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Guler A, Yilmaz A, Oncer N, Sever NI, Cengiz Sahin S, Kavakcıoglu Yardimci B, Yilmaz M. Machine learning-assisted SERS approach enables the biochemical discrimination in Bcl-2 and Mcl-1 expressing yeast cells treated with ketoconazole and fluconazole antifungals. Talanta 2024; 276:126248. [PMID: 38776770 DOI: 10.1016/j.talanta.2024.126248] [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: 03/01/2024] [Revised: 05/01/2024] [Accepted: 05/10/2024] [Indexed: 05/25/2024]
Abstract
Antifungal medications are important due to their potential application in cancer treatment either on their own or with traditional treatments. The mechanisms that prevent the effects of these medications and restrict their usage in cancer treatment are not completely understood. The evaluation and discrimination of the possible protective effects of the anti-apoptotic members of the Bcl-2 family of proteins, critical regulators of mitochondrial apoptosis, against antifungal drug-induced cell death has still scientific uncertainties that must be considered. Novel, simple, and reliable strategies are highly demanded to identify the biochemical signature of this phenomenon. However, the complex nature of cells poses challenges for the analysis of cellular biochemical changes or classification. In this study, for the first time, we investigated the probable protective activities of Bcl-2 and Mcl-1 proteins against cell damage induced by ketoconazole (KET) and fluconazole (FLU) antifungal drugs in a yeast model through surface-enhanced Raman spectroscopy (SERS) approach. The proposed SERS platform created robust Raman spectra with a high signal-to-noise ratio. The analysis of SERS spectral data via advanced unsupervised and supervised machine learning methods enabled unquestionable differentiation (100 %) in samples and biomolecular identification. Various SERS bands related to lipids and proteins observed in the analyses suggest that the expression of these anti-apoptotic proteins reduces oxidative biomolecule damage induced by the antifungals. Also, cell viability assay, Annexin V-FITC/PI double staining, and total oxidant and antioxidant status analyses were performed to support Raman measurements. We strongly believe that the proposed approach paves the way for the evaluation of various biochemical structures/changes in various cells.
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Affiliation(s)
- Ayşenur Guler
- Chemistry Department, Graduate School of Natural and Applied Sciences, Pamukkale University, Denizli, Turkey
| | - Asli Yilmaz
- Department of Molecular Biology & Genetics, Faculty of Science, Ataturk University, Erzurum, Turkey
| | - Nazli Oncer
- Department of Nanoscience and Nanoengineering, Graduate School of Natural and Applied Sciences, Ataturk University, Erzurum, Turkey
| | - Nurettin Ilter Sever
- Department of Molecular Biology & Genetics, Faculty of Science, Pamukkale University, Denizli, Turkey
| | - Sevilay Cengiz Sahin
- Department of Molecular Biology & Genetics, Faculty of Science, Pamukkale University, Denizli, Turkey
| | - Berna Kavakcıoglu Yardimci
- Department of Chemistry, Faculty of Science, Pamukkale University, Denizli, Turkey; Advanced Technology Application and Research Center, Pamukkale University, Denizli, Turkey.
| | - Mehmet Yilmaz
- Department of Nanoscience and Nanoengineering, Graduate School of Natural and Applied Sciences, Ataturk University, Erzurum, Turkey; Department of Chemical Engineering, Faculty of Engineering, Ataturk University, Erzurum, Turkey.
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Felicia WXL, Rovina K, ‘Aqilah NMN, Vonnie JM, Yin KW, Huda N. Assessing Meat Freshness via Nanotechnology Biosensors: Is the World Prepared for Lightning-Fast Pace Methods? BIOSENSORS 2023; 13:217. [PMID: 36831985 PMCID: PMC9954215 DOI: 10.3390/bios13020217] [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: 12/01/2022] [Revised: 01/11/2023] [Accepted: 01/12/2023] [Indexed: 06/18/2023]
Abstract
In the rapidly evolving field of food science, nanotechnology-based biosensors are one of the most intriguing techniques for tracking meat freshness. Purine derivatives, especially hypoxanthine and xanthine, are important signs of food going bad, especially in meat and meat products. This article compares the analytical performance parameters of traditional biosensor techniques and nanotechnology-based biosensor techniques that can be used to find purine derivatives in meat samples. In the introduction, we discussed the significance of purine metabolisms as analytes in the field of food science. Traditional methods of analysis and biosensors based on nanotechnology were also briefly explained. A comprehensive section of conventional and nanotechnology-based biosensing techniques is covered in detail, along with their analytical performance parameters (selectivity, sensitivity, linearity, and detection limit) in meat samples. Furthermore, the comparison of the methods above was thoroughly explained. In the last part, the pros and cons of the methods and the future of the nanotechnology-based biosensors that have been created are discussed.
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Affiliation(s)
- Wen Xia Ling Felicia
- Faculty of Food Science and Nutrition, Universiti Malaysia Sabah, Kota Kinabalu 88400, Sabah, Malaysia
| | - Kobun Rovina
- Faculty of Food Science and Nutrition, Universiti Malaysia Sabah, Kota Kinabalu 88400, Sabah, Malaysia
| | - Nasir Md Nur ‘Aqilah
- Faculty of Food Science and Nutrition, Universiti Malaysia Sabah, Kota Kinabalu 88400, Sabah, Malaysia
| | - Joseph Merillyn Vonnie
- Faculty of Food Science and Nutrition, Universiti Malaysia Sabah, Kota Kinabalu 88400, Sabah, Malaysia
| | - Koh Wee Yin
- Faculty of Food Science and Nutrition, Universiti Malaysia Sabah, Kota Kinabalu 88400, Sabah, Malaysia
| | - Nurul Huda
- Faculty of Sustainable Agriculture, Universiti Malaysia Sabah, Locked Bag No. 3, Sandakan 90509, Sabah, Malaysia
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Li B, Ma Y, Han X, Hu P, Lu X. Enhanced Sum Frequency Generation for Monolayers on Au Relative to Silica: Local Field Factors and SPR Effect. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:659-667. [PMID: 36580605 DOI: 10.1021/acs.langmuir.2c03016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Using metals as signal magnified substrates, surface plasmon-enhanced sum frequency generation (SFG) vibrational spectroscopy is a promising technique to probe weak molecular-level signals at surfaces and interfaces. In this study, the vibrational signals of the n-alkane monolayer on the gold (Au) and silica substrates are investigated using the broadband femtosecond SFG. The enhancement factors are discovered to be up to ∼1076 and ∼31 for the methyl symmetric and asymmetric stretching (ss and as) modes of the monolayer, respectively. By systematically analyzing the second-order nonlinear susceptibility tensor components (χijks), the Fresnel coefficients (Fijks), and the surface plasmon resonance (SPR) effect, we find that the interplay between Fijk and χijk terms and the SPR effect dominate the SFG signal enhancement. Our study reveals that the relative contributions of different influencing factors (i.e., Fresnel coefficients and SPR) to the SFG signal enhancement provide an approach to interpreting enhanced SFG vibrational signals detected from probe molecules on distinct substrates and may finally guide the design of the experimental methodology to improve the detection sensitivity and signal-to-noise ratio.
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Affiliation(s)
- Bolin Li
- Anhui Key Laboratory of Condensed Matter Physics at Extreme Conditions, High Magnetic Field Laboratory (HMFL), Hefei Institutes of Physical Science (HFIPS), Chinese Academy of Sciences, Hefei, Anhui230031, P. R. China
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing210096, China
| | - Yonghao Ma
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing210096, China
| | - Xiaofeng Han
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing210096, China
| | - Pengcheng Hu
- School of Medical Imaging, Xuzhou Medical College, Xuzhou, Jiangsu221004, China
| | - Xiaolin Lu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing210096, China
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Ustun O, Yilmaz A, Yilmaz M. Catalytic and SERS activities of WO 3-based nanowires: the effect of oxygen vacancies, silver nanoparticle doping, and the type of organic dye. Phys Chem Chem Phys 2022; 24:18615-18626. [PMID: 35894693 DOI: 10.1039/d2cp00034b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Oxygen vacancies in tungsten trioxide (WO3) nanostructures (WO3-x) dominate the major characteristics of the material and determine their activity in various applications including photocatalysis and surface-enhanced Raman spectroscopy (SERS). Despite some studies performed in the last decade, the photocatalytic activity toward different pollutants and SERS activity toward different Raman reporter molecules are still unclear and may provide valuable insights into this research field. Therefore, in this study, we propose WO3-x nanowires (NWs) both as ideal photocatalysts for the degradation of organic pollutants such as crystal violet (CV), methylene blue (MB), malachite green (MG), and rhodamine 6G (R6G) and a SERS platform for the detection of these molecules. In the first step, WO3-x NWs were fabricated through the solvothermal method. Afterward, the oxygen vacancy content of WO3-x NWs was manipulated by the addition of silver ions or H2O2. Although H2O2 led to a remarkable decrease in oxygen vacancies (WO3), the addition of silver ions led to the formation of Ag nanostructures on WO3-x NWs (WO3-x@Ag). Interestingly, the combination of WO3-x and WO3-x@Ag nanosystems with all dye molecules resulted in the formation of H-aggregates due to the strong electrostatic interaction between the nanostructure and dye molecules and then its photocatalytic degradation, while regular degradation of dyes was observed for WO3. In SERS activity tests, each NP system exhibited different activities depending on various parameters including the chemical nature of the nanosystem, the degree of oxygen vacancy, the interaction of the Raman reporter molecule with the surface of the NP, and the resultant formation of H-aggregates or photocatalytic degradation. The combination of MB with WO3-x, WO3-x@Ag, and WO3 created enhancement factors such as 1.6 × 103, 5.4 × 103, and 6.2 × 103, respectively. This report showed that the parameters mentioned here must be considered in detail to evaluate the photocatalytic and SERS activity of the WO3-based nanosystem.
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Affiliation(s)
- Oguzhan Ustun
- Department of Nanoscience and Nanoengineering, Ataturk University, 25240 Erzurum, Turkey.
| | - Asli Yilmaz
- Department of Molecular Biology and Genetics, Ataturk University, 25240 Erzurum, Turkey
| | - Mehmet Yilmaz
- Department of Nanoscience and Nanoengineering, Ataturk University, 25240 Erzurum, Turkey. .,Department of Chemical Engineering, Ataturk University, 25240 Erzurum, Turkey
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Serginay N, Dizaji AN, Mazlumoglu H, Karatas E, Yilmaz A, Yilmaz M. Antibacterial activity and cytotoxicity of bioinspired poly(L-DOPA)-mediated silver nanostructure-decorated titanium dioxide nanowires. Colloids Surf A Physicochem Eng Asp 2022. [DOI: 10.1016/j.colsurfa.2022.128350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Xie Y. Fabrication of Highly Ordered Ag/TiO2 Nanopore Array as a Self-Cleaning and Recycling SERS Substrate. Aust J Chem 2021. [DOI: 10.1071/ch21142] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Silver nanoparticles deposited on a titania nanopore array (Ag/TiO2 NPA) has been designed as a surface-enhanced Raman scattering (SERS) substrate for sensitive and recycling application of organic molecule detection. A TiO2 NPA was fabricated by a surface oxidization reaction of a titanium sheet by a double anodization process. A Ag/TiO2 NPA was then formed by depositing silver nanoparticles onto the TiO2 NPA by a cycling chemical reduction deposition process. The Ag/TiO2 NPA has a uniform mono-layer dispersion of Ag nanoparticles with a size of 30–50 nm on TiO2 nanopores with a diameter of 100–110 nm. The Ag/TiO2 NPA SERS substrate could facilitate interfacial adsorption of Rhodamine 6G (R6G), which achieves a sensitive detection limit of 10−8 M R6G through SERS spectrum measurement. The Ag/TiO2 NPA SERS substrate achieves an analytical enhancement factor value of 2.6 × 105. The Ag/TiO2 NRA could promote the UV light-excited photocatalytic degradation reaction of R6G adsorbed on its surface which gives rise to a refreshed Ag/TiO2 NRA under UV irradiation for 60 min and accordingly behave as a self-cleaning and recycling SERS substrate. The Ag/TiO2 NPA exhibits a much higher R6G degradation reaction rate constant (0.05764 min−1) than the TiO2 NPA (0.02600 min−1), indicating its superior photocatalytic activity and self-cleaning activity. The refreshed Ag/TiO2 NPA was able to be recycled for the Raman detection of R6G, maintaining a high stability, reproducibility, and cyclability. The highly ordered Ag/TiO2 NPA with well controlled Ag nanoparticle dispersion and TiO2 nanopore shape could act as a suitable SERS substrate for recycling and self-cleaning application for stable and sensitive molecule detection.
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