D. Tziotis - Academia.edu (original) (raw)
Papers by D. Tziotis
Talanta, 2014
In the previous reports about cognitive dysfunction, cerebellum was thought to be a less affected... more In the previous reports about cognitive dysfunction, cerebellum was thought to be a less affected tissue by genetic or environmental alterations in comparison to other tissues in the brain including hippocampus under the same conditions. In this work, we investigated two types of metabolomic alterations inside the cerebellum tissue. The first one addressed the differences in the metabolomics profiles between Transgenic (Tg) CRND8 of Alzheimer's disease mice and non-transgenic (non-Tg) littermates. The second one addressed the metabolic differences between wild type mice exposed to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) and wild type mice which are not exposed to this toxic compound. For these two investigations, ultrahigh resolution Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR/MS) was implemented. As a result, the significant changes of each comparison were tentatively annotated by the high mass accuracy generated from the measurements in the negative ion mode. The biosynthesis of amino acids was also enhanced pronouncedly, and perturbation of purine metabolism was also observed in Tg mice compared to non-Tg littermates. In another animal model, the reduced levels of amino acids were found whereas the intermediate levels in purine metabolism and fatty acids including fatty acid conjugated metabolites were elevated in cerebellar tissues of mice exposed to TCDD compared to control group. Collectively, it was demonstrated that FT-ICR/MS was a powerful tool for interpretation of the elemental compositions of the peaks, revealing that the metabolic perturbations in cerebellar tissues of mice were induced by either genetic manipulation or environmental factor. Therefore, the non-targeted approach, alternatively, provides various metabolic phenotypes for the systems-level mirror of the complex etiology of neurotoxicity in the cerebellum.
European Journal of Mass Spectrometry, 2011
Here, we propose a novel computational and visual approach for the analysis of high field Fourier... more Here, we propose a novel computational and visual approach for the analysis of high field Fourier transform ion cyclotron resonance mass spectra (FTICR/MS) based on successive and multiple atomic and Kendrick analogous mass difference analyses. Compositional networks based on elemental compositions and functional networks based on selected functional groups equivalents enable improved assignment options of elemental composition and classification of organic complexity with tunable validation windows. The approach is demonstrated through the analysis of a 12T FTICR mass spectrum of an intricate water soluble extract of a secondary organic aerosol with a previously established abundance in CHNOS molecules.
Analytical and Bioanalytical Chemistry, 2013
Infections with Chlamydia pneumoniae cause several respiratory diseases, such as community-acquir... more Infections with Chlamydia pneumoniae cause several respiratory diseases, such as community-acquired pneumonia, bronchitis or sinusitis. Here, we present an integrated non-targeted metabolomics analysis applying ultra-high-resolution mass spectrometry and ultra-performance liquid chromatography mass spectrometry to determine metabolite alterations in C. pneumoniae-infected HEp-2 cells. Most important permutations are elaborated using uni- and multivariate statistical analysis, logD retention time regression and mass defect-based network analysis. Classes of metabolites showing high variations upon infection are lipids, carbohydrates and amino acids. Moreover, we observed several non-annotated compounds as predominantly abundant after infection, which are promising biomarker candidates for drug-target and diagnostic research.
Successful Strategies to Generate and Analyze Metabolic Data, 2013
ABSTRACT This chapter contains sections titled: Introduction Metabolomics Technologies Principles... more ABSTRACT This chapter contains sections titled: Introduction Metabolomics Technologies Principles of FTICR-MS Proceeding in Metabolomics Application Example in Metabolomics Using FTICR-MS Exhaled Breath Condensate Conclusion and Remarks References
Journal of Geophysical Research: Biogeosciences, 2013
1] Similarities between the Atacama Desert (Chile) and Mars include extreme aridity, highly oxidi... more 1] Similarities between the Atacama Desert (Chile) and Mars include extreme aridity, highly oxidizing chemistry, and intense ultraviolet radiation that promoted the photochemical production of perchlorates and nitrates. Concentration of these ions under hyperarid conditions led to the formation of nitrate-and perchlorate-bearing deposits in ephemeral lakes, followed by later deposition of chlorides and sulfates. At some locations, such as the Salar Grande, hypersaline deposits have remained unaltered for millions of years. We conducted a drilling campaign in deposits of the Salar to characterize the preservation state of biological molecules. A 5 m deep discontinuous core was recovered and subjected to multitechnique analysis including the antibody microarray-based biosensor LDChip300 and the SOLID (Signs Of Life Detector) instrument, complemented by geophysical, mineralogical, geochemical, and molecular analysis. We identified two units based on the mineralogy: the upper one, from the surface to~320 cm depth characterized by a predominance of halite and anhydrite, and the lower one, from 320 to 520 cm, with a drop in halite and anhydrite and an enrichment in nitrate and perchlorate. Organic compounds including biomolecules were detected in association with the different depositional and mineralogical units, demonstrating the high capacity for molecular preservation. Hypersaline environments preserve biomolecules over geologically significant timescales; therefore, salt-bearing materials should be high-priority targets for the search for evidence of life on Mars.
PLoS Pathogens, 2013
The Chlamydiae are a highly successful group of obligate intracellular bacteria, whose members ar... more The Chlamydiae are a highly successful group of obligate intracellular bacteria, whose members are remarkably diverse, ranging from major pathogens of humans and animals to symbionts of ubiquitous protozoa. While their infective developmental stage, the elementary body (EB), has long been accepted to be completely metabolically inert, it has recently been shown to sustain some activities, including uptake of amino acids and protein biosynthesis. In the current study, we performed an in-depth characterization of the metabolic capabilities of EBs of the amoeba symbiont Protochlamydia amoebophila. A combined metabolomics approach, including fluorescence microscopy-based assays, isotope-ratio mass spectrometry (IRMS), ion cyclotron resonance Fourier transform mass spectrometry (ICR/FT-MS), and ultra-performance liquid chromatography mass spectrometry (UPLC-MS) was conducted, with a particular focus on the central carbon metabolism. In addition, the effect of nutrient deprivation on chlamydial infectivity was analyzed. Our investigations revealed that host-free P. amoebophila EBs maintain respiratory activity and metabolize D-glucose, including substrate uptake as well as host-free synthesis of labeled metabolites and release of labeled CO 2 from 13 C-labeled D-glucose. The pentose phosphate pathway was identified as major route of D-glucose catabolism and host-independent activity of the tricarboxylic acid (TCA) cycle was observed. Our data strongly suggest anabolic reactions in P. amoebophila EBs and demonstrate that under the applied conditions D-glucose availability is essential to sustain metabolic activity. Replacement of this substrate by L-glucose, a non-metabolizable sugar, led to a rapid decline in the number of infectious particles. Likewise, infectivity of Chlamydia trachomatis, a major human pathogen, also declined more rapidly in the absence of nutrients. Collectively, these findings demonstrate that D-glucose is utilized by P. amoebophila EBs and provide evidence that metabolic activity in the extracellular stage of chlamydiae is of major biological relevance as it is a critical factor affecting maintenance of infectivity. Citation: Sixt BS, Siegl A, Mü ller C, Watzka M, Wultsch A, et al. (2013) Metabolic Features of Protochlamydia amoebophila Elementary Bodies -A Link between Activity and Infectivity in Chlamydiae. PLoS Pathog 9(8): e1003553.
BioFactors, 2008
Recent advances in the use of liquid chromatography-mass spectrometry for the study of metabolomi... more Recent advances in the use of liquid chromatography-mass spectrometry for the study of metabolomics are reviewed. Sample preparations of biofluids and practical aspects of ultra-high pressure liquid chromatography are discussed. Applicability of different kinds of mass spectrometers for metabolite profiling is described. New tools-ion mobility spectroscopy and automated chip-based nanoelectrospray system with potentials to be applied in the metabolomics analysis are described.
A new Fourier transform ion cyclotron resonance mass spectrometer is described in three sections:... more A new Fourier transform ion cyclotron resonance mass spectrometer is described in three sections: magnet, vacuum system, and electronics/data system. Each component is described in detail (e.g., manufacturer’s part numbers, drawings, circuit schematics, etc.). Of special interest is the high-frequency signal generation and processing required to extend the lower-mass limit for singly charged ions to 1 u. In particular, two
Biogeosciences, 2012
Atmospheric aerosols impose direct and indirect effects on the climate system, for example, by ab... more Atmospheric aerosols impose direct and indirect effects on the climate system, for example, by absorption of radiation in relation to cloud droplets size, on chemical and organic composition and cloud dynamics. The first step in the formation of Organic primary aerosols, i.e. the transfer of dissolved organic matter from the marine surface into the atmosphere, was studied. We present a molecular level description of this phenomenon using the high resolution analytical tools of Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) and nuclear magnetic resonance spectroscopy (NMR). Our experiments confirm the chemoselective transfer of natural organic molecules, especially of aliphatic compounds from the surface water into the atmosphere via bubble bursting processes. Transfer from marine surface water to the atmosphere involves a chemical gradient governed by the physicochemical properties of the involved molecules when comparing elemental compositions and differentiating CHO, CHNO, CHOS and CHNOS bearing compounds. Typical chemical fingerprints of compounds enriched in the aerosol phase were CHO and CHOS molecular series, smaller molecules of higher aliphaticity and lower oxygen content, and typical surfactants. A nontargeted metabolomics analysis demonstrated that many of these molecules corresponded to homologous series of oxo-, hydroxy-, methoxy-, branched fatty acids and mono-, di-and tricarboxylic acids as well as monoterpenes and sugars. These surface active biomolecules were preferentially transferred from surface water into the atmosphere via bubble bursting processes to form a significant fraction of primary organic aerosols. This way of sea spray production leaves a selective biological signature of the surface water in the corresponding aerosol that may be transported into higher altitudes up to the lower atmosphere, thus contributing to the formation of secondary organic aerosol on a global scale or transported laterally with possible deposition in the context of global biogeocycling.
Talanta, 2014
In the previous reports about cognitive dysfunction, cerebellum was thought to be a less affected... more In the previous reports about cognitive dysfunction, cerebellum was thought to be a less affected tissue by genetic or environmental alterations in comparison to other tissues in the brain including hippocampus under the same conditions. In this work, we investigated two types of metabolomic alterations inside the cerebellum tissue. The first one addressed the differences in the metabolomics profiles between Transgenic (Tg) CRND8 of Alzheimer's disease mice and non-transgenic (non-Tg) littermates. The second one addressed the metabolic differences between wild type mice exposed to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) and wild type mice which are not exposed to this toxic compound. For these two investigations, ultrahigh resolution Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR/MS) was implemented. As a result, the significant changes of each comparison were tentatively annotated by the high mass accuracy generated from the measurements in the negative ion mode. The biosynthesis of amino acids was also enhanced pronouncedly, and perturbation of purine metabolism was also observed in Tg mice compared to non-Tg littermates. In another animal model, the reduced levels of amino acids were found whereas the intermediate levels in purine metabolism and fatty acids including fatty acid conjugated metabolites were elevated in cerebellar tissues of mice exposed to TCDD compared to control group. Collectively, it was demonstrated that FT-ICR/MS was a powerful tool for interpretation of the elemental compositions of the peaks, revealing that the metabolic perturbations in cerebellar tissues of mice were induced by either genetic manipulation or environmental factor. Therefore, the non-targeted approach, alternatively, provides various metabolic phenotypes for the systems-level mirror of the complex etiology of neurotoxicity in the cerebellum.
European Journal of Mass Spectrometry, 2011
Here, we propose a novel computational and visual approach for the analysis of high field Fourier... more Here, we propose a novel computational and visual approach for the analysis of high field Fourier transform ion cyclotron resonance mass spectra (FTICR/MS) based on successive and multiple atomic and Kendrick analogous mass difference analyses. Compositional networks based on elemental compositions and functional networks based on selected functional groups equivalents enable improved assignment options of elemental composition and classification of organic complexity with tunable validation windows. The approach is demonstrated through the analysis of a 12T FTICR mass spectrum of an intricate water soluble extract of a secondary organic aerosol with a previously established abundance in CHNOS molecules.
Analytical and Bioanalytical Chemistry, 2013
Infections with Chlamydia pneumoniae cause several respiratory diseases, such as community-acquir... more Infections with Chlamydia pneumoniae cause several respiratory diseases, such as community-acquired pneumonia, bronchitis or sinusitis. Here, we present an integrated non-targeted metabolomics analysis applying ultra-high-resolution mass spectrometry and ultra-performance liquid chromatography mass spectrometry to determine metabolite alterations in C. pneumoniae-infected HEp-2 cells. Most important permutations are elaborated using uni- and multivariate statistical analysis, logD retention time regression and mass defect-based network analysis. Classes of metabolites showing high variations upon infection are lipids, carbohydrates and amino acids. Moreover, we observed several non-annotated compounds as predominantly abundant after infection, which are promising biomarker candidates for drug-target and diagnostic research.
Successful Strategies to Generate and Analyze Metabolic Data, 2013
ABSTRACT This chapter contains sections titled: Introduction Metabolomics Technologies Principles... more ABSTRACT This chapter contains sections titled: Introduction Metabolomics Technologies Principles of FTICR-MS Proceeding in Metabolomics Application Example in Metabolomics Using FTICR-MS Exhaled Breath Condensate Conclusion and Remarks References
Journal of Geophysical Research: Biogeosciences, 2013
1] Similarities between the Atacama Desert (Chile) and Mars include extreme aridity, highly oxidi... more 1] Similarities between the Atacama Desert (Chile) and Mars include extreme aridity, highly oxidizing chemistry, and intense ultraviolet radiation that promoted the photochemical production of perchlorates and nitrates. Concentration of these ions under hyperarid conditions led to the formation of nitrate-and perchlorate-bearing deposits in ephemeral lakes, followed by later deposition of chlorides and sulfates. At some locations, such as the Salar Grande, hypersaline deposits have remained unaltered for millions of years. We conducted a drilling campaign in deposits of the Salar to characterize the preservation state of biological molecules. A 5 m deep discontinuous core was recovered and subjected to multitechnique analysis including the antibody microarray-based biosensor LDChip300 and the SOLID (Signs Of Life Detector) instrument, complemented by geophysical, mineralogical, geochemical, and molecular analysis. We identified two units based on the mineralogy: the upper one, from the surface to~320 cm depth characterized by a predominance of halite and anhydrite, and the lower one, from 320 to 520 cm, with a drop in halite and anhydrite and an enrichment in nitrate and perchlorate. Organic compounds including biomolecules were detected in association with the different depositional and mineralogical units, demonstrating the high capacity for molecular preservation. Hypersaline environments preserve biomolecules over geologically significant timescales; therefore, salt-bearing materials should be high-priority targets for the search for evidence of life on Mars.
PLoS Pathogens, 2013
The Chlamydiae are a highly successful group of obligate intracellular bacteria, whose members ar... more The Chlamydiae are a highly successful group of obligate intracellular bacteria, whose members are remarkably diverse, ranging from major pathogens of humans and animals to symbionts of ubiquitous protozoa. While their infective developmental stage, the elementary body (EB), has long been accepted to be completely metabolically inert, it has recently been shown to sustain some activities, including uptake of amino acids and protein biosynthesis. In the current study, we performed an in-depth characterization of the metabolic capabilities of EBs of the amoeba symbiont Protochlamydia amoebophila. A combined metabolomics approach, including fluorescence microscopy-based assays, isotope-ratio mass spectrometry (IRMS), ion cyclotron resonance Fourier transform mass spectrometry (ICR/FT-MS), and ultra-performance liquid chromatography mass spectrometry (UPLC-MS) was conducted, with a particular focus on the central carbon metabolism. In addition, the effect of nutrient deprivation on chlamydial infectivity was analyzed. Our investigations revealed that host-free P. amoebophila EBs maintain respiratory activity and metabolize D-glucose, including substrate uptake as well as host-free synthesis of labeled metabolites and release of labeled CO 2 from 13 C-labeled D-glucose. The pentose phosphate pathway was identified as major route of D-glucose catabolism and host-independent activity of the tricarboxylic acid (TCA) cycle was observed. Our data strongly suggest anabolic reactions in P. amoebophila EBs and demonstrate that under the applied conditions D-glucose availability is essential to sustain metabolic activity. Replacement of this substrate by L-glucose, a non-metabolizable sugar, led to a rapid decline in the number of infectious particles. Likewise, infectivity of Chlamydia trachomatis, a major human pathogen, also declined more rapidly in the absence of nutrients. Collectively, these findings demonstrate that D-glucose is utilized by P. amoebophila EBs and provide evidence that metabolic activity in the extracellular stage of chlamydiae is of major biological relevance as it is a critical factor affecting maintenance of infectivity. Citation: Sixt BS, Siegl A, Mü ller C, Watzka M, Wultsch A, et al. (2013) Metabolic Features of Protochlamydia amoebophila Elementary Bodies -A Link between Activity and Infectivity in Chlamydiae. PLoS Pathog 9(8): e1003553.
BioFactors, 2008
Recent advances in the use of liquid chromatography-mass spectrometry for the study of metabolomi... more Recent advances in the use of liquid chromatography-mass spectrometry for the study of metabolomics are reviewed. Sample preparations of biofluids and practical aspects of ultra-high pressure liquid chromatography are discussed. Applicability of different kinds of mass spectrometers for metabolite profiling is described. New tools-ion mobility spectroscopy and automated chip-based nanoelectrospray system with potentials to be applied in the metabolomics analysis are described.
A new Fourier transform ion cyclotron resonance mass spectrometer is described in three sections:... more A new Fourier transform ion cyclotron resonance mass spectrometer is described in three sections: magnet, vacuum system, and electronics/data system. Each component is described in detail (e.g., manufacturer’s part numbers, drawings, circuit schematics, etc.). Of special interest is the high-frequency signal generation and processing required to extend the lower-mass limit for singly charged ions to 1 u. In particular, two
Biogeosciences, 2012
Atmospheric aerosols impose direct and indirect effects on the climate system, for example, by ab... more Atmospheric aerosols impose direct and indirect effects on the climate system, for example, by absorption of radiation in relation to cloud droplets size, on chemical and organic composition and cloud dynamics. The first step in the formation of Organic primary aerosols, i.e. the transfer of dissolved organic matter from the marine surface into the atmosphere, was studied. We present a molecular level description of this phenomenon using the high resolution analytical tools of Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) and nuclear magnetic resonance spectroscopy (NMR). Our experiments confirm the chemoselective transfer of natural organic molecules, especially of aliphatic compounds from the surface water into the atmosphere via bubble bursting processes. Transfer from marine surface water to the atmosphere involves a chemical gradient governed by the physicochemical properties of the involved molecules when comparing elemental compositions and differentiating CHO, CHNO, CHOS and CHNOS bearing compounds. Typical chemical fingerprints of compounds enriched in the aerosol phase were CHO and CHOS molecular series, smaller molecules of higher aliphaticity and lower oxygen content, and typical surfactants. A nontargeted metabolomics analysis demonstrated that many of these molecules corresponded to homologous series of oxo-, hydroxy-, methoxy-, branched fatty acids and mono-, di-and tricarboxylic acids as well as monoterpenes and sugars. These surface active biomolecules were preferentially transferred from surface water into the atmosphere via bubble bursting processes to form a significant fraction of primary organic aerosols. This way of sea spray production leaves a selective biological signature of the surface water in the corresponding aerosol that may be transported into higher altitudes up to the lower atmosphere, thus contributing to the formation of secondary organic aerosol on a global scale or transported laterally with possible deposition in the context of global biogeocycling.