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Deng J, Zhang W, Zhang L, Qin C, Wang H, Ling W. Micro-interfacial behavior of antibiotic-resistant bacteria and antibiotic resistance genes in the soil environment: A review. ENVIRONMENT INTERNATIONAL 2024; 191:108972. [PMID: 39180776 DOI: 10.1016/j.envint.2024.108972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 08/11/2024] [Accepted: 08/19/2024] [Indexed: 08/26/2024]
Abstract
Overutilization and misuse of antibiotics in recent decades markedly intensified the rapid proliferation and diffusion of antibiotic resistance genes (ARGs) within the environment, thereby elevating ARGs to the status of a global public health crisis. Recognizing that soil acts as a critical reservoir for ARGs, environmental researchers have made great progress in exploring the sources, distribution, and spread of ARGs in soil. However, the microscopic state and micro-interfacial behavior of ARGs in soil remains inadequately understood. In this study, we reviewed the micro-interfacial behaviors of antibiotic-resistant bacteria (ARB) in soil and porous media, predominantly including migration-deposition, adsorption, and biofilm formation. Meanwhile, adsorption, proliferation, and degradation were identified as the primary micro-interfacial behaviors of ARGs in the soil, with component of soil serving as significant determinant. Our work contributes to the further comprehension of the microstates and processes of ARB and ARGs in the soil environments and offers a theoretical foundation for managing and mitigating the risks associated with ARG contamination.
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Affiliation(s)
- Jibao Deng
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Wenkang Zhang
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Lingyu Zhang
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Chao Qin
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Hefei Wang
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China.
| | - Wanting Ling
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China.
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2
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Xu Y, Yan ZS, Ma YQ, Ding HM. Topology- and size-dependent binding of DNA nanostructures to the DNase I. Int J Biol Macromol 2024; 257:128703. [PMID: 38072351 DOI: 10.1016/j.ijbiomac.2023.128703] [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: 08/03/2023] [Revised: 12/01/2023] [Accepted: 12/07/2023] [Indexed: 12/17/2023]
Abstract
The susceptibility of DNA nanomaterials to enzymatic degradation in biological environments is a significant obstacle limiting their broad applications in biomedicine. While DNA nanostructures exhibit some resistance to nuclease degradation, the underlying mechanism of this resistance remains elusive. In this study, the interaction of tetrahedral DNA nanostructures (TDNs) and double-stranded DNA (dsDNA) with DNase I is investigated using all-atom molecular dynamics simulations. Our results indicate that DNase I can effectively bind to all dsDNA molecules, and certain key residues strongly interact with the nucleic bases of DNA. However, the binding of DNase I to TDNs exhibits a non-monotonic behavior based on size; TDN15 and TDN26 interact weakly with DNase I (∼ - 75 kcal/mol), whereas TDN21 forms a strong binding with DNase I (∼ - 110 kcal/mol). Furthermore, the topological properties of the DNA nanostructures are analyzed, and an under-twisting (∼32°) of the DNA helix is observed in TDN15 and TDN26. Importantly, this under-twisting results in an increased width of the minor groove in TDN15 and TDN26, which primarily explains their reduced binding affinity to DNase I comparing to the dsDNA. Overall, this study demonstrated a novel mechanism for local structural control of DNA at the nanoscale by adjusting the twisting induced by length.
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Affiliation(s)
- Yao Xu
- National Laboratory of Solid State Microstructures and Department of Physics, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
| | - Zeng-Shuai Yan
- National Laboratory of Solid State Microstructures and Department of Physics, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
| | - Yu-Qiang Ma
- National Laboratory of Solid State Microstructures and Department of Physics, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China.
| | - Hong-Ming Ding
- Center for Soft Condensed Matter Physics and Interdisciplinary Research, School of Physical Science and Technology, Soochow University, Suzhou 215006, China.
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Sun Y, Li X, Chen R, Liu F, Wei S. Recent advances in structural characterization of biomacromolecules in foods via small-angle X-ray scattering. Front Nutr 2022; 9:1039762. [PMID: 36466419 PMCID: PMC9714470 DOI: 10.3389/fnut.2022.1039762] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 11/03/2022] [Indexed: 08/04/2023] Open
Abstract
Small-angle X-ray scattering (SAXS) is a method for examining the solution structure, oligomeric state, conformational changes, and flexibility of biomacromolecules at a scale ranging from a few Angstroms to hundreds of nanometers. Wide time scales ranging from real time (milliseconds) to minutes can be also covered by SAXS. With many advantages, SAXS has been extensively used, it is widely used in the structural characterization of biomacromolecules in food science and technology. However, the application of SAXS in charactering the structure of food biomacromolecules has not been reviewed so far. In the current review, the principle, theoretical calculations and modeling programs are summarized, technical advances in the experimental setups and corresponding applications of in situ capabilities: combination of chromatography, time-resolved, temperature, pressure, flow-through are elaborated. Recent applications of SAXS for monitoring structural properties of biomacromolecules in food including protein, carbohydrate and lipid are also highlighted, and limitations and prospects for developing SAXS based on facility upgraded and artificial intelligence to study the structural properties of biomacromolecules are finally discussed. Future research should focus on extending machine time, simplifying SAXS data treatment, optimizing modeling methods in order to achieve an integrated structural biology based on SAXS as a practical tool for investigating the structure-function relationship of biomacromolecules in food industry.
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Affiliation(s)
- Yang Sun
- College of Vocational and Technical Education, Yunnan Normal University, Kunming, China
| | - Xiujuan Li
- Pharmaceutical Department, The Affiliated Taian City Central Hospital of Qingdao University, Taian, China
| | - Ruixin Chen
- College of Vocational and Technical Education, Yunnan Normal University, Kunming, China
| | - Fei Liu
- College of Vocational and Technical Education, Yunnan Normal University, Kunming, China
| | - Song Wei
- Tumor Precise Intervention and Translational Medicine Laboratory, The Affiliated Taian City Central Hospital of Qingdao University, Taian, China
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Ehm T, Philipp J, Barkey M, Ober M, Brinkop AT, Simml D, von Westphalen M, Nickel B, Beck R, Rädler JO. 3D-printed SAXS chamber for controlled in situ dialysis and optical characterization. JOURNAL OF SYNCHROTRON RADIATION 2022; 29:1014-1019. [PMID: 35787568 PMCID: PMC9255564 DOI: 10.1107/s1600577522005136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 05/12/2022] [Indexed: 06/15/2023]
Abstract
3D printing changes the scope of how samples can be mounted for small-angle X-ray scattering (SAXS). In this paper a 3D-printed X-ray chamber, which allows for in situ exchange of buffer and in situ optical transmission spectroscopy, is presented. The chamber is made of cyclic olefin copolymers (COC), including COC X-ray windows providing ultra-low SAXS background. The design integrates a membrane insert for in situ dialysis of the 100 µl sample volume against a reservoir, which enables measurements of the same sample under multiple conditions using an in-house X-ray setup equipped with a 17.4 keV molybdenum source. The design's capabilities are demonstrated by measuring reversible structural changes in lipid and polymer systems as a function of salt concentration and pH. In the same chambers optical light transmission spectroscopy was carried out measuring the optical turbidity of the mesophases and local pH values using pH-responsive dyes. Microfluidic exchange and optical spectroscopy combined with in situ X-ray scattering enables vast applications for the study of responsive materials.
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Affiliation(s)
- Tamara Ehm
- School of Physics and Astronomy, Center for Physics and Chemistry of Living Systems, and Center for Nanoscience and Nanotechnology, Tel Aviv University, Ramat Aviv, Israel
- Faculty of Physics, Ludwig-Maximilians-Universität, Geschwister-Scholl-Platz 1, Munich, Germany
| | - Julian Philipp
- Faculty of Physics, Ludwig-Maximilians-Universität, Geschwister-Scholl-Platz 1, Munich, Germany
| | - Martin Barkey
- Faculty of Physics, Ludwig-Maximilians-Universität, Geschwister-Scholl-Platz 1, Munich, Germany
| | - Martina Ober
- Faculty of Physics, Ludwig-Maximilians-Universität, Geschwister-Scholl-Platz 1, Munich, Germany
| | - Achim Theo Brinkop
- Faculty of Physics, Ludwig-Maximilians-Universität, Geschwister-Scholl-Platz 1, Munich, Germany
| | - David Simml
- Faculty of Physics, Ludwig-Maximilians-Universität, Geschwister-Scholl-Platz 1, Munich, Germany
| | - Miriam von Westphalen
- Faculty of Physics, Ludwig-Maximilians-Universität, Geschwister-Scholl-Platz 1, Munich, Germany
| | - Bert Nickel
- Faculty of Physics, Ludwig-Maximilians-Universität, Geschwister-Scholl-Platz 1, Munich, Germany
| | - Roy Beck
- School of Physics and Astronomy, Center for Physics and Chemistry of Living Systems, and Center for Nanoscience and Nanotechnology, Tel Aviv University, Ramat Aviv, Israel
| | - Joachim O. Rädler
- Faculty of Physics, Ludwig-Maximilians-Universität, Geschwister-Scholl-Platz 1, Munich, Germany
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Djebbi K, Shi B, Weng T, Bahri M, Elaguech MA, Liu J, Tlili C, Wang D. Highly Sensitive Fluorescence Assay for miRNA Detection: Investigation of the DNA Spacer Effect on the DSN Enzyme Activity toward Magnetic-Bead-Tethered Probes. ACS OMEGA 2022; 7:2224-2233. [PMID: 35071911 PMCID: PMC8771974 DOI: 10.1021/acsomega.1c05775] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 12/29/2021] [Indexed: 05/28/2023]
Abstract
Researchers have recently designed various biosensors combining magnetic beads (MBs) and duplex-specific nuclease (DSN) enzyme to detect miRNAs. Yet, the interfacial mechanisms for surface-based hybridization and DSN-assisted target recycling are relatively not well understood. Thus, herein, we developed a highly sensitive and selective fluorescent biosensor to study the phenomenon that occurs on the local microenvironment surrounding the MB-tethered DNA probe via detecting microRNA-21 as a model. Using the above strategy, we investigated the influence of different DNA spacers, base-pair orientations, and surface densities on DSN-assisted target recycling. As a result, we were able to detect as low as 170 aM of miR-21 under the optimized conditions. Moreover, this approach exhibits a high selectivity in a fully matched target compared to a single-base mismatch, allowing the detection of miRNAs in serum with improved recovery. These results are attributed to the synergetic effect between the DSN enzyme activity and the neutral DNA spacer (triethylene glycol: TEG) to improve the miRNA detection's sensitivity. Finally, our strategy could create new paths for detecting microRNAs since it obliterates the enzyme-mediated cascade reaction used in previous studies, which is more expensive, more time-consuming, less sensitive, and requires double catalytic reactions.
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Affiliation(s)
- Khouloud Djebbi
- Chongqing
Institute of Green and Intelligent Technology, Chinese Academy of
Sciences, Chongqing 400714, P. R. China
- Chongqing
School, University of Chinese Academy of
Sciences (UCAS), Chongqing 400714, P. R. China
- University
of Chinese Academy of Sciences (UCAS), Beijing 100049, P. R. China
| | - Biao Shi
- Chongqing
Institute of Green and Intelligent Technology, Chinese Academy of
Sciences, Chongqing 400714, P. R. China
- Chongqing
School, University of Chinese Academy of
Sciences (UCAS), Chongqing 400714, P. R. China
| | - Ting Weng
- Chongqing
Institute of Green and Intelligent Technology, Chinese Academy of
Sciences, Chongqing 400714, P. R. China
- Chongqing
School, University of Chinese Academy of
Sciences (UCAS), Chongqing 400714, P. R. China
| | - Mohamed Bahri
- Chongqing
Institute of Green and Intelligent Technology, Chinese Academy of
Sciences, Chongqing 400714, P. R. China
- Chongqing
School, University of Chinese Academy of
Sciences (UCAS), Chongqing 400714, P. R. China
- University
of Chinese Academy of Sciences (UCAS), Beijing 100049, P. R. China
| | - Mohamed Amin Elaguech
- Chongqing
Institute of Green and Intelligent Technology, Chinese Academy of
Sciences, Chongqing 400714, P. R. China
- Chongqing
School, University of Chinese Academy of
Sciences (UCAS), Chongqing 400714, P. R. China
- University
of Chinese Academy of Sciences (UCAS), Beijing 100049, P. R. China
| | - Jin Liu
- Chongqing
School, University of Chinese Academy of
Sciences (UCAS), Chongqing 400714, P. R. China
- Department
of Pathology, Chongqing General Hospital, University of Chinese Academy of Sciences (UCAS), Chongqing 400013, P. R. China
| | - Chaker Tlili
- Chongqing
Institute of Green and Intelligent Technology, Chinese Academy of
Sciences, Chongqing 400714, P. R. China
- Chongqing
School, University of Chinese Academy of
Sciences (UCAS), Chongqing 400714, P. R. China
| | - Deqiang Wang
- Chongqing
Institute of Green and Intelligent Technology, Chinese Academy of
Sciences, Chongqing 400714, P. R. China
- Chongqing
School, University of Chinese Academy of
Sciences (UCAS), Chongqing 400714, P. R. China
- University
of Chinese Academy of Sciences (UCAS), Beijing 100049, P. R. China
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Breger JC, Susumu K, Lasarte-Aragonés G, Díaz SA, Brask J, Medintz IL. Quantum Dot Lipase Biosensor Utilizing a Custom-Synthesized Peptidyl-Ester Substrate. ACS Sens 2020; 5:1295-1304. [PMID: 32096987 DOI: 10.1021/acssensors.9b02291] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Lipases are an important class of lipid hydrolyzing enzymes that play significant roles in many aspects of cell biology and digestion; they also have large roles in commercial food and biofuel preparation and are being targeted for pharmaceutical development. Given these, and many other biotechnological roles, sensitive and specific biosensors capable of monitoring lipase activity in a quantitative manner are critical. Here, we describe a Förster resonance energy transfer (FRET)-based biosensor that originates from a custom-synthesized ester substrate displaying a peptide at one end and a dye acceptor at the other. These substrates were ratiometrically self-assembled to luminescent semiconductor quantum dot (QD) donors by metal affinity coordination using the appended peptide's terminal hexahistidine motif to give rise to the full biosensing construct. This resulted in a high rate of FRET between the QD donor and the proximal substrate's dye acceptor. The lipase hydrolyzed the intervening target ester bond in the peptide substrate which, in turn, displaced the dye acceptor containing component and altered the rate of FRET in a concentration-dependent manner. Specifics of the substrate's stepwise synthesis are described along with the sensors assembly, characterization, and application in a quantitative proof-of-concept demonstration assay that is based on an integrated Michaelis-Menten kinetic approach. The utility of this unique nanoparticle-based architecture within a sensor configuration is then discussed.
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Affiliation(s)
- Joyce C. Breger
- Center for Bio/Molecular Science and Engineering, U.S. Naval Research Laboratory, Code 6900, Washington, District of Columbia 20375, United States
| | - Kimihiro Susumu
- Optical Sciences Division, U.S. Naval Research Laboratory, Code 5600, Washington, District of Columbia 20375, United States
- KeyW Corporation, Hanover, Maryland 21076, United States
| | - Guillermo Lasarte-Aragonés
- Center for Bio/Molecular Science and Engineering, U.S. Naval Research Laboratory, Code 6900, Washington, District of Columbia 20375, United States
- Department of Bioengineering, George Mason University, Fairfax, Virginia 22030, United States
| | - Sebastián A. Díaz
- Center for Bio/Molecular Science and Engineering, U.S. Naval Research Laboratory, Code 6900, Washington, District of Columbia 20375, United States
| | - Jesper Brask
- Novozymes A/S, Biologiens Vej 2, 2800 Kgs. Lyngby, Denmark
| | - Igor L. Medintz
- Center for Bio/Molecular Science and Engineering, U.S. Naval Research Laboratory, Code 6900, Washington, District of Columbia 20375, United States
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