@article {3787,
	title = {Physiological and transcriptome profiling of Chlorella sorokiniana: A study on azo dye wastewater decolorization},
	journal = {Journal of Hazardous Materials},
	volume = {460},
	year = {2023},
	pages = {132450},
	abstract = {<p>Over decades, synthetic dyes have become increasingly dominated by azo dyes posing a significant environmental risk due to their toxicity. Microalgae-based systems may offer an alternative for treatment of azo dye effluents to conventional physical-chemical methods. Here, microalgae were tested to decolorize industrial azo dye wastewater (ADW). Chlorella sorokiniana showed the highest decolorization efficiency in a preliminary screening test. Subsequently, the optimization of the experimental design resulted in 70\% decolorization in a photobioreactor. Tolerance of this strain was evidenced using multiple approaches (growth and chlorophyll content assays, scanning electron microscopy (SEM), and antioxidant level measurements). Raman microspectroscopy was employed for the quantification of ADW-specific compounds accumulated by the microalgal biomass. Finally, RNA-seq revealed the transcriptome profile of C. sorokiniana exposed to ADW for 72\&nbsp;h. Activated DNA repair and primary metabolism provided sufficient energy for microalgal growth to overcome the adverse toxic conditions. Furthermore, several transporter genes, oxidoreductases-, and glycosyltransferases-encoding genes were upregulated to effectively sequestrate and detoxify the ADW. This work demonstrates the potential utilization of C. sorokiniana as a tolerant strain for industrial wastewater treatment, emphasizing the regulation of its molecular mechanisms to cope with unfavorable growth conditions.</p>},
	keywords = {BF, MF},
	issn = {0304-3894},
	doi = {https://doi.org/10.1016/j.jhazmat.2023.132450},
	url = {https://www.sciencedirect.com/science/article/pii/S0304389423017338},
	author = {Vladimira Tarbajova and Martina Kolackova and Pavel Chaloupsky and Marketa Dobesova and Petr Capal and Zdenek Pilat and Ota Samek and Pavel Zem{\'a}nek and Pavel Svec and Dagmar Skopalova Sterbova and Marketa Vaculovicova and Lukas Richtera and Alfredo P{\'e}rez-de-Mora and Vojtech Adam and Dalibor Huska}
}
@article {3729,
	title = {Rapid Identification of Pathogens Causing Bloodstream Infections by Raman Spectroscopy and Raman Tweezers},
	journal = {Microbiology Spectrum},
	volume = {11},
	year = {2023},
	pages = {e00028-23},
	keywords = {BF, MF},
	doi = {10.1128/spectrum.00028-23},
	url = {https://journals.asm.org/doi/abs/10.1128/spectrum.00028-23},
	author = {Katar{\'\i}na Rebro{\v s}ov{\'a} and Silvie Bernatov{\'a} and Martin {\v S}iler and Jan Ma{\v s}ek and Ota Samek and Jan Je{\v z}ek and Martin Kizovsk{\'y} and Veronika Hol{\'a} and Pavel Zem{\'a}nek and Filip R{\r u}{\v z}i{\v c}ka}
}
@article {3796,
	title = {Rapid identification of pathogens in blood serum via Raman tweezers in combination with advanced processing methods},
	journal = {Biomed. Opt. Express},
	volume = {14},
	year = {2023},
	month = {Dec},
	pages = {6410{\textendash}6421},
	keywords = {AIF, BF, LF, MF},
	doi = {10.1364/BOE.503628},
	url = {https://opg.optica.org/boe/abstract.cfm?URI=boe-14-12-6410},
	author = {Ond{\v r}ej Vacul{\'\i}k and Silvie Bernatov{\'a} and Katar{\'\i}na Rebro{\v s}ov{\'a} and Ota Samek and Luk{\'a}{\v s} {\v S}ilhan and Filip R{\r u} {\v z}i{\v c}ka and Mojm{\'\i}r {\v S}er{\'y} and Martin {\v S}iler and Jan Je{\v z} ek and Pavel Zem{\'a}nek}
}
@article {3504,
	title = {Raman spectroscopy{\textemdash}a tool for rapid differentiation among microbes causing urinary tract infections},
	journal = {Analytica Chimica Acta},
	volume = {1191},
	year = {2022},
	pages = {339292},
	keywords = {BF, KF, MF},
	issn = {0003-2670},
	doi = {https://doi.org/10.1016/j.aca.2021.339292},
	url = {https://www.sciencedirect.com/science/article/pii/S0003267021011181},
	author = {Katar{\'\i}na Rebro{\v s}ov{\'a} and Silvie Bernatov{\'a} and Martin {\v S}iler and Magdalena Uhlirova and Ota Samek and Jan Je{\v z}ek and Veronika Hol{\'a} and Filip R{\r u}{\v z}i{\v c}ka and Pavel Zem{\'a}nek}
}
@article { PilatSENS18SERS,
	title = {Detection of chloroalkanes by surface-enhanced raman spectroscopy in microfluidic chips},
	journal = {Sensors},
	volume = {18},
	year = {2018},
	pages = {3212},
	keywords = {BF, MF},
	doi = {10.3390/s18103212},
	author = {Z. Pil{\'a}t and Kizovsk{\'y}, M. and J Je{\v z}ek and Kr{\'a}tk{\'y}, S. and Sobota, J. and M {\v S}iler and O. Samek and Bury{\v s}ka, T. and Va{\v n}{\'a}{\v c}ek, P. and Damborsk{\'y}, J. and Prokop, Z. and P. Zem{\'a}nek}
}
@article { PilatSENS18Ecoli,
	title = {Microfluidic Cultivation and Laser Tweezers Raman Spectroscopy of E-coli under Antibiotic Stress},
	journal = {Sensors},
	volume = {18},
	year = {2018},
	pages = {1623},
	keywords = {BF, MF},
	doi = {10.3390/s18051623},
	author = {Z. Pil{\'a}t and Silva Bernatov{\'a} and J Je{\v z}ek and Kirchhoff, J. and Tannert, A. and Neugebauer, U. and O. Samek and P. Zem{\'a}nek}
}
@article {RebrosovsaFB17,
	title = {Differentiation between Staphylococcus aureus and Staphylococcus epidermidis strains using Raman spectroscopy},
	journal = {Future Microbiology},
	volume = {12},
	year = {2017},
	pages = {10},
	keywords = {BF, MF},
	doi = {10.2217/fmb-2016-0224},
	author = {K. Rebro{\v s}ov{\'a} and M {\v S}iler and O. Samek and F. R{\r u}{\v z}i{\v c}ka and Silva Bernatov{\'a} and J Je{\v z}ek and P. Zem{\'a}nek and V. Hol{\'a}}
}
@article {PilatSENS17,
	title = {Effects of Infrared Optical Trapping on Saccharomyces cerevisiae in a Microfluidic System},
	journal = {Sensors},
	volume = {17},
	year = {2017},
	pages = {2640},
	keywords = {BF, MF},
	doi = {10.3390/s17112640},
	author = {Z. Pil{\'a}t and A. Jon{\'a}{\v s} and J Je{\v z}ek and P. Zem{\'a}nek}
}
@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},
	keywords = {BF, MF},
	doi = {10.1017/S1431927617006456},
	author = {K. Hrubanov{\'a} and V. Krzy{\v z}{\'a}nek and O. Samek and R. Skoup{\'y} and M {\v S}iler and J Je{\v z}ek and S. Obru{\v c}a and P. Zem{\'a}nek}
}
@article {RebrosovaSR17,
	title = {Rapid identification of staphylococci by Raman spectroscopy},
	journal = {Sci. Rep.},
	volume = {7},
	year = {2017},
	pages = {14846},
	keywords = {BF, MF},
	doi = {10.1038/s41598-017-13940-w},
	author = {K. Rebro{\v s}ov{\'a} and M {\v S}iler and O. Samek and F. R{\r u}{\v z}i{\v c}ka and S. Bernatov{\'a} and V. Hol{\'a} and J Je{\v z}ek and P. Zem{\'a}nek and J. Sokolov{\'a} and P. Petr{\'a}{\v s}}
}
@article { JonasJOSAB17,
	title = {Thermal tuning of spectral emission from optically trapped liquid-crystal droplet resonators},
	journal = {J. Opt. Soc. Am. B},
	volume = {34},
	year = {2017},
	pages = {1855-1864},
	keywords = {BF, MF},
	doi = {10.1364/JOSAB.34.001855},
	author = {A. Jon{\'a}{\v s} and Z. Pil{\'a}t and J Je{\v z}ek and Silva Bernatov{\'a} and T. Fo{\v r}t and P. Zem{\'a}nek and Mehdi Aas and Alper Kiraz}
}
