1
|
Li S, Luo N, Li C, Mao S, Huang H. Diversity and distribution analysis of eukaryotic communities in the Xiangshan Bay, East China sea by metabarcoding approach. MARINE ENVIRONMENTAL RESEARCH 2024; 197:106451. [PMID: 38492505 DOI: 10.1016/j.marenvres.2024.106451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 01/04/2024] [Accepted: 03/11/2024] [Indexed: 03/18/2024]
Abstract
Eukaryotic communities play an important role in the coastal ecosystem of Xiangshan Bay, a narrow semi-closed bay famous for fisheries and marine farming. However, information on the diversity and composition of eukaryotic communities in Xiangshan Bay remains unclear. In this study, the metabarcoding approach was utilized to comprehensively investigate the eukaryotic plankton community structure and dominant taxa, particularly eukaryotic microalgae, in the Xiangshan Bay over a period of four months in 2018. The results showed that the three major phyla were Arthropoda, Chlorophyta, and Bacillariophyta. The richness indices revealed that species richness peaked in February and was at its lowest in May. Diversity indices showed that the samples collected in May had the lowest diversity. Centropages was detected in the samples of all months, however, its highest dominance was observed in the samples collected in February. In addition, compared to other months, a greater proportion of eukaryotic microalgae was witnessed in March. The three eukaryotic algae with highest abundances in March were Cyclotella, Prorocentrum, and Thalassiosira. Moreover, high diversity of pico-sized (0.2-2.0 μm) phytoplankton (which are often easily missed by microscopy) was discovered in this study by using metabarcoding approach. This study highlights the strength and significance of the metabarcoding approach to uncover a large number of eukaryotic species which remains undetectable during application of conventional approaches. The findings of this study reveals that the eukaryotic community structure varies noticeably in both time and space throughout sampling period, with temperature being the most important environmental factor influencing these changes. This study lays a solid foundation to understand eukaryotic plankton composition, temporal and spatial dynamics and the distribution mechanism of eukaryotic plankton community in Xiangshan Bay, providing theoretical reference for further studies related to marine ecology.
Collapse
Affiliation(s)
- Shuangqing Li
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, 315211, China.
| | - Ningjian Luo
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, 315211, China.
| | - Chuang Li
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, 315211, China.
| | - Shuoqian Mao
- Ningbo Institute of Oceanography, Ningbo, 315832, China.
| | - Hailong Huang
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, 315211, China.
| |
Collapse
|
2
|
Wei L, Zhu D, Cheng Q, Gao Z, Wang H, Qiu J. Aptamer-Based fluorescent DNA biosensor in antibiotics detection. Food Res Int 2024; 179:114005. [PMID: 38342532 DOI: 10.1016/j.foodres.2024.114005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 01/03/2024] [Accepted: 01/08/2024] [Indexed: 02/13/2024]
Abstract
The inappropriate employment of antibiotics across diverse industries has engendered profound apprehensions concerning their cumulative presence within human bodies and food commodities. Consequently, many nations have instituted stringent measures limiting the admissible quantities of antibiotics in food items. Nonetheless, conventional techniques employed for antibiotic detection prove protracted and laborious, prompting a dire necessity for facile, expeditious, and uncomplicated detection methodologies. In this regard, aptamer-based fluorescent DNA biosensors (AFBs) have emerged as a sanguine panacea to surmount the limitations of traditional detection modalities. These ingenious biosensors harness the binding prowess of aptamers, singular strands of DNA/RNA, to selectively adhere to specific target antibiotics. Notably, the AFBs demonstrate unparalleled selectivity, affinity, and sensitivity in detecting antibiotics. This comprehensive review meticulously expounds upon the strides achieved in AFBs for antibiotic detection, particularly emphasizing the labeling modality and the innovative free-label approach. It also elucidates the design principles behind a diverse array of AFBs. Additionally, a succinct survey of signal amplification strategies deployed within these biosensors is provided. The central objective of this review is to apprise researchers from diverse disciplines of the contemporary trends in AFBs for antibiotic detection. By doing so, it aspires to instigate a concerted endeavor toward the development of heightened sensitivity and pioneering AFBs, thereby contributing to the perpetual advancement of antibiotic detection methodologies.
Collapse
Affiliation(s)
- Luke Wei
- Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, People's Republic of China
| | - Dingze Zhu
- Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, People's Republic of China
| | - Qiuyue Cheng
- Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, People's Republic of China
| | - Zihan Gao
- Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, People's Republic of China
| | - Honglei Wang
- Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, People's Republic of China
| | - Jieqiong Qiu
- Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, People's Republic of China.
| |
Collapse
|
3
|
Enders A, Grünberger A, Bahnemann J. Towards Small Scale: Overview and Applications of Microfluidics in Biotechnology. Mol Biotechnol 2024; 66:365-377. [PMID: 36515858 PMCID: PMC10881759 DOI: 10.1007/s12033-022-00626-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 11/26/2022] [Indexed: 12/15/2022]
Abstract
Thanks to recent and continuing technological innovations, modern microfluidic systems are increasingly offering researchers working across all fields of biotechnology exciting new possibilities (especially with respect to facilitating high throughput analysis, portability, and parallelization). The advantages offered by microfluidic devices-namely, the substantially lowered chemical and sample consumption they require, the increased energy and mass transfer they offer, and their comparatively small size-can potentially be leveraged in every sub-field of biotechnology. However, to date, most of the reported devices have been deployed in furtherance of healthcare, pharmaceutical, and/or industrial applications. In this review, we consider examples of microfluidic and miniaturized systems across biotechnology sub-fields. In this context, we point out the advantages of microfluidics for various applications and highlight the common features of devices and the potential for transferability to other application areas. This will provide incentives for increased collaboration between researchers from different disciplines in the field of biotechnology.
Collapse
Affiliation(s)
- Anton Enders
- Institute of Technical Chemistry, Leibniz University Hannover, Callinstraße 5, 30167, Hannover, Germany
| | - Alexander Grünberger
- Institute of Process Engineering in Life Sciences: Microsystems in Bioprocess Engineering, Karlsruhe Institute of Technology, Fritz-Haber-Weg 2, 76131, Karlsruhe, Germany
| | - Janina Bahnemann
- Institute of Physics, University of Augsburg, Universitätsstraße 1, 86159, Augsburg, Germany.
| |
Collapse
|
4
|
Yao Y, Luo N, Zong Y, Jia M, Rao Y, Huang H, Jiang H. Recombinase Polymerase Amplification Combined with Lateral Flow Dipstick Assay for the Rapid and Sensitive Detection of Pseudo-nitzschia multiseries. Int J Mol Sci 2024; 25:1350. [PMID: 38279350 PMCID: PMC10816074 DOI: 10.3390/ijms25021350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 01/03/2024] [Accepted: 01/19/2024] [Indexed: 01/28/2024] Open
Abstract
The harmful algal bloom (HAB) species Pseudo-nitzschia multiseries is widely distributed worldwide and is known to produce the neurotoxin domoic acid, which harms marine wildlife and humans. Early detection and preventative measures are more critical than late management. However, the major challenge related to early detection is the accurate and sensitive detection of microalgae present in low abundance. Therefore, developing a sensitive and specific method that can rapidly detect P. multiseries is critical for expediting the monitoring and prediction of HABs. In this study, a novel assay method, recombinase polymerase amplification combined with lateral flow dipstick (RPA-LFD), is first developed for the detection of P. multiseries. To obtain the best test results, several important factors that affected the amplification effect were optimized. The internal transcribed spacer sequence of the nuclear ribosomal DNA from P. multiseries was selected as the target region. The results showed that the optimal amplification temperature and time for the recombinase polymerase amplification (RPA) of P. multiseries were 37 °C and 15 min. The RPA products could be visualized directly using the lateral flow dipstick after only 3 min. The RPA-LFD assay sensitivity for detection of recombinant plasmid DNA (1.9 × 100 pg/μL) was 100 times more sensitive than that of RPA, and the RPA-LFD assay sensitivity for detection of genomic DNA (2.0 × 102 pg/μL) was 10 times more sensitive than that of RPA. Its feasibility in the detection of environmental samples was also verified. In conclusion, these results indicated that the RPA-LFD detection of P. multiseries that was established in this study has high efficiency, sensitivity, specificity, and practicability. Management measures made based on information gained from early detection methods may be able to prevent certain blooms. The use of a highly sensitive approach for early warning detection of P. multiseries is essential to alleviate the harmful impacts of HABs on the environment, aquaculture, and human health.
Collapse
Affiliation(s)
- Yuqing Yao
- School of Marine Sciences, Ningbo University, Ningbo 315211, China; (Y.Y.); (N.L.); (Y.Z.); (M.J.); (Y.R.)
| | - Ningjian Luo
- School of Marine Sciences, Ningbo University, Ningbo 315211, China; (Y.Y.); (N.L.); (Y.Z.); (M.J.); (Y.R.)
| | - Yujie Zong
- School of Marine Sciences, Ningbo University, Ningbo 315211, China; (Y.Y.); (N.L.); (Y.Z.); (M.J.); (Y.R.)
| | - Meng Jia
- School of Marine Sciences, Ningbo University, Ningbo 315211, China; (Y.Y.); (N.L.); (Y.Z.); (M.J.); (Y.R.)
| | - Yichen Rao
- School of Marine Sciences, Ningbo University, Ningbo 315211, China; (Y.Y.); (N.L.); (Y.Z.); (M.J.); (Y.R.)
| | - Hailong Huang
- School of Marine Sciences, Ningbo University, Ningbo 315211, China; (Y.Y.); (N.L.); (Y.Z.); (M.J.); (Y.R.)
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519080, China
| | - Haibo Jiang
- School of Marine Sciences, Ningbo University, Ningbo 315211, China; (Y.Y.); (N.L.); (Y.Z.); (M.J.); (Y.R.)
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519080, China
| |
Collapse
|
5
|
Pal P, Anand U, Saha SC, Sundaramurthy S, Okeke ES, Kumar M, Radha, Bontempi E, Albertini E, Dey A, Di Maria F. Novel CRISPR/Cas technology in the realm of algal bloom biomonitoring: Recent trends and future perspectives. ENVIRONMENTAL RESEARCH 2023; 231:115989. [PMID: 37119838 DOI: 10.1016/j.envres.2023.115989] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 04/09/2023] [Accepted: 04/24/2023] [Indexed: 05/26/2023]
Abstract
In conjunction with global climate change, progressive ocean warming, and acclivity in pollution and anthropogenic eutrophication, the incidence of harmful algal blooms (HABs) and cyanobacterial harmful algal blooms (CHABs) continue to expand in distribution, frequency, and magnitude. Algal bloom-related toxins have been implicated in human health disorders and ecological dysfunction and are detrimental to the national and global economy. Biomonitoring programs based on traditional monitoring protocols were characterised by some limitations that can be efficiently overdone using the CRISPR/Cas technology. In the present review, the potential and challenges of exploiting the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-Cas technology for early detection of HABs and CHABs-associated toxigenic species were analysed. Based on more than 30 scientific papers, the main results indicate the great potential of CRISPR/Cas technology for this issue, even if the high sensitivity detected for the Cas12 and Cas13 platforms represents a possible interference risk.
Collapse
Affiliation(s)
- Pracheta Pal
- Department of Life Sciences, Presidency University, 86/1 College Street, Kolkata, 700073, West Bengal, India
| | - Uttpal Anand
- Zuckerberg Institute for Water Research, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Midreshet Ben-Gurion, 8499000, Israel
| | - Suchismita Chatterjee Saha
- Department of Zoology, Nabadwip Vidyasagar College (affiliated to the University of Kalyani), Nabadwip, West Bengal, 741302, India
| | - Suresh Sundaramurthy
- Department of Chemical Engineering, Maulana Azad National Institute of Technology, Bhopal, 462003, Madhya Pradesh, India
| | - Emmanuel Sunday Okeke
- Department of Biochemistry, Faculty of Biological Sciences & Natural Science Unit, School of General Studies, University of Nigeria, Nsukka, Enugu State, 410001, Nigeria; Institute of Environmental Health and Ecological Security, School of the Environment and Safety, Jiangsu University, 301 Xuefu Rd., 212013, Zhenjiang, Jiangsu, China
| | - Manoj Kumar
- Chemical and Biochemical Processing Division, ICAR - Central Institute for Research on Cotton Technology, Mumbai, 400019, Maharashtra, India
| | - Radha
- School of Biological and Environmental Sciences, Shoolini University of Biotechnology and Management Sciences, Solan, 173229, Himachal Pradesh, India
| | - Elza Bontempi
- INSTM and Chemistry for Technologies Laboratory, Department of Mechanical and Industrial Engineering, University of Brescia, Via Branze 38, 25123, Brescia, Italy
| | - Emidio Albertini
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, University of Perugia, Borgo XX Giugno 74, 06121, Perugia, Italy.
| | - Abhijit Dey
- Department of Life Sciences, Presidency University, 86/1 College Street, Kolkata, 700073, West Bengal, India.
| | - Francesco Di Maria
- Dipartimento di Ingegneria, University of Perugia, Via G. Duranti 93, 06125, Perugia, Italy.
| |
Collapse
|
6
|
Wang L, Chen X, Pan F, Yao G, Chen J. Development of a rapid detection method for Karenia mikimotoi by using CRISPR-Cas12a. Front Microbiol 2023; 14:1205765. [PMID: 37608945 PMCID: PMC10440436 DOI: 10.3389/fmicb.2023.1205765] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 07/20/2023] [Indexed: 08/24/2023] Open
Abstract
Harmful algal blooms (HABs), mainly formed by dinoflagellates, have detrimental effects on marine ecosystems and public health. Therefore, detecting HABs is crucial for early warning and prevention of HABs as well as the mitigation of their adverse effects. Although various methods, such as light microscopy, electron microscopy, real-time PCR, and microarrays, have already been established for the detection of HABs, they are still cumbersome to be exploited in the field. Therefore, rapid nucleic detection methods such as recombinase polymerase amplification (RPA) and loop-mediated isothermal amplification (LAMP)-lateral flow dipstick (LFD) have been developed for monitoring bloom-forming algae. However, the CRISPR/Cas-based detection of HABs has yet to be applied to this field. In this study, we developed a method for detecting Karenia mikimotoi (K. mikimotoi), a typical ichthyotoxic dinoflagellate responsible for global blooms. Our method utilized Cas12a from Lachnospiraceae bacterium ND2006 (LbCas12a) to target and cleave the internal transcribed spacer (ITS) of K. mikimotoi, guided by RNA. We leveraged the target-activated non-specific single-stranded deoxyribonuclease cleavage activity of LbCas12a to generate signals that can be detected using fluorescence-read machines or LFDs. By combining RPA and LbCas12a with reporters, we significantly enhanced the sensitivity, enabling the detection of ITS-harboring plasmids at concentrations as low as 9.8 aM and genomic DNA of K. mikimotoi at levels as low as 3.6 × 10-5 ng/μl. Moreover, we simplified the genomic DNA extraction method using cellulose filter paper (CFP) by directly eluting the DNA into RPA reactions, reducing the extraction time to < 30 s. The entire process, from genomic DNA extraction to result reporting, takes less than an hour, enabling the identification of nearly a single cell. In conclusion, our method provided an easy, specific, and sensitive approach for detecting K. mikimotoi, offering the potential for efficient monitoring and management of K. mikimotoi blooms.
Collapse
Affiliation(s)
- Lu Wang
- Fujian Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, Fuzhou Institute of Oceanography, Minjiang University, Fuzhou, China
| | - Xiaoyao Chen
- Fishery Resources Monitoring Center of Fujian Province, Fuzhou, China
| | - Feifei Pan
- Fishery Resources Monitoring Center of Fujian Province, Fuzhou, China
| | - Guangshan Yao
- Fujian Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, Fuzhou Institute of Oceanography, Minjiang University, Fuzhou, China
| | - Jianming Chen
- Fujian Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, Fuzhou Institute of Oceanography, Minjiang University, Fuzhou, China
| |
Collapse
|
7
|
Durán-Vinet B, Araya-Castro K, Zaiko A, Pochon X, Wood SA, Stanton JAL, Jeunen GJ, Scriver M, Kardailsky A, Chao TC, Ban DK, Moarefian M, Aran K, Gemmell NJ. CRISPR-Cas-Based Biomonitoring for Marine Environments: Toward CRISPR RNA Design Optimization Via Deep Learning. CRISPR J 2023; 6:316-324. [PMID: 37439822 PMCID: PMC10494903 DOI: 10.1089/crispr.2023.0019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 05/30/2023] [Indexed: 07/14/2023] Open
Abstract
Almost all of Earth's oceans are now impacted by multiple anthropogenic stressors, including the spread of nonindigenous species, harmful algal blooms, and pathogens. Early detection is critical to manage these stressors effectively and to protect marine systems and the ecosystem services they provide. Molecular tools have emerged as a promising solution for marine biomonitoring. One of the latest advancements involves utilizing CRISPR-Cas technology to build programmable, rapid, ultrasensitive, and specific diagnostics. CRISPR-based diagnostics (CRISPR-Dx) has the potential to allow robust, reliable, and cost-effective biomonitoring in near real time. However, several challenges must be overcome before CRISPR-Dx can be established as a mainstream tool for marine biomonitoring. A critical unmet challenge is the need to design, optimize, and experimentally validate CRISPR-Dx assays. Artificial intelligence has recently been presented as a potential approach to tackle this challenge. This perspective synthesizes recent advances in CRISPR-Dx and machine learning modeling approaches, showcasing CRISPR-Dx potential to progress as a rising molecular tool candidate for marine biomonitoring applications.
Collapse
Affiliation(s)
- Benjamín Durán-Vinet
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand; Berkeley, Berkeley, California, USA
- Scientific and Technological Bioresource Nucleus (BIOREN-UFRO), Universidad de La Frontera, Temuco, Chile; Berkeley, Berkeley, California, USA
| | - Karla Araya-Castro
- Scientific and Technological Bioresource Nucleus (BIOREN-UFRO), Universidad de La Frontera, Temuco, Chile; Berkeley, Berkeley, California, USA
| | - Anastasija Zaiko
- Cawthron Institute, Nelson, New Zealand; Berkeley, Berkeley, California, USA
- Institute of Marine Science, University of Auckland, Auckland, New Zealand; Berkeley, Berkeley, California, USA
- Sequench Ltd, Nelson, New Zealand; Berkeley, Berkeley, California, USA
| | - Xavier Pochon
- Cawthron Institute, Nelson, New Zealand; Berkeley, Berkeley, California, USA
- Institute of Marine Science, University of Auckland, Auckland, New Zealand; Berkeley, Berkeley, California, USA
| | - Susanna A. Wood
- Cawthron Institute, Nelson, New Zealand; Berkeley, Berkeley, California, USA
| | - Jo-Ann L. Stanton
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand; Berkeley, Berkeley, California, USA
| | - Gert-Jan Jeunen
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand; Berkeley, Berkeley, California, USA
- Department of Marine Sciences, University of Otago, Dunedin, New Zealand; Berkeley, Berkeley, California, USA
| | - Michelle Scriver
- Cawthron Institute, Nelson, New Zealand; Berkeley, Berkeley, California, USA
- Institute of Marine Science, University of Auckland, Auckland, New Zealand; Berkeley, Berkeley, California, USA
| | - Anya Kardailsky
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand; Berkeley, Berkeley, California, USA
- Department of Zoology, University of Otago, Dunedin, New Zealand; Berkeley, Berkeley, California, USA
| | - Tzu-Chiao Chao
- Institute of Environmental Change and Society, Department of Biology, University of Regina, Regina, Canada; Berkeley, Berkeley, California, USA
| | - Deependra K. Ban
- Keck Graduate Institute, The Claremont Colleges, Claremont, California, USA; Berkeley, Berkeley, California, USA
| | - Maryam Moarefian
- Keck Graduate Institute, The Claremont Colleges, Claremont, California, USA; Berkeley, Berkeley, California, USA
| | - Kiana Aran
- Keck Graduate Institute, The Claremont Colleges, Claremont, California, USA; Berkeley, Berkeley, California, USA
- Cardea Bio Inc., San Diego, California, USA; and Berkeley, Berkeley, California, USA
- University of California, Berkeley, Berkeley, California, USA
| | - Neil J. Gemmell
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand; Berkeley, Berkeley, California, USA
| |
Collapse
|
8
|
Dong H, Liu X, Gan L, Fan D, Sun X, Zhang Z, Wu P. Nucleic acid aptamer-based biosensors and their application in thrombin analysis. Bioanalysis 2023. [PMID: 37326345 DOI: 10.4155/bio-2023-0058] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023] Open
Abstract
Thrombin is a multifunctional serine protease that plays an important role in coagulation and anticoagulation processes. Aptamers have been widely applied in biosensors due to their high specificity, low cost and good biocompatibility. This review summarizes recent advances in thrombin quantification using aptamer-based biosensors. The primary focus is optical sensors and electrochemical sensors, along with their applications in thrombin analysis and disease diagnosis.
Collapse
Affiliation(s)
- Hang Dong
- State Key Laboratory of Targeting Oncology, National Center for International Research of Bio-Targeting Theranostics, Guangxi Key Laboratory of Bio-Targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis & Therapy, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Xiyu Liu
- State Key Laboratory of Targeting Oncology, National Center for International Research of Bio-Targeting Theranostics, Guangxi Key Laboratory of Bio-Targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis & Therapy, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Lu Gan
- State Key Laboratory of Targeting Oncology, National Center for International Research of Bio-Targeting Theranostics, Guangxi Key Laboratory of Bio-Targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis & Therapy, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Dianfa Fan
- State Key Laboratory of Targeting Oncology, National Center for International Research of Bio-Targeting Theranostics, Guangxi Key Laboratory of Bio-Targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis & Therapy, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Xinjun Sun
- State Key Laboratory of Targeting Oncology, National Center for International Research of Bio-Targeting Theranostics, Guangxi Key Laboratory of Bio-Targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis & Therapy, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Zhikun Zhang
- State Key Laboratory of Targeting Oncology, National Center for International Research of Bio-Targeting Theranostics, Guangxi Key Laboratory of Bio-Targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis & Therapy, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Pan Wu
- State Key Laboratory of Targeting Oncology, National Center for International Research of Bio-Targeting Theranostics, Guangxi Key Laboratory of Bio-Targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis & Therapy, Guangxi Medical University, Nanning, Guangxi, 530021, China
- Pharmaceutical College, Guangxi Medical University, Nanning, Guangxi, 530021, China
| |
Collapse
|
9
|
Hatfield RG, Ryder D, Tidy AM, Hartnell DM, Dean KJ, Batista FM. Combining Nanopore Sequencing with Recombinase Polymerase Amplification Enables Identification of Dinoflagellates from the Alexandrium Genus, Providing a Rapid, Field Deployable Tool. Toxins (Basel) 2023; 15:372. [PMID: 37368673 DOI: 10.3390/toxins15060372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 05/24/2023] [Accepted: 05/26/2023] [Indexed: 06/29/2023] Open
Abstract
The armoured dinoflagellate Alexandrium can be found throughout many of the world's temperate and tropical marine environments. The genus has been studied extensively since approximately half of its members produce a family of potent neurotoxins, collectively called saxitoxin. These compounds represent a significant threat to animal and environmental health. Moreover, the consumption of bivalve molluscs contaminated with saxitoxin poses a threat to human health. The identification of Alexandrium cells collected from sea water samples using light microscopy can provide early warnings of a toxic event, giving harvesters and competent authorities time to implement measures that safeguard consumers. However, this method cannot reliably resolve Alexandrium to a species level and, therefore, is unable to differentiate between toxic and non-toxic variants. The assay outlined in this study uses a quick recombinase polymerase amplification and nanopore sequencing method to first target and amplify a 500 bp fragment of the ribosomal RNA large subunit and then sequence the amplicon so that individual species from the Alexandrium genus can be resolved. The analytical sensitivity and specificity of the assay was assessed using seawater samples spiked with different Alexandrium species. When using a 0.22 µm membrane to capture and resuspend cells, the assay was consistently able to identify a single cell of A. minutum in 50 mL of seawater. Phylogenetic analysis showed the assay could identify the A. catenella, A. minutum, A. tamutum, A. tamarense, A. pacificum, and A. ostenfeldii species from environmental samples, with just the alignment of the reads being sufficient to provide accurate, real-time species identification. By using sequencing data to qualify when the toxic A. catenella species was present, it was possible to improve the correlation between cell counts and shellfish toxicity from r = 0.386 to r = 0.769 (p ≤ 0.05). Furthermore, a McNemar's paired test performed on qualitative data highlighted no statistical differences between samples confirmed positive or negative for toxic species of Alexandrium by both phylogenetic analysis and real time alignment with the presence or absence of toxins in shellfish. The assay was designed to be deployed in the field for the purposes of in situ testing, which required the development of custom tools and state-of-the-art automation. The assay is rapid and resilient to matrix inhibition, making it suitable as a potential alternative detection method or a complementary one, especially when applying regulatory controls.
Collapse
Affiliation(s)
- Robert G Hatfield
- Centre for Environment Fisheries and Aquaculture Science, Weymouth DT48UB, UK
| | - David Ryder
- Centre for Environment Fisheries and Aquaculture Science, Weymouth DT48UB, UK
| | - Annabel M Tidy
- Centre for Environment Fisheries and Aquaculture Science, Weymouth DT48UB, UK
| | - David M Hartnell
- Centre for Environment Fisheries and Aquaculture Science, Weymouth DT48UB, UK
| | - Karl J Dean
- Centre for Environment Fisheries and Aquaculture Science, Weymouth DT48UB, UK
| | - Frederico M Batista
- Centre for Environment Fisheries and Aquaculture Science, Weymouth DT48UB, UK
| |
Collapse
|
10
|
Pan J, Deng F, Chen J. A fluorescent biosensor for Cd 2+ detection in water samples based on Cd 2+-fueled wheel DNAzyme walker and its logic gate applications. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 864:161046. [PMID: 36549523 DOI: 10.1016/j.scitotenv.2022.161046] [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: 11/01/2022] [Revised: 12/12/2022] [Accepted: 12/15/2022] [Indexed: 06/17/2023]
Abstract
A fluorescent biosensor was developed for Cd2+ detection based on a Cd2+-fueled wheel DNAzyme walker. Cd2+ can activate the wheel to roll along the DNA walking tracks through DNAzyme cleavage and toehold-mediated strand displacement. The substrate strand was modified with BHQ and Cy5. Through continuous cleavage reactions toward the substrate strands, a high fluorescence signal can be obtained. The biosensor is ultrasensitive, and the detection limit is 0.2 pM (S/N = 3). The fluorescent assay is robust and has been applied to the determination of Cd2+ in real water samples with good accuracy and reliability. Using Cd2+, Pb2+, and Hg2+ as the three inputs, we also construct a concatenated AND logic gate. The input combination of (111) can produce an output of 1. Other input combinations produce an output of 0. Our proposed detection platform and logic system hold great promise for the ultrasensitive and intelligent sensing of different heavy metal ions in water samples.
Collapse
Affiliation(s)
- Jiafeng Pan
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Fang Deng
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Junhua Chen
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China.
| |
Collapse
|
11
|
Xu S, Lyu P, Zheng X, Yang H, Xia B, Li H, Zhang H, Ma S. Monitoring and control methods of harmful algal blooms in Chinese freshwater system: a review. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:56908-56927. [PMID: 35708805 DOI: 10.1007/s11356-022-21382-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 06/06/2022] [Indexed: 06/15/2023]
Abstract
Harmful algal blooms (HABs) are a worldwide problem with substantial adverse effects on the aquatic environment as well as human health, which have prompted researchers to study measures to stem and control them. Meanwhile, it is key to research and develop monitoring methods to establish early warning HABs. However, both the current monitoring methods and control methods have some shortcomings, making the field application limited. Thus, we need to improve current approaches for monitoring and controlling HABs efficiently. Based on the freshwater system features in China, we review various monitoring and control methods of HABs, summarize and discuss the problems with these methods, and propose the future development direction of monitoring and control HABs. Finally, we envision that it can combine physical, chemical, and biological methods to inhibit HAB expansion in the future, complementing each other with advantages. Further, we promise to establish a long-term strategy of controlling HABs with various algicidal bacteria co-cultivate for field applications in China. Efforts in studying algicidal bacteria must be increased to better control HABs and mitigate the risks of aquatic ecosystems and human health in China.
Collapse
Affiliation(s)
- Shengjun Xu
- Shenzhen BLY Landscape & Architecture Planning & Design Institute, Shenzhen, 518055, China
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Ping Lyu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Xiaoxu Zheng
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Haijun Yang
- Shenzhen BLY Landscape & Architecture Planning & Design Institute, Shenzhen, 518055, China
| | - Bing Xia
- Shenzhen BLY Landscape & Architecture Planning & Design Institute, Shenzhen, 518055, China
| | - Hui Li
- Shenzhen BLY Landscape & Architecture Planning & Design Institute, Shenzhen, 518055, China
| | - Hao Zhang
- South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Shuanglong Ma
- College of Resources and Environmental Sciences, Henan Agricultural University, Zhengzhou, 450002, China.
| |
Collapse
|
12
|
Chip-Based and Wearable Tools for Isothermal Amplification and Electrochemical Analysis of Nucleic Acids. CHEMOSENSORS 2022. [DOI: 10.3390/chemosensors10070278] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The determination of nucleic acids has become an analytical diagnostic method with many applications in fields such as biomedical sciences, environmental monitoring, forensic identification, and food safety. Among the different methods for nucleic acid analysis, those based on the polymerase chain reaction (PCR) are nowadays considered the gold standards. Isothermal amplification methods are an interesting alternative, especially in the design of chip-based architectures. Biosensing platforms hold great promise for the simple and rapid detection of nucleic acids since they can be embedded in lab-on-a-chip tools to perform nucleic acid extraction, amplification, and detection steps. Electrochemical transduction schemes are particularly interesting in the design of small and portable devices due to miniaturization, low-energy consumption, and multianalyte detection capability. The aim of this review is to summarize the different applications of isothermal amplification methods combined with electrochemical biosensing techniques in the development of lab-on-a-chip tools and wearable sensors. Different isothermal amplification methods are revised, and examples of different applications are discussed. Finally, a discussion on patented devices is also included.
Collapse
|
13
|
Fu H, Zhang C, Wang Y, Chen G. Advances in multiplex molecular detection technologies for harmful algae. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:43745-43757. [PMID: 35449333 DOI: 10.1007/s11356-022-20269-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 04/11/2022] [Indexed: 06/14/2023]
Abstract
As the eutrophication of natural water bodies becomes more and more serious, the frequency of outbreaks of harmful algal blooms (HABs) mainly formed by harmful algae also increases. HABs have become a global ecological problem that poses a serious threat to human health and food safety. Therefore, it is extremely important to establish methods that can rapidly detect harmful algal species for early warning of HABs. The traditional morphology-based identification method is inefficient and inaccurate. In recent years, the rapid development of molecular biology techniques has provided new ideas for the detection of harmful algae and has become a research hotspot. The current molecular detection methods for harmful algal species mainly include fluorescence in situ hybridization, sandwich hybridization, and quantitative PCR (qPCR), but all of these methods can only detect single harmful algal species at a time. The establishment of methods for the simultaneous detection of multiple harmful algal species has become a new trend in the development of molecular detection technology because various harmful algal species may coexist in the natural water environment. The established molecular techniques for multiple detections of harmful algae mainly include gene chip, multiplex PCR, multiplex qPCR, massively parallel sequencing, antibody chip, and multiple isothermal amplification. This review mainly focuses on the principles, advantages and disadvantages, application progress, and application prospects of these multiple detection technologies, aiming at providing effective references not only for the fisheries but also for economic activities, environment, and human health.
Collapse
Affiliation(s)
- Hanyu Fu
- College of Oceanology, Harbin Institute of Technology (Weihai), Weihai, 264209, People's Republic of China
| | - Chunyun Zhang
- 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, 150009, People's Republic of China.
| |
Collapse
|
14
|
Ginés I, Gaiani G, Ruhela A, Skouridou V, Campàs M, Masip L. Nucleic acid lateral flow dipstick assay for the duplex detection of Gambierdiscus australes and Gambierdiscus excentricus. HARMFUL ALGAE 2021; 110:102135. [PMID: 34887012 DOI: 10.1016/j.hal.2021.102135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 11/02/2021] [Accepted: 11/08/2021] [Indexed: 06/13/2023]
Abstract
The proliferation of harmful microalgae endangers aquatic ecosystems and can have serious economic implications on a global level. Harmful microalgae and their associated toxins also pose a threat to human health since they can cause seafood-borne diseases such as ciguatera. Implementation of DNA-based molecular methods together with appropriate detection strategies in monitoring programs can support the efforts for effective prevention of potential outbreaks. A PCR-lateral flow assay (PCR-LFA) in dipstick format was developed in this work for the detection of two Gambierdiscus species, G. australes and G. excentricus, which are known to produce highly potent neurotoxins known as ciguatoxins and have been associated with ciguatera outbreaks. Duplex PCR amplification of genomic DNA from strains of these species utilizing species-specific ssDNA tailed primers and a common primer containing the binding sequence of scCro DNA binding protein resulted in the generation of hybrid ssDNA-dsDNA amplicons. These were captured on the dipsticks via hybridization with complementary probes and detected with a scCro/carbon nanoparticle (scCro/CNPs) conjugate. The two different test zones on the dipsticks allowed the discrimination of the two species and the assay exhibited high sensitivity, 6.3 pg/μL of genomic DNA from both G. australes and G. excentricus. The specificity of the approach was also demonstrated using genomic DNA from non-target Gambierdiscus species and other microalgae genera which did not produce any signals. The possibility to use cells directly for amplification instead of purified genomic DNA suggested the compatibility of the approach with field sample testing. Future work is required to further explore the potential use of the strategy for on-site analysis and its applicability to other toxic species.
Collapse
Affiliation(s)
- Iris Ginés
- Departament d'Enginyeria Química, Universitat Rovira i Virgili, 26 Països Catalans, 43007 Tarragona, Spain
| | - Greta Gaiani
- IRTA, Ctra Poble Nou km 5.5, 43540 Sant Carles de la Ràpita, Spain
| | - Ankur Ruhela
- Departament d'Enginyeria Química, Universitat Rovira i Virgili, 26 Països Catalans, 43007 Tarragona, Spain
| | - Vasso Skouridou
- Departament d'Enginyeria Química, Universitat Rovira i Virgili, 26 Països Catalans, 43007 Tarragona, Spain
| | - Mònica Campàs
- IRTA, Ctra Poble Nou km 5.5, 43540 Sant Carles de la Ràpita, Spain
| | - Lluis Masip
- Departament d'Enginyeria Química, Universitat Rovira i Virgili, 26 Països Catalans, 43007 Tarragona, Spain.
| |
Collapse
|
15
|
Pearson LA, D'Agostino PM, Neilan BA. Recent developments in quantitative PCR for monitoring harmful marine microalgae. HARMFUL ALGAE 2021; 108:102096. [PMID: 34588118 DOI: 10.1016/j.hal.2021.102096] [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: 06/14/2021] [Revised: 08/17/2021] [Accepted: 08/19/2021] [Indexed: 06/13/2023]
Abstract
Marine microalgae produce a variety of specialised metabolites that have toxic effects on humans, farmed fish, and marine wildlife. Alarmingly, many of these compounds bioaccumulate in the tissues of shellfish and higher trophic organisms, including species consumed by humans. Molecular methods are emerging as a potential alternative and complement to the conventional microscopic diagnosis of toxic or otherwise harmful microalgal species. Quantitative PCR (qPCR) in particular, has gained popularity over the past decade as a sensitive, rapid, and cost-effective method for monitoring harmful microalgae. Assays targeting taxonomic marker genes provide the opportunity to identify and quantify (or semi-quantify) microalgal species and importantly to pre-empt bloom events. Moreover, the discovery of paralytic shellfish toxin biosynthesis genes in dinoflagellates has enabled researchers to directly monitor toxigenic species in coastal waters and fisheries. This review summarises the recent developments in qPCR detection methods for harmful microalgae, with emphasis on emerging toxin gene monitoring technologies.
Collapse
Affiliation(s)
- Leanne A Pearson
- School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Paul M D'Agostino
- Chair of Technical Biochemistry, Technical University of Dresden, Dresden, Germany
| | - Brett A Neilan
- School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW, 2308, Australia.
| |
Collapse
|
16
|
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
|
17
|
Biosensors Based on Isothermal DNA Amplification for Bacterial Detection in Food Safety and Environmental Monitoring. SENSORS 2021; 21:s21020602. [PMID: 33467078 PMCID: PMC7831002 DOI: 10.3390/s21020602] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 01/11/2021] [Accepted: 01/14/2021] [Indexed: 02/06/2023]
Abstract
The easy and rapid spread of bacterial contamination and the risk it poses to human health makes evident the need for analytical methods alternative to conventional time-consuming laboratory-based techniques for bacterial detection. To tackle this demand, biosensors based on isothermal DNA amplification methods have emerged, which avoid the need for thermal cycling, thus facilitating their integration into small and low-cost devices for in situ monitoring. This review focuses on the breakthroughs made on biosensors based on isothermal amplification methods for the detection of bacteria in the field of food safety and environmental monitoring. Optical and electrochemical biosensors based on loop mediated isothermal amplification (LAMP), rolling circle amplification (RCA), recombinase polymerase amplification (RPA), helicase dependent amplification (HDA), strand displacement amplification (SDA), and isothermal strand displacement polymerisation (ISDPR) are described, and an overview of their current advantages and limitations is provided. Although further efforts are required to harness the potential of these emerging analytical techniques, the coalescence of the different isothermal amplification techniques with the wide variety of biosensing detection strategies provides multiple possibilities for the efficient detection of bacteria far beyond the laboratory bench.
Collapse
|