Auxin, a plant hormone, is able to stimulate growth and to control developmental processes. To get a deeper level of understanding of how auxin activity is regulated in planta, we have developed a sensitive and selective mass spectrometry-based protocol for multiplex quantification of indole 3-acetic acid (IAA) as well as its precursors and degradation products. As part of the protocol development, we have also established a derivatization protocol for the IAA precursors IPyA and IAAld, compounds that are highly labile during sample extraction and purification. This article describes a standard isotope dilution method for quantitative profiling of the IAA metabolome in small amounts of plant tissues. © 2016 by John Wiley & Sons, Inc.

• Klíčová slova
• IAA, LC-MS/MS, SPE, auxin, metabolite profiling,
• Publikační typ
• časopisecké články MeSH

Perfusion cell culture processes allow the steady-state culture of mammalian cells at high viable cell density, which is beneficial for overall product yields and homogeneity of product quality in the manufacturing of therapeutic proteins. In this study, the extent of metabolic steady state and the change of the metabolite profile between different steady states of an industrial Chinese hamster ovary (CHO) cell line producing a monoclonal antibody (mAb) was investigated in stirred tank perfusion bioreactors. Matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF-MS) of daily cell extracts revealed more than a hundred peaks, among which 76 metabolites were identified by tandem MS (MS/MS) and high resolution Fourier transform ion cyclotron resonance (FT-ICR) MS. Nucleotide ratios (Uridine (U)-ratio, nucleotide triphosphate (NTP)-ratio and energy charge (EC)) and multivariate analysis of all features indicated a consistent metabolite profile for a stable culture performed at 40 × 106 cells/mL over 26 days of culture. Conversely, the reactor was operated continuously so as to reach three distinct steady states one after the other at 20, 60, and 40 × 106 cells/mL. In each case, a stable metabolite profile was achieved after an initial transient phase of approximately three days at constant cell density when varying between these set points. Clear clustering according to cell density was observed by principal component analysis, indicating steady-state dependent metabolite profiles. In particular, varying levels of nucleotides, nucleotide sugar, and lipid precursors explained most of the variance between the different cell density set points. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 33:879-890, 2017.

• Klíčová slova
• MALDI-TOF mass spectrometry, animal cell culture, metabolite profiling, perfusion cultivation,
• MeSH
• bioreaktory * MeSH
• buněčné kultury * MeSH
• CHO buňky MeSH
• Cricetulus MeSH
• kultivované buňky MeSH
• metabolom * MeSH
• monoklonální protilátky biosyntéza   MeSH
• multivariační analýza MeSH
• perfuze * MeSH
• spektrometrie hmotnostní - ionizace laserem za účasti matrice MeSH
• spektroskopie infračervená s Fourierovou transformací MeSH
• tandemová hmotnostní spektrometrie MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• monoklonální protilátky MeSH

The discovery of tyrosine kinase inhibitors (TKIs) brought a major breakthrough in the treatment of patients with chronic myeloid leukemia (CML). Pathogenetic CML events are closely linked with the Bcr-Abl protein with tyrosine kinase activity. TKIs block the ATP-binding site; therefore, the signal pathways leading to malignant transformation are no longer active. However, there is limited information about the impact of TKI treatment on the metabolome of CML patients. Using liquid chromatography mass spectrometric metabolite profiling and multivariate statistical methods, we analyzed plasma and leukocyte samples of patients newly diagnosed with CML, patients treated with hydroxyurea and TKIs (imatinib, dasatinib, nilotinib), and healthy controls. The global metabolic profiles clearly distinguished the newly diagnosed CML patients and the patients treated with hydroxyurea from those treated with TKIs and the healthy controls. The major changes were found in glycolysis, the citric acid cycle, and amino acid metabolism. We observed differences in the levels of amino acids and acylcarnitines between those patients responding to imatinib treatment and those who were resistant to it. According to our findings, the metabolic profiling may be potentially used as an additional tool for the assessment of response/resistance to imatinib.

• Klíčová slova
• chronic myeloid leukemia, drug resistance, hydroxyurea, metabolomics, tyrosine kinase inhibitors,
• MeSH
• aminokyseliny metabolismus   MeSH
• chronická myeloidní leukemie krev   metabolismus   MeSH
• citrátový cyklus účinky léků   MeSH
• glykolýza účinky léků   MeSH
• hydroxymočovina farmakologie   terapeutické užití   MeSH
• imatinib mesylát farmakologie   terapeutické užití   MeSH
• inhibitory proteinkinas farmakologie   MeSH
• krevní plazma chemie   metabolismus   MeSH
• leukocyty chemie   metabolismus   MeSH
• lidé MeSH
• metabolom * MeSH
• metabolomika metody   MeSH
• monitorování léčiv metody   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• aminokyseliny MeSH
• hydroxymočovina MeSH
• imatinib mesylát MeSH
• inhibitory proteinkinas MeSH

BACKGROUND: Medulloblastoma (MB) is the most common malignant tumour of the central nervous system in children. MB is considered to be high risk tumour propensity to metastasize. In the Czech Republic, approximately 10-12 children are affected annually by this tumour. Recent progress in molecular diagnostics helps to refine the diagnosis and estimate clinical prognosis of the disease. Currently, MBs are subclassified into WNT-activated, SHH-activated, group 3, and 4 based on molecular pathways that drive their tumorigenesis. Each subtype differs in its histopathology, clinical features, genomic changes and gene expressions. The aim of our study is to classify patients MBs into four basic molecular groups and compare our results with published data. MATERIAL AND METHODS: In our study we analysed expression profiles using Affymetrix GeneChip Human Gene 1.0. ST Array (Thermo Fisher Scientific, MA, USA). As input material RNA extracted from the fresh frozen tissue was used. Molecular classification based on the method established by P. Northcott in 2011 was performed. RESULTS: From April 2015 to February 2019, 21 patients with MBs were included in our study. Median age of the patients at the time of diagnosis was 6 years, 14 boys and 7 girls were enrolled. Gene expression profiling and molecular classification of MBs was performed. Based on this methodology, we found the most frequently represented subgroup of MB was group 4 (9 patients, 43%), followed by group 3 (5 patients, 24%), SHH-activated MB (4 patients, 19%) and the least represented subgroup was WNT-activated MB (3 patients, 14%). Results of molecular subgroup classification of MBs were successfully correlated with histopathological findings and other molecular-genetic examinations. CONCLUSION: Molecular classification of MBs has been established in our institution allowing better understanding of this heterogeneous disease and helping clinicians in therapeutic planning in affected patients. This work was supported by the Czech Ministry of Health grant No. 16-33209A. All rights reserved. he authors declare they have no potential confl icts of interest concerning drugs, products, or services used in the study. The Editorial Board declares that the manuscript met the ICMJE recommendation for biomedical papers. Submitted: 1. 3. 2019 Accepted: 4. 3. 2019.

• Klíčová slova
• gene expression profiling, medulloblastoma, pediatric oncology, precision medicine,
• MeSH
• dítě MeSH
• genom lidský * MeSH
• lidé MeSH
• meduloblastom klasifikace   genetika   patologie   MeSH
• nádorové biomarkery genetika   MeSH
• nádory mozečku klasifikace   genetika   patologie   MeSH
• prognóza MeSH
• stanovení celkové genové exprese * MeSH
• výpočetní biologie metody   MeSH
• Check Tag
• dítě MeSH
• lidé MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• Geografické názvy
• Česká republika MeSH
• Názvy látek
• nádorové biomarkery MeSH

Auxin (indole-3-acetic acid, IAA) plays fundamental roles as a signalling molecule during numerous plant growth and development processes. The formation of local auxin gradients and auxin maxima/minima, which is very important for these processes, is regulated by auxin metabolism (biosynthesis, degradation, and conjugation) as well as transport. When studying auxin metabolism pathways it is crucial to combine data obtained from genetic investigations with the identification and quantification of individual metabolites. Thus, to facilitate efforts to elucidate auxin metabolism and its roles in plants, we have developed a high-throughput method for simultaneously quantifying IAA and its key metabolites in minute samples (<10 mg FW) of Arabidopsis thaliana tissues by in-tip micro solid-phase extraction and fast LC-tandem MS. As a proof of concept, we applied the method to a collection of Arabidopsis mutant lines and identified lines with altered IAA metabolite profiles using multivariate data analysis. Finally, we explored the correlation between IAA metabolite profiles and IAA-related phenotypes. The developed rapid analysis of large numbers of samples (>100 samples d-1) is a valuable tool to screen for novel regulators of auxin metabolism and homeostasis among large collections of genotypes.

• MeSH
• Arabidopsis genetika   metabolismus   MeSH
• chromatografie kapalinová MeSH
• extrakce na pevné fázi MeSH
• kyseliny indoloctové metabolismus   MeSH
• multivariační analýza MeSH
• mutace * MeSH
• rostlinné proteiny analýza   MeSH
• tandemová hmotnostní spektrometrie MeSH
• vysoce účinné nukleotidové sekvenování metody   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• kyseliny indoloctové MeSH
• rostlinné proteiny MeSH

The plant nucleus plays an irreplaceable role in cellular control and regulation by auxin (indole-3-acetic acid, IAA) mainly because canonical auxin signaling takes place here. Auxin can enter the nucleus from either the endoplasmic reticulum or cytosol. Therefore, new information about the auxin metabolome (auxinome) in the nucleus can illuminate our understanding of subcellular auxin homeostasis. Different methods of nuclear isolation from various plant tissues have been described previously, but information about auxin metabolite levels in nuclei is still fragmented and insufficient. Herein, we tested several published nucleus isolation protocols based on differential centrifugation or flow cytometry. The optimized sorting protocol leading to promising yield, intactness, and purity was then combined with an ultra-sensitive mass spectrometry analysis. Using this approach, we can present the first complex report on the auxinome of isolated nuclei from cell cultures of Arabidopsis and tobacco. Moreover, our results show dynamic changes in auxin homeostasis at the intranuclear level after treatment of protoplasts with free IAA, or indole as a precursor of auxin biosynthesis. Finally, we can conclude that the methodological procedure combining flow cytometry and mass spectrometry offers new horizons for the study of auxin homeostasis at the subcellular level.

• Klíčová slova
• auxin, auxin metabolism, flow cytometry, nucleus, subcellular fractionation,
• MeSH
• Arabidopsis účinky léků   metabolismus   ultrastruktura   MeSH
• buněčné jádro účinky léků   metabolismus   ultrastruktura   MeSH
• buněčné kultury MeSH
• centrifugace metody   MeSH
• frakcionace buněk přístrojové vybavení   metody   MeSH
• hmotnostní spektrometrie MeSH
• homeostáza fyziologie   MeSH
• indoly metabolismus   farmakologie   MeSH
• kyseliny indoloctové metabolismus   MeSH
• protoplasty chemie   MeSH
• průtoková cytometrie MeSH
• regulátory růstu rostlin metabolismus   MeSH
• rostlinné buňky účinky léků   metabolismus   ultrastruktura   MeSH
• tabák účinky léků   metabolismus   ultrastruktura   MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• indole MeSH Prohlížeč
• indoly MeSH
• kyseliny indoloctové MeSH
• regulátory růstu rostlin MeSH

Within streptophyte green algae Zygnematophyceae are the sister group to the land plants that inherited several traits conferring stress protection. Zygnema sp., a mat-forming alga thriving in extreme habitats, was collected from a field site in Svalbard, where the bottom layers are protected by the top layers. The two layers were investigated by a metatranscriptomic approach and GC-MS-based metabolite profiling. In the top layer, 6569 genes were significantly upregulated and 149 were downregulated. Upregulated genes coded for components of the photosynthetic apparatus, chlorophyll synthesis, early light-inducible proteins, cell wall and carbohydrate metabolism, including starch-degrading enzymes. An increase in maltose in the top layer and degraded starch grains at the ultrastructural levels corroborated these findings. Genes involved in amino acid, redox metabolism and DNA repair were upregulated. A total of 29 differentially accumulated metabolites (out of 173 identified ones) confirmed higher metabolic turnover in the top layer. For several of these metabolites, differential accumulation matched the transcriptional changes of enzymes involved in associated pathways. In summary, the findings support the hypothesis that in a Zygnema mat the top layer shields the bottom layers from abiotic stress factors such as excessive irradiation.

• MeSH
• Chlorophyta genetika   metabolismus   MeSH
• ekosystém MeSH
• fotosyntéza genetika   MeSH
• fyziologický stres MeSH
• metabolom MeSH
• Streptophyta genetika   metabolismus   MeSH
• transkriptom MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Geografické názvy
• Arktida MeSH
• Svalbard MeSH

We present a biological profile of 16 Aspergillus niger environmental isolates from different types of soils and solid substrates across a pH range, from an ultra-acidic (<3.5) to a very strongly alkaline (>9.0) environment. The soils and solid substrates also differ in varying degrees of anthropic pollution, which in most cases is caused by several centuries of mining activity at old mining sites, sludge beds, ore deposits, stream sediments, and coal dust. The values of toxic elements (As, Sb, Zn, Cu, Pb) very often exceed the limit values. The isolates possess different macro- and micromorphological features. All the identifications of Aspergillus niger isolates were confirmed by molecular PCR analysis and their similarity was expressed by RAMP analysis. The biochemical profile of isolates based on FF-MicroPlate tests from the Biolog system showed identical biochemical reactions in 50 tests, while in 46 tests the utilisation reactions differed. The highest similarity of strains isolated from substrates with the same pH, as well as the most suitable biochemical tests for analysis of the phenotypic similarity of isolated strains, were confirmed when evaluating the biochemical profile using multicriterial analysis in the Canoco program. The isolates were screened for mycotoxin production by thin-layer chromatography (TLC), as well. Two of them were able to synthesise ochratoxin A, while none produced fumonisins under experimental conditions. Presence of toxic compounds in contaminated sites may affect environmental microscopic fungi and cause the genome alteration, which may result in changes of their physiology, including the production of different (secondary) metabolites, such as mycotoxins.

• Klíčová slova
• Aspergillus niger environmental isolates, Biolog FF MicroplateTM, extrolite profile, molecular analyses, multi-criteria data analysis,
• Publikační typ
• časopisecké články MeSH

Flavonoids, including anthocyanins, are polyphenolic compounds present in fruits, vegetables and dietary supplements. They can be absorbed from the intestine to the bloodstream or pass into the large intestine. Various bacterial species and enzymes are present along the entire intestine. The aim of the present work was to investigate the intestinal metabolism of selected dietary polyphenol and polyphenol glycosides (quercetin, cyanidin-3-O-glucoside, cyanidin-3-O-galactoside, and delphinidin-3-O-galactoside) by human fecal bacteria. Moreover, the metabolism of metabolites formed from these compounds in human colon carcinoma cells (Caco-2) was also point of the interest. Test compounds were added to fresh human stool in broth or to Caco-2 cells in medium and then incubated for 6 or 20 h at 37°C. After incubation, samples were prepared for LC/MS determination. Main metabolic pathways were deglycosylation, hydrogenation, methylation, hydroxylation, and decomposition. 2,4,5-trihydroxybenzaldehyde, as a metabolite of cyanidin glycosides, was detected after incubation for the first time. Metabolites formed by fecal bacteria were further glucuronidated or methylated by intestinal enzymes. This metabolite profiling of natural compounds has helped to better understand the complex metabolism in the human intestine and this work also has shown the connection of metabolism of natural substances by intestinal bacteria followed by metabolism in intestinal cells.

• Klíčová slova
• Caco-2, Fecal bacteria, Flavonoids, Human, Metabolomics,
• MeSH
• Bacteria metabolismus   MeSH
• Caco-2 buňky MeSH
• feces mikrobiologie   MeSH
• flavonoidy metabolismus   MeSH
• glykosidy metabolismus   MeSH
• lidé MeSH
• metabolické sítě a dráhy MeSH
• metabolom * MeSH
• nádory tračníku metabolismus   MeSH
• polyfenoly metabolismus   MeSH
• střevní sliznice metabolismus   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• flavonoidy MeSH
• glykosidy MeSH
• polyfenoly MeSH

Senna Mill. (Fabaceae) is an important medicinal plant distributed worldwide. Senna alexandrina (S. alexandrina), the officinal species of the genus, is one of the most well-known herbal medicines traditionally used to treat constipation and digestive diseases. Senna italica (S. italica), another species of the genus, is native to an area ranging from Africa to the Indian subcontinent, including Iran. In Iran, this plant has been used traditionally as a laxative. However, very little phytochemical information and pharmacological reports investigating its safety of use are available. In the current study, we compared LC-ESIMS metabolite profiles of the methanol extract of S. italica with that of S. alexandrina and measured the content of sennosides A and B as the biomarkers in this genus. By this, we were able to examine the feasibility of using S. italica as a laxative agent like S. alexandrina. In addition, the hepatotoxicity of both species was evaluated against HepG2 cancer cell lines using HPLC-based activity profiling to localize the hepatotoxic components and evaluate their safety of use. Interestingly, the results showed that the phytochemical profiles of the plants were similar but with some differences, particularly in their relative contents. Glycosylated flavonoids, anthraquinones, dianthrones, benzochromenones, and benzophenones constituted the main components in both species. Nevertheless, some differences, particularly in the relative amount of some compounds, were observed. According to the LC-MS results, the amounts of sennoside A in S. alexandrina and S. italica were 1.85 ± 0.095% and 1.00 ± 0.38%, respectively. Moreover, the amounts of sennoside B in S. alexandrina and S. italica were 0.41 ± 0.12 % and 0.32 ± 0.17%, respectively. Furthermore, although both extracts showed significant hepatotoxicity at concentrations of 50 and 100 µg/mL, they were almost non-toxic at lower concentrations. Taken together, according to the results, the metabolite profiles of S. italica and S. alexandrina showed many compounds in common. However, further phytochemical, pharmacological, and clinical studies are necessary to examine the efficacy and safety of S. italica as a laxative agent.

• Klíčová slova
• LC-ESIMS, LC-MS/MS, Senna alexandrina, Senna italica, hepatotoxicity, sennosides,
• Publikační typ
• časopisecké články MeSH