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Lee SM, Balakrishnan HK, Doeven EH, Yuan D, Guijt RM. Chemical Trends in Sample Preparation for Nucleic Acid Amplification Testing (NAAT): A Review. BIOSENSORS 2023; 13:980. [PMID: 37998155 PMCID: PMC10669371 DOI: 10.3390/bios13110980] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 11/02/2023] [Accepted: 11/07/2023] [Indexed: 11/25/2023]
Abstract
Nucleic acid amplification testing facilitates the detection of disease through specific genomic sequences and is attractive for point-of-need testing (PONT); in particular, the early detection of microorganisms can alert early response systems to protect the public and ecosystems from widespread outbreaks of biological threats, including infectious diseases. Prior to nucleic acid amplification and detection, extensive sample preparation techniques are required to free nucleic acids and extract them from the sample matrix. Sample preparation is critical to maximize the sensitivity and reliability of testing. As the enzymatic amplification reactions can be sensitive to inhibitors from the sample, as well as from chemicals used for lysis and extraction, avoiding inhibition is a significant challenge, particularly when minimising liquid handling steps is also desirable for the translation of the assay to a portable format for PONT. The reagents used in sample preparation for nucleic acid testing, covering lysis and NA extraction (binding, washing, and elution), are reviewed with a focus on their suitability for use in PONT.
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Affiliation(s)
- Soo Min Lee
- Centre for Regional and Rural Futures (CeRRF), Deakin University, Locked Bag 20000, Geelong, VIC 3220, Australia
| | - Hari Kalathil Balakrishnan
- Department of Chemical Engineering, Khalifa University, Abu Dhabi P.O. Box 127788, United Arab Emirates;
| | - Egan H. Doeven
- School of Life and Environmental Sciences, Deakin University, Locked Bag 20000, Geelong, VIC 3220, Australia;
| | - Dan Yuan
- School of Mechanical and Mining Engineering, The University of Queensland, Brisbane, QLD 4072, Australia;
| | - Rosanne M. Guijt
- Centre for Regional and Rural Futures (CeRRF), Deakin University, Locked Bag 20000, Geelong, VIC 3220, Australia
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2
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Kundrod KA, Barra M, Wilkinson A, Smith CA, Natoli ME, Chang MM, Coole JB, Santhanaraj A, Lorenzoni C, Mavume C, Atif H, Montealegre JR, Scheurer ME, Castle PE, Schmeler KM, Richards-Kortum RR. An integrated isothermal nucleic acid amplification test to detect HPV16 and HPV18 DNA in resource-limited settings. Sci Transl Med 2023; 15:eabn4768. [PMID: 37343083 PMCID: PMC10566637 DOI: 10.1126/scitranslmed.abn4768] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 06/01/2023] [Indexed: 06/23/2023]
Abstract
High-risk human papillomavirus (HPV) DNA testing is widely acknowledged as the most sensitive cervical cancer screening method but has limited availability in resource-limited settings, where the burden of cervical cancer is highest. Recently, HPV DNA tests have been developed for use in resource-limited settings, but they remain too costly for widespread use and require instruments that are often limited to centralized laboratories. To help meet the global need for low-cost cervical cancer screening, we developed a prototype, sample-to-answer, point-of-care test for HPV16 and HPV18 DNA. Our test relies on isothermal DNA amplification and lateral flow detection, two technologies that reduce the need for complex instrumentation. We integrated all test components into a low-cost, manufacturable platform, and performance of the integrated test was evaluated with synthetic samples, provider-collected clinical samples in a high-resource setting in the United States, and self-collected clinical samples in a low-resource setting in Mozambique. We demonstrated a clinically relevant limit of detection of 1000 HPV16 or HPV18 DNA copies per test. The test requires six user steps, yields results in 45 min, and can be performed using a benchtop instrument and minicentrifuge by minimally trained personnel. The projected per-test cost is <$5, and the projected instrumentation cost is <$1000. These results show the feasibility of a sample-to-answer, point-of-care HPV DNA test. With the inclusion of other HPV types, this test has the potential to fill a critical gap for decentralized and globally accessible cervical cancer screening.
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Affiliation(s)
- Kathryn A Kundrod
- Department of Bioengineering, Rice University, Houston, TX, USA
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Maria Barra
- Department of Bioengineering, Rice University, Houston, TX, USA
| | | | - Chelsey A Smith
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Mary E Natoli
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Megan M Chang
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Jackson B Coole
- Department of Bioengineering, Rice University, Houston, TX, USA
| | | | - Cesaltina Lorenzoni
- Ministério da Saúde de Moçambique (MISAU), Hospital Central de Maputo, Hospital Geral de Mavalane, Universidade Eduardo Mondlane (UEM), Maputo, Mozambique
| | - Celda Mavume
- Ministério da Saúde de Moçambique (MISAU), Hospital Central de Maputo, Hospital Geral de Mavalane, Universidade Eduardo Mondlane (UEM), Maputo, Mozambique
| | - Hira Atif
- Ministério da Saúde de Moçambique (MISAU), Hospital Central de Maputo, Hospital Geral de Mavalane, Universidade Eduardo Mondlane (UEM), Maputo, Mozambique
| | | | - Michael E Scheurer
- Department of Pediatrics-Hematology/Oncology, Baylor College of Medicine, Houston, TX, USA
| | - Philip E Castle
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
- Division of Cancer Prevention, National Cancer Institute, Rockville, MD, USA
| | - Kathleen M Schmeler
- Department of Gynecologic Oncology & Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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3
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Smith CA, Chang MM, Kundrod KA, Novak EN, Parra SG, López L, Mavume C, Lorenzoni C, Maza M, Salcedo MP, Carns JL, Baker E, Montealegre J, Scheurer M, Castle PE, Schmeler KM, Richards-Kortum RR. A low-cost, paper-based hybrid capture assay to detect high-risk HPV DNA for cervical cancer screening in low-resource settings. LAB ON A CHIP 2023; 23:451-465. [PMID: 36562325 PMCID: PMC9890501 DOI: 10.1039/d2lc00885h] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 12/10/2022] [Indexed: 06/17/2023]
Abstract
Cervical cancer is a leading cause of cancer death for women in low-resource settings. The World Health Organization recommends that cervical cancer screening programs incorporate HPV DNA testing, but available tests are expensive, require laboratory infrastructure, and cannot be performed at the point-of-care. We developed a two-dimensional paper network (2DPN), hybrid-capture, signal amplification assay and a point-of-care sample preparation protocol to detect high-risk HPV DNA from exfoliated cervical cells within an hour. The test does not require expensive equipment and has an estimated cost of <$3 per test without the need for batching. We evaluated performance of the paper HPV DNA assay with short synthetic and genomic HPV DNA targets, HPV positive and negative cellular samples, and two sets of clinical samples. The first set of clinical samples consisted of 16 biobanked, provider-collected cervical samples from a study in El Salvador previously tested with careHPV and subsequently tested in a controlled laboratory environment. The paper HPV DNA test correctly identified eight of eight HPV-negative clinical samples and seven of eight HPV-positive clinical samples. We then performed a field evaluation of the paper HPV DNA test in a hospital laboratory in Mozambique. Cellular controls generated expected results throughout field testing with fully lyophilized sample preparation and 2DPN reagents. When evaluated with 16 residual self-collected cervicovaginal samples previously tested by the GeneXpert HPV assay ("Xpert"), the accuracy of the HPV DNA paper test in the field was reduced compared to testing in the controlled laboratory environment, with positive results obtained for all eight HPV-positive samples as well as seven of eight HPV-negative samples. Further evaluation showed reduction in performance was likely due in part to increased concentration of exfoliated cells in the self-collected clinical samples from Mozambique compared with provider-collected samples from El Salvador. Finally, a formal usability assessment was conducted with users in El Salvador and Mozambique; the assay was rated as acceptable to perform after minimal training. With additional optimization for higher cell concentrations and inclusion of an internal cellular control, the paper HPV DNA assay offers promise as a low-cost, point-of-care cervical cancer screening test in low-resource settings.
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Affiliation(s)
- Chelsey A Smith
- Department of Bioengineering, Rice University, Houston, TX, USA.
| | - Megan M Chang
- Department of Bioengineering, Rice University, Houston, TX, USA.
| | | | - Emilie N Novak
- Department of Bioengineering, Rice University, Houston, TX, USA.
| | - Sonia G Parra
- Department of Bioengineering, Rice University, Houston, TX, USA.
| | - Leticia López
- Basic Health International, San Salvador, El Salvador
| | | | - Cesaltina Lorenzoni
- Hospital Central de Maputo, Maputo, Mozambique
- Ministerio da Saude de Moçambique (MISAU), Maputo, Mozambique
| | - Mauricio Maza
- Basic Health International, San Salvador, El Salvador
| | - Mila P Salcedo
- Department of Gynecologic Oncology & Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Jennifer L Carns
- Department of Bioengineering, Rice University, Houston, TX, USA.
| | - Ellen Baker
- Department of Gynecologic Oncology & Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Jane Montealegre
- Department of Pediatrics-Hematology/Oncology, Baylor College of Medicine, Houston, TX, USA
| | - Michael Scheurer
- Department of Pediatrics-Hematology/Oncology, Baylor College of Medicine, Houston, TX, USA
| | - Philip E Castle
- Divisions of Cancer Prevention and Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Kathleen M Schmeler
- Department of Gynecologic Oncology & Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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4
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Zhao J, Li N, Zhou X, Yu Z, Lan M, Chen S, Miao J, Li Y, Li G, Yang F. Electrolysis of Bacteria Based on Microfluidic Technology. MICROMACHINES 2023; 14:144. [PMID: 36677205 PMCID: PMC9864792 DOI: 10.3390/mi14010144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/24/2022] [Accepted: 01/01/2023] [Indexed: 06/17/2023]
Abstract
Cell lysis is a key step for studying the structure and function of proteins in cells and an important intermediate step in drug screening, cancer diagnosis, and genome analysis. The current cell lysis methods still suffer from limitations, such as the need for large instruments, a long and time-consuming process, a large sample volume, chemical reagent contamination, and their unsuitability for the small amount of bacteria lysis required for point-of-care testing (POCT) devices. Therefore, a fast, chemical-free, portable, and non-invasive device needs to be developed. In the present study, we designed an integrated microfluidic chip to achieve E. coli lysis by applying an alternating current (AC) electric field and investigated the effects of voltage, frequency, and flow rate on the lysis. The results showed that the lysis efficiency of the bacteria was increased with a higher voltage, lower frequency, and lower flow rate. When the voltage was at 10 Vp-p, the lysis efficiency was close to 100%. The study provided a simple, rapid, reagent-free, and high-efficiency cleavage method for biology and biomedical applications involving bacteria lysis.
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Stettinius A, Holmes H, Zhang Q, Mehochko I, Winters M, Hutchison R, Maxwell A, Holliday J, Vlaisavljevich E. DNA release from plant tissue using focused ultrasound extraction (FUSE). APPLICATIONS IN PLANT SCIENCES 2023; 11:e11510. [PMID: 36818781 PMCID: PMC9934592 DOI: 10.1002/aps3.11510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 10/31/2022] [Accepted: 11/02/2022] [Indexed: 06/18/2023]
Abstract
PREMISE Sample preparation in genomics is a critical step that is often overlooked in molecular workflows and impacts the success of downstream genetic applications. This study explores the use of a recently developed focused ultrasound extraction (FUSE) technique to enable the rapid release of DNA from plant tissues for genetic analysis. METHODS FUSE generates a dense acoustic cavitation bubble cloud that pulverizes targeted tissue into acellular debris. This technique was applied to leaf samples of American chestnut (Castanea dentata), tulip poplar (Liriodendron tulipifera), red maple (Acer rubrum), and chestnut oak (Quercus montana). RESULTS We observed that FUSE can extract high quantities of DNA in 9-15 min, compared to the 30 min required for control DNA extraction methods. FUSE extracted DNA quantities of 24.33 ± 6.51 ng/mg and 35.32 ± 9.21 ng/mg from American chestnut and red maple, respectively, while control methods yielded 6.22 ± 0.87 ng/mg and 11.51 ± 1.95 ng/mg, respectively. The quality of the DNA released by FUSE allowed for successful amplification and next-generation sequencing. DISCUSSION These results indicate that FUSE can improve DNA extraction efficiency for leaf tissues. Continued development of this technology aims to adapt to field-deployable systems to increase the cataloging of genetic biodiversity, particularly in low-resource biodiversity hotspots.
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Affiliation(s)
- Alexia Stettinius
- Department of Biomedical Engineering and MechanicsVirginia Polytechnic Institute and State UniversityBlacksburgVirginiaUSA
| | - Hal Holmes
- Department of Biomedical Engineering and MechanicsVirginia Polytechnic Institute and State UniversityBlacksburgVirginiaUSA
- Conservation X LabsSeattleWashingtonUSA
| | - Qian Zhang
- Department of Forest Resources and Environmental ConservationVirginia Polytechnic Institute and State UniversityBlacksburgVirginiaUSA
| | - Isabelle Mehochko
- Department of Biomedical Engineering and MechanicsVirginia Polytechnic Institute and State UniversityBlacksburgVirginiaUSA
| | | | - Ruby Hutchison
- Department of Biomedical Engineering and MechanicsVirginia Polytechnic Institute and State UniversityBlacksburgVirginiaUSA
| | - Adam Maxwell
- Department of UrologyUniversity of WashingtonSeattleWashingtonUSA
| | - Jason Holliday
- Department of Forest Resources and Environmental ConservationVirginia Polytechnic Institute and State UniversityBlacksburgVirginiaUSA
| | - Eli Vlaisavljevich
- Department of Biomedical Engineering and MechanicsVirginia Polytechnic Institute and State UniversityBlacksburgVirginiaUSA
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6
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Jang M, Kim S, Song J, Kim S. Rapid and simple detection of influenza virus via isothermal amplification lateral flow assay. Anal Bioanal Chem 2022; 414:4685-4696. [PMID: 35501506 PMCID: PMC9060413 DOI: 10.1007/s00216-022-04090-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 04/12/2022] [Accepted: 04/19/2022] [Indexed: 12/03/2022]
Abstract
Respiratory illness caused by influenza virus is a serious public health problem worldwide. As the symptoms of influenza virus infection are similar to those of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, it is essential to distinguish these two viruses. Therefore, to properly respond to a pathogen, a detection method that is capable of rapid and accurate diagnosis in a hospital or at home is required. To satisfy this need, we applied loop-mediated isothermal amplification (LAMP) and an isothermal nucleic acid amplification technique, along with a system to analyze the results without specialized equipment, a lateral flow assay (LFA). Using the platform developed in this study, all processes, from sample preparation to detection, can be performed without special equipment. Unlike existing PCR methods, the nucleic acid amplification can be performed in the field because hot packs do not require electricity. Thus, the designed platform can provide rapid results without the need to transport the samples to a laboratory or hospital. These advantages are not limited to operations in developing countries with poor access to medical systems. In conclusion, the developed technology is a promising tool for infectious disease management that allows for rapid identification of infectious diseases and appropriate treatment of patients.
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Affiliation(s)
- Minju Jang
- Department of Bionanotechnology, Gachon University, Seongnam, 13120, Republic of Korea
| | - SeJin Kim
- 33, Sagimakgol-ro 62beon-gil, Jungwon-gu, Seongnam, 13211, Republic of Korea
| | - Junkyu Song
- 33, Sagimakgol-ro 62beon-gil, Jungwon-gu, Seongnam, 13211, Republic of Korea
| | - Sanghyo Kim
- Department of Bionanotechnology, Gachon University, Seongnam, 13120, Republic of Korea.
- 33, Sagimakgol-ro 62beon-gil, Jungwon-gu, Seongnam, 13211, Republic of Korea.
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7
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Chen FE, Trick AY, Hasnain AC, Hsieh K, Chen L, Shin DJ, Wang TH. Ratiometric PCR in a Portable Sample-to-Result Device for Broad-Based Pathogen Identification. Anal Chem 2022; 94:9372-9379. [PMID: 35730588 DOI: 10.1021/acs.analchem.2c01357] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Polymerase chain reaction (PCR)-based diagnostic testing is the gold standard method for pathogen identification (ID) with recent developments enabling automated PCR tests for point-of-care (POC) use. However, multiplexed identification of several pathogens in PCR assays typically requires optics for an equivalent number of fluorescence channels, increasing instrumentation's complexity and cost. In this study, we first developed ratiometric PCR that surpassed one target per color barrier to allow multiplexed identification while minimizing optical components for affordable POC use. We realized it by amplifying pathogenic targets with fluorescently labeled hydrolysis probes with a specific ratio of red-to-green fluorophores for each bacterial species. We then coupled ratiometric PCR and automated magnetic beads-based sample preparation within a thermoplastic cartridge and a portable droplet magnetofluidic platform. We named the integrated workflow POC-ratioPCR. We demonstrated that the POC-ratioPCR could detect one out of six bacterial targets related to urinary tract infections (UTIs) in a single reaction using only two-color channels. We further evaluated POC-ratioPCR using mock bacterial urine samples spiked with good agreement. The POC-ratioPCR presents a simple and effective method for enabling broad-based POC PCR identification of pathogens directly from crude biosamples with low optical instrumentation complexity.
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Affiliation(s)
- Fan-En Chen
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Alexander Y Trick
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Alexander C Hasnain
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Kuangwen Hsieh
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Liben Chen
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Dong Jin Shin
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Tza-Huei Wang
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States.,Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States.,Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland 21218, United States
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8
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Nasrollahi F, Haghniaz R, Hosseini V, Davoodi E, Mahmoodi M, Karamikamkar S, Darabi MA, Zhu Y, Lee J, Diltemiz SE, Montazerian H, Sangabathuni S, Tavafoghi M, Jucaud V, Sun W, Kim H, Ahadian S, Khademhosseini A. Micro and Nanoscale Technologies for Diagnosis of Viral Infections. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2100692. [PMID: 34310048 PMCID: PMC8420309 DOI: 10.1002/smll.202100692] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 03/19/2021] [Indexed: 05/16/2023]
Abstract
Viral infection is one of the leading causes of mortality worldwide. The growth of globalization significantly increases the risk of virus spreading, making it a global threat to future public health. In particular, the ongoing coronavirus disease 2019 (COVID-19) pandemic outbreak emphasizes the importance of devices and methods for rapid, sensitive, and cost-effective diagnosis of viral infections in the early stages by which their quick and global spread can be controlled. Micro and nanoscale technologies have attracted tremendous attention in recent years for a variety of medical and biological applications, especially in developing diagnostic platforms for rapid and accurate detection of viral diseases. This review addresses advances of microneedles, microchip-based integrated platforms, and nano- and microparticles for sampling, sample processing, enrichment, amplification, and detection of viral particles and antigens related to the diagnosis of viral diseases. Additionally, methods for the fabrication of microchip-based devices and commercially used devices are described. Finally, challenges and prospects on the development of micro and nanotechnologies for the early diagnosis of viral diseases are highlighted.
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Affiliation(s)
- Fatemeh Nasrollahi
- Terasaki Institute for Biomedical Innovation (TIBI)Los AngelesCA90024USA
- Department of BioengineeringUniversity of California‐Los AngelesLos AngelesCA90095USA
| | - Reihaneh Haghniaz
- Terasaki Institute for Biomedical Innovation (TIBI)Los AngelesCA90024USA
- Department of BioengineeringUniversity of California‐Los AngelesLos AngelesCA90095USA
| | - Vahid Hosseini
- Terasaki Institute for Biomedical Innovation (TIBI)Los AngelesCA90024USA
- Department of BioengineeringUniversity of California‐Los AngelesLos AngelesCA90095USA
| | - Elham Davoodi
- Terasaki Institute for Biomedical Innovation (TIBI)Los AngelesCA90024USA
- Department of BioengineeringUniversity of California‐Los AngelesLos AngelesCA90095USA
- Department of Mechanical and Mechatronics EngineeringUniversity of WaterlooWaterlooONN2L 3G1Canada
| | - Mahboobeh Mahmoodi
- Department of BioengineeringUniversity of California‐Los AngelesLos AngelesCA90095USA
- Department of Biomedical EngineeringYazd BranchIslamic Azad UniversityYazd8915813135Iran
| | | | - Mohammad Ali Darabi
- Terasaki Institute for Biomedical Innovation (TIBI)Los AngelesCA90024USA
- Department of BioengineeringUniversity of California‐Los AngelesLos AngelesCA90095USA
| | - Yangzhi Zhu
- Terasaki Institute for Biomedical Innovation (TIBI)Los AngelesCA90024USA
| | - Junmin Lee
- Terasaki Institute for Biomedical Innovation (TIBI)Los AngelesCA90024USA
| | - Sibel Emir Diltemiz
- Department of BioengineeringUniversity of California‐Los AngelesLos AngelesCA90095USA
- Department of ChemistryFaculty of ScienceEskisehir Technical UniversityEskisehir26470Turkey
| | - Hossein Montazerian
- Terasaki Institute for Biomedical Innovation (TIBI)Los AngelesCA90024USA
- Department of BioengineeringUniversity of California‐Los AngelesLos AngelesCA90095USA
| | | | - Maryam Tavafoghi
- Department of BioengineeringUniversity of California‐Los AngelesLos AngelesCA90095USA
| | - Vadim Jucaud
- Terasaki Institute for Biomedical Innovation (TIBI)Los AngelesCA90024USA
| | - Wujin Sun
- Terasaki Institute for Biomedical Innovation (TIBI)Los AngelesCA90024USA
| | - Han‐Jun Kim
- Terasaki Institute for Biomedical Innovation (TIBI)Los AngelesCA90024USA
| | - Samad Ahadian
- Terasaki Institute for Biomedical Innovation (TIBI)Los AngelesCA90024USA
| | - Ali Khademhosseini
- Terasaki Institute for Biomedical Innovation (TIBI)Los AngelesCA90024USA
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Pahlow S, Hentschel S, Horbert P, Romero C, Lehniger L, Wagner S, Popp J, Weber K. Isolation of pathogenic bacteria from sputum samples using a 3D-printed cartridge system. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2021; 13:4884-4895. [PMID: 34590629 DOI: 10.1039/d1ay00924a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Within this contribution we introduce a 3D-printed cartridge system enabling the convenient and cost-efficient sample preparation from sputum for subsequent PCR based detection schemes. The developed fluidic system operates on pneumatic actuations. The closed system ensures a very low probability for contamination during sample processing, which is crucial when using a highly sensitive detection method such as PCR. The enrichment of the bacterial cells is achieved using different types of amine-functionalized particles. Our particle-based sample preparation approach yields intact and viable bacterial cells. Accordingly, not only PCR-based detection schemes can be employed, but also spectroscopic methods and biochemical tests, which require cultivation steps, are possible. The cartridge design in principle is compatible with magnetic and non-magnetic particle types. We investigated both variants and found that the performance of expanded glass beads is superior over the magnetic particles within the cartridge. Owing to the rather large size of the expanded glass beads, the dimensions of the channels can be enlarged, leading to lower hydrodynamic resistances, which is beneficial when processing viscous samples such as sputum. We verified the performance of our system using both artificial and real sputum samples containing Escherichia coli and Moraxella catarrhalis.
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Affiliation(s)
- Susanne Pahlow
- Friedrich Schiller University Jena, Institute of Physical Chemistry and Abbe Center of Photonics, Helmholtzweg 4, 07743 Jena, Germany.
- InfectoGnostics Research Campus Jena, Center for Applied Research, Philosophenweg 7, 07743 Jena, Germany
- Leibniz Institute of Photonic Technology - Member of the Research Alliance "Leibniz Health Technologies", Albert-Einstein-Straße 9, 07745 Jena, Germany
| | - Stefanie Hentschel
- Friedrich Schiller University Jena, Institute of Physical Chemistry and Abbe Center of Photonics, Helmholtzweg 4, 07743 Jena, Germany.
- InfectoGnostics Research Campus Jena, Center for Applied Research, Philosophenweg 7, 07743 Jena, Germany
- Leibniz Institute of Photonic Technology - Member of the Research Alliance "Leibniz Health Technologies", Albert-Einstein-Straße 9, 07745 Jena, Germany
| | - Peter Horbert
- Leibniz Institute of Photonic Technology - Member of the Research Alliance "Leibniz Health Technologies", Albert-Einstein-Straße 9, 07745 Jena, Germany
| | - Cynthia Romero
- Friedrich Schiller University Jena, Institute of Physical Chemistry and Abbe Center of Photonics, Helmholtzweg 4, 07743 Jena, Germany.
- Leibniz Institute of Photonic Technology - Member of the Research Alliance "Leibniz Health Technologies", Albert-Einstein-Straße 9, 07745 Jena, Germany
| | - Lydia Lehniger
- Friedrich Schiller University Jena, Institute of Physical Chemistry and Abbe Center of Photonics, Helmholtzweg 4, 07743 Jena, Germany.
- InfectoGnostics Research Campus Jena, Center for Applied Research, Philosophenweg 7, 07743 Jena, Germany
- Leibniz Institute of Photonic Technology - Member of the Research Alliance "Leibniz Health Technologies", Albert-Einstein-Straße 9, 07745 Jena, Germany
| | - Sascha Wagner
- Leibniz Institute of Photonic Technology - Member of the Research Alliance "Leibniz Health Technologies", Albert-Einstein-Straße 9, 07745 Jena, Germany
| | - Jürgen Popp
- Friedrich Schiller University Jena, Institute of Physical Chemistry and Abbe Center of Photonics, Helmholtzweg 4, 07743 Jena, Germany.
- InfectoGnostics Research Campus Jena, Center for Applied Research, Philosophenweg 7, 07743 Jena, Germany
- Leibniz Institute of Photonic Technology - Member of the Research Alliance "Leibniz Health Technologies", Albert-Einstein-Straße 9, 07745 Jena, Germany
| | - Karina Weber
- Friedrich Schiller University Jena, Institute of Physical Chemistry and Abbe Center of Photonics, Helmholtzweg 4, 07743 Jena, Germany.
- InfectoGnostics Research Campus Jena, Center for Applied Research, Philosophenweg 7, 07743 Jena, Germany
- Leibniz Institute of Photonic Technology - Member of the Research Alliance "Leibniz Health Technologies", Albert-Einstein-Straße 9, 07745 Jena, Germany
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10
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Nichols ZE, Geddes CD. Sample Preparation and Diagnostic Methods for a Variety of Settings: A Comprehensive Review. Molecules 2021; 26:5666. [PMID: 34577137 PMCID: PMC8470389 DOI: 10.3390/molecules26185666] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 09/14/2021] [Accepted: 09/14/2021] [Indexed: 11/16/2022] Open
Abstract
Sample preparation is an essential step for nearly every type of biochemical analysis in use today. Among the most important of these analyses is the diagnosis of diseases, since their treatment may rely greatly on time and, in the case of infectious diseases, containing their spread within a population to prevent outbreaks. To address this, many different methods have been developed for use in the wide variety of settings for which they are needed. In this work, we have reviewed the literature and report on a broad range of methods that have been developed in recent years and their applications to point-of-care (POC), high-throughput screening, and low-resource and traditional clinical settings for diagnosis, including some of those that were developed in response to the coronavirus disease 2019 (COVID-19) pandemic. In addition to covering alternative approaches and improvements to traditional sample preparation techniques such as extractions and separations, techniques that have been developed with focuses on integration with smart devices, laboratory automation, and biosensors are also discussed.
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Affiliation(s)
- Zach E. Nichols
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, 1000 Hilltop Drive, Baltimore, MD 21250, USA;
- Institute of Fluorescence, University of Maryland, Baltimore County, 701 E Pratt Street, Baltimore, MD 21270, USA
| | - Chris D. Geddes
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, 1000 Hilltop Drive, Baltimore, MD 21250, USA;
- Institute of Fluorescence, University of Maryland, Baltimore County, 701 E Pratt Street, Baltimore, MD 21270, USA
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11
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Bao M, Chen Q, Xu Z, Jensen EC, Liu C, Waitkus JT, Yuan X, He Q, Qin P, Du K. Challenges and Opportunities for Clustered Regularly Interspaced Short Palindromic Repeats Based Molecular Biosensing. ACS Sens 2021; 6:2497-2522. [PMID: 34143608 DOI: 10.1021/acssensors.1c00530] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Clustered regularly interspaced short palindromic repeats, CRISPR, has recently emerged as a powerful molecular biosensing tool for nucleic acids and other biomarkers due to its unique properties such as collateral cleavage nature, room temperature reaction conditions, and high target-recognition specificity. Numerous platforms have been developed to leverage the CRISPR assay for ultrasensitive biosensing applications. However, to be considered as a new gold standard, several key challenges for CRISPR molecular biosensing must be addressed. In this paper, we briefly review the history of biosensors, followed by the current status of nucleic acid-based detection methods. We then discuss the current challenges pertaining to CRISPR-based nucleic acid detection, followed by the recent breakthroughs addressing these challenges. We focus upon future advancements required to enable rapid, simple, sensitive, specific, multiplexed, amplification-free, and shelf-stable CRISPR-based molecular biosensors.
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Affiliation(s)
- Mengdi Bao
- Department of Mechanical Engineering, Rochester Institute of Technology, Rochester, New York 14623, United States
| | - Qun Chen
- Center of Precision Medicine and Healthcare, Tsinghua-Berkeley Shenzhen Institute, Shenzhen, Guangdong Province 518055, China
| | - Zhiheng Xu
- Department of Mechanical Engineering, Rochester Institute of Technology, Rochester, New York 14623, United States
| | - Erik C. Jensen
- HJ Science & Technology Inc., San Leandro, California 94710, United States
| | - Changyue Liu
- Center of Precision Medicine and Healthcare, Tsinghua-Berkeley Shenzhen Institute, Shenzhen, Guangdong Province 518055, China
| | - Jacob T. Waitkus
- Department of Mechanical Engineering, Rochester Institute of Technology, Rochester, New York 14623, United States
| | - Xi Yuan
- Center of Precision Medicine and Healthcare, Tsinghua-Berkeley Shenzhen Institute, Shenzhen, Guangdong Province 518055, China
| | - Qian He
- Center of Precision Medicine and Healthcare, Tsinghua-Berkeley Shenzhen Institute, Shenzhen, Guangdong Province 518055, China
| | - Peiwu Qin
- Center of Precision Medicine and Healthcare, Tsinghua-Berkeley Shenzhen Institute, Shenzhen, Guangdong Province 518055, China
| | - Ke Du
- Department of Mechanical Engineering, Rochester Institute of Technology, Rochester, New York 14623, United States
- Department of Microsystems Engineering, Rochester Institute of Technology, Rochester, New York 14623, United States
- School of Chemistry and Materials Science, Rochester Institute of Technology, Rochester, New York 14623, United States
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12
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Chondrogiannis G, Khaliliazar S, Toldrà A, Réu P, Hamedi MM. Nitrocellulose-bound achromopeptidase for point-of-care nucleic acid tests. Sci Rep 2021; 11:6140. [PMID: 33731748 PMCID: PMC7969615 DOI: 10.1038/s41598-021-85481-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 02/24/2021] [Indexed: 11/23/2022] Open
Abstract
Enzymes are the cornerstone of modern biotechnology. Achromopeptidase (ACP) is a well-known enzyme that hydrolyzes a number of proteins, notably proteins on the surface of Gram-positive bacteria. It is therefore used for sample preparation in nucleic acid tests. However, ACP inhibits DNA amplification which makes its integration difficult. Heat is commonly used to inactivate ACP, but it can be challenging to integrate heating into point-of-care devices. Here, we use recombinase polymerase amplification (RPA) together with ACP, and show that when ACP is immobilized on nitrocellulose paper, it retains its enzymatic function and can easily and rapidly be activated using agitation. The nitrocellulose-bound ACP does, however, not leak into the solution, preventing the need for deactivation through heat or by other means. Nitrocellulose-bound ACP thus opens new possibilities for paper-based Point-of-Care (POC) devices.
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Affiliation(s)
- Georgios Chondrogiannis
- School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Shirin Khaliliazar
- School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Anna Toldrà
- School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Pedro Réu
- School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden.
| | - Mahiar M Hamedi
- School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden.
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13
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Oroojalian F, Beygi M, Baradaran B, Mokhtarzadeh A, Shahbazi MA. Immune Cell Membrane-Coated Biomimetic Nanoparticles for Targeted Cancer Therapy. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2006484. [PMID: 33577127 DOI: 10.1002/smll.202006484] [Citation(s) in RCA: 204] [Impact Index Per Article: 68.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 11/20/2020] [Indexed: 06/12/2023]
Abstract
Nanotechnology has provided great opportunities for managing neoplastic conditions at various levels, from preventive and diagnostic to therapeutic fields. However, when it comes to clinical application, nanoparticles (NPs) have some limitations in terms of biological stability, poor targeting, and rapid clearance from the body. Therefore, biomimetic approaches, utilizing immune cell membranes, are proposed to solve these issues. For example, macrophage or neutrophil cell membrane coated NPs are developed with the ability to interact with tumor tissue to suppress cancer progression and metastasis. The functionality of these particles largely depends on the surface proteins of the immune cells and their preserved function during membrane extraction and coating process on the NPs. Proteins on the outer surface of immune cells can render a wide range of activities to the NPs, including prolonged blood circulation, remarkable competency in recognizing antigens for enhanced targeting, better cellular interactions, gradual drug release, and reduced toxicity in vivo. In this review, nano-based systems coated with immune cells-derived membranous layers, their detailed production process, and the applicability of these biomimetic systems in cancer treatment are discussed. In addition, future perspectives and challenges for their clinical translation are also presented.
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Affiliation(s)
- Fatemeh Oroojalian
- Department of Advanced Sciences and Technologies in Medicine, School of Medicine, North Khorasan University of Medical Sciences, Bojnurd, 94531-55166, Iran
- Natural Products and Medicinal Plants Research Center, North Khorasan University of Medical Sciences, Bojnurd, 94531-55166, Iran
| | - Mohammad Beygi
- Department of Agricultural Engineering, Isfahan University of Technology (IUT), Isfahan, 84156-83111, Iran
| | - Behzad Baradaran
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, 51666-14731, Iran
| | - Ahad Mokhtarzadeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, 51666-14731, Iran
| | - Mohammad-Ali Shahbazi
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Helsinki, FI-00014, Finland
- Zanjan Pharmaceutical Nanotechnology Research Center (ZPNRC), Zanjan University of Medical Sciences, Zanjan, 45139-56184, Iran
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14
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Holmes HR, Haywood M, Hutchison R, Zhang Q, Edsall C, Hall TL, Baisch D, Holliday J, Vlaisavljevich E. Focused ultrasound extraction (FUSE) for the rapid extraction of DNA from tissue matrices. Methods Ecol Evol 2020. [DOI: 10.1111/2041-210x.13505] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hal R. Holmes
- Department of Biomedical Engineering and Mechanics Virginia Polytechnic Institute and State University Blacksburg VA USA
- Conservation X Labs Seattle WA USA
| | - Morgan Haywood
- Department of Biomedical Engineering and Mechanics Virginia Polytechnic Institute and State University Blacksburg VA USA
| | - Ruby Hutchison
- Department of Biomedical Engineering and Mechanics Virginia Polytechnic Institute and State University Blacksburg VA USA
| | - Qian Zhang
- Department of Forest Resources and Environmental Conservation Virginia Polytechnic Institute and State University Blacksburg VA USA
| | - Connor Edsall
- Department of Biomedical Engineering and Mechanics Virginia Polytechnic Institute and State University Blacksburg VA USA
| | - Timothy L. Hall
- Department of Biomedical Engineering University of Michigan Ann Arbor MI USA
| | | | - Jason Holliday
- Department of Forest Resources and Environmental Conservation Virginia Polytechnic Institute and State University Blacksburg VA USA
| | - Eli Vlaisavljevich
- Department of Biomedical Engineering and Mechanics Virginia Polytechnic Institute and State University Blacksburg VA USA
- Center for Engineered Health, Virginia Tech Institute for Critical Technology and Applied Science Blacksburg VA USA
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15
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Murray LP, Mace CR. Usability as a guiding principle for the design of paper-based, point-of-care devices - A review. Anal Chim Acta 2020; 1140:236-249. [PMID: 33218486 DOI: 10.1016/j.aca.2020.09.063] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 09/28/2020] [Accepted: 09/30/2020] [Indexed: 12/14/2022]
Abstract
Due to their portability, versatility for supporting multiple assay formats, and potential for resulting in low-cost assays, paper-based analytical devices (PADs) are an increasingly popular format as a platform for the development of point-of-care tests. However, very few PADs have been translated successfully to their intended environments outside of academic settings. Often overlooked as a factor that inhibits translation, usability is a vital characteristic of any successful point-of-care test. Recent advancements in PAD design have demonstrated improved usability by simplifying various aspects of user operation, including sample collection, sample processing, device operation, detection, and readout/interpretation. Field testing at various stages of device design can offer critical feedback about device usability, especially when it involves the proposed end-user or other stakeholders. By highlighting advances in usability, we aim to encourage thoughtful and rigorous design at the academic prototyping stage to address one outstanding hurdle that limits the number of PADs that make it from the benchtop to the point-of-care.
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Affiliation(s)
- Lara P Murray
- Department of Chemistry, Tufts University, Medford, MA, 02155, USA
| | - Charles R Mace
- Department of Chemistry, Tufts University, Medford, MA, 02155, USA.
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16
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Lu H, Mutafopulos K, Heyman JA, Spink P, Shen L, Wang C, Franke T, Weitz DA. Rapid additive-free bacteria lysis using traveling surface acoustic waves in microfluidic channels. LAB ON A CHIP 2019; 19:4064-4070. [PMID: 31690904 DOI: 10.1039/c9lc00656g] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
We report an additive-free method to lyse bacteria and extract nucleic acids and protein using a traveling surface acoustic wave (TSAW) coupled to a microfluidic device. We characterize the effects of the TSAW on E. coli by measuring the viability of cells exposed to the sound waves and find that about 90% are dead. In addition, we measure the protein and nucleic acids released from the cells and show that we recover about 20% of the total material. The lysis method should work for all types of bacteria. These results demonstrate the feasibility of using TSAW to lyse bacteria in a manner that is independent of the type of bacteria.
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Affiliation(s)
- Haiwei Lu
- State Key Laboratory for Manufacturing Systems Engineering, Xi'an Jiaotong University, Xi'an 710049, People's Republic of China and School of Engineering and Applied Sciences, Harvard University, Cambridge, USA.
| | - Kirk Mutafopulos
- School of Engineering and Applied Sciences, Harvard University, Cambridge, USA.
| | - John A Heyman
- School of Engineering and Applied Sciences, Harvard University, Cambridge, USA.
| | - Pascal Spink
- School of Engineering and Applied Sciences, Harvard University, Cambridge, USA.
| | - Liang Shen
- State Key Laboratory for Manufacturing Systems Engineering, Xi'an Jiaotong University, Xi'an 710049, People's Republic of China
| | - Chaohui Wang
- State Key Laboratory for Manufacturing Systems Engineering, Xi'an Jiaotong University, Xi'an 710049, People's Republic of China
| | - Thomas Franke
- Biomedical Engineering, School of Engineering, University of Glasgow, Glasgow, UK
| | - David A Weitz
- School of Engineering and Applied Sciences, Harvard University, Cambridge, USA. and Department of Physics, Harvard University, Cambridge, USA and Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
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17
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Land KJ. The Many Roads to an Ideal Paper-based Device. PAPER-BASED DIAGNOSTICS 2018. [PMCID: PMC7119996 DOI: 10.1007/978-3-319-96870-4_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The recent Zika and Ebola virus outbreaks highlight the need for low-cost diagnostics that can be rapidly deployed and used outside of established clinical infrastructure. This demand for robust point-of-care (POC) diagnostics is further driven by the increasing burden of drug-resistant diseases, concern for food and water safety, and bioterrorism. As has been discussed in previous chapters, paper-based tests provide a simple and compelling solution to such needs.
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Affiliation(s)
- Kevin J. Land
- Council for Scientific and Industrial Research, Pretoria, South Africa
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18
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Liu H, Zhao F, Jin CE, Koo B, Lee EY, Zhong L, Yun K, Shin Y. Large Instrument- and Detergent-Free Assay for Ultrasensitive Nucleic Acids Isolation via Binary Nanomaterial. Anal Chem 2018; 90:5108-5115. [PMID: 29561136 DOI: 10.1021/acs.analchem.7b05136] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Nucleic acid-based diagnostics are widely used for clinical applications due to their powerful recognition of biomolecule properties. Isolation and purification of nucleic acids such as DNA and RNA in the diagnostic system have been severely hampered in point-of-care testing because of low recovery yields, degradation of nucleic acids due to the use of chaotropic detergent and high temperature, and the requirement of large instruments such as centrifuges and thermal controllers. Here, we report a novel large instrument- and detergent-free assay via binary nanomaterial for ultrasensitive nucleic acid isolation and detection from cells (eukaryotic and prokaryotic). This binary nanomaterial couples a zinc oxide nanomultigonal shuttle (ZnO NMS) for cell membrane rupture without detergent and temperature control and diatomaceous earth with dimethyl suberimidate complex (DDS) for the capture and isolation of nucleic acids (NA) from cells. The ZnO NMS was synthesized to a size of 500 nm to permit efficient cell lysis at room temperature within 2 min using the biological, chemical, and physical properties of the nanomaterial. By combining the ZnO NMS with the DDS and proteinase K, the nucleic acid extraction could be completed in 15 min with high quantity and quality. For bacterial cells, DNA isolation with the binary nanomaterial yielded 100 times more DNA, than a commercial spin column based reference kit, as determined by the NanoDrop spectrophotometer. We believe that this binary nanomaterial will be a useful tool for rapid and sensitive nucleic acid isolation and detection without large instruments and detergent in the field of molecular diagnostics.
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Affiliation(s)
- Huifang Liu
- Department of Convergence Medicine, Asan Medical Center, University of Ulsan College of Medicine and Biomedical Engineering Research Center, Asan Institute of Life Sciences , Asan Medical Center , 88 Olympicro-43gil , Songpa-gu, Seoul 05505 , Republic of Korea
| | - Fei Zhao
- Department of Convergence Medicine, Asan Medical Center, University of Ulsan College of Medicine and Biomedical Engineering Research Center, Asan Institute of Life Sciences , Asan Medical Center , 88 Olympicro-43gil , Songpa-gu, Seoul 05505 , Republic of Korea
| | - Choong Eun Jin
- Department of Convergence Medicine, Asan Medical Center, University of Ulsan College of Medicine and Biomedical Engineering Research Center, Asan Institute of Life Sciences , Asan Medical Center , 88 Olympicro-43gil , Songpa-gu, Seoul 05505 , Republic of Korea
| | - Bonhan Koo
- Department of Convergence Medicine, Asan Medical Center, University of Ulsan College of Medicine and Biomedical Engineering Research Center, Asan Institute of Life Sciences , Asan Medical Center , 88 Olympicro-43gil , Songpa-gu, Seoul 05505 , Republic of Korea
| | - Eun Yeong Lee
- Department of Convergence Medicine, Asan Medical Center, University of Ulsan College of Medicine and Biomedical Engineering Research Center, Asan Institute of Life Sciences , Asan Medical Center , 88 Olympicro-43gil , Songpa-gu, Seoul 05505 , Republic of Korea
| | - Linlin Zhong
- Department of Bionanotechnology , Gachon University , Gyeonggi-do 13120 , Republic of Korea
| | - Kyusik Yun
- Department of Bionanotechnology , Gachon University , Gyeonggi-do 13120 , Republic of Korea
| | - Yong Shin
- Department of Convergence Medicine, Asan Medical Center, University of Ulsan College of Medicine and Biomedical Engineering Research Center, Asan Institute of Life Sciences , Asan Medical Center , 88 Olympicro-43gil , Songpa-gu, Seoul 05505 , Republic of Korea
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19
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Basha IHK, Ho ETW, Yousuff CM, Hamid NHB. Towards Multiplex Molecular Diagnosis-A Review of Microfluidic Genomics Technologies. MICROMACHINES 2017; 8:E266. [PMID: 30400456 PMCID: PMC6190060 DOI: 10.3390/mi8090266] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 06/30/2017] [Accepted: 07/16/2017] [Indexed: 12/21/2022]
Abstract
Highly sensitive and specific pathogen diagnosis is essential for correct and timely treatment of infectious diseases, especially virulent strains, in people. Point-of-care pathogen diagnosis can be a tremendous help in managing disease outbreaks as well as in routine healthcare settings. Infectious pathogens can be identified with high specificity using molecular methods. A plethora of microfluidic innovations in recent years have now made it increasingly feasible to develop portable, robust, accurate, and sensitive genomic diagnostic devices for deployment at the point of care. However, improving processing time, multiplexed detection, sensitivity and limit of detection, specificity, and ease of deployment in resource-limited settings are ongoing challenges. This review outlines recent techniques in microfluidic genomic diagnosis and devices with a focus on integrating them into a lab on a chip that will lead towards the development of multiplexed point-of-care devices of high sensitivity and specificity.
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Affiliation(s)
- Ismail Hussain Kamal Basha
- Department of Electrical and Electronic Engineering, Universiti Teknologi PETRONAS, 32610 Seri Iskandar, Perak Darul Ridzuan, Malaysia.
| | - Eric Tatt Wei Ho
- Department of Electrical and Electronic Engineering, Universiti Teknologi PETRONAS, 32610 Seri Iskandar, Perak Darul Ridzuan, Malaysia.
| | - Caffiyar Mohamed Yousuff
- Department of Electrical and Electronic Engineering, Universiti Teknologi PETRONAS, 32610 Seri Iskandar, Perak Darul Ridzuan, Malaysia.
| | - Nor Hisham Bin Hamid
- Department of Electrical and Electronic Engineering, Universiti Teknologi PETRONAS, 32610 Seri Iskandar, Perak Darul Ridzuan, Malaysia.
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20
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Gong MM, Sinton D. Turning the Page: Advancing Paper-Based Microfluidics for Broad Diagnostic Application. Chem Rev 2017. [PMID: 28627178 DOI: 10.1021/acs.chemrev.7b00024] [Citation(s) in RCA: 323] [Impact Index Per Article: 46.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Infectious diseases are a major global health issue. Diagnosis is a critical first step in effectively managing their spread. Paper-based microfluidic diagnostics first emerged in 2007 as a low-cost alternative to conventional laboratory testing, with the goal of improving accessibility to medical diagnostics in developing countries. In this review, we examine the advances in paper-based microfluidic diagnostics for medical diagnosis in the context of global health from 2007 to 2016. The theory of fluid transport in paper is first presented. The next section examines the strategies that have been employed to control fluid and analyte transport in paper-based assays. Tasks such as mixing, timing, and sequential fluid delivery have been achieved in paper and have enabled analytical capabilities comparable to those of conventional laboratory methods. The following section examines paper-based sample processing and analysis. The most impactful advancement here has been the translation of nucleic acid analysis to a paper-based format. Smartphone-based analysis is another exciting development with potential for wide dissemination. The last core section of the review highlights emerging health applications, such as male fertility testing and wearable diagnostics. We conclude the review with the future outlook, remaining challenges, and emerging opportunities.
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Affiliation(s)
- Max M Gong
- Department of Mechanical and Industrial Engineering, University of Toronto , 5 King's College Road, Toronto, Ontario, Canada M5S 3G8.,Department of Biomedical Engineering, Wisconsin Institutes for Medical Research, University of Wisconsin-Madison , 1111 Highland Avenue, Madison, Wisconsin 53705, United States
| | - David Sinton
- Department of Mechanical and Industrial Engineering, University of Toronto , 5 King's College Road, Toronto, Ontario, Canada M5S 3G8
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21
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Shehadul Islam M, Aryasomayajula A, Selvaganapathy PR. A Review on Macroscale and Microscale Cell Lysis Methods. MICROMACHINES 2017. [PMCID: PMC6190294 DOI: 10.3390/mi8030083] [Citation(s) in RCA: 209] [Impact Index Per Article: 29.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The lysis of cells in order to extract the nucleic acids or proteins inside it is a crucial unit operation in biomolecular analysis. This paper presents a critical evaluation of the various methods that are available both in the macro and micro scale for cell lysis. Various types of cells, the structure of their membranes are discussed initially. Then, various methods that are currently used to lyse cells in the macroscale are discussed and compared. Subsequently, popular methods for micro scale cell lysis and different microfluidic devices used are detailed with their advantages and disadvantages. Finally, a comparison of different techniques used in microfluidics platform has been presented which will be helpful to select method for a particular application.
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22
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Microfluidics: innovative approaches for rapid diagnosis of antibiotic-resistant bacteria. Essays Biochem 2017; 61:91-101. [PMID: 28258233 DOI: 10.1042/ebc20160059] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 01/14/2017] [Accepted: 01/18/2017] [Indexed: 11/17/2022]
Abstract
The emergence of antibiotic-resistant bacteria has become a major global health concern. Rapid and accurate diagnostic strategies to determine the antibiotic susceptibility profile prior to antibiotic prescription and treatment are critical to control drug resistance. The standard diagnostic procedures for the detection of antibiotic-resistant bacteria, which rely mostly on phenotypic characterization, are time consuming, insensitive and often require skilled personnel, making them unsuitable for point-of-care (POC) diagnosis. Various molecular techniques have therefore been implemented to help speed up the process and increase sensitivity. Over the past decade, microfluidic technology has gained great momentum in medical diagnosis as a series of fluid handling steps in a laboratory can be simplified and miniaturized on to a small platform, allowing marked reduction of sample amount, high portability and tremendous possibility for integration with other detection technologies. These advantages render the microfluidic system a great candidate to be developed into an easy-to-use sample-to-answer POC diagnosis suitable for application in remote clinical settings. This review provides an overview of the current development of microfluidic technologies for the nucleic acid based and phenotypic-based detections of antibiotic resistance.
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23
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Lafleur LK, Bishop JD, Heiniger EK, Gallagher RP, Wheeler MD, Kauffman P, Zhang X, Kline EC, Buser JR, Kumar S, Byrnes SA, Vermeulen NMJ, Scarr NK, Belousov Y, Mahoney W, Toley BJ, Ladd PD, Lutz BR, Yager P. A rapid, instrument-free, sample-to-result nucleic acid amplification test. LAB ON A CHIP 2016; 16:3777-87. [PMID: 27549897 DOI: 10.1039/c6lc00677a] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The prototype demonstrated here is the first fully integrated sample-to-result diagnostic platform for performing nucleic acid amplification tests that requires no permanent instrument or manual sample processing. The multiplexable autonomous disposable nucleic acid amplification test (MAD NAAT) is based on two-dimensional paper networks, which enable sensitive chemical detection normally reserved for laboratories to be carried out anywhere by untrained users. All reagents are stored dry in the disposable test device and are rehydrated by stored buffer. The paper network is physically multiplexed to allow independent isothermal amplification of multiple targets; each amplification reaction is also chemically multiplexed with an internal amplification control. The total test time is less than one hour. The MAD NAAT prototype was used to characterize a set of human nasal swab specimens pre-screened for methicillin-resistant Staphylococcus aureus (MRSA) bacteria. With qPCR as the quantitative reference method, the lowest input copy number in the range where the MAD NAAT prototype consistently detected MRSA in these specimens was ∼5 × 10(3) genomic copies (∼600 genomic copies per biplexed amplification reaction).
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Affiliation(s)
- Lisa K Lafleur
- Department of Bioengineering, University of Washington, Seattle, USA.
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24
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Comparison of point-of-care-compatible lysis methods for bacteria and viruses. J Microbiol Methods 2016; 128:80-87. [DOI: 10.1016/j.mimet.2016.07.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Revised: 07/12/2016] [Accepted: 07/12/2016] [Indexed: 11/18/2022]
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