@article {4129, title = {Assembly for semi-correlation analysis of samples using cryogenic scanning electron microscopy and cryogenic Raman micro-spectroscopy}, journal = {MEASUREMENT SCIENCE AND TECHNOLOGY}, volume = {36}, year = {2025}, month = {MAY 31}, pages = {055903}, issn = {0957-0233}, doi = {10.1088/1361-6501/adc94a} } @conference {4126, title = {Preparation and pilot experiments on microfluidic chip with surface acoustic waves}, booktitle = {23rd Slovak-Czech-Polish Optical Conference on Wave and Quantum Aspects of Contemporary Optics}, year = {2025}, publisher = {International Society for Optics and Photonics}, organization = {International Society for Optics and Photonics}, doi = {10.1117/12.3056740}, url = {https://doi.org/10.1117/12.3056740} } @article {4130, title = {Surface-Enhanced Raman Spectroscopy for Adenine Detection in Five Selected Bacterial Strains Under Stress Conditions}, journal = {SENSORS}, volume = {25}, year = {2025}, month = {JUL 26}, pages = {4629}, doi = {10.3390/s25154629} } @article {3991, title = {MicrobioRaman: an open-access web repository for microbiological Raman spectroscopy data}, journal = {NATURE MICROBIOLOGY}, volume = {9}, year = {2024}, month = {MAY}, issn = {2058-5276}, doi = {10.1038/s41564-024-01656-3} } @article {3992, title = {Microplastics in animal nutrition: Occurrence, spread, and hazard in animals}, journal = {JOURNAL OF AGRICULTURE AND FOOD RESEARCH}, volume = {17}, year = {2024}, month = {SEP}, pages = {101258}, issn = {2666-1543}, doi = {10.1016/j.jafr.2024.101258} } @article {3773, title = {Identification of staphyloxanthin and derivates in yellow-pigmented Staphylococcus capitis subsp. capitis}, journal = {Frontiers in Microbiology}, volume = {14}, year = {2023}, doi = {10.3389/fmicb.2023.1272734}, url = {https://www.frontiersin.org/articles/10.3389/fmicb.2023.1272734} } @article {3728, title = {SERS-Tags: Selective Immobilization and Detection of Bacteria by Strain-Specific Antibodies and Surface-Enhanced Raman Scattering}, journal = {Biosensors}, volume = {13}, year = {2023}, pages = {182}, issn = {2079-6374}, doi = {10.3390/bios13020182}, url = {https://www.mdpi.com/2079-6374/13/2/182} } @article {3575, title = {Raman Spectroscopy-A Novel Method for Identification and Characterization of Microbes on a Single-Cell Level in Clinical Settings}, journal = {FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY}, volume = {12}, year = {2022}, month = {APR 22}, pages = {866463}, issn = {2235-2988}, doi = {10.3389/fcimb.2022.866463} } @article {3459, title = {The potential of SERS as an AST methodology in clinical settings}, journal = {NANOPHOTONICS}, volume = {10}, year = {2021}, month = {AUG}, pages = {2537-2561}, issn = {2192-8606}, doi = {10.1515/nanoph-2021-0095} } @article {3417, title = {Raman Microspectroscopic Analysis of Selenium Bioaccumulation by Green Alga Chlorella vulgaris}, journal = {Biosensors}, volume = {11}, year = {2021}, pages = {115}, issn = {2079-6374}, doi = {10.3390/bios11040115}, url = {https://www.mdpi.com/2079-6374/11/4/115} } @article {3460, title = {The Use of Raman Spectroscopy to Monitor Metabolic Changes in Stressed Metschnikowia sp. Yeasts}, journal = {Microorganisms}, volume = {9}, year = {2021}, pages = {277}, abstract = {

Raman spectroscopy is a universal method designed for the analysis of a wide range of physical, chemical and biological systems or various surfaces. This technique is suitable to monitor various components of cells, tissues or microorganisms. The advantages include very fast non-contact and non-destructive analysis and no or minimal need for sample treatment. The yeasts Metschnikowia can be considered as industrially usable producers of pulcherrimin or single-cell lipids, depending on cultivation conditions and external stress. In the present study, Raman spectroscopy was used as an effective tool to identify both pulcherrimin and lipids in single yeast cells. The analysis of pulcherrimin is very demanding; so far, there is no optimal procedure to analyze or identify this pigment. Based on results, the strong dependence of pulcherrimin production on the ferric ion concentration was found with the highest yield in media containing 0.1 g/L iron. Further, production of lipids in Metschnikowia cells was studied at different temperatures and C:N ratios, using Raman spectroscopy to follow fatty acids composition, under different regimes, by monitoring the iodine number. The results of Raman spectroscopy were comparable with the fatty acid analysis obtained by gas chromatography. This study therefore supported use of Raman spectroscopy for biotechnological applications as a simple tool in the identification and analysis both the pulcherrimin and microbial lipids. This method provides a quick and relatively accurate estimation of targeted metabolites with minimal sample modification and allows to monitor metabolic changes over time of cultivation.

}, issn = {2076-2607}, doi = {10.3390/microorganisms9020277}, url = {https://www.mdpi.com/2076-2607/9/2/277} } @article {3482, title = {Use of Waste Substrates for the Lipid Production by Yeasts of the Genus Metschnikowia{\textemdash}Screening Study}, journal = {Microorganisms}, volume = {9}, year = {2021}, pages = {2295}, abstract = {

Oleogenic yeasts are characterized by the ability to accumulate increased amounts of lipids under certain conditions. These microbial lipids differ in their fatty acid composition, which allows them to be widely used in the biotechnology industry. The interest of biotechnologists is closely linked to the rising prices of fossil fuels in recent years. Their negative environmental impact is caused by significantly increased demand for biodiesel. The composition of microbial lipids is very similar to vegetable oils, which provides great potential for use in the production of biodiesel. In addition, some oleogenic microorganisms are capable of producing lipids with a high proportion of unsaturated fatty acids. The presented paper{\textquoteright}s main aim was to study the production of lipids and lipid substances by yeasts of the genus Metschnikowia, to cultivate crude waste animal fat to study its utilization by yeasts, and to apply the idea of circular economy in the biotechnology of Metschnikowia yeasts. The work focuses on the influence of various stress factors in the cultivation process, such as reduced temperature or nutritional stress through the use of various waste substrates, together with manipulating the ratio of carbon and nitrogen sources in the medium. Yeast production properties were monitored by several instrumental techniques, including gas chromatography and Raman spectroscopy. The amount of lipids and in particular the fatty acid composition varied depending on the strains studied and the culture conditions used. The ability of yeast to produce significant amounts of unsaturated fatty acids was also demonstrated in the work. The most suitable substrate for lipid production was a medium containing glycerol, where the amount of accumulated lipids in the yeast M. pulcherrima 1232 was up to 36\%. In our work, the crude animal fat was used for the production of high-value lipids, which to the best of our knowledge is a new result. Moreover, quantitative screening of lipase enzyme activity cultivated on animal fat substrate on selected yeasts of the genus Metschnikowia was performed. We found that for the yeast utilizing glycerol, animal fat seems to be an excellent source of carbon. Therefore, the yeast conversion of crude processed animal fat to value-added products is a valuable process for the biotechnology and food industry.

}, issn = {2076-2607}, doi = {10.3390/microorganisms9112295}, url = {https://www.mdpi.com/2076-2607/9/11/2295} } @article {3189, title = {Identification of ability to form biofilm in Candida parapsilosis and Staphylococcus epidermidis by Raman spectroscopy}, journal = {Future Microbiology}, volume = {14}, year = {2019}, pages = {509-517}, abstract = {

Aim: Finding rapid, reliable diagnostic methods is a big challenge in clinical microbiology. Raman spectroscopy is an optical method used for multiple applications in scientific fields including microbiology. This work reports its potential in identifying biofilm positive strains of Candida parapsilosis and Staphylococcus epidermidis. Materials \& methods: We tested 54 S. epidermidis strains (23 biofilm positive, 31 negative) and 51 C. parapsilosis strains (27 biofilm positive, 24 negative) from colonies on Mueller-Hinton agar plates, using Raman spectroscopy. Results: The accuracy was 98.9\% for C. parapsilosis and 96.1\% for S. epidermidis. Conclusion: The method showed great potential for identifying biofilm positive bacterial and yeast strains. We suggest that Raman spectroscopy might become a useful aid in clinical diagnostics.

}, doi = {10.2217/fmb-2018-0297}, url = {https://doi.org/10.2217/fmb-2018-0297} } @article {3104, title = {Wavelength-Dependent Optical Force Aggregation of Gold Nanorods for SERS in a Microfluidic Chip}, journal = {J. Phys. Chem. C}, volume = {123}, year = {2019}, pages = {5608-5615}, doi = {10.1021/acs.jpcc.8b12493} } @article { SedlacekAMB19, title = {What keeps polyhydroxyalkanoates in bacterial cells amorphous? A derivation from stress exposure experiments}, journal = {Appl. Microbiol. Biotech.}, volume = {103}, number = {4}, year = {2019}, pages = {1905-1917}, doi = {10.1007/s00253-018-09584-z} } @article { ProchazkaSAB18, title = {Combination of laser-induced breakdown spectroscopy and Raman spectroscopy for multivariate classification of bacteria}, journal = {Spec. Acta Part B}, volume = {139}, year = {2018}, pages = {6-12}, doi = {10.1016/j.sab.2017.11.004} } @article { PilatSENS18SERS, title = {Detection of chloroalkanes by surface-enhanced raman spectroscopy in microfluidic chips}, journal = {Sensors}, volume = {18}, year = {2018}, pages = {3212}, doi = {10.3390/s18103212} } @article { PilatSENS18Ecoli, title = {Microfluidic Cultivation and Laser Tweezers Raman Spectroscopy of E-coli under Antibiotic Stress}, journal = {Sensors}, volume = {18}, year = {2018}, pages = {1623}, doi = {10.3390/s18051623} } @article { HrubanovaSENS18, title = {Monitoring Candida parapsilosis and Staphylococcus epidermidis Biofilms by a Combination of Scanning Electron Microscopy and Raman Spectroscopy}, journal = {Sensors}, volume = {18}, number = {12}, year = {2018}, pages = {4089}, doi = {10.3390/s18124089} } @article {RebrosovsaFB17, title = {Differentiation between Staphylococcus aureus and Staphylococcus epidermidis strains using Raman spectroscopy}, journal = {Future Microbiology}, volume = {12}, year = {2017}, pages = {10}, doi = {10.2217/fmb-2016-0224} } @article {HrubanovaMM17, title = {Morphological and Production Changes in Planktonic and Biofilm Cells Monitored Using SEM and Raman Spectroscopy}, journal = {Microscopy and Microanalysis}, volume = {23}, year = {2017}, pages = {S1}, doi = {10.1017/S1431927617006456} } @article {ObrucaNB17, title = {The presence of PHB granules in cytoplasm protects non-halophilic bacterial cells against the harmful impact of hypertonic environments}, journal = {New Biotechnol.}, volume = {39}, year = {2017}, pages = {10}, doi = {10.1016/j.nbt.2017.07.008} } @article {RebrosovaSR17, title = {Rapid identification of staphylococci by Raman spectroscopy}, journal = {Sci. Rep.}, volume = {7}, year = {2017}, pages = {14846}, doi = {10.1038/s41598-017-13940-w} } @article { MravecFEMSML16, title = {Accumulation of PHA granules in Cupriavidus necator as seen by confocal fluorescence microscopy}, journal = {FEMS Microbiology Letters}, volume = {363}, year = {2016}, pages = {10}, doi = {10.1093/femsle/fnw094} } @article { ObrucaPLOSONE16, title = {Accumulation of Poly(3-hydroxybutyrate) Helps Bacterial Cells to Survive Freezing}, journal = {PLoS ONE}, volume = {11}, year = {2016}, pages = {e0157778}, doi = {10.1371/journal.pone.0157778} } @article { ObrucaAMB16, title = {Evaluation of 3-hydroxybutyrate as an enzyme-protective agent against heating and oxidative damage and its potential role in stress response of poly(3-hydroxybutyrate) accumulating cells}, journal = {Appl Microbiol Biotechnol}, volume = {100}, year = {2016}, pages = {1365-1376}, doi = {10.1007/s00253-015-7162-4} } @article { HrubanovaMM16, title = {Morphological and Production Changes in Stressed Red Yeasts Monitored Using SEM and Raman Spectroscopy}, journal = {Microscopy and Microanalysis}, volume = {22}, year = {2016}, pages = {S3}, doi = {10.1017/S1431927616006577} } @article {SamekSENS16, title = {Quantitative Raman Spectroscopy Analysis of Polyhydroxyalkanoates Produced by Cupriavidus necator H16}, journal = {Sensors}, volume = {16}, year = {2016}, pages = {1808}, doi = {10.3390/s16111808} } @article { KrzyzanekMM15, title = {Cryo-SEM and Raman Spectroscopy Study of the Involvement of Polyhydroxyalkanoates in Stress Response of Bacteria}, journal = {Microscopy and Microanalysis}, volume = {21}, number = {S3}, year = {2015}, pages = {183-184}, doi = {10.1017/S1431927615001713} } @article { SamekJBO15, title = {Identification of individual biofilm-forming bacterial cells using Raman tweezers}, journal = {J. Biomed. Opt.}, volume = {20}, number = {5}, year = {2015}, doi = {10.1117/1.JBO.20.5.051038} } @article { MlynarikovaSENS15, title = {Influence of Culture Media on Microbial Fingerprints Using Raman Spectroscopy}, journal = {Sensors}, volume = {15}, year = {2015}, pages = {29635-29647}, doi = {10.3390/s151129635} } @article { HrubanovaMM15, title = {Monitoring of Multilayered Bacterial Biofilm Morphology by Cryo-SEM for Raman Spectroscopy Measurements}, journal = {Microscopy and Microanalysis}, volume = {21}, year = {2015}, pages = {187-188}, doi = {10.1017/S1431927615001737} } @article { BurdikovaDS15, title = {SEM and Raman Spectroscopy Applied to Biomass Analysis for Application in the Field of Biofuels and Food Industry}, journal = {Dairy Sci. Technol.}, volume = {95}, year = {2015}, pages = {687-700}, doi = {10.1007/s13594-015-0253-2} } @article { SamekMM15, title = {SEM and Raman Spectroscopy Applied to Biomass Analysis for Application in the Field of Biofuels and Food Industry}, journal = {Microscopy and Microanalysis}, volume = {21}, year = {2015}, pages = {1775-1776}, doi = {10.1017/S1431927615009654} } @article {PorizkaSENS14, title = {Algal Biomass Analysis by Laser-Based Analytical Techniques{\textemdash}A Review}, journal = {Sensors}, volume = {14}, year = {2014}, pages = {17725-17752}, doi = {10.3390/s140917725} } @article { SamekIJMC14, title = {Candida parapsilosis Biofilm Identification by Raman Spectroscopy}, journal = {Int. J. Mol. Sci.}, volume = {15}, year = {2014}, pages = {23924-23935}, doi = {10.3390/ijms151223924} } @article { BernatovaMol13, title = {Following the mechanisms of bacteriostatic versus bacericidal action using Raman spectroscopy}, journal = {Molecules}, volume = {18}, year = {2013}, pages = {13188-13199}, doi = {10.3390/molecules181113188} } @article {PorizkaSAB12, title = {Application of laser-induced breakdown spectroscopy to the analysis of algal biomass for industrial biotechnology}, journal = {Spectrochim. Acta B}, volume = {74-75}, year = {2012}, pages = {169-176}, doi = {10.1016/j.sab.2012.06.014} } @article { PilatJAP2012, title = {Raman microspectroscopy of algal lipid bodies: beta-carotene quantification}, journal = {J. Appl. Phycol.}, volume = {24}, year = {2012}, pages = {541-546}, doi = {10.1007/s10811-011-9754-4} } @article { SamekLPL11, title = {Characterization of oil-producing microalgae using Raman spectroscopy}, journal = {Laser Phys. Lett.}, volume = {8}, year = {2011}, pages = {701{\textendash}709}, doi = {10.1002/lapl.201110060} } @article { SamekLPL10, title = {The potential of Raman spectroscopy for the identification of biofilm formation by Staphylococcus epidermidis}, journal = {Laser Phys. Lett.}, volume = {7}, year = {2010}, pages = {378{\textendash}383}, type = {Article}, doi = {10.1002/lapl.200910154} } @article { Samek2010, title = {Raman Microspectroscopy of Individual Algal Cells: Sensing Unsaturation of Storage Lipids in vivo}, journal = {Sensors}, volume = {10}, year = {2010}, pages = {8635{\textendash}8651}, doi = {10.3390/s100908635} }