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Abdul Rashid JI, Yusof NA, Abdullah J, Shomiad Shueb RH. Strategies in the optimization of DNA hybridization conditions and its role in electrochemical detection of dengue virus (DENV) using response surface methodology (RSM). RSC Adv 2023; 13:18748-18759. [PMID: 37362605 PMCID: PMC10286818 DOI: 10.1039/d3ra00216k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 04/28/2023] [Indexed: 06/28/2023] Open
Abstract
In recent years, limited research has been conducted on enhancing DNA hybridization-based biosensor approaches using statistical models. This study explores the application of response surface methodology (RSM) to improve the performance of a DNA hybridization biosensor for dengue virus (DENV) detection. The biosensor is based on silicon nanowires decorated with gold nanoparticles (SiNWs/AuNPs) and utilizes methylene blue as a redox indicator. The DNA hybridization process between the immobilized DNA probe and the target DENV gene was monitored using differential pulse voltammetry (DPV) based on the reduction of methylene blue. Fourier-transform infrared spectroscopy (FTIR) and electrochemical impedance spectroscopy (EIS) were employed to confirm successful DNA hybridization events on the modified screen-printed gold electrode (SPGE) surface. Several parameters, including pH buffer, NaCl concentration, temperature, and hybridization time, were simultaneously optimized, with NaCl concentration having the most significant impact on DNA hybridization events. This study enhances the understanding of the role of each parameter in influencing DNA hybridization detection in electrochemical biosensors. The optimized biosensor demonstrated the ability to detect complementary oligonucleotide and amplified DENV gene concentrations as low as 0.0891 ng µL-1 (10 pM) and 2.8 ng µL-1, respectively. The developed biosensor shows promise for rapid clinical diagnosis of dengue virus infection.
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Affiliation(s)
- Jahwarhar Izuan Abdul Rashid
- Department of Chemistry and Biology, Centre for Defence Foundation Studies, National Defence University of Malaysia Sungai Besi Camp 57000 Kuala Lumpur Malaysia
| | - Nor Azah Yusof
- Department of Chemistry, Faculty of Science, Universiti Putra Malaysia Serdang Selangor 43400 Malaysia
| | - Jaafar Abdullah
- Department of Chemistry, Faculty of Science, Universiti Putra Malaysia Serdang Selangor 43400 Malaysia
| | - Rafidah Hanim Shomiad Shueb
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia 16150 Kubang Kerian Kelantan Malaysia
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Taufiq S, Waqar M, Sharif MN, Abbas SR. Towards portable rapid TB biosensor: Detecting Mycobacterium tuberculosis in raw sputum samples using functionalized screen printed electrodes. Bioelectrochemistry 2023; 150:108353. [PMID: 36603412 DOI: 10.1016/j.bioelechem.2022.108353] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 12/12/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022]
Abstract
Due to lack of robust, sensitive and low cost detection strategies, Tuberculosis (TB) remains a significant global health issue. WHO reports 1.5 million deaths per year, ∼80 % cases occur in low- to middle-income countries, where resource limitations complicate the diagnosis. Robust detection of TB infection is important to contain the spread and treat disease. We developed a label-free DNA biosensor based on commercially available screen printed electrodes (SPEs) (DropSens and Zensors) that can detect TB robustly, sensitively, and specifically via DNA hybridization with its IS6110 gene marker, in purified DNA and raw sputum samples. The fabricated biosensor was morphologically characterized by scanning electron microscopy coupled with energy dispersive X-ray spectroscopy. Cyclic voltammetry and Differential Pulse Voltammetry was used for electrochemical analysis of the modified electrode. The fabricated biosensor demonstrated satisfactory selectivity for Mycobacterium tuberculosis (MTB) against Salmonella typhimurium and Escherichia coli and was able to detect MTB; the limit of detection (LOD) of 1.90 nM with R2 = 0.993, when analyzed over a range of concentrations of DNA (0.5-10 nM). It is being exploited to detect target MTB from clinical samples, without DNA purification. The approach is robust, sensitive, and specific, requires low sample volume and can be extended towards portable point of care diagnosis of TB.
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Affiliation(s)
- Saman Taufiq
- Department of Industrial Biotechnology, Atta ur Rahman School of Applied Biosciences, National University of Science and Technology (NUST), Islamabad, Pakistan; Biosensors and Therapeutics Lab, School of Interdisciplinary Engineering and Sciences (SINES), NUST, Islamabad, Pakistan.
| | - Muhammad Waqar
- Department of Industrial Biotechnology, Atta ur Rahman School of Applied Biosciences, National University of Science and Technology (NUST), Islamabad, Pakistan
| | - Muhammad Nauman Sharif
- Department of Industrial Biotechnology, Atta ur Rahman School of Applied Biosciences, National University of Science and Technology (NUST), Islamabad, Pakistan; Biosensors and Therapeutics Lab, School of Interdisciplinary Engineering and Sciences (SINES), NUST, Islamabad, Pakistan.
| | - Shah Rukh Abbas
- Department of Industrial Biotechnology, Atta ur Rahman School of Applied Biosciences, National University of Science and Technology (NUST), Islamabad, Pakistan; Biosensors and Therapeutics Lab, School of Interdisciplinary Engineering and Sciences (SINES), NUST, Islamabad, Pakistan.
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Hussain MH, Mohsin MZ, Zaman WQ, Yu J, Zhao X, Wei Y, Zhuang Y, Mohsin A, Guo M. Multiscale engineering of microbial cell factories: A step forward towards sustainable natural products industry. Synth Syst Biotechnol 2022; 7:586-601. [PMID: 35155840 PMCID: PMC8816652 DOI: 10.1016/j.synbio.2021.12.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 12/08/2021] [Accepted: 12/30/2021] [Indexed: 01/09/2023] Open
Abstract
Microbial cell factories (bacteria and fungi) are the leading producers of beneficial natural products such as lycopene, carotene, herbal medicine, and biodiesel etc. These microorganisms are considered efficient due to their effective bioprocessing strategy (monoculture- and consortial-based approach) under distinct processing conditions. Meanwhile, the advancement in genetic and process optimization techniques leads to enhanced biosynthesis of natural products that are known functional ingredients with numerous applications in the food, cosmetic and medical industries. Natural consortia and monoculture thrive in nature in a small proportion, such as wastewater, food products, and soils. In similitude to natural consortia, it is possible to engineer artificial microbial consortia and program their behaviours via synthetic biology tools. Therefore, this review summarizes the optimization of genetic and physicochemical parameters of the microbial system for improved production of natural products. Also, this review presents a brief history of natural consortium and describes the functional properties of monocultures. This review focuses on synthetic biology tools that enable new approaches to design synthetic consortia; and highlights the syntropic interactions that determine the performance and stability of synthetic consortia. In particular, the effect of processing conditions and advanced genetic techniques to improve the productibility of both monoculture and consortial based systems have been greatly emphasized. In this context, possible strategies are also discussed to give an insight into microbial engineering for improved production of natural products in the future. In summary, it is concluded that the coupling of genomic modifications with optimum physicochemical factors would be promising for producing a robust microbial cell factory that shall contribute to the increased production of natural products.
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Affiliation(s)
- Muhammad Hammad Hussain
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, PR China
| | - Muhammad Zubair Mohsin
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, PR China
| | - Waqas Qamar Zaman
- Institute of Environmental Sciences and Engineering, School of Civil and Environmental Engineering, National University of Sciences and Technology (NUST), Sector H-12, Islamabad, 44000, Pakistan
| | - Junxiong Yu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, PR China
| | - Xueli Zhao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, PR China
| | - Yanlong Wei
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, PR China
| | - Yingping Zhuang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, PR China
| | - Ali Mohsin
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, PR China
- Corresponding author. East China University of Science and Technology, 130 Meilong Rd, Shanghai, 200237, PR China.
| | - Meijin Guo
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, PR China
- Corresponding author. P.O. box 329#, East China University of Science and Technology, 130 Meilong Rd., Shanghai, 200237, PR China.
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Hai H, Chen C, Chen D, Li P, Shan Y, Li J. A sensitive electrochemiluminescence DNA biosensor based on the signal amplification of ExoIII enzyme-assisted hybridization chain reaction combined with nanoparticle-loaded multiple probes. Mikrochim Acta 2021; 188:125. [PMID: 33723966 DOI: 10.1007/s00604-021-04777-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Accepted: 02/23/2021] [Indexed: 10/21/2022]
Abstract
An electrochemiluminescence (ECL) DNA biosensor based on ExoIII exonuclease assistance and hybridization chain reaction (HCR) amplification technology has been constructed. ExoIII exonuclease and triple-helix DNA molecular switch are used in detecting a target in circulation. By combining HCR with AuNPs@DNA, a novel signal probe is built, which enables multiple signal amplification and the high-sensitive detection of transgenic rice BT63 DNA. The Fe3O4@Au solution is added to a magneto-controlled glassy carbon electrode, and sulfhydryl-modified capture DNA (CP) is immobilized on Fe3O4@Au through the Au-S bond. Mercaptoethanol is added to close sites and prevent the nonspecific adsorption of CP on the magnetron glassy carbon electrode. A target DNA is added to a constructed triple-helix DNA molecular centrifuge tube for reaction. Owing to base complementation and the reversible switching of the triple-helix DNA molecular state, the target DNA turns on the triple-helix DNA molecular switch and hybridizes with a long-strand recognition probe (RP) to form a double-stranded DNA (dsDNA). Exonuclease ExoIII is added to specifically recognize and cut the dsDNA and to release the target DNA. The target DNA strand then circulates back completely to open the multiple triple-helix DNA molecular switch, releasing a large number of signal transduction probes (STP). To hybridize with CP, a large amount of STP is added to the electrode. Finally, a AuNPs@DNA signal probe is added to hybridize with STP. H1 and H2 probes are added for the hybridization chain reaction and the indefinite extension of the primer strand on the probe. Then, tris-(bipyridyl)ruthenium(II) is added for ECL signal detection with PBS-tri-n-propylamine as the base solution. In the concentration range 1.0 × 10-16 to 1.0 × 10-8 mol/L of the target DNA, good linear relationship was achieved with the corresponding ECL signal. The detection limit is 3.6 × 10-17 mol/L. The spiked recovery of the rice samples range from 97.2 to 101.5%. The sensor is highly sensitive and has good selectivity, stability, and reproducibility. A novel electrochemiluminescence biosensor with extremely higher sensitivity was prepared for the determination of ultra-trace amount transgenic rice BT63 DNA. The sensitivity was significantly improved by multiple signal enhancements. Firstly, a large number of signal transduction probes are released when the triple-helix DNA molecular switch unlock after recycles assisted by ExoIII exonuclease under target BT63 DNA; and then the signal transduction probes hybridize with the signal probes of AuNPs@(DNA-HCR) produced through hybridization chain reaction. Finally, the signal probes which were embedded with a large amount of electrochemiluminescence reagent produce high luminescence intensity. The detection limit was 3.6 × 10-17 mol/L, which is almost the most sensitive methods reported.
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Affiliation(s)
- Hong Hai
- Guangxi Key Laboratory of Electrochemical and Magnetochemical Function Materials, College of Chemistry and Bioengineering, Guilin University of Technology, Guilin, 541004, Guangxi, China
| | - Ciping Chen
- Guangxi Key Laboratory of Electrochemical and Magnetochemical Function Materials, College of Chemistry and Bioengineering, Guilin University of Technology, Guilin, 541004, Guangxi, China
| | - Dongli Chen
- Guangxi Key Laboratory of Electrochemical and Magnetochemical Function Materials, College of Chemistry and Bioengineering, Guilin University of Technology, Guilin, 541004, Guangxi, China
| | - Peijun Li
- Guangxi Key Laboratory of Electrochemical and Magnetochemical Function Materials, College of Chemistry and Bioengineering, Guilin University of Technology, Guilin, 541004, Guangxi, China
| | - Yang Shan
- Guangxi Key Laboratory of Electrochemical and Magnetochemical Function Materials, College of Chemistry and Bioengineering, Guilin University of Technology, Guilin, 541004, Guangxi, China.,Hunan Institute of Agriculture Product Processing, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
| | - Jianping Li
- Guangxi Key Laboratory of Electrochemical and Magnetochemical Function Materials, College of Chemistry and Bioengineering, Guilin University of Technology, Guilin, 541004, Guangxi, China.
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Bhalla N, Pan Y, Yang Z, Payam AF. Opportunities and Challenges for Biosensors and Nanoscale Analytical Tools for Pandemics: COVID-19. ACS NANO 2020; 14:7783-7807. [PMID: 32551559 PMCID: PMC7319134 DOI: 10.1021/acsnano.0c04421] [Citation(s) in RCA: 214] [Impact Index Per Article: 53.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 06/18/2020] [Indexed: 05/05/2023]
Abstract
Biosensors and nanoscale analytical tools have shown huge growth in literature in the past 20 years, with a large number of reports on the topic of 'ultrasensitive', 'cost-effective', and 'early detection' tools with a potential of 'mass-production' cited on the web of science. Yet none of these tools are commercially available in the market or practically viable for mass production and use in pandemic diseases such as coronavirus disease 2019 (COVID-19). In this context, we review the technological challenges and opportunities of current bio/chemical sensors and analytical tools by critically analyzing the bottlenecks which have hindered the implementation of advanced sensing technologies in pandemic diseases. We also describe in brief COVID-19 by comparing it with other pandemic strains such as that of severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) for the identification of features that enable biosensing. Moreover, we discuss visualization and characterization tools that can potentially be used not only for sensing applications but also to assist in speeding up the drug discovery and vaccine development process. Furthermore, we discuss the emerging monitoring mechanism, namely wastewater-based epidemiology, for early warning of the outbreak, focusing on sensors for rapid and on-site analysis of SARS-CoV2 in sewage. To conclude, we provide holistic insights into challenges associated with the quick translation of sensing technologies, policies, ethical issues, technology adoption, and an overall outlook of the role of the sensing technologies in pandemics.
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Affiliation(s)
- Nikhil Bhalla
- Nanotechnology
and Integrated Bioengineering Centre (NIBEC), School of Engineering, Ulster University, Shore Road, BT37
0QB Jordanstown, Northern Ireland, United Kingdom
- Healthcare
Technology Hub, Ulster University, Shore Road, BT37 0QB Jordanstown, Northern
Ireland, United Kingdom
| | - Yuwei Pan
- Cranfield
Water Science Institute, Cranfield University, Cranfield, Bedfordshire MK43 0AL, United Kingdom
| | - Zhugen Yang
- Cranfield
Water Science Institute, Cranfield University, Cranfield, Bedfordshire MK43 0AL, United Kingdom
| | - Amir Farokh Payam
- Nanotechnology
and Integrated Bioengineering Centre (NIBEC), School of Engineering, Ulster University, Shore Road, BT37
0QB Jordanstown, Northern Ireland, United Kingdom
- Healthcare
Technology Hub, Ulster University, Shore Road, BT37 0QB Jordanstown, Northern
Ireland, United Kingdom
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Tan J, Peng B, Tang L, Feng C, Wang J, Yu J, Ouyang X, Zhu X. Enhanced photoelectric conversion efficiency: A novel h-BN based self-powered photoelectrochemical aptasensor for ultrasensitive detection of diazinon. Biosens Bioelectron 2019; 142:111546. [PMID: 31387026 DOI: 10.1016/j.bios.2019.111546] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 07/24/2019] [Accepted: 07/27/2019] [Indexed: 01/10/2023]
Abstract
This work presents a novel hexagonal boron nitride (h-BN) based self-powered photoelectrochemical (PEC) aptasensor for ultrasensitive detection of diazinon (DZN) with excellent photoelectric conversion efficiency. It was the first time that h-BN based materials were applied to PEC aptasensor, in which the construction of Z-scheme heterojunction of h-BN and graphitic carbon nitride (CN) via doping sulfur into h-BN was innovatively proposed. Meanwhile, Au nanoparticles (AuNPs) were utilized for the surface plasmon resonance (SPR) effect and the formation of new recombination centers. The charge transfer mechanism was expounded and verified by the electron spin resonance (ESR) spin-trap technique. The proposed PEC aptasensor for determination of DZN exhibited a wide linear range from 0.01 to 10000 nM and a low detection limit of 6.8 pM with superb selectivity and remarkable stability. Moreover, the constructed PEC aptasensor performed well with excellent recoveries in three different real samples. This work illustrated that PEC aptasensor is a promising alternative to conventional analytical technologies for the detection of DZN and other organophosphorus (OP) pesticides. The designing ideas of the proposed h-BN based material can provide a foothold for the innovative construction of photoactive materials for PEC bioanalysis.
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Affiliation(s)
- Jisui Tan
- College of Environmental Science and Engineering, Hunan University, Changsha, 410082, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, 410082, Hunan, China
| | - Bo Peng
- College of Environmental Science and Engineering, Hunan University, Changsha, 410082, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, 410082, Hunan, China
| | - Lin Tang
- College of Environmental Science and Engineering, Hunan University, Changsha, 410082, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, 410082, Hunan, China.
| | - Chengyang Feng
- College of Environmental Science and Engineering, Hunan University, Changsha, 410082, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, 410082, Hunan, China
| | - Jiajia Wang
- College of Environmental Science and Engineering, Hunan University, Changsha, 410082, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, 410082, Hunan, China
| | - Jiangfang Yu
- College of Environmental Science and Engineering, Hunan University, Changsha, 410082, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, 410082, Hunan, China
| | - Xilian Ouyang
- College of Environmental Science and Engineering, Hunan University, Changsha, 410082, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, 410082, Hunan, China
| | - Xu Zhu
- College of Environmental Science and Engineering, Hunan University, Changsha, 410082, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, 410082, Hunan, China
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Tang L, Ouyang X, Peng B, Zeng G, Zhu Y, Yu J, Feng C, Fang S, Zhu X, Tan J. Highly sensitive detection of microcystin-LR under visible light using a self-powered photoelectrochemical aptasensor based on a CoO/Au/g-C 3N 4 Z-scheme heterojunction. NANOSCALE 2019; 11:12198-12209. [PMID: 31199416 DOI: 10.1039/c9nr03004b] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Based on the unique photoelectrochemical properties of a CoO/Au/g-C3N4 Z-scheme heterojunction, a self-powered photoelectrochemical (PEC) aptasensor was constructed for the detection of microcystin-leucine arginine (MC-LR). Z-scheme heterojunctions can promote the separation of a photo-induced electron-hole pair, and the surface plasmonic resonance (SPR) of Au nanoparticles can significantly enhance the adsorption of visible light. Importantly, MC-LR molecules were captured by aptamers initially immobilized on the modified electrode due to their high affinity, and then oxidized by the photogenerated holes, which caused an amplified photocurrent signal, allowing the quantitative analysis of MC-LR by measuring the photocurrent intensity change. This PEC MC-LR aptasensor showed high sensitivity and selectivity within a wide linear response range from 0.1 pM to 10 nM and a detection limit of 0.01 pM. The application of this sensor in the analysis of lake water samples provided accurate results with a relative standard deviation (RSD) of 2.6%-4.2%.
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Affiliation(s)
- Lin Tang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, China. and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, Hunan, China
| | - Xilian Ouyang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, China. and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, Hunan, China
| | - Bo Peng
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, China. and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, Hunan, China
| | - Guangming Zeng
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, China. and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, Hunan, China
| | - Yuan Zhu
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, China. and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, Hunan, China
| | - Jiangfang Yu
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, China. and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, Hunan, China
| | - Chengyang Feng
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, China. and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, Hunan, China
| | - Siyuan Fang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, China. and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, Hunan, China
| | - Xu Zhu
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, China. and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, Hunan, China
| | - Jisui Tan
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, China. and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, Hunan, China
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Meng Q, Xu X, Zhang W, Men M, Xu B, Deng L, Bello A, Jiang X, Sheng S, Wu X. Bacterial community succession in dairy manure composting with a static composting technique. Can J Microbiol 2019; 65:436-449. [DOI: 10.1139/cjm-2018-0560] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Qingxin Meng
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, P.R. China
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, P.R. China
| | - Xiuhong Xu
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, P.R. China
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, P.R. China
| | - Wenhao Zhang
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, P.R. China
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, P.R. China
| | - Mengqi Men
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, P.R. China
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, P.R. China
| | - Benshu Xu
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, P.R. China
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, P.R. China
| | - Liting Deng
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, P.R. China
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, P.R. China
| | - Ayodeji Bello
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, P.R. China
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, P.R. China
| | - Xin Jiang
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, P.R. China
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, P.R. China
| | - Siyuan Sheng
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, P.R. China
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, P.R. China
| | - Xiaotong Wu
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, P.R. China
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, P.R. China
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Duan Y, Awasthi SK, Chen H, Liu T, Zhang Z, Zhang L, Awasthi MK, Taherzadeh MJ. Evaluating the impact of bamboo biochar on the fungal community succession during chicken manure composting. BIORESOURCE TECHNOLOGY 2019; 272:308-314. [PMID: 30384205 DOI: 10.1016/j.biortech.2018.10.045] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Revised: 10/17/2018] [Accepted: 10/19/2018] [Indexed: 06/08/2023]
Abstract
The objective of this study was to investigate the fungal community succession and variations in chicken manure (CM) compost with different concentration of bamboo biochar (BB) as additive via the using of metagenomics method. The consequent obviously revealed that Chytridiomycota, Mucoromycota, Ascomycota and Basidiomycota were the dominant phylum, while Batrachochytrium, Funneliformis, Mucor, Phizophagus and Pyronema were the pre-dominant genera in each treatment. Redundancy analyses indicated that higher dosage of biochar applied treatments has significant correlation between fungal communities and environmental factors. The diversity of fungal community was analogous but the relative abundance (RA) was inconsistent among the all treatments. In addition, the principal component analysis was also confirmed that T5 and T6 treatments have considerably correlation than other treatments. However, the mean value of RA remained maximum in higher dosage of biochar blended treatments. Ultimately, the RA of different fungal genus and species were influenced in CM compost by the BB amendment.
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Affiliation(s)
- Yumin Duan
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, China
| | - Sanjeev Kumar Awasthi
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, China
| | - Hongyu Chen
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, China
| | - Tao Liu
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, China
| | - Zengqiang Zhang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, China
| | - Linsen Zhang
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi Province 712100, China
| | - Mukesh Kumar Awasthi
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, China.
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Peng B, Tang L, Zeng G, Fang S, Ouyang X, Long B, Zhou Y, Deng Y, Liu Y, Wang J. Self-powered photoelectrochemical aptasensor based on phosphorus doped porous ultrathin g-C3N4 nanosheets enhanced by surface plasmon resonance effect. Biosens Bioelectron 2018; 121:19-26. [DOI: 10.1016/j.bios.2018.08.042] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 08/12/2018] [Accepted: 08/18/2018] [Indexed: 11/25/2022]
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Mohammed AM, Ibraheem IJ, Obaid A, Bououdina M. Nanostructured ZnO-based biosensor: DNA immobilization and hybridization. SENSING AND BIO-SENSING RESEARCH 2017. [DOI: 10.1016/j.sbsr.2017.07.003] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
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12
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Electrochemical DNA biosensor for the detection of human papillomavirus E6 gene inserted in recombinant plasmid. ARAB J CHEM 2016. [DOI: 10.1016/j.arabjc.2014.05.023] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
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13
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Enzyme catalytic amplification of miRNA-155 detection with graphene quantum dot-based electrochemical biosensor. Biosens Bioelectron 2016; 77:451-6. [DOI: 10.1016/j.bios.2015.09.068] [Citation(s) in RCA: 136] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 09/18/2015] [Accepted: 09/29/2015] [Indexed: 02/06/2023]
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14
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Zhou Y, Tang L, Zeng G, Zhang C, Xie X, Liu Y, Wang J, Tang J, Zhang Y, Deng Y. Label free detection of lead using impedimetric sensor based on ordered mesoporous carbon–gold nanoparticles and DNAzyme catalytic beacons. Talanta 2016; 146:641-7. [DOI: 10.1016/j.talanta.2015.06.063] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 06/15/2015] [Accepted: 06/20/2015] [Indexed: 11/26/2022]
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15
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Zhou Y, Tang L, Xie X, Zeng G, Wang J, Deng Y, Yang G, Zhang C, Zhang Y, Chen J. Sensitive impedimetric biosensor based on duplex-like DNA scaffolds and ordered mesoporous carbon nitride for silver(I) ion detection. Analyst 2015; 139:6529-35. [PMID: 25346956 DOI: 10.1039/c4an01607f] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
This study demonstrates a new, unlabeled immobilized DNA-based biosensor with ordered mesoporous carbon nitride material (MCN) for the detection of Ag(+) by electrochemical impedance spectroscopy (EIS) with [Fe(CN)6](4-/3-) as the redox couple. The unlabeled immobilized DNA initially formed the hairpin-like structure through hybridization with the probe, and then changed to duplex-like structure upon interaction with Ag(+) in solution to form a C-Ag(+)-C complex at electrode surface. As a result, the interfacial charge-transfer resistance of the electrode towards the [Fe(CN)6](4-/3-) redox couple was changed. Thus, a declined charge transfer resistance (Rct) was obtained, corresponding to Ag(+) concentration. MCN provide an excellent platform for DNA immobilization and faster electron transfer. Impedance data were analyzed with the help of Randles equivalent circuit. The lower detection limit of the biosensor for Ag(+) is 5 × 10(-11) M with good specificity. All results showed that this novel approach provides a reliable method for Ag(+) detection with sensitivity and specificity, potentially useful for practical applications. Moreover, other DNA detection methods for more heavy metals may be obtained from this idea and applied in the environmental field.
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Affiliation(s)
- Yaoyu Zhou
- College of Environmental Science and Engineering, Hunan University, Ministry of Education, Changsha 410082, China.
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16
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Huang Z, Chen G, Zeng G, Chen A, Zuo Y, Guo Z, Tan Q, Song Z, Niu Q. Polyvinyl alcohol-immobilized Phanerochaete chrysosporium and its application in the bioremediation of composite-polluted wastewater. JOURNAL OF HAZARDOUS MATERIALS 2015; 289:174-183. [PMID: 25725339 DOI: 10.1016/j.jhazmat.2015.02.043] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Revised: 02/13/2015] [Accepted: 02/15/2015] [Indexed: 06/04/2023]
Abstract
A novel biosorbent, polyvinyl alcohol (PVA)-immobilized Phanerochaete chrysosporium, was applied to the bioremediation of composite-polluted wastewater, containing both cadmium and 2,4-dichlorophenol (2,4-DCP). The optimum removal efficiency achieved was 78% for Cd(II) and 95.4% for 2,4-DCP at initial concentrations of 20 mg/L Cd(II) and 40 mg/L 2,4-DCP. PPBs had significantly enhanced the resistance of P. chrysosporium to 2,4-DCP, leading to the degradation rates of 2,4-DCP beyond 90% with varying initial 2,4-DCP concentrations. This research demonstrated that 2,4-DCP and secreted proteins might be used as carbon and nitrogen sources by PVA-immobilized P. chrysosporium beads (PPBs) for Cd(II) removal. Fourier transform infrared spectroscopy analysis showed that hydroxyl and carboxyl groups on the surface of PPBs were dominant in Cd(II) binding. The mechanism underlying the degradation of 2,4-DCP into fumaric acid and 1-hexanol was investigated. The adsorption-desorption studies indicated that PPBs kept up to 98.9% of desorption efficiency over three cycles.
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Affiliation(s)
- Zhenzhen Huang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Guiqiu Chen
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China.
| | - Guangming Zeng
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China.
| | - Anwei Chen
- College of Resources and Environment, Hunan Agricultural University, Changsha 410128, PR China
| | - Yanan Zuo
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Zhi Guo
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Qiong Tan
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Zhongxian Song
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming 650500, PR China
| | - Qiuya Niu
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
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17
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Muti M, Soysal M, Nacak FM, Gençdağ K, Karagözler AE. A Novel DNA Probe Based on Molecularly Imprinted Polymer Modified Electrode for the Electrochemical Monitoring of DNA. ELECTROANAL 2015. [DOI: 10.1002/elan.201400672] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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18
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Zhou Y, Tang L, Zeng G, Zhu J, Dong H, Zhang Y, Xie X, Wang J, Deng Y. A novel biosensor for silver(i) ion detection based on nanoporous gold and duplex-like DNA scaffolds with anionic intercalator. RSC Adv 2015. [DOI: 10.1039/c5ra10686a] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A novel biosensor for silver(i) ion detection based on nanoporous gold and duplex-like DNA scaffolds with anionic intercalator.
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Affiliation(s)
- Yaoyu Zhou
- College of Environmental Science and Engineering
- Hunan University
- Changsha
- China
- Key Laboratory of Environmental Biology and Pollution Control (Hunan University)
| | - Lin Tang
- College of Environmental Science and Engineering
- Hunan University
- Changsha
- China
- Key Laboratory of Environmental Biology and Pollution Control (Hunan University)
| | - Guangming Zeng
- College of Environmental Science and Engineering
- Hunan University
- Changsha
- China
- Key Laboratory of Environmental Biology and Pollution Control (Hunan University)
| | - Jingjing Zhu
- College of Environmental Science and Engineering
- Hunan University
- Changsha
- China
- Key Laboratory of Environmental Biology and Pollution Control (Hunan University)
| | - Haoran Dong
- College of Environmental Science and Engineering
- Hunan University
- Changsha
- China
- Key Laboratory of Environmental Biology and Pollution Control (Hunan University)
| | - Yi Zhang
- College of Environmental Science and Engineering
- Hunan University
- Changsha
- China
- Key Laboratory of Environmental Biology and Pollution Control (Hunan University)
| | - Xia Xie
- College of Environmental Science and Engineering
- Hunan University
- Changsha
- China
- Key Laboratory of Environmental Biology and Pollution Control (Hunan University)
| | - Jiajia Wang
- College of Environmental Science and Engineering
- Hunan University
- Changsha
- China
- Key Laboratory of Environmental Biology and Pollution Control (Hunan University)
| | - Yaocheng Deng
- College of Environmental Science and Engineering
- Hunan University
- Changsha
- China
- Key Laboratory of Environmental Biology and Pollution Control (Hunan University)
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19
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Zhou Y, Tang L, Zeng G, Chen J, Wang J, Fan C, Yang G, Zhang Y, Xie X. Amplified and selective detection of manganese peroxidase genes based on enzyme-scaffolded-gold nanoclusters and mesoporous carbon nitride. Biosens Bioelectron 2014; 65:382-9. [PMID: 25461185 DOI: 10.1016/j.bios.2014.10.063] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 10/23/2014] [Accepted: 10/27/2014] [Indexed: 11/28/2022]
Abstract
This work has demonstrated an amplified and selective detection platform using enzyme-scaffolded-gold nanoclusters as signal label, coupling with mesoporous carbon nitride (MCN) and gold nanoparticles (GNPs) modified glassy carbon electrode (GCE). Streptavidin-horseradish peroxidase (SA-HRP) has been integrated with gold nanoclusters (GNCs) as scaffold using a simple, fast and non-toxic method. The mechanisms of enzymatic amplification, redox cycling and signal amplification by this biosensor were discussed in detail. GNCs might perform important roles as electrocatalyst as well as electron transducer in these processes. The concentrations of reagents and the reaction times of these reagents were optimized to improve the analytical performances. Under the optimized condition, the signal response to enzyme-scaffolded-gold nanoclusters catalyzed reaction was linearly related to the natural logarithm of the target nucleic acid concentration in the range from 10(-17)M to 10(-9)M with a correlation coefficient of 0.9946, and the detection limit was 8.0×10(-18)M (S/N=3). Besides, synthesized oligonucleotide as well as Phanerochaete chrysosporium MnP fragments amplified using polymerase chain reaction and digested by restriction endonucleases were tested. Furthermore, this biosensor exhibited good precision, stability, sensitivity, and selectivity, and discriminated satisfactorily against mismatched nucleic acid samples of similar lengths.
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Affiliation(s)
- Yaoyu Zhou
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, Hunan, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, Hunan, PR China
| | - Lin Tang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, Hunan, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, Hunan, PR China.
| | - Guangming Zeng
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, Hunan, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, Hunan, PR China.
| | - Jun Chen
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, Hunan, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, Hunan, PR China
| | - Jiajia Wang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, Hunan, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, Hunan, PR China
| | - Changzheng Fan
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, Hunan, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, Hunan, PR China
| | - Guide Yang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, Hunan, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, Hunan, PR China
| | - Yi Zhang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, Hunan, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, Hunan, PR China
| | - Xia Xie
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, Hunan, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, Hunan, PR China
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20
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Tang L, Chen J, Zeng G, Zhu Y, Zhang Y, Zhou Y, Xie X, Yang G, Zhang S. Ordered Mesoporous Carbon and Thiolated Polyaniline Modified Electrode for Simultaneous Determination of Cadmium(II) and Lead(II) by Anodic Stripping Voltammetry. ELECTROANAL 2014. [DOI: 10.1002/elan.201400350] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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21
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Sun X, Jia M, Guan L, Ji J, Zhang Y, Tang L, Li Z. Multilayer graphene-gold nanocomposite modified stem-loop DNA biosensor for peanut allergen-Ara h1 detection. Food Chem 2014; 172:335-42. [PMID: 25442562 DOI: 10.1016/j.foodchem.2014.09.042] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Revised: 06/20/2014] [Accepted: 09/10/2014] [Indexed: 11/19/2022]
Abstract
In this study, we developed an electrochemically-amplified, stem-loop DNA biosensor to detect the peanut allergen Ara h1. Specifically, we electrodeposited a multilayer graphene-gold nanocomposite onto a glassy carbon electrode and then immobilised a thiolated hairpin DNA-biotin probe onto the modified electrode surface. The multilayer graphene-gold composite has good dispersion ability, and can amplify the electrochemical signal due to its high electron-transfer efficiency. The probe was switched to an "off" state in the presence of target DNA. The prepared biosensor demonstrated a linear response ranging from 10(-16) to 10(-13)M, with an ultrasensitive detection limit of 0.041 fM. Moreover, the biosensor showed excellent selectivity, as well as the ability to discriminate between a complementary target and a one-base mismatch or non-complementary sequence. Results show that this prepared DNA biosensor can be successfully used to detect the peanut allergen Ara h1 in a peanut milk beverage. Findings can be applied to the prevention of allergic reactions, thus improving human health and safety.
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Affiliation(s)
- Xiulan Sun
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University, Wuxi, Jiangsu 214122, China.
| | - Min Jia
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Lu Guan
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Jian Ji
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Yinzhi Zhang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Lili Tang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Zaijun Li
- School of Chemical and Material Engineering of Jiangnan University, Wuxi, Jiangsu 214122, China
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22
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Yang J, Palla M, Bosco FG, Rindzevicius T, Alstrøm TS, Schmidt MS, Boisen A, Ju J, Lin Q. Surface-enhanced Raman spectroscopy based quantitative bioassay on aptamer-functionalized nanopillars using large-area Raman mapping. ACS NANO 2013; 7:5350-9. [PMID: 23713574 PMCID: PMC3915935 DOI: 10.1021/nn401199k] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Surface-enhanced Raman spectroscopy (SERS) has been used in a variety of biological applications due to its high sensitivity and specificity. Here, we report a SERS-based biosensing approach for quantitative detection of biomolecules. A SERS substrate bearing gold-decorated silicon nanopillars is functionalized with aptamers for sensitive and specific detection of target molecules. In this study, TAMRA-labeled vasopressin molecules in the picomolar regime (1 pM to 1 nM) are specifically captured by aptamers on the nanostructured SERS substrate and monitored by using an automated SERS signal mapping technique. From the experimental results, we show concentration-dependent SERS responses in the picomolar range by integrating SERS signal intensities over a scanning area. It is also noted that our signal mapping approach significantly improves statistical reproducibility and accounts for spot-to-spot variation in conventional SERS quantification. Furthermore, we have developed an analytical model capable of predicting experimental intensity distributions on the substrates for reliable quantification of biomolecules. Lastly, we have calculated the minimum needed area of Raman mapping for efficient and reliable analysis of each measurement. Combining our SERS mapping analysis with an aptamer-functionalized nanopillar substrate is found to be extremely efficient for detection of low-abundance biomolecules.
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Affiliation(s)
- Jaeyoung Yang
- Department of Mechanical Engineering, Columbia University, New York, New York 10027, United States
| | - Mirko Palla
- Department of Mechanical Engineering, Columbia University, New York, New York 10027, United States
- Department of Chemical Engineering, Columbia University, New York, New York 10027, United States
| | - Filippo Giacomo Bosco
- Department of Micro & Nanotechnology, Technical University of Denmark, Lyngby 2800, Denmark
| | - Tomas Rindzevicius
- Department of Micro & Nanotechnology, Technical University of Denmark, Lyngby 2800, Denmark
| | - Tommy Sonne Alstrøm
- Department of Applied Mathematics and Computer Science, Technical University of Denmark, Lyngby 2800, Denmark
| | | | - Anja Boisen
- Department of Micro & Nanotechnology, Technical University of Denmark, Lyngby 2800, Denmark
| | - Jingyue Ju
- Department of Chemical Engineering, Columbia University, New York, New York 10027, United States
| | - Qiao Lin
- Department of Mechanical Engineering, Columbia University, New York, New York 10027, United States
- Address correspondence to:
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23
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Nanostructured rough gold electrodes as platforms to enhance the sensitivity of electrochemical genosensors. Anal Chim Acta 2013; 788:141-7. [PMID: 23845493 DOI: 10.1016/j.aca.2013.06.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Revised: 06/05/2013] [Accepted: 06/12/2013] [Indexed: 11/24/2022]
Abstract
An electrochemical DNA genosensor constructed by using rough gold as electrode support is reported in this work. The electrode surface nanopatterning was accomplished by repetitive square-wave perturbing potential (RSWPP). A synthetic 25-mer DNA capture probe, modified at the 5' end with a hexaalkylthiol, able to hybridize with a specific sequence of lacZ gene from the Enterobacteriaceae bacterial family was assembled to the rough gold surface. A 25 bases synthetic sequence fully complementary to the thiolated DNA capture probe and a 326 bases fragment of lacZ containing a fully matched sequence with the capture probe, which was amplified by a specific asymmetric polymerase chain reaction (aPCR), were employed as target sequences. The hybridization event was electrochemically monitored by using two different indicators, hexaammineruthenium (III) chloride showing an electrostatic DNA binding mode, and pentaamineruthenium-[3-(2-phenanthren-9-yl-vinyl)-pyridine] (in brief RuL) which binds to double stranded DNA (dsDNA) following an intercalative mechanism. After optimization of the different variables involved in the hybridization and detection reactions, detection limits of 5.30 pg μL(-1) and 10 pg μL(-1) were obtained for the 25-mer synthetic target DNA and the aPCR amplicon, respectively. A RSD value of 6% was obtained for measurements carried out with 3 different genosensors prepared in the same manner.
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24
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Functionalized ensembles of nanoelectrodes as affinity biosensors for DNA hybridization detection. Biosens Bioelectron 2013; 40:265-70. [DOI: 10.1016/j.bios.2012.07.041] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2012] [Revised: 07/02/2012] [Accepted: 07/21/2012] [Indexed: 11/23/2022]
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25
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Ramulu T, Venu R, Sinha B, Lim B, Jeon S, Yoon S, Kim C. Nanowires array modified electrode for enhanced electrochemical detection of nucleic acid. Biosens Bioelectron 2013; 40:258-64. [DOI: 10.1016/j.bios.2012.07.034] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2012] [Revised: 07/19/2012] [Accepted: 07/20/2012] [Indexed: 11/28/2022]
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26
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Luo C, Lei Y, Yan L, Yu T, Li Q, Zhang D, Ding S, Ju H. A Rapid and Sensitive Aptamer-Based Electrochemical Biosensor for Direct Detection of Escherichia Coli O111. ELECTROANAL 2012. [DOI: 10.1002/elan.201100700] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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27
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Laccase biosensor using magnetic multiwalled carbon nanotubes and chitosan/silica hybrid membrane modified magnetic carbon paste electrode. ACTA ACUST UNITED AC 2011. [DOI: 10.1007/s11771-011-0913-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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28
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Narcisi V, Mascini M, Perez G, Del Carlo M, Tiscar PG, Yamanaka H, Compagnone D. Electrochemical genosensors for the detection of Bonamia parasite. Selection of single strand-DNA (ssDNA) probes by simulation of the secondary structure folding. Talanta 2011; 85:1927-32. [DOI: 10.1016/j.talanta.2011.07.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2011] [Revised: 06/27/2011] [Accepted: 07/07/2011] [Indexed: 10/18/2022]
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29
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Li Z, Zeng G, Tang L, Zhang Y, Li Y, Pang Y, Luo J, Liu Y. Electrochemical DNA sensor for simultaneous detection of genes encoding two functional enzymes involved in lignin degradation. Biochem Eng J 2011. [DOI: 10.1016/j.bej.2011.04.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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30
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Liu C, Zeng GM, Tang L, Zhang Y, Li YP, Liu YY, Li Z, Wu MS, Luo J. Electrochemical detection of Pseudomonas aeruginosa 16S rRNA using a biosensor based on immobilized stem–loop structured probe. Enzyme Microb Technol 2011; 49:266-71. [DOI: 10.1016/j.enzmictec.2011.06.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2010] [Revised: 06/02/2011] [Accepted: 06/06/2011] [Indexed: 10/18/2022]
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31
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Simultaneous cadmium removal and 2,4-dichlorophenol degradation from aqueous solutions by Phanerochaete chrysosporium. Appl Microbiol Biotechnol 2011; 91:811-21. [PMID: 21556917 DOI: 10.1007/s00253-011-3313-4] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2011] [Revised: 04/02/2011] [Accepted: 04/05/2011] [Indexed: 10/18/2022]
Abstract
Phanerochaete chrysosporium has been recognised as an effective bioremediation agent due to its unique degradation to xenobiotic and biosorption ability to heavy metals. However, few studies have focused on the simultaneous removal of heavy metals and organic pollutants. The aim of this work was to study the feasibility of simultaneous cadmium removal and 2,4-dichlorophenol (2,4-DCP) degradation in P. chrysosporium liquid cultures. The removal efficiencies were pH dependent and the maximum removal efficiencies were observed at pH 6.5 under an initial cadmium concentration of 5 mg/L and an initial 2,4-DCP concentration of 20 mg/L. The removal efficiencies for cadmium and 2,4-DCP reached 63.62% and 83.90%, respectively, under the optimum conditions. The high production levels of lignin peroxidase (7.35 U/mL) and manganese peroxidase (8.30 U/mL) resulted in an increase in 2,4-DCP degradation. The protein content decreased with increasing cadmium concentration. The surface characteristics and functional groups of the biomass were studied by scanning electron microscopy and a Fourier-transformed infrared spectrometer. The results showed that the use of P. chrysosporium is promising for the simultaneous removal of cadmium and 2,4-DCP from liquid media.
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32
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Zeng G, Li Z, Tang L, Wu M, Lei X, Liu Y, Liu C, Pang Y, Zhang Y. Gold nanoparticles/water-soluble carbon nanotubes/aromatic diamine polymer composite films for highly sensitive detection of cellobiose dehydrogenase gene. Electrochim Acta 2011. [DOI: 10.1016/j.electacta.2011.03.035] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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33
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Zeng G, Yu Z, Chen Y, Zhang J, Li H, Yu M, Zhao M. Response of compost maturity and microbial community composition to pentachlorophenol (PCP)-contaminated soil during composting. BIORESOURCE TECHNOLOGY 2011; 102:5905-5911. [PMID: 21414773 DOI: 10.1016/j.biortech.2011.02.088] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2010] [Revised: 02/10/2011] [Accepted: 02/22/2011] [Indexed: 05/30/2023]
Abstract
Two composting piles were prepared by adding to a mixture of rice straw, vegetables and bran: (i) raw soil free from pentachlorophenol (PCP) contamination (pile A) and (ii) PCP-contaminated soil (pile B). It was shown by the results that compost maturity characterized by water soluble carbon (WSC), TOC/TN ratio, germination index (GI) and dehydrogenase activity (DA) was significantly affected by PCP exposure, which resulted in an inferior degree of maturity for pile B. DGGE analysis revealed an inhibited effect of PCP on compost microbial abundance. The bacteria community shifts were mainly consistent with composting factors such as temperature, pH, moisture content and substrates. By contrast, the fungal communities were more sensitive to PCP contamination due to the significant correlation between fungal community shifts and PCP removal. Therefore, the different microbial community compositions for properly evaluating the degree of maturity and PCP contamination were suggested.
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Affiliation(s)
- Guangming Zeng
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China.
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Zhang J, Zeng G, Chen Y, Yu M, Yu Z, Li H, Yu Y, Huang H. Effects of physico-chemical parameters on the bacterial and fungal communities during agricultural waste composting. BIORESOURCE TECHNOLOGY 2011; 102:2950-2956. [PMID: 21146982 DOI: 10.1016/j.biortech.2010.11.089] [Citation(s) in RCA: 158] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2010] [Revised: 11/18/2010] [Accepted: 11/19/2010] [Indexed: 05/30/2023]
Abstract
The goal of this study was to identify and prioritize some of the physico-chemical parameters that contributed to bacterial and fungal community compositions during agricultural waste composting. Relationships between those parameters and microbial community compositions determined by PCR-DGGE were simultaneously evaluated by redundancy analysis (RDA). The results showed that the temporal variation of bacterial community composition was significantly related to water soluble carbon (WSC), ammonium and nitrate (P<0.05), while the most variation in distribution of fungal community composition was statistically explained by pile temperature, WSC, and moisture content (P<0.05). Significant amounts of the variation (54.9% and 56.0% for bacterial and fungal species data, respectively) were explained by those parameters, suggesting that those parameters were the most likely ones to influence, or be influenced by the bacterial and fungal species. Variation partitioning analyses indicated that WSC and pile temperature showed predominant effect on the bacterial and fungal community composition, respectively.
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Affiliation(s)
- Jiachao Zhang
- College of Environmental Science and Engineering, Hunan University, Changsha, PR China
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35
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Campuzano S, Pedrero M, García JL, García E, García P, Pingarrón JM. Development of amperometric magnetogenosensors coupled to asymmetric PCR for the specific detection of Streptococcus pneumoniae. Anal Bioanal Chem 2011; 399:2413-20. [DOI: 10.1007/s00216-010-4645-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2010] [Revised: 12/21/2010] [Accepted: 12/21/2010] [Indexed: 10/18/2022]
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36
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Zhang Y, Zeng GM, Tang L, Li YP, Chen LJ, Pang Y, Li Z, Feng CL, Huang GH. An electrochemical DNA sensor based on a layers–film construction modified electrode. Analyst 2011; 136:4204-10. [DOI: 10.1039/c1an15526a] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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37
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Kinetic and analytical comparison of horseradish peroxidase on bare- and redox-modified single-walled carbon nanotubes. Electrochim Acta 2010. [DOI: 10.1016/j.electacta.2010.08.054] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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38
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Tosar J, Brañas G, Laíz J. Electrochemical DNA hybridization sensors applied to real and complex biological samples. Biosens Bioelectron 2010; 26:1205-17. [DOI: 10.1016/j.bios.2010.08.053] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2010] [Revised: 07/30/2010] [Accepted: 08/17/2010] [Indexed: 11/28/2022]
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Chen G, Zeng G, Du C, Huang D, Tang L, Wang L, Shen G. Transfer of heavy metals from compost to red soil and groundwater under simulated rainfall conditions. JOURNAL OF HAZARDOUS MATERIALS 2010; 181:211-6. [PMID: 20510509 DOI: 10.1016/j.jhazmat.2010.04.118] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2009] [Revised: 02/04/2010] [Accepted: 04/29/2010] [Indexed: 05/12/2023]
Abstract
It is well known that compost can be polluted with heavy metals. A self-designed soil column system was used to clarify the leaching or residue of heavy metals when compost was added to red soil. Less than 4% of Cu and more than 58.3% of Zn were transferred to groundwater. Maximum concentrations of Cu and Zn in leachate were 22 and 246 microg/L, respectively. pH in leachate decreased during 6.75-11.25 h, comparing with the control. Electrical conductivity was higher in the treatment of compost polluted by both Cu and Zn than that polluted only by Cu. Over 75.3% of Cu and 78.2% of Zn remained in the residual formation. Maximum bioavailability parameters in soil were 0.099 for Cu and 0.160 for Zn. Long-term field experiments with cycling application are needed to study the cycling effect on heavy metal residue in soil or leaching to the groundwater in the future.
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Affiliation(s)
- Guiqiu Chen
- College of Environmental Science and Engineering, Hunan University, Changsha, China.
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Liang YS, Yuan XZ, Zeng GM, Hu CL, Zhong H, Huang DL, Tang L, Zhao JJ. Biodelignification of rice straw by Phanerochaete chrysosporium in the presence of dirhamnolipid. Biodegradation 2010; 21:615-24. [PMID: 20131085 DOI: 10.1007/s10532-010-9329-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2009] [Accepted: 01/14/2010] [Indexed: 11/29/2022]
Abstract
Lignin degradation by white-rot fungi has received considerable attention as a means for reducing accumulation of lignocellulosic wastes in the environment. The stimulatory effect of surfactants on fungal lignocellulose bioconversion also has attracted wide interest. In this study the influence of dirhamnolipid biosurfactant on biodegradation of rice straw by Phanerochaete chrysosporium was investigated. It was shown that the biodelignification process of rice straw can be significantly enhanced by the presence of dirhamnolipid biosurfactant. In particular, the dirhamnolipid at the concentration of 0.007% increased the peak activity of lignin peroxidase (LiP) by 86% without affecting the manganese peroxidase (MnP) activity. The water-soluble organic carbon (WSOC) contents in the straw substrates as well as the microbial growth and activity were effectively improved by dirhamnolipid, while the degradation rate of lignin increased by 54% with dirhamnolipid of 0.007%. Observed chemical structural and morphological changes showed that the straw substrates were delignified in the presence of dirhamnolipid with the formation of terrace-like fragments separated from the inner cellular fibers and the release of simple compounds. Variation partitioning analysis revealed that the dirhamnolipid addition induced a significant straw biodelignification which explained 22.1% (P = 0.013) of the variance.
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Affiliation(s)
- Yun-Shan Liang
- College of Environmental Science and Engineering, Hunan University, 410082, Changsha, People's Republic of China
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41
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Hvastkovs EG, Buttry DA. Recent advances in electrochemical DNA hybridization sensors. Analyst 2010; 135:1817-29. [DOI: 10.1039/c0an00113a] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Park JY, Park SM. DNA hybridization sensors based on electrochemical impedance spectroscopy as a detection tool. SENSORS 2009; 9:9513-32. [PMID: 22303136 PMCID: PMC3267184 DOI: 10.3390/s91209513] [Citation(s) in RCA: 123] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2009] [Revised: 10/28/2009] [Accepted: 11/11/2009] [Indexed: 12/18/2022]
Abstract
Recent advances in label free DNA hybridization sensors employing electrochemical impedance spectroscopy (EIS) as a detection tool are reviewed. These sensors are based on the modulation of the blocking ability of an electrode modified with a probe DNA by an analyte, i.e., target DNA. The probe DNA is immobilized on a self-assembled monolayer, a conducting polymer film, or a layer of nanostructures on the electrode such that desired probe DNA would selectively hybridize with target DNA. The rate of charge transfer from the electrode thus modified to a redox indicator, e.g., [Fe(CN)6]3−/4−, which is measured by EIS in the form of charge transfer resistance (Rct), is modulated by whether or not, as well as how much, the intended target DNA is selectively hybridized. Efforts made to enhance the selectivity as well as the sensitivity of DNA sensors and to reduce the EIS measurement time are briefly described along with brief future perspectives in developing DNA sensors.
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Affiliation(s)
- Jin-Young Park
- Department of Chemistry, Pohang University of Science & Technology, Pohang 790-784, Korea; E-Mail:
| | - Su-Moon Park
- Interdisciplinary School of Green Energy Engineering, Ulsan National Institute of Science & Technology, Ulsan 689-805, Korea
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +82-52-217-2916; Fax: +82-52-217-2909
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Wu CC, Ko FH, Yang YS, Hsia DL, Lee BS, Su TS. Label-free biosensing of a gene mutation using a silicon nanowire field-effect transistor. Biosens Bioelectron 2009; 25:820-5. [PMID: 19765969 DOI: 10.1016/j.bios.2009.08.031] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2009] [Revised: 08/03/2009] [Accepted: 08/21/2009] [Indexed: 11/26/2022]
Abstract
We have developed a silicon nanowire field-effect transistor (NWFET) that allows deoxyribonucleic acid (DNA) biosensing. The nanowire (NW) was fabricated on a silicon-on-insulator wafer to provide effective ohmic contact. The NWFET sensor displayed n-channel depletion characteristics. To demonstrate the sensing capacity of the NWFET, we employed the BRAF(V599E) mutation gene, which correlates to the occurrence of cancers, as the target DNA sequence. The threshold voltage of the NWFET increased when the mutation gene was hybridized with the capture DNA strands on the nanowire, and decreased to the original level after de-hybridization of the gene. The shift in the drain current-gate voltage (I(D)-V(G)) curves revealed that the electrical signal had a logarithmic relationship with respect to the concentration of the mutation gene of up to six orders of magnitude, with the detection limit in the sub-femtomolar level. The detection results of mismatched DNA sequences, including one- and five-base-mismatched DNA strands, could be distinguished from complementary DNA gene by this sensor. The excellent electrical results obtained using this label-free NWFET sensor suggest that such devices might be potentially useful tools for biological research and oncogene screening.
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Affiliation(s)
- Chi-Chang Wu
- Department of Materials Science and Engineering, National Chiao Tung University, Hsinchu 300, Taiwan
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Luo X, Hsing IM. Electrochemical techniques on sequence-specific PCR amplicon detection for point-of-care applications. Analyst 2009; 134:1957-64. [PMID: 19768201 DOI: 10.1039/b912653h] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Nucleic acid based analysis provides accurate differentiation among closely affiliated species and this species- and sequence-specific detection technique would be particularly useful for point-of-care (POC) testing for prevention and early detection of highly infectious and damaging diseases. Electrochemical (EC) detection and polymerase chain reaction (PCR) are two indispensable steps, in our view, in a nucleic acid based point-of-care testing device as the former, in comparison with the fluorescence counterpart, provides inherent advantages of detection sensitivity, device miniaturization and operation simplicity, and the latter offers an effective way to boost the amount of targets to a detectable quantity. In this mini-review, we will highlight some of the interesting investigations using the combined EC detection and PCR amplification approaches for end-point detection and real-time monitoring. The promise of current approaches and the direction for future investigations will be discussed. It would be our view that the synergistic effect of the combined EC-PCR steps in a portable device provides a promising detection technology platform that will be ready for point-of-care applications in the near future.
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Affiliation(s)
- Xiaoteng Luo
- Bioengineering Graduate Program, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
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