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The electrophoretic motion of cylindrical macroions inside a nanochannel using molecular dynamics simulation. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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Buszewski B, Maślak E, Złoch M, Railean-Plugaru V, Kłodzińska E, Pomastowski P. A new approach to identifying pathogens, with particular regard to viruses, based on capillary electrophoresis and other analytical techniques. Trends Analyt Chem 2021; 139:116250. [PMID: 34776563 PMCID: PMC8573725 DOI: 10.1016/j.trac.2021.116250] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Fast determination, identification and characterization of pathogens is a significant challenge in many fields, from industry to medicine. Standard approaches (e.g., culture media and biochemical tests) are known to be very time-consuming and labor-intensive. Conversely, screening techniques demand a quick and low-cost grouping of microbial isolates, and current analysis call for broad reports of pathogens, involving the application of molecular, microscopy, and electromigration techniques, DNA fingerprinting and also MALDI-TOF methods. The present COVID-19 pandemic is a crisis that affects rich and poor countries alike. Detection of SARS-CoV-2 in patient samples is a critical tool for monitoring disease spread, guiding therapeutic decisions and devising social distancing protocols. The goal of this review is to present an innovative methodology based on preparative separation of pathogens by electromigration techniques in combination with simultaneous analysis of the proteome, lipidome, and genome using laser desorption/ionization analysis.
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Affiliation(s)
- Bogusław Buszewski
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Torun, 87-100, Torun, Poland.,Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University in Torun, 87-100, Torun, Poland
| | - Ewelina Maślak
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Torun, 87-100, Torun, Poland.,Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University in Torun, 87-100, Torun, Poland
| | - Michał Złoch
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Torun, 87-100, Torun, Poland
| | - Viorica Railean-Plugaru
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Torun, 87-100, Torun, Poland
| | - Ewa Kłodzińska
- Institute of Sport - National Research Institute, Department of Analytical Chemistry and Instrumental Analysis, 01-982, Warsaw, Poland
| | - Paweł Pomastowski
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Torun, 87-100, Torun, Poland
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CoVrimer: A tool for aligning SARS-CoV-2 primer sequences and selection of conserved/degenerate primers. Genomics 2021; 113:3174-3184. [PMID: 34293476 PMCID: PMC8289724 DOI: 10.1016/j.ygeno.2021.07.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 05/30/2021] [Accepted: 07/17/2021] [Indexed: 01/17/2023]
Abstract
As mutations in SARS-CoV-2 virus accumulate rapidly, novel primers that amplify this virus sensitively and specifically are in demand. We have developed a webserver named CoVrimer by which users can search for and align existing or newly designed conserved/degenerate primer pair sequences against the viral genome and assess the mutation load of both primers and amplicons. CoVrimer uses mutation data obtained from an online platform established by NGDC-CNCB (12 May 2021) to identify genomic regions, either conserved or with low levels of mutations, from which potential primer pairs are designed and provided to the user for filtering based on generalized and SARS-CoV-2 specific parameters. Alignments of primers and probes can be visualized with respect to the reference genome, indicating variant details and the level of conservation. Consequently, CoVrimer is likely to help researchers with the challenges posed by viral evolution and is freely available at http://konulabapps.bilkent.edu.tr:3838/CoVrimer/.
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