1
|
Reynolds J, Loeffler RS, Leigh PJ, Lopez HA, Yoon JY. Recent Uses of Paper Microfluidics in Isothermal Nucleic Acid Amplification Tests. BIOSENSORS 2023; 13:885. [PMID: 37754119 PMCID: PMC10526735 DOI: 10.3390/bios13090885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/08/2023] [Accepted: 09/11/2023] [Indexed: 09/28/2023]
Abstract
Isothermal nucleic acid amplification tests have recently gained popularity over polymerase chain reaction (PCR), as they only require a constant temperature and significantly simplify nucleic acid amplification. Recently, numerous attempts have been made to incorporate paper microfluidics into these isothermal amplification tests. Paper microfluidics (including lateral flow strips) have been used to extract nucleic acids, amplify the target gene, and detect amplified products, all toward automating the process. We investigated the literature from 2020 to the present, i.e., since the onset of the COVID-19 pandemic, during which a significant surge in isothermal amplification tests has been observed. Paper microfluidic detection has been used extensively for recombinase polymerase amplification (RPA) and its related methods, along with loop-mediated isothermal amplification (LAMP) and rolling circle amplification (RCA). Detection was conducted primarily with colorimetric and fluorometric methods, although a few publications demonstrated flow distance- and surface-enhanced Raman spectroscopic (SERS)-based detection. A good number of publications could be found that demonstrated both amplification and detection on paper microfluidic platforms. A small number of publications could be found that showed extraction or all three procedures (i.e., fully integrated systems) on paper microfluidic platforms, necessitating the need for future work.
Collapse
Affiliation(s)
- Jocelyn Reynolds
- Department of Biomedical Engineering, The University of Arizona, Tucson, AZ 85721, USA; (J.R.); (R.S.L.); (P.J.L.)
| | - Reid S. Loeffler
- Department of Biomedical Engineering, The University of Arizona, Tucson, AZ 85721, USA; (J.R.); (R.S.L.); (P.J.L.)
| | - Preston J. Leigh
- Department of Biomedical Engineering, The University of Arizona, Tucson, AZ 85721, USA; (J.R.); (R.S.L.); (P.J.L.)
| | - Hannah A. Lopez
- Department of Neuroscience, The University of Arizona, Tucson, AZ 85721, USA;
| | - Jeong-Yeol Yoon
- Department of Biomedical Engineering, The University of Arizona, Tucson, AZ 85721, USA; (J.R.); (R.S.L.); (P.J.L.)
| |
Collapse
|
2
|
Liu F, Zhang C, Wang Y, Chen G. A review of the current and emerging detection methods of marine harmful microalgae. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 815:152913. [PMID: 34999066 DOI: 10.1016/j.scitotenv.2022.152913] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 12/13/2021] [Accepted: 12/31/2021] [Indexed: 06/14/2023]
Abstract
In recent years, the scale and frequency of outbreaks of harmful algal blooms (HABs) have increased year by year due to the intensification of seawater eutrophication and global climate change. HABs have become a global marine ecological and environmental problem, which poses a serious threat to human health, marine ecological security, and economic development. The establishment of detection technology for harmful microalgae is fundamental to the early warning and prevention of HABs. To date, several detection methods have been developed for harmful microalgae, they however lack a unified classification standard. It is difficult to use a reasonable mix of all the developed methods to improve the accuracy of detection results. Here, all of the established detection methods for harmful microalgae were reviewed, including morphological structure-based detection methods, cytochrome-based detection techniques, immunoassays, and nucleic acid-based detection methods. The principles, advantages, and weaknesses of these methods were highlighted. Their application in the detection of harmful microalgae was summarized. Overall, different detection methods are suitable for different purposes. Further development of more accurate, cost-effective, efficient, and rapid detection technology is required in the future. This review is expected to provide a reference for research related to the monitoring of marine environment, early warning of HABs, and the molecular identification of harmful microalgae.
Collapse
Affiliation(s)
- Fuguo Liu
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai 264209, PR China; School of Environment, Harbin Institute of Technology, Harbin 150090, PR China
| | - Chunyun Zhang
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai 264209, PR China; School of Marine Sciences, Ningbo University, Ningbo 315211, PR China.
| | - Yuanyuan Wang
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai 264209, PR China
| | - Guofu Chen
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai 264209, PR China.
| |
Collapse
|
3
|
Zhang C, Chen Q, Liu F, Liu Y, Wang Y, Chen G. Rapid detection of Chattonella marina by PCR combined with dot lateral flow strip. JOURNAL OF APPLIED PHYCOLOGY 2022; 34:449-460. [PMID: 35079200 PMCID: PMC8778489 DOI: 10.1007/s10811-021-02667-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 11/30/2021] [Accepted: 11/30/2021] [Indexed: 06/14/2023]
Abstract
UNLABELLED In this study a novel technique referred to as PCR combined with dot lateral flow strip (PCDS) is proposed and its application to the detection of harmful microalgae was explored. For this purpose, using Chattonella marina as a test algal species, PCR targeting the D1-D2 region of large subunit ribosomal gene of this alga was performed with the tagged specific primers. The amplicons were then analyzed with the manually prepared dot lateral flow strip, and the strip could produce a test dot and a control dot that are naked-eye detectable, indicating the successful establishment of PCDS. The established PCDS assay does not require expensive instruments for the detection, and the results can be observed visually after adding 7.5 μL of PCR amplicons in combination with 92.5 μL of chromatography buffer to the sample pad of the strip for about 10 min. The PCR conditions were optimized to enhance the effectiveness of detection. The cross-reactivity test with 23 microalgae species, including Chattonella marina, showed good specificity of the PCDS. The detection limit of PCDS was 1.25 × 10-2 ng µL-1 for genomic DNA and 101 cells mL-1 for crude cell extracts, which can meet the detection needs. In summary, the PCDS proposed in this study has low cost, clear, and intuitive detection results and good specificity and sensitivity, providing a novel detection method for C. marina. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s10811-021-02667-x.
Collapse
Affiliation(s)
- Chunyun Zhang
- College of Oceanology, Harbin Institute of Technology (Weihai), Weihai, 264209 People’s Republic of China
- School of Environment, Harbin Institute of Technology, Harbin, 264209 People’s Republic of China
- School of Marine Sciences, Ningbo University, Ningbo, 315211 People’s Republic of China
| | - Qixin Chen
- College of Oceanology, Harbin Institute of Technology (Weihai), Weihai, 264209 People’s Republic of China
| | - Fuguo Liu
- College of Oceanology, Harbin Institute of Technology (Weihai), Weihai, 264209 People’s Republic of China
- School of Environment, Harbin Institute of Technology, Harbin, 264209 People’s Republic of China
| | - Yin Liu
- College of Oceanology, Harbin Institute of Technology (Weihai), Weihai, 264209 People’s Republic of China
| | - Yuanyuan Wang
- College of Oceanology, Harbin Institute of Technology (Weihai), Weihai, 264209 People’s Republic of China
| | - Guofu Chen
- College of Oceanology, Harbin Institute of Technology (Weihai), Weihai, 264209 People’s Republic of China
- School of Environment, Harbin Institute of Technology, Harbin, 264209 People’s Republic of China
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Wenhua West Road, Weihai, 2# Shandong Province China
| |
Collapse
|
4
|
Garafutdinov RR, Sakhabutdinova AR, Gilvanov AR, Chemeris AV. Rolling Circle Amplification as a Universal Method for the Analysis of a Wide Range of Biological Targets. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2021; 47:1172-1189. [PMID: 34931113 PMCID: PMC8675116 DOI: 10.1134/s1068162021060078] [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: 03/26/2021] [Revised: 04/14/2021] [Accepted: 04/16/2021] [Indexed: 11/23/2022]
Abstract
Detection and quantification of biotargets are important analytical tasks, which are solved using a wide range of various methods. In recent years, methods based on the isothermal amplification of nucleic acids (NAs) have been extensively developed. Among them, a special place is occupied by rolling circle amplification (RCA), which is used not only for the detection of a specific NA but also for the analysis of other biomolecules, and is also a versatile platform for the development of highly sensitive methods and convenient diagnostic devices. The present review reveals a number of methodical aspects of RCA-mediated analysis; in particular, the data on its key molecular participants are presented, the methods for increasing the efficiency and productivity of RCA are described, and different variants of reporter systems are briefly characterized. Differences in the techniques of RCA-mediated analysis of biotargets of various types are shown. Some examples of using different RCA variants for the solution of specific diagnostic problems are given.
Collapse
Affiliation(s)
- R. R. Garafutdinov
- Institute of Biochemistry and Genetics, Ufa Federal Research Center, Russian Academy of Sciences, 450054 Ufa, Russia
| | - A. R. Sakhabutdinova
- Institute of Biochemistry and Genetics, Ufa Federal Research Center, Russian Academy of Sciences, 450054 Ufa, Russia
| | - A. R. Gilvanov
- Institute of Biochemistry and Genetics, Ufa Federal Research Center, Russian Academy of Sciences, 450054 Ufa, Russia
| | - A. V. Chemeris
- Institute of Biochemistry and Genetics, Ufa Federal Research Center, Russian Academy of Sciences, 450054 Ufa, Russia
| |
Collapse
|
5
|
How does the Internet of Things (IoT) help in microalgae biorefinery? Biotechnol Adv 2021; 54:107819. [PMID: 34454007 DOI: 10.1016/j.biotechadv.2021.107819] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 07/27/2021] [Accepted: 08/22/2021] [Indexed: 12/14/2022]
Abstract
Microalgae biorefinery is a platform for the conversion of microalgal biomass into a variety of value-added products, such as biofuels, bio-based chemicals, biomaterials, and bioactive substances. Commercialization and industrialization of microalgae biorefinery heavily rely on the capability and efficiency of large-scale cultivation of microalgae. Thus, there is an urgent need for novel technologies that can be used to monitor, automatically control, and precisely predict microalgae production. In light of this, innovative applications of the Internet of things (IoT) technologies in microalgae biorefinery have attracted tremendous research efforts. IoT has potential applications in a microalgae biorefinery for the automatic control of microalgae cultivation, monitoring and manipulation of microalgal cultivation parameters, optimization of microalgae productivity, identification of toxic algae species, screening of target microalgae species, classification of microalgae species, and viability detection of microalgal cells. In this critical review, cutting-edge IoT technologies that could be adopted to microalgae biorefinery in the upstream and downstream processing are described comprehensively. The current advances of the integration of IoT with microalgae biorefinery are presented. What this review discussed includes automation, sensors, lab-on-chip, and machine learning, which are the main constituent elements and advanced technologies of IoT. Specifically, future research directions are discussed with special emphasis on the development of sensors, the application of microfluidic technology, robotized microalgae, high-throughput platforms, deep learning, and other innovative techniques. This review could contribute greatly to the novelty and relevance in the field of IoT-based microalgae biorefinery to develop smarter, safer, cleaner, greener, and economically efficient techniques for exhaustive energy recovery during the biorefinery process.
Collapse
|
6
|
Durán-Vinet B, Araya-Castro K, Chao TC, Wood SA, Gallardo V, Godoy K, Abanto M. Potential applications of CRISPR/Cas for next-generation biomonitoring of harmful algae blooms: A review. HARMFUL ALGAE 2021; 103:102027. [PMID: 33980455 DOI: 10.1016/j.hal.2021.102027] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 03/01/2021] [Accepted: 03/21/2021] [Indexed: 06/12/2023]
Abstract
Research on harmful algal and cyanobacterial blooms (HABs and CHABs) has risen dramatically due to their increasing global distribution, frequency, and intensity. These blooms jeopardize public health, ecosystem function, sustainability and can have negative economic impacts. Numerous monitoring programs have been established using light microscopy, liquid chromatography coupled to mass spectrometry (LC-MS), ELISA, and spectrophotometry to monitor HABs/CHABs outbreaks. Recently, DNA/RNA-based molecular methods have been integrated into these programs to replace or complement traditional methods through analyzing environmental DNA and RNA (eDNA/eRNA) with techniques such as quantitative polymerase chain reaction (qPCR), fluorescent in situ hybridization (FISH), sandwich hybridization assay (SHA), isothermal amplification methods, and microarrays. These have enabled the detection of rare or cryptic species, enhanced sample throughput, and reduced costs and the need for visual taxonomic expertise. However, these methods have limitations, such as the need for high capital investment in equipment or detection uncertainties, including determining whether organisms are viable. In this review, we discuss the potential of newly developed molecular diagnosis technology based on Clustered Regularly Interspaced Short Palindromic Repeats/Cas proteins (CRISPR/Cas), which utilizes the prokaryotic adaptative immune systems of bacteria and archaea. Cas12 and Cas13-based platforms can detect both DNA and RNA with attomolar sensitivity within an hour. CRISPR/Cas diagnostic is a rapid, inexpensive, specific, and ultrasensitive technology that, with some further development, will provide many new platforms that can be used for HABs/CHABs biomonitoring and research.
Collapse
Affiliation(s)
- B Durán-Vinet
- Scientific and Technological Bioresource Nucleus (BIOREN-UFRO), Genomics and Bioinformatics Unit, Universidad de La Frontera, Av. Francisco Salazar, 1145 Temuco, Chile; Bachelor of Biotechnology (Honours) Program, Faculty of Agricultural and Forestry Sciences, Universidad de La Frontera, Av. Francisco Salazar, 1145 Temuco, Chile.
| | - K Araya-Castro
- Doctoral Program in Science of Natural Resources, Universidad de La Frontera, Av. Francisco Salazar, 1145 Temuco, Chile
| | - T C Chao
- Institute of Environmental Change & Society, Department of Biology, University of Regina, Wascana Parkway, 3737 Regina, Canada
| | - S A Wood
- Coastal and Freshwater Group, Cawthron Institute, 98 Halifax Street East, Nelson 7010, New Zealand
| | - V Gallardo
- Scientific and Technological Bioresource Nucleus (BIOREN-UFRO), Genomics and Bioinformatics Unit, Universidad de La Frontera, Av. Francisco Salazar, 1145 Temuco, Chile; Bachelor of Biotechnology (Honours) Program, Faculty of Agricultural and Forestry Sciences, Universidad de La Frontera, Av. Francisco Salazar, 1145 Temuco, Chile
| | - K Godoy
- Scientific and Technological Bioresource Nucleus (BIOREN-UFRO), Microscopy and Flow Cytometry Unit, Universidad de La Frontera, Av. Francisco Salazar, 1145 Temuco, Chile
| | - M Abanto
- Scientific and Technological Bioresource Nucleus (BIOREN-UFRO), Genomics and Bioinformatics Unit, Universidad de La Frontera, Av. Francisco Salazar, 1145 Temuco, Chile
| |
Collapse
|