@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}, keywords = {BF, MF}, issn = {0957-0233}, doi = {10.1088/1361-6501/adc94a}, author = {Laznicka, Tomas and Kizovsk{\'y}, Martin and Hrubanov{\'a}, Kamila and Je{\v z}ek, Jan and Mrazova, Katerina and Obru{\v c}a, Stanislav and Samek, Ota and Krzy{\v z}{\'a}nek, Vladislav} } @inbook {4132, title = {Chapter 26 - Hyphenated Raman and laser spectroscopy for the characterization of microplastics in tissues}, booktitle = {Applied Raman Spectroscopy}, year = {2025}, pages = {441-451}, publisher = {Elsevier}, organization = {Elsevier}, abstract = {

This chapter is dedicated to the possibility of combining Raman spectroscopy with other spectroscopic methods, namely laser-induced breakdown spectroscopy (LIBS) in the detection and characterization of microplastics embedded in tissues of selected model organisms. The idea is to take advantage of the complementarity of the two methods, which originates in the way of laser-tissue interaction that both techniques utilize for sample analysis. Their joint use yields complete chemical information, that is, Raman spectroscopy provides molecular information, whereas LIBS provides atomic information as is well-described in the literature. Ultimately, the tandem LIBS{\textendash}Raman analysis can be done from the same spot of the sample. Moreover, these two methods need very similar components and thus can share the majority of the laboratory setup. The chapter gives an overview of hyphenated Raman and LIBS systems, advancements in this field, and options for data processing of joint Raman and LIBS analyses. Data fusion of Raman spectroscopy and LIBS is also discussed. Special attention will be given to the detection and characterization of microplastics using Raman and LIBS systems, as microplastic pollution has attracted considerable attention in recent years, with news of microplastic detection in recent areas and also in human bodies resonating publicly. Raman spectroscopy may be utilized in the detection of microplastics and recent works support this. With the help of LIBS, which can elucidate further the potential risks of weathered microplastics, the hyphenated approach may be the way forward for in situ detection and characterization of microplastics.

}, keywords = {BF, MF}, isbn = {978-0-443-21834-7}, doi = {https://doi.org/10.1016/B978-0-443-21834-7.00026-8}, url = {https://www.sciencedirect.com/science/article/pii/B9780443218347000268}, author = {Pavel Po{\v r}{\'\i}zka and Daniel Holub and Martin Kizovsk{\'y} and Ota Samek and Jozef Kaiser and Gabriela Kal{\v c}{\'\i}kov{\'a}}, editor = {Vivek Kumar Singh} } @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}, keywords = {BF, MF}, doi = {10.3390/s25154629}, author = {Ghazalova, Mona and Modlitbova, Pavlina and Samek, Ota and Rebro{\v s}ov{\'a}, Katar{\'\i}na and {\v S}iler, Martin and Je{\v z}ek, Jan and Pil{\'a}t, Zden{\v e}k} } @article {3864, title = {Biomedical Optics Express Feature Issue Introduction: Optical Manipulation and Its Applications (OMA) 2023}, journal = {BIOMEDICAL OPTICS EXPRESS}, volume = {15}, year = {2024}, month = {FEB 1}, pages = {1192-1194}, keywords = {BF, MF}, issn = {2156-7085}, doi = {10.1364/BOE.519305}, author = {Jones, Philip and Bernatov{\'a}, Silvie and Kotsifaki, Domna G.} } @article {3991, title = {MicrobioRaman: an open-access web repository for microbiological Raman spectroscopy data}, journal = {NATURE MICROBIOLOGY}, volume = {9}, year = {2024}, month = {MAY}, keywords = {BF, MF}, issn = {2058-5276}, doi = {10.1038/s41564-024-01656-3}, author = {Lee, Kang Soo and Landry, Zachary and Athar, Awais and Alcolombri, Uria and Ayutthaya, Pratchaya Pramoj Na and Berry, David and de Bettignies, Philippe and Cheng, Ji-Xin and Csucs, Gabor and Cui, Li and Deckert, Volker and Dieing, Thomas and Dionne, Jennifer and Doskocil, Ondrej and D{\textquoteright}Souza, Glen and Garcia-Timermans, Cristina and Gierlinger, Notburga and Goda, Keisuke and Hatzenpichler, Roland and Henshaw, Richard J. and Huang, Wei E. and Iermak, Ievgeniia and Ivleva, Natalia P. and Kneipp, Janina and Kubryk, Patrick and Kuesel, Kirsten and Lee, Tae Kwon and Lee, Sung Sik and Ma, Bo and Martinez-Perez, Clara and Matousek, Pavel and Meckenstock, Rainer U. and Min, Wei and Mojzes, Peter and Mueller, Oliver and Kumar, Naresh and Nielsen, Per Halkjaer and Notingher, Ioan and Palatinszky, Marton and Pereira, Fatima C. and Pezzotti, Giuseppe and Pil{\'a}t, Zden{\v e}k and Plesinger, Filip and Popp, Juergen and Probst, Alexander J. and Riva, Alessandra and Saleh, Amr. A. E. and Samek, Ota and Sapers, Haley M. and Schubert, Olga T. and Stubbusch, Astrid K. M. and Tadesse, Loza F. and Taylor, Gordon T. and Wagner, Michael and Wang, Jing and Yin, Huabing and Yue, Yang and Zenobi, Renato and Zini, Jacopo and Sarkans, Ugis and Stocker, Roman} } @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}, keywords = {BF, MF}, issn = {2666-1543}, doi = {10.1016/j.jafr.2024.101258}, author = {Khan, Aamir and Qadeer, Abdul and Wajid, Abdul and Ullah, Qudrat and Rahman, Sajid Ur and Ullah, Kaleem and Safi, Sher Zaman and Ticha, Lenka and Skalickova, Sylvie and Chilala, Pompido and Bernatov{\'a}, Silvie and Samek, Ota and Horky, Pavel} } @article {3989, title = {Raman microspectroscopy and laser-induced breakdown spectroscopy for the analysis of polyethylene microplastics in human soft tissues}, journal = {Heliyon}, volume = {10}, year = {2024}, pages = {e37844}, abstract = {

People are exposed to microplastics (MPs) on a large scale in everyday life. However, it is not clear whether MPs can also be distributed and retained in certain tissues. Therefore, the development of analytical methods capable of detecting MPs in specific human organs/tissues is of utmost importance. In this study, the use and combination of spectroscopic techniques, namely Raman microspectroscopy and laser-induced breakdown spectroscopy (LIBS), was tested for the detection of polyethylene (PE) MPs in human tonsils. Preliminary results showed that Raman microspectroscopy was able to detect MPs down to 1\ μm in size and LIBS down to 10\ μm. In the next step, human tonsils were spiked with PE MPs, and digested. The filtered particles were analyzed using Raman microspectroscopy and LIBS, and complemented by X-ray fluorescence (XRF). The results showed that Raman microspectroscopy could reliably detect PE MPs in spiked human tonsils, while LIBS and XRF served as a reference analytical method to characterize particles that could not be classified by Raman microspectroscopy for their non-organic origin. The results of this study, supported by a current feasibility study conducted on clinical samples, demonstrated the reliability and feasibility of this approach for monitoring MPs in biotic samples.

}, keywords = {BF, MF}, issn = {2405-8440}, doi = {https://doi.org/10.1016/j.heliyon.2024.e37844}, url = {https://www.sciencedirect.com/science/article/pii/S2405844024138753}, author = {Vikt{\'o}ria Parobkov{\'a} and Daniel Holub and Martin Kizovsk{\'y} and Gabriela Kal{\v c}{\'\i}kov{\'a} and Ula Rozman and Milan Ur{\'\i}k and Karel Novotn{\'y} and Ota Samek and Tom{\'a}{\v s} Zikmund and Pavel Po{\v r}{\'\i}zka and Jozef Kaiser} } @article {3865, title = {Unraveling the ecotoxicological effects of micro and nano-plastics on aquatic organisms and human health}, journal = {Frontiers in Environmental Science}, volume = {12}, year = {2024}, abstract = {

Plastic pollution ranks among the most severe environmental disasters caused by humans, generating millions of tonnes of waste annually. The extensive and unregulated use of plastics has led to ecotoxicity and environmental imbalance. Microplastics (MPs) are prevalent in aquatic environments, and these MPs further degrade into even smaller particles known as nano-plastics (NPs). Both MPs and NPs impact the environment by readily absorbing organic pollutants and pathogens from their surroundings, owing to their bigger surface area to volume ratio. This review focuses on the source of origin, bioaccumulation, and potential impact of MPs and NPs on aquatic organisms and human health. Additionally, the review explores various methods employed for identification and quantification of these particles in aquatic ecosystems. Sufficient information is available on their characteristics, distributions, and effects on marine ecosystems compared with freshwater ecosystems. For plastic particles \<10\ μm, more toxicological effects were observed compared with larger size particles, in aquatic life. Understanding the mechanism of action and ecotoxicological effects of micro/nano-plastics on the health of aquatic life across various trophic levels, as well as human health, is of utmost importance. We address knowledge gaps and provide insights into future research approaches for a better understanding of the interactive mechanisms between binary pollutants.

}, keywords = {BF, MF}, issn = {2296-665X}, doi = {10.3389/fenvs.2024.1390510}, url = {https://www.frontiersin.org/articles/10.3389/fenvs.2024.1390510}, author = {Naz, Saima and Chatha, Ahmad Manan Mustafa and Khan, Nisar Ahmed and Ullah, Qudrat and Zaman, Faisal and Qadeer, Abdul and Khan, Ibrar Muhammad and Danabas, Durali and Kiran, Azka and Skalickova, Sylvie and Bernatov{\'a}, Silvie and Khan, Muhammad Zahoor and Horky, Pavel} } @article {3737, title = {Aspergillus niger as a cell factory for the production of pyomelanin, a molecule with UV-C radiation shielding activity}, journal = {Frontiers in Microbiology}, volume = {14}, year = {2023}, keywords = {BF, MF}, issn = {1664-302X}, doi = {10.3389/fmicb.2023.1233740}, url = {https://www.frontiersin.org/articles/10.3389/fmicb.2023.1233740}, author = {Koch, Stella Marie and Freidank-Pohl, Carsten and Siontas, Oliver and Cortesao, Marta and Mota, Afonso and Runzheimer, Katharina and Jung, Sascha and Rebro{\v s}ov{\'a}, Katar{\'\i}na and {\v S}iler, Martin and Moeller, Ralf and Meyer, Vera} } @article {3773, title = {Identification of staphyloxanthin and derivates in yellow-pigmented Staphylococcus capitis subsp. capitis}, journal = {Frontiers in Microbiology}, volume = {14}, year = {2023}, keywords = {BF, MF}, doi = {10.3389/fmicb.2023.1272734}, url = {https://www.frontiersin.org/articles/10.3389/fmicb.2023.1272734}, author = {Siems, Katharina and Runzheimer, Katharina and Rebro{\v s}ov{\'a}, Katar{\'\i}na and Etzbach, Lara and Auerhammer, Alina and Rehm, Anna and Schwengers, Oliver and {\v S}iler, Martin and Samek, Ota and R{\r u}{\v z}i{\v c}ka, Filip and Moeller, Ralf} } @article {3632, title = {Laser-based techniques: Novel tools for the identification and characterization of aged microplastics with developed biofilm}, journal = {Chemosphere}, volume = {313}, year = {2023}, pages = {137373}, abstract = {

Microplastics found in the environment are often covered with a biofilm, which makes their analysis difficult. Therefore, the biofilm is usually removed before analysis, which may affect the microplastic particles or lead to their loss during the procedure. In this work, we used laser-based analytical techniques and evaluated their performance in detecting, characterizing, and classifying pristine and aged microplastics with a developed biofilm. Five types of microplastics from different polymers were selected (polyamide, polyethylene, polyethylene terephthalate, polypropylene, and polyvinyl chloride) and aged under controlled conditions in freshwater and wastewater. The development of biofilm and the changes in the properties of the microplastic were evaluated. The pristine and aged microplastics were characterized by standard methods (e.g., optical and scanning electron microscopy, and Raman spectroscopy), and then laser-induced breakdown spectroscopy (LIBS) and laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) were used. The results show that LIBS could identify different types of plastics regardless of the ageing and major biotic elements of the biofilm layer. LA-ICP-MS showed a high sensitivity to metals, which can be used as markers for various plastics. In addition, LA-ICP-MS can be employed in studies to monitor the adsorption and desorption (leaching) of metals during the ageing of microplastics. The use of these laser-based analytical techniques was found to be beneficial in the study of environmentally relevant microplastics.

}, keywords = {BF, MF}, issn = {0045-6535}, doi = {https://doi.org/10.1016/j.chemosphere.2022.137373}, url = {https://www.sciencedirect.com/science/article/pii/S0045653522038668}, author = {Pavel Po{\v r}{\'\i}zka and Lukas Brunnbauer and Michaela Porkert and Ula Rozman and Gregor Marolt and Daniel Holub and Martin Kizovsk{\'y} and Mark{\'e}ta Bene{\v s}ov{\'a} and Ota Samek and Andreas Limbeck and Jozef Kaiser and Gabriela Kal{\v c}{\'\i}kov{\'a}} } @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 = {

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\ 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.

}, 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 {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}, keywords = {BF, MF}, issn = {2079-6374}, doi = {10.3390/bios13020182}, url = {https://www.mdpi.com/2079-6374/13/2/182}, author = {Bene{\v s}ov{\'a}, Mark{\'e}ta and Bernatov{\'a}, Silvie and Mika, Filip and Pokorn{\'a}, Zuzana and Je{\v z}ek, Jan and {\v S}iler, Martin and Samek, Ota and R{\r u}{\v z}i{\v c}ka, Filip and Rebro{\v s}ov{\'a}, Katar{\'\i}na and Zem{\'a}nek, Pavel and Pil{\'a}t, Zden{\v e}k} } @article {3631, title = {Absolute frequencies of H13C14N hydrogen cyanide transitions in the 1.5-{\textmu}m region with the saturated spectroscopy and a sub-kHz scanning laser}, journal = {Opt. Lett.}, volume = {47}, year = {2022}, month = {Nov}, pages = {5704{\textendash}5707}, abstract = {

The wide span and high density of lines in its rovibrational spectrum render hydrogen cyanide a useful spectroscopic media for referencing absolute frequencies of lasers in optical communication and dimensional metrology. We determined, for the first time to the best of our knowledge, the molecular transitions{\textquoteright} center frequencies of the H13C14N isotope in the range from 1526 nm to 1566 nm with 1.3\&\#x00A0;{\texttimes}\&\#x00A0;10\textminus10 fractional uncertainty. We investigated the molecular transitions with a highly coherent and widely tunable scanning laser that was precisely referenced to a hydrogen maser through an optical frequency comb. We demonstrated an approach to stabilize the operational conditions needed to maintain the constantly low pressure of the hydrogen cyanide to carry out the saturated spectroscopy with the third-harmonic synchronous demodulation. We demonstrated approximately a forty-fold improvement in the line centers{\textquoteright} resolution compared to the previous result.

}, keywords = {BF, MF}, doi = {10.1364/OL.467633}, url = {https://opg.optica.org/ol/abstract.cfm?URI=ol-47-21-5704}, author = {Jan Hrabina and Martin Hosek and Simon Rerucha and Martin Cizek and Zdenek Pilat and Massimo Zucco and Josef Lazar and Ondrej Cip} } @article {3503, title = {Endoscopic Imaging Using a Multimode Optical Fibre Calibrated with Multiple Internal References}, journal = {Photonics}, volume = {9}, year = {2022}, pages = {37}, keywords = {BF, KF, MF}, doi = {10.3390/photonics9010037}, url = {https://www.mdpi.com/2304-6732/9/1/37}, author = {J{\'a}kl, Petr and {\v S}iler, Martin and Je{\v z}ek, Jan and Cifuentes, Angel and Tr{\"a}g{\r a}rdh, Johanna and Zem{\'a}nek, Pavel and Cizmar, Tomas} } @article {3574, title = {Glycogen, poly(3-hydroxybutyrate) and pigment accumulation in three Synechocystis strains when exposed to a stepwise increasing salt stress}, journal = {JOURNAL OF APPLIED PHYCOLOGY}, volume = {34}, year = {2022}, month = {JUN}, pages = {1227-1241}, keywords = {BF, MF}, issn = {0921-8971}, doi = {10.1007/s10811-022-02693-3}, author = {Meixner, K. and Daffert, C. and Dalnodar, D. and Mrazova, K. and Hrubanov{\'a}, K. and Krzyzanek, V and Nebes{\'a}{\v r}ov{\'a}, J. and Samek, O. and Sedrlova, Z. and Slaninov{\'a}, E. and Sedl{\'a}{\v c}ek, P. and Obru{\v c}a, S. and Fritz, I} } @article {3589, title = {In Vivo Contrast Imaging of Rat Heart with Carbon Dioxide Foam}, journal = {SENSORS}, volume = {22}, year = {2022}, month = {JUL}, pages = {5124}, keywords = {BF, MF}, doi = {10.3390/s22145124}, author = {Karalko, Anton and Kesa, Peter and Jelinek, Frantisek and Sefc, Ludek and Je{\v z}ek, Jan and Zem{\'a}nek, Pavel and Grus, Tomas} } @article {3576, title = {The potential of combining laser-induced breakdown spectroscopy and Raman spectroscopy data for the analysis of wood samples}, journal = {Spectrochimica Acta Part B: Atomic Spectroscopy}, volume = {195}, year = {2022}, pages = {106487}, abstract = {

We report on combining the surface analysis technique of Laser-induced Breakdown Spectroscopy (LIBS) with Raman spectroscopy. The combination of both techniques enables to study the chemical composition of the sample in a broader context when combining elemental and molecular information. Obtained elemental and molecular spectra are characteristic for individual biological samples (e.g., organs and cells) and are considered as a fingerprint. In this study, Raman spectroscopy is used for the detection of important molecular complexes in selected wood samples, e.g., accurate lignin and cellulose content on distinct spots of the sample surface. We chose Raman as a standard reference technique that is used for the lignin/cellulose ratio estimation. To complement the molecular information, LIBS technique was employed for the imaging of essential nutrients, e.g., Ca, Na, and K. Consequently, the contribution from both analytical techniques was combined and changes in the molecular content were visually correlated to the abundance of nutrition elements and show a direct dependence between the two signal responses. Thus, we can get specific answers to relation of lignin and cellulose formation with nutrients within the plant tissue. This evidence may then be helpful for the study of the effect of various environmental and stress factors.

}, keywords = {BF, MF}, issn = {0584-8547}, doi = {https://doi.org/10.1016/j.sab.2022.106487}, url = {https://www.sciencedirect.com/science/article/pii/S0584854722001318}, author = {Daniel Holub and Pavel Po{\v r}{\'\i}zka and Martin Kizovsk{\'y} and David Prochazka and Ota Samek and Josef Kaiser} } @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}, keywords = {BF, MF}, issn = {2235-2988}, doi = {10.3389/fcimb.2022.866463}, author = {Rebro{\v s}ov{\'a}, Katar{\'\i}na and Samek, Ota and Kizovsk{\'y}, Martin and Bernatov{\'a}, Silvie and Hol{\'a}, Veronika and R{\r u}{\v z}i{\v c}ka, Filip} } @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 {3577, title = {The role of polyhydroxyalkanoates in adaptation of Cupriavidus necator to osmotic pressure and high concentration of copper ions}, journal = {International Journal of Biological Macromolecules}, volume = {206}, year = {2022}, pages = {977-989}, abstract = {

Polyhydroxyalkanoates (PHA) are abundant microbial polyesters accumulated in the form of intracellular granules by numerous prokaryotes primarily as storage of carbon and energy. Apart from their storage function, the presence of PHA also enhances the robustness of the microbial cells against various stressors. In this work, we investigated the role of PHA in Cupriavidus necator, a model organism concerning PHA metabolism, for adaptation to osmotic pressure and copper ions. In long-term laboratory evolution experiments, the bacterial culture was cultivated in presence of elevated doses of sodium chloride or copper ions (incubations lasted 78 passages for Cu2+ and 68 passages for NaCl) and the evolved strains were compared with the wild-type strain in terms of growth and PHA production capacity, cell morphology (investigated by various electron microscopy techniques), activities of selected enzymes involved in PHA metabolism and other crucial metabolic pathways, the chemical composition of bacterial biomass (determined by infrared and Raman spectroscopy) and also considering robustness against various stressors. The results confirmed the important role of PHA metabolism for adaptation to both tested stressors.

}, keywords = {BF, MF}, issn = {0141-8130}, doi = {https://doi.org/10.1016/j.ijbiomac.2022.03.102}, url = {https://www.sciencedirect.com/science/article/pii/S0141813022005712}, author = {Ivana Novackova and Vendula Hrabalova and Eva Slaninova and Petr Sedlacek and Ota Samek and Martin Koller and Vladislav Krzyzanek and Kamila Hrubanova and Katerina Mrazova and Jana Nebesarova and Stanislav Obruca} } @article {3481, title = {Optically transportable optofluidic microlasers with liquid crystal cavities tuned by the electric field}, journal = {ACS Applied Materials \& Interfaces}, volume = {13}, year = {2021}, month = {OCT 21}, pages = {50657-50667}, keywords = {BF, LF, MF}, doi = {10.1021/acsami.1c11936}, author = {Jonas, Alexandr and Pil{\'a}t, Zden{\v e}k and Je{\v z}ek, Jan and Bernatov{\'a}, Silvie and Jedli{\v c}ka, Petr and Aas, Mehdi and Kiraz, Alper and Zem{\'a}nek, Pavel} } @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}, keywords = {BF, MF}, issn = {2192-8606}, doi = {10.1515/nanoph-2021-0095}, author = {Samek, Ota and Bernatov{\'a}, Silvie and Dohnal, Fadi} } @article {3417, title = {Raman Microspectroscopic Analysis of Selenium Bioaccumulation by Green Alga Chlorella vulgaris}, journal = {Biosensors}, volume = {11}, year = {2021}, pages = {115}, keywords = {BF, MF}, issn = {2079-6374}, doi = {10.3390/bios11040115}, url = {https://www.mdpi.com/2079-6374/11/4/115}, author = {Kizovsk{\'y}, Martin and Pil{\'a}t, Zden{\v e}k and Mylenko, Mykola and Hrouzek, Pavel and Kuta, Jan and Skoup{\'y}, Radim and Krzy{\v z}{\'a}nek, Vladislav and Hrubanov{\'a}, Kamila and Adamczyk, Olga and Je{\v z}ek, Jan and Bernatov{\'a}, Silvie and Klementov{\'a}, Tereza and Gjevik, Al{\v z}b{\v e}ta and {\v S}iler, Martin and Samek, Ota and Zem{\'a}nek, Pavel} } @article {3410, title = {Rapid detection of antibiotic sensitivity of Staphylococcus aureus by Raman tweezers}, journal = {Eur. Phys. J. Plus}, volume = {136}, year = {2021}, pages = {233}, keywords = {BF, KF, MF}, doi = {10.1140/epjp/s13360-021-01152-1}, url = {https://doi.org/10.1140/epjp/s13360-021-01152-1}, author = {Bernatov{\'a}, S. and K. Rebro{\v s}ov{\'a} and Pil{\'a}t, Z. and M. {\v S}er{\'y} and Gjevik, A. and Samek, O. and Je{\v z}ek, J. and {\v S}iler, M. and Kizovsk{\'y}, M. and Klementov{\'a}, T. and Hol{\'a}, V. and F. R{\r u}{\v z}i{\v c}ka and Zem{\'a}nek, P.} } @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.

}, keywords = {BF, MF}, issn = {2076-2607}, doi = {10.3390/microorganisms9020277}, url = {https://www.mdpi.com/2076-2607/9/2/277}, author = {N{\v e}mcov{\'a}, Andrea and Gonov{\'a}, Dominika and Samek, Ota and Sipiczki, Matthias and Breierov{\'a}, Emilia and M{\'a}rov{\'a}, Ivana} } @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.

}, keywords = {BF, MF}, issn = {2076-2607}, doi = {10.3390/microorganisms9112295}, url = {https://www.mdpi.com/2076-2607/9/11/2295}, author = {N{\v e}mcov{\'a}, Andrea and Szotkowski, Martin and Samek, Ota and Cag{\'a}{\v n}ov{\'a}, Linda and Sipiczki, Matthias and M{\'a}rov{\'a}, Ivana} } @article {3337, title = {Analysis of bacteriophage-host interaction by Raman tweezers}, journal = {Analytical Chemistry}, volume = {92}, year = {2020}, pages = {12304{\textendash}12311}, keywords = {BF, KF, MF}, author = {Pil{\'a}t, Z and Jon{\'a}{\v s}, A and Pil{\'a}tov{\'a}, J and Klementov{\'a}, T and Bernatov{\'a}, S and {\v S}iler, M and Ma{\v n}ka, T and Kizovsk{\'y}, M and R{\r u}{\v z}i{\v c}ka, F and Pan{\r u}{\v c}ek, R and Neugebauer, U and Samek, O and Zem{\'a}nek, P} } @article {3187, title = {Controlled Oil/Water Partitioning of Hydrophobic Substrates Extending the Bioanalytical Applications of Droplet-Based Microfluidics}, journal = {Anal. Chem.}, volume = {91}, year = {2019}, pages = {10008-10015}, keywords = {BF, MF}, doi = {10.1021/acs.analchem.9b01839}, author = {Bury{\v s}ka, T. and Va{\v s}ina, M. and Gielen, F. and Va{\v n}{\'a}{\v c}ek, P. and van Vliet, L. and Je{\v z}ek, J. and Pil{\'a}t, Z. and Zem{\'a}nek, P. and Damborsk{\'y}, J. and Hollfelder, F. and Prokop, Z.} } @article {3105, title = {The effects of the treatment conditions on the dissolution profile of ethylcellulose coated pellets}, journal = {Europ. J. of Pharmaceutical Sci.}, volume = {132}, year = {2019}, pages = {86-95}, keywords = {BF, MF}, doi = {10.1016/j.ejps.2019.02.034}, author = {Pavlokov{\'a}, S. and Mu{\v s}el{\'\i}k, J. and Sabadkov{\'a}, D. and Bernatov{\'a}, S. and Samek, O. and Neumann, D. and Franc, A.} } @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.

}, keywords = {BF, KF, MF}, doi = {10.2217/fmb-2018-0297}, url = {https://doi.org/10.2217/fmb-2018-0297}, author = {Rebro{\v s}ov{\'a}, Katar{\'\i}na and {\v S}iler, Martin and Samek, Ota and R{\r u}{\v z}i{\v c}ka, Filip and Bernatov{\'a}, Silvie and Je{\v z}ek, Jan and Zem{\'a}nek, Pavel and Hol{\'a}, Veronika} } @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}, keywords = {BF, MF}, doi = {10.1021/acs.jpcc.8b12493}, author = {Bernatov{\'a}, Silvie and Donato, Maria Grazia and Je{\v z}ek, Jan and Pil{\'a}t, Z. and Samek, Ota and Magazzu, Alessandro and Marag{\`o}, Onofrio M. and Zem{\'a}nek, Pavel and Gucciardi, Pietro G.} } @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}, keywords = {BF, MF}, doi = {10.1007/s00253-018-09584-z}, author = {P. Sedl{\'a}{\v c}ek and Slaninov{\'a}, E. and Enev, V. and Koller, M. and J. Nebes{\'a}{\v r}ov{\'a} and I. M{\'a}rov{\'a} and K. Hrubanov{\'a} and V. Krzy{\v z}{\'a}nek and O. Samek and S. Obru{\v c}a} } @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}, keywords = {BF, MF}, doi = {10.1016/j.sab.2017.11.004}, author = {D. Proch{\'a}zka and M. Mazura and O. Samek and K. Rebro{\v s}ov{\'a} and P. Po{\v r}{\'\i}zka and J. Klus and P. Proch{\'a}zkov{\'a} and J. Novotn{\'y} and K. Novotn{\'y} and J. Kaiser} } @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 { 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}, keywords = {BF, MF}, doi = {10.3390/s18124089}, author = {K. Hrubanov{\'a} and V. Krzy{\v z}{\'a}nek and J. Nebes{\'a}{\v r}ov{\'a} and F. R{\r u}{\v z}i{\v c}ka and Z. Pil{\'a}t and O. Samek} } @article {OzbakirRSOS18, title = {A new type of microphotoreactor with integrated optofluidic waveguide based on solid-air nanoporous aerogels}, journal = {Royal Society Open Science}, volume = {5}, year = {2018}, pages = {180802}, keywords = {BF, MF}, doi = {10.1098/rsos.180802}, author = {Ozbakir, Y. and A. Jon{\'a}{\v s} and Alper Kiraz and Erkey, C.} } @article {RashidJLT18, title = {Optofluidic Dye Lasers Based on Holey Fibers: Modeling and Performance Analysis}, journal = {J. Lightwave. Technol.}, volume = {36}, year = {2018}, pages = {4114-4122}, keywords = {BF, MF}, doi = {10.1109/JLT.2018.2860684}, author = {Rashid, Zeeshan and A. Jon{\'a}{\v s} and Buczynski, Ryszard and Alper Kiraz} } @article {RashidASS18, title = {Reversible switching of wetting properties and erasable patterning of polymer surfaces using plasma oxidation and thermal treatment}, journal = {Appl. Surf. Sci.}, volume = {441}, year = {2018}, pages = {841-852}, keywords = {BF, MF}, doi = {10.1016/j.apsusc.2018.02.089}, author = {Rashid, Zeeshan and Atay, Ipek and Soydan, Seren and Yagci, M. Baris and A. Jon{\'a}{\v s} and Yilgor, Emel and Alper Kiraz and Yilgor, Iskender} } @article {BalochSAA18, title = {Sensitivity of compositional measurement of high-pressure fluid mixtures using microcantilever frequency response}, journal = {Sensors Actuators A}, volume = {278}, year = {2018}, pages = {111-126}, keywords = {BF, MF}, doi = {/10.1016/j.sna.2018.05.025}, author = {Baloch, Shadi Khan and A. Jon{\'a}{\v s} and Alper Kiraz and Alaca, B. Erdem and Erkey, Can} } @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 {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}, keywords = {BF, MF}, doi = {10.1016/j.nbt.2017.07.008}, author = {S. Obru{\v c}a and P. Sedl{\'a}{\v c}ek and F. Mravec and V. Krzy{\v z}{\'a}nek and J. Nebes{\'a}{\v r}ov{\'a} and O. Samek and D. Ku{\v c}era and Pavla Bene{\v s}ov{\'a} and K. Hrubanov{\'a} and M. Milerov{\'a} and I. M{\'a}rov{\'a}} } @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} }