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Rathnayake RAC, Zhao Z, McLaughlin N, Li W, Yan Y, Chen LL, Xie Q, Wu CD, Mathew MT, Wang RR. Machine learning enabled multiplex detection of periodontal pathogens by surface-enhanced Raman spectroscopy. Int J Biol Macromol 2024; 257:128773. [PMID: 38096932 DOI: 10.1016/j.ijbiomac.2023.128773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 11/02/2023] [Accepted: 12/11/2023] [Indexed: 12/21/2023]
Abstract
Periodontitis is a chronic inflammation of the periodontium caused by a persistent bacterial infection, resulting in destruction of the supporting structures of teeth. Analysis of microbial composition in saliva can inform periodontal status. Actinobacillus actinomycetemcomitans (Aa), Porphyromonas gingivalis (Pg), and Streptococcus mutans (Sm) are among reported periodontal pathogens, and were used as model systems in this study. Our atomic force microscopic (AFM) study revealed that these pathogens are biological nanorods with dimensions of 0.6-1.1 μm in length and 500-700 nm in width. Current bacterial detection methods often involve complex preparation steps and require labeled reporting motifs. Employing surface-enhanced Raman spectroscopy (SERS), we revealed cell-type specific Raman signatures of these pathogens for label-free detection. It overcame the complexity associated with spectral overlaps among different bacterial species, relying on high signal-to-noise ratio (SNR) spectra carefully collected from pure species samples. To enable simple, rapid, and multiplexed detection, we harnessed advanced machine learning techniques to establish predictive models based on a large set of raw spectra of each bacterial species and their mixtures. Using these models, given a raw spectrum collected from a bacterial suspension, simultaneous identification of all three species in the test sample was achieved at 95.6 % accuracy. This sensing modality can be applied to multiplex detection of a broader range and a larger set of periodontal pathogens, paving the way for hassle-free detection of oral bacteria in saliva with little to no sample preparation.
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Affiliation(s)
- Rathnayake A C Rathnayake
- Department of Chemistry, Illinois Institute of Technology, Chicago, IL 60616, United States of America
| | - Zhenghao Zhao
- Department of Computer Science, Illinois Institute of Technology, Chicago, IL 60616, United States of America
| | - Nathan McLaughlin
- Department of Surgery, University of Illinois Chicago, Chicago, IL 60612, United States of America
| | - Wei Li
- Department of Pediatric Dentistry, University of Illinois Chicago, Chicago, IL 60612, United States of America
| | - Yan Yan
- Department of Computer Science, Illinois Institute of Technology, Chicago, IL 60616, United States of America.
| | - Liaohai L Chen
- Department of Surgery, University of Illinois Chicago, Chicago, IL 60612, United States of America
| | - Qian Xie
- Department of Endodontics, University of Illinois Chicago, Chicago, IL, United States of America
| | - Christine D Wu
- Department of Pediatric Dentistry, University of Illinois Chicago, Chicago, IL 60612, United States of America
| | - Mathew T Mathew
- Department of Restorative Dentistry, University of Illinois Chicago, Chicago, IL 60612, United States of America; Department of Biomedical Sciences, University of Illinois Rockford, Rockford, IL 61107, United States of America
| | - Rong R Wang
- Department of Chemistry, Illinois Institute of Technology, Chicago, IL 60616, United States of America.
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Tarannum T, Ahmed S. Recent development in antiviral surfaces: Impact of topography and environmental conditions. Heliyon 2023; 9:e16698. [PMID: 37260884 PMCID: PMC10227326 DOI: 10.1016/j.heliyon.2023.e16698] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 05/23/2023] [Accepted: 05/24/2023] [Indexed: 06/02/2023] Open
Abstract
The transmission of viruses is largely dependent on contact with contaminated virus-laden communal surfaces. While frequent surface disinfection and antiviral coating techniques are put forth by researchers as a plan of action to tackle transmission in dire situations like the Covid-19 pandemic caused by SARS-CoV-2 virus, these procedures are often laborious, time-consuming, cost-intensive, and toxic. Hence, surface topography-mediated antiviral surfaces have been gaining more attention in recent times. Although bioinspired hydrophobic antibacterial nanopatterned surfaces mimicking the natural sources is a very prevalent and successful strategy, the antiviral prospect of these surfaces is yet to be explored. Few recent studies have explored the potential of nanopatterned antiviral surfaces. In this review, we highlighted surface properties that have an impact on virus attachment and persistence, particularly focusing and emphasizing on the prospect of the nanotextured surface with enhanced properties to be used as antiviral surface. In addition, recent developments in surface nanopatterning techniques depending on the nano-scaled dimensions have been discussed. The impacts of environments and surface topology on virus inactivation have also been reviewed.
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Alexei Pichardo-Orta F, Luna OAP, Cordero JRV. A frontal air intake may improve the natural ventilation in urban buses. Sci Rep 2022; 12:21256. [PMID: 36482072 PMCID: PMC9732044 DOI: 10.1038/s41598-022-25868-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 12/06/2022] [Indexed: 12/13/2022] Open
Abstract
In this report we analyze the air flow across the open windows (natural ventilation) of an urban bus model and the consequent dispersion of aerosols emitted in the passengers area. The methods include computational fluid dynamics simulations and three ways to characterize the dispersion of passive tracers: a continuous concentration-based model, a discrete random model and a parametric scalar based on the so-called mean age of air. We also conducted experiments using a 1:10 scale bus model and [Formula: see text] as a passive tracer to assess the ventilation characteristics. We found that dispersion and expulsion of aerosols is driven by a negative pressure in the standard bus design equipped with lateral windows. Also, the average age of air is 6 minutes while the air flow promotes aerosol accumulation to the front (driver's area). To speed up the expulsion of aerosols and reduce their in-cabin accumulation, we propose a bus bodywork prototype having a frontal air intake. All the numerical models and experiments conducted in this work agreed that the expulsion of aerosols in this novel configuration is significantly increased while the average age of air is reduced to 50 seconds. The average air flow also changes with the presence of frontal air intakes and, as a consequence, the expulsion of aerosols is now driven by a frontal velocity field.
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Affiliation(s)
- F Alexei Pichardo-Orta
- Instituto de Física, Universidad Autónoma de San Luis Potosí, Álvaro Obregón 64, 78000, San Luis Potosí, S.L.P., México
| | - Oscar Adrián Patiño Luna
- Instituto de Física, Universidad Autónoma de San Luis Potosí, Álvaro Obregón 64, 78000, San Luis Potosí, S.L.P., México
| | - J Rodrigo Vélez Cordero
- Investigadores por México-Instituto de Física, Universidad Autónoma de San Luis Potosí, Álvaro Obregón 64, 78000, San Luis Potosí, S.L.P., México.
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Gómez-López VM, Jubinville E, Rodríguez-López MI, Trudel-Ferland M, Bouchard S, Jean J. Inactivation of Foodborne Viruses by UV Light: A Review. Foods 2021; 10:foods10123141. [PMID: 34945692 PMCID: PMC8701782 DOI: 10.3390/foods10123141] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 11/29/2021] [Accepted: 12/15/2021] [Indexed: 12/13/2022] Open
Abstract
Viruses on some foods can be inactivated by exposure to ultraviolet (UV) light. This green technology has little impact on product quality and, thus, could be used to increase food safety. While its bactericidal effect has been studied extensively, little is known about the viricidal effect of UV on foods. The mechanism of viral inactivation by UV results mainly from an alteration of the genetic material (DNA or RNA) within the viral capsid and, to a lesser extent, by modifying major and minor viral proteins of the capsid. In this review, we examine the potential of UV treatment as a means of inactivating viruses on food processing surfaces and different foods. The most common foodborne viruses and their laboratory surrogates; further explanation on the inactivation mechanism and its efficacy in water, liquid foods, meat products, fruits, and vegetables; and the prospects for the commercial application of this technology are discussed. Lastly, we describe UV’s limitations and legislation surrounding its use. Based on our review of the literature, viral inactivation in water seems to be particularly effective. While consistent inactivation through turbid liquid food or the entire surface of irregular food matrices is more challenging, some treatments on different food matrices seem promising.
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Affiliation(s)
- Vicente M. Gómez-López
- Catedra Alimentos para la Salud, Universidad Católica San Antonio de Murcia, Campus de los Jerónimos, E-30107 Murcia, Spain;
| | - Eric Jubinville
- Institute of Nutraceuticals and Functional Foods, Département des Sciences des Aliments, Université Laval, Québec, QC G1V 0A6, Canada; (E.J.); (M.T.-F.); (S.B.)
| | - María Isabel Rodríguez-López
- Departamento de Tecnología de la Alimentación y Nutrición, Universidad Católica San Antonio de Murcia, Campus de los Jerónimos, E-30107 Murcia, Spain;
| | - Mathilde Trudel-Ferland
- Institute of Nutraceuticals and Functional Foods, Département des Sciences des Aliments, Université Laval, Québec, QC G1V 0A6, Canada; (E.J.); (M.T.-F.); (S.B.)
| | - Simon Bouchard
- Institute of Nutraceuticals and Functional Foods, Département des Sciences des Aliments, Université Laval, Québec, QC G1V 0A6, Canada; (E.J.); (M.T.-F.); (S.B.)
| | - Julie Jean
- Institute of Nutraceuticals and Functional Foods, Département des Sciences des Aliments, Université Laval, Québec, QC G1V 0A6, Canada; (E.J.); (M.T.-F.); (S.B.)
- Correspondence: ; Tel.: +1-418-656-2131 (ext. 413849)
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Ghasemi H, Yazdani H, Fini EH, Mansourpanah Y. Interactions of SARS-CoV-2 with inanimate surfaces in built and transportation environments. SUSTAINABLE CITIES AND SOCIETY 2021; 72:103031. [PMID: 36570725 PMCID: PMC9761300 DOI: 10.1016/j.scs.2021.103031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 05/13/2021] [Accepted: 05/16/2021] [Indexed: 05/11/2023]
Abstract
Understanding the interactions and transmission of pathogens with/via inanimate surfaces common in the built environment and public transport vehicles is critical to promoting sustainable and resilient urban development. Here, molecular dynamics (MD) simulations are used to study the adhesion of SARS-CoV-2 (the causative agent of COVID-19) to some of these surfaces at different temperatures (same for surfaces and ambiance) ranging from -23 to 60 °C. Surfaces simulated are aluminum, copper, copper oxide, polyethylene (PE), and silicon dioxide (SiO2). Steered MD (SMD) simulations are also used to investigate the transfer of the virus from PE and SiO2 when a contaminated surface is touched. The virus shows the lowest and highest adhesions to PE and SiO2, respectively (20 vs 534 eV). Influence of temperature is not found to be noticeable. Using simulated water molecules to represent moisture on the skin, SMD simulations show that water molecules can lift the virus from the PE surface but damage the virus when lifting it from the the SiO2 surface. The results suggest that the PE surface is a more favorable surface to transmit the virus than the other surfaces simulated in this study. The results are compared with those reported in a few experimental studies.
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Affiliation(s)
- Hamid Ghasemi
- Department of Civil and Environmental Engineering, Howard University, 2300 Sixth St NW #1026, Washington, DC 20059, USA
| | - Hessam Yazdani
- Department of Civil and Environmental Engineering, Howard University, 2300 Sixth St NW #1026, Washington, DC 20059, USA
| | - Elham H Fini
- School of Sustainable Engineering and the Built Environment, Arizona State University, 660 S. College Avenue, Tempe, AZ 85287, USA
| | - Yaghoub Mansourpanah
- Membrane Research Laboratory, Lorestan University, Khorramabad, 68137-17133, Iran
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Akhmetova AI, Yaminsky IV. High resolution imaging of viruses: Scanning probe microscopy and related techniques. Methods 2021; 197:30-38. [PMID: 34157416 DOI: 10.1016/j.ymeth.2021.06.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 05/26/2021] [Accepted: 06/17/2021] [Indexed: 11/19/2022] Open
Abstract
Scanning probe microscopy is a group of measurements that provides 3D visualization of viruses in different environmental conditions including liquids and air. Besides 3D topography it is possible to measure the properties like mechanical rigidity and stability, adhesion, tendency to crystallization, surface charge, etc. Choosing the right substrate and scanning parameters makes it much easier to obtain reliable data. Rational interpretation of experimental results should take into account possible artifacts, proper filtering and data presentation using specially designed software packages. Animal and human virus characterization is in the focus of many intensive studies because of their potential harm to higher organisms. The article focuses on high-resolution visualization of plant viruses. Tobacco mosaic virus, potato viruses X and B and others are not dangerous for the human being and are widely used in different applications such as vaccine preparation, construction of building units in nanotechnology and material science applications, nanoparticle production and delivery, and even metrology. The methods of virus's deposition, visualization, and consequent image processing and interpretation are described in details. Specific examples of viruses imaging are illustrated using the FemtoScan Online software, which has typical and all the necessary built-in functions for constructing three-dimensional images, their processing and analysis. Despite visible progress in visualizing the viruses using probe microscopy, many unresolved problems still remain. At present time the probe microscopy data on viruses is not systemized. There is no descriptive atlas of the images and morphology as revealed by this type of high resolution microscopy. It is worth emphasizing that new virus investigation methods will appear due to the progress of science.
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Affiliation(s)
- Assel I Akhmetova
- Lomonosov Moscow State University, 1, Leninskie Gory, Moscow, 119991, GSP-1, Russia; Advanced Technologies Center, 4-5-47, Stroitelei str., Moscow, 119311, Russia
| | - Igor V Yaminsky
- Lomonosov Moscow State University, 1, Leninskie Gory, Moscow, 119991, GSP-1, Russia; Advanced Technologies Center, 4-5-47, Stroitelei str., Moscow, 119311, Russia.
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Tharayil A, Rajakumari R, Chirayil CJ, Thomas S, Kalarikkal N. A short review on nanotechnology interventions against COVID-19. EMERGENT MATERIALS 2021; 4:131-141. [PMID: 33554045 PMCID: PMC7856851 DOI: 10.1007/s42247-021-00163-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 01/12/2021] [Indexed: 05/02/2023]
Abstract
The COVID-19 has affected all major aspects of the society in a global perspective. The role of nanotechnology is much sought after in fighting this pandemic. Advanced materials based on nanotechnology are the basis of several technologies starting from masks and personal protection equipment to specific diagnostic tools that could diminish the impact of COVID-19. Development of nanotechnology-based products is therefore an absolute necessity for fight against COVID-19. We examine the fundamental concepts related to virology, histopathologic findings and how nanotechnology can help in fighting the disease. In this review we discuss the state of the art and ongoing nanotechnology-based strategies like antiviral coatings, 3D printing and therapeutics to fight against this deadly disease. The importance of using nanoparticles in point of care tests and biosensors is also highlighted.
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Affiliation(s)
- Abhimanyu Tharayil
- School of Energy Materials, Mahatma Gandhi University, Kottayam, Kerala 686560 India
| | - R. Rajakumari
- International and Inter-University Centre for Nanoscience and Nanotechnology, Mahatma Gandhi University, Kottayam, Kerala 686560 India
| | | | - Sabu Thomas
- School of Energy Materials, Mahatma Gandhi University, Kottayam, Kerala 686560 India
- International and Inter-University Centre for Nanoscience and Nanotechnology, Mahatma Gandhi University, Kottayam, Kerala 686560 India
- School of Chemical Sciences, Mahatma Gandhi University, Kottayam, Kerala 686560 India
| | - Nandakumar Kalarikkal
- International and Inter-University Centre for Nanoscience and Nanotechnology, Mahatma Gandhi University, Kottayam, Kerala 686560 India
- School of Pure and Applied Physics, Mahatma Gandhi University, Kottayam, Kerala 686560 India
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8
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Computer simulations of the interaction between SARS-CoV-2 spike glycoprotein and different surfaces. Biointerphases 2020; 15:051008. [PMID: 33105999 DOI: 10.1116/6.0000502] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
A prominent feature of coronaviruses is the presence of a large glycoprotein spike protruding from a lipidic membrane. This glycoprotein spike determines the interaction of coronaviruses with the environment and the host. In this paper, we perform all atomic molecular dynamics simulations of the interaction between the SARS-CoV-2 trimeric glycoprotein spike and surfaces of materials. We considered a material with high hydrogen bonding capacity (cellulose) and a material capable of strong hydrophobic interactions (graphite). Initially, the spike adsorbs to both surfaces through essentially the same residues belonging to the receptor binding subunit of its three monomers. Adsorption onto cellulose stabilizes in this configuration, with the help of a large number of hydrogen bonds developed between cellulose and the three receptor-binding domains of the glycoprotein spike. In the case of adsorption onto graphite, the initial adsorption configuration is not stable and the surface induces a substantial deformation of the glycoprotein spike with a large number of adsorbed residues not pertaining to the binding subunits of the spike monomers.
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