Silvie Bernatová

Bio: Silvie Bernatová is an academic researcher from Academy of Sciences of the Czech Republic. The author has contributed to research in topics: Raman spectroscopy & Optical tweezers. The author has an hindex of 12, co-authored 41 publications receiving 355 citations.

Following the Mechanisms of Bacteriostatic versus Bactericidal Action Using Raman Spectroscopy

Abstract: Antibiotics cure infections by influencing bacterial growth or viability. Antibiotics can be divided to two groups on the basis of their effect on microbial cells through two main mechanisms, which are either bactericidal or bacteriostatic. Bactericidal antibiotics kill the bacteria and bacteriostatic antibiotics suppress the growth of bacteria (keep them in the stationary phase of growth). One of many factors to predict a favorable clinical outcome of the potential action of antimicrobial chemicals may be provided using in vitro bactericidal/bacteriostatic data (e.g., minimum inhibitory concentrations-MICs). Consequently, MICs are used in clinical situations mainly to confirm resistance, and to determine the in vitro activities of new antimicrobials. We report on the combination of data obtained from MICs with information on microorganisms' "fingerprint" (e.g., DNA/RNA, and proteins) provided by Raman spectroscopy. Thus, we could follow mechanisms of the bacteriostatic versus bactericidal action simply by detecting the Raman bands corresponding to DNA. The Raman spectra of Staphylococcus epidermidis treated with clindamycin (a bacteriostatic agent) indeed show little effect on DNA which is in contrast with the action of ciprofloxacin (a bactericidal agent), where the Raman spectra show a decrease in strength of the signal assigned to DNA, suggesting DNA fragmentation.

Rapid identification of staphylococci by Raman spectroscopy.

Abstract: Clinical treatment of the infections caused by various staphylococcal species differ depending on the actual cause of infection. Therefore, it is necessary to develop a fast and reliable method for identification of staphylococci. Raman spectroscopy is an optical method used in multiple scientific fields. Recent studies showed that the method has a potential for use in microbiological research, too. Our work here shows a possibility to identify staphylococci by Raman spectroscopy. We present a method that enables almost 100% successful identification of 16 of the clinically most important staphylococcal species directly from bacterial colonies grown on a Mueller-Hinton agar plate. We obtained characteristic Raman spectra of 277 staphylococcal strains belonging to 16 species from a 24-hour culture of each strain grown on the Mueller-Hinton agar plate using the Raman instrument. The results show that it is possible to distinguish among the tested species using Raman spectroscopy and therefore it has a great potential for use in routine clinical diagnostics.

Raman microspectroscopy of algal lipid bodies: β-carotene quantification

Abstract: Advanced optical instruments can serve for analysis and manipulation of individual living cells and their internal structures. We have used Raman microspectroscopic analysis for assessment of β-carotene concentration in algal lipid bodies (LBs) in vivo. Some algae contain β-carotene in high amounts in their LBs, including strains which are considered useful in biotechnology for lipid and pigment production. We have devised a simple method to measure the concentration of β-carotene in a mixture of algal storage lipids from the ratio of their Raman vibrations. This finding may allow fast acquisition of β-carotene concentration valuable, e.g., for Raman microspectroscopy assisted cell sorting for selection of the overproducing strains. Furthermore, we demonstrate that β-carotene concentration can be proportional to LB volume and light intensity during the cultivation. We combine optical manipulation and analysis on a microfluidic platform in order to achieve fast, effective, and non-invasive sorting based on the spectroscopic features of the individual living cells. The resultant apparatus could find its use in demanding biotechnological applications such as selection of rare natural mutants or artificially modified cells resulting from genetic manipulations.

Candida parapsilosis Biofilm Identification by Raman Spectroscopy

Abstract: Colonies of Candida parapsilosis on culture plates were probed directly in situ using Raman spectroscopy for rapid identification of specific strains separated by a given time intervals (up to months apart). To classify the Raman spectra, data analysis was performed using the approach of principal component analysis (PCA). The analysis of the data sets generated during the scans of individual colonies reveals that despite the inhomogeneity of the biological samples unambiguous associations to individual strains (two biofilm-positive and two biofilm-negative) could be made.

Microfluidic Cultivation and Laser Tweezers Raman Spectroscopy of E. coli under Antibiotic Stress.

Abstract: Analyzing the cells in various body fluids can greatly deepen the understanding of the mechanisms governing the cellular physiology. Due to the variability of physiological and metabolic states, it is important to be able to perform such studies on individual cells. Therefore, we developed an optofluidic system in which we precisely manipulated and monitored individual cells of Escherichia coli. We tested optical micromanipulation in a microfluidic chamber chip by transferring individual bacteria into the chambers. We then subjected the cells in the chambers to antibiotic cefotaxime and we observed the changes by using time-lapse microscopy. Separately, we used laser tweezers Raman spectroscopy (LTRS) in a different micro-chamber chip to manipulate and analyze individual cefotaxime-treated E. coli cells. Additionally, we performed conventional Raman micro-spectroscopic measurements of E. coli cells in a micro-chamber. We found observable changes in the cellular morphology (cell elongation) and in Raman spectra, which were consistent with other recently published observations. The principal component analysis (PCA) of Raman data distinguished between the cefotaxime treated cells and control. We tested the capabilities of the optofluidic system and found it to be a reliable and versatile solution for this class of microbiological experiments.

Laser-induced breakdown spectroscopy.

Abstract: ■ CONTENTS General Information: Books, Reviews, and Conferences 640 Fundamentals 641 Interaction of Laser Beam with Matter 641 Factors Affecting Laser Ablation and LaserInduced Plasma Formation 642 Influence of Target on the Laser-Induced Plasmas 642 Influence of Laser Parameters on the LaserInduced Plasmas 643 Laser Wavelength (λ) 643 Laser Pulse Duration (τ) 643 Laser Pulse Energy (E) 645 Influence of Ambient Gas on the Laser-Induced Plasmas 645 LIBS Methods 647 Double Pulse LIBS 647 Femtosecond LIBS 651 Resonant LIBS 652 Ranging Approaches 652 Applications 654 Surface Inspection, Depth Profiling, and LIBS Imaging 654 Cultural Heritage 654 Industrial Analysis 655 Environmental Monitoring 656 Biomedical and Pharmaceutical Analysis 658 Security and Forensics 659 Analysis of Liquids and Submerged Solids 660 Space Exploration and Isotopic Analysis 662 Space Exploration 662 Isotopic Analysis 662 Conclusions and Future Outlook 663 Author Information 664 Corresponding Author 664 Notes 664 Biographies 664 Acknowledgments 664 References 664

Surface-enhanced Raman spectroscopy: benefits, trade-offs and future developments

Abstract: Surface-enhanced Raman spectroscopy (SERS) is a vibrational spectroscopy technique with sensitivity down to the single molecule level that provides fine molecular fingerprints, allowing for direct identification of target analytes. Extensive theoretical and experimental research, together with continuous development of nanotechnology, has significantly broadened the scope of SERS and made it a hot research field in chemistry, physics, materials, biomedicine, and so on. However, SERS has not been developed into a routine analytical technique, and continuous efforts have been made to address the problems preventing its real-world application. The present minireview focuses on analyzing current and potential strategies to tackle problems and realize the SERS performance necessary for translation to practical applications.

Deep learning and artificial intelligence methods for Raman and surface-enhanced Raman scattering

Abstract: Machine learning is shaping up our lives in many ways. In analytical sciences, machine learning provides an unprecedented opportunity to extract information from complex or big datasets in chromatography, mass spectrometry, NMR, and spectroscopy, among others. This is especially the case in Raman and surface-enhanced Raman scattering (SERS) techniques where vibrational spectra of complex chemical mixtures are acquired as large datasets for the analysis or imaging of chemical systems. The classical linear methods of processing the information no longer suffice and thus machine learning methods for extracting the chemical information from Raman and SERS experiments have been implemented recently. In this review, we will provide a brief overview of the most common machine learning techniques employed in Raman, a guideline for new users to implement machine learning in their data analysis process, and an overview of modern applications of machine learning in Raman and SERS.

Raman spectroscopy: techniques and applications in the life sciences

Abstract: Raman spectroscopy is an increasingly popular technique in many areas including biology and medicine. It is based on Raman scattering, a phenomenon in which incident photons lose or gain energy via interactions with vibrating molecules in a sample. These energy shifts can be used to obtain information regarding molecular composition of the sample with very high accuracy. Applications of Raman spectroscopy in the life sciences have included quantification of biomolecules, hyperspectral molecular imaging of cells and tissue, medical diagnosis, and others. This review briefly presents the physical origin of Raman scattering explaining the key classical and quantum mechanical concepts. Variations of the Raman effect will also be considered, including resonance, coherent, and enhanced Raman scattering. We discuss the molecular origins of prominent bands often found in the Raman spectra of biological samples. Finally, we examine several variations of Raman spectroscopy techniques in practice, looking at their applications, strengths, and challenges. This review is intended to be a starting resource for scientists new to Raman spectroscopy, providing theoretical background and practical examples as the foundation for further study and exploration.