1
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Sundaramoorthy A, Bharanidharan G, Prakasarao A, Ganesan S. Characterization and classification of pathogenic bacteria using native fluorescence and spectral deconvolution. JOURNAL OF BIOPHOTONICS 2024; 17:e202300566. [PMID: 38847123 DOI: 10.1002/jbio.202300566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 04/24/2024] [Accepted: 04/24/2024] [Indexed: 07/13/2024]
Abstract
Identification and classification of pathogenic bacterial strains is of current interest for the early treatment of diseases. In this work, protein fluorescence from eight different pathogenic bacterial strains were characterized using steady state and time resolved fluorescence spectroscopy. The spectral deconvolution method was also employed to decompose the emission contribution from different intrinsic fluorophores and extracted various key parameters, such as intensity, emission maxima, emission line width of the fluorophores, and optical redox ratio. The change in average lifetime values across different bacterial strains exhibits good statistical significance (p ≤ 0.01). The variations in the photophysical characteristics of bacterial strains are due to the different conformational states of the proteins. The stepwise multiple linear discriminate analysis of fluorescence emission spectra at 280 nm excitation across eight different bacterial strains classifies the original groups and cross validated group with 100% and 99.5% accuracy, respectively.
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Affiliation(s)
| | | | - Aruna Prakasarao
- Department of Medical Physics, Anna University, Chennai, Tamilnadu, India
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2
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Markovitsi D. On the Use of the Intrinsic DNA Fluorescence for Monitoring Its Damage: A Contribution from Fundamental Studies. ACS OMEGA 2024; 9:26826-26837. [PMID: 38947837 PMCID: PMC11209687 DOI: 10.1021/acsomega.4c02256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 05/02/2024] [Accepted: 05/08/2024] [Indexed: 07/02/2024]
Abstract
The assessment of DNA damage by means of appropriate fluorescent probes is widely spread. In the specific case of UV-induced damage, it has been suggested to use the emission of dimeric photoproducts as an internal indicator for the efficacy of spermicidal lamps. However, in the light of fundamental studies on the UV-induced processes, outlined in this review, this is not straightforward. It is by now well established that, in addition to photodimers formed via an electronic excited state, photoionization also takes place with comparable or higher quantum yields, depending on the irradiation wavelength. Among the multitude of final lesions, some have been fully characterized, but others remain unknown; some of them may emit, while others go undetected upon monitoring fluorescence, the result being strongly dependent on both the irradiation and the excitation wavelength. In contrast, the fluorescence of undamaged nucleobases associated with emission from ππ* states, localized or excitonic, appearing at wavelengths shorter than 330 nm is worthy of being explored to this end. Despite its low quantum yield, it is readily detected nowadays. Its intensity decreases due to the disappearance of the reacting nucleobases and the loss of exciton coherence provoked by the presence of lesions, independently of their type. Thus, it could potentially provide valuable information about the DNA damage induced, not only by UV radiation but also by other sanitizing or therapeutic agents.
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Affiliation(s)
- Dimitra Markovitsi
- Université Paris-Saclay, CNRS,
Institut de Chimie Physique, UMR8000, 91405 Orsay, France
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3
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Lv HZ, Chen J, Zhao Y, Li Y, Cao SH, Cai WP, Shen L, Lu Y, Li YQ. A novel derivative synchronous fluorescence method for the rapid, non-destructive and intuitive differentiation of denitrifying bacteria. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 356:120587. [PMID: 38520848 DOI: 10.1016/j.jenvman.2024.120587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 01/30/2024] [Accepted: 03/10/2024] [Indexed: 03/25/2024]
Abstract
It is challenging to differentiate bacteria residing in the same habitat by direct observation. This difficulty impedes the harvest, application and manipulation of functional bacteria in environmental engineering. In this study, we developed a novel method for rapid differentiation of living denitrifying bacteria based on derivative synchronous fluorescence spectroscopy, as exemplified by three heterotrophic nitrification-aerobic denitrification bacteria having the maximum nitrogen removal efficiencies greater than 90%. The intact bacteria and their living surroundings can be analyzed as an integrated target, which eliminates the need for the complex pre-processing of samples. Under the optimal synchronous scanning parameter (Δλ = 40 nm), each bacterium possesses a unique fluorescence spectral structure and the derivative synchronous fluorescence technique can significantly improve the spectral resolution compared to other conventional fluorescence methods, which enables the rapid differentiation of different bacteria through derivative synchronous fluorescence spectra as fast as 2 min per spectrum. Additionally, the derivative synchronous fluorescence technique can extract the spectral signals contributed by bacterial extracellular substances produced in the biological nitrogen removal process. Moreover, the results obtained from our method can reflect the real-time denitrification properties of bacteria in the biological nitrogen removal process of wastewater. All these merits highlight derivative synchronous fluorescence spectroscopy as a promising analytic method in the environmental field.
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Affiliation(s)
- Huang-Zhou Lv
- Department of Chemistry and the MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, PR China
| | - Jinliang Chen
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, The Key Laboratory for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen, 361005, PR China
| | - Yan Zhao
- Department of Chemistry and the MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, PR China; Technology Center, China Tobacco Fujian Industrial Co., Ltd., Xiamen, 361021, PR China
| | - Yu Li
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, The Key Laboratory for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen, 361005, PR China
| | - Shuo-Hui Cao
- Department of Chemistry and the MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, PR China; Department of Electronic Science, Xiamen University Xiamen, 361005, PR China
| | - Wei-Peng Cai
- Xiamen Municipal Center for Disease Control and Prevention, Xiamen, 361021, PR China
| | - Liang Shen
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, The Key Laboratory for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen, 361005, PR China.
| | - Yinghua Lu
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, The Key Laboratory for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen, 361005, PR China
| | - Yao-Qun Li
- Department of Chemistry and the MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, PR China.
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4
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Öberg R, Sil TB, Johansson AC, Malyshev D, Landström L, Johansson S, Andersson M, Andersson PO. UV-Induced Spectral and Morphological Changes in Bacterial Spores for Inactivation Assessment. J Phys Chem B 2024; 128:1638-1646. [PMID: 38326108 PMCID: PMC10895659 DOI: 10.1021/acs.jpcb.3c07062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 01/23/2024] [Accepted: 01/24/2024] [Indexed: 02/09/2024]
Abstract
The ability to detect and inactivate spore-forming bacteria is of significance within, for example, industrial, healthcare, and defense sectors. Not only are stringent protocols necessary for the inactivation of spores but robust procedures are also required to detect viable spores after an inactivation assay to evaluate the procedure's success. UV radiation is a standard procedure to inactivate spores. However, there is limited understanding regarding its impact on spores' spectral and morphological characteristics. A further insight into these UV-induced changes can significantly improve the design of spore decontamination procedures and verification assays. This work investigates the spectral and morphological changes to Bacillus thuringiensis spores after UV exposure. Using absorbance and fluorescence spectroscopy, we observe an exponential decay in the spectral intensity of amino acids and protein structures, as well as a logistic increase in dimerized DPA with increased UV exposure on bulk spore suspensions. Additionally, using micro-Raman spectroscopy, we observe DPA release and protein degradation with increased UV exposure. More specifically, the protein backbone's 1600-1700 cm-1 amide I band decays slower than other amino acid-based structures. Last, using electron microscopy and light scattering measurements, we observe shriveling of the spore bodies with increased UV radiation, alongside the leaking of core content and disruption of proteinaceous coat and exosporium layers. Overall, this work utilized spectroscopy and electron microscopy techniques to gain new understanding of UV-induced spore inactivation relating to spore degradation and CaDPA release. The study also identified spectroscopic indicators that can be used to determine spore viability after inactivation. These findings have practical applications in the development of new spore decontamination and inactivation validation methods.
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Affiliation(s)
- Rasmus Öberg
- Swedish
Defence Research Agency (FOI), Umeå 90621, Sweden
- Department
of Physics, Umeå University, Umeå 90736, Sweden
| | - Timir B. Sil
- Department
of Physics, Umeå University, Umeå 90736, Sweden
| | | | | | - Lars Landström
- Swedish
Defence Research Agency (FOI), Norra Sorunda 13794, Sweden
| | | | - Magnus Andersson
- Department
of Physics, Umeå University, Umeå 90736, Sweden
- Umeå
Centre for Microbial Research (UCMR), Umeå 90736, Sweden
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5
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Keniry A, Blewitt ME. Chromatin-mediated silencing on the inactive X chromosome. Development 2023; 150:dev201742. [PMID: 37991053 DOI: 10.1242/dev.201742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2023]
Abstract
In mammals, the second X chromosome in females is silenced to enable dosage compensation between XX females and XY males. This essential process involves the formation of a dense chromatin state on the inactive X (Xi) chromosome. There is a wealth of information about the hallmarks of Xi chromatin and the contribution each makes to silencing, leaving the tantalising possibility of learning from this knowledge to potentially remove silencing to treat X-linked diseases in females. Here, we discuss the role of each chromatin feature in the establishment and maintenance of the silent state, which is of crucial relevance for such a goal.
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Affiliation(s)
- Andrew Keniry
- Epigenetics and Development Division, The Walter and Eliza Hall Institute for Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
- The Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Marnie E Blewitt
- Epigenetics and Development Division, The Walter and Eliza Hall Institute for Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
- The Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
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6
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Xu J, Xu J, Tong Z, Yu S, Liu B, Mu X, Du B, Liu Z, Wang J, Liu D. Investigating the impact of attenuated fluorescence spectra on protein discrimination. OPTICS EXPRESS 2023; 31:35507-35518. [PMID: 38017719 DOI: 10.1364/oe.499362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 09/18/2023] [Indexed: 11/30/2023]
Abstract
The optical remote sensing techniques are promising for the real-time detection, and identification of different types of hazardous biological materials. However, the received fluorescent spectra from a remote distance suffer from the atmospheric attenuation effect upon the spectral shape. To investigate the influence of atmospheric attenuation on characterizing, and classifying biological agents, the laboratory-measured fluorescence data of fourteen proteins combined with the atmospheric transmission factors of the MODTRAN model were conducted with different detection ranges. The multivariate analysis techniques of principal component analysis (PCA) and linear discriminant analysis (LDA), and the predictors of Random Forest and XGBoost were employed to assess the separability and distinguishability of different spectra recorded. The results showed that the spectral-shift effect on attenuated spectra varied as a function of the detection range, the atmospheric visibility, and the spectral distribution. According to the PCA and LDA analysis, the distribution of decomposed factors changed in the spectral explanatory power with the increasing attenuation effect, which was consistent with the hierarchical clustering results. Random Forest exhibited higher performance in classifying protein samples than that of XGBoost, while the two methods performed similarly in identifying harmful and harmless subgroups of proteins. Fewer subgroups decreased the sensitivity of the classification accuracy to the attenuation effect. Our analysis demonstrated that combining atmospheric transport models to build a fluorescence spectral database is essential for fast identification between spectra, and reduced classification criteria could facilitate the compatibility of spectral database and classification algorithms.
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7
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Ali H, Anwar S. Validation of conventional and synchronous fluorescence emission of potable water. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 297:122751. [PMID: 37084682 DOI: 10.1016/j.saa.2023.122751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 04/04/2023] [Accepted: 04/12/2023] [Indexed: 05/03/2023]
Abstract
Water from filter plants and bottled water is generally safe to drink but regular quality monitoring of these facilities requires development of quick analytical technique to ensure public safety and health. This study presented the variation of two components in spectra of conventional fluorescence spectroscopy (CFS) and four components in synchronous fluorescence spectroscopy (SFS) to assess the quality of 25 water samples from different sources. Poor quality water either due to organic or inorganic contaminants presented high intensity fluorescence emission in the blue green region and low intensity water Raman peak unlike an intense water Raman peak originated from pure water when excited at 365 nm. Emission intensity in the blue green region and water Raman peak can be used as a marker for quick screening of water quality. Although few discrepancies were observed in CF spectra of samples with intense Raman peak but were found to be positive for bacterial contamination, thus questioning the sensitivity of CFS that needs to be addressed. Whereas, SFS presented highly selective and detailed picture of water contaminants emitting aromatic amino acid, fulvic and humic like fluorescence. It is suggested that the specificity of CFS can be enhanced by coupling it with SFS or use of multiple excitation wavelengths to target different fluorophores for water quality analysis.
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Affiliation(s)
- Hina Ali
- Agriculture and Biophotonics Division, National Institute of Lasers and Optronics College, Pakistan Institute of Engineering and Applied Sciences, Nilore 45650, Islamabad, Pakistan.
| | - Shahzad Anwar
- Agriculture and Biophotonics Division, National Institute of Lasers and Optronics College, Pakistan Institute of Engineering and Applied Sciences, Nilore 45650, Islamabad, Pakistan
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8
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Kuwana R, Yamazawa R, Asada R, Ito K, Furuta M, Takamatsu H. Excessive ultraviolet C irradiation causes spore protein denaturation and prohibits the initiation of spore germination in Bacillus subtilis. JOURNAL OF MICROORGANISM CONTROL 2023; 28:15-25. [PMID: 37277954 DOI: 10.4265/jmc.28.1_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Ultraviolet (UV) -C is widely used to kill bacteria as it damages chromosomal DNA. We analyzed the denaturation of the protein function of Bacillus subtilis spores after UV-C irradiation. Almost all of the B. subtilis spores germinated in Luria-Bertani (LB) liquid medium, but the colony-forming unit (CFU) of the spores on LB agar plates decreased to approximately 1/103 by 100 mJ/cm2 of UV-C irradiation. Some of the spores germinated in LB liquid medium under phase-contrast microscopy, but almost no colonies formed on the LB agar plates after 1 J/cm2 of UV-C irradiation. The fluorescence of the green fluorescent protein (GFP) -fused spore proteins, YeeK-GFP, YeeK is a coat protein, decreased following UV-C irradiation of over 1 J/cm2, while that of SspA-GFP, SspA is a core protein, decreased following UV-C irradiation of over 2 J/ cm2, respectively. These results revealed that UV-C affected on coat proteins more than core proteins. We conclude that 25 to 100 mJ/cm2 of UV-C irradiation can cause DNA damage, and more than 1 J/cm2 of UV-C irradiation can cause the denaturation of spore proteins involved in germination. Our study would contribute to improve the technology to detect the bacterial spores, especially after UV sterilization.
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Affiliation(s)
| | | | - Ryoko Asada
- Graduate School of Engineering, Department of Quantum and Radiation Technology, Osaka Metropolitan University
| | - Kiyoshi Ito
- Faculty of Pharmaceutical Sciences, Setsunan University
| | - Masakazu Furuta
- Graduate School of Engineering, Department of Quantum and Radiation Technology, Osaka Metropolitan University
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9
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Application of stacking ensemble learning model in quantitative analysis of biomaterial activity. Microchem J 2022. [DOI: 10.1016/j.microc.2022.108075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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10
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Rapid detection of φX-174 virus based on synchronous fluorescence of tryptophan. Anal Bioanal Chem 2022; 415:509-515. [PMID: 36441232 PMCID: PMC9702944 DOI: 10.1007/s00216-022-04436-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 11/09/2022] [Accepted: 11/10/2022] [Indexed: 11/29/2022]
Abstract
The development of rapid methods for the detection of virus particles based on their intrinsic fluorescence (the native auto-fluorescence that originates from the non-labeled analyte) is challenging. Pure viruses may be detected in filtered solutions, based on the strong fluorescence of the amino acid tryptophan (Trp) in their proteins. Nevertheless, Trp also exists in high quantities in the hosts and host cultivation media. In this work, we developed a new method for the detection of the naked φX-174 virus. We show that a separation of φX-174 from its Escherichia coli host (grown on the standard cultivation medium nutrient agar) by simple extraction and filtration is not sufficient for its detection based on the intrinsic fluorescence since ~ 70% of the Trp fluorescence is derived from impurities. We formulate a new cultivation medium with a very low Trp concentration. We apply synchronous fluorescence measurements to show that no Trp fluorescence is detected in the extract solution upon incubation of this medium substrate with ammonium acetate extraction buffer. Finally, we apply synchronous fluorescence to detect φX-174 based on the spectral fingerprint of its native Trp content. Such a method is more rapid than usual traditional separation and detection methods which can take several hours and does not require any addition of labeling agents such as fluorescent dyes or antibodies for the detection. As other virus species contain Trp as one of the amino acids presents in their proteins, this method has the potential to apply to the detection of other viral species.
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11
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Pakuła A, Żołnowski W, Paśko S, Kursa O, Marć P, Jaroszewicz LR. Multispectral Portable Fibre-Optic Reflectometer for the Classification of the Origin of Chicken Eggshells in the Case of Mycoplasma synoviae Infections. SENSORS (BASEL, SWITZERLAND) 2022; 22:8690. [PMID: 36433286 PMCID: PMC9692302 DOI: 10.3390/s22228690] [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: 10/14/2022] [Revised: 11/04/2022] [Accepted: 11/09/2022] [Indexed: 06/16/2023]
Abstract
The proper classification of the origins of food products is a crucial issue all over the world nowadays. In this paper, the authors present a device-a multispectral portable fibre-optic reflectometer and signal processing patch-together with a machine-learning algorithm for the classification of the origins of chicken eggshells in the case of Mycoplasma synoviae infection. The sensor device was developed based on previous studies with a continuous spectrum in transmittance and selected spectral lines in reflectance. In the described case, the sensor is based on the integration of reflected spectral data from short spectral bands from the VIS and NIR region, which are produced by single-colour LEDs and introduced to the sample via a fibre bundle. The measurement is carried out in a sequence, and the reflected signal is pre-processed to be put in the machine learning algorithm. The support vector machine algorithm is used together with three different types of data normalization. The obtained results of the F-score factor for classification of the origins of samples show that the percentages of eggs coming from Mycoplasma synoviae infected hens are up to 87% for white and 96% for brown eggshells.
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Affiliation(s)
- Anna Pakuła
- Institute of Micromechanics and Photonics, Warsaw University of Technology, Św. A. Boboli 8, 02-525 Warsaw, Poland
- Faculty of New Technologies and Chemistry, Military University of Technology, ul. gen. Sylwestra Kaliskiego 2, 00-908 Warsaw, Poland
| | - Wojciech Żołnowski
- Institute of Optoelectronics, Military University of Technology, ul. gen. Sylwestra Kaliskiego 2, 00-908 Warsaw, Poland
| | - Sławomir Paśko
- Institute of Micromechanics and Photonics, Warsaw University of Technology, Św. A. Boboli 8, 02-525 Warsaw, Poland
| | - Olimpia Kursa
- Department of Poultry Diseases, National Veterinary Research Institute, Al. Partyzantów 57, 24-100 Puławy, Poland
| | - Paweł Marć
- Faculty of New Technologies and Chemistry, Military University of Technology, ul. gen. Sylwestra Kaliskiego 2, 00-908 Warsaw, Poland
| | - Leszek R. Jaroszewicz
- Faculty of New Technologies and Chemistry, Military University of Technology, ul. gen. Sylwestra Kaliskiego 2, 00-908 Warsaw, Poland
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12
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Yang T, Ou J, Yildirim E. Xist exerts gene-specific silencing during XCI maintenance and impacts lineage-specific cell differentiation and proliferation during hematopoiesis. Nat Commun 2022; 13:4464. [PMID: 35915095 PMCID: PMC9343370 DOI: 10.1038/s41467-022-32273-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 07/21/2022] [Indexed: 11/12/2022] Open
Abstract
X chromosome inactivation (XCI) is a dosage compensation phenomenon that occurs in females. Initiation of XCI depends on Xist RNA, which triggers silencing of one of the two X chromosomes, except for XCI escape genes that continue to be biallelically expressed. In the soma XCI is stably maintained with continuous Xist expression. How Xist impacts XCI maintenance remains an open question. Here we conditionally delete Xist in hematopoietic system of mice and report differentiation and cell cycle defects in female hematopoietic stem and progenitor cells (HSPCs). By utilizing female HSPCs and mouse embryonic fibroblasts, we find that X-linked genes show variable tolerance to Xist loss. Specifically, XCI escape genes exhibit preferential transcriptional upregulation, which associates with low H3K27me3 occupancy and high chromatin accessibility that accommodates preexisting binding of transcription factors such as Yin Yang 1 (YY1) at the basal state. We conclude that Xist is necessary for gene-specific silencing during XCI maintenance and impacts lineage-specific cell differentiation and proliferation during hematopoiesis. Here the authors investigate the functional relevance of X-chromosome inactivation (XCI) regulator Xist in hematopoiesis. They find that Xist loss leads to changes in the ratio of hematopoietic progenitor cells and results in chromatin accessibility and transcriptional upregulation on the inactive X chromosome, including XCI escape genes known to be associated with cell cycle and immune response.
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Affiliation(s)
- Tianqi Yang
- Department of Cell Biology, Duke University Medical Center, Durham, NC, 27710, USA.,Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC, 27710, USA.,Duke Regeneration Center, Duke University, Durham, NC, 27710, USA.,Duke Cancer Institute, Duke University Medical Center, Durham, NC, 27710, USA
| | - Jianhong Ou
- Department of Cell Biology, Duke University Medical Center, Durham, NC, 27710, USA.,Duke Regeneration Center, Duke University, Durham, NC, 27710, USA
| | - Eda Yildirim
- Department of Cell Biology, Duke University Medical Center, Durham, NC, 27710, USA. .,Duke Regeneration Center, Duke University, Durham, NC, 27710, USA. .,Duke Cancer Institute, Duke University Medical Center, Durham, NC, 27710, USA.
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13
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Wang W, Rahman A, Huang Q, Vikesland PJ. Surface-enhanced Raman spectroscopy enabled evaluation of bacterial inactivation. WATER RESEARCH 2022; 220:118668. [PMID: 35689895 DOI: 10.1016/j.watres.2022.118668] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/21/2022] [Accepted: 05/23/2022] [Indexed: 06/15/2023]
Abstract
An improved understanding of bacterial inactivation mechanisms will provide useful insights for infectious disease control and prevention. We evaluated bacterial response to several inactivation methods using surface-enhanced Raman spectroscopy (SERS). The results indicate that changes in the SERS signal are highly related to cellular disruption and that cellular changes arising after cell inactivation cannot be ignored. The membrane integrity of heat and the combination of UV254 and free chlorine (UV254/chlorine) treated Pseudomonas syringae (P. syringae) cells were severely disrupted, leading to significantly increased peak intensities. Conversely, ethanol treated bacteria exhibited intact cell morphologies and the SERS spectra remained virtually unchanged. On the basis of time dependent SERS signals, we extracted dominant SERS patterns. Peaks related to nucleic acids accounted for the main changes observed during heat, UV254, and UV254/chlorine treatment, likely due to their outward diffusion from the cell cytoplasm. For free chlorine treated P. syringae, carbohydrates and proteins on the cell membrane were denatured or lost, resulting in a decrease in related peak intensities. The nucleobases were likely oxidized when treated with UV254 and chlorine, thus leading to shifts in the related peaks. The generality of the method was verified using two additional bacterial strains: Escherichia coli and Bacillus subtilis as well as in different water matrices. The results suggest that SERS spectral analysis is a promising means to examine bacterial stress response at the molecular level and has applicability in diverse environmental implementations.
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Affiliation(s)
- Wei Wang
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24061, USA; Virginia Tech Institute of Critical Technology and Applied Science (ICTAS) Sustainable Nanotechnology Center (VTSuN), Blacksburg, Virginia 24061, USA
| | - Asifur Rahman
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24061, USA; Virginia Tech Institute of Critical Technology and Applied Science (ICTAS) Sustainable Nanotechnology Center (VTSuN), Blacksburg, Virginia 24061, USA
| | - Qishen Huang
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24061, USA; Virginia Tech Institute of Critical Technology and Applied Science (ICTAS) Sustainable Nanotechnology Center (VTSuN), Blacksburg, Virginia 24061, USA
| | - Peter J Vikesland
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24061, USA; Virginia Tech Institute of Critical Technology and Applied Science (ICTAS) Sustainable Nanotechnology Center (VTSuN), Blacksburg, Virginia 24061, USA.
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14
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Yousefi H, Samani SE, Khan S, Prasad A, Shakeri A, Li Y, Filipe CDM, Didar TF. LISzyme Biosensors: DNAzymes Embedded in an Anti-biofouling Platform for Hands-free Real-Time Detection of Bacterial Contamination in Milk. ACS NANO 2022; 16:29-37. [PMID: 34872243 DOI: 10.1021/acsnano.1c05766] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Nonspecific binding is a significant challenge associated with biosensors in complex food textures. To overcome this, we have developed LISzymes, which are DNAzymes incorporated in lubricant-infused surfaces (LISs). Using milk as a complex background matrix, we show that LISzyme biosensors are significantly more effective in preventing nonspecific binding compared to other commonly used "blocking" methods. The use of lubricant infusion to treat sensing surfaces results in a 4-fold increase in the signal-to-noise ratio obtained with the DNAzyme with respect to untreated surfaces, when detecting the presence of specific bacteria in milk. This is a striking improvement upon previous DNAzyme sensors. We also show that the use of LISs does not affect the DNAzyme's ability to effectively and specifically detect its target─a protein specifically produced by Escherichia coli (E. coli), in a complex sample matrix such as milk. LISzymes drastically improve DNAzyme performance, resulting in target detection associated with E. coli at concentrations as low as 250 CFU/mL in milk in less than an hour, which is currently not possible using other optical platforms. LISzymes are promising tools for the real-time monitoring of food contamination and may prove valuable within many other biosensing applications.
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Affiliation(s)
- Hanie Yousefi
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario M5S 3M2, Canada
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15
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Kumaravel S, Jian SE, Huang ST, Huang CH, Hong WZ. Convenient and ultrasensitive detection of live Salmonella using ratiometric electrochemical molecular substrates. Anal Chim Acta 2022; 1190:339244. [PMID: 34857137 DOI: 10.1016/j.aca.2021.339244] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 10/30/2021] [Accepted: 11/01/2021] [Indexed: 01/12/2023]
Abstract
Salmonella contamination is a major concern in food and public health safety, and carrying out episodic monitoring of Salmonella contamination in food and water bodies is essential for safeguarding public health and the economy. Therefore, there is an urgent need to develop an easy-to-operate Salmonella-targeting point-of-care detection platform. To this end, we designed two activity-based latent ratiometric electrochemical molecular substrates, denoted as Sal-CAF and Sal-NBAF, specifically for achieving easy, rapid, and selective profiling of Salmonella esterase (a Salmonella biomarker) under physiological conditions. The octyl esters of the substrates were cleaved by the esterase and triggered the trimethyl lock to eject the electron-rich aminoferrocene derivatives (CAF and NBAF), and the corresponding electrochemical signals were tracked at the negative region (-0.08 V vs Ag/AgCl) of the voltammetric spectrum. The Sal-CAF substrate was used to determine the concentration of Salmonella in a wide dynamic range (1.03 × 105-1.1 × 1010 CFU mL-1) with a low detection limit of 39.27 × 103 CFU mL-1. The developed probes were tested against various bacteria but were only activated by live Salmonella. Furthermore, the Sal-CAF probe was used directly in quantifying spiked live Salmonella spiked in milk samples and also used to effectively monitor and quantify Salmonella production in real-time. These achievements indicated the Sal-CAF probe to be a promising platform for point-of-care Salmonella analysis.
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Affiliation(s)
- Sakthivel Kumaravel
- Department of Chemical Engineering and Biotechnology, National Taipei University of Technology, Taipei, 106, Taiwan; Institute of Biochemical and Biomedical Engineering, National Taipei University of Technology, Taipei, 106, Taiwan.
| | - Sheng-En Jian
- Department of Chemical Engineering and Biotechnology, National Taipei University of Technology, Taipei, 106, Taiwan; Institute of Biochemical and Biomedical Engineering, National Taipei University of Technology, Taipei, 106, Taiwan
| | - Sheng-Tung Huang
- Department of Chemical Engineering and Biotechnology, National Taipei University of Technology, Taipei, 106, Taiwan; Institute of Biochemical and Biomedical Engineering, National Taipei University of Technology, Taipei, 106, Taiwan.
| | - Chih-Hung Huang
- Institute of Biochemical and Biomedical Engineering, National Taipei University of Technology, Taipei, 106, Taiwan
| | - Wei-Zhe Hong
- Institute of Biochemical and Biomedical Engineering, National Taipei University of Technology, Taipei, 106, Taiwan
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16
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Dhankhar D, Nagpal A, Li R, Chen J, Cesario TC, Rentzepis PM. Resonance Raman Spectra for the In Situ Identification of Bacteria Strains and Their Inactivation Mechanism. APPLIED SPECTROSCOPY 2021; 75:1146-1154. [PMID: 33605151 DOI: 10.1177/0003702821992834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The resonance Raman spectra of bacterial carotenoids have been employed to identify bacterial strains and their intensity changes as a function of ultraviolet (UV) radiation dose have been used to differentiate between live and dead bacteria. In addition, the resonance-enhanced Raman spectra enabled us to detect bacteria in water at much lower concentrations (∼108 cells/mL) than normally detected spectroscopically. A handheld spectrometer capable of recording resonance Raman spectra in situ was designed, constructed, and was used to record the spectra. In addition to bacteria, the method presented in this paper may also be used to identify fungi, viruses, and plants, in situ, and detect infections within a very short period of time.
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Affiliation(s)
- Dinesh Dhankhar
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, USA
| | - Anushka Nagpal
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, USA
| | - Runze Li
- School of Physical Science and Technology, Shanghai Tech University, Shanghai, China
| | - Jie Chen
- Center for Ultrafast Science and Technology, Key Laboratory for Laser Plasmas (Ministry of Education), School of Physics and Astronomy, Collaborative Innovation Center of IFSA (CICIFSA), 12474Shanghai Jiao Tong University, Shanghai, China
| | - Thomas C Cesario
- School of Medicine, University of California at Irvine, Irvine, USA
| | - Peter M Rentzepis
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, USA
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17
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Dhankhar D, Nagpal A, Rentzepis PM. Cell-phone camera Raman spectrometer. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2021; 92:054101. [PMID: 34243331 DOI: 10.1063/5.0046281] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 03/17/2021] [Indexed: 06/13/2023]
Abstract
In this report, we describe the design, construction, and operation of a cell-phone-based Raman and emission spectral detector, which when coupled to a diffraction grating and cell-phone camera system provides means for the detection, recording, and identification of chemicals, drugs, and biological molecules, in situ by means of their Raman and fluorescence spectra. The newly constructed cell-phone spectrometer system was used to record Raman spectra from various chemicals and biological molecules including the resonance enhanced Raman spectra of carrots and bacteria. In addition, we present the quantitative analysis of alcohol-water Raman spectra, performed using our cell-phone spectrometer. The designed and constructed system was also used for constructing Raman images of the samples by utilizing a position scanning stage in conjunction with the system. This compact and portable system is well suited for in situ field applications of Raman and fluorescence spectroscopy and may also be an integrated feature of future cell-phones.
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Affiliation(s)
- Dinesh Dhankhar
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, Texas 77843, USA
| | - Anushka Nagpal
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, Texas 77843, USA
| | - Peter M Rentzepis
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, Texas 77843, USA
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18
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Beattie JR, Esmonde-White FWL. Exploration of Principal Component Analysis: Deriving Principal Component Analysis Visually Using Spectra. APPLIED SPECTROSCOPY 2021; 75:361-375. [PMID: 33393349 DOI: 10.1177/0003702820987847] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Spectroscopy rapidly captures a large amount of data that is not directly interpretable. Principal component analysis is widely used to simplify complex spectral datasets into comprehensible information by identifying recurring patterns in the data with minimal loss of information. The linear algebra underpinning principal component analysis is not well understood by many applied analytical scientists and spectroscopists who use principal component analysis. The meaning of features identified through principal component analysis is often unclear. This manuscript traces the journey of the spectra themselves through the operations behind principal component analysis, with each step illustrated by simulated spectra. Principal component analysis relies solely on the information within the spectra, consequently the mathematical model is dependent on the nature of the data itself. The direct links between model and spectra allow concrete spectroscopic explanation of principal component analysis , such as the scores representing "concentration" or "weights". The principal components (loadings) are by definition hidden, repeated and uncorrelated spectral shapes that linearly combine to generate the observed spectra. They can be visualized as subtraction spectra between extreme differences within the dataset. Each PC is shown to be a successive refinement of the estimated spectra, improving the fit between PC reconstructed data and the original data. Understanding the data-led development of a principal component analysis model shows how to interpret application specific chemical meaning of the principal component analysis loadings and how to analyze scores. A critical benefit of principal component analysis is its simplicity and the succinctness of its description of a dataset, making it powerful and flexible.
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M KR, Misra S, Mitra SK. Microparticle Suspensions and Bacteria-Laden Droplets: Are They the Same in Terms of Wetting Signature? LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:1588-1595. [PMID: 33459022 DOI: 10.1021/acs.langmuir.0c03365] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Adhesion behavior of microbial pathogens on commonly encountered surfaces is one of the most pertinent questions now. We present the characterization of bacteria-laden droplets and quantify the adhesion forces on highly repellent surfaces with the help of a simple experimental setup. Comparing the force signature measured directly using an in-house capillary deflection-based droplet force apparatus, we report an anomalous adhesion behavior of live bacteria (E. coli)-laden droplets on repellent surfaces, which stands in stark contrast to the observed adhesion signature when the doping agent is changed to inert microparticles or the same bacteria in an incapacitated state. We showed that the regular contact angle measurements using optical goniometry is unable to differentiate between the live bacteria and the dead ones (including microparticles) and thus delineate its limitations and the complementary nature of the adhesion measurements in understanding the fundamental interfacial interaction of living organisms on solid surfaces.
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Affiliation(s)
- Kiran Raj M
- Micro & Nano-scale Transport Laboratory, Waterloo Institute for Nanotechnology, Department of Mechanical and Mechatronics Engineering, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| | - Sirshendu Misra
- Micro & Nano-scale Transport Laboratory, Waterloo Institute for Nanotechnology, Department of Mechanical and Mechatronics Engineering, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| | - Sushanta K Mitra
- Micro & Nano-scale Transport Laboratory, Waterloo Institute for Nanotechnology, Department of Mechanical and Mechatronics Engineering, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
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20
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Ghoshal S, Chowdhury P, Ray S, Mitra M, Kanjilal SD, Sen S, Dasgupta AK, Sengupta S. Population genetic and biophysical evidences reveal that purifying selection shapes the genetic landscape of Plasmodium falciparum RH ligands in Chhattisgarh and West Bengal, India. Malar J 2020; 19:367. [PMID: 33054833 PMCID: PMC7557104 DOI: 10.1186/s12936-020-03433-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 10/01/2020] [Indexed: 11/17/2022] Open
Abstract
Background Reticulocyte binding protein-like homologs (RHs) are currently being evaluated as anti-erythrocytic stage vaccine targets against Plasmodium falciparum malaria. Present study explores the possible evolutionary drivers shaping the genetic organization of Pfrhs in Indian parasite population. It simultaneously evaluates a putative gain-of-function variant of PfRH5, a keystone member of PfRH family. Methods Receptor binding regions of Pfrh1, Pfrh2a/b, Pfrh4 and whole Pfrh5 were amplified using blood samples of P. falciparum malaria patients from Chhattisgarh and West Bengal and sequenced. Assembled sequences were analysed using MEGA7 and DnaSPv6. Binding affinities of recombinant PfRH5 proteins with basigin (BSG) were compared using in silico (CHARMM and AUTODOCK) and in vitro (Circular dichroism, fluorescence spectroscopy and isothermal titration calorimetry) methods. Results Pfrh1 (0.5), Pfrh2a/b (0.875), Pfrh4 (0.667) and Pfrh5 (0.778) sequence changes corresponded to low frequency (< 0.05) variants which resulted in an overall negative Tajima’s D. Since mismatch distribution of none of the Pfrh loci corroborated with the model of demographic expansion, a possible role of natural selection formulating Pfrh sequence diversity was investigated. Among the 5 members, Pfrh5 displayed very high dN/dS (5.7) ratio. Nevertheless, the model of selective sweep due to presence of any advantageous substitutions could not be invoked as polymorphic nonsynonymous sites (17/18) for Pfrh5 exceeded significantly over the divergent (62/86) ones (p = 0.0436). The majority of extant PfRH5 sequences (52/83) differed from the reference Pf3D7 allele by a single amino acid mismatch (C203Y). This non-conservative alteration was predicted to lower the total interaction energy of that PfRH5variant with BSG, compared to PfRH53D7. Biophysical evidences validated the proposition that PfRH5variant formed a more stable complex with BSG. Thermodynamic association constant for interaction of BSG with PfRH5variant was also found to be higher (Kavariant = 3.63E6 ± 2.02E6 M−1 and Ka3D7 = 1.31E6 ± 1.21E6 M−1). Conclusions Together, the study indicates that the genetic architecture of Pfrhs is principally shaped by purifying selection. The most abundant and ubiquitous PfRH5 variant harbouring 203Y, exhibits a greater affinity for BSG compared to PfRH53D7 possessing 203C allele. The study underscores the importance of selecting the functional allele that best represents circulating strains in natural parasite populations as vaccine targets.
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Affiliation(s)
- Sharmistha Ghoshal
- Department of Biochemistry, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700 019, West Bengal, India
| | - Pramita Chowdhury
- Department of Biochemistry, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700 019, West Bengal, India
| | - Sanhita Ray
- Department of Biochemistry, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700 019, West Bengal, India
| | - Mitashree Mitra
- School of Studies in Anthropology. Pt, Ravishankar Shukla University, Raipur, 492010, Chhattisgarh, India
| | - Sumana Datta Kanjilal
- Department of Pediatric Medicine, Institute of Post Graduate Medical Education & Research, Kolkata, West Bengal, India
| | - Srikanta Sen
- Mitra Tower, Lake Town, Block-A, Kolkata, 700 089, India
| | - Anjan Kr Dasgupta
- Department of Biochemistry, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700 019, West Bengal, India
| | - Sanghamitra Sengupta
- Department of Biochemistry, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700 019, West Bengal, India.
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21
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Two-terminal DC mode measurements for sensing of growth phases of multi-species microbial population in nutrient broth. SENSING AND BIO-SENSING RESEARCH 2020. [DOI: 10.1016/j.sbsr.2020.100349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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22
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Dhankhar D, Li R, Nagpal A, Chen J, Krishnamoorthi A, Rentzepis PM. A novel approach for remote detection of bacteria using simple charge-coupled device cameras and telescope. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2020; 91:074106. [PMID: 32752878 DOI: 10.1063/5.0010701] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 06/25/2020] [Indexed: 06/11/2023]
Abstract
We have designed, constructed, and utilized a charge-coupled device system, integrated with a small Newtonian telescope, capable of long distance recording of bacterial fluorescence and synchronous spectra for the detection of bacteria, their component molecules, and other species. This newly developed optical system utilizes commercial monochrome cameras that we have used to detect various bacterial strains, such as Escherichia coli, and determine their concentrations. In addition, using this system, we were able to differentiate between live and dead bacteria after treatment with ultraviolet light or antibiotics.
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Affiliation(s)
- Dinesh Dhankhar
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, Texas 77843, USA
| | - Runze Li
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, Texas 77843, USA
| | - Anushka Nagpal
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, Texas 77843, USA
| | - Jie Chen
- Center for Ultrafast Science and Technology, Key Laboratory for Laser Plasmas (Ministry of Education), School of Physics and Astronomy, Collaborative Innovation Center of IFSA (CICIFSA), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Arjun Krishnamoorthi
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, Texas 77843, USA
| | - Peter M Rentzepis
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, Texas 77843, USA
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23
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Kumar S, Gopinathan R, Chandra GK, Umapathy S, Saini DK. Rapid detection of bacterial infection and viability assessment with high specificity and sensitivity using Raman microspectroscopy. Anal Bioanal Chem 2020; 412:2505-2516. [PMID: 32072214 DOI: 10.1007/s00216-020-02474-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 01/05/2020] [Accepted: 01/30/2020] [Indexed: 01/15/2023]
Abstract
Infectious diseases caused by bacteria still pose major diagnostic challenges in spite of the availability of various molecular approaches. Irrespective of the type of infection, rapid identification of the causative pathogen with a high degree of sensitivity and specificity is essential for initiating appropriate treatment. While existing methods like PCR possess high sensitivity, they are incapable of identifying the viability status of the pathogen and those which can, like culturing, are inherently slow. To overcome these limitations, we developed a diagnostic platform based on Raman microspectroscopy, capable of detecting biochemical signatures from a single bacterium for identification as well as viability assessment. The study also establishes a decontamination protocol for handling live pathogenic bacteria which does not affect identification and viability testing, showing applicability in the analysis of sputum samples containing pathogenic mycobacterial strains. The minimal sample processing along with multivariate analysis of spectroscopic signatures provides an interface for automatic classification, allowing the prediction of unknown samples by mapping signatures onto available datasets. Also, the novelty of the current work is the demonstration of simultaneous identification and viability assessment at a single bacterial level for pathogenic bacteria. Graphical abstract.
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Affiliation(s)
- Srividya Kumar
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore, 560012, India
| | - Renu Gopinathan
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore, 560012, India
| | - Goutam Kumar Chandra
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore, 560012, India.,Department of Physics, NIT Calicut, Calicut, Kerala, 673601, India
| | - Siva Umapathy
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore, 560012, India. .,Department of Instrumentation and Applied Physics, Indian Institute of Science, Bangalore, 560012, India.
| | - Deepak Kumar Saini
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore, 560012, India. .,Centre for Biosystems Science and Engineering, Indian Institute of Science, Bangalore, 560012, India. .,Centre for Infectious Diseases Research, Indian Institute of Science, Bangalore, 560012, India.
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24
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Inkinen J, Ahonen M, Iakovleva E, Karppinen P, Mielonen E, Mäkinen R, Mannonen K, Koivisto J. Contamination detection by optical measurements in a real-life environment: A hospital case study. JOURNAL OF BIOPHOTONICS 2020; 13:e201960069. [PMID: 31613045 PMCID: PMC7065611 DOI: 10.1002/jbio.201960069] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 09/30/2019] [Accepted: 10/06/2019] [Indexed: 05/05/2023]
Abstract
Organic dirt on touch surfaces can be biological contaminants (microbes) or nutrients for those but is often invisible by the human eye causing challenges for evaluating the need for cleaning. Using hyperspectral scanning algorithm, touch surface cleanliness monitoring by optical imaging was studied in a real-life hospital environment. As the highlight, a human eye invisible stain from a dirty chair armrest was revealed manually with algorithms including threshold levels for intensity and clustering analysis with two excitation lights (green and red) and one bandpass filter (wavelength λ = 500 nm). The same result was confirmed by automatic k-means clustering analysis from the entire dirty data of visible light (red, green and blue) and filters 420 to 720 nm with 20 nm increments. Overall, the collected touch surface samples (N = 156) indicated the need for cleaning in some locations by the high culturable bacteria and adenosine triphosphate counts despite the lack of visible dirt. Examples of such locations were toilet door lock knobs and busy registration desk armchairs. Thus, the studied optical imaging system utilizing the safe visible light area shows a promising method for touch surface cleanliness evaluation in real-life environments.
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Affiliation(s)
- Jenni Inkinen
- Aalto University, School of Science, Department of Applied PhysicsComplex Systems and MaterialsAaltoFinland
| | - Merja Ahonen
- Satakunta University of Applied Sciences, Faculty of TechnologyWANDER Nordic Water and Materials InstituteRaumaFinland
| | - Evgenia Iakovleva
- Aalto University, School of Science, Department of Applied PhysicsComplex Systems and MaterialsAaltoFinland
| | - Pasi Karppinen
- Aalto University, School of Science, Department of Applied PhysicsComplex Systems and MaterialsAaltoFinland
| | - Eelis Mielonen
- Aalto University, School of Science, Department of Applied PhysicsComplex Systems and MaterialsAaltoFinland
| | - Riika Mäkinen
- Satakunta University of Applied Sciences, Faculty of TechnologyWANDER Nordic Water and Materials InstituteRaumaFinland
| | - Katriina Mannonen
- Satakunta University of Applied Sciences, Faculty of TechnologyWANDER Nordic Water and Materials InstituteRaumaFinland
| | - Juha Koivisto
- Aalto University, School of Science, Department of Applied PhysicsComplex Systems and MaterialsAaltoFinland
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25
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A tryptophan synchronous and normal fluorescence study on bacteria inactivation mechanism. Proc Natl Acad Sci U S A 2019; 116:18822-18826. [PMID: 31481620 DOI: 10.1073/pnas.1909722116] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The UV photodissociation kinetics of tryptophan amino acid, Trp, attached to the membrane of bacteria, Escherichia coli and Bacillus subtilis, have been studied by means of normal and synchronous fluorescence. Our experimental data suggest that the fluorescence intensity of Trp increases during the first minute of irradiation with 250 nm to ∼ 280 nm, 7 mW/cm2 UV light, and subsequently decreases with continuous irradiation. During this short, less than a minute, period of time, 70% of the 107 cell per milliliter bacteria are inactivated. This increase in fluorescence intensity is not observed when tryptophan is in the free state, namely, not attached to a protein, but dissolved in water or saline solution. This increase in fluorescence is attributed to the additional fluorescence of tryptophan molecules formed by protein unfolding, the breakage of the bond that attaches Trp to the bacterial protein membrane, or possibly caused by the irradiation of 2 types of tryptophan residues that photolyze with different quantum yields.
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Prongmanee W, Alam I, Asanithi P. Hydroxyapatite/Graphene oxide composite for electrochemical detection of L-Tryptophan. J Taiwan Inst Chem Eng 2019. [DOI: 10.1016/j.jtice.2019.06.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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27
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Singh S, Moudgil A, Mishra N, Das S, Mishra P. Vancomycin functionalized WO3 thin film-based impedance sensor for efficient capture and highly selective detection of Gram-positive bacteria. Biosens Bioelectron 2019; 136:23-30. [DOI: 10.1016/j.bios.2019.04.029] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 04/05/2019] [Accepted: 04/15/2019] [Indexed: 01/08/2023]
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28
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Gahlaut SK, Kalyani N, Sharan C, Mishra P, Singh J. Smartphone based dual mode in situ detection of viability of bacteria using Ag nanorods array. Biosens Bioelectron 2019; 126:478-484. [DOI: 10.1016/j.bios.2018.11.025] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 11/05/2018] [Accepted: 11/15/2018] [Indexed: 01/01/2023]
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29
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Vedarethinam V, Huang L, Xu W, Zhang R, Gurav DD, Sun X, Yang J, Chen R, Qian K. Detection and Inhibition of Bacteria on a Dual-Functional Silver Platform. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1803051. [PMID: 30358085 DOI: 10.1002/smll.201803051] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 10/08/2018] [Indexed: 05/24/2023]
Abstract
Detection and inhibition of bacteria are universally required in clinics and daily life for health care. Developing a dual-functional material is challenging and in demand, engaging advanced applications for both defined bioanalysis and targeted biotoxicity. Herein, magnetic silver nanoshells are designed as a multifunctional platform for the detection and inhibition of bacteria. The optimized magnetic silver nanoshells enable direct laser desorption/ionization mass spectrometry based metabolic analysis of bacteria (≈10 µL-1 ), in complex biofluids. The serum infection process (0-10 h) is monitored by statistics toward clinical classification. Moreover, magnetic silver nanoshells facilitate surface adhesion on bacteria due to nanoscale surface roughness and thus display long-term antibacterial effects. Bacteria metabolism is studied with metabolic biomarkers (e.g., malate and lysine) identified during inhibition, showing cell membrane destruction and dysfunctional protein synthesis mechanisms. This work not only guides the design of material-based approaches for bioanalysis and biotoxicity, but contributes to bacteria-related diagnosis by using specific metabolic biomarkers for sensitive detection and new insights by monitoring metabolomic change of bacteria for antibacterial applications.
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Affiliation(s)
- Vadanasundari Vedarethinam
- School of Biomedical Engineering, Children's Hospital of Shanghai, and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Lin Huang
- School of Biomedical Engineering, Children's Hospital of Shanghai, and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Wei Xu
- School of Biomedical Engineering, Children's Hospital of Shanghai, and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Ru Zhang
- School of Biomedical Engineering, Children's Hospital of Shanghai, and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Deepanjali D Gurav
- School of Biomedical Engineering, Children's Hospital of Shanghai, and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Xuming Sun
- School of Biomedical Engineering, Children's Hospital of Shanghai, and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Jing Yang
- School of Biomedical Engineering, Children's Hospital of Shanghai, and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Ruoping Chen
- School of Biomedical Engineering, Children's Hospital of Shanghai, and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Kun Qian
- School of Biomedical Engineering, Children's Hospital of Shanghai, and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
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30
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Li R, Dhankhar D, Chen J, Cesario TC, Rentzepis PM. Determination of live:dead bacteria as a function of antibiotic treatment. J Microbiol Methods 2018; 154:73-78. [PMID: 30332616 DOI: 10.1016/j.mimet.2018.10.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Revised: 10/08/2018] [Accepted: 10/13/2018] [Indexed: 10/28/2022]
Abstract
Antibiotics are drugs that react against, kill, or inhibit the growth of bacteria. The method most often employed to evaluate the effectiveness of an antibiotic to kill bacteria requires at least 16 to 24 h for bacterial incubation. The requirement of long periods of time for the determination of the number of bacteria still alive after antibiotic treatment, may, in many cases, be detrimental to the patient's health. In addition, with increasing of bacterial antibiotic resistance, the need to utilize methods for distinguishing between live and dead bacteria within a short period of time after treatment with antibiotic agents, is becoming more crucial. To that effect, we have utilized a hand-held double monochromator to record in situ and within minutes the synchronous and normal fluorescence spectra of bacteria and other species. The fluorescence spectra of bacterial components such as tryptophan, tyrosine and DNA are clearly displayed. In addition, principal component analysis, PCA, makes it possible to display live and dead bacteria separately and determine the ratio of live:dead bacteria before and after treatment with antibiotics.
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Affiliation(s)
- Runze Li
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, Texas 77843, United States
| | - Dinesh Dhankhar
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, Texas 77843, United States
| | - Jie Chen
- Center for Ultrafast Science and Technology, Key Laboratory for Laser Plasmas (Ministry of Education), School of Physics and Astronomy, Collaborative Innovation Center of IFSA (CICIFSA), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Thomas C Cesario
- School of Medicine, University of California, Irvine, CA 92697, United States
| | - Peter M Rentzepis
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, Texas 77843, United States.
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