-19 drugs, either repurposed or new, and their targeted delivery to infected sites are summarized. We conclude by providing future perspectives and research directions that are critical to effectively prevent or respond to future pandemics.
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Affiliation(s)
- E Alperay Tarim
- Department of Bioengineering, Izmir Institute of Technology, Izmir, Turkey
| | - Muge Anil Inevi
- Department of Bioengineering, Izmir Institute of Technology, Izmir, Turkey
| | - Ilayda Ozkan
- Department of Bioengineering, Izmir Institute of Technology, Izmir, Turkey
| | - Seren Kecili
- Department of Bioengineering, Izmir Institute of Technology, Izmir, Turkey
| | - Eyup Bilgi
- Department of Bioengineering, Izmir Institute of Technology, Izmir, Turkey
| | - M Semih Baslar
- Department of Bioengineering, Izmir Institute of Technology, Izmir, Turkey
| | - Engin Ozcivici
- Department of Bioengineering, Izmir Institute of Technology, Izmir, Turkey
| | | | - H Cumhur Tekin
- Department of Bioengineering, Izmir Institute of Technology, Izmir, Turkey.
- METU MEMS Center, Ankara, Turkey.
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3
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Recent Advances in Drug Delivery System Fabricated by Microfluidics for Disease Therapy. Bioengineering (Basel) 2022; 9:bioengineering9110625. [DOI: 10.3390/bioengineering9110625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/16/2022] [Accepted: 10/26/2022] [Indexed: 11/16/2022] Open
Abstract
Traditional drug therapy faces challenges such as drug distribution throughout the body, rapid degradation and excretion, and extensive adverse reactions. In contrast, micro/nanoparticles can controllably deliver drugs to target sites to improve drug efficacy. Unlike traditional large-scale synthetic systems, microfluidics allows manipulation of fluids at the microscale and shows great potential in drug delivery and precision medicine. Well-designed microfluidic devices have been used to fabricate multifunctional drug carriers using stimuli-responsive materials. In this review, we first introduce the selection of materials and processing techniques for microfluidic devices. Then, various well-designed microfluidic chips are shown for the fabrication of multifunctional micro/nanoparticles as drug delivery vehicles. Finally, we describe the interaction of drugs with lymphatic vessels that are neglected in organs-on-chips. Overall, the accelerated development of microfluidics holds great potential for the clinical translation of micro/nanoparticle drug delivery systems for disease treatment.
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Abstract
Despite tremendous gains over the past decade, methods for characterizing proteins have generally lagged behind those for nucleic acids, which are characterized by extremely high sensitivity, dynamic range, and throughput. However, the ability to directly characterize proteins at nucleic acid levels would address critical biological challenges such as more sensitive medical diagnostics, deeper protein quantification, large-scale measurement, and discovery of alternate protein isoforms and modifications and would open new paths to single-cell proteomics. In response to this need, there has been a push to radically improve protein sequencing technologies by taking inspiration from high-throughput nucleic acid sequencing, with a particular focus on developing practical methods for single-molecule protein sequencing (SMPS). SMPS technologies fall generally into three categories: sequencing by degradation (e.g., mass spectrometry or fluorosequencing), sequencing by transit (e.g., nanopores or quantum tunneling), and sequencing by affinity (as in DNA hybridization-based approaches). We describe these diverse approaches, which range from those that are already experimentally well-supported to the merely speculative, in this nascent field striving to reformulate proteomics.
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Affiliation(s)
- Brendan M Floyd
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, Texas, USA; ,
| | - Edward M Marcotte
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, Texas, USA; ,
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Bisht A, Mishra A, Bisht H, Tripathi RM. Nanomaterial Based Biosensors for Detection of Viruses Including SARS-CoV-2: A Review. JOURNAL OF ANALYSIS AND TESTING 2021; 5:327-340. [PMID: 34777896 PMCID: PMC8572656 DOI: 10.1007/s41664-021-00200-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Accepted: 08/17/2021] [Indexed: 12/23/2022]
Abstract
The COVID-19 outbreak led to an uncontrollable situation and was later declared a global pandemic. RT-PCR is one of the reliable methods for the detection of COVID-19, but it requires transporting samples to sophisticated laboratories and takes a significant amount of time to amplify the viral genome. Therefore, there is an urgent need for a large-scale, rapid, specific, and portable detection kit. Nowadays nanomaterials-based detection technology has been developed and it showed advancement over the conventional methods in selectivity and sensitivity. This review aims at summarising some of the most promising nanomaterial-based sensing technologies for detecting SARS-CoV-2. Nanomaterials possess unique physical, chemical, electrical and optical properties, which can be exploited for the application in biosensors. Furthermore, nanomaterials work on the same scale as biological processes and can be easily functionalized with substrates of interest. These devices do not require extraordinary sophistication and are suitable for use by common individuals without high-tech laboratories. Electrochemical and colorimetric methods similar to glucometer and pregnancy test kits are discussed and reviewed as potential diagnostic devices for COVID-19. Other devices working on the principle of immune response and microarrays are also discussed as possible candidates. Nanomaterials such as metal nanoparticles, graphene, quantum dots, and CNTs enhance the limit of detection and accuracy of the biosensors to give spontaneous results. The challenges of industrial-scale production of these devices are also discussed. If mass production is successfully developed, these sensors can ramp up the testing to provide the accurate number of people affected by the virus, which is extremely critical in today's scenario.
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Affiliation(s)
- Ayushi Bisht
- Amity Institute of Biotechnology, Amity University, Noida, 201303 India
| | - Abhishek Mishra
- Amity Institute of Nanotechnology, Amity University, Noida, 201303 India
| | - Harender Bisht
- Reliance Industries Limited, Motikhavdi, Jamnagar, 361140 India
| | - R. M. Tripathi
- Amity Institute of Nanotechnology, Amity University, Noida, 201303 India
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Shen L, Wang P, Ke Y. DNA Nanotechnology-Based Biosensors and Therapeutics. Adv Healthc Mater 2021; 10:e2002205. [PMID: 34085411 DOI: 10.1002/adhm.202002205] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 02/19/2021] [Indexed: 12/19/2022]
Abstract
Over the past few decades, DNA nanotechnology engenders a vast variety of programmable nanostructures utilizing Watson-Crick base pairing. Due to their precise engineering, unprecedented programmability, and intrinsic biocompatibility, DNA nanostructures cannot only interact with small molecules, nucleic acids, proteins, viruses, and cancer cells, but also can serve as nanocarriers to deliver different therapeutic agents. Such addressability innate to DNA nanostructures enables their use in various fields of biomedical applications such as biosensors and cancer therapy. This review is begun with a brief introduction of the development of DNA nanotechnology, followed by a summary of recent applications of DNA nanostructures in biosensors and therapeutics. Finally, challenges and opportunities for practical applications of DNA nanotechnology are discussed.
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Affiliation(s)
- Luyao Shen
- Wallace H. Coulter Department of Biomedical Engineering Georgia Institute of Technology and Emory University Atlanta GA 30322 USA
- Institute of Molecular Medicine Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine State Key Laboratory of Oncogenes and Related Genes Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200127 China
| | - Pengfei Wang
- Institute of Molecular Medicine Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine State Key Laboratory of Oncogenes and Related Genes Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200127 China
| | - Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering Georgia Institute of Technology and Emory University Atlanta GA 30322 USA
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A Sample-In-Answer-Out Microfluidic System for the Molecular Diagnostics of 24 HPV Genotypes Using Palm-Sized Cartridge. MICROMACHINES 2021; 12:mi12030263. [PMID: 33806512 PMCID: PMC8000143 DOI: 10.3390/mi12030263] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 02/25/2021] [Accepted: 03/01/2021] [Indexed: 12/23/2022]
Abstract
This paper proposes an automated microfluidic system for molecular diagnostics that integrates the functions of a traditional polymerase chain reaction (PCR) laboratory into a palm-sized microfluidic cartridge (CARD) made of polystyrene. The CARD integrates 4 independent microfluidic sample lanes, which can independently complete a sample test, and each sample lane integrates the 3 functional areas of the sample preparation area, PCR amplification area, and product analysis area. By using chemical cell lysis, magnetic silica bead-based DNA extraction, combined with multi-PCR-reverse dot hybridization with microarray, 24 HPV genotypes can be typing tested in CARD. With a custom-made automated CARD operating platform, the entire process can be automatically carried out, achieving sample-in-answer-out. The custom-made operation platform is developed based on a liquid handling station-type, which can automatically load off-chip reagents without placing reagents in CARD in advance. The platform can control six CARDs to work simultaneously, detect 24 samples at a time. The results show that the limit of detection of the microfluidic system is 200 copies/test, and the positive detection rate of clinical samples by this system is 100%, which is an effective method for detection of HPV.
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8
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Enhancement of Fluid Mixing with U-Shaped Channels on a Rotating Disc. MICROMACHINES 2020; 11:mi11121110. [PMID: 33334076 PMCID: PMC7765561 DOI: 10.3390/mi11121110] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 12/11/2020] [Accepted: 12/13/2020] [Indexed: 01/15/2023]
Abstract
In this study, centrifugal microfluidics with a simple geometry of U-shaped structure was designed, fabricated and analyzed to attain rapid and efficient fluid mixing. Visualization experiments together with numerical simulations were carried out to investigate the mixing behavior for the microfluidics with single, double and triple U-shaped structures, where each of the U-structures consisted of four consecutive 90° bends. It is found that the U-shaped structure markedly enhances mixing by transverse secondary flow that is originated from the Coriolis-induced vortices and further intensified by the Dean force generated as the stream turns along the 90° bends. The secondary flow becomes stronger with increasing rotational speed and with more U-shaped structures, hence higher mixing performance. The mixing efficiency measured for the three types of mixers shows a sharp increase with increasing rotational speed in the lower range. As the rotational speed further increases, nearly complete mixing can be achieved at 600 rpm for the triple-U mixer and at 720 rpm for the double-U mixer, while a maximum efficiency level of 83-86% is reached for the single-U mixer. The simulation results that reveal detailed characteristics of the flow and concentration fields are in good agreement with the experiments.
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9
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Zhao Y, Feng Y, Zhang Y, Xia P, Xiao Z, Wang Z, Yan H. Combining competitive sequestration with nonlinear hybridization chain reaction amplification: an ultra-specific and highly sensitive sensing strategy for single-nucleotide variants. Anal Chim Acta 2020; 1130:107-116. [PMID: 32892930 DOI: 10.1016/j.aca.2020.07.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 07/06/2020] [Accepted: 07/14/2020] [Indexed: 12/11/2022]
Abstract
Highly specific and sensitive detection of single-nucleotide variants (SNVs) is of central importance in disease diagnosis and pharmacogenomics. However, it remains a great challenge to successfully detect very low amounts of mutant SNV sequences in real samples in which a SNV sequence may be surrounded by high levels of closely related wild-type sequences. Herein, we propose an ultra-specific and highly sensitive SNV sensing strategy by combining the competitive sequestration with the nonlinear hybridization chain reaction (HCR) amplification. The rationally designed sequestration hairpin can effectively sequester the large amount of wild-type sequence and thus dramatically improve the hybridization specificity in recognizing SNVs. To improve the detection sensitivity, a new fluorescent signal probe is fabricated by intercalating SYBR Green I dye into the nonlinear HCR based DNA dendrimer to further bind with SNVs for signal amplification. The hyperbranched DNA dendrimer possesses large numbers of DNA duplexes for dye intercalation, thus the signal probe shows strong fluorescence intensity, leading to large fluorescence signal amplification. Taking advantage of the improved hybridization specificity of the competitive sequestration and the enhanced fluorescence response of the nonlinear HCR amplification, the developed sensing strategy enables ultra-specific and highly sensitive detection of SNVs. Taking human pancreatic cancers and colorectal carcinomas related KRAS gene mutations as models, the developed strategy shows remarkably high specificity against 17 SNVs (discrimination factors ranged from 126 to 1001 with a median of 310), and achieves high sensitivity for 6 KRAS mutations (the best resultant detection limit reached 15 pM for KRAS G13D (c.38G > A)). Notably, combined with PCR amplification, our SNV sensing strategy could detect KRAS G12D (c.35G > A) from extracted human genomic DNA samples at abundance as low as 0.05%. This work expands the rule set of designing specific and sensitive SNV sensing strategies and shows promising potential application in clinical diagnosis.
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Affiliation(s)
- Yan Zhao
- MOE Key Laboratory of Material Physics and Chemistry Under Extraordinary Conditions, School of Science, Northwestern Polytechnical University, Xi'an, 710129, China.
| | - Yuanbo Feng
- MOE Key Laboratory of Material Physics and Chemistry Under Extraordinary Conditions, School of Science, Northwestern Polytechnical University, Xi'an, 710129, China
| | - Yuanbo Zhang
- MOE Key Laboratory of Material Physics and Chemistry Under Extraordinary Conditions, School of Science, Northwestern Polytechnical University, Xi'an, 710129, China
| | - Pu Xia
- Key Laboratory of Spectral Imaging Technology, Xi'an Institute of Optics and Precision Mechanics, Chinese Academy of Sciences, Xi'an, 710119, China
| | - Zihan Xiao
- Queen Mary University of London Engineering School, NPU, Northwestern Polytechnical University, Xi'an, 710129, China
| | - Ziheng Wang
- Queen Mary University of London Engineering School, NPU, Northwestern Polytechnical University, Xi'an, 710129, China
| | - Hongxia Yan
- MOE Key Laboratory of Material Physics and Chemistry Under Extraordinary Conditions, School of Science, Northwestern Polytechnical University, Xi'an, 710129, China.
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10
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Canós Valero A, Kislov D, Gurvitz EA, Shamkhi HK, Pavlov AA, Redka D, Yankin S, Zemánek P, Shalin AS. Nanovortex-Driven All-Dielectric Optical Diffusion Boosting and Sorting Concept for Lab-on-a-Chip Platforms. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:1903049. [PMID: 32537397 PMCID: PMC7284221 DOI: 10.1002/advs.201903049] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 02/10/2020] [Accepted: 02/24/2020] [Indexed: 05/29/2023]
Abstract
The ever-growing field of microfluidics requires precise and flexible control over fluid flows at reduced scales. Current constraints demand a variety of controllable components to carry out several operations inside microchambers and microreactors. In this context, brand-new nanophotonic approaches can significantly enhance existing capabilities providing unique functionalities via finely tuned light-matter interactions. A concept is proposed, featuring dual on-chip functionality: boosted optically driven diffusion and nanoparticle sorting. High-index dielectric nanoantennae is specially designed to ensure strongly enhanced spin-orbit angular momentum transfer from a laser beam to the scattered field. Hence, subwavelength optical nanovortices emerge driving spiral motion of plasmonic nanoparticles via the interplay between curl-spin optical forces and radiation pressure. The nanovortex size is an order of magnitude smaller than that provided by conventional beam-based approaches. The nanoparticles mediate nanoconfined fluid motion enabling moving-part-free nanomixing inside a microchamber. Moreover, exploiting the nontrivial size dependence of the curled optical forces makes it possible to achieve precise nanoscale sorting of gold nanoparticles, demanded for on-chip separation and filtering. Altogether, a versatile platform is introduced for further miniaturization of moving-part-free, optically driven microfluidic chips for fast chemical analysis, emulsion preparation, or chemical gradient generation with light-controlled navigation of nanoparticles, viruses or biomolecules.
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Affiliation(s)
| | - Denis Kislov
- ITMO UniversityKronverksky prospect 49St. Petersburg197101Russia
| | - Egor A. Gurvitz
- ITMO UniversityKronverksky prospect 49St. Petersburg197101Russia
| | - Hadi K. Shamkhi
- ITMO UniversityKronverksky prospect 49St. Petersburg197101Russia
| | - Alexander A. Pavlov
- Institute of Nanotechnology of Microelectronics of the Russian Academy of Sciences (INME RAS)Nagatinskaya Street, House 16A, Building 11Moscow119991Russia
| | - Dmitrii Redka
- Electrotechnical University “LETI” (ETU)5 Prof. Popova StreetSaint Petersburg197376Russia
| | - Sergey Yankin
- LLC COMSOLBolshaya Sadovaya St. 10Moscow123001Russia
| | - Pavel Zemánek
- Czech Academy of SciencesInstitute of Scientific InstrumentsKrálovopolská 147Brno612 64Czech Republic
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11
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Tripathy S, Singh SG. Label-Free Electrochemical Detection of DNA Hybridization: A Method for COVID-19 Diagnosis. TRANSACTIONS OF THE INDIAN NATIONAL ACADEMY OF ENGINEERING : AN INTERNATIONAL JOURNAL OF ENGINEERING AND TECHNOLOGY 2020; 5:205-209. [PMID: 38624377 PMCID: PMC7247285 DOI: 10.1007/s41403-020-00103-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 05/13/2020] [Indexed: 01/03/2023]
Abstract
This paper presents label-free electrochemical transduction as a suitable scheme for COVID-19-specific viral RNA/c-DNA detection, with an aim to facilitate point of care diagnosis. In lieu of this, we discuss the proposed electrochemical biosensing scheme, based on electrodeposited gold nanoparticles as the transducing elements. Specific to this approach, here, the protocols associated with the immobilization of the single-stranded probe nucleotide on to the biosensor, have also been laid out. This paper also discusses the methods of electrochemical analysis, to be used for data acquisition and subsequent calibration, in relation to target analyte detection. Towards facilitating portable diagnosis, development of miniaturized sensors and their integration with readout units have also been discussed.
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Affiliation(s)
- Suryasnata Tripathy
- Department of Electrical Engineering, Indian Institute of Technology, Hyderabad, Telangana 502285 India
| | - Shiv Govind Singh
- Department of Electrical Engineering, Indian Institute of Technology, Hyderabad, Telangana 502285 India
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12
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Kang Y, Cheon NY, Cha J, Kim A, Kim HI, Lee L, Kim KO, Jo K, Lee JY. High-throughput single-molecule imaging system using nanofabricated trenches and fluorescent DNA-binding proteins. Biotechnol Bioeng 2020; 117:1640-1648. [PMID: 32162675 DOI: 10.1002/bit.27331] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 03/02/2020] [Accepted: 03/11/2020] [Indexed: 12/18/2022]
Abstract
DNA curtain is a high-throughput system, integrating a lipid bilayer, fluorescence imaging, and microfluidics to probe protein-DNA interactions in real-time and has provided in-depth understanding of DNA metabolism. Especially, the microfluidic platform of a DNA curtain is highly suitable for a biochip. In the DNA curtain, DNA molecules are aligned along chromium nanobarriers, which are fabricated on a slide surface, and visualized using an intercalating dye, YOYO-1. Although the chromium barriers confer precise geometric alignment of DNA, reuse of the slides is limited by wear of the barriers during cleaning. YOYO-1 is rapidly photobleached and causes photocleavage of DNA under continuous laser illumination, restricting DNA observation to a brief time window. To address these challenges, we developed a new nanopatterned slide, upon which carved nanotrenches serve as diffusion barriers. The nanotrenches were robust under harsh cleaning conditions, facilitating the maintenance of surface cleanliness that is essential to slide reuse. We also stained DNA with a fluorescent protein with a DNA-binding motif, fluorescent protein-DNA binding peptide (FP-DBP). FP-DBP was slowly photobleached and did not cause DNA photocleavage. This new DNA curtain system enables a more stable and repeatable investigation of real-time protein-DNA interactions and will serve as a good platform for lab-on-a-chip.
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Affiliation(s)
- Yujin Kang
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Na Young Cheon
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Jongjin Cha
- Department of Physics and Astronomy, Seoul National University, Seoul, Republic of Korea
| | - Ayoung Kim
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Hyung-Il Kim
- UNIST Central Research Facilities (UCRF), Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Luda Lee
- UNIST Central Research Facilities (UCRF), Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Kang O Kim
- UNIST Central Research Facilities (UCRF), Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Kyubong Jo
- Department of Chemistry and Integrated Biotechnology, Sogang University, Seoul, Republic of Korea
| | - Ja Yil Lee
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea.,Center for Genomic Integrity, Institute for Basic Science, Ulsan, Republic of Korea
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13
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Ostromohov N, Rofman B, Bercovici M, Kaigala G. Electrokinetic Scanning Probe. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e1904268. [PMID: 31885215 DOI: 10.1002/smll.201904268] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 11/25/2019] [Indexed: 06/10/2023]
Abstract
The theoretical analysis and experimental demonstration of a new concept are presented for a non-contact scanning probe, in which transport of fluid and molecules is controlled by electric fields. The electrokinetic scanning probe (ESP) enables local chemical and biochemical interactions with surfaces in liquid environments. The physical mechanism and design criteria for such a probe are presented, and its compatibility with a wide range of processing solutions and pH values are demonstrated. The applicability of the probe is shown for surface patterning in conjunction with localized heating and 250-fold analyte stacking.
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Affiliation(s)
- Nadya Ostromohov
- Faculty of Mechanical Engineering, Technion-Israel Institute of Technology, Haifa, 3200003, Israel
- IBM Research-Zurich, Saeumerstrasse 4, CH-8803, Rueschlikon, Switzerland
| | - Baruch Rofman
- Faculty of Mechanical Engineering, Technion-Israel Institute of Technology, Haifa, 3200003, Israel
| | - Moran Bercovici
- Faculty of Mechanical Engineering, Technion-Israel Institute of Technology, Haifa, 3200003, Israel
| | - Govind Kaigala
- IBM Research-Zurich, Saeumerstrasse 4, CH-8803, Rueschlikon, Switzerland
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14
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Geissler M, Brassard D, Clime L, Pilar AVC, Malic L, Daoud J, Barrère V, Luebbert C, Blais BW, Corneau N, Veres T. Centrifugal microfluidic lab-on-a-chip system with automated sample lysis, DNA amplification and microarray hybridization for identification of enterohemorrhagic Escherichia coli culture isolates. Analyst 2020; 145:6831-6845. [DOI: 10.1039/d0an01232g] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Automated workflow that starts with a colony isolate and ends with a fluorescence signal on a DNA microarray.
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Affiliation(s)
- Matthias Geissler
- Life Sciences Division
- National Research Council of Canada
- Boucherville
- Canada
| | - Daniel Brassard
- Life Sciences Division
- National Research Council of Canada
- Boucherville
- Canada
| | - Liviu Clime
- Life Sciences Division
- National Research Council of Canada
- Boucherville
- Canada
| | | | - Lidija Malic
- Life Sciences Division
- National Research Council of Canada
- Boucherville
- Canada
| | - Jamal Daoud
- Life Sciences Division
- National Research Council of Canada
- Boucherville
- Canada
| | | | | | - Burton W. Blais
- Ontario Laboratory Network
- Canadian Food Inspection Agency
- Ottawa
- Canada
| | | | - Teodor Veres
- Life Sciences Division
- National Research Council of Canada
- Boucherville
- Canada
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15
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Rosenfeld A, Brehm M, Welle A, Trouillet V, Heissler S, Benz M, Levkin PA. Solid-phase combinatorial synthesis using microarrays of microcompartments with light-induced on-chip cell screening. Mater Today Bio 2019; 3:100022. [PMID: 32159150 PMCID: PMC7061619 DOI: 10.1016/j.mtbio.2019.100022] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 07/19/2019] [Accepted: 07/25/2019] [Indexed: 12/31/2022] Open
Abstract
The process of drug discovery includes individual synthesis and characterization of drug candidates, followed by a biological screening, which is separated from synthesis in space and time. This approach suffers from low throughput and associated high costs, which in turn lead to inefficiency in the field of drug discovery. Here, we present a miniaturized platform combining combinatorial solid-phase synthesis with high-throughput cell screenings. The method is based on the formation of nanoporous poly(2-hydroxyethyl methacrylate-co-ethylene dimethacrylate) layers patterned with hydrophilic spots separated from each other by superhydrophobic liquid-impermeable barriers. The porous polymer inside the hydrophilic spots is used as a support to conduct solid-phase synthesis. The hydrophilic spots can be then filled with droplets containing either reagents for synthesis or live cells. Upon irradiation with UV light, products of solid-phase synthesis are released from the porous polymer because of the photo-cleavable linkers used and diffuse into separate droplets. The light-induced release of the products allows the control of the release spatially, temporally, and quantitatively. To demonstrate the versatility and usability of the platform for various cell lines, we have successfully implemented peptide synthesis to create an exemplary chemical library and demonstrated high cell viability after the UV-triggered small-molecule release.
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Affiliation(s)
- A Rosenfeld
- Karlsruhe Institute of Technology (KIT), Institute of Toxicology and Genetics (ITG), Hermann-von Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - M Brehm
- Karlsruhe Institute of Technology (KIT), Institute of Toxicology and Genetics (ITG), Hermann-von Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - A Welle
- Karlsruhe Institute of Technology (KIT), Institute of Functional Interfaces, Hermann-von Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany.,Karlsruhe Institute of Technology (KIT), Karlsruhe Nano Micro Facility, Hermann-von Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - V Trouillet
- Karlsruhe Institute of Technology (KIT), Karlsruhe Nano Micro Facility, Hermann-von Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany.,Karlsruhe Institute of Technology (KIT), Institute for Applied Materials, Hermann-von Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - S Heissler
- Karlsruhe Institute of Technology (KIT), Institute of Functional Interfaces, Hermann-von Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - M Benz
- Karlsruhe Institute of Technology (KIT), Institute of Toxicology and Genetics (ITG), Hermann-von Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - P A Levkin
- Karlsruhe Institute of Technology (KIT), Institute of Toxicology and Genetics (ITG), Hermann-von Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany.,Karlsruhe Institute of Technology (KIT), Institute of Organic Chemistry, 76131, Karlsruhe, Germany
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16
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Development of certified reference material NMIJ CRM 6205-a for the validation of DNA quantification methods: accurate mass concentrations of 600-bp DNA solutions having artificial sequences. Anal Bioanal Chem 2019; 411:6091-6100. [PMID: 31289897 DOI: 10.1007/s00216-019-01992-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 06/03/2019] [Accepted: 06/18/2019] [Indexed: 10/26/2022]
Abstract
Two 600-bp DNA solutions (DNA600-G and DNA600-T) were developed as certified reference material, NMIJ CRM 6205-a, for the validation of DNA quantification methods. Both DNA600-G and DNA600-T are ideal as "spike-in control" because these materials have artificial nucleic acid sequences. The certified values were determined as the mass concentration of total DNA (whole DNA materials in sample solution regardless of sequence) at 25 °C by formic acid hydrolysis/liquid chromatography-isotope dilution mass spectrometry (LC-IDMS) and inductively coupled plasma-mass spectrometry (ICP-MS) based on the amount of phosphorus. DNAs were synthesized, and plasmids including the synthesized DNAs were cloned into Escherichia coli DH5α. The amplified plasmids were digested with a restriction enzyme and highly purified. Then, the purified DNAs were diluted with water to approximately 1 ng/μL. By using the CRM-validated methods in fields where DNA quantification is required, the reliability of DNA quantification could be improved. Graphical abstract.
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17
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Chu A, Nguyen D, Talathi SS, Wilson AC, Ye C, Smith WL, Kaplan AD, Duoss EB, Stolaroff JK, Giera B. Automated detection and sorting of microencapsulation via machine learning. LAB ON A CHIP 2019; 19:1808-1817. [PMID: 30982831 DOI: 10.1039/c8lc01394b] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Microfluidic-based microencapsulation requires significant oversight to prevent material and quality loss due to sporadic disruptions in fluid flow that routinely arise. State-of-the-art microcapsule production is laborious and relies on experts to monitor the process, e.g. through a microscope. Unnoticed defects diminish the quality of collected material and/or may cause irreversible clogging. To address these issues, we developed an automated monitoring and sorting system that operates on consumer-grade hardware in real-time. Using human-labeled microscope images acquired during typical operation, we train a convolutional neural network that assesses microencapsulation. Based on output from the machine learning algorithm, an integrated valving system collects desirable microcapsules or diverts waste material accordingly. Although the system notifies operators to make necessary adjustments to restore microencapsulation, we can extend the system to automate corrections. Since microfluidic-based production platforms customarily collect image and sensor data, machine learning can help to scale up and improve microfluidic techniques beyond microencapsulation.
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Affiliation(s)
- Albert Chu
- Lawrence Livermore National Laboratory, Livermore, California 94550, USA.
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18
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Chemiresistive DNA hybridization sensor with electrospun nanofibers: A method to minimize inter-device variability. Biosens Bioelectron 2019; 133:24-31. [DOI: 10.1016/j.bios.2019.03.031] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 03/02/2019] [Accepted: 03/17/2019] [Indexed: 02/08/2023]
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19
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Choi Y, Schmidt C, Tinnefeld P, Bald I, Rödiger S. A new reporter design based on DNA origami nanostructures for quantification of short oligonucleotides using microbeads. Sci Rep 2019; 9:4769. [PMID: 30886341 PMCID: PMC6423227 DOI: 10.1038/s41598-019-41136-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 02/28/2019] [Indexed: 01/05/2023] Open
Abstract
The DNA origami technique has great potential for the development of brighter and more sensitive reporters for fluorescence based detection schemes such as a microbead-based assay in diagnostic applications. The nanostructures can be programmed to include multiple dye molecules to enhance the measured signal as well as multiple probe strands to increase the binding strength of the target oligonucleotide to these nanostructures. Here we present a proof-of-concept study to quantify short oligonucleotides by developing a novel DNA origami based reporter system, combined with planar microbead assays. Analysis of the assays using the VideoScan digital imaging platform showed DNA origami to be a more suitable reporter candidate for quantification of the target oligonucleotides at lower concentrations than a conventional reporter that consists of one dye molecule attached to a single stranded DNA. Efforts have been made to conduct multiplexed analysis of different targets as well as to enhance fluorescence signals obtained from the reporters. We therefore believe that the quantification of short oligonucleotides that exist in low copy numbers is achieved in a better way with the DNA origami nanostructures as reporters.
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Affiliation(s)
- Youngeun Choi
- University of Potsdam, Department of Chemistry, Physical Chemistry, 14476, Potsdam, Germany.,BAM Federal Institute for Materials Research and Testing, 12489, Berlin, Germany
| | - Carsten Schmidt
- Brandenbrug University of Technology Cottbus-Senftenberg, Institute of Biotechnology, 01968, Senftenberg, Germany
| | - Philip Tinnefeld
- Department Chemie and Center for NanoScience, Ludwig-Maximilians-Universitaet Muenchen, Butenandtstr, 5-13 Haus E, 81377, Muenchen, Germany
| | - Ilko Bald
- University of Potsdam, Department of Chemistry, Physical Chemistry, 14476, Potsdam, Germany. .,BAM Federal Institute for Materials Research and Testing, 12489, Berlin, Germany.
| | - Stefan Rödiger
- Brandenbrug University of Technology Cottbus-Senftenberg, Institute of Biotechnology, 01968, Senftenberg, Germany.
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20
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Conformation and Dynamics of Long-Chain End-Tethered Polymers in Microchannels. Polymers (Basel) 2019; 11:polym11030488. [PMID: 30960472 PMCID: PMC6473708 DOI: 10.3390/polym11030488] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 02/25/2019] [Accepted: 02/27/2019] [Indexed: 12/14/2022] Open
Abstract
Polyelectrolytes constitute an important group of materials, used for such different purposes as the stabilization of emulsions and suspensions or oil recovery. They are also studied and utilized in the field of microfluidics. With respect to the latter, a part of the interest in polyelectrolytes inside microchannels stems from genetic analysis, considering that deoxyribonucleic acid (DNA) molecules are polyelectrolytes. This review summarizes the single-molecule experimental and molecular dynamics simulation-based studies of end-tethered polyelectrolytes, especially addressing their relaxation dynamics and deformation characteristics under various external forces in micro-confined environments. In most of these studies, DNA is considered as a model polyelectrolyte. Apart from summarizing the results obtained in that area, the most important experimental and simulation techniques are explained.
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21
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Xiong Q, Lim AE, Lim Y, Lam YC, Duan H. Dynamic Magnetic Nanomixers for Improved Microarray Assays by Eliminating Diffusion Limitation. Adv Healthc Mater 2019; 8:e1801022. [PMID: 30511823 DOI: 10.1002/adhm.201801022] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Revised: 10/21/2018] [Indexed: 12/12/2022]
Abstract
Microarrays are widely used in high-throughput analysis of DNA, protein, and small molecules. However, the majority of microarray assays need improved assay speed and sensitivity due to the slow molecular diffusion from bulk solutions to probe surfaces. Here, a new class of magnetic nanomixers in DNA and protein microarray assays is reported to eliminate the diffusion constraint through dynamic mixing. It is demonstrated that the dynamic nanomixers can improve the assay kinetics at least by a factor of 4 and 2 for DNA and protein microarray assays, respectively. By using the dynamic nanomixers, the sensitivities of detecting Escherichia coli O157:H7 DNA and prostate specific antigen increase by more than four-fold. The dynamic mixing also greatly reduces the spot-to-spot variation to below 10% across a broad concentration range, providing more accurate assay results. In comparison with existing methods, this magnetic nanomixer-based approach offers rapid turnaround, improved sensitivity, good accuracy, low cost, simple operation, and excellent compatibility with commercial microarrays.
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Affiliation(s)
- Qirong Xiong
- School of Chemical and Biomedical EngineeringNanyang Technological University 70 Nanyang Drive Singapore 637457 Singapore
| | - An Eng Lim
- School of Mechanical and Aerospace EngineeringNanyang Technological University 50 Nanyang Avenue Singapore 639798 Singapore
| | - Yun Lim
- School of Chemical and Biomedical EngineeringNanyang Technological University 70 Nanyang Drive Singapore 637457 Singapore
| | - Yee Cheong Lam
- School of Mechanical and Aerospace EngineeringNanyang Technological University 50 Nanyang Avenue Singapore 639798 Singapore
| | - Hongwei Duan
- School of Chemical and Biomedical EngineeringNanyang Technological University 70 Nanyang Drive Singapore 637457 Singapore
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22
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Huang SH, Chang YS, Juang JMJ, Chang KW, Tsai MH, Lu TP, Lai LC, Chuang EY, Huang NT. An automated microfluidic DNA microarray platform for genetic variant detection in inherited arrhythmic diseases. Analyst 2019; 143:1367-1377. [PMID: 29423467 DOI: 10.1039/c7an01648d] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In this study, we developed an automated microfluidic DNA microarray (AMDM) platform for point mutation detection of genetic variants in inherited arrhythmic diseases. The platform allows for automated and programmable reagent sequencing under precise conditions of hybridization flow and temperature control. It is composed of a commercial microfluidic control system, a microfluidic microarray device, and a temperature control unit. The automated and rapid hybridization process can be performed in the AMDM platform using Cy3 labeled oligonucleotide exons of SCN5A genetic DNA, which produces proteins associated with sodium channels abundant in the heart (cardiac) muscle cells. We then introduce a graphene oxide (GO)-assisted DNA microarray hybridization protocol to enable point mutation detection. In this protocol, a GO solution is added after the staining step to quench dyes bound to single-stranded DNA or non-perfectly matched DNA, which can improve point mutation specificity. As proof-of-concept we extracted the wild-type and mutant of exon 12 and exon 17 of SCN5A genetic DNA from patients with long QT syndrome or Brugada syndrome by touchdown PCR and performed a successful point mutation discrimination in the AMDM platform. Overall, the AMDM platform can greatly reduce laborious and time-consuming hybridization steps and prevent potential contamination. Furthermore, by introducing the reciprocating flow into the microchannel during the hybridization process, the total assay time can be reduced to 3 hours, which is 6 times faster than the conventional DNA microarray. Given the automatic assay operation, shorter assay time, and high point mutation discrimination, we believe that the AMDM platform has potential for low-cost, rapid and sensitive genetic testing in a simple and user-friendly manner, which may benefit gene screening in medical practice.
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Affiliation(s)
- Shu-Hong Huang
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, Taiwan.
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23
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Lee DJ, Mai J, Huang TJ. Microfluidic approaches for cell-based molecular diagnosis. BIOMICROFLUIDICS 2018; 12:051501. [PMID: 30271515 PMCID: PMC6138474 DOI: 10.1063/1.5030891] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 08/27/2018] [Indexed: 06/08/2023]
Abstract
The search for next-generation biomarkers has enabled cell-based diagnostics in a number of disciplines ranging from oncology to pharmacogenetics. However, cell-based diagnostics are still far from clinical reality due to the complex assays and associated protocols which typically require cell isolation, lysis, DNA extraction, amplification, and detection steps. Leveraging recent advances in microfluidics, many biochemical assays have been translated onto microfluidic platforms. We have compared and summarized recent advances in modular approaches toward the realization of fully-integrated, cell-based molecular diagnostics for clinical and point-of-care applications.
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Affiliation(s)
- Dong Jun Lee
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, USA
| | - John Mai
- Alfred E. Mann Institute for Biomedical Engineering, University of Southern California, Los Angeles, California 90089, USA
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24
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Seder I, Kim DM, Hwang SH, Sung H, Kim DE, Kim SJ. Microfluidic chip with movable layers for the manipulation of biochemicals. LAB ON A CHIP 2018; 18:1867-1874. [PMID: 29877550 DOI: 10.1039/c8lc00382c] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
A simple and effective platform that can conglomerate various microfluidic functions in a single chip is essential for many bioassays, especially for point-of-care testing applications. Here, a chip that exploits surface tension in solutions with movable top and bottom layers is presented, for use in fluid transport, mixing, maintaining metered volumes, and biomolecule capture and release. The chip has open chambers in vertically mobile top layers and rotationally mobile bottom layers to exploit surface tension in biochemical solutions, and implements control over fluid motion. To manipulate biomolecules, a vertically mobile tip with a permanent magnet at the top layer performs collection, transport, release, and dispersion of magnetic beads. Thus, the chip orchestrates various fluidic control functions without using on-chip valves and pumps that increase operational and structural complexity. To demonstrate its utility, the chip performs automated DNA extraction by obtaining genomic DNA from a sample containing cells. Our approach provides a useful and effective alternative to numerous platforms that use active and passive on-chip components for bioassays.
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Affiliation(s)
- Islam Seder
- Department of Mechanical Engineering, Konkuk University, Seoul, 05029, Republic of Korea.
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25
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Development of Microplatforms to Mimic the In Vivo Architecture of CNS and PNS Physiology and Their Diseases. Genes (Basel) 2018; 9:genes9060285. [PMID: 29882823 PMCID: PMC6027402 DOI: 10.3390/genes9060285] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 05/28/2018] [Accepted: 05/31/2018] [Indexed: 12/16/2022] Open
Abstract
Understanding the mechanisms that govern nervous tissues function remains a challenge. In vitro two-dimensional (2D) cell culture systems provide a simplistic platform to evaluate systematic investigations but often result in unreliable responses that cannot be translated to pathophysiological settings. Recently, microplatforms have emerged to provide a better approximation of the in vivo scenario with better control over the microenvironment, stimuli and structure. Advances in biomaterials enable the construction of three-dimensional (3D) scaffolds, which combined with microfabrication, allow enhanced biomimicry through precise control of the architecture, cell positioning, fluid flows and electrochemical stimuli. This manuscript reviews, compares and contrasts advances in nervous tissues-on-a-chip models and their applications in neural physiology and disease. Microplatforms used for neuro-glia interactions, neuromuscular junctions (NMJs), blood-brain barrier (BBB) and studies on brain cancer, metastasis and neurodegenerative diseases are addressed. Finally, we highlight challenges that can be addressed with interdisciplinary efforts to achieve a higher degree of biomimicry. Nervous tissue microplatforms provide a powerful tool that is destined to provide a better understanding of neural health and disease.
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26
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Veselinovic J, Li Z, Daggumati P, Seker E. Electrically Guided DNA Immobilization and Multiplexed DNA Detection with Nanoporous Gold Electrodes. NANOMATERIALS 2018; 8:nano8050351. [PMID: 29883441 PMCID: PMC5977365 DOI: 10.3390/nano8050351] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 05/17/2018] [Accepted: 05/18/2018] [Indexed: 12/21/2022]
Abstract
Molecular diagnostics have significantly advanced the early detection of diseases, where the electrochemical sensing of biomarkers (e.g., DNA, RNA, proteins) using multiple electrode arrays (MEAs) has shown considerable promise. Nanostructuring the electrode surface results in higher surface coverage of capture probes and more favorable orientation, as well as transport phenomena unique to nanoscale, ultimately leading to enhanced sensor performance. The central goal of this study is to investigate the influence of electrode nanostructure on electrically-guided immobilization of DNA probes for nucleic acid detection in a multiplexed format. To that end, we used nanoporous gold (np-Au) electrodes that reduced the limit of detection (LOD) for DNA targets by two orders of magnitude compared to their planar counterparts, where the LOD was further improved by an additional order of magnitude after reducing the electrode diameter. The reduced electrode diameter also made it possible to create a np-Au MEA encapsulated in a microfluidic channel. The electro-grafting reduced the necessary incubation time to immobilize DNA probes into the porous electrodes down to 10 min (25-fold reduction compared to passive immobilization) and allowed for grafting a different DNA probe sequence onto each electrode in the array. The resulting platform was successfully used for the multiplexed detection of three different biomarker genes relevant to breast cancer diagnosis.
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Affiliation(s)
- Jovana Veselinovic
- Department of Chemical Engineering, University of California-Davis, Davis, CA 95616, USA.
| | - Zidong Li
- Department of Biomedical Engineering, University of California-Davis, Davis, CA 95616, USA.
| | - Pallavi Daggumati
- Department of Electrical and Computer Engineering, University of California-Davis, Davis, CA 95616, USA.
| | - Erkin Seker
- Department of Electrical and Computer Engineering, University of California-Davis, Davis, CA 95616, USA.
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27
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Martinović T, Šrajer Gajdošik M, Josić D. Sample preparation in foodomic analyses. Electrophoresis 2018; 39:1527-1542. [DOI: 10.1002/elps.201800029] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 03/12/2018] [Accepted: 03/27/2018] [Indexed: 12/30/2022]
Affiliation(s)
| | | | - Djuro Josić
- Department of Biotechnology; University of Rijeka; Rijeka Croatia
- Department of Medicine; Brown Medical School; Brown University; Providence RI USA
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28
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Guo XL, Wei Y, Lou Q, Zhu Y, Fang Q. Manipulating Femtoliter to Picoliter Droplets by Pins for Single Cell Analysis and Quantitative Biological Assay. Anal Chem 2018; 90:5810-5817. [PMID: 29648445 DOI: 10.1021/acs.analchem.8b00343] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Herein, we developed an automated and flexible system for performing miniaturized liquid-liquid reactions and assays in the femtoliter to picoliter range, by combining the contact printing and the droplet-based microfluidics techniques. The system mainly consisted of solid pins and an oil-covered hydrophilic micropillar array chip fixed on an automated x- y- z translation stage. A novel droplet manipulation mode called "dipping-depositing-moving" (DDM) was proposed, which was based on the programmable combination of three basic operations, dipping liquids and depositing liquids with the solid pins and moving the two-dimensional oil-covered hydrophilic pillar microchip. With the DDM mode, flexible generation and manipulation of small droplets with volumes down to 179 fL could be achieved. For overcoming the scale phenomenon specially appeared in picoliter-scale droplets, we used a design of water moat to protect the femtoliter to picoliter droplets from volume loss through the cover oil during the droplet generation, manipulation, reaction and assay processes. Moreover, we also developed a precise quantitative method, quantitative droplet dilution method, to accurately measure the volumes of femtoliter to picoliter droplets. To demonstrate its feasibility and adaptability, we applied the present system in the determination of kinetics parameter for matrix metalloproteinases (MMP-9) in 1.81 pL reactors and the measurement the activity of β-galactosidase in single cells (HepG2 cells) in picoliter droplet array. The ultrasmall volumes of the droplet reactors avoided the excessive dilution to the reaction solutions and enabled the highly sensitive measurement of enzyme activity in the single cell level.
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Affiliation(s)
- Xiao-Li Guo
- Institute of Microanalytical Systems, Department of Chemistry and Innovation Center for Cell Signaling Network , Zhejiang University , Hangzhou , 310058 , China
| | - Yan Wei
- Institute of Microanalytical Systems, Department of Chemistry and Innovation Center for Cell Signaling Network , Zhejiang University , Hangzhou , 310058 , China
| | - Qi Lou
- Institute of Microanalytical Systems, Department of Chemistry and Innovation Center for Cell Signaling Network , Zhejiang University , Hangzhou , 310058 , China
| | - Ying Zhu
- Institute of Microanalytical Systems, Department of Chemistry and Innovation Center for Cell Signaling Network , Zhejiang University , Hangzhou , 310058 , China
| | - Qun Fang
- Institute of Microanalytical Systems, Department of Chemistry and Innovation Center for Cell Signaling Network , Zhejiang University , Hangzhou , 310058 , China
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29
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Campana O, Wlodkowic D. Ecotoxicology Goes on a Chip: Embracing Miniaturized Bioanalysis in Aquatic Risk Assessment. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:932-946. [PMID: 29284083 DOI: 10.1021/acs.est.7b03370] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Biological and environmental sciences are, more than ever, becoming highly dependent on technological and multidisciplinary approaches that warrant advanced analytical capabilities. Microfluidic lab-on-a-chip technologies are perhaps one the most groundbreaking offshoots of bioengineering, enabling design of an entirely new generation of bioanalytical instrumentation. They represent a unique approach to combine microscale engineering and physics with specific biological questions, providing technological advances that allow for fundamentally new capabilities in the spatiotemporal analysis of molecules, cells, tissues, and even small metazoan organisms. While these miniaturized analytical technologies experience an explosive growth worldwide, with a substantial promise of a direct impact on biosciences, it seems that lab-on-a-chip systems have so far escaped the attention of aquatic ecotoxicologists. In this Critical Review, potential applications of the currently existing and emerging chip-based technologies for aquatic ecotoxicology and water quality monitoring are highlighted. We also offer suggestions on how aquatic ecotoxicology can benefit from adoption of microfluidic lab-on-a-chip devices for accelerated bioanalysis.
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Affiliation(s)
- Olivia Campana
- Instituto de Ciencias Marinas de Andalucía, CSIC , Puerto Real, 11519, Spain
| | - Donald Wlodkowic
- School of Science, RMIT University , Melbourne, Victoria 3083, Australia
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30
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Abstract
Nucleic acid aptamers have tremendous potential as molecular recognition elements in biomedical targeting, analytical arrays, and self-signaling sensors. However, practical limitations and inefficiencies in the process of selecting novel aptamers (SELEX) have hampered widespread adoption of aptamer technologies. Many factors have recently contributed to more effective aptamer screening, but no influence has done more to increase the efficiency, scale, and automation of aptamer selection than that of new microfluidic SELEX techniques. This review introduces aptamers as a powerful chemical and biological tool, briefly highlights traditional SELEX techniques and their limitations, covers in detail the recent advancements in microfluidic methods of aptamer selection and characterization, and suggests possible future directions of the field.
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Affiliation(s)
- Sean K Dembowski
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA.
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31
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Li R, Zhang X, Lv X, Geng L, Li Y, Qin K, Deng Y. Microvalve controlled multi-functional microfluidic chip for divisional cell co-culture. Anal Biochem 2017; 539:48-53. [DOI: 10.1016/j.ab.2017.10.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 10/09/2017] [Accepted: 10/10/2017] [Indexed: 12/22/2022]
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32
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Knob R, Nelson DB, Robison RA, Woolley AT. Sequence-specific DNA solid-phase extraction in an on-chip monolith: Towards detection of antibiotic resistance genes. J Chromatogr A 2017; 1523:309-315. [PMID: 28734608 PMCID: PMC5675797 DOI: 10.1016/j.chroma.2017.07.028] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 07/05/2017] [Accepted: 07/09/2017] [Indexed: 12/13/2022]
Abstract
Antibiotic resistance of bacteria is a growing problem and presents a challenge for prompt treatment in patients with sepsis. Currently used methods rely on culturing or amplification; however, these steps are either time consuming or suffer from interference issues. A microfluidic device was made from black polypropylene, with a monolithic column modified with a capture oligonucleotide for sequence selective solid-phase extraction of a complementary target from a lysate sample. Porous properties of the monolith allow flow and hybridization of a target complementary to the probe immobilized on the column surface. Good flow-through properties enable extraction of a 100μL sample and elution of target DNA in 12min total time. Using a fluorescently labeled target oligonucleotide related to Verona Integron-Mediated Metallo-β-lactamase it was possible to extract and detect a 1pM sample with 83% recovery. Temperature-mediated elution by heating above the duplex melting point provides a clean extract without any agents that interfere with base pairing, allowing various labeling methods or further downstream processing of the eluent. Further integration of this extraction module with a system for isolation and lysis of bacteria from blood, as well as combining with single-molecule detection should allow rapid determination of antibiotic resistance.
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Affiliation(s)
- Radim Knob
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, USA
| | - Daniel B Nelson
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA
| | - Richard A Robison
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA
| | - Adam T Woolley
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, USA.
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Rizzi G, Lee JR, Guldberg P, Dufva M, Wang SX, Hansen MF. Denaturation strategies for detection of double stranded PCR products on GMR magnetic biosensor array. Biosens Bioelectron 2017; 93:155-160. [DOI: 10.1016/j.bios.2016.09.031] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 09/08/2016] [Accepted: 09/10/2016] [Indexed: 01/08/2023]
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34
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Wang R, Wang Y, Zhang D, Si G, Zhu L, Du L, Kou S, Badugu R, Rosenfeld M, Lin J, Wang P, Ming H, Yuan XL, Lakowicz JR. Diffraction-Free Bloch Surface Waves. ACS NANO 2017; 11:5383-5390. [PMID: 28505412 PMCID: PMC5777330 DOI: 10.1021/acsnano.7b02358] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Here, we demonstrate a diffraction-free Bloch surface wave sustained on all-dielectric multilayers that does not diffract after being passed through three obstacles or across a single mode fiber. It can propagate in a straight line for distances longer than 110 μm at a wavelength of 633 nm and could be applied as an in-plane optical virtual probe both in air and in an aqueous environment. Its ability to be used in water, its long diffraction-free distance, and its tolerance to multiple obstacles make this wave ideal for certain applications in areas such as the biological sciences, where many measurements are made on glass surfaces or for which an aqueous environment is required, and for high-speed interconnections between chips, where low loss is necessary.
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Affiliation(s)
- Ruxue Wang
- Department of Optics and Optical Engineering, University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - Yong Wang
- Department of Optics and Optical Engineering, University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - Douguo Zhang
- Department of Optics and Optical Engineering, University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - Guangyuan Si
- School of Engineering, RMIT University, Melbourne, VIC 3001, Australia
| | - Liangfu Zhu
- Department of Optics and Optical Engineering, University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - Luping Du
- Nanophotonics Research Centre, Shenzhen University & Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Shanshan Kou
- Department of Chemistry and Physics, La Trobe Institute for Molecular Sciences (LIMS), La Trobe University, Melbourne, Victoria 3086, Australia
| | - Ramachandram Badugu
- Center for Fluorescence Spectroscopy, Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, United States
| | - Mary Rosenfeld
- Center for Fluorescence Spectroscopy, Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, United States
| | - Jiao Lin
- School of Engineering, RMIT University, Melbourne, VIC 3001, Australia
- Nanophotonics Research Centre, Shenzhen University & Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Pei Wang
- Department of Optics and Optical Engineering, University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - Hai Ming
- Department of Optics and Optical Engineering, University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - Xiaocong Larry Yuan
- Nanophotonics Research Centre, Shenzhen University & Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Joseph R. Lakowicz
- Center for Fluorescence Spectroscopy, Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, United States
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Li C, Jia Z, Li P, Wen H, Lv G, Huang X. Parallel Detection of Refractive Index Changes in a Porous Silicon Microarray Based on Digital Images. SENSORS 2017; 17:s17040750. [PMID: 28368332 PMCID: PMC5421710 DOI: 10.3390/s17040750] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2017] [Revised: 03/30/2017] [Accepted: 03/31/2017] [Indexed: 11/16/2022]
Abstract
A new technique for the refractive index change with high-sensitivity measurements was proposed by the digital image of porous silicon (PSi) microarray utilization in this paper. Under the irradiation of a He-Ne laser, the surface images of the PSi array cells with the microcavity structure were obtained by the digital imaging equipment, whereas the refractive index change of each array cells was detected by calculating the average gray value of the image and the refractive index change measurement sensitivity was 10-4. This technique could be utilized in the label-free and parallel detection of refraction index changes induced by a biological reaction in the microarray or the chip.
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Affiliation(s)
- Chuanxi Li
- School of Physical Science and Technology, Xinjiang University, Urumqi 830046, China.
| | - Zhenhong Jia
- College of Information Science and Engineering, Xinjiang University, Urumqi 830046, China.
| | - Peng Li
- School of Physical Science and Technology, Xinjiang University, Urumqi 830046, China.
| | - Hao Wen
- The First Affiliated Hospital of Xinjiang Medical University, Urumqi 830054, China.
| | - Guodong Lv
- The First Affiliated Hospital of Xinjiang Medical University, Urumqi 830054, China.
| | - Xiaohui Huang
- College of Information Science and Engineering, Xinjiang University, Urumqi 830046, China.
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36
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Tang AHL, Yeung P, Chan GCF, Chan BP, Wong KKY, Tsia KK. Time-stretch microscopy on a DVD for high-throughput imaging cell-based assay. BIOMEDICAL OPTICS EXPRESS 2017; 8:640-652. [PMID: 28270973 PMCID: PMC5330545 DOI: 10.1364/boe.8.000640] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 12/21/2016] [Accepted: 12/25/2016] [Indexed: 06/06/2023]
Abstract
Cell-based assay based on time-stretch imaging is recognized to be well-suited for high-throughput phenotypic screening. However, this ultrafast imaging technique has primarily been limited to suspension-cell assay, leaving a wide range of solid-substrate assay formats uncharted. Moreover, time-stretch imaging is generally restricted to intrinsic biophysical phenotyping, but lacks the biomolecular signatures of the cells. To address these challenges, we develop a spinning time-stretch imaging assay platform based on the functionalized digital versatile disc (DVD). We demonstrate that adherent cell culture and biochemically-specific cell-capture can now be assayed with time-stretch microscopy, thanks to the high-speed DVD spinning motion that naturally enables on-the-fly cellular imaging at an ultrafast line-scan rate of >10MHz. As scanning the whole DVD at such a high speed enables ultra-large field-of-view imaging, it could be favorable for scaling both the assay throughput and content as demanded in many applications, e.g. drug discovery, and rare cancer cell screening.
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Affiliation(s)
- Anson H. L. Tang
- Department of Electrical and Electronic Engineering, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - P. Yeung
- Department of Mechanical Engineering, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Godfrey C. F. Chan
- Department of Paediatrics & Adolescent Medicine, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Barbara P. Chan
- Department of Mechanical Engineering, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Kenneth K. Y. Wong
- Department of Electrical and Electronic Engineering, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Kevin K. Tsia
- Department of Electrical and Electronic Engineering, The University of Hong Kong, Pokfulam, Hong Kong, China
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37
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Abstract
The development of microfabricated devices that will provide high-throughput quantitative data and high resolution in a fast, repeatable and reproducible manner is essential for plant biology research.
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Affiliation(s)
- Meltem Elitaş
- Department of Mechatronics
- Faculty of Engineering and Natural Sciences
- Sabanci University
- 34956, Istanbul
- Turkey
| | - Meral Yüce
- Nanotechnology Research and Application Centre
- Sabanci University
- 34956, Istanbul
- Turkey
| | - Hikmet Budak
- Department of Molecular Biology
- Genetics and Bioengineering
- Faculty of Engineering and Natural Sciences
- Sabanci University
- 34956, Istanbul
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38
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39
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Ostromohov N, Bercovici M, Kaigala GV. Delivery of minimally dispersed liquid interfaces for sequential surface chemistry. LAB ON A CHIP 2016; 16:3015-23. [PMID: 27354032 DOI: 10.1039/c6lc00473c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
We present a method for sequential delivery of reagents to a reaction site with minimal dispersion of their interfaces. Using segmented flow to encapsulate the reagents as droplets, the dispersion between reagent plugs remains confined in a limited volume, while being transmitted to the reaction surface. In close proximity to the target surface, we use a passive array of microstructures for removal of the oil phase such that the original reagent sequence is reconstructed, and only the aqueous phase reaches the reaction surface. We provide a detailed analysis of the conditions under which the method can be applied and demonstrate maintaining a transition time of 560 ms between reagents transported to a reaction site over a distance of 60 cm. We implemented the method using a vertical microfluidic probe on an open surface, allowing contact-free interaction with biological samples, and demonstrated two examples of assays implemented using the method: measurements of receptor-ligand reaction kinetics and of the fluorescence response of immobilized GFP to local variations in pH. We believe that the method can be useful for studying the dynamic response of cells and proteins to various stimuli, as well as for highly automated multi-step assays.
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Affiliation(s)
- N Ostromohov
- Faculty of Mechanical Engineering, Technion - Israel Institute of Technology, Haifa 3200003, Israel. and IBM Research-Zurich, Saeumerstrasse 4, CH-8803 Rueschlikon, Switzerland.
| | - M Bercovici
- Faculty of Mechanical Engineering, Technion - Israel Institute of Technology, Haifa 3200003, Israel.
| | - G V Kaigala
- IBM Research-Zurich, Saeumerstrasse 4, CH-8803 Rueschlikon, Switzerland.
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40
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Ramirez LMS, He M, Mailloux S, George J, Wang J. Facile and High-Throughput Synthesis of Functional Microparticles with Quick Response Codes. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2016; 12:3259-3269. [PMID: 27151936 DOI: 10.1002/smll.201600456] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Revised: 04/04/2016] [Indexed: 06/05/2023]
Abstract
Encoded microparticles are high demand in multiplexed assays and labeling. However, the current methods for the synthesis and coding of microparticles either lack robustness and reliability, or possess limited coding capacity. Here, a massive coding of dissociated elements (MiCODE) technology based on innovation of a chemically reactive off-stoichimetry thiol-allyl photocurable polymer and standard lithography to produce a large number of quick response (QR) code microparticles is introduced. The coding process is performed by photobleaching the QR code patterns on microparticles when fluorophores are incorporated into the prepolymer formulation. The fabricated encoded microparticles can be released from a substrate without changing their features. Excess thiol functionality on the microparticle surface allows for grafting of amine groups and further DNA probes. A multiplexed assay is demonstrated using the DNA-grafted QR code microparticles. The MiCODE technology is further characterized by showing the incorporation of BODIPY-maleimide (BDP-M) and Nile Red fluorophores for coding and the use of microcontact printing for immobilizing DNA probes on microparticle surfaces. This versatile technology leverages mature lithography facilities for fabrication and thus is amenable to scale-up in the future, with potential applications in bioassays and in labeling consumer products.
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Affiliation(s)
- Lisa Marie S Ramirez
- Multiplex Biotechnology Laboratory, Department of Chemistry, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - Muhan He
- Multiplex Biotechnology Laboratory, Department of Chemistry, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - Shay Mailloux
- Multiplex Biotechnology Laboratory, Department of Chemistry, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - Justin George
- Multiplex Biotechnology Laboratory, Department of Chemistry, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - Jun Wang
- Multiplex Biotechnology Laboratory, Department of Chemistry, University at Albany, State University of New York, Albany, NY, 12222, USA
- Cancer Research Center, University at Albany, State University of New York, Rensselaer, NY, 12144, USA
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41
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Haisch C. Raman-based microarray readout: a review. Anal Bioanal Chem 2016; 408:4535-45. [PMID: 26973235 DOI: 10.1007/s00216-016-9444-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Revised: 02/16/2016] [Accepted: 02/23/2016] [Indexed: 11/26/2022]
Abstract
For a quarter of a century, microarrays have been part of the routine analytical toolbox. Label-based fluorescence detection is still the commonest optical readout strategy. Since the 1990s, a continuously increasing number of label-based as well as label-free experiments on Raman-based microarray readout concepts have been reported. This review summarizes the possible concepts and methods and their advantages and challenges. A common label-based strategy is based on the binding of selective receptors as well as Raman reporter molecules to plasmonic nanoparticles in a sandwich immunoassay, which results in surface-enhanced Raman scattering signals of the reporter molecule. Alternatively, capture of the analytes can be performed by receptors on a microarray surface. Addition of plasmonic nanoparticles again leads to a surface-enhanced Raman scattering signal, not of a label but directly of the analyte. This approach is mostly proposed for bacteria and cell detection. However, although many promising readout strategies have been discussed in numerous publications, rarely have any of them made the step from proof of concept to a practical application, let alone routine use. Graphical Abstract Possible realization of a SERS (Surface-Enhanced Raman Scattering) system for microarray readout.
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Affiliation(s)
- Christoph Haisch
- Technische Universität München, Marchioninistrasse 17, 81377, Munich, Germany.
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42
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Li J, Zrazhevskiy P, Gao X. Eliminating Size-Associated Diffusion Constraints for Rapid On-Surface Bioassays with Nanoparticle Probes. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2016; 12:1035-1043. [PMID: 26749053 PMCID: PMC4815929 DOI: 10.1002/smll.201503101] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 11/30/2015] [Indexed: 05/21/2023]
Abstract
Nanoparticle probes enable implementation of advanced on-surface assay formats, but impose often underappreciated size-associated constraints, in particular on assay kinetics and sensitivity. The present study highlights substantially slower diffusion-limited assay kinetics due to the rapid development of a nanoprobe depletion layer next to the surface, which static incubation and mixing of bulk solution employed in conventional assay setups often fail to disrupt. In contrast, cyclic solution draining and replenishing yields reaction-limited assay kinetics irrespective of the probe size. Using common surface bioassays, enzyme-linked immunosorbent assays and immunofluorescence, this study shows that this conceptually distinct approach effectively "erases" size-dependent diffusion constraints, providing a straightforward route to rapid on-surface bioassays employing bulky probes and procedures involving multiple labeling cycles, such as multicycle single-cell molecular profiling. For proof-of-concept, the study demonstrates that the assay time can be shortened from hours to minutes with the same probe concentration and, at a typical incubation time, comparable target labeling can be achieved with up to eight times lower nanoprobe concentration. The findings are expected to enable realization of novel assay formats and stimulate development of rapid on-surface bioassays with nanoparticle probes.
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Affiliation(s)
- Junwei Li
- Department of Bioengineering, University of Washington, Seattle, WA, 98195, USA
| | - Pavel Zrazhevskiy
- Department of Bioengineering, University of Washington, Seattle, WA, 98195, USA
| | - Xiaohu Gao
- Department of Bioengineering, University of Washington, Seattle, WA, 98195, USA
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43
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Abstract
The DNA microarray technology is currently a useful biomedical tool which has been developed for a variety of diagnostic applications. However, the development pathway has not been smooth and the technology has faced some challenges. The reliability of the microarray data and also the clinical utility of the results in the early days were criticized. These criticisms added to the severe competition from other techniques, such as next-generation sequencing (NGS), impacting the growth of microarray-based tests in the molecular diagnostic market.Thanks to the advances in the underlying technologies as well as the tremendous effort offered by the research community and commercial vendors, these challenges have mostly been addressed. Nowadays, the microarray platform has achieved sufficient standardization and method validation as well as efficient probe printing, liquid handling and signal visualization. Integration of various steps of the microarray assay into a harmonized and miniaturized handheld lab-on-a-chip (LOC) device has been a goal for the microarray community. In this respect, notable progress has been achieved in coupling the DNA microarray with the liquid manipulation microsystem as well as the supporting subsystem that will generate the stand-alone LOC device.In this chapter, we discuss the major challenges that microarray technology has faced in its almost two decades of development and also describe the solutions to overcome the challenges. In addition, we review the advancements of the technology, especially the progress toward developing the LOC devices for DNA diagnostic applications.
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Affiliation(s)
| | - Abootaleb Sedighi
- Department of Chemistry, Simon Fraser University, Burnaby, BC, Canada, V5A 1S6
| | - Paul C H Li
- Department of Chemistry, Simon Fraser University, Burnaby, BC, Canada, V5A 1S6.
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44
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Microfluidic solvent extraction, stripping, and phase disengagement for high-value platinum chloride solutions. Chem Eng Sci 2015. [DOI: 10.1016/j.ces.2015.08.055] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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45
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Holden MT, Carter MCD, Wu CH, Wolfer J, Codner E, Sussman MR, Lynn DM, Smith LM. Photolithographic Synthesis of High-Density DNA and RNA Arrays on Flexible, Transparent, and Easily Subdivided Plastic Substrates. Anal Chem 2015; 87:11420-8. [PMID: 26494264 PMCID: PMC4945104 DOI: 10.1021/acs.analchem.5b02893] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The photolithographic fabrication of high-density DNA and RNA arrays on flexible and transparent plastic substrates is reported. The substrates are thin sheets of poly(ethylene terephthalate) (PET) coated with cross-linked polymer multilayers that present hydroxyl groups suitable for conventional phosphoramidite-based nucleic acid synthesis. We demonstrate that by modifying array synthesis procedures to accommodate the physical and chemical properties of these materials, it is possible to synthesize plastic-backed oligonucleotide arrays with feature sizes as small as 14 μm × 14 μm and feature densities in excess of 125 000/cm(2), similar to specifications attainable using rigid substrates such as glass or glassy carbon. These plastic-backed arrays are tolerant to a wide range of hybridization temperatures, and improved synthetic procedures are described that enable the fabrication of arrays with sequences up to 50 nucleotides in length. These arrays hybridize with S/N ratios comparable to those fabricated on otherwise identical arrays prepared on glass or glassy carbon. This platform supports the enzymatic synthesis of RNA arrays and proof-of-concept experiments are presented showing that the arrays can be readily subdivided into smaller arrays (or "millichips") using common laboratory-scale laser cutting tools. These results expand the utility of oligonucleotide arrays fabricated on plastic substrates and open the door to new applications for these important bioanalytical tools.
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Affiliation(s)
- Matthew T. Holden
- Department of Chemistry, University of Wisconsin - Madison, WI, 53706, USA
| | | | - Cheng-Hsien Wu
- Department of Chemistry, University of Wisconsin - Madison, WI, 53706, USA
| | - Jamison Wolfer
- Biotechnology Center, University of Wisconsin - Madison, WI, 53706, USA
- Department of Biochemistry, University of Wisconsin - Madison, WI, 53706, USA
- Genome Center of Wisconsin, University of Wisconsin - Madison, WI, 53706, USA
| | - Eric Codner
- Department of Chemical and Biological Engineering, University of Wisconsin - Madison, WI, 53706, USA
| | - Michael R. Sussman
- Biotechnology Center, University of Wisconsin - Madison, WI, 53706, USA
- Department of Biochemistry, University of Wisconsin - Madison, WI, 53706, USA
- Genome Center of Wisconsin, University of Wisconsin - Madison, WI, 53706, USA
| | - David M. Lynn
- Department of Chemistry, University of Wisconsin - Madison, WI, 53706, USA
- Department of Chemical and Biological Engineering, University of Wisconsin - Madison, WI, 53706, USA
| | - Lloyd M. Smith
- Department of Chemistry, University of Wisconsin - Madison, WI, 53706, USA
- Biotechnology Center, University of Wisconsin - Madison, WI, 53706, USA
- Genome Center of Wisconsin, University of Wisconsin - Madison, WI, 53706, USA
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46
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Kim J, Bae S, Song S, Chung K, Kwon S. Fiber composite slices for multiplexed immunoassays. BIOMICROFLUIDICS 2015; 9:044109. [PMID: 26339310 PMCID: PMC4522008 DOI: 10.1063/1.4927590] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 07/17/2015] [Indexed: 05/11/2023]
Abstract
Fabrication methods for the development of multiplexed immunoassay platforms primarily depend on the individual functionalization of reaction chambers to achieve a heterogeneous reacting substrate composition, which increases the overall manufacturing time and cost. Here, we describe a new type of low-cost fabrication method for a scalable immunoassay platform based on cotton threads. The manufacturing process involves the fabrication of functionalized fibers and the arrangement of these fibers into a bundle; this bundle is then sectioned to make microarray-like particles with a predefined surface architecture. With these sections, composed of heterogeneous thread fragments with different types of antibodies, we demonstrated quantitative and 7-plex immunoassays. We expect that this methodology will prove to be a versatile, low-cost, and highly scalable method for the fabrication of multiplexed bioassay platforms.
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Affiliation(s)
- Jiyun Kim
- Nano Systems Institute, Seoul National University , Seoul 151-744, South Korea
| | | | | | - Keumsim Chung
- QuantaMatrix Inc., Se oul National University , Seoul 151-744, South Korea
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47
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Tseng WC, Hsu KC, Shiea CS, Huang YL. Recent trends in nanomaterial-based microanalytical systems for the speciation of trace elements: A critical review. Anal Chim Acta 2015; 884:1-18. [DOI: 10.1016/j.aca.2015.02.041] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 02/11/2015] [Accepted: 02/16/2015] [Indexed: 01/05/2023]
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48
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Aramesh M, Shimoni O, Fox K, Karle TJ, Lohrmann A, Ostrikov K, Prawer S, Cervenka J. Ultra-high-density 3D DNA arrays within nanoporous biocompatible membranes for single-molecule-level detection and purification of circulating nucleic acids. NANOSCALE 2015; 7:5998-6006. [PMID: 25744416 DOI: 10.1039/c4nr07351g] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Extracellular nucleic acids freely circulating in blood and other physiologic fluids are important biomarkers for non-invasive diagnostics and early detection of cancer and other diseases, yet difficult to detect because they exist in very low concentrations and large volumes. Here we demonstrate a new broad-range sensor platform for ultrasensitive and selective detection of circulating DNA down to the single-molecule level. The biosensor is based on a chemically functionalized nanoporous diamond-like carbon (DLC) coated alumina membrane. The few nanometer-thick, yet perfect and continuous DLC-coating confers the chemical stability and biocompatibility of the sensor, allowing its direct application in biological conditions. The selective detection is based on complementary hybridization of a fluorescently-tagged circulating cancer oncomarker (a 21-mer nucleic acid) with covalently immobilized DNA on the surface of the membrane. The captured DNAs are detected in the nanoporous structure of the sensor using confocal scanning laser microscopy. The flow-through membrane sensor demonstrates broad-range sensitivity, spanning from 10(15) molecules per cm(2) down to single molecules, which is several orders of magnitude improvement compared to the flat DNA microarrays. Our study suggests that these flow-through type nanoporous sensors represent a new powerful platform for large volume sampling and ultrasensitive detection of different chemical biomarkers.
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Affiliation(s)
- M Aramesh
- School of Physics, The University of Melbourne, Melbourne, Victoria 3010, Australia.
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49
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Xu Y, Wang X. Fluid and cell behaviors along a 3D printed alginate/gelatin/fibrin channel. Biotechnol Bioeng 2015; 112:1683-95. [PMID: 25727058 DOI: 10.1002/bit.25579] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 02/17/2015] [Indexed: 02/06/2023]
Abstract
Three-dimensional (3D) cell manipulation is available with the integration of microfluidic technology and rapid prototyping techniques. High-Fidelity (Hi-Fi) constructs hold enormous therapeutic potential for organ manufacturing and regenerative medicine. In the present paper we introduced a quasi-three-dimensional (Q3D) model with parallel biocompatible alginate/gelatin/fibrin hurdles. The behaviors of fluids and cells along the microfluidic channels with various widths were studied. Cells inside the newly designed microfluidic channels attached and grew well. Morphological changes of adipose-derived stem cells (ADSCs) in both two-dimensional (2D) and 3D milieu were found on the printed constructs. Endothelialization occurred with the co-cultures of ADSCs and hepatocytes. This study provides insights into the interactions among fluids, cells and biomaterials, the behaviors of fluids and cells along the microfluidic channels, and the applications of Q3D techniques.
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Affiliation(s)
- Yufan Xu
- Department of Mechanical Engineering, Key Laboratory for Advanced Materials Processing Technology, Ministry of Education & Center of Organ Manufacturing, Tsinghua University, Beijing, 100084, P.R. China
| | - Xiaohong Wang
- Department of Mechanical Engineering, Key Laboratory for Advanced Materials Processing Technology, Ministry of Education & Center of Organ Manufacturing, Tsinghua University, Beijing, 100084, P.R. China. .,State Key Laboratory of Materials Processing and Die & Mould Technology, Huazhong University of Science and Technology, Wuhan, 430074, P.R. China.
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Wang S, Sun Y, Gan W, Liu Y, Xiang G, Wang D, Wang L, Cheng J, Liu P. An automated microfluidic system for single-stranded DNA preparation and magnetic bead-based microarray analysis. BIOMICROFLUIDICS 2015; 9:024102. [PMID: 25825617 PMCID: PMC4352165 DOI: 10.1063/1.4914024] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 02/18/2015] [Indexed: 05/25/2023]
Abstract
We present an integrated microfluidic device capable of performing single-stranded DNA (ssDNA) preparation and magnetic bead-based microarray analysis with a white-light detection for detecting mutations that account for hereditary hearing loss. The entire operation process, which includes loading of streptavidin-coated magnetic beads (MBs) and biotin-labeled polymerase chain reaction products, active dispersion of the MBs with DNA for binding, alkaline denaturation of DNA, dynamic hybridization of the bead-labeled ssDNA to a tag array, and white-light detection, can all be automatically accomplished in a single chamber of the microchip, which was operated on a self-contained instrument with all the necessary components for thermal control, fluidic control, and detection. Two novel mixing valves with embedded polydimethylsiloxane membranes, which can alternately generate a 3-μl pulse flow at a peak rate of around 160 mm/s, were integrated into the chip for thoroughly dispersing magnetic beads in 2 min. The binding efficiency of biotinylated oligonucleotides to beads was measured to be 80.6% of that obtained in a tube with the conventional method. To critically test the performance of this automated microsystem, we employed a commercial microarray-based detection kit for detecting nine mutation loci that account for hereditary hearing loss. The limit of detection of the microsystem was determined as 2.5 ng of input K562 standard genomic DNA using this kit. In addition, four blood samples obtained from persons with mutations were all correctly typed by our system in less than 45 min per run. The fully automated, "amplicon-in-answer-out" operation, together with the white-light detection, makes our system an excellent platform for low-cost, rapid genotyping in clinical diagnosis.
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