Application of Raman spectroscopy to study the inactivation process of bacterial microorganisms

Raman spectroscopy (RS) is one of the promising approaches for structural and functional studies of various biological objects, including bacterial microorganisms. Both traditional biochemical tests and genetic methods which require expensive reagents, consumables and are time-consuming are used for bacterial analysis. Spectroscopic methods are positioned as noninvasive, highly sensitive, and requiring minimal sample preparation. In this work we investigated the possibility of using the RS method using optical sensors based on gold anisotropic nanoparticles. The applicability of the method was demonstrated by studying the effect of a broad-spectrum cephalosporin antibiotic and an extract of Viburnum opulus L (VO) on Escherichia coli (E. Coli) colonies. The studies were performed by Raman spectroscopy using a Virsa spectrometer (Renishaw). Raman signal amplification was carried out using two original optical sensors proposed by the authors. To create sensors, we used a chemical method of depositing gold nanostars on APTES-modified quartz glasses and a physical method for creating sensors based on anodizing titanium surfaces. The results of the study showed the high sensitivity and information content of the proposed method. The possibility of using the RS method for studying the inactivation of bacterial microorganisms is shown. Spectral Raman bands of E. Coli were determined and identified before and after exposure to VO extract and antibiotic as a control. A decrease in the intensity of spectral modes corresponding to amino acids and purine metabolites was found in the average Raman spectrum of E. Coli after exposure to VO extract. For the first time, a study of the antimicrobial effect of an aqueous extract of VO fruits was carried out by the method of Raman scattering. It has been shown that the use of plant extracts, including VO fruit extracts, to inactivate the vital activity of bacterial colonies is a promising approach to the search for new alternative antibacterial agents. The results obtained are in good agreement with the already known scientific studies and confirm the effectiveness of the proposed method

Ordinary differential equations and Boolean networks in application to modelling of 6-mercaptopurine metabolism

We consider two approaches to modelling the cell metabolism of 6-mercaptopurine, one of the important chemotherapy drugs used for treating acute lymphocytic leukaemia: kinetic ordinary differential equations, and Boolean networks supplied with one controlling node, which takes continual values. We analyse their interplay with respect to taking into account ATP concentration as a key parameter of switching between different pathways. It is shown that the Boolean networks, which allow avoiding the complexity of general kinetic modelling, preserve the possibility of reproducing the principal switching mechanism.</jats:p

The Cascade Hilbert-Zero Decomposition: A Novel Method for Peaks Resolution and Its Application to Raman Spectra

Raman spectra of biological objects are sufficiently complex since they are comprised of wide diffusive spectral peaks over a noisy background. This makes the resolution of individual closely positioned components a complicated task. Here we propose a method for constructing an approximation of such systems by a series, respectively, to shifts of the Gaussian functions with different adjustable dispersions. It is based on the coordination of the Gaussian peaks’ location with the zeros of the signal’s Hilbert transform. The resolution of overlapping peaks is achieved by applying this procedure in a hierarchical cascade way, subsequently excluding peaks of each level of decomposition. Both the mathematical rationale for the localization of intervals, where the zero crossing of the Hilbert-transformed uni- and multimodal mixtures of Gaussians occurs, and the step-by-step outline of the numerical algorithm are provided and discussed. As a practical case study, we analyze results of the processing of a complicated Raman spectrum obtained from a strain of Mycobacterium tuberculosis. However, the proposed method can be applied to signals of different origins formed by overlapped localized pulses too

The Cascade Hilbert-Zero Decomposition: A Novel Method for Peaks Resolution and Its Application to Raman Spectra

Raman spectra of biological objects are sufficiently complex since they are comprised of wide diffusive spectral peaks over a noisy background. This makes the resolution of individual closely positioned components a complicated task. Here we propose a method for constructing an approximation of such systems by a series, respectively, to shifts of the Gaussian functions with different adjustable dispersions. It is based on the coordination of the Gaussian peaks’ location with the zeros of the signal’s Hilbert transform. The resolution of overlapping peaks is achieved by applying this procedure in a hierarchical cascade way, subsequently excluding peaks of each level of decomposition. Both the mathematical rationale for the localization of intervals, where the zero crossing of the Hilbert-transformed uni- and multimodal mixtures of Gaussians occurs, and the step-by-step outline of the numerical algorithm are provided and discussed. As a practical case study, we analyze results of the processing of a complicated Raman spectrum obtained from a strain of Mycobacterium tuberculosis. However, the proposed method can be applied to signals of different origins formed by overlapped localized pulses too.</jats:p