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Zhou H, Xu L, Ren Z, Zhu J, Lee C. Machine learning-augmented surface-enhanced spectroscopy toward next-generation molecular diagnostics. NANOSCALE ADVANCES 2023; 5:538-570. [PMID: 36756499 PMCID: PMC9890940 DOI: 10.1039/d2na00608a] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 11/06/2022] [Indexed: 06/17/2023]
Abstract
The world today is witnessing the significant role and huge demand for molecular detection and screening in healthcare and medical diagnosis, especially during the outbreak of COVID-19. Surface-enhanced spectroscopy techniques, including Surface-Enhanced Raman Scattering (SERS) and Infrared Absorption (SEIRA), provide lattice and molecular vibrational fingerprint information which is directly linked to the molecular constituents, chemical bonds, and configuration. These properties make them an unambiguous, nondestructive, and label-free toolkit for molecular diagnostics and screening. However, new issues in molecular diagnostics, such as increasing molecular species, faster spread of viruses, and higher requirements for detection accuracy and sensitivity, have brought great challenges to detection technology. Advancements in artificial intelligence and machine learning (ML) techniques show promising potential in empowering SERS and SEIRA with rapid analysis and automatic data processing to jointly tackle the challenge. This review introduces the combination of ML and SERS/SEIRA by investigating how ML algorithms can be beneficial to SERS/SEIRA, discussing the general process of combining ML and SEIRA/SERS, highlighting the molecular diagnostics and screening applications based on ML-combined SEIRA/SERS, and providing perspectives on the future development of ML-integrated SEIRA/SERS. In general, this review offers comprehensive knowledge about the recent advances and the future outlook regarding ML-integrated SEIRA/SERS for molecular diagnostics and screening.
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Affiliation(s)
- Hong Zhou
- Department of Electrical and Computer Engineering, National University of Singapore Singapore 117583
- Center for Intelligent Sensors and MEMS (CISM), National University of Singapore Singapore 117608
| | - Liangge Xu
- Department of Electrical and Computer Engineering, National University of Singapore Singapore 117583
- Center for Intelligent Sensors and MEMS (CISM), National University of Singapore Singapore 117608
- National Key Laboratory of Special Environment Composite Technology, Harbin Institute of Technology Harbin 150001 China
| | - Zhihao Ren
- Department of Electrical and Computer Engineering, National University of Singapore Singapore 117583
- Center for Intelligent Sensors and MEMS (CISM), National University of Singapore Singapore 117608
| | - Jiaqi Zhu
- National Key Laboratory of Special Environment Composite Technology, Harbin Institute of Technology Harbin 150001 China
| | - Chengkuo Lee
- Department of Electrical and Computer Engineering, National University of Singapore Singapore 117583
- Center for Intelligent Sensors and MEMS (CISM), National University of Singapore Singapore 117608
- NUS Suzhou Research Institute (NUSRI) Suzhou 215123 China
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2
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Do H, Madukoma CS, Sundaresan V, Shrout JD, Hoffman AJ, Bohn PW. Spatiotemporal distribution of chemical signatures exhibited by Myxococcus xanthus in response to metabolic conditions. Anal Bioanal Chem 2021; 414:1691-1698. [PMID: 34850244 DOI: 10.1007/s00216-021-03795-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 11/16/2021] [Accepted: 11/18/2021] [Indexed: 11/25/2022]
Abstract
Myxococcus xanthus is a common soil bacterium with a complex life cycle, which is known for production of secondary metabolites. However, little is known about the effects of nutrient availability on M. xanthus metabolite production. In this study, we utilize confocal Raman microscopy (CRM) to examine the spatiotemporal distribution of chemical signatures secreted by M. xanthus and their response to varied nutrient availability. Ten distinct spectral features are observed by CRM from M. xanthus grown on nutrient-rich medium. However, when M. xanthus is constrained to grow under nutrient-limited conditions, by starving it of casitone, it develops fruiting bodies, and the accompanying Raman microspectra are dramatically altered. The reduced metabolic state engendered by the absence of casitone in the medium is associated with reduced, or completely eliminated, features at 1140 cm-1, 1560 cm-1, and 1648 cm-1. In their place, a feature at 1537 cm-1 is observed, this feature being tentatively assigned to a transitional phase important for cellular adaptation to varying environmental conditions. In addition, correlating principal component analysis heat maps with optical images illustrates how fruiting bodies in the center co-exist with motile cells at the colony edge. While the metabolites responsible for these Raman features are not completely identified, three M. xanthus peaks at 1004, 1151, and 1510 cm-1 are consistent with the production of lycopene. Thus, a combination of CRM imaging and PCA enables the spatial mapping of spectral signatures of secreted factors from M. xanthus and their correlation with metabolic conditions.
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Affiliation(s)
- Hyein Do
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Chinedu S Madukoma
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Vignesh Sundaresan
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Joshua D Shrout
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA.,Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Anthony J Hoffman
- Department of Electrical Engineering, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Paul W Bohn
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, 46556, USA. .,Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN, 46556, USA.
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3
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Vaitiekūnaitė D, Snitka V. Differentiation of Closely Related Oak-Associated Gram-Negative Bacteria by Label-Free Surface Enhanced Raman Spectroscopy (SERS). Microorganisms 2021; 9:1969. [PMID: 34576865 PMCID: PMC8466144 DOI: 10.3390/microorganisms9091969] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/08/2021] [Accepted: 09/14/2021] [Indexed: 12/02/2022] Open
Abstract
Due to the harmful effects of chemical fertilizers and pesticides, the need for an eco-friendly solution to improve soil fertility has become a necessity, thus microbial biofertilizer research is on the rise. Plant endophytic bacteria inhabiting internal tissues represent a novel niche for research into new biofertilizer strains. However, the number of species and strains that need to be differentiated and identified to facilitate faster screening in future plant-bacteria interaction studies, is enormous. Surface enhanced Raman spectroscopy (SERS) may provide a platform for bacterial discrimination and identification, which, compared with the traditional methods, is relatively rapid, uncomplicated and ensures high specificity. In this study, we attempted to differentiate 18 bacterial isolates from two oaks via morphological, physiological, biochemical tests and SERS spectra analysis. Previous 16S rRNA gene fragment sequencing showed that three isolates belong to Paenibacillus, 3-to Pantoea and 12-to Pseudomonas genera. Additional tests were not able to further sort these bacteria into strain-specific groups. However, the obtained label-free SERS bacterial spectra along with the high-accuracy principal component (PCA) and discriminant function analyses (DFA) demonstrated the possibility to differentiate these bacteria into variant strains. Furthermore, we collected information about the biochemical characteristics of selected isolates. The results of this study suggest a promising application of SERS in combination with PCA/DFA as a rapid, non-expensive and sensitive method for the detection and identification of plant-associated bacteria.
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Affiliation(s)
- Dorotėja Vaitiekūnaitė
- Laboratory of Forest Plant Biotechnology, Institute of Forestry, Lithuanian Research Centre for Agriculture and Forestry, Liepų Str. 1, Girionys, 53101 Kaunas, Lithuania
| | - Valentinas Snitka
- Research Center for Microsystems and Nanotechnology, Kaunas University of Technology, Studentu Str. 65, 51369 Kaunas, Lithuania;
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4
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Cao T, Weaver AA, Baek S, Jia J, Shrout JD, Bohn PW. Depth distributions of signaling molecules in Pseudomonas aeruginosa biofilms mapped by confocal Raman microscopy. J Chem Phys 2021; 154:204201. [PMID: 34241187 DOI: 10.1063/5.0052785] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Pseudomonas aeruginosa is an opportunistic human pathogen implicated in both acute and chronic diseases, which resists antibiotic treatment, in part by forming physical and chemical barriers such as biofilms. Here, we explore the use of confocal Raman imaging to characterize the three-dimensional (3D) spatial distribution of alkyl quinolones (AQs) in P. aeruginosa biofilms by reconstructing depth profiles from hyperspectral Raman data. AQs are important to quorum sensing (QS), virulence, and other actions of P. aeruginosa. Three-dimensional distributions of three different AQs (PQS, HQNO, and HHQ) were observed to have a significant depth, suggesting 3D anisotropic shapes-sheet-like rectangular solids for HQNO and extended cylinders for PQS. Similar to observations from 2D imaging studies, spectral features characteristic of AQs (HQNO or PQS) and the amide I vibration from peptide-containing species were found to correlate with the PQS cylinders typically located at the tips of the HQNO rectangular solids. In the QS-deficient mutant lasIrhlI, a small globular component was observed, whose highly localized nature and similarity in size to a P. aeruginosa cell suggest that the feature arises from HHQ localized in the vicinity of the cell from which it was secreted. The difference in the shapes and sizes of the aggregates of the three AQs in wild-type and mutant P. aeruginosa is likely related to the difference in the cellular response to growth conditions, environmental stress, metabolic levels, or other structural and biochemical variations inside biofilms. This study provides a new route to characterizing the 3D structure of biofilms and shows the potential of confocal Raman imaging to elucidate the nature of heterogeneous biofilms in all three spatial dimensions. These capabilities should be applicable as a tool in studies of infectious diseases.
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Affiliation(s)
- Tianyuan Cao
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Abigail A Weaver
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Seol Baek
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Jin Jia
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Joshua D Shrout
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Paul W Bohn
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
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Biological and clinical significance of quorum sensing alkylquinolones: current analytical and bioanalytical methods for their quantification. Anal Bioanal Chem 2021; 413:4599-4618. [PMID: 33959788 DOI: 10.1007/s00216-021-03356-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 03/21/2021] [Accepted: 04/16/2021] [Indexed: 12/27/2022]
Abstract
Quorum sensing (QS) is a sophisticated bacterial communication system which plays a key role in the virulence and biofilm formation of many pathogens. The Pseudomonas aeruginosa QS network consists of four sets of connected systems (las, rlh, pqs and iqs) hierarchically organized. The pqs system involves characteristic autoinducers (AI), most of them sharing an alkylquinolone (AQ) structure, and is able to carry out several relevant biological functions besides its main signalling activity. Their role in bacterial physiology and pathogenicity has been widely studied. Indeed, the presence of these metabolites in several body fluids and infected tissues has pointed to their potential value as biomarkers of infection. In this review, we summarize the most recent findings about the biological implications and the clinical significance of the main P. aeruginosa AQs. These findings have encouraged the development of analytical and bioanalytical techniques addressed to assess the role of these metabolites in bacterial growth and survival, during pathogenesis or as biomarkers of infections. The availability of highly sensitive reliable analytical methods suitable for clinical analysis would allow getting knowledge about pathogenesis and disease prognosis or progression, supporting clinicians on the decision-making process for the management of these infections and guiding them on the application of more effective and appropriate treatments. The benefits from the implementation of the point-of-care (PoC)-type testing in infectious disease diagnostics, which are seen to improve patient outcomes by promoting earlier therapeutic interventions, are also discussed.
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Jia J, Ellis JF, Cao T, Fu K, Morales-Soto N, Shrout JD, Sweedler JV, Bohn PW. Biopolymer Patterning-Directed Secretion in Mucoid and Nonmucoid Strains of Pseudomonas aeruginosa Revealed by Multimodal Chemical Imaging. ACS Infect Dis 2021; 7:598-607. [PMID: 33620198 DOI: 10.1021/acsinfecdis.0c00765] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Quinolone, pyocyanin, and rhamnolipid production were studied in Pseudomonas aeruginosa by spatially patterning mucin, a glycoprotein important to infection of lung epithelia. Mass spectrometric imaging and confocal Raman microscopy are combined to probe P. aeruginosa biofilms from mucoid and nonmucoid strains grown on lithographically defined patterns. Quinolone signatures from biofilms on patterned vs unpatterned and mucin vs mercaptoundecanoic acid (MUA) surfaces were compared. Microbial attachment is accompanied by secretion of 2-alkyl-4-quinolones as well as rhamnolipids from the mucoid and nonmucoid strains. Pyocyanin was also detected both in the biofilm and in the supernatant in the mucoid strain only. Significant differences in the spatiotemporal distributions of secreted factors are observed between strains and among different surface patterning conditions. The mucoid strain is sensitive to composition and patterning while the nonmucoid strain is not, and in promoting community development in the mucoid strain, nonpatterned surfaces are better than patterned, and mucin is better than MUA. Also, the mucoid strain secretes the virulence factor pyocyanin in a way that correlates with distress. A change in the relative abundance for two rhamnolipids is observed in the mucoid strain during exposure to mucin, whereas minimal variation is observed in the nonmucoid strain. Differences between mucoid and nonmucoid strains are consistent with their strain-specific phenology, in which the mucoid strain develops highly protected and withdrawn biofilms that achieve Pseudomonas quinolone signal production under limited conditions.
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Affiliation(s)
- Jin Jia
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Joanna F. Ellis
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801,United States
| | - Tianyuan Cao
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Kaiyu Fu
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Nydia Morales-Soto
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, Indiana 46556,United States
| | - Joshua D. Shrout
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, Indiana 46556,United States
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Jonathan V. Sweedler
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801,United States
| | - Paul W. Bohn
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, United States
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7
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Beloin C, McDougald D. Speciality Grand Challenge for "Biofilms". Front Cell Infect Microbiol 2021; 11:632429. [PMID: 33692967 PMCID: PMC7937965 DOI: 10.3389/fcimb.2021.632429] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 01/28/2021] [Indexed: 12/23/2022] Open
Affiliation(s)
- Christophe Beloin
- Genetics of Biofilms Laboratory, Institut Pasteur, UMR CNRS2001, Paris, France
| | - Diane McDougald
- iîhree lnstitute, University of Technology Sydney, Sydney, NSW, Australia.,Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
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8
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Spatiotemporal Distribution of Pseudomonas aeruginosa Alkyl Quinolones under Metabolic and Competitive Stress. mSphere 2020; 5:5/4/e00426-20. [PMID: 32699119 PMCID: PMC7376503 DOI: 10.1128/msphere.00426-20] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Alkyl quinolones (AQs), including Pseudomonas quinolone signal (PQS), made by the opportunistic pathogen Pseudomonas aeruginosa have been associated with both population density and stress. The regulation of AQ production is known to be complex, and the stimuli that modulate AQ responses are not fully clear. Here, we have used hyperspectral Raman chemical imaging to examine the temporal and spatial profiles of AQs exhibited by P. aeruginosa under several potentially stressful conditions. We found that metabolic stress, effected by carbon limitation, or competition stress, effected by proximity to other species, resulted in accelerated PQS production. This competition effect did not require cell-to-cell interaction, as evidenced by the fact that the addition of supernatants from either Escherichia coli or Staphylococcus aureus led to early appearance of PQS. Lastly, the fact that these modulations were observed for PQS but not for all AQs suggests a high level of complexity in AQ regulation that remains to be discerned. Pseudomonas aeruginosa is an opportunistic human pathogen important to diseases such as cystic fibrosis. P. aeruginosa has multiple quorum-sensing (QS) systems, one of which utilizes the signaling molecule 2-heptyl-3-hydroxy-4-quinolone (Pseudomonas quinolone signal [PQS]). Here, we use hyperspectral Raman imaging to elucidate the spatiotemporal PQS distributions that determine how P. aeruginosa regulates surface colonization and its response to both metabolic stress and competition from other bacterial strains. These chemical imaging experiments illustrate the strong link between environmental challenges, such as metabolic stress caused by nutritional limitations or the presence of another bacterial species, and PQS signaling. Metabolic stress elicits a complex response in which limited nutrients induce the bacteria to produce PQS earlier, but the bacteria may also pause PQS production entirely if the nutrient concentration is too low. Separately, coculturing P. aeruginosa in the proximity of another bacterial species, or its culture supernatant, results in earlier production of PQS. However, these differences in PQS appearance are not observed for all alkyl quinolones (AQs) measured; the spatiotemporal response of 2-heptyl-4-hydroxyquinoline N-oxide (HQNO) is highly uniform for most conditions. These insights on the spatiotemporal distributions of quinolones provide additional perspective on the behavior of P. aeruginosa in response to different environmental cues. IMPORTANCE Alkyl quinolones (AQs), including Pseudomonas quinolone signal (PQS), made by the opportunistic pathogen Pseudomonas aeruginosa have been associated with both population density and stress. The regulation of AQ production is known to be complex, and the stimuli that modulate AQ responses are not fully clear. Here, we have used hyperspectral Raman chemical imaging to examine the temporal and spatial profiles of AQs exhibited by P. aeruginosa under several potentially stressful conditions. We found that metabolic stress, effected by carbon limitation, or competition stress, effected by proximity to other species, resulted in accelerated PQS production. This competition effect did not require cell-to-cell interaction, as evidenced by the fact that the addition of supernatants from either Escherichia coli or Staphylococcus aureus led to early appearance of PQS. Lastly, the fact that these modulations were observed for PQS but not for all AQs suggests a high level of complexity in AQ regulation that remains to be discerned.
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9
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Do H, Kwon SR, Fu K, Morales-Soto N, Shrout JD, Bohn PW. Electrochemical Surface-Enhanced Raman Spectroscopy of Pyocyanin Secreted by Pseudomonas aeruginosa Communities. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:7043-7049. [PMID: 31042392 PMCID: PMC8006532 DOI: 10.1021/acs.langmuir.9b00184] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Pyocyanin (PYO) is one of many toxins secreted by the opportunistic human pathogenic bacterium Pseudomonas aeruginosa. Direct detection of PYO in biofilms is crucial because PYO can provide important information about infection-related virulence mechanisms in P. aeruginosa. Because PYO is both redox-active and Raman-active, we seek to simultaneously acquire both spectroscopic and redox state information about PYO. The combination of surface-enhanced Raman spectroscopy (SERS) and voltammetry is used here to provide insights into the molecular redox behavior of PYO while controlling the SERS and electrochemical (EC) response of PYO with external stimuli, such as pH and applied potential. Furthermore, PYO secretion from biofilms of different P. aeruginosa strains is compared. Both SERS spectra and EC behavior are observed to change with pH, and several pH-dependent bands are identified in the SERS spectra, which can potentially be used to probe the local environment. Comparison of the voltammetric behavior of wild-type and a PYO-deficient mutant unequivocally identifies PYO as a major component of the secretome. Spectroelectrochemical studies of the PYO standard reveal decreasing SERS intensities of PYO bands under reducing conditions. Extending these experiments to pellicle biofilms shows similar behavior with applied potential, and SERS imaging indicates that secreted PYO is localized in regions approximately the size of P. aeruginosa cells. The in situ spectroelectrochemical biofilm characterization approach developed here suggests that EC-SERS monitoring of secreted molecules can be used diagnostically and correlated with the progress of infection.
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Affiliation(s)
- Hyein Do
- Department of Chemistry and Biochemistry,
University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Seung-Ryong Kwon
- Department of Chemical and Biomolecular
Engineering, University of Notre Dame, Notre Dame, Indiana 46556, United
States
| | - Kaiyu Fu
- Department of Chemistry and Biochemistry,
University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Nydia Morales-Soto
- Department of Civil and Environmental
Engineering and Earth Sciences, University of Notre Dame, Notre Dame, Indiana
46556, United States
| | - Joshua D. Shrout
- Department of Civil and Environmental
Engineering and Earth Sciences, University of Notre Dame, Notre Dame, Indiana
46556, United States
- Department of Biological Sciences, University of
Notre Dame, Notre Dame, Indiana 46556, United States
| | - Paul W. Bohn
- Department of Chemistry and Biochemistry,
University of Notre Dame, Notre Dame, Indiana 46556, United States
- Department of Chemical and Biomolecular
Engineering, University of Notre Dame, Notre Dame, Indiana 46556, United
States
- Corresponding Author
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Jia F, Barber E, Turasan H, Seo S, Dai R, Liu L, Li X, Bhunia AK, Kokini JL. Detection of Pyocyanin Using a New Biodegradable SERS Biosensor Fabricated Using Gold Coated Zein Nanostructures Further Decorated with Gold Nanoparticles. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:4603-4610. [PMID: 30964288 DOI: 10.1021/acs.jafc.8b07317] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In this paper, a biodegradable gold coated zein film surface enhanced Raman spectroscopy (SERS) platform, with gold nanoparticles (AuNPs) deposited on the surface to further enhance the Raman signal, was used to detect pyocyanin (PYO), the toxin secreted by Pseudomonas aeruginosa. An inverted pyramid structure imprinted on a zein film and gold coated during the transfer process was further improved with the deposition and fixing of gold nanoparticles, which resulted in enhancement of the SERS signal by approximately a decade. This new platform served as a lab-on-a-chip sensor to enable the sensitive and rapid detection of PYO in drinking water. The size, distribution, and morphology of the zein film nanostructures including the presence and distribution of gold nanoparticles were characterized by scanning electron microscopy (SEM). The new zein-based platform has the advantage of being largely biodegradable compared with commercial silicon- or glass-based platforms. The limit of detection for PYO using the newly developed zein-based SERS sensor platform was calculated as 25 μM, considerably lower than the concentration of PYO in the blood of people with cystic fibrosis which has been reported to be 70 μM.
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Affiliation(s)
- Fei Jia
- College of Food Science and Nutritional Engineering , China Agricultural University , Beijing , 100083 , China
- Department of Food Science , Purdue University , West Lafayette , Indiana 47906 , United States
| | - Emma Barber
- Department of Food Science , Purdue University , West Lafayette , Indiana 47906 , United States
| | - Hazal Turasan
- Department of Food Science , Purdue University , West Lafayette , Indiana 47906 , United States
| | - Sujin Seo
- Department of Electrical and Computer Engineering , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Ruitong Dai
- College of Food Science and Nutritional Engineering , China Agricultural University , Beijing , 100083 , China
| | - Logan Liu
- Department of Electrical and Computer Engineering , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Xingmin Li
- College of Food Science and Nutritional Engineering , China Agricultural University , Beijing , 100083 , China
| | - Arun K Bhunia
- Department of Food Science , Purdue University , West Lafayette , Indiana 47906 , United States
| | - Jozef L Kokini
- Department of Food Science , Purdue University , West Lafayette , Indiana 47906 , United States
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11
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Cao T, Morales-Soto N, Jia J, Baig NF, Dunham SJB, Ellis J, Sweedler JV, Shrout JD, Bohn PW. Spatiotemporal Dynamics of Molecular Messaging in Bacterial Co-Cultures Studied by Multimodal Chemical Imaging. PROCEEDINGS OF SPIE--THE INTERNATIONAL SOCIETY FOR OPTICAL ENGINEERING 2019; 10863:108630A. [PMID: 33790492 PMCID: PMC8009051 DOI: 10.1117/12.2501349] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Microbial community behavior is coupled to a set of genetically-regulated chemical signals that correlate with cell density - the quorum sensing (QS) system - and there is growing appreciation that the QS-regulated behavior of bacteria is chemically, spatially, and temporally complex. In addition, while it has been known for some time that different species use different QS networks, we are beginning to appreciate that different strains of the same bacterial species also differ in their QS networks. Here we combine mass spectrometric imaging (MSI) and confocal Raman microscopy (CRM) approaches to investigate co-cultures involving different strains (FRD1 and PAO1C) of the same species (Pseudomonas aeruginosa) as well as those involving different species (P. aeruginosa and E. coli). Combining MSI and CRM makes it possible to supersede the limits imposed by individual imaging approaches and enables the spatial mapping of individual bacterial species and their microbial products within a mixed bacterial community growing in situ on surfaces. MSI is used to delineate the secretion of a specific rhamnolipid surfactant as well as alkyl quinolone (AQ) messengers between FRD1 and PAO1C strains of P. aeruginosa, showing that the spatial distribution and production rate of AQ messengers in PAO1C far outstrips that of FRD1. In the case of multiple species, CRM is used to show that the prolific secretion of AQs by the PAO1C strain of P. aeruginosa is used to mediate its interaction with co-cultured E. coli.
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Affiliation(s)
- Tianyuan Cao
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA
| | - Nydia Morales-Soto
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Jin Jia
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA
| | - Nameera F Baig
- Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720
| | - Sage J B Dunham
- Entech Instruments, 2207 Agate Court, Simi Valley, CA 93065
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL 61801
| | - Joseph Ellis
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL 61801
| | - Jonathan V Sweedler
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL 61801
| | - Joshua D Shrout
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, IN, USA
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Paul W Bohn
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN, USA
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12
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Dunham SJB, Ellis JF, Baig NF, Morales-Soto N, Cao T, Shrout JD, Bohn PW, Sweedler JV. Quantitative SIMS Imaging of Agar-Based Microbial Communities. Anal Chem 2018; 90:5654-5663. [PMID: 29623707 PMCID: PMC5930052 DOI: 10.1021/acs.analchem.7b05180] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
After several decades of widespread use for mapping elemental ions and small molecular fragments in surface science, secondary ion mass spectrometry (SIMS) has emerged as a powerful analytical tool for molecular imaging in biology. Biomolecular SIMS imaging has primarily been used as a qualitative technique; although the distribution of a single analyte can be accurately determined, it is difficult to map the absolute quantity of a compound or even to compare the relative abundance of one molecular species to that of another. We describe a method for quantitative SIMS imaging of small molecules in agar-based microbial communities. The microbes are cultivated on a thin film of agar, dried under nitrogen, and imaged directly with SIMS. By use of optical microscopy, we show that the area of the agar is reduced by 26 ± 2% (standard deviation) during dehydration, but the overall biofilm morphology and analyte distribution are largely retained. We detail a quantitative imaging methodology, in which the ion intensity of each analyte is (1) normalized to an external quadratic regression curve, (2) corrected for isomeric interference, and (3) filtered for sample-specific noise and lower and upper limits of quantitation. The end result is a two-dimensional surface density image for each analyte. The sample preparation and quantitation methods are validated by quantitatively imaging four alkyl-quinolone and alkyl-quinoline N-oxide signaling molecules (including Pseudomonas quinolone signal) in Pseudomonas aeruginosa colony biofilms. We show that the relative surface densities of the target biomolecules are substantially different from values inferred through direct intensity comparison and that the developed methodologies can be used to quantitatively compare as many ions as there are available standards.
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Affiliation(s)
- Sage J. B. Dunham
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana- Champaign, Urbana, IL 61801
| | - Joseph F. Ellis
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana- Champaign, Urbana, IL 61801
| | - Nameera F. Baig
- Department of Chemistry and Biochemistry, and Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556
| | - Nydia Morales-Soto
- Department of Civil and Environmental Engineering and Earth Sciences, and Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556
| | - Tianyuan Cao
- Department of Chemistry and Biochemistry, and Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556
| | - Joshua D. Shrout
- Department of Civil and Environmental Engineering and Earth Sciences, and Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556
| | - Paul W. Bohn
- Department of Chemistry and Biochemistry, and Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556
| | - Jonathan V. Sweedler
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana- Champaign, Urbana, IL 61801
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