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Lane LA, Zhang J, Wang Y. AMP coated SERS NanoTags with hydrophobic locking: Maximizing brightness, stability, and cellular targetability. J Colloid Interface Sci 2024; 663:295-308. [PMID: 38402824 DOI: 10.1016/j.jcis.2024.02.113] [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: 12/05/2023] [Revised: 01/16/2024] [Accepted: 02/13/2024] [Indexed: 02/27/2024]
Abstract
Developing innovative surface-enhanced Raman scattering (SERS) nanotags continues to attract significant attention due to their unparalleled sensitivity and specificity for in vitro diagnostic and in vivo tumor imaging applications. Here, we report a new class of bright and stable SERS nanotags using alkylmercaptan-PEG (AMP) polymers. Due to its amphiphilic structure and a thiol anchoring group, these polymers strongly absorb onto gold nanoparticles, leading to an inner hydrophobic layer and an outer hydrophilic PEG layer. The inner hydrophobic layer serves to "lock in" the Raman reporter molecules adsorbed on the particle surface via favorable hydrophobic interactions that also allow denser PEG coatings, which "lock out" other molecules from competitive binding or adsorbing to the gold surface, thereby providing superior colloidal and signal stability. The higher grafting densities of AMP polymers compared to conventional thiolated PEG also led to dramatic increases in cellular target selectivity, with specific-to-nonspecific binding ratios reaching beyond an order of magnitude difference. Experimental evaluations and theoretical considerations of dielectric polarization and light scattering indicate that the hydrophobic layer provides a more favorable dielectric environment with less plasmon dampening, greater particle scattering efficiency, and increased Raman reporter polarizability. Accordingly, SERS nanotags with AMP polymer coatings are observed to be considerably brighter (∼10-fold). Furthermore, the AMP-coated SERS nanotag's increased intensity and avidity can boost cellular detection sensitivity by nearly two orders of magnitude.
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Affiliation(s)
- Lucas A Lane
- International Ph.D. Program in Biomedical Engineering, College of Biomedical Engineering, Taipei Medical University, Taipei, Taiwan, ROC.
| | - Jinglei Zhang
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Jiangsu Province 210093, China
| | - Yiqing Wang
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Jiangsu Province 210093, China.
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2
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Liu Y, Su G, Wang W, Wei H, Dang L. A novel multifunctional SERS microfluidic sensor based on ZnO/Ag nanoflower arrays for label-free ultrasensitive detection of bacteria. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:2085-2092. [PMID: 38511545 DOI: 10.1039/d4ay00018h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
This study proposes a microfluidic platform for rapid enrichment and ultrasensitive SERS detection of bacteria. The platform comprises ZnO nanoflower arrays decorated with silver nanoparticles to enhance the SERS sensitivity. The ZnO nanoflower array substrate with a 3D reticular columnar structure is prepared using the hydrothermal method. SEM analysis depicts the 3.05 μm gap distribution of the substrate array to intercept the most bacteria in the particle sizes range of 0.5 to 3 μm. Then, silver nanoparticles are deposited on the ZnO nano-array surface by liquid evaporation self-assembly. TEM and SEM analysis indicate nanosize of Ag particles, evenly distributed on the substrate, enhancing the SERS efficiency and improving sensing reproducibility. The probe molecules (R6G) are tested to demonstrate the high SERS activity of the proposed microfluidic sensor. Then, Escherichia coli, Staphylococcus aureus, Enterococcus faecalis, and Bacillus subtilis are selected, demonstrating the sensor's excellent bacterial capture and sensitive recognition capabilities, with a detection limit as low as 102 CFU mL-1. Additionally, the antibacterial properties of ZnO/Ag heterojunction nanostructures are studied, suggesting their ability to inactivate bacteria. Compared with the traditional Au-enhanced chip, the sensor preparation is easy, safe, reliable, and low-cost. Moreover, the ZnO nano-array exhibits a large specific surface area, high interception ability, stronger and uniform SERS performance, and effective and reliable detection of trace pathogens. This work provides potential future ZnO/Ag microfluidic SERS sensor applications for rapid, unlabeled, and trace pathogens detection in clinical and environmental applications, potentially achieving breakthroughs in early detection, prevention, and treatment.
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Affiliation(s)
- Yue Liu
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China.
| | - Guanwen Su
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China.
| | - Wei Wang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China.
| | - Hongyuan Wei
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China.
| | - Leping Dang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China.
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Frempong SB, Salbreiter M, Mostafapour S, Pistiki A, Bocklitz TW, Rösch P, Popp J. Illuminating the Tiny World: A Navigation Guide for Proper Raman Studies on Microorganisms. Molecules 2024; 29:1077. [PMID: 38474589 DOI: 10.3390/molecules29051077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 02/13/2024] [Accepted: 02/18/2024] [Indexed: 03/14/2024] Open
Abstract
Raman spectroscopy is an emerging method for the identification of bacteria. Nevertheless, a lot of different parameters need to be considered to establish a reliable database capable of identifying real-world samples such as medical or environmental probes. In this review, the establishment of such reliable databases with the proper design in microbiological Raman studies is demonstrated, shining a light into all the parts that require attention. Aspects such as the strain selection, sample preparation and isolation requirements, the phenotypic influence, measurement strategies, as well as the statistical approaches for discrimination of bacteria, are presented. Furthermore, the influence of these aspects on spectra quality, result accuracy, and read-out are discussed. The aim of this review is to serve as a guide for the design of microbiological Raman studies that can support the establishment of this method in different fields.
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Affiliation(s)
- Sandra Baaba Frempong
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University, Helmholtzweg 4, 07743 Jena, Germany
- InfectoGnostics Research Campus Jena, Center of Applied Research, Philosophenweg 7, 07743 Jena, Germany
| | - Markus Salbreiter
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University, Helmholtzweg 4, 07743 Jena, Germany
- InfectoGnostics Research Campus Jena, Center of Applied Research, Philosophenweg 7, 07743 Jena, Germany
| | - Sara Mostafapour
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University, Helmholtzweg 4, 07743 Jena, Germany
| | - Aikaterini Pistiki
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University, Helmholtzweg 4, 07743 Jena, Germany
- InfectoGnostics Research Campus Jena, Center of Applied Research, Philosophenweg 7, 07743 Jena, Germany
- Leibniz-Institute of Photonic Technology, Member of the Leibniz Research Alliance-Leibniz Health Technologies, Albert-Einstein-Str. 9, 07745 Jena, Germany
| | - Thomas W Bocklitz
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University, Helmholtzweg 4, 07743 Jena, Germany
- Leibniz-Institute of Photonic Technology, Member of the Leibniz Research Alliance-Leibniz Health Technologies, Albert-Einstein-Str. 9, 07745 Jena, Germany
| | - Petra Rösch
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University, Helmholtzweg 4, 07743 Jena, Germany
- InfectoGnostics Research Campus Jena, Center of Applied Research, Philosophenweg 7, 07743 Jena, Germany
| | - Jürgen Popp
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University, Helmholtzweg 4, 07743 Jena, Germany
- InfectoGnostics Research Campus Jena, Center of Applied Research, Philosophenweg 7, 07743 Jena, Germany
- Leibniz-Institute of Photonic Technology, Member of the Leibniz Research Alliance-Leibniz Health Technologies, Albert-Einstein-Str. 9, 07745 Jena, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, 07743 Jena, Germany
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Kurdadze T, Lamadie F, Nehme KA, Teychené S, Biscans B, Rodriguez-Ruiz I. On-Chip Photonic Detection Techniques for Non-Invasive In Situ Characterizations at the Microfluidic Scale. SENSORS (BASEL, SWITZERLAND) 2024; 24:1529. [PMID: 38475065 DOI: 10.3390/s24051529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 02/21/2024] [Accepted: 02/22/2024] [Indexed: 03/14/2024]
Abstract
Microfluidics has emerged as a robust technology for diverse applications, ranging from bio-medical diagnostics to chemical analysis. Among the different characterization techniques that can be used to analyze samples at the microfluidic scale, the coupling of photonic detection techniques and on-chip configurations is particularly advantageous due to its non-invasive nature, which permits sensitive, real-time, high throughput, and rapid analyses, taking advantage of the microfluidic special environments and reduced sample volumes. Putting a special emphasis on integrated detection schemes, this review article explores the most relevant advances in the on-chip implementation of UV-vis, near-infrared, terahertz, and X-ray-based techniques for different characterizations, ranging from punctual spectroscopic or scattering-based measurements to different types of mapping/imaging. The principles of the techniques and their interest are discussed through their application to different systems.
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Affiliation(s)
- Tamar Kurdadze
- CEA, DES, ISEC, DMRC, Univ Montpellier, 30207 Bagnols-sur-Ceze, Marcoule, France
| | - Fabrice Lamadie
- CEA, DES, ISEC, DMRC, Univ Montpellier, 30207 Bagnols-sur-Ceze, Marcoule, France
| | - Karen A Nehme
- Laboratoire de Génie Chimique, CNRS, UMR 5503, 4 Allée Emile Monso, 31432 Toulouse, France
| | - Sébastien Teychené
- Laboratoire de Génie Chimique, CNRS, UMR 5503, 4 Allée Emile Monso, 31432 Toulouse, France
| | - Béatrice Biscans
- Laboratoire de Génie Chimique, CNRS, UMR 5503, 4 Allée Emile Monso, 31432 Toulouse, France
| | - Isaac Rodriguez-Ruiz
- Laboratoire de Génie Chimique, CNRS, UMR 5503, 4 Allée Emile Monso, 31432 Toulouse, France
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Xie M, Zhu Y, Li Z, Yan Y, Liu Y, Wu W, Zhang T, Li Z, Wang H. Key steps for improving bacterial SERS signals in complex samples: Separation, recognition, detection, and analysis. Talanta 2024; 268:125281. [PMID: 37832450 DOI: 10.1016/j.talanta.2023.125281] [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: 07/18/2023] [Revised: 09/09/2023] [Accepted: 10/05/2023] [Indexed: 10/15/2023]
Abstract
Rapid and reliable detection of pathogenic bacteria is absolutely essential for research in environmental science, food quality, and medical diagnostics. Surface-enhanced Raman spectroscopy (SERS), as an emerging spectroscopic technique, has the advantages of high sensitivity, good selectivity, rapid detection speed, and portable operation, which has been broadly used in the detection of pathogenic bacteria in different kinds of complex samples. However, the SERS detection method is also challenging in dealing with the detection difficulties of bacterial samples in complex matrices, such as interference from complex matrices, confusion of similar bacteria, and complexity of data processing. Therefore, researchers have developed some technologies to assist in SERS detection of bacteria, including both the front-end process of obtaining bacterial sample data and the back-end data processing process. The review summarizes the key steps for improving bacterial SERS signals in complex samples: separation, recognition, detection, and analysis, highlighting the principles of each step and the key roles for SERS pathogenic bacteria analysis, and the interconnectivity between each step. In addition, the current challenges in the practical application of SERS technology and the development trends are discussed. The purpose of this review is to deepen researchers' understanding of the various stages of using SERS technology to detect bacteria in complex sample matrices, and help them find new breakthroughs in different stages to facilitate the detection and control of bacteria in complex samples.
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Affiliation(s)
- Maomei Xie
- College of Pharmaceutical Engineering of Traditional Chinese Medicine (TCM), Tianjin University of TCM, Tianjin, 301617, China
| | - Yiting Zhu
- College of Pharmaceutical Engineering of Traditional Chinese Medicine (TCM), Tianjin University of TCM, Tianjin, 301617, China
| | - Zhiyao Li
- College of Pharmaceutical Engineering of Traditional Chinese Medicine (TCM), Tianjin University of TCM, Tianjin, 301617, China
| | - Yueling Yan
- College of Pharmaceutical Engineering of Traditional Chinese Medicine (TCM), Tianjin University of TCM, Tianjin, 301617, China
| | - Yidan Liu
- College of Pharmaceutical Engineering of Traditional Chinese Medicine (TCM), Tianjin University of TCM, Tianjin, 301617, China
| | - Wenbo Wu
- College of Pharmaceutical Engineering of Traditional Chinese Medicine (TCM), Tianjin University of TCM, Tianjin, 301617, China
| | - Tong Zhang
- College of Pharmaceutical Engineering of Traditional Chinese Medicine (TCM), Tianjin University of TCM, Tianjin, 301617, China
| | - Zheng Li
- College of Pharmaceutical Engineering of Traditional Chinese Medicine (TCM), Tianjin University of TCM, Tianjin, 301617, China; Haihe Laboratory of Modern Chinese Medicine, Tianjin, 301617, China; State Key Laboratory of Component-based Chinese Medicine, Tianjin University of TCM, Tianjin, 301617, China.
| | - Haixia Wang
- College of Pharmaceutical Engineering of Traditional Chinese Medicine (TCM), Tianjin University of TCM, Tianjin, 301617, China; Haihe Laboratory of Modern Chinese Medicine, Tianjin, 301617, China; State Key Laboratory of Component-based Chinese Medicine, Tianjin University of TCM, Tianjin, 301617, China.
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6
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Zeng P, Guan Q, Zhang Q, Yu L, Yan X, Hong Y, Duan L, Wang C. SERS detection of foodborne pathogens in beverage with Au nanostars. Mikrochim Acta 2023; 191:28. [PMID: 38093122 DOI: 10.1007/s00604-023-06105-2] [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: 08/02/2023] [Accepted: 11/15/2023] [Indexed: 12/18/2023]
Abstract
The aim of this study is to develop a simple but rapid method for the determination of foodborne pathogens in complex matrices (beverages) by surface enhanced Raman spectroscopy (SERS) combined with Au nanostar solid-phase substrates. The star-shaped singlet Au nanostructure was formed on the surface of a stainless steel sheet by chemical replacement reaction. Rhodamine 6G verified the sensitivity and reproducibility of this substrate, and the relative standard deviations of the SERS intensity at 1312 cm-1, 1364 cm-1, and 1510 cm-1 displacements were 3.40%, 5.64%, and 3.48%, respectively. By detecting four pathogens in beverage samples on Au nanostar substrates, the utility of the SERS assay was demonstrated, while the combination of principal component analysis (PCA) and hierarchical cluster analysis (HCA) further enabled the isolation and identification of pathogens. The results of spiked beverages were validated in conventional culture identification and Vitek 2 Compact biochemical identification system experiments. Thus, this research demonstrated that Au nanostar substrates can be effectively utilized for the recognition of pathogenic bacteria and have immense promise to advance the progress of quick detection of foodborne pathogens and food safety.
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Affiliation(s)
- Pei Zeng
- School of Food Science & Engineering, Jiangxi Agricultural University, Nanchang, 330045, People's Republic of China
| | - Qi Guan
- School of Food Science & Engineering, Jiangxi Agricultural University, Nanchang, 330045, People's Republic of China
| | - Qianqian Zhang
- School of Food Science & Engineering, Jiangxi Agricultural University, Nanchang, 330045, People's Republic of China
| | - Lili Yu
- School of Food Science & Engineering, Jiangxi Agricultural University, Nanchang, 330045, People's Republic of China
| | - Xianzai Yan
- School of Food Science & Engineering, Jiangxi Agricultural University, Nanchang, 330045, People's Republic of China
| | - Yanping Hong
- School of Food Science & Engineering, Jiangxi Agricultural University, Nanchang, 330045, People's Republic of China
| | - Luying Duan
- School of Food Science & Engineering, Jiangxi Agricultural University, Nanchang, 330045, People's Republic of China
| | - Chunrong Wang
- School of Food Science & Engineering, Jiangxi Agricultural University, Nanchang, 330045, People's Republic of China.
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Gao F, Li F, Wang J, Yu H, Li X, Chen H, Wang J, Qin D, Li Y, Liu S, Zhang X, Wang ZH. SERS-Based Optical Nanobiosensors for the Detection of Alzheimer's Disease. BIOSENSORS 2023; 13:880. [PMID: 37754114 PMCID: PMC10526933 DOI: 10.3390/bios13090880] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 08/21/2023] [Accepted: 08/23/2023] [Indexed: 09/28/2023]
Abstract
Alzheimer's disease (AD) is a leading cause of dementia, impacting millions worldwide. However, its complex neuropathologic features and heterogeneous pathophysiology present significant challenges for diagnosis and treatment. To address the urgent need for early AD diagnosis, this review focuses on surface-enhanced Raman scattering (SERS)-based biosensors, leveraging the excellent optical properties of nanomaterials to enhance detection performance. These highly sensitive and noninvasive biosensors offer opportunities for biomarker-driven clinical diagnostics and precision medicine. The review highlights various types of SERS-based biosensors targeting AD biomarkers, discussing their potential applications and contributions to AD diagnosis. Specific details about nanomaterials and targeted AD biomarkers are provided. Furthermore, the future research directions and challenges for improving AD marker detection using SERS sensors are outlined.
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Affiliation(s)
- Feng Gao
- Department of Neurology, Renmin Hospital of Wuhan University, Wuhan 430060, China; (F.G.); (F.L.); (J.W.); (H.Y.); (X.L.); (H.C.); (J.W.); (D.Q.); (Y.L.); (S.L.); (X.Z.)
- Center for Neurodegenerative Disease Research, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Fang Li
- Department of Neurology, Renmin Hospital of Wuhan University, Wuhan 430060, China; (F.G.); (F.L.); (J.W.); (H.Y.); (X.L.); (H.C.); (J.W.); (D.Q.); (Y.L.); (S.L.); (X.Z.)
- Center for Neurodegenerative Disease Research, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Jianhao Wang
- Department of Neurology, Renmin Hospital of Wuhan University, Wuhan 430060, China; (F.G.); (F.L.); (J.W.); (H.Y.); (X.L.); (H.C.); (J.W.); (D.Q.); (Y.L.); (S.L.); (X.Z.)
- Center for Neurodegenerative Disease Research, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Hang Yu
- Department of Neurology, Renmin Hospital of Wuhan University, Wuhan 430060, China; (F.G.); (F.L.); (J.W.); (H.Y.); (X.L.); (H.C.); (J.W.); (D.Q.); (Y.L.); (S.L.); (X.Z.)
- Center for Neurodegenerative Disease Research, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Xiang Li
- Department of Neurology, Renmin Hospital of Wuhan University, Wuhan 430060, China; (F.G.); (F.L.); (J.W.); (H.Y.); (X.L.); (H.C.); (J.W.); (D.Q.); (Y.L.); (S.L.); (X.Z.)
- Center for Neurodegenerative Disease Research, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Hongyu Chen
- Department of Neurology, Renmin Hospital of Wuhan University, Wuhan 430060, China; (F.G.); (F.L.); (J.W.); (H.Y.); (X.L.); (H.C.); (J.W.); (D.Q.); (Y.L.); (S.L.); (X.Z.)
- Center for Neurodegenerative Disease Research, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Jiabei Wang
- Department of Neurology, Renmin Hospital of Wuhan University, Wuhan 430060, China; (F.G.); (F.L.); (J.W.); (H.Y.); (X.L.); (H.C.); (J.W.); (D.Q.); (Y.L.); (S.L.); (X.Z.)
- Center for Neurodegenerative Disease Research, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Dongdong Qin
- Department of Neurology, Renmin Hospital of Wuhan University, Wuhan 430060, China; (F.G.); (F.L.); (J.W.); (H.Y.); (X.L.); (H.C.); (J.W.); (D.Q.); (Y.L.); (S.L.); (X.Z.)
- Center for Neurodegenerative Disease Research, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Yiyi Li
- Department of Neurology, Renmin Hospital of Wuhan University, Wuhan 430060, China; (F.G.); (F.L.); (J.W.); (H.Y.); (X.L.); (H.C.); (J.W.); (D.Q.); (Y.L.); (S.L.); (X.Z.)
- Center for Neurodegenerative Disease Research, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Songyan Liu
- Department of Neurology, Renmin Hospital of Wuhan University, Wuhan 430060, China; (F.G.); (F.L.); (J.W.); (H.Y.); (X.L.); (H.C.); (J.W.); (D.Q.); (Y.L.); (S.L.); (X.Z.)
- Center for Neurodegenerative Disease Research, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Xi Zhang
- Department of Neurology, Renmin Hospital of Wuhan University, Wuhan 430060, China; (F.G.); (F.L.); (J.W.); (H.Y.); (X.L.); (H.C.); (J.W.); (D.Q.); (Y.L.); (S.L.); (X.Z.)
- Center for Neurodegenerative Disease Research, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Zhi-Hao Wang
- Department of Neurology, Renmin Hospital of Wuhan University, Wuhan 430060, China; (F.G.); (F.L.); (J.W.); (H.Y.); (X.L.); (H.C.); (J.W.); (D.Q.); (Y.L.); (S.L.); (X.Z.)
- Center for Neurodegenerative Disease Research, Renmin Hospital of Wuhan University, Wuhan 430060, China
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Baranova AA, Tyurin AP, Korshun VA, Alferova VA. Sensing of Antibiotic-Bacteria Interactions. Antibiotics (Basel) 2023; 12:1340. [PMID: 37627760 PMCID: PMC10451291 DOI: 10.3390/antibiotics12081340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/15/2023] [Accepted: 08/17/2023] [Indexed: 08/27/2023] Open
Abstract
Sensing of antibiotic-bacteria interactions is an important area of research that has gained significant attention in recent years. Antibiotic resistance is a major public health concern, and it is essential to develop new strategies for detecting and monitoring bacterial responses to antibiotics in order to maintain effective antibiotic development and antibacterial treatment. This review summarizes recent advances in sensing strategies for antibiotic-bacteria interactions, which are divided into two main parts: studies on the mechanism of action for sensitive bacteria and interrogation of the defense mechanisms for resistant ones. In conclusion, this review provides an overview of the present research landscape concerning antibiotic-bacteria interactions, emphasizing the potential for method adaptation and the integration of machine learning techniques in data analysis, which could potentially lead to a transformative impact on mechanistic studies within the field.
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Affiliation(s)
| | | | | | - Vera A. Alferova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia; (A.A.B.); (A.P.T.); (V.A.K.)
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9
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Loiko N, Tereshkina K, Kovalenko V, Moiseenko A, Tereshkin E, Sokolova OS, Krupyanskii Y. DNA-Binding Protein Dps Protects Escherichia coli Cells against Multiple Stresses during Desiccation. BIOLOGY 2023; 12:853. [PMID: 37372138 DOI: 10.3390/biology12060853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 06/06/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023]
Abstract
Gradual dehydration is one of the frequent lethal yet poorly understood stresses that bacterial cells constantly face in the environment when their micro ecotopes dry out, as well as in industrial processes. Bacteria successfully survive extreme desiccation through complex rearrangements at the structural, physiological, and molecular levels, in which proteins are involved. The DNA-binding protein Dps has previously been shown to protect bacterial cells from many adverse effects. In our work, using engineered genetic models of E. coli to produce bacterial cells with overproduction of Dps protein, the protective function of Dps protein under multiple desiccation stresses was demonstrated for the first time. It was shown that the titer of viable cells after rehydration in the experimental variants with Dps protein overexpression was 1.5-8.5 times higher. Scanning electron microscopy was used to show a change in cell morphology upon rehydration. It was also proved that immobilization in the extracellular matrix, which is greater when the Dps protein is overexpressed, helps the cells survive. Transmission electron microscopy revealed disruption of the crystal structure of DNA-Dps crystals in E. coli cells that underwent desiccation stress and subsequent watering. Coarse-grained molecular dynamics simulations showed the protective function of Dps in DNA-Dps co-crystals during desiccation. The data obtained are important for improving biotechnological processes in which bacterial cells undergo desiccation.
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Affiliation(s)
- Nataliya Loiko
- Winogradsky Institute of Microbiology, Fundamentals of Biotechnology Federal Research Center, Russian Academy of Sciences, 117312 Moscow, Russia
| | - Ksenia Tereshkina
- Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Vladislav Kovalenko
- Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Andrey Moiseenko
- Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119991 Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Eduard Tereshkin
- Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Olga S Sokolova
- Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Yurii Krupyanskii
- Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119991 Moscow, Russia
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