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Mao S, Zhao J, Ding X, Vuong VA, Song J, Que L. Integrated Sensing Chip for Ultrasensitive Label-Free Detection of the Products of Loop-Mediated Isothermal Amplification. ACS Sens 2023; 8:2255-2262. [PMID: 37276452 DOI: 10.1021/acssensors.3c00227] [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] [Indexed: 06/07/2023]
Abstract
Loop-mediated isothermal amplification (LAMP) is a nucleic acid amplification technique that has been widely used for the detection of pathogens in many organisms. Current LAMP-based sensors usually require the LAMP products to be labeled in order for them to be detected. Here, we present a novel label-free LAMP chip, which consists of a nanopore thin-film sensor embedded inside a LAMP reaction chamber. A fraction of LAMP primers is immobilized on the sensor surface, allowing the LAMP products to be synthesized and bound to the sensor surface via immobilized primers. After the LAMP reaction components are removed from the reaction chamber, the amplified LAMP products bound to the sensor surface give rise to significantly increased transducing signals, which can be measured by a portable optical spectrometer through an optical fiber probe. As a demonstration, we used the LAMP chip to detect the causal agent of late blight, Phytophthora infestans, which is one of the most devastating plant pathogens and poses a major threat to sustainable crop production worldwide. We show that this chip can detect as low as 1 fg/μL of P. infestans DNA in 30 min, which corresponds to an attomolar level of 1.6 × 10-6 attomole/μL and is at least 10 times more sensitive than the currently available methods. This label-free sensing technology holds great promise to open up a new avenue for ultrasensitive, highly specific, rapid, and cost-effective point-of-care diagnostics of plant, animal, human, and foodborne pathogens.
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Affiliation(s)
- Subin Mao
- Electrical and Computer Engineering Department, Iowa State University, Ames, Iowa 50011, United States
| | - Jinping Zhao
- Texas A&M AgriLife Research Center at Dallas, Texas A&M University System, Dallas, Texas 75252, United States
| | - Xiaoke Ding
- Electrical and Computer Engineering Department, Iowa State University, Ames, Iowa 50011, United States
| | - Van Anh Vuong
- Texas A&M AgriLife Research Center at Dallas, Texas A&M University System, Dallas, Texas 75252, United States
| | - Junqi Song
- Texas A&M AgriLife Research Center at Dallas, Texas A&M University System, Dallas, Texas 75252, United States
- Department of Plant Pathology & Microbiology, Texas A&M University, College Station, Texas 77843, United States
| | - Long Que
- Electrical and Computer Engineering Department, Iowa State University, Ames, Iowa 50011, United States
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Li M, Guo Q, Liang M, Zhao Q, Lin T, Gao H, Hieno A, Kageyama K, Zhang X, Cui L, Yan Y, Qiang Y. Population Dynamics, Effective Soil Factors, and LAMP Detection Systems for Phytophthora Species Associated with Kiwifruit Diseases in China. PLANT DISEASE 2022; 106:846-853. [PMID: 34661453 DOI: 10.1094/pdis-04-21-0852-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
China has the largest area of kiwifruit production in the world. Pathogens associated with root diseases of kiwi trees have not been investigated extensively. In this research, three Phytophthora species, Phytophthora cactorum, Phytophthora cinnamomi, and Phytophthora lateralis, which are pathogenic to kiwi trees in the main planting areas of China, were studied. The population densities of these species in 128 soil samples from 32 kiwi orchards in 2017 and 2018 were measured using multiplex real-time quantitative PCR based on the ras-related protein gene Ypt1. P. cactorum was the most widely distributed of the three species in orchards of the Zhouzhi and Meixian prefectures. We used redundancy analysis to examine soil factors in the kiwi orchards to understand their effects on the population densities of the Phytophthora species. The redundancy analysis indicated that soil temperature and pH were significantly correlated with the abundance of P. cactorum and P. cinnamomi. In addition, two loop-mediated isothermal amplification detection systems for P. cactorum were developed based on the tigA gene. The color-change detection system proved to be accurate, sensitive, and faster than quantitative PCR. The results of this study, along with the loop-mediated isothermal amplification detection systems, will be of great use in the control of Phytophthora diseases for the production of kiwifruits in China.
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Affiliation(s)
- Mingzhu Li
- National Engineering Laboratory for Resource Developing of Endangered Chinese Crude Drugs in Northwest China, Shaanxi Normal University, Xi'an 710119, China
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Qian Guo
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Mengyi Liang
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Qing Zhao
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Tao Lin
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Han Gao
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Ayaka Hieno
- River Basin Research Center, Gifu University, Gifu 501-1193, Japan
| | - Koji Kageyama
- River Basin Research Center, Gifu University, Gifu 501-1193, Japan
| | - Xin Zhang
- National Engineering Laboratory for Resource Developing of Endangered Chinese Crude Drugs in Northwest China, Shaanxi Normal University, Xi'an 710119, China
| | - Langjun Cui
- National Engineering Laboratory for Resource Developing of Endangered Chinese Crude Drugs in Northwest China, Shaanxi Normal University, Xi'an 710119, China
| | - Yaping Yan
- National Engineering Laboratory for Resource Developing of Endangered Chinese Crude Drugs in Northwest China, Shaanxi Normal University, Xi'an 710119, China
| | - Yi Qiang
- National Engineering Laboratory for Resource Developing of Endangered Chinese Crude Drugs in Northwest China, Shaanxi Normal University, Xi'an 710119, China
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Penkov NV, Goltyaev MV, Astashev ME, Serov DA, Moskovskiy MN, Khort DO, Gudkov SV. The Application of Terahertz Time-Domain Spectroscopy to Identification of Potato Late Blight and Fusariosis. Pathogens 2021; 10:pathogens10101336. [PMID: 34684285 PMCID: PMC8537707 DOI: 10.3390/pathogens10101336] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/10/2021] [Accepted: 10/14/2021] [Indexed: 11/16/2022] Open
Abstract
Fusarium and late blight (fungal diseases of cereals and potatoes) are among the main causes of crop loss worldwide. A key element of success in the fight against phytopathogens is the timely identification of infected plants and seeds. That is why the development of new methods for identifying phytopathogens is a priority for agriculture. The terahertz time-domain spectroscopy (THz-TDS) is a promising method for assessing the quality of materials. For the first time, we used THz-TDS for assessing the infection of seeds of cereals (oats, wheat and barley) with fusarium and potato tubers of different varieties (Nadezhda and Meteor) with late blight. We evaluated the refractive index, absorption coefficient and complex dielectric permittivity in healthy and infected plants. The presence of phytopathogens on seeds was confirmed by microscopy and PCR. It is shown, that Late blight significantly affected all the studied spectral characteristics. The nature of the changes depended on the variety of the analyzed plants and the localization of the analyzed tissue relative to the focus of infection. Fusarium also significantly affected all the studied spectral characteristics. It was found that THz-TDS method allows you to clearly establish the presence or absence of a phytopathogens, in the case of late blight, to assess the degree and depth of damage to plant tissues.
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Affiliation(s)
- Nikita V. Penkov
- Institute of Cell Biophysics RAS, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, 142290 Pushchino, Russia; (N.V.P.); (M.V.G.); (D.A.S.)
| | - Mikhail V. Goltyaev
- Institute of Cell Biophysics RAS, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, 142290 Pushchino, Russia; (N.V.P.); (M.V.G.); (D.A.S.)
| | - Maxim E. Astashev
- Prokhorov General Physics Institute of the Russian Academy of Sciences, 119991 Moscow, Russia;
| | - Dmitry A. Serov
- Institute of Cell Biophysics RAS, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, 142290 Pushchino, Russia; (N.V.P.); (M.V.G.); (D.A.S.)
- Prokhorov General Physics Institute of the Russian Academy of Sciences, 119991 Moscow, Russia;
| | - Maxim N. Moskovskiy
- Federal State Budgetary Scientific Institution “Federal Scientific Agroengineering Center VIM”, 109428 Moscow, Russia; (M.N.M.); (D.O.K.)
| | - Dmitriy O. Khort
- Federal State Budgetary Scientific Institution “Federal Scientific Agroengineering Center VIM”, 109428 Moscow, Russia; (M.N.M.); (D.O.K.)
| | - Sergey V. Gudkov
- Prokhorov General Physics Institute of the Russian Academy of Sciences, 119991 Moscow, Russia;
- Correspondence:
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