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Meena GG, Jain A, Parks JW, Stambaugh A, Patterson JL, Hawkins AR, Schmidt H. Integration of sample preparation and analysis into an optofluidic chip for multi-target disease detection. LAB ON A CHIP 2018; 18:3678-3686. [PMID: 30376021 PMCID: PMC6264894 DOI: 10.1039/c8lc00966j] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Detection of molecular biomarkers with high specificity and sensitivity from biological samples requires both sophisticated sample preparation and subsequent analysis. These tasks are often carried out on separate platforms which increases required sample volumes and the risk of errors, sample loss, and contamination. Here, we present an optofluidic platform which combines an optical detection section with single nucleic acid strand sensitivity, and a sample processing unit capable of on-chip, specific extraction and labeling of nucleic acid and protein targets in complex biological matrices. First, on-chip labeling and detection of individual lambda DNA molecules down to concentrations of 8 fM is demonstrated. Subsequently, we demonstrate the simultaneous capture, fluorescence tagging and detection of both Zika specific nucleic acid and NS-1 protein targets in both buffer and human serum. We show that the dual DNA and protein assay allows for successful differentiation and diagnosis of Zika against cross-reacting species like dengue.
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Affiliation(s)
- Gopikrishnan G Meena
- School of Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.
| | - Aadhar Jain
- School of Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.
| | - Joshua W Parks
- School of Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.
| | - Alexandra Stambaugh
- School of Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.
| | - Jean L Patterson
- Department of Virology and Immunology, Texas Biomedical Research Institute, 7620 NW Loop 410, San Antonio, TX 78227, USA
| | - Aaron R Hawkins
- ECEn Department, Brigham Young University, 459 Clyde Building, Provo, UT 84602, USA
| | - Holger Schmidt
- School of Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.
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52
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BLACK JENNIFERA, GANJALIZADEH VAHID, PARKS JOSHUAW, SCHMIDT HOLGER. Multi-channel velocity multiplexing of single virus detection on an optofluidic chip. OPTICS LETTERS 2018; 43:4425-4428. [PMID: 30211881 PMCID: PMC6309855 DOI: 10.1364/ol.43.004425] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Liquid-core waveguide-based optofluidic devices have proven to be valuable tools for analysis of biological samples in fluid. They have enabled single bioparticle sensitivity while maintaining in-plane detection via light-induced fluorescence. The incorporation of multi-spot excitation with multimode interference (MMI) waveguides has enabled spatially and spectrally multiplexed detection of single viruses on an oxide-based optofluidic platform. Here, we introduce a new way of MMI-based multiplexing where multiple analysis channels are placed within a single multi-spot pattern. This stacked channel design enables both velocity and spectral multiplexing of single particles. The principle is demonstrated with differentiated detection of single H3N2 and H1N1 viruses on a polydimethylsiloxane platform.
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53
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Stambaugh A, Parks JW, Stott MA, Meena GG, Hawkins AR, Schmidt H. Optofluidic detection of Zika nucleic acid and protein biomarkers using multimode interference multiplexing. BIOMEDICAL OPTICS EXPRESS 2018; 9:3725-3730. [PMID: 30338150 PMCID: PMC6191625 DOI: 10.1364/boe.9.003725] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 06/05/2018] [Accepted: 06/13/2018] [Indexed: 05/03/2023]
Abstract
The recent massive Zika virus (ZIKV) outbreak illustrates the need for rapid and specific diagnostic techniques. Detecting ZIKV in biological samples poses unique problems: antibody detection of ZIKV is insufficient due to cross-reactivity of Zika antibodies with other flaviviruses, and nucleic acid and protein biomarkers for ZIKV are detectable at different stages of infection. Here, we describe a new optofluidic approach for the parallel detection of different molecular biomarkers using multimode interference (MMI) waveguides. We report differentiated, multiplex detection of both ZIKV biomarker types using multi-spot excitation at two visible wavelengths with over 98% fidelity by combining several analysis techniques.
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Affiliation(s)
- Alexandra Stambaugh
- School of Engineering, University of California, Santa Cruz, 1156 High St., Santa Cruz, CA 95064, USA
| | - Joshua W. Parks
- School of Engineering, University of California, Santa Cruz, 1156 High St., Santa Cruz, CA 95064, USA
| | - Matthew A. Stott
- ECEn Department, Brigham Young University, 459 Clyde Building, Provo, UT 84602, USA
| | - Gopikrishnan G. Meena
- School of Engineering, University of California, Santa Cruz, 1156 High St., Santa Cruz, CA 95064, USA
| | - Aaron R. Hawkins
- ECEn Department, Brigham Young University, 459 Clyde Building, Provo, UT 84602, USA
| | - Holger Schmidt
- School of Engineering, University of California, Santa Cruz, 1156 High St., Santa Cruz, CA 95064, USA
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54
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Clark DJ, Tyson J, Sails AD, Krishna S, Staines HM. The current landscape of nucleic acid tests for filovirus detection. J Clin Virol 2018; 103:27-36. [PMID: 29625392 PMCID: PMC5958242 DOI: 10.1016/j.jcv.2018.03.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 03/14/2018] [Indexed: 11/03/2022]
Abstract
Filoviruses can cause severe hemorrhagic fever in humans and non-human primates. There is an urgent need for rapid diagnosis of filoviruses during outbreaks. Filovirus diagnostics have advanced since the 2014–2016 Ebolavirus outbreak. NATs are the gold standard for filovirus detection. NAT-based diagnostic speed, portability and multiplexing have all improved.
Nucleic acid testing (NAT) for pathogenic filoviruses plays a key role in surveillance and to control the spread of infection. As they share clinical features with other pathogens, the initial spread of these viruses can be misdiagnosed. Tests that can identify a pathogen in the initial stages of infection are essential to control outbreaks. Since the Ebola virus disease (EVD) outbreak in 2014–2016 several tests have been developed that are faster than previous tests and more suited for field use. Furthermore, the ability to test for a range of pathogens simultaneously has been expanded to improve clinical pathway management of febrile syndromes. This review provides an overview of these novel diagnostic tests.
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Affiliation(s)
- David J Clark
- Centre for Diagnostics & Antimicrobial Resistance, Institute for Infection & Immunity, St. George's University of London, Cranmer Terrace, London SW17 0RE, UK; Institute for Infection & Immunity, St. George's University of London, Cranmer Terrace, London SW17 0RE, UK.
| | - John Tyson
- QuantuMDx, Lugano Building, 57 Melbourne Street, Newcastle-upon-Tyne, NE1 2JQ, UK
| | - Andrew D Sails
- QuantuMDx, Lugano Building, 57 Melbourne Street, Newcastle-upon-Tyne, NE1 2JQ, UK
| | - Sanjeev Krishna
- Centre for Diagnostics & Antimicrobial Resistance, Institute for Infection & Immunity, St. George's University of London, Cranmer Terrace, London SW17 0RE, UK; Institute for Infection & Immunity, St. George's University of London, Cranmer Terrace, London SW17 0RE, UK; St. George's University Hospitals NHS Foundation Trust, Blackshaw Road, Tooting, London SW17 0QT, UK
| | - Henry M Staines
- Centre for Diagnostics & Antimicrobial Resistance, Institute for Infection & Immunity, St. George's University of London, Cranmer Terrace, London SW17 0RE, UK; Institute for Infection & Immunity, St. George's University of London, Cranmer Terrace, London SW17 0RE, UK
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55
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Ngo HT, Freedman E, Odion RA, Strobbia P, De Silva Indrasekara AS, Vohra P, Taylor SM, Vo-Dinh T. Direct Detection of Unamplified Pathogen RNA in Blood Lysate using an Integrated Lab-in-a-Stick Device and Ultrabright SERS Nanorattles. Sci Rep 2018; 8:4075. [PMID: 29511216 PMCID: PMC5840326 DOI: 10.1038/s41598-018-21615-3] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 01/23/2018] [Indexed: 12/19/2022] Open
Abstract
Direct detection of genetic biomarkers in body fluid lysate without target amplification will revolutionize nucleic acid-based diagnostics. However, the low concentration of target sequences makes this goal challenging. We report a method for direct detection of pathogen RNA in blood lysate using a bioassay using surface-enhanced Raman spectroscopy (SERS)-based detection integrated in a "lab-in-a-stick" portable device. Two levels of signal enhancement were employed to achieve the sensitivity required for direct detection. Each target sequence was tagged with an ultrabright SERS-encoded nanorattle with ultrahigh SERS signals, and these tagged target sequences were concentrated into a focused spot for detection using hybridization sandwiches with magnetic microbeads. Furthermore, the washing process was automated by integration into a "lab-in-a-stick" portable device. We could directly detect synthetic target with a limit of detection of 200 fM. More importantly, we detected plasmodium falciparum malaria parasite RNA directly in infected red blood cells lysate. To our knowledge, this is the first report of SERS-based direct detection of pathogen nucleic acid in blood lysate without nucleic acid extraction or target amplification. The results show the potential of our integrated bioassay for field use and point-of-care diagnostics.
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Affiliation(s)
- Hoan T Ngo
- Fitzpatrick Institute for Photonics, Duke University, Durham, NC, 27708, USA
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
- Biomedical Engineering Department, International University, Vietnam National University-Ho Chi Minh City (VNU-HCMC), Ho Chi Minh City, Vietnam
| | - Elizabeth Freedman
- Fitzpatrick Institute for Photonics, Duke University, Durham, NC, 27708, USA
- Department of Medicine & Duke Global Health Institute, Duke University, Durham, NC, 27708, USA
| | - Ren Abelard Odion
- Fitzpatrick Institute for Photonics, Duke University, Durham, NC, 27708, USA
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
| | - Pietro Strobbia
- Fitzpatrick Institute for Photonics, Duke University, Durham, NC, 27708, USA
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
| | - Agampodi Swarnapali De Silva Indrasekara
- Fitzpatrick Institute for Photonics, Duke University, Durham, NC, 27708, USA
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
| | - Priya Vohra
- Fitzpatrick Institute for Photonics, Duke University, Durham, NC, 27708, USA
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
- Division of Head and Neck Surgery and Communication Sciences, Duke University, Durham, NC, 27708, USA
| | - Steve M Taylor
- Fitzpatrick Institute for Photonics, Duke University, Durham, NC, 27708, USA
- Department of Medicine & Duke Global Health Institute, Duke University, Durham, NC, 27708, USA
| | - Tuan Vo-Dinh
- Fitzpatrick Institute for Photonics, Duke University, Durham, NC, 27708, USA.
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA.
- Department of Chemistry, Duke University, Durham, NC, 27708, USA.
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56
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Abstract
This critical review summarizes the developments in the integration of micro-optical elements with microfluidic platforms for facilitating detection and automation of bio-analytical applications.
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Affiliation(s)
- Hui Yang
- Institute of Biomedical and Health Engineering
- Shenzhen Institutes of Advanced Technology
- Chinese Academy of Science
- 518055 Shenzhen
- China
| | - Martin A. M. Gijs
- Laboratory of Microsystems
- Ecole Polytechnique Fédérale de Lausanne
- 1015 Lausanne
- Switzerland
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57
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Sui Z, Li T, An R, Wu W, Komiyama M, Liang X. Tandem blocking of PCR extension to form a single-stranded overhang for facile, visual, and ultrasensitive gene detection. RSC Adv 2018; 8:15652-15658. [PMID: 35539451 PMCID: PMC9080086 DOI: 10.1039/c8ra01471j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 04/18/2018] [Indexed: 11/25/2022] Open
Abstract
In order to detect a predetermined gene in a field test, a facile, visual, and ultrasensitive approach without the need of special and expensive machines is required. In this study, a gene in the Ebola virus was targeted as an example for diagnosis. The key strategy is to incorporate molecular blockers (azobenzene-bearing moieties or thymine dimers) in tandem in one of the PCR primers and stop the polymerase extension there to form a single-stranded overhang. The PCR product was added to the dispersion of gold nanoparticles which were labelled with a probe oligonucleotide. When the Ebola virus-specific gene existed in the specimen, the oligonucleotide on the gold particles formed a double-helix with the single-stranded overhang, and thus the dispersion remained red in color. In the absence of the gene, however, the dispersion rapidly turned to blue because of nanoparticle aggregation. The difference was explicit even when the initial specimen involved only 1 copy of the gene. Accordingly, “whether the patient is infected by the virus or not” can be easily and visually judged by the naked eye. Here we present a simple but practically useful assay for gene detection. This strategy employs the advantages of both PCR and Au colloidal science, and thus satisfactorily fulfills the factors required for Point-of-Care detection.![]()
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Affiliation(s)
- Zhe Sui
- College of Food Science and Engineering
- Ocean University of China
- Qingdao 266003
- China
| | - Tong Li
- College of Food Science and Engineering
- Ocean University of China
- Qingdao 266003
- China
| | - Ran An
- College of Food Science and Engineering
- Ocean University of China
- Qingdao 266003
- China
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology
| | - Wei Wu
- College of Food Science and Engineering
- Ocean University of China
- Qingdao 266003
- China
| | - Makoto Komiyama
- College of Food Science and Engineering
- Ocean University of China
- Qingdao 266003
- China
- National Institute for Materials Science (NIMS)
| | - Xingguo Liang
- College of Food Science and Engineering
- Ocean University of China
- Qingdao 266003
- China
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology
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58
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Wei L, Yan W, Ho D. Recent Advances in Fluorescence Lifetime Analytical Microsystems: Contact Optics and CMOS Time-Resolved Electronics. SENSORS (BASEL, SWITZERLAND) 2017; 17:E2800. [PMID: 29207568 PMCID: PMC5751615 DOI: 10.3390/s17122800] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 11/30/2017] [Accepted: 12/01/2017] [Indexed: 01/01/2023]
Abstract
Fluorescence spectroscopy has become a prominent research tool with wide applications in medical diagnostics and bio-imaging. However, the realization of combined high-performance, portable, and low-cost spectroscopic sensors still remains a challenge, which has limited the technique to the laboratories. A fluorescence lifetime measurement seeks to obtain the characteristic lifetime from the fluorescence decay profile. Time-correlated single photon counting (TCSPC) and time-gated techniques are two key variations of time-resolved measurements. However, commercial time-resolved analysis systems typically contain complex optics and discrete electronic components, which lead to bulkiness and a high cost. These two limitations can be significantly mitigated using contact sensing and complementary metal-oxide-semiconductor (CMOS) implementation. Contact sensing simplifies the optics, whereas CMOS technology enables on-chip, arrayed detection and signal processing, significantly reducing size and power consumption. This paper examines recent advances in contact sensing and CMOS time-resolved circuits for the realization of fully integrated fluorescence lifetime measurement microsystems. The high level of performance from recently reported prototypes suggests that the CMOS-based contact sensing microsystems are emerging as sound technologies for application-specific, low-cost, and portable time-resolved diagnostic devices.
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Affiliation(s)
- Liping Wei
- Department of Materials Science and Engineering, City University of Hong Kong, Hong Kong 999077, China.
| | - Wenrong Yan
- Department of Materials Science and Engineering, City University of Hong Kong, Hong Kong 999077, China.
| | - Derek Ho
- Department of Materials Science and Engineering, City University of Hong Kong, Hong Kong 999077, China.
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59
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Singh RK, Dhama K, Malik YS, Ramakrishnan MA, Karthik K, Khandia R, Tiwari R, Munjal A, Saminathan M, Sachan S, Desingu PA, Kattoor JJ, Iqbal HMN, Joshi SK. Ebola virus - epidemiology, diagnosis, and control: threat to humans, lessons learnt, and preparedness plans - an update on its 40 year's journey. Vet Q 2017; 37:98-135. [PMID: 28317453 DOI: 10.1080/01652176.2017.1309474] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Ebola virus (EBOV) is an extremely contagious pathogen and causes lethal hemorrhagic fever disease in man and animals. The recently occurred Ebola virus disease (EVD) outbreaks in the West African countries have categorized it as an international health concern. For the virus maintenance and transmission, the non-human primates and reservoir hosts like fruit bats have played a vital role. For curbing the disease timely, we need effective therapeutics/prophylactics, however, in the absence of any approved vaccine, timely diagnosis and monitoring of EBOV remains of utmost importance. The technologically advanced vaccines like a viral-vectored vaccine, DNA vaccine and virus-like particles are underway for testing against EBOV. In the absence of any effective control measure, the adaptation of high standards of biosecurity measures, strict sanitary and hygienic practices, strengthening of surveillance and monitoring systems, imposing appropriate quarantine checks and vigilance on trade, transport, and movement of visitors from EVD endemic countries remains the answer of choice for tackling the EBOV spread. Herein, we converse with the current scenario of EBOV giving due emphasis on animal and veterinary perspectives along with advances in diagnosis and control strategies to be adopted, lessons learned from the recent outbreaks and the global preparedness plans. To retrieve the evolutionary information, we have analyzed a total of 56 genome sequences of various EBOV species submitted between 1976 and 2016 in public databases.
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Affiliation(s)
- Raj Kumar Singh
- a ICAR-Indian Veterinary Research Institute , Bareilly , India
| | - Kuldeep Dhama
- b Division of Pathology, ICAR-Indian Veterinary Research Institute , Bareilly , India
| | - Yashpal Singh Malik
- c Division of Biological Standardization, ICAR-Indian Veterinary Research Institute , Bareilly , India
| | | | - Kumaragurubaran Karthik
- e Divison of Bacteriology and Mycology, ICAR-Indian Veterinary Research Institute , Bareilly , India
| | - Rekha Khandia
- f Department of Biochemistry and Genetics , Barkatullah University , Bhopal , India
| | - Ruchi Tiwari
- g Department of Veterinary Microbiology and Immunology , College of Veterinary Sciences, Deen Dayal Upadhayay Pashu Chikitsa Vigyan Vishwavidyalay Evum Go-Anusandhan Sansthan (DUVASU) , Mathura , India
| | - Ashok Munjal
- f Department of Biochemistry and Genetics , Barkatullah University , Bhopal , India
| | - Mani Saminathan
- b Division of Pathology, ICAR-Indian Veterinary Research Institute , Bareilly , India
| | - Swati Sachan
- h Immunology Section, ICAR-Indian Veterinary Research Institute , Bareilly , India
| | | | - Jobin Jose Kattoor
- c Division of Biological Standardization, ICAR-Indian Veterinary Research Institute , Bareilly , India
| | - Hafiz M N Iqbal
- i School of Engineering and Science, Tecnologico de Monterrey , Monterrey , Mexico
| | - Sunil Kumar Joshi
- j Cellular Immunology Lab , Frank Reidy Research Center for Bioelectrics , School of Medical Diagnostics & Translational Sciences, Old Dominion University , Norfolk , VA , USA
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60
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Du K, Park M, Griffiths A, Carrion R, Patterson J, Schmidt H, Mathies R. Microfluidic System for Detection of Viral RNA in Blood Using a Barcode Fluorescence Reporter and a Photocleavable Capture Probe. Anal Chem 2017; 89:12433-12440. [PMID: 29073356 PMCID: PMC5990416 DOI: 10.1021/acs.analchem.7b03527] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
A microfluidic sample preparation multiplexer (SPM) and assay procedure is developed to improve amplification-free detection of Ebola virus RNA from blood. While a previous prototype successfully detected viral RNA following off-chip RNA extraction from infected cells, the new device and protocol can detect Ebola virus in raw blood with clinically relevant sensitivity. The Ebola RNA is hybridized with sequence specific capture and labeling DNA probes in solution and then the complex is pulled down onto capture beads for purification and concentration. After washing, the captured RNA target is released by irradiating the photocleavable DNA capture probe with ultraviolet (UV) light. The released, labeled, and purified RNA is detected by a sensitive and compact fluorometer. Exploiting these capabilities, a detection limit of 800 attomolar (aM) is achieved without target amplification. The new SPM can run up to 80 assays in parallel using a pneumatic multiplexing architecture. Importantly, our new protocol does not require time-consuming and problematic off-chip probe conjugation and washing. This improved SPM and labeling protocol is an important step toward a useful POC device and assay.
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Affiliation(s)
- Ke Du
- Department of Chemistry, University of California at Berkeley, Berkeley, California 94720, United States
| | - Myeongkee Park
- Department of Chemistry, University of California at Berkeley, Berkeley, California 94720, United States
| | - Anthony Griffiths
- Department of Virology and Immunology, Texas Biomedical Research Institute, 7620 NW Loop 410, San Antonio, Texas 78227, United States
| | - Ricardo Carrion
- Department of Virology and Immunology, Texas Biomedical Research Institute, 7620 NW Loop 410, San Antonio, Texas 78227, United States
| | - Jean Patterson
- Department of Virology and Immunology, Texas Biomedical Research Institute, 7620 NW Loop 410, San Antonio, Texas 78227, United States
| | - Holger Schmidt
- School of Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Richard Mathies
- Department of Chemistry, University of California at Berkeley, Berkeley, California 94720, United States
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61
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Ozcelik D, Jain A, Stambaugh A, Stott MA, Parks JW, Hawkins A, Schmidt H. Scalable Spatial-Spectral Multiplexing of Single-Virus Detection Using Multimode Interference Waveguides. Sci Rep 2017; 7:12199. [PMID: 28939852 PMCID: PMC5610187 DOI: 10.1038/s41598-017-12487-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 09/06/2017] [Indexed: 11/09/2022] Open
Abstract
Simultaneous detection of multiple pathogens and samples (multiplexing) is one of the key requirements for diagnostic tests in order to enable fast, accurate and differentiated diagnoses. Here, we introduce a novel, highly scalable, photonic approach to multiplex analysis with single virus sensitivity. A solid-core multimode interference (MMI) waveguide crosses multiple fluidic waveguide channels on an optofluidic chip to create multi-spot excitation patterns that depend on both the wavelength and location of the channel along the length of the MMI waveguide. In this way, joint spectral and spatial multiplexing is implemented that encodes both spatial and spectral information in the time dependent fluorescence signal. We demonstrate this principle by using two excitation wavelengths and three fluidic channels to implement a 6x multiplex assay with single virus sensitivity. High fidelity detection and identification of six different viruses from a standard influenza panel is reported. This multimodal multiplexing strategy scales favorably to large numbers of targets or large numbers of clinical samples. Further, since single particles are detected unbound in flow, the technique can be broadly applied to direct detection of any fluorescent target, including nucleic acids and proteins.
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Affiliation(s)
- Damla Ozcelik
- School of Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA
| | - Aadhar Jain
- School of Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA
| | - Alexandra Stambaugh
- School of Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA
| | - Matthew A Stott
- ECEn Department, 459 Clyde Building, Brigham Young University, Provo, UT, 84602, USA
| | - Joshua W Parks
- School of Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA
| | - Aaron Hawkins
- ECEn Department, 459 Clyde Building, Brigham Young University, Provo, UT, 84602, USA
| | - Holger Schmidt
- School of Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA.
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62
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Zeisberger M, Schmidt MA. Analytic model for the complex effective index of the leaky modes of tube-type anti-resonant hollow core fibers. Sci Rep 2017; 7:11761. [PMID: 28924224 PMCID: PMC5603564 DOI: 10.1038/s41598-017-12234-5] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 09/06/2017] [Indexed: 12/31/2022] Open
Abstract
Due to their promising applications, hollow-core fibers, in particular, their anti-resonant versions, have recently attracted the attention of the photonics community. Here, we introduce a model that approximates, using the reflection of a wave on a single planar film, modal guidance in tube-type anti-resonant waveguides whose core diameters are large compared to the wavelength. The model yields analytic expressions for the real and imaginary parts of the complex effective index of the leaky modes supported, and is valid in all practically relevant situations, excellently matching all the important dispersion and loss parameters. Essential principles such as the fourth power dependence of the modal loss on the core radius at all wavelengths and the geometry-independent transition refractive index, below which modal discrimination favors the fundamental mode are discussed. As application examples, we use our model for understanding higher-order mode suppression in revolver-type fibers and for uncovering the tuning capabilities associated with nonlinear pulse propagation.
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Affiliation(s)
- Matthias Zeisberger
- Leibniz Institute of Photonic Technology, Albert-Einstein-Str. 9, 07745, Jena, Germany.
| | - Markus A Schmidt
- Leibniz Institute of Photonic Technology, Albert-Einstein-Str. 9, 07745, Jena, Germany
- Otto Schott Institute of Materials Research (OSIM), Friedrich Schiller University of Jena, Fraunhoferstr. 6, 07743, Jena, Germany
- Abbe Center of Photonics and Faculty of Physics, Friedrich Schiller University Jena, Max-Wien-Platz 1, Jena, 07743, Germany
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63
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Chen Y, Ren R, Pu H, Guo X, Chang J, Zhou G, Mao S, Kron M, Chen J. Field-Effect Transistor Biosensor for Rapid Detection of Ebola Antigen. Sci Rep 2017; 7:10974. [PMID: 28887479 PMCID: PMC5591202 DOI: 10.1038/s41598-017-11387-7] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 08/23/2017] [Indexed: 01/12/2023] Open
Abstract
The Ebola virus transmits a highly contagious, frequently fatal human disease for which there is no specific antiviral treatment. Therefore, rapid, accurate, and early diagnosis of Ebola virus disease (EVD) is critical to public health containment efforts, particularly in developing countries where resources are few and EVD is endemic. We have developed a reduced graphene oxide-based field-effect transistor method for real-time detection of the Ebola virus antigen. This method uses the attractive semiconductor characteristics of graphene-based material, and instantaneously yields highly sensitive and specific detection of Ebola glycoprotein. The feasibility of this method for clinical application in point-of-care technology is evaluated using Ebola glycoprotein suspended in diluted PBS buffer, human serum, and plasma. These results demonstrate the successful fabrication of a promising field-effect transistor biosensor for EVD diagnosis.
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Affiliation(s)
- Yantao Chen
- Department of Mechanical Engineering, University of Wisconsin-Milwaukee, 3200 N. Cramer Street, Milwaukee, WI, 53211, USA.,Tianjin Key Laboratory for Photoelectric Materials & Devices, School of Materials Science and Engineering, Tianjin University of Technology, Tianjin, 300384, P.R. China
| | - Ren Ren
- Department of Mechanical Engineering, University of Wisconsin-Milwaukee, 3200 N. Cramer Street, Milwaukee, WI, 53211, USA
| | - Haihui Pu
- Department of Mechanical Engineering, University of Wisconsin-Milwaukee, 3200 N. Cramer Street, Milwaukee, WI, 53211, USA
| | - Xiaoru Guo
- Department of Mechanical Engineering, University of Wisconsin-Milwaukee, 3200 N. Cramer Street, Milwaukee, WI, 53211, USA
| | - Jingbo Chang
- Department of Mechanical Engineering, University of Wisconsin-Milwaukee, 3200 N. Cramer Street, Milwaukee, WI, 53211, USA
| | - Guihua Zhou
- Department of Mechanical Engineering, University of Wisconsin-Milwaukee, 3200 N. Cramer Street, Milwaukee, WI, 53211, USA
| | - Shun Mao
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai, 200092, P.R. China
| | - Michael Kron
- Department of Medicine, Division of Infectious Diseases, Biotechnology and Bioengineering Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA.
| | - Junhong Chen
- Department of Mechanical Engineering, University of Wisconsin-Milwaukee, 3200 N. Cramer Street, Milwaukee, WI, 53211, USA.
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64
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Zhang L, Ding B, Chen Q, Feng Q, Lin L, Sun J. Point-of-care-testing of nucleic acids by microfluidics. Trends Analyt Chem 2017. [DOI: 10.1016/j.trac.2017.07.013] [Citation(s) in RCA: 114] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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65
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Optofluidic Lab-on-a-Chip Fluorescence Sensor Using Integrated Buried ARROW (bARROW) Waveguides. MICROMACHINES 2017; 8. [PMID: 29201455 PMCID: PMC5708584 DOI: 10.3390/mi8080252] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Optofluidic, lab-on-a-chip fluorescence sensors were fabricated using buried anti-resonant reflecting optical waveguides (bARROWs). The bARROWs are impervious to the negative water absorption effects that typically occur in waveguides made using hygroscopic, plasma-enhanced chemical vapor deposition (PECVD) oxides. These sensors were used to detect fluorescent microbeads and had an average signal-to-noise ratio (SNR) that was 81.3% higher than that of single-oxide ARROW fluorescence sensors. While the single-oxide ARROW sensors were annealed at 300 °C to drive moisture out of the waveguides, the bARROW sensors required no annealing process to obtain a high SNR.
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66
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Szydzik C, Gavela AF, Herranz S, Roccisano J, Knoerzer M, Thurgood P, Khoshmanesh K, Mitchell A, Lechuga LM. An automated optofluidic biosensor platform combining interferometric sensors and injection moulded microfluidics. LAB ON A CHIP 2017; 17:2793-2804. [PMID: 28682395 DOI: 10.1039/c7lc00524e] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
A primary limitation preventing practical implementation of photonic biosensors within point-of-care platforms is their integration with fluidic automation subsystems. For most diagnostic applications, photonic biosensors require complex fluid handling protocols; this is especially prominent in the case of competitive immunoassays, commonly used for detection of low-concentration, low-molecular weight biomarkers. For this reason, complex automated microfluidic systems are needed to realise the full point-of-care potential of photonic biosensors. To fulfil this requirement, we propose an on-chip valve-based microfluidic automation module, capable of automating such complex fluid handling. This module is realised through application of a PDMS injection moulding fabrication technique, recently described in our previous work, which enables practical fabrication of normally closed pneumatically actuated elastomeric valves. In this work, these valves are configured to achieve multiplexed reagent addressing for an on-chip diaphragm pump, providing the sample and reagent processing capabilities required for automation of cyclic competitive immunoassays. Application of this technique simplifies fabrication and introduces the potential for mass production, bringing point-of-care integration of complex automated microfluidics into the realm of practicality. This module is integrated with a highly sensitive, label-free bimodal waveguide photonic biosensor, and is demonstrated in the context of a proof-of-concept biosensing assay, detecting the low-molecular weight antibiotic tetracycline.
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Affiliation(s)
- C Szydzik
- School of Engineering, RMIT University, Melbourne, Australia
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67
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Persichetti G, Grimaldi IA, Testa G, Bernini R. Multifunctional optofluidic lab-on-chip platform for Raman and fluorescence spectroscopic microfluidic analysis. LAB ON A CHIP 2017; 17:2631-2639. [PMID: 28664956 DOI: 10.1039/c7lc00460e] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
A multifunctional lab-on-a-chip platform for spectroscopic analysis of liquid samples based on an optofluidic jet waveguide is reported. The optofluidic detection scheme is achieved through the total internal reflection arising in a liquid jet of only 150 μm diameter, leading to highly efficient signal excitation and collection. This results in an optofluidic chip with an alignment-free spectroscopic detection scheme, which avoids any background from the sample container. This platform has been designed for multiwavelength fluorescence and Raman spectroscopy. The chip integrates a recirculation system that reduces the required sample volume. The evaluation of the device performance has been accomplished by means of fluorescence measurements performed on eosin Y in water solutions, achieving a limit of detection of 33 pM. The sensor has been applied in Raman spectroscopy of water-ethanol solutions, leading to a limit of detection of 0.18%. As additional application, analysis of riboflavin using fluorescence detection demonstrates the possibility of detecting this vitamin at the 560 pM level (0.21 ng l-1). Although measurements have been performed by means of a compact and low-cost spectrometer, in both cases the micro-jet optofluidic chip achieved similar performances if not better than high-end benchtop based laboratory equipment. This approach paves the way towards portable lab-on-a-chip devices for high sensitivity environmental and biochemical sensing, using optical spectroscopy.
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Affiliation(s)
- G Persichetti
- Institute for Electromagnetic Monitoring of the Environment (IREA), National Research Council (CNR), Naples, Italy.
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68
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Ozcelik D, Cai H, Leake KD, Hawkins AR, Schmidt H. Optofluidic bioanalysis: fundamentals and applications. NANOPHOTONICS 2017; 6:647-661. [PMID: 29201591 PMCID: PMC5708574 DOI: 10.1515/nanoph-2016-0156] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Over the past decade, optofluidics has established itself as a new and dynamic research field for exciting developments at the interface of photonics, microfluidics, and the life sciences. The strong desire for developing miniaturized bioanalytic devices and instruments, in particular, has led to novel and powerful approaches to integrating optical elements and biological fluids on the same chip-scale system. Here, we review the state-of-the-art in optofluidic research with emphasis on applications in bioanalysis and a focus on waveguide-based approaches that represent the most advanced level of integration between optics and fluidics. We discuss recent work in photonically reconfigurable devices and various application areas. We show how optofluidic approaches have been pushing the performance limits in bioanalysis, e.g. in terms of sensitivity and portability, satisfying many of the key requirements for point-of-care devices. This illustrates how the requirements for bianalysis instruments are increasingly being met by the symbiotic integration of novel photonic capabilities in a miniaturized system.
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Affiliation(s)
- Damla Ozcelik
- School of Engineering, University of California-Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Hong Cai
- School of Engineering, University of California-Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Kaelyn D. Leake
- School of Engineering, University of California-Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Aaron R. Hawkins
- ECEn Department, 459 Clyde Building, Brigham Young University, Provo, UT 84602, USA
| | - Holger Schmidt
- Corresponding author: Holger Schmidt, School of Engineering, University of California-Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA,
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69
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Wall T, Hammon S, Hamilton E, Zacheu G, Orfila M, Schmidt H, Hawkins AR. Mitigating Water Absorption in Waveguides Made From Unannealed PECVD SiO 2. IEEE PHOTONICS TECHNOLOGY LETTERS : A PUBLICATION OF THE IEEE LASER AND ELECTRO-OPTICS SOCIETY 2017; 29:806-809. [PMID: 29200798 PMCID: PMC5708587 DOI: 10.1109/lpt.2017.2686354] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Water absorption was studied in two types of waveguides made from unannealed plasma enhanced chemical vapor deposition (PECVD) SiO2. Standard rib anti-resonant reflecting optical waveguides (ARROWs) were fabricated with thin films of different intrinsic stress and indices of refraction. Buried ARROWs (bARROWs) with low and high refractive index differences between the core and cladding regions were also fabricated from the same types of PECVD films. All waveguides were subjected to a heated, high humidity environment and their optical throughput was tested over time. Due to water absorption in the SiO2 films, the optical throughput of all of the ARROWs decreased with time spent in the wet environment. The ARROWs with the lowest stress SiO2 had the slowest rate of throughput change. High index difference bARROWs showed no decrease in optical throughput after 40 days in the wet environment and are presented as a solution for environmentally stable waveguides made from unannealed PECVD SiO2.
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Affiliation(s)
- Thomas Wall
- Department of Electrical and Computer Engineering, Brigham Young University, Provo, UT 84602 USA
| | - Steven Hammon
- Department of Electrical and Computer Engineering, Brigham Young University, Provo, UT 84602 USA
| | - Erik Hamilton
- Department of Electrical and Computer Engineering, Brigham Young University, Provo, UT 84602 USA
| | - Gabriel Zacheu
- Department of Electrical and Computer Engineering, Brigham Young University, Provo, UT 84602 USA
| | - Marcos Orfila
- Department of Electrical and Computer Engineering, Brigham Young University, Provo, UT 84602 USA
| | - Holger Schmidt
- School of Engineering, University of Californnia at Santa Cruz, Santa Cruz, CA 95064 USA
| | - Aaron R Hawkins
- Department of Electrical and Computer Engineering, Brigham Young University, Provo, UT 84602 USA
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Abstract
Aerogels—solid materials keeping their internal structure of interconnected submicron-sized pores intact upon exchanging the pore liquid with a gas—were first synthesized in 1932 by Samuel Kistler. Overall, an aerogel is a special form of a highly porous material with a very low solid density and it is composed of individual nano-sized particles or fibers that are connected to form a three-dimensional network. The unique properties of these materials, such as open pores and high surface areas, are attributed to their high porosity and irregular solid structure, which can be tuned through proper selection of the preparation conditions. Moreover, their low refractive index makes them a remarkable solid-cladding material for developing liquid-core optofluidic waveguides based on total internal reflection of light. This paper is a comprehensive review of the literature on the use of aerogels for optofluidic waveguide applications. First, an overview of different types of aerogels and their physicochemical properties is presented. Subsequently, possible techniques to fabricate channels in aerogel monoliths are discussed and methods to make the channel surfaces hydrophobic are described in detail. Studies in the literature on the characterization of light propagation in liquid-filled channels within aerogel monoliths as well as their light-guiding characteristics are discussed. Finally, possible applications of aerogel-based optofluidic waveguides are described.
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Affiliation(s)
- Yaprak Özbakır
- Department of Chemical and Biological Engineering, Koc University, 34450 Sarıyer, Istanbul, Turkey;
- Department of Physics, Koc University, 34450 Sarıyer, Istanbul, Turkey
| | - Alexandr Jonas
- Department of Physics, Istanbul Technical University, 34469 Maslak, Istanbul, Turkey
- Correspondence: (A.J.); (A.K.); (C.E.); Tel.: +90-212-338-1866 (A.J. & A.K. & C.E.)
| | - Alper Kiraz
- Department of Physics, Koc University, 34450 Sarıyer, Istanbul, Turkey
- Department of Electrical and Electronics Engineering, Koc University, 34450 Sarıyer, Istanbul, Turkey
- Correspondence: (A.J.); (A.K.); (C.E.); Tel.: +90-212-338-1866 (A.J. & A.K. & C.E.)
| | - Can Erkey
- Department of Chemical and Biological Engineering, Koc University, 34450 Sarıyer, Istanbul, Turkey;
- Correspondence: (A.J.); (A.K.); (C.E.); Tel.: +90-212-338-1866 (A.J. & A.K. & C.E.)
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71
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Du K, Cai H, Park M, Wall TA, Stott MA, Alfson KJ, Griffiths A, Carrion R, Patterson JL, Hawkins AR, Schmidt H, Mathies RA. Multiplexed efficient on-chip sample preparation and sensitive amplification-free detection of Ebola virus. Biosens Bioelectron 2017; 91:489-496. [PMID: 28073029 DOI: 10.1016/j.bios.2016.12.071] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Revised: 12/26/2016] [Accepted: 12/30/2016] [Indexed: 12/23/2022]
Abstract
An automated microfluidic sample preparation multiplexer (SPM) has been developed and evaluated for Ebola virus detection. Metered air bubbles controlled by microvalves are used to improve bead-solution mixing thereby enhancing the hybridization of the target Ebola virus RNA with capture probes bound to the beads. The method uses thermally stable 4-formyl benzamide functionalized (4FB) magnetic beads rather than streptavidin coated beads with a high density of capture probes to improve the target capture efficiency. Exploiting an on-chip concentration protocol in the SPM and the single molecule detection capability of the antiresonant reflecting optical waveguide (ARROW) biosensor chip, a detection limit of 0.021pfu/mL for clinical samples is achieved without target amplification. This RNA target capture efficiency is two orders of magnitude higher than previous results using streptavidin beads and the limit of detection (LOD) improves 10×. The wide dynamic range of this technique covers the whole clinically applicable concentration range. In addition, the current sample preparation time is ~1h which is eight times faster than previous work. This multiplexed, miniaturized sample preparation microdevice establishes a key technology that intended to develop next generation point-of-care (POC) detection system.
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Affiliation(s)
- K Du
- Department of Chemistry, University of California at Berkeley, Berkeley, CA 94720, USA
| | - H Cai
- School of Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | - M Park
- Department of Chemistry, University of California at Berkeley, Berkeley, CA 94720, USA
| | - T A Wall
- ECEn Department, Brigham Young University, 459 Clyde Building, Provo, UT 84602, USA
| | - M A Stott
- ECEn Department, Brigham Young University, 459 Clyde Building, Provo, UT 84602, USA
| | - K J Alfson
- Department of Virology and Immunology, Texas Biomedical Research Institute, 7620 NW Loop 410, San Antonio, TX 78227, USA
| | - A Griffiths
- Department of Virology and Immunology, Texas Biomedical Research Institute, 7620 NW Loop 410, San Antonio, TX 78227, USA
| | - R Carrion
- Department of Virology and Immunology, Texas Biomedical Research Institute, 7620 NW Loop 410, San Antonio, TX 78227, USA
| | - J L Patterson
- Department of Virology and Immunology, Texas Biomedical Research Institute, 7620 NW Loop 410, San Antonio, TX 78227, USA
| | - A R Hawkins
- ECEn Department, Brigham Young University, 459 Clyde Building, Provo, UT 84602, USA
| | - H Schmidt
- School of Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.
| | - R A Mathies
- Department of Chemistry, University of California at Berkeley, Berkeley, CA 94720, USA.
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72
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Nayak S, Blumenfeld NR, Laksanasopin T, Sia SK. Point-of-Care Diagnostics: Recent Developments in a Connected Age. Anal Chem 2017; 89:102-123. [PMID: 27958710 PMCID: PMC5793870 DOI: 10.1021/acs.analchem.6b04630] [Citation(s) in RCA: 281] [Impact Index Per Article: 40.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Samiksha Nayak
- Department of Biomedical Engineering, Columbia University, 351 Engineering Terrace, 1210 Amsterdam Avenue, New York, NY 10027, USA
| | - Nicole R. Blumenfeld
- Department of Biomedical Engineering, Columbia University, 351 Engineering Terrace, 1210 Amsterdam Avenue, New York, NY 10027, USA
| | - Tassaneewan Laksanasopin
- Biological Engineering Program, Faculty of Engineering, King Mongkut’s University of Technology Thonburi, 126 Pracha Uthit Rd., Bang Mod, Thung Khru, Bangkok 10140, Thailand
| | - Samuel K. Sia
- Department of Biomedical Engineering, Columbia University, 351 Engineering Terrace, 1210 Amsterdam Avenue, New York, NY 10027, USA
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73
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Cai H, Stott MA, Ozcelik D, Parks JW, Hawkins AR, Schmidt H. On-chip wavelength multiplexed detection of cancer DNA biomarkers in blood. BIOMICROFLUIDICS 2016; 10:064116. [PMID: 28058082 PMCID: PMC5176344 DOI: 10.1063/1.4968033] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 11/06/2016] [Indexed: 05/03/2023]
Abstract
We have developed an optofluidic analysis system that processes biomolecular samples starting from whole blood and then analyzes and identifies multiple targets on a silicon-based molecular detection platform. We demonstrate blood filtration, sample extraction, target enrichment, and fluorescent labeling using programmable microfluidic circuits. We detect and identify multiple targets using a spectral multiplexing technique based on wavelength-dependent multi-spot excitation on an antiresonant reflecting optical waveguide chip. Specifically, we extract two types of melanoma biomarkers, mutated cell-free nucleic acids -BRAFV600E and NRAS, from whole blood. We detect and identify these two targets simultaneously using the spectral multiplexing approach with up to a 96% success rate. These results point the way toward a full front-to-back chip-based optofluidic compact system for high-performance analysis of complex biological samples.
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Affiliation(s)
- H Cai
- School of Engineering, University of California , Santa Cruz. 1156 High Street, Santa Cruz, California 95064, USA
| | - M A Stott
- Department of Electrical and Computer Engineering, Brigham Young University , 459 Clyde Building, Provo, Utah 84602, USA
| | - D Ozcelik
- School of Engineering, University of California , Santa Cruz. 1156 High Street, Santa Cruz, California 95064, USA
| | - J W Parks
- School of Engineering, University of California , Santa Cruz. 1156 High Street, Santa Cruz, California 95064, USA
| | - A R Hawkins
- Department of Electrical and Computer Engineering, Brigham Young University , 459 Clyde Building, Provo, Utah 84602, USA
| | - H Schmidt
- School of Engineering, University of California , Santa Cruz. 1156 High Street, Santa Cruz, California 95064, USA
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74
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Parks J, Wall T, Cai H, Hawkins A, Schmidt H. Enhancement of ARROW Photonic Device Performance via Thermal Annealing of PECVD-based SiO 2 Waveguides. IEEE JOURNAL OF SELECTED TOPICS IN QUANTUM ELECTRONICS : A PUBLICATION OF THE IEEE LASERS AND ELECTRO-OPTICS SOCIETY 2016; 22:10.1109/JSTQE.2016.2549801. [PMID: 27547024 PMCID: PMC4987089 DOI: 10.1109/jstqe.2016.2549801] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Silicon-based optofluidic devices are very attractive for applications in biophotonics and chemical sensing. Understanding and controlling the properties of their dielectric waveguides is critical for the performance of these chips. We report that thermal annealing of PECVD-grown silicon dioxide (SiO2) ridge waveguides results in considerable improvements to optical transmission and particle detection. There are two fundamental changes that yield higher optical transmission: (1) propagation loss in solid-core waveguides is reduced by over 70%, and (2) coupling efficiencies between solid- and liquid-core waveguides are optimized. The combined effects result in improved optical chip transmission by a factor of 100-1000 times. These improvements are shown to arise from the elimination of a high-index layer at the surface of the SiO2 caused by water absorption into the porous oxide. The effects of this layer on optical transmission and mode confinement are shown to be reversible by alternating subjection of waveguides to water and subsequent low temperature annealing. Finally, we show that annealing improves detection of fluorescent analytes in optofluidic chips with a signal-to-noise ratio improvement of 166x and a particle detection efficiency improvement of 94%.
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Affiliation(s)
- J.W. Parks
- School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064 USA
| | - T.A. Wall
- Department of Electrical and Computer Engineering, Brigham Young University, Provo, UT 84602 USA
| | - H. Cai
- School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064 USA
| | - A.R. Hawkins
- Department of Electrical and Computer Engineering, Brigham Young University, Provo, UT 84602 USA
| | - H. Schmidt
- School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064 USA
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75
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Stott MA, Black J, Hamilton E, Schmidt H, Hawkins AR. Optimization of Y-splitting antiresonant reflecting optical waveguides-based rib waveguides. OPTICAL ENGINEERING (REDONDO BEACH, CALIF.) 2016; 55:100505. [PMID: 28190900 PMCID: PMC5298892 DOI: 10.1117/1.oe.55.10.100505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Antiresonant reflecting optical waveguide power splitters, designed for use around the 635-nm wavelength, are characterized for multiple split angles ranging from 0.5 deg to 9 deg. Theoretical expectations and simulations predict lowest transmission losses at this split junction for the lowest angles. This is confirmed by the experimental structures built in SiO2 films on silicon substrates. A fabrication nonideality affects the achievable splitting angle. Design considerations are discussed based on tradeoffs between loss and the required length for a Y-splitter.
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Affiliation(s)
- Matthew A. Stott
- Brigham Young University, Electrical and Computer Engineering, 459 Clyde Building, Provo, Utah 84602, United States
| | - Jennifer Black
- University of California, Santa Cruz, School of Engineering, 1156 High Street, Santa Cruz, California 95064, United States
| | - Erik Hamilton
- Brigham Young University, Electrical and Computer Engineering, 459 Clyde Building, Provo, Utah 84602, United States
| | - Holger Schmidt
- University of California, Santa Cruz, School of Engineering, 1156 High Street, Santa Cruz, California 95064, United States
| | - Aaron R. Hawkins
- Brigham Young University, Electrical and Computer Engineering, 459 Clyde Building, Provo, Utah 84602, United States
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76
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Parks JW, Schmidt H. Flexible optofluidic waveguide platform with multi-dimensional reconfigurability. Sci Rep 2016; 6:33008. [PMID: 27597164 PMCID: PMC5011725 DOI: 10.1038/srep33008] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 08/18/2016] [Indexed: 01/16/2023] Open
Abstract
Dynamic reconfiguration of photonic function is one of the hallmarks of optofluidics. A number of approaches have been taken to implement optical tunability in microfluidic devices. However, a device architecture that allows for simultaneous high-performance microfluidic fluid handling as well as dynamic optical tuning has not been demonstrated. Here, we introduce such a platform based on a combination of solid- and liquid-core polydimethylsiloxane (PDMS) waveguides that also provides fully functioning microvalve-based sample handling. A combination of these waveguides forms a liquid-core multimode interference waveguide that allows for multi-modal tuning of waveguide properties through core liquids and pressure/deformation. We also introduce a novel lifting-gate lightvalve that simultaneously acts as a fluidic microvalve and optical waveguide, enabling mechanically reconfigurable light and fluid paths and seamless incorporation of controlled particle analysis. These new functionalities are demonstrated by an optical switch with >45 dB extinction ratio and an actuatable particle trap for analysis of biological micro- and nanoparticles.
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Affiliation(s)
- Joshua W Parks
- School of Engineering, University of CA Santa Cruz, 1156 High Street, Santa Cruz, CA 95064 USA
| | - Holger Schmidt
- School of Engineering, University of CA Santa Cruz, 1156 High Street, Santa Cruz, CA 95064 USA
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77
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Ozcelik D, Stott MA, Parks JW, Black JA, Wall TA, Hawkins AR, Schmidt H. Signal-to-noise Enhancement in Optical Detection of Single Viruses with Multi-spot Excitation. IEEE JOURNAL OF SELECTED TOPICS IN QUANTUM ELECTRONICS : A PUBLICATION OF THE IEEE LASERS AND ELECTRO-OPTICS SOCIETY 2016; 22:4402406. [PMID: 27524876 PMCID: PMC4978512 DOI: 10.1109/jstqe.2015.2503321] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
We present fluorescence detection of single H1N1 viruses with enhanced signal to noise ratio (SNR) achieved by multi-spot excitation in liquid-core anti-resonant reflecting optical waveguides (ARROWs). Solid-core Y-splitting ARROW waveguides are fabricated orthogonal to the liquid-core section of the chip, creating multiple excitation spots for the analyte. We derive expressions for the SNR increase after signal processing, and analyze its dependence on signal levels and spot number. Very good agreement between theoretical calculations and experimental results is found. SNR enhancements up to 5x104 are demonstrated.
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Affiliation(s)
- Damla Ozcelik
- School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064 USA
| | - Matthew A. Stott
- Department of Electrical and Computer Engineering, Brigham Young University, Provo, UT 84602 USA
| | - Joshua W. Parks
- School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064 USA
| | - Jennifer A. Black
- School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064 USA
| | - Thomas A. Wall
- Department of Electrical and Computer Engineering, Brigham Young University, Provo, UT 84602 USA
| | - Aaron R. Hawkins
- Department of Electrical and Computer Engineering, Brigham Young University, Provo, UT 84602 USA
| | - Holger Schmidt
- School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064 USA
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78
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Pitt WG, Alizadeh M, Husseini GA, McClellan DS, Buchanan CM, Bledsoe CG, Robison RA, Blanco R, Roeder BL, Melville M, Hunter AK. Rapid separation of bacteria from blood-review and outlook. Biotechnol Prog 2016; 32:823-39. [PMID: 27160415 DOI: 10.1002/btpr.2299] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 05/03/2016] [Indexed: 12/11/2022]
Abstract
The high morbidity and mortality rate of bloodstream infections involving antibiotic-resistant bacteria necessitate a rapid identification of the infectious organism and its resistance profile. Traditional methods based on culturing the blood typically require at least 24 h, and genetic amplification by PCR in the presence of blood components has been problematic. The rapid separation of bacteria from blood would facilitate their genetic identification by PCR or other methods so that the proper antibiotic regimen can quickly be selected for the septic patient. Microfluidic systems that separate bacteria from whole blood have been developed, but these are designed to process only microliter quantities of whole blood or only highly diluted blood. However, symptoms of clinical blood infections can be manifest with bacterial burdens perhaps as low as 10 CFU/mL, and thus milliliter quantities of blood must be processed to collect enough bacteria for reliable genetic analysis. This review considers the advantages and shortcomings of various methods to separate bacteria from blood, with emphasis on techniques that can be done in less than 10 min on milliliter-quantities of whole blood. These techniques include filtration, screening, centrifugation, sedimentation, hydrodynamic focusing, chemical capture on surfaces or beads, field-flow fractionation, and dielectrophoresis. Techniques with the most promise include screening, sedimentation, and magnetic bead capture, as they allow large quantities of blood to be processed quickly. Some microfluidic techniques can be scaled up. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:823-839, 2016.
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Affiliation(s)
- William G Pitt
- Dept. of Chemical Engineering, Brigham Young University, Provo, UT
| | - Mahsa Alizadeh
- Dept. of Chemical Engineering, Brigham Young University, Provo, UT
| | - Ghaleb A Husseini
- Dept. of Chemical Engineering, American University of Sharjah, Sharjah, UAE
| | | | - Clara M Buchanan
- Dept. of Chemical Engineering, Brigham Young University, Provo, UT
| | - Colin G Bledsoe
- Dept. of Chemical Engineering, Brigham Young University, Provo, UT
| | - Richard A Robison
- Dept. of Microbiology and Molecular Biology, Brigham Young University, Provo, UT
| | - Rae Blanco
- Dept. of Chemical Engineering, Brigham Young University, Provo, UT
| | | | - Madison Melville
- Dept. of Chemical Engineering, Brigham Young University, Provo, UT
| | - Alex K Hunter
- Dept. of Chemical Engineering, Brigham Young University, Provo, UT
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79
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Lee Y, Kim Y, Lee D, Roy D, Park JW. Quantification of Fewer than Ten Copies of a DNA Biomarker without Amplification or Labeling. J Am Chem Soc 2016; 138:7075-81. [DOI: 10.1021/jacs.6b02791] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
| | | | | | - Dhruvajyoti Roy
- Nanogea Inc., 6162 Bristol Parkway, Culver City, California 90230, United States
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80
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81
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Wall TA, Chu RP, Parks JW, Ozcelik D, Schmidt H, Hawkins AR. Improved environmental stability for plasma enhanced chemical vapor deposition SiO 2 waveguides using buried channel designs. OPTICAL ENGINEERING (REDONDO BEACH, CALIF.) 2016; 55:040501. [PMID: 28190901 PMCID: PMC5298888 DOI: 10.1117/1.oe.55.4.040501] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Ridge and buried channel waveguides (BCWs) made using plasma-enhanced chemical vapor deposition SiO2 were fabricated and tested after being subjected to long 85°C water baths. The water bath was used to investigate the effects of any water absorption in the ridge and BCWs. Optical mode spreading and power throughput were measured over a period of three weeks. The ridge waveguides quickly absorbed water within the critical guiding portion of the waveguide. This caused a nonuniformity in the refractive index profile, leading to poor modal confinement after only seven days. The BCWs possessed a low index top cladding layer of SiO2, which caused an increase in the longevity of the waveguides, and after 21 days, the BCW samples still maintained ~20% throughput, much higher than the ridge waveguides, which had a throughput under 5%.
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Affiliation(s)
- Thomas A. Wall
- Brigham Young University, Electrical and Computer Engineering, 459 Clyde Building, Provo, Utah 84602, United States
| | - Roger P. Chu
- Brigham Young University, Electrical and Computer Engineering, 459 Clyde Building, Provo, Utah 84602, United States
| | - Joshua W. Parks
- University of California, Santa Cruz, Baskin Engineering, Room 40, 1156 High Street, Santa Cruz, California 95064, United States
| | - Damla Ozcelik
- University of California, Santa Cruz, Baskin Engineering, Room 40, 1156 High Street, Santa Cruz, California 95064, United States
| | - Holger Schmidt
- University of California, Santa Cruz, Baskin Engineering, Room 40, 1156 High Street, Santa Cruz, California 95064, United States
| | - Aaron R. Hawkins
- Brigham Young University, Electrical and Computer Engineering, 459 Clyde Building, Provo, Utah 84602, United States
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82
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Testa G, Persichetti G, Bernini R. Liquid Core ARROW Waveguides: A Promising Photonic Structure for Integrated Optofluidic Microsensors. MICROMACHINES 2016; 7:mi7030047. [PMID: 30407419 PMCID: PMC6190334 DOI: 10.3390/mi7030047] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Revised: 02/29/2016] [Accepted: 03/07/2016] [Indexed: 12/11/2022]
Abstract
In this paper, we introduce a liquid core antiresonant reflecting optical waveguide (ARROW) as a novel optofluidic device that can be used to create innovative and highly functional microsensors. Liquid core ARROWs, with their dual ability to guide the light and the fluids in the same microchannel, have shown great potential as an optofluidic tool for quantitative spectroscopic analysis. ARROWs feature a planar architecture and, hence, are particularly attractive for chip scale integrated system. Step by step, several improvements have been made in recent years towards the implementation of these waveguides in a complete on-chip system for highly-sensitive detection down to the single molecule level. We review applications of liquid ARROWs for fluids sensing and discuss recent results and trends in the developments and applications of liquid ARROW in biomedical and biochemical research. The results outlined show that the strong light matter interaction occurring in the optofluidic channel of an ARROW and the versatility offered by the fabrication methods makes these waveguides a very promising building block for optofluidic sensor development.
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Affiliation(s)
- Genni Testa
- Istituto per il Rilevamento Elettromagnetico dell'Ambiente, Consiglio Nazionale delle Ricerche (IREA-CNR), Via Diocleziano 328, 80124 Naples, Italy.
| | - Gianluca Persichetti
- Istituto per il Rilevamento Elettromagnetico dell'Ambiente, Consiglio Nazionale delle Ricerche (IREA-CNR), Via Diocleziano 328, 80124 Naples, Italy.
| | - Romeo Bernini
- Istituto per il Rilevamento Elettromagnetico dell'Ambiente, Consiglio Nazionale delle Ricerche (IREA-CNR), Via Diocleziano 328, 80124 Naples, Italy.
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83
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Liu S, Hawkins AR, Schmidt H. Optofluidic devices with integrated solid-state nanopores. Mikrochim Acta 2016; 183:1275-1287. [PMID: 27046940 DOI: 10.1007/s00604-016-1758-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
This review (with 90 refs.) covers the state of the art in optofluidic devices with integrated solid-state nanopores for use in detection and sensing. Following an introduction into principles of optofluidics and solid-state nanopore technology, we discuss features of solid-state nanopore based assays using optofluidics. This includes the incorporation of solid-state nanopores into optofluidic platforms based on liquid-core anti-resonant reflecting optical waveguides (ARROWs), methods for their fabrication, aspects of single particle detection and particle manipulation. We then describe the new functionalities provided by solid-state nanopores integrated into optofluidic chips, in particular acting as smart gates for correlated electro-optical detection and discrimination of nanoparticles. This enables the identification of viruses and λ-DNA, particle trajectory simulations, enhancing sensitivity by tuning the shape of nanopores. The review concludes with a summary and an outlook.
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Affiliation(s)
- Shuo Liu
- School of Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Aaron R Hawkins
- ECEn Department, 459 Clyde Building, Brigham Young University, Provo, UT 84602, USA
| | - Holger Schmidt
- School of Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
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84
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Md Ali MA, Ostrikov K(K, Khalid FA, Majlis BY, Kayani AA. Active bioparticle manipulation in microfluidic systems. RSC Adv 2016. [DOI: 10.1039/c6ra20080j] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The motion of bioparticles in a microfluidic environment can be actively controlled using several tuneable mechanisms, including hydrodynamic, electrophoresis, dielectrophoresis, magnetophoresis, acoustophoresis, thermophoresis and optical forces.
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Affiliation(s)
- Mohd Anuar Md Ali
- Institute of Microengineering and Nanoelectronics
- Universiti Kebangsaan Malaysia
- Bangi
- Malaysia
| | - Kostya (Ken) Ostrikov
- School of Chemistry, Physics, and Mechanical Engineering
- Queensland University of Technology
- Brisbane
- Australia
- CSIRO-QUT Joint Sustainable Processes and Devices Laboratory
| | - Fararishah Abdul Khalid
- Faculty of Technology Management and Technopreneurship
- Universiti Teknikal Malaysia Melaka
- Malaysia
| | - Burhanuddin Y. Majlis
- Institute of Microengineering and Nanoelectronics
- Universiti Kebangsaan Malaysia
- Bangi
- Malaysia
| | - Aminuddin A. Kayani
- Institute of Microengineering and Nanoelectronics
- Universiti Kebangsaan Malaysia
- Bangi
- Malaysia
- Center for Advanced Materials and Green Technology
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85
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Leake KD, Olson MAB, Ozcelik D, Hawkins AR, Schmidt H. Spectrally reconfigurable integrated multi-spot particle trap. OPTICS LETTERS 2015; 40:5435-8. [PMID: 26625019 PMCID: PMC4833011 DOI: 10.1364/ol.40.005435] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Optical manipulation of small particles in the form of trapping, pushing, or sorting has developed into a vast field with applications in the life sciences, biophysics, and atomic physics. Recently, there has been increasing effort toward integration of particle manipulation techniques with integrated photonic structures on self-contained optofluidic chips. Here, we use the wavelength dependence of multi-spot pattern formation in multimode interference (MMI) waveguides to create a new type of reconfigurable, integrated optical particle trap. Interfering lateral MMI modes create multiple trapping spots in an intersecting fluidic channel. The number of trapping spots can be dynamically controlled by altering the trapping wavelength. This novel, spectral reconfigurability is utilized to deterministically move single and multiple particles between different trapping locations along the channel. This fully integrated multi-particle trap can form the basis of high throughput biophotonic assays on a chip.
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Affiliation(s)
- Kaelyn D. Leake
- School of Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, USA
| | - Michael A. B. Olson
- Department of Electrical and Computer Engineering, Brigham Young University, 459 Clyde Building, Provo, Utah 84602, USA
| | - Damla Ozcelik
- School of Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, USA
| | - Aaron R. Hawkins
- Department of Electrical and Computer Engineering, Brigham Young University, 459 Clyde Building, Provo, Utah 84602, USA
| | - Holger Schmidt
- Department of Electrical and Computer Engineering, Brigham Young University, 459 Clyde Building, Provo, Utah 84602, USA
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