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Sample records for spectrometry-based saliva metabolomics

  1. Fusion of mass spectrometry-based metabolomics data

    NARCIS (Netherlands)

    Smilde, Age K.; van der Werf, Mariët J.; Bijlsma, Sabina; van der Werff-van der Vat, Bianca J. C.; Jellema, Renger H.

    2005-01-01

    A general method is presented for combining mass spectrometry-based metabolomics data. Such data are becoming more and more abundant, and proper tools for fusing these types of data sets are needed. Fusion of metabolomics data leads to a comprehensive view on the metabolome of an organism or

  2. Mass spectrometry-based metabolomics for tuberculosis meningitis.

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    Zhang, Peixu; Zhang, Weiguanliu; Lang, Yue; Qu, Yan; Chu, Fengna; Chen, Jiafeng; Cui, Li

    2018-04-18

    Tuberculosis meningitis (TBM) is a prevalent form of extra-pulmonary tuberculosis that causes substantial morbidity and mortality. Diagnosis of TBM is difficult because of the limited sensitivity of existing laboratory techniques. A metabolomics approach can be used to investigate the sets of metabolites of both bacteria and host, and has been used to clarify the mechanisms underlying disease development, and identify metabolic changes, leadings to improved methods for diagnosis, treatment, and prognostication. Mass spectrometry (MS) is a major analysis platform used in metabolomics, and MS-based metabolomics provides wide metabolite coverage, because of its high sensitivity, and is useful for the investigation of Mycobacterium tuberculosis (Mtb) and related diseases. It has been used to investigate TBM diagnosis; however, the processes involved in the MS-based metabolomics approach are complex and flexible, and often consist of several steps, and small changes in the methods used can have a huge impact on the final results. Here, the process of MS-based metabolomics is summarized and its applications in Mtb and Mtb-related diseases discussed. Moreover, the current status of TBM metabolomics is described. Copyright © 2018. Published by Elsevier B.V.

  3. Advantages and Pitfalls of Mass Spectrometry Based Metabolome Profiling in Systems Biology.

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    Aretz, Ina; Meierhofer, David

    2016-04-27

    Mass spectrometry-based metabolome profiling became the method of choice in systems biology approaches and aims to enhance biological understanding of complex biological systems. Genomics, transcriptomics, and proteomics are well established technologies and are commonly used by many scientists. In comparison, metabolomics is an emerging field and has not reached such high-throughput, routine and coverage than other omics technologies. Nevertheless, substantial improvements were achieved during the last years. Integrated data derived from multi-omics approaches will provide a deeper understanding of entire biological systems. Metabolome profiling is mainly hampered by its diversity, variation of metabolite concentration by several orders of magnitude and biological data interpretation. Thus, multiple approaches are required to cover most of the metabolites. No software tool is capable of comprehensively translating all the data into a biologically meaningful context yet. In this review, we discuss the advantages of metabolome profiling and main obstacles limiting progress in systems biology.

  4. Advantages and Pitfalls of Mass Spectrometry Based Metabolome Profiling in Systems Biology

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    Ina Aretz

    2016-04-01

    Full Text Available Mass spectrometry-based metabolome profiling became the method of choice in systems biology approaches and aims to enhance biological understanding of complex biological systems. Genomics, transcriptomics, and proteomics are well established technologies and are commonly used by many scientists. In comparison, metabolomics is an emerging field and has not reached such high-throughput, routine and coverage than other omics technologies. Nevertheless, substantial improvements were achieved during the last years. Integrated data derived from multi-omics approaches will provide a deeper understanding of entire biological systems. Metabolome profiling is mainly hampered by its diversity, variation of metabolite concentration by several orders of magnitude and biological data interpretation. Thus, multiple approaches are required to cover most of the metabolites. No software tool is capable of comprehensively translating all the data into a biologically meaningful context yet. In this review, we discuss the advantages of metabolome profiling and main obstacles limiting progress in systems biology.

  5. The Role of Mass Spectrometry-Based Metabolomics in Medical Countermeasures Against Radiation

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    Patterson, Andrew D.; Lanz, Christian; Gonzalez, Frank J.; Idle, Jeffrey R.

    2013-01-01

    Radiation metabolomics can be defined as the global profiling of biological fluids to uncover latent, endogenous small molecules whose concentrations change in a dose-response manner following exposure to ionizing radiation. In response to the potential threat of nuclear or radiological terrorism, the Center for High-Throughput Minimally Invasive Radiation Biodosimetry (CMCR) was established to develop field-deployable biodosimeters based, in principle, on rapid analysis by mass spectrometry of readily and easily obtainable biofluids. In this review, we briefly summarize radiation biology and key events related to actual and potential nuclear disasters, discuss the important contributions the field of mass spectrometry has made to the field of radiation metabolomics, and summarize current discovery efforts to use mass spectrometry-based metabolomics to identify dose-responsive urinary constituents, and ultimately to build and deploy a noninvasive high-throughput biodosimeter. PMID:19890938

  6. Towards the chiral metabolomics: Liquid chromatography–mass spectrometry based DL-amino acid analysis after labeling with a new chiral reagent, (S)-2,5-dioxopyrrolidin-1-yl-1-(4,6-dimethoxy-1,3,5-triazin-2-yl) pyrrolidine-2-carboxylate, and the application to saliva of healthy volunteers

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    Mochizuki, Toshiki; Takayama, Takahiro; Todoroki, Kenichiro; Inoue, Koichi; Min, Jun Zhe; Toyo’oka, Toshimasa, E-mail: toyooka@u-shizuoka-ken.ac.jp

    2015-05-22

    seemed to be negligible. Based on the results using L-Ala-d{sub 3}, the D-Ala in saliva seemed to be produced due to the racemization with some enzymes such as racemase. The racemization reaction was reversible, i.e., D-Ala-d{sub 3} was also racemized to L-Ala-d{sub 3} in saliva. Thus, care should be taken during the analysis of DL-amino acids in saliva. The present method using DMT-(S)-Pro-OSu may be applicable for the determination of chiral amine metabolomics, because the resulting derivatives produce the same product ions without relation to the compounds and show highly sensitive detection in the SRM mode of MS/MS. Consequently, DMT-(S)-Pro-OSu seems to be a useful chiral derivatization reagent for the determination of amines and amino acids in biological samples.

  7. Web-based resources for mass-spectrometry-based metabolomics: a user's guide.

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    Tohge, Takayuki; Fernie, Alisdair R

    2009-03-01

    In recent years, a plethora of web-based tools aimed at supporting mass-spectrometry-based metabolite profiling and metabolomics applications have appeared. Given the huge hurdles presented by the chemical diversity and dynamic range of the metabolites present in the plant kingdom, profiling the levels of a broad range of metabolites is highly challenging. Given the scale and costs involved in defining the plant metabolome, it is imperative that data are effectively shared between laboratories pursuing this goal. However, ensuring accurate comparison of samples run on the same machine within the same laboratory, let alone cross-machine and cross-laboratory comparisons, requires both careful experimentation and data interpretation. In this review, we present an overview of currently available software that aids either in peak identification or in the related field of peak alignment as well as those with utility in defining structural information of compounds and metabolic pathways.

  8. Mass spectrometry-based metabolomics: Targeting the crosstalk between gut microbiota and brain in neurodegenerative disorders.

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    Luan, Hemi; Wang, Xian; Cai, Zongwei

    2017-11-12

    Metabolomics seeks to take a "snapshot" in a time of the levels, activities, regulation and interactions of all small molecule metabolites in response to a biological system with genetic or environmental changes. The emerging development in mass spectrometry technologies has shown promise in the discovery and quantitation of neuroactive small molecule metabolites associated with gut microbiota and brain. Significant progress has been made recently in the characterization of intermediate role of small molecule metabolites linked to neural development and neurodegenerative disorder, showing its potential in understanding the crosstalk between gut microbiota and the host brain. More evidence reveals that small molecule metabolites may play a critical role in mediating microbial effects on neurotransmission and disease development. Mass spectrometry-based metabolomics is uniquely suitable for obtaining the metabolic signals in bidirectional communication between gut microbiota and brain. In this review, we summarized major mass spectrometry technologies including liquid chromatography-mass spectrometry, gas chromatography-mass spectrometry, and imaging mass spectrometry for metabolomics studies of neurodegenerative disorders. We also reviewed the recent advances in the identification of new metabolites by mass spectrometry and metabolic pathways involved in the connection of intestinal microbiota and brain. These metabolic pathways allowed the microbiota to impact the regular function of the brain, which can in turn affect the composition of microbiota via the neurotransmitter substances. The dysfunctional interaction of this crosstalk connects neurodegenerative diseases, including Parkinson's disease, Alzheimer's disease and Huntington's disease. The mass spectrometry-based metabolomics analysis provides information for targeting dysfunctional pathways of small molecule metabolites in the development of the neurodegenerative diseases, which may be valuable for the

  9. Mass spectrometry-based metabolomics: applications to biomarker and metabolic pathway research.

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    Zhang, Aihua; Sun, Hui; Yan, Guangli; Wang, Ping; Wang, Xijun

    2016-01-01

    Mass spectrometry-based metabolomics has become increasingly popular in molecular medicine. High-definition mass spectrometry (MS), coupled with pattern recognition methods, have been carried out to obtain comprehensive metabolite profiling and metabolic pathway of large biological datasets. This sets the scene for a new and powerful diagnostic approach. Analysis of the key metabolites in body fluids has become an important part of improving disease diagnosis. With technological advances in analytical techniques, the ability to measure low-molecular-weight metabolites in bio-samples provides a powerful platform for identifying metabolites that are uniquely correlated with a specific human disease. MS-based metabolomics can lead to enhanced understanding of disease mechanisms and to new diagnostic markers and has a strong potential to contribute to improving early diagnosis of diseases. This review will highlight the importance and benefit with certain characteristic examples of MS-metabolomics for identifying metabolic pathways and metabolites that accurately screen for potential diagnostic biomarkers of diseases. Copyright © 2015 John Wiley & Sons, Ltd.

  10. Mass Spectrometry-Based Quantitative Metabolomics Revealed a Distinct Lipid Profile in Breast Cancer Patients

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    Yun Yen

    2013-04-01

    Full Text Available Breast cancer accounts for the largest number of newly diagnosed cases in female cancer patients. Although mammography is a powerful screening tool, about 20% of breast cancer cases cannot be detected by this method. New diagnostic biomarkers for breast cancer are necessary. Here, we used a mass spectrometry-based quantitative metabolomics method to analyze plasma samples from 55 breast cancer patients and 25 healthy controls. A number of 30 patients and 20 age-matched healthy controls were used as a training dataset to establish a diagnostic model and to identify potential biomarkers. The remaining samples were used as a validation dataset to evaluate the predictive accuracy for the established model. Distinct separation was obtained from an orthogonal partial least squares-discriminant analysis (OPLS-DA model with good prediction accuracy. Based on this analysis, 39 differentiating metabolites were identified, including significantly lower levels of lysophosphatidylcholines and higher levels of sphingomyelins in the plasma samples obtained from breast cancer patients compared with healthy controls. Using logical regression, a diagnostic equation based on three metabolites (lysoPC a C16:0, PC ae C42:5 and PC aa C34:2 successfully differentiated breast cancer patients from healthy controls, with a sensitivity of 98.1% and a specificity of 96.0%.

  11. Effect of masticatory stimulation on the quantity and quality of saliva and the salivary metabolomic profile.

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    Nobuyuki Okuma

    Full Text Available This study characterized the changes in quality and quantity of saliva, and changes in the salivary metabolomic profile, to understand the effects of masticatory stimulation.Stimulated and unstimulated saliva samples were collected from 55 subjects and salivary hydrophilic metabolites were comprehensively quantified using capillary electrophoresis-time-of-flight mass spectrometry.In total, 137 metabolites were identified and quantified. The concentrations of 44 metabolites in stimulated saliva were significantly higher than those in unstimulated saliva. Pathway analysis identified the upregulation of the urea cycle and synthesis and degradation pathways of glycine, serine, cysteine and threonine in stimulated saliva. A principal component analysis revealed that the effect of masticatory stimulation on salivary metabolomic profiles was less dependent on sample population sex, age, and smoking. The concentrations of only 1 metabolite in unstimulated saliva, and of 3 metabolites stimulated saliva, showed significant correlation with salivary secretion volume, indicating that the salivary metabolomic profile and salivary secretion volume were independent factors.Masticatory stimulation affected not only salivary secretion volume, but also metabolite concentration patterns. A low correlation between the secretion volume and these patterns supports the conclusion that the salivary metabolomic profile may be a new indicator to characterize masticatory stimulation.

  12. Untargeted mass spectrometry-based metabolomic profiling of pleural effusions: fatty acids as novel cancer biomarkers for malignant pleural effusions.

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    Lam, Ching-Wan; Law, Chun-Yiu

    2014-09-05

    Untargeted mass spectrometry-based metabolomic profiling is a powerful analytical method used for broad-spectrum identification and quantification of metabolites in biofluids in human health and disease states. In this study, we exploit metabolomic profiling for cancer biomarker discovery for diagnosis of malignant pleural effusions. We envisage the result will be clinically useful since currently there are no cancer biomarkers that are accurate enough for the diagnosis of malignant pleural effusions. Metabolomes of 32 malignant pleural effusions from lung cancer patients and 18 benign effusions from patients with pulmonary tuberculosis were analyzed using reversed-phase liquid chromatography tandem mass spectrometry (LC-MS/MS) using AB SCIEX TripleTOF 5600. MS spectra were analyzed using XCMS, PeakView, and LipidView. Metabolome-Wide Association Study (MWAS) was performed by Receiver Operating Characteristic Curve Explorer and Tester (ROCCET). Insignificant markers were filtered out using a metabolome-wide significance level (MWSL) with p-value pleural effusions. Using a ratio of FFA 18:1-to-ceramide (d18:1/16:0), the area-under-ROC was further increased to 0.99 (95% CI = 0.91-1.00) with sensitivity 93.8% and specificity 100.0%. Using untargeted metabolomic profiling, the diagnostic cancer biomarker with the largest area-under-ROC can be determined objectively. This lipogenic phenotype could be explained by overexpression of fatty acid synthase (FASN) in cancer cells. The diagnostic performance of FFA 18:1-to-ceramide (d18:1/16:0) ratio supports its use for diagnosis of malignant pleural effusions.

  13. The Recent Developments in Sample Preparation for Mass Spectrometry-Based Metabolomics.

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    Gong, Zhi-Gang; Hu, Jing; Wu, Xi; Xu, Yong-Jiang

    2017-07-04

    Metabolomics is a critical member in systems biology. Although great progress has been achieved in metabolomics, there are still some problems in sample preparation, data processing and data interpretation. In this review, we intend to explore the roles, challenges and trends in sample preparation for mass spectrometry- (MS-) based metabolomics. The newly emerged sample preparation methods were also critically examined, including laser microdissection, in vivo sampling, dried blood spot, microwave, ultrasound and enzyme-assisted extraction, as well as microextraction techniques. Finally, we provide some conclusions and perspectives for sample preparation in MS-based metabolomics.

  14. Conventional and Advanced Separations in Mass Spectrometry-Based Metabolomics: Methodologies and Applications

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    Heyman, Heino M.; Zhang, Xing; Tang, Keqi; Baker, Erin Shammel; Metz, Thomas O.

    2016-02-16

    Metabolomics is the quantitative analysis of all metabolites in a given sample. Due to the chemical complexity of the metabolome, optimal separations are required for comprehensive identification and quantification of sample constituents. This chapter provides an overview of both conventional and advanced separations methods in practice for reducing the complexity of metabolite extracts delivered to the mass spectrometer detector, and covers gas chromatography (GC), liquid chromatography (LC), capillary electrophoresis (CE), supercritical fluid chromatography (SFC) and ion mobility spectrometry (IMS) separation techniques coupled with mass spectrometry (MS) as both uni-dimensional and as multi-dimensional approaches.

  15. Mass spectrometry-based metabolomic fingerprinting for screening cold tolerance in Arabidopsis thaliana accessions

    Czech Academy of Sciences Publication Activity Database

    Václavík, L.; Mishra, Anamika; Mishra, Kumud; Hajslova, J.

    2013-01-01

    Roč. 405, č. 8 (2013), s. 2671-2683 ISSN 1618-2642 R&D Projects: GA MŠk(CZ) ED1.1.00/02.0073; GA MŠk OC08055 Institutional support: RVO:67179843 Keywords : cold tolerance * Arabidopsis thaliana * metabolomic fingerprinting * LC-MS * DART-MS * chemometric analysis Subject RIV: EH - Ecology, Behaviour Impact factor: 3.578, year: 2013

  16. Advances in high-resolution mass spectrometry based on metabolomics studies for food--a review.

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    Rubert, Josep; Zachariasova, Milena; Hajslova, Jana

    2015-01-01

    Food authenticity becomes a necessity for global food policies, since food placed in the market without fail has to be authentic. It has always been a challenge, since in the past minor components, called also markers, have been mainly monitored by chromatographic methods in order to authenticate the food. Nevertheless, nowadays, advanced analytical methods have allowed food fingerprints to be achieved. At the same time they have been also combined with chemometrics, which uses statistical methods in order to verify food and to provide maximum information by analysing chemical data. These sophisticated methods based on different separation techniques or stand alone have been recently coupled to high-resolution mass spectrometry (HRMS) in order to verify the authenticity of food. The new generation of HRMS detectors have experienced significant advances in resolving power, sensitivity, robustness, extended dynamic range, easier mass calibration and tandem mass capabilities, making HRMS more attractive and useful to the food metabolomics community, therefore becoming a reliable tool for food authenticity. The purpose of this review is to summarise and describe the most recent metabolomics approaches in the area of food metabolomics, and to discuss the strengths and drawbacks of the HRMS analytical platforms combined with chemometrics.

  17. Global mass spectrometry based metabolomics profiling of erythrocytes infected with Plasmodium falciparum.

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    Theodore R Sana

    data acquisition. Untargeted and targeted data mining workflows, when used together to perform pathway-inferred metabolomics, have the benefit of obviating MS/MS confirmation for every detected compound.

  18. Ultrasensitive determination of mercury in human saliva by atomic fluorescence spectrometry based on solidified floating organic drop microextraction

    International Nuclear Information System (INIS)

    Yuan, C.-G.; Wang, J.; Jin, Y.

    2012-01-01

    We report on a new, rapid and simple method for the determination of ultra-trace quantities of mercury ion in human saliva. It is based on solidified floating organic drop microextraction and detection by cold vapor atomic fluorescence spectrometry (CV-AFS). Mercury ion was complexed with diethyldithiocarbamate, and the hydrophobic complex was then extracted into fine droplets of 1-undecanol. By cooling in an ice bath after extraction, the droplets in solution solidify to form a single ball floating on the surface of solution. The solidified micro drop containing the mercury complex was then transferred for determination by CV-AFS. The effects of pH value, concentration of chelating reagent, quantity of 1-undecanol, sample volume, equilibration temperature and time were investigated. Under the optimum conditions, the preconcentration of a 25-mL sample is accomplished with an enrichment factor of 182. The limit of detection is 2.5 ng L -1 . The relative standard deviation for seven replicate determinations at 0.1 ng mL -1 level is 4.1%. The method was applied to the determination of mercury in saliva samples collected from four volunteers. Two volunteers having dental amalgam fillings had 0.4 ng mL -1 mercury in their saliva, whereas mercury was not detectable in the saliva of two volunteers who had no dental fillings. (author)

  19. Pre-analytic evaluation of volumetric absorptive microsampling and integration in a mass spectrometry-based metabolomics workflow.

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    Volani, Chiara; Caprioli, Giulia; Calderisi, Giovanni; Sigurdsson, Baldur B; Rainer, Johannes; Gentilini, Ivo; Hicks, Andrew A; Pramstaller, Peter P; Weiss, Guenter; Smarason, Sigurdur V; Paglia, Giuseppe

    2017-10-01

    Volumetric absorptive microsampling (VAMS) is a novel approach that allows single-drop (10 μL) blood collection. Integration of VAMS with mass spectrometry (MS)-based untargeted metabolomics is an attractive solution for both human and animal studies. However, to boost the use of VAMS in metabolomics, key pre-analytical questions need to be addressed. Therefore, in this work, we integrated VAMS in a MS-based untargeted metabolomics workflow and investigated pre-analytical strategies such as sample extraction procedures and metabolome stability at different storage conditions. We first evaluated the best extraction procedure for the polar metabolome and found that the highest number and amount of metabolites were recovered upon extraction with acetonitrile/water (70:30). In contrast, basic conditions (pH 9) resulted in divergent metabolite profiles mainly resulting from the extraction of intracellular metabolites originating from red blood cells. In addition, the prolonged storage of blood samples at room temperature caused significant changes in metabolome composition, but once the VAMS devices were stored at - 80 °C, the metabolome remained stable for up to 6 months. The time used for drying the sample did also affect the metabolome. In fact, some metabolites were rapidly degraded or accumulated in the sample during the first 48 h at room temperature, indicating that a longer drying step will significantly change the concentration in the sample. Graphical abstract Volumetric absorptive microsampling (VAMS) is a novel technology that allows single-drop blood collection and, in combination with mass spectrometry (MS)-based untargeted metabolomics, represents an attractive solution for both human and animal studies. In this work, we integrated VAMS in a MS-based untargeted metabolomics workflow and investigated pre-analytical strategies such as sample extraction procedures and metabolome stability at different storage conditions. The latter revealed that

  20. The same microbiota and a potentially discriminant metabolome in the saliva of omnivore, ovo-lacto-vegetarian and Vegan individuals.

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    De Filippis, Francesca; Vannini, Lucia; La Storia, Antonietta; Laghi, Luca; Piombino, Paola; Stellato, Giuseppina; Serrazanetti, Diana I; Gozzi, Giorgia; Turroni, Silvia; Ferrocino, Ilario; Lazzi, Camilla; Di Cagno, Raffaella; Gobbetti, Marco; Ercolini, Danilo

    2014-01-01

    The salivary microbiota has been linked to both oral and non-oral diseases. Scant knowledge is available on the effect of environmental factors such as long-term dietary choices on the salivary microbiota and metabolome. This study analyzed the microbial diversity and metabolomic profiles of the saliva of 161 healthy individuals who followed an omnivore or ovo-lacto-vegetarian or vegan diet. A large core microbiota was identified, including 12 bacterial genera, found in >98% of the individuals. The subjects could be stratified into three "salivary types" that differed on the basis of the relative abundance of the core genera Prevotella, Streptococcus/Gemella and Fusobacterium/Neisseria. Statistical analysis indicated no effect of dietary habit on the salivary microbiota. Phylogenetic beta-diversity analysis consistently showed no differences between omnivore, ovo-lacto-vegetarian and vegan individuals. Metabolomic profiling of saliva using (1)H-NMR and GC-MS/SPME identified diet-related biomarkers that enabled a significant discrimination between the 3 groups of individuals on the basis of their diet. Formate, urea, uridine and 5-methyl-3-hexanone could discriminate samples from omnivores, whereas 1-propanol, hexanoic acid and proline were characteristic of non-omnivore diets. Although the salivary metabolome can be discriminating for diet, the microbiota has a remarkable inter-individual stability and did not vary with dietary habits. Microbial homeostasis might be perturbed with sub-standard oral hygiene or other environmental factors, but there is no current indication that a choice of an omnivore, ovo-lacto-vegetarian or vegan diet can lead to a specific composition of the oral microbiota with consequences on the oral homeostasis.

  1. The same microbiota and a potentially discriminant metabolome in the saliva of omnivore, ovo-lacto-vegetarian and Vegan individuals.

    Directory of Open Access Journals (Sweden)

    Francesca De Filippis

    Full Text Available The salivary microbiota has been linked to both oral and non-oral diseases. Scant knowledge is available on the effect of environmental factors such as long-term dietary choices on the salivary microbiota and metabolome. This study analyzed the microbial diversity and metabolomic profiles of the saliva of 161 healthy individuals who followed an omnivore or ovo-lacto-vegetarian or vegan diet. A large core microbiota was identified, including 12 bacterial genera, found in >98% of the individuals. The subjects could be stratified into three "salivary types" that differed on the basis of the relative abundance of the core genera Prevotella, Streptococcus/Gemella and Fusobacterium/Neisseria. Statistical analysis indicated no effect of dietary habit on the salivary microbiota. Phylogenetic beta-diversity analysis consistently showed no differences between omnivore, ovo-lacto-vegetarian and vegan individuals. Metabolomic profiling of saliva using (1H-NMR and GC-MS/SPME identified diet-related biomarkers that enabled a significant discrimination between the 3 groups of individuals on the basis of their diet. Formate, urea, uridine and 5-methyl-3-hexanone could discriminate samples from omnivores, whereas 1-propanol, hexanoic acid and proline were characteristic of non-omnivore diets. Although the salivary metabolome can be discriminating for diet, the microbiota has a remarkable inter-individual stability and did not vary with dietary habits. Microbial homeostasis might be perturbed with sub-standard oral hygiene or other environmental factors, but there is no current indication that a choice of an omnivore, ovo-lacto-vegetarian or vegan diet can lead to a specific composition of the oral microbiota with consequences on the oral homeostasis.

  2. Potential of human saliva for nuclear magnetic resonance-based metabolomics and for health-related biomarker identification

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    Bertram, Hanne Christine; Eggers, Nina; Eller, Nanna

    2009-01-01

    In the present study, the ability of (1)H nuclear magnetic resonance (NMR) for metabolic profiling of human saliva samples was investigated. High-resolution (1)H NMR spectra were obtained, and signals were assigned to various metabolites mainly representing small organic acids and amino acids...... in intensities of several metabolites including trimethylamine oxide (TMAO), choline, propionate, alanine, methanol, and N-acetyl groups. No effects of gender and body mass index (BMI) on the salivary metabolite profile were detected. The relationships between the salivary metabolome and glycated hemoglobin...

  3. Vitroprocines, new antibiotics against Acinetobacter baumannii, discovered from marine Vibrio sp. QWI-06 using mass-spectrometry-based metabolomics approach

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    Liaw, Chih-Chuang; Chen, Pei-Chin; Shih, Chao-Jen; Tseng, Sung-Pin; Lai, Ying-Mi; Hsu, Chi-Hsin; Dorrestein, Pieter C.; Yang, Yu-Liang

    2015-08-01

    A robust and convenient research strategy integrating state-of-the-art analytical techniques is needed to efficiently discover novel compounds from marine microbial resources. In this study, we identified a series of amino-polyketide derivatives, vitroprocines A-J, from the marine bacterium Vibrio sp. QWI-06 by an integrated approach using imaging mass spectroscopy and molecular networking, as well as conventional bioactivity-guided fractionation and isolation. The structure-activity relationship of vitroprocines against Acinetobacter baumannii is proposed. In addition, feeding experiments with 13C-labeled precursors indicated that a pyridoxal 5‧-phosphate-dependent mechanism is involved in the biosynthesis of vitroprocines. Elucidation of amino-polyketide derivatives from a species of marine bacteria for the first time demonstrates the potential of this integrated metabolomics approach to uncover marine bacterial biodiversity.

  4. A pilot study of the metabolomic profiles of saliva from female orthodontic patients with external apical root resorption.

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    Zhou, Jinglin; Hu, Huimin; Huang, Renhuan

    2018-03-01

    Orthodontically induced external apical root resorption (OIEARR) is one of the most severe complications of orthodontic treatment, which is hard to diagnose at early stage by merely radiographic examination. This study aimed to identify salivary metabolic products using unbiased metabolic profiling in order to discover biomarkers that may indicate OIEARR. Unstimulated saliva samples were analyzed from 19 healthy orthodontic patients with EARR (n=8) and non-EARR (n=11). Metabolite profiling was performed using 1 H Nuclear Magnetic Resonance (NMR) spectroscopy. A total of 187 metabolites were found in saliva samples. With supervised partial least squares discriminant analysis and regression analysis, samples from 2 groups were well separated, attributed by a series of metabolites of interest, including butyrate, propane-1,2-diol, α-linolenic acid (Ala), α-glucose, urea, fumarate, formate, guanosine, purine, etc. Indicating the increased inflammatory responses in the periodontal tissues possibly associated with energy metabolism and oxidative stress. The effective separation capacity of 1 H NMR based metabolomics suggested potential feasibility of clinical application in monitoring periodontal and apical condition in orthodontic patients during treatment and make early diagnosis of OIEARR. Metabolites detected in this study need further validation to identify exact biomarkers of OIEARR. Saliva biomarkers may assist in diagnosis and monitoring of this disease. Copyright © 2018 Elsevier B.V. All rights reserved.

  5. Influences of Normalization Method on Biomarker Discovery in Gas Chromatography-Mass Spectrometry-Based Untargeted Metabolomics: What Should Be Considered?

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    Chen, Jiaqing; Zhang, Pei; Lv, Mengying; Guo, Huimin; Huang, Yin; Zhang, Zunjian; Xu, Fengguo

    2017-05-16

    Data reduction techniques in gas chromatography-mass spectrometry-based untargeted metabolomics has made the following workflow of data analysis more lucid. However, the normalization process still perplexes researchers, and its effects are always ignored. In order to reveal the influences of normalization method, five representative normalization methods (mass spectrometry total useful signal, median, probabilistic quotient normalization, remove unwanted variation-random, and systematic ratio normalization) were compared in three real data sets with different types. First, data reduction techniques were used to refine the original data. Then, quality control samples and relative log abundance plots were utilized to evaluate the unwanted variations and the efficiencies of normalization process. Furthermore, the potential biomarkers which were screened out by the Mann-Whitney U test, receiver operating characteristic curve analysis, random forest, and feature selection algorithm Boruta in different normalized data sets were compared. The results indicated the determination of the normalization method was difficult because the commonly accepted rules were easy to fulfill but different normalization methods had unforeseen influences on both the kind and number of potential biomarkers. Lastly, an integrated strategy for normalization method selection was recommended.

  6. Determination of total concentration of chemically labeled metabolites as a means of metabolome sample normalization and sample loading optimization in mass spectrometry-based metabolomics.

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    Wu, Yiman; Li, Liang

    2012-12-18

    For mass spectrometry (MS)-based metabolomics, it is important to use the same amount of starting materials from each sample to compare the metabolome changes in two or more comparative samples. Unfortunately, for biological samples, the total amount or concentration of metabolites is difficult to determine. In this work, we report a general approach of determining the total concentration of metabolites based on the use of chemical labeling to attach a UV absorbent to the metabolites to be analyzed, followed by rapid step-gradient liquid chromatography (LC) UV detection of the labeled metabolites. It is shown that quantification of the total labeled analytes in a biological sample facilitates the preparation of an appropriate amount of starting materials for MS analysis as well as the optimization of the sample loading amount to a mass spectrometer for achieving optimal detectability. As an example, dansylation chemistry was used to label the amine- and phenol-containing metabolites in human urine samples. LC-UV quantification of the labeled metabolites could be optimally performed at the detection wavelength of 338 nm. A calibration curve established from the analysis of a mixture of 17 labeled amino acid standards was found to have the same slope as that from the analysis of the labeled urinary metabolites, suggesting that the labeled amino acid standard calibration curve could be used to determine the total concentration of the labeled urinary metabolites. A workflow incorporating this LC-UV metabolite quantification strategy was then developed in which all individual urine samples were first labeled with (12)C-dansylation and the concentration of each sample was determined by LC-UV. The volumes of urine samples taken for producing the pooled urine standard were adjusted to ensure an equal amount of labeled urine metabolites from each sample was used for the pooling. The pooled urine standard was then labeled with (13)C-dansylation. Equal amounts of the (12)C

  7. Discovery of safety biomarkers for atorvastatin in rat urine using mass spectrometry based metabolomics combined with global and targeted approach

    International Nuclear Information System (INIS)

    Kumar, Bhowmik Salil; Lee, Young-Joo; Yi, Hong Jae; Chung, Bong Chul; Jung, Byung Hwa

    2010-01-01

    In order to develop a safety biomarker for atorvastatin, this drug was orally administrated to hyperlipidemic rats, and a metabolomic study was performed. Atorvastatin was given in doses of either 70 mg kg -1 day -1 or 250 mg kg -1 day -1 for a period of 7 days (n = 4 for each group). To evaluate any abnormal effects of the drug, physiological and plasma biochemical parameters were measured and histopathological tests were carried out. Safety biomarkers were derived by comparing these parameters and using both global and targeted metabolic profiling. Global metabolic profiling was performed using liquid chromatography/time of flight/mass spectrometry (LC/TOF/MS) with multivariate data analysis. Several safety biomarker candidates that included various steroids and amino acids were discovered as a result of global metabolic profiling, and they were also confirmed by targeted metabolic profiling using gas chromatography/mass spectrometry (GC/MS) and capillary electrophoresis/mass spectrometry (CE/MS). Serum biochemical and histopathological tests were used to detect abnormal drug reactions in the liver after repeating oral administration of atorvastatin. The metabolic differences between control and the drug-treated groups were compared using PLS-DA score plots. These results were compared with the physiological and plasma biochemical parameters and the results of a histopathological test. Estrone, cortisone, proline, cystine, 3-ureidopropionic acid and histidine were proposed as potential safety biomarkers related with the liver toxicity of atorvastatin. These results indicate that the combined application of global and targeted metabolic profiling could be a useful tool for the discovery of drug safety biomarkers.

  8. Discovery of safety biomarkers for atorvastatin in rat urine using mass spectrometry based metabolomics combined with global and targeted approach

    Energy Technology Data Exchange (ETDEWEB)

    Kumar, Bhowmik Salil [Bioanalysis and Biotransformation Research Center, Korea Institute of Science and Technology, P.O. Box 131, Cheongryang, Seoul 130-650 (Korea, Republic of); University of Science and Technology, (305-333) 113 Gwahangno, Yuseong-gu, Daejeon (Korea, Republic of); Lee, Young-Joo; Yi, Hong Jae [College of Pharmacy, Kyung Hee University, Hoegi-dong, Dongdaemun-gu, Seoul 130-791 (Korea, Republic of); Chung, Bong Chul [Bioanalysis and Biotransformation Research Center, Korea Institute of Science and Technology, P.O. Box 131, Cheongryang, Seoul 130-650 (Korea, Republic of); Jung, Byung Hwa, E-mail: jbhluck@kist.re.kr [Bioanalysis and Biotransformation Research Center, Korea Institute of Science and Technology, P.O. Box 131, Cheongryang, Seoul 130-650 (Korea, Republic of); University of Science and Technology, (305-333) 113 Gwahangno, Yuseong-gu, Daejeon (Korea, Republic of)

    2010-02-19

    In order to develop a safety biomarker for atorvastatin, this drug was orally administrated to hyperlipidemic rats, and a metabolomic study was performed. Atorvastatin was given in doses of either 70 mg kg{sup -1} day{sup -1} or 250 mg kg{sup -1} day{sup -1} for a period of 7 days (n = 4 for each group). To evaluate any abnormal effects of the drug, physiological and plasma biochemical parameters were measured and histopathological tests were carried out. Safety biomarkers were derived by comparing these parameters and using both global and targeted metabolic profiling. Global metabolic profiling was performed using liquid chromatography/time of flight/mass spectrometry (LC/TOF/MS) with multivariate data analysis. Several safety biomarker candidates that included various steroids and amino acids were discovered as a result of global metabolic profiling, and they were also confirmed by targeted metabolic profiling using gas chromatography/mass spectrometry (GC/MS) and capillary electrophoresis/mass spectrometry (CE/MS). Serum biochemical and histopathological tests were used to detect abnormal drug reactions in the liver after repeating oral administration of atorvastatin. The metabolic differences between control and the drug-treated groups were compared using PLS-DA score plots. These results were compared with the physiological and plasma biochemical parameters and the results of a histopathological test. Estrone, cortisone, proline, cystine, 3-ureidopropionic acid and histidine were proposed as potential safety biomarkers related with the liver toxicity of atorvastatin. These results indicate that the combined application of global and targeted metabolic profiling could be a useful tool for the discovery of drug safety biomarkers.

  9. Mass Spectrometry-Based Metabolomics of Agave Sap (Agave salmiana after Its Inoculation with Microorganisms Isolated from Agave Sap Concentrate Selected to Enhance Anticancer Activity

    Directory of Open Access Journals (Sweden)

    Luis M. Figueroa

    2017-11-01

    Full Text Available Saponins have been correlated with the reduction of cancer cell growth and the apoptotic effect of agave sap concentrate. Empirical observations of this artisanal Mexican food have shown that fermentation occurs after agave sap is concentrated, but little is known about the microorganisms that survive after cooking, or their effects on saponins and other metabolites. The aim of this study was to evaluate the changes in metabolites found in agave (A. salmiana sap after its fermentation with microorganisms isolated from agave sap concentrate, and demonstrate its potential use to enhance anticancer activity. Microorganisms were isolated by dilution plating and identified by 16S rRNA analysis. Isolates were used to ferment agave sap, and their corresponding butanolic extracts were compared with those that enhanced the cytotoxic activity on colon (Caco-2 and liver (Hep-G2 cancer cells. Metabolite changes were investigated by mass spectrometry-based metabolomics. Among 69 isolated microorganisms, the actinomycetes Arthrobacter globiformis and Gordonia sp. were used to analyze the metabolites, along with bioactivity changes. From the 939 ions that were mainly responsible for variation among fermented samples at 48 h, 96 h, and 192 h, four were correlated to anticancer activity. It was shown that magueyoside B, a kammogenin glycoside, was found at higher intensities in the samples fermented with Gordonia sp. that reduced Hep-G2 viability better than controls. These findings showed that microorganisms from agave sap concentrate change agave sap metabolites such as saponins. Butanolic extracts obtained after agave sap fermentation with Arthrobacter globiformis or Gordonia sp. increased the cancer cell growth inhibitory effect on colon or liver cancer cells, respectively.

  10. Metabolomics

    DEFF Research Database (Denmark)

    Kamstrup-Nielsen, Maja Hermann

    Metabolomics is the analysis of the whole metabolome and the focus in metabolomics studies is to measure as many metabolites as possible. The use of chemometrics in metabolomics studies is widespread, but there is a clear lack of validation in the developed models. The focus in this thesis has been...... how to properly handle complex metabolomics data, in order to achieve reliable and valid multivariate models. This has been illustrated by three case studies with examples of forecasting breast cancer and early detection of colorectal cancer based on data from nuclear magnetic resonance (NMR...... is a presentation of a core consistency diagnostic aiding in determining the number of components in a PARAFAC2 model. It is of great importance to validate especially PLS-DA models and if not done properly, the developed models might reveal spurious groupings. Furthermore, data from metabolomics studies contain...

  11. MetCCS predictor: a web server for predicting collision cross-section values of metabolites in ion mobility-mass spectrometry based metabolomics.

    Science.gov (United States)

    Zhou, Zhiwei; Xiong, Xin; Zhu, Zheng-Jiang

    2017-07-15

    In metabolomics, rigorous structural identification of metabolites presents a challenge for bioinformatics. The use of collision cross-section (CCS) values of metabolites derived from ion mobility-mass spectrometry effectively increases the confidence of metabolite identification, but this technique suffers from the limit number of available CCS values. Currently, there is no software available for rapidly generating the metabolites' CCS values. Here, we developed the first web server, namely, MetCCS Predictor, for predicting CCS values. It can predict the CCS values of metabolites using molecular descriptors within a few seconds. Common users with limited background on bioinformatics can benefit from this software and effectively improve the metabolite identification in metabolomics. The web server is freely available at: http://www.metabolomics-shanghai.org/MetCCS/ . jiangzhu@sioc.ac.cn. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

  12. Galaxy-M: a Galaxy workflow for processing and analyzing direct infusion and liquid chromatography mass spectrometry-based metabolomics data.

    Science.gov (United States)

    Davidson, Robert L; Weber, Ralf J M; Liu, Haoyu; Sharma-Oates, Archana; Viant, Mark R

    2016-01-01

    Metabolomics is increasingly recognized as an invaluable tool in the biological, medical and environmental sciences yet lags behind the methodological maturity of other omics fields. To achieve its full potential, including the integration of multiple omics modalities, the accessibility, standardization and reproducibility of computational metabolomics tools must be improved significantly. Here we present our end-to-end mass spectrometry metabolomics workflow in the widely used platform, Galaxy. Named Galaxy-M, our workflow has been developed for both direct infusion mass spectrometry (DIMS) and liquid chromatography mass spectrometry (LC-MS) metabolomics. The range of tools presented spans from processing of raw data, e.g. peak picking and alignment, through data cleansing, e.g. missing value imputation, to preparation for statistical analysis, e.g. normalization and scaling, and principal components analysis (PCA) with associated statistical evaluation. We demonstrate the ease of using these Galaxy workflows via the analysis of DIMS and LC-MS datasets, and provide PCA scores and associated statistics to help other users to ensure that they can accurately repeat the processing and analysis of these two datasets. Galaxy and data are all provided pre-installed in a virtual machine (VM) that can be downloaded from the GigaDB repository. Additionally, source code, executables and installation instructions are available from GitHub. The Galaxy platform has enabled us to produce an easily accessible and reproducible computational metabolomics workflow. More tools could be added by the community to expand its functionality. We recommend that Galaxy-M workflow files are included within the supplementary information of publications, enabling metabolomics studies to achieve greater reproducibility.

  13. Liquid Chromatography–Mass Spectrometry Based Metabolomics Study of Cloned versus Normal Pigs Fed Either Restricted or Ad Libitum High-Energy Diets

    DEFF Research Database (Denmark)

    Christensen, Kirstine Lykke; Hedemann, Mette Skou; Jørgensen, Henry

    2012-01-01

    Genetically identical cloned pigs should in principle eliminate biological variation and provide more pronounced effects when subjected to, e.g., dietary interventions, but little is known about how phenotype and phenotypic variation is affected by cloning. Therefore, an investigation...... of the metabolome of cloned pigs compared to normal control pigs was performed to elucidate the variation and possible differences in the metabolic phenotypes during a dietary intervention. A total of 19 control pigs and 17 cloned pigs were given the same high-energy dense diet either ad libitum or in a restricted...... manner (60% of ad libitum) for 6 months, and plasma was subjected to liquid chromatography–mass spectrometry nontargeted metabolomics and biochemical analyses. Low systemic levels of IGF-1 could indicate altered growth conditions and energy metabolism in cloned pigs. In response to ad libitum feeding...

  14. The mzTab data exchange format: communicating mass-spectrometry-based proteomics and metabolomics experimental results to a wider audience.

    Science.gov (United States)

    Griss, Johannes; Jones, Andrew R; Sachsenberg, Timo; Walzer, Mathias; Gatto, Laurent; Hartler, Jürgen; Thallinger, Gerhard G; Salek, Reza M; Steinbeck, Christoph; Neuhauser, Nadin; Cox, Jürgen; Neumann, Steffen; Fan, Jun; Reisinger, Florian; Xu, Qing-Wei; Del Toro, Noemi; Pérez-Riverol, Yasset; Ghali, Fawaz; Bandeira, Nuno; Xenarios, Ioannis; Kohlbacher, Oliver; Vizcaíno, Juan Antonio; Hermjakob, Henning

    2014-10-01

    The HUPO Proteomics Standards Initiative has developed several standardized data formats to facilitate data sharing in mass spectrometry (MS)-based proteomics. These allow researchers to report their complete results in a unified way. However, at present, there is no format to describe the final qualitative and quantitative results for proteomics and metabolomics experiments in a simple tabular format. Many downstream analysis use cases are only concerned with the final results of an experiment and require an easily accessible format, compatible with tools such as Microsoft Excel or R. We developed the mzTab file format for MS-based proteomics and metabolomics results to meet this need. mzTab is intended as a lightweight supplement to the existing standard XML-based file formats (mzML, mzIdentML, mzQuantML), providing a comprehensive summary, similar in concept to the supplemental material of a scientific publication. mzTab files can contain protein, peptide, and small molecule identifications together with experimental metadata and basic quantitative information. The format is not intended to store the complete experimental evidence but provides mechanisms to report results at different levels of detail. These range from a simple summary of the final results to a representation of the results including the experimental design. This format is ideally suited to make MS-based proteomics and metabolomics results available to a wider biological community outside the field of MS. Several software tools for proteomics and metabolomics have already adapted the format as an output format. The comprehensive mzTab specification document and extensive additional documentation can be found online. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

  15. The mzTab Data Exchange Format: Communicating Mass-spectrometry-based Proteomics and Metabolomics Experimental Results to a Wider Audience*

    Science.gov (United States)

    Griss, Johannes; Jones, Andrew R.; Sachsenberg, Timo; Walzer, Mathias; Gatto, Laurent; Hartler, Jürgen; Thallinger, Gerhard G.; Salek, Reza M.; Steinbeck, Christoph; Neuhauser, Nadin; Cox, Jürgen; Neumann, Steffen; Fan, Jun; Reisinger, Florian; Xu, Qing-Wei; del Toro, Noemi; Pérez-Riverol, Yasset; Ghali, Fawaz; Bandeira, Nuno; Xenarios, Ioannis; Kohlbacher, Oliver; Vizcaíno, Juan Antonio; Hermjakob, Henning

    2014-01-01

    The HUPO Proteomics Standards Initiative has developed several standardized data formats to facilitate data sharing in mass spectrometry (MS)-based proteomics. These allow researchers to report their complete results in a unified way. However, at present, there is no format to describe the final qualitative and quantitative results for proteomics and metabolomics experiments in a simple tabular format. Many downstream analysis use cases are only concerned with the final results of an experiment and require an easily accessible format, compatible with tools such as Microsoft Excel or R. We developed the mzTab file format for MS-based proteomics and metabolomics results to meet this need. mzTab is intended as a lightweight supplement to the existing standard XML-based file formats (mzML, mzIdentML, mzQuantML), providing a comprehensive summary, similar in concept to the supplemental material of a scientific publication. mzTab files can contain protein, peptide, and small molecule identifications together with experimental metadata and basic quantitative information. The format is not intended to store the complete experimental evidence but provides mechanisms to report results at different levels of detail. These range from a simple summary of the final results to a representation of the results including the experimental design. This format is ideally suited to make MS-based proteomics and metabolomics results available to a wider biological community outside the field of MS. Several software tools for proteomics and metabolomics have already adapted the format as an output format. The comprehensive mzTab specification document and extensive additional documentation can be found online. PMID:24980485

  16. Gas chromatography-mass spectrometry based metabolomic approach for optimization and toxicity evaluation of earthworm sub-lethal responses to carbofuran.

    Directory of Open Access Journals (Sweden)

    Mohana Krishna Reddy Mudiam

    Full Text Available Despite recent advances in understanding mechanism of toxicity, the development of biomarkers (biochemicals that vary significantly with exposure to chemicals for pesticides and environmental contaminants exposure is still a challenging task. Carbofuran is one of the most commonly used pesticides in agriculture and said to be most toxic carbamate pesticide. It is necessary to identify the biochemicals that can vary significantly after carbofuran exposure on earthworms which will help to assess the soil ecotoxicity. Initially, we have optimized the extraction conditions which are suitable for high-throughput gas chromatography mass spectrometry (GC-MS based metabolomics for the tissue of earthworm, Metaphire posthuma. Upon evaluation of five different extraction solvent systems, 80% methanol was found to have good extraction efficiency based on the yields of metabolites, multivariate analysis, total number of peaks and reproducibility of metabolites. Later the toxicity evaluation was performed to characterize the tissue specific metabolomic perturbation of earthworm, Metaphire posthuma after exposure to carbofuran at three different concentration levels (0.15, 0.3 and 0.6 mg/kg of soil. Seventeen metabolites, contributing to the best classification performance of highest dose dependent carbofuran exposed earthworms from healthy controls were identified. This study suggests that GC-MS based metabolomic approach was precise and sensitive to measure the earthworm responses to carbofuran exposure in soil, and can be used as a promising tool for environmental eco-toxicological studies.

  17. Assessment of protein modifications in liver of rats under chronic treatment with paracetamol (acetaminophen) using two complementary mass spectrometry-based metabolomic approaches.

    Science.gov (United States)

    Mast, Carole; Lyan, Bernard; Joly, Charlotte; Centeno, Delphine; Giacomoni, Franck; Martin, Jean-François; Mosoni, Laurent; Dardevet, Dominique; Pujos-Guillot, Estelle; Papet, Isabelle

    2015-04-29

    Liver protein can be altered under paracetamol (APAP) treatment. APAP-protein adducts and other protein modifications (oxidation/nitration, expression) play a role in hepatotoxicity induced by acute overdoses, but it is unknown whether liver protein modifications occur during long-term treatment with non-toxic doses of APAP. We quantified APAP-protein adducts and assessed other protein modifications in the liver from rats under chronic (17 days) treatment with two APAP doses (0.5% or 1% of APAP in the diet w/w). A targeted metabolomic method was validated and used to quantify APAP-protein adducts as APAP-cysteine adducts following proteolytic hydrolysis. The limit of detection was found to be 7ng APAP-cysteine/mL hydrolysate i.e. an APAP-Cys to tyrosine ratio of 0.016‰. Other protein modifications were assessed on the same protein hydrolysate by untargeted metabolomics including a new strategy to process the data and identify discriminant molecules. These two complementary mass spectrometry (MS)-based metabolic approaches enabled the assessment of a wide range of protein modifications induced by chronic treatment with APAP. APAP-protein adducts were detected even in the absence of glutathione depletion and hepatotoxicity, i.e. in the 0.5% APAP group, and increased by 218% in the 1% APAP group compared to the 0.5% APAP group. At the same time, the untargeted metabolomic method revealed a decrease in the binding of cysteine, cysteinyl-glycine and GSH to thiol groups of protein cysteine residues, an increase in the oxidation of tryptophan and proline residues and a modification in protein expression. This wide range of modifications in liver proteins occurred in rats under chronic treatment with APAP that did not induce hepatotoxicity. Copyright © 2015 Elsevier B.V. All rights reserved.

  18. Investigation of the Antifatigue Effects of Korean Ginseng on Professional Athletes by Gas Chromatography-Time-of-Flight-Mass Spectrometry-Based Metabolomics.

    Science.gov (United States)

    Yan, Bei; Liu, Yao; Shi, Aixin; Wang, Zhihong; Aa, Jiye; Huang, Xiaoping; Liu, Yi

    2018-05-01

    Ginseng is usually used for alleviating fatigue. The purpose of this paper was to evaluate the regulatory effect of Korean ginseng on the metabolic pattern in professional athletes, and, further, to explore the underlying mechanism of the antifatigue effect of Korean ginseng. GC-time-of-flight-MS was used to profile serum samples from professional athletes before training and after 15 and 30 day training, and professional athletes administered with Korean ginseng in the meanwhile. Biochemical parameters of all athletes were also analyzed. For the athlete control group, strength-endurance training resulted in an elevation of creatine kinase (CK) and blood urea nitrogen (BUN), and a reduction in blood hemoglobin, and a dynamic trajectory of the metabolomic profile which were related to fatigue. Korean ginseng treatment not only lead to a marked reduction in CK and blood urea nitrogen (BUN) in serum, but also showed regulatory effects on the serum metabolic profile and restored scores plots close to normal, suggesting that the change in metabolic profiling could reflect the antifatigue effect of Korean ginseng. Furthermore, perturbed levels of 11 endogenous metabolites were regulated by Korean ginseng significantly, which might be primarily involved in lipid metabolism, energy balance, and chemical signaling. These findings suggest that metabolomics is a potential tool for the evaluation of the antifatigue effect of Korean ginseng and for the elucidation of its pharmacological mechanism.

  19. Metabolome analysis for discovering biomarkers of gastroenterological cancer.

    Science.gov (United States)

    Suzuki, Makoto; Nishiumi, Shin; Matsubara, Atsuki; Azuma, Takeshi; Yoshida, Masaru

    2014-09-01

    Improvements in analytical technologies have made it possible to rapidly determine the concentrations of thousands of metabolites in any biological sample, which has resulted in metabolome analysis being applied to various types of research, such as clinical, cell biology, and plant/food science studies. The metabolome represents all of the end products and by-products of the numerous complex metabolic pathways operating in a biological system. Thus, metabolome analysis allows one to survey the global changes in an organism's metabolic profile and gain a holistic understanding of the changes that occur in organisms during various biological processes, e.g., during disease development. In clinical metabolomic studies, there is a strong possibility that differences in the metabolic profiles of human specimens reflect disease-specific states. Recently, metabolome analysis of biofluids, e.g., blood, urine, or saliva, has been increasingly used for biomarker discovery and disease diagnosis. Mass spectrometry-based techniques have been extensively used for metabolome analysis because they exhibit high selectivity and sensitivity during the identification and quantification of metabolites. Here, we describe metabolome analysis using liquid chromatography-mass spectrometry, gas chromatography-mass spectrometry, and capillary electrophoresis-mass spectrometry. Furthermore, the findings of studies that attempted to discover biomarkers of gastroenterological cancer are also outlined. Finally, we discuss metabolome analysis-based disease diagnosis. Copyright © 2014 Elsevier B.V. All rights reserved.

  20. Web Server for Peak Detection, Baseline Correction, and Alignment in Two-Dimensional Gas Chromatography Mass Spectrometry-Based Metabolomics Data.

    Science.gov (United States)

    Tian, Tze-Feng; Wang, San-Yuan; Kuo, Tien-Chueh; Tan, Cheng-En; Chen, Guan-Yuan; Kuo, Ching-Hua; Chen, Chi-Hsin Sally; Chan, Chang-Chuan; Lin, Olivia A; Tseng, Y Jane

    2016-11-01

    Two-dimensional gas chromatography time-of-flight mass spectrometry (GC×GC/TOF-MS) is superior for chromatographic separation and provides great sensitivity for complex biological fluid analysis in metabolomics. However, GC×GC/TOF-MS data processing is currently limited to vendor software and typically requires several preprocessing steps. In this work, we implement a web-based platform, which we call GC 2 MS, to facilitate the application of recent advances in GC×GC/TOF-MS, especially for metabolomics studies. The core processing workflow of GC 2 MS consists of blob/peak detection, baseline correction, and blob alignment. GC 2 MS treats GC×GC/TOF-MS data as pictures and clusters the pixels as blobs according to the brightness of each pixel to generate a blob table. GC 2 MS then aligns the blobs of two GC×GC/TOF-MS data sets according to their distance and similarity. The blob distance and similarity are the Euclidean distance of the first and second retention times of two blobs and the Pearson's correlation coefficient of the two mass spectra, respectively. GC 2 MS also directly corrects the raw data baseline. The analytical performance of GC 2 MS was evaluated using GC×GC/TOF-MS data sets of Angelica sinensis compounds acquired under different experimental conditions and of human plasma samples. The results show that GC 2 MS is an easy-to-use tool for detecting peaks and correcting baselines, and GC 2 MS is able to align GC×GC/TOF-MS data sets acquired under different experimental conditions. GC 2 MS is freely accessible at http://gc2ms.web.cmdm.tw .

  1. Rapid resolution liquid chromatography coupled with quadrupole time-of-flight mass spectrometry-based metabolomics approach to study the effects of jieduquyuziyin prescription on systemic lupus erythematosus.

    Science.gov (United States)

    Ding, Xinghong; Hu, Jinbo; Wen, Chengping; Ding, Zhishan; Yao, Li; Fan, Yongsheng

    2014-01-01

    Jieduquyuziyin prescription (JP), a traditional Chinese medicine (TCM) prescription, has been widely used for the clinical treatment of systemic lupus erythematosus (SLE). However, the complex chemical constituents of JP and the multifactorial pathogenesis of SLE make research on the therapeutic mechanism of JP in SLE challenging. In this paper, a serum metabolomics approach based on rapid resolution liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (RRLC-Q-TOF/MS) was employed to acquire the metabolic characteristics of serum samples obtained from mice in the SLE model group, JP-treated group, prednisone acetate (PA)-treated group and control group. The orthogonal partial least squares (OPLS) was applied to recognize metabolic patterns, and an obvious separation of groups was obtained. Thirteen metabolites, namely, phosphatidylethanolamine (PE 20:3), hepoxilin B3, lyso- phosphatidylethanolamine (lyso-PE 22:6), 12S-hydroxypentaenoic acid (12S-HEPE), traumatic acid, serotonin, platelet-activating factor (PAF), phosphatidylcholine (PC 20:5),eicosapentaenoic acid (EPA), 12(S)-hydroxyei- cosatetraenoic acid (12S-HETE), 14-hydroxy docosahexaenoic acid (14-HDOHE), lyso-phosphatidylcholine (lyso-PC 20:4), and indole acetaldehyde, were identified and characterized as differential metabolites involved in the pathogenesis of SLE. After treatment with JP, the relative content of 12(S)-HETE, PAF, 12(S)-HEPE, EPA, PE (20:3), Lyso-PE(22:6), and 14-HDOHE were effectively regulated, which suggested that the therapeutic effects of JP on SLE may involve regulating disturbances to the metabolism of unsaturated fatty acid, tryptophan and phospholipid. This research also demonstrated that metabolomics is a powerful tool for researching complex disease mechanisms and evaluating the mechanism of action of TCM.

  2. Gas Chromatography/Mass Spectrometry-Based Metabolomic Profiling Reveals Alterations in Mouse Plasma and Liver in Response to Fava Beans.

    Science.gov (United States)

    Xiao, Man; Du, Guankui; Zhong, Guobing; Yan, Dongjing; Zeng, Huazong; Cai, Wangwei

    2016-01-01

    Favism is a life-threatening hemolytic anemia resulting from the intake of fava beans by susceptible individuals with low erythrocytic glucose 6-phosphate dehydrogenase (G6PD) activity. However, little is known about the metabolomic changes in plasma and liver after the intake of fava beans in G6PD normal and deficient states. In this study, gas chromatography/mass spectrometry was used to analyze the plasma and liver metabolic alterations underlying the effects of fava beans in C3H- and G6PD-deficient (G6PDx) mice, and to find potential biomarkers and metabolic changes associated with favism. Our results showed that fava beans induced oxidative stress in both C3H and G6PDx mice. Significantly, metabolomic differences were observed in plasma and liver between the control and fava bean treated groups of both C3H and G6PDx mice. The levels of 7 and 21 metabolites in plasma showed significant differences between C3H-control (C3H-C)- and C3H fava beans-treated (C3H-FB) mice, and G6PDx-control (G6PDx-C)- and G6PDx fava beans-treated (G6PDx-FB) mice, respectively. Similarly, the levels of 7 and 25 metabolites in the liver showed significant differences between C3H and C3H-FB, and G6PDx and G6PDx-FB, respectively. The levels of oleic acid, linoleic acid, and creatinine were significantly increased in the plasma of both C3H-FB and G6PDx-FB mice. In the liver, more metabolic alterations were observed in G6PDx-FB mice than in C3H-FB mice, and were involved in a sugar, fatty acids, amino acids, cholesterol biosynthesis, the urea cycle, and the nucleotide metabolic pathway. These findings suggest that oleic acid, linoleic acid, and creatinine may be potential biomarkers of the response to fava beans in C3H and G6PDx mice and therefore that oleic acid and linoleic acid may be involved in oxidative stress induced by fava beans. This study demonstrates that G6PD activity in mice can affect their metabolic pathways in response to fava beans.

  3. Gas Chromatography/Mass Spectrometry-Based Metabolomic Profiling Reveals Alterations in Mouse Plasma and Liver in Response to Fava Beans.

    Directory of Open Access Journals (Sweden)

    Man Xiao

    Full Text Available Favism is a life-threatening hemolytic anemia resulting from the intake of fava beans by susceptible individuals with low erythrocytic glucose 6-phosphate dehydrogenase (G6PD activity. However, little is known about the metabolomic changes in plasma and liver after the intake of fava beans in G6PD normal and deficient states. In this study, gas chromatography/mass spectrometry was used to analyze the plasma and liver metabolic alterations underlying the effects of fava beans in C3H- and G6PD-deficient (G6PDx mice, and to find potential biomarkers and metabolic changes associated with favism. Our results showed that fava beans induced oxidative stress in both C3H and G6PDx mice. Significantly, metabolomic differences were observed in plasma and liver between the control and fava bean treated groups of both C3H and G6PDx mice. The levels of 7 and 21 metabolites in plasma showed significant differences between C3H-control (C3H-C- and C3H fava beans-treated (C3H-FB mice, and G6PDx-control (G6PDx-C- and G6PDx fava beans-treated (G6PDx-FB mice, respectively. Similarly, the levels of 7 and 25 metabolites in the liver showed significant differences between C3H and C3H-FB, and G6PDx and G6PDx-FB, respectively. The levels of oleic acid, linoleic acid, and creatinine were significantly increased in the plasma of both C3H-FB and G6PDx-FB mice. In the liver, more metabolic alterations were observed in G6PDx-FB mice than in C3H-FB mice, and were involved in a sugar, fatty acids, amino acids, cholesterol biosynthesis, the urea cycle, and the nucleotide metabolic pathway. These findings suggest that oleic acid, linoleic acid, and creatinine may be potential biomarkers of the response to fava beans in C3H and G6PDx mice and therefore that oleic acid and linoleic acid may be involved in oxidative stress induced by fava beans. This study demonstrates that G6PD activity in mice can affect their metabolic pathways in response to fava beans.

  4. Fenofibrate Metabolism in the Cynomolgus Monkey using Ultraperformance Liquid Chromatography-Quadrupole Time-of-Flight Mass Spectrometry-Based MetabolomicsS⃞

    Science.gov (United States)

    Liu, Aiming; Patterson, Andrew D.; Yang, Zongtao; Zhang, Xinying; Liu, Wei; Qiu, Fayang; Sun, He; Krausz, Kristopher W.; Idle, Jeffrey R.; Gonzalez, Frank J.; Dai, Renke

    2009-01-01

    Fenofibrate, widely used for the treatment of dyslipidemia, activates the nuclear receptor, peroxisome proliferator-activated receptor α. However, liver toxicity, including liver cancer, occurs in rodents treated with fibrate drugs. Marked species differences occur in response to fibrate drugs, especially between rodents and humans, the latter of which are resistant to fibrate-induced cancer. Fenofibrate metabolism, which also shows species differences, has not been fully determined in humans and surrogate primates. In the present study, the metabolism of fenofibrate was investigated in cynomolgus monkeys by ultraperformance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC-QTOFMS)-based metabolomics. Urine samples were collected before and after oral doses of fenofibrate. The samples were analyzed in both positive-ion and negative-ion modes by UPLC-QTOFMS, and after data deconvolution, the resulting data matrices were subjected to multivariate data analysis. Pattern recognition was performed on the retention time, mass/charge ratio, and other metabolite-related variables. Synthesized or purchased authentic compounds were used for metabolite identification and structure elucidation by liquid chromatographytandem mass spectrometry. Several metabolites were identified, including fenofibric acid, reduced fenofibric acid, fenofibric acid ester glucuronide, reduced fenofibric acid ester glucuronide, and compound X. Another two metabolites (compound B and compound AR), not previously reported in other species, were characterized in cynomolgus monkeys. More importantly, previously unknown metabolites, fenofibric acid taurine conjugate and reduced fenofibric acid taurine conjugate were identified, revealing a previously unrecognized conjugation pathway for fenofibrate. PMID:19251819

  5. Ion trace detection algorithm to extract pure ion chromatograms to improve untargeted peak detection quality for liquid chromatography/time-of-flight mass spectrometry-based metabolomics data.

    Science.gov (United States)

    Wang, San-Yuan; Kuo, Ching-Hua; Tseng, Yufeng J

    2015-03-03

    Able to detect known and unknown metabolites, untargeted metabolomics has shown great potential in identifying novel biomarkers. However, elucidating all possible liquid chromatography/time-of-flight mass spectrometry (LC/TOF-MS) ion signals in a complex biological sample remains challenging since many ions are not the products of metabolites. Methods of reducing ions not related to metabolites or simply directly detecting metabolite related (pure) ions are important. In this work, we describe PITracer, a novel algorithm that accurately detects the pure ions of a LC/TOF-MS profile to extract pure ion chromatograms and detect chromatographic peaks. PITracer estimates the relative mass difference tolerance of ions and calibrates the mass over charge (m/z) values for peak detection algorithms with an additional option to further mass correction with respect to a user-specified metabolite. PITracer was evaluated using two data sets containing 373 human metabolite standards, including 5 saturated standards considered to be split peaks resultant from huge m/z fluctuation, and 12 urine samples spiked with 50 forensic drugs of varying concentrations. Analysis of these data sets show that PITracer correctly outperformed existing state-of-art algorithm and extracted the pure ion chromatograms of the 5 saturated standards without generating split peaks and detected the forensic drugs with high recall, precision, and F-score and small mass error.

  6. Global metabolomic analysis of human saliva and plasma from healthy and diabetic subjects, with and without periodontal disease.

    Directory of Open Access Journals (Sweden)

    Virginia M Barnes

    Full Text Available Recent studies suggest that periodontal disease and type 2 diabetes mellitus are bi-directionally associated. Identification of a molecular signature for periodontitis using unbiased metabolic profiling could allow identification of biomarkers to assist in the diagnosis and monitoring of both diabetes and periodontal disease. This cross-sectional study identified plasma and salivary metabolic products associated with periodontitis and/or diabetes in order to discover biomarkers that may differentiate or demonstrate an interaction of these diseases. Saliva and plasma samples were analyzed from 161 diabetic and non-diabetic human subjects with a healthy periodontium, gingivitis and periodontitis. Metabolite profiling was performed using Metabolon's platform technology. A total of 772 metabolites were found in plasma and 475 in saliva. Diabetics had significantly higher levels of glucose and α-hydroxybutyrate, the established markers of diabetes, for all periodontal groups of subjects. Comparison of healthy, gingivitis and periodontitis saliva samples within the non-diabetic group confirmed findings from previous studies that included increased levels of markers of cellular energetic stress, increased purine degradation and glutathione metabolism through increased levels of oxidized glutathione and cysteine-glutathione disulfide, markers of oxidative stress, including increased purine degradation metabolites (e.g. guanosine and inosine, increased amino acid levels suggesting protein degradation, and increased ω-3 (docosapentaenoate and ω-6 fatty acid (linoleate and arachidonate signatures. Differences in saliva between diabetic and non-diabetic cohorts showed altered signatures of carbohydrate, lipid and oxidative stress exist in the diabetic samples. Global untargeted metabolic profiling of human saliva in diabetics replicated the metabolite signature of periodontal disease progression in non-diabetic patients and revealed unique metabolic

  7. Quantification in untargeted mass spectrometry-based metabolomics

    NARCIS (Netherlands)

    Kloet, Frans Meindert van der

    2014-01-01

    The aim of this thesis was to develop concepts and methods to extract qualitative and quantitative information about metabolites from untargeted mass spectrometric data of biological samples. Several typical challenges in data handling were addressed that prevent a straightforward interpretation

  8. Metabolomics in transfusion medicine.

    Science.gov (United States)

    Nemkov, Travis; Hansen, Kirk C; Dumont, Larry J; D'Alessandro, Angelo

    2016-04-01

    Biochemical investigations on the regulatory mechanisms of red blood cell (RBC) and platelet (PLT) metabolism have fostered a century of advances in the field of transfusion medicine. Owing to these advances, storage of RBCs and PLT concentrates has become a lifesaving practice in clinical and military settings. There, however, remains room for improvement, especially with regard to the introduction of novel storage and/or rejuvenation solutions, alternative cell processing strategies (e.g., pathogen inactivation technologies), and quality testing (e.g., evaluation of novel containers with alternative plasticizers). Recent advancements in mass spectrometry-based metabolomics and systems biology, the bioinformatics integration of omics data, promise to speed up the design and testing of innovative storage strategies developed to improve the quality, safety, and effectiveness of blood products. Here we review the currently available metabolomics technologies and briefly describe the routine workflow for transfusion medicine-relevant studies. The goal is to provide transfusion medicine experts with adequate tools to navigate through the otherwise overwhelming amount of metabolomics data burgeoning in the field during the past few years. Descriptive metabolomics data have represented the first step omics researchers have taken into the field of transfusion medicine. However, to up the ante, clinical and omics experts will need to merge their expertise to investigate correlative and mechanistic relationships among metabolic variables and transfusion-relevant variables, such as 24-hour in vivo recovery for transfused RBCs. Integration with systems biology models will potentially allow for in silico prediction of metabolic phenotypes, thus streamlining the design and testing of alternative storage strategies and/or solutions. © 2015 AABB.

  9. Metabolomic Studies of Oral Biofilm, Oral Cancer, and Beyond

    Directory of Open Access Journals (Sweden)

    Jumpei Washio

    2016-06-01

    Full Text Available Oral diseases are known to be closely associated with oral biofilm metabolism, while cancer tissue is reported to possess specific metabolism such as the ‘Warburg effect’. Metabolomics might be a useful method for clarifying the whole metabolic systems that operate in oral biofilm and oral cancer, however, technical limitations have hampered such research. Fortunately, metabolomics techniques have developed rapidly in the past decade, which has helped to solve these difficulties. In vivo metabolomic analyses of the oral biofilm have produced various findings. Some of these findings agreed with the in vitro results obtained in conventional metabolic studies using representative oral bacteria, while others differed markedly from them. Metabolomic analyses of oral cancer tissue not only revealed differences between metabolomic profiles of cancer and normal tissue, but have also suggested a specific metabolic system operates in oral cancer tissue. Saliva contains a variety of metabolites, some of which might be associated with oral or systemic disease; therefore, metabolomics analysis of saliva could be useful for identifying disease-specific biomarkers. Metabolomic analyses of the oral biofilm, oral cancer, and saliva could contribute to the development of accurate diagnostic, techniques, safe and effective treatments, and preventive strategies for oral and systemic diseases.

  10. Metabolomic Studies of Oral Biofilm, Oral Cancer, and Beyond.

    Science.gov (United States)

    Washio, Jumpei; Takahashi, Nobuhiro

    2016-06-02

    Oral diseases are known to be closely associated with oral biofilm metabolism, while cancer tissue is reported to possess specific metabolism such as the 'Warburg effect'. Metabolomics might be a useful method for clarifying the whole metabolic systems that operate in oral biofilm and oral cancer, however, technical limitations have hampered such research. Fortunately, metabolomics techniques have developed rapidly in the past decade, which has helped to solve these difficulties. In vivo metabolomic analyses of the oral biofilm have produced various findings. Some of these findings agreed with the in vitro results obtained in conventional metabolic studies using representative oral bacteria, while others differed markedly from them. Metabolomic analyses of oral cancer tissue not only revealed differences between metabolomic profiles of cancer and normal tissue, but have also suggested a specific metabolic system operates in oral cancer tissue. Saliva contains a variety of metabolites, some of which might be associated with oral or systemic disease; therefore, metabolomics analysis of saliva could be useful for identifying disease-specific biomarkers. Metabolomic analyses of the oral biofilm, oral cancer, and saliva could contribute to the development of accurate diagnostic, techniques, safe and effective treatments, and preventive strategies for oral and systemic diseases.

  11. A robust and versatile mass spectrometry platform for comprehensive assessment of the thiol redox metabolome

    Directory of Open Access Journals (Sweden)

    T.R. Sutton

    2018-06-01

    . Additional determination of acid-labile sulfide/thiols was demonstrated in human blood cells, urine and saliva. Using this simplified mass spectrometry-based workflow the thiol redox metabolome can be determined in samples from clinical and translational studies, providing a novel prognostic/diagnostic platform for patient stratification, drug monitoring, and identification of new therapeutic approaches in redox diseases. Keywords: Oxidative stress, Redox status, Reactive species interactome, Glutathione, Hydrogen sulfide, Persulfides, Thiol-maleimide michael addition

  12. Saliva and dental erosion

    Directory of Open Access Journals (Sweden)

    Marília Afonso Rabelo Buzalaf

    2012-10-01

    Full Text Available Dental erosion is a multifactorial condition. The consideration of chemical, biological and behavioral factors is fundamental for its prevention and therapy. Among the biological factors, saliva is one of the most important parameters in the protection against erosive wear. Objective: This review discusses the role of salivary factors on the development of dental erosion. Material and Methods: A search was undertaken on MeDLINe website for papers from 1969 to 2010. The keywords used in the research were "saliva", "acquired pellicle", "salivary flow", "salivary buffering capacity" and "dental erosion". Inclusion of studies, data extraction and quality assessment were undertaken independently and in duplicate by two members of the review team. Disagreements were solved by discussion and consensus or by a third party. Results: Several characteristics and properties of saliva play an important role in dental erosion. Salivary clearance gradually eliminates the acids through swallowing and saliva presents buffering capacity causing neutralization and buffering of dietary acids. Salivary flow allows dilution of the acids. In addition, saliva is supersaturated with respect to tooth mineral, providing calcium, phosphate and fluoride necessary for remineralization after an erosive challenge. Furthermore, many proteins present in saliva and acquired pellicle play an important role in dental erosion. Conclusions: Saliva is the most important biological factor affecting the progression of dental erosion. Knowledge of its components and properties involved in this protective role can drive the development of preventive measures targeting to enhance its known beneficial effects.

  13. Saliva and dental erosion.

    Science.gov (United States)

    Buzalaf, Marília Afonso Rabelo; Hannas, Angélicas Reis; Kato, Melissa Thiemi

    2012-01-01

    Dental erosion is a multifactorial condition. The consideration of chemical, biological and behavioral factors is fundamental for its prevention and therapy. Among the biological factors, saliva is one of the most important parameters in the protection against erosive wear. This review discusses the role of salivary factors on the development of dental erosion. A search was undertaken on MeDLINe website for papers from 1969 to 2010. The keywords used in the research were "saliva", "acquired pellicle", "salivary flow", "salivary buffering capacity" and "dental erosion". Inclusion of studies, data extraction and quality assessment were undertaken independently and in duplicate by two members of the review team. Disagreements were solved by discussion and consensus or by a third party. Several characteristics and properties of saliva play an important role in dental erosion. Salivary clearance gradually eliminates the acids through swallowing and saliva presents buffering capacity causing neutralization and buffering of dietary acids. Salivary flow allows dilution of the acids. In addition, saliva is supersaturated with respect to tooth mineral, providing calcium, phosphate and fluoride necessary for remineralization after an erosive challenge. Furthermore, many proteins present in saliva and acquired pellicle play an important role in dental erosion. Saliva is the most important biological factor affecting the progression of dental erosion. Knowledge of its components and properties involved in this protective role can drive the development of preventive measures targeting to enhance its known beneficial effects.

  14. Nutritional Metabolomics

    DEFF Research Database (Denmark)

    Gürdeniz, Gözde

    strategy influences the patterns identified as important for the nutritional question under study. Therefore, in depth understanding of the study design and the specific effects of the analytical technology on the produced data is extremely important to achieve high quality data handling. Besides data......Metabolomics provides a holistic approach to investigate the perturbations in human metabolism with respect to a specific exposure. In nutritional metabolomics, the research question is generally related to the effect of a specific food intake on metabolic profiles commonly of plasma or urine....... Application of multiple analytical strategies may provide comprehensive information to reach a valid answer to these research questions. In this thesis, I investigated several analytical technologies and data handling strategies in order to evaluate their effects on the biological answer. In metabolomics, one...

  15. Saliva and wound healing.

    Science.gov (United States)

    Brand, Henk S; Ligtenberg, Antoon J M; Veerman, Enno C I

    2014-01-01

    Oral wounds heal faster and with less scar formation than skin wounds. One of the key factors involved is saliva, which promotes wound healing in several ways. Saliva creates a humid environment, thus improving the survival and functioning of inflammatory cells that are crucial for wound healing. In addition, saliva contains several proteins which play a role in the different stages of wound healing. Saliva contains substantial amounts of tissue factor, which dramatically accelerates blood clotting. Subsequently, epidermal growth factor in saliva promotes the proliferation of epithelial cells. Secretory leucocyte protease inhibitor inhibits the tissue-degrading activity of enzymes like elastase and trypsin. Absence of this protease inhibitor delays oral wound healing. Salivary histatins in vitro promote wound closure by enhancing cell spreading and cell migration, but do not stimulate cell proliferation. A synthetic cyclic variant of histatin exhibits a 1,000-fold higher activity than linear histatin, which makes this cyclic variant a promising agent for the development of a new wound healing medication. Conclusively, recognition of the many roles salivary proteins play in wound healing makes saliva a promising source for the development of new drugs involved in tissue regeneration.

  16. Mass Spectrometry-Based Biomarker Discovery.

    Science.gov (United States)

    Zhou, Weidong; Petricoin, Emanuel F; Longo, Caterina

    2017-01-01

    The discovery of candidate biomarkers within the entire proteome is one of the most important and challenging goals in proteomic research. Mass spectrometry-based proteomics is a modern and promising technology for semiquantitative and qualitative assessment of proteins, enabling protein sequencing and identification with exquisite accuracy and sensitivity. For mass spectrometry analysis, protein extractions from tissues or body fluids and subsequent protein fractionation represent an important and unavoidable step in the workflow for biomarker discovery. Following extraction of proteins, the protein mixture must be digested, reduced, alkylated, and cleaned up prior to mass spectrometry. The aim of our chapter is to provide comprehensible and practical lab procedures for sample digestion, protein fractionation, and subsequent mass spectrometry analysis.

  17. Oestrogens in saliva

    International Nuclear Information System (INIS)

    Rothschild, R.S.; Levine, L.S.; Hattingh, J.

    1981-01-01

    Matched plasma and saliva samples were obtained from a non-pregnant and pregnant group (last trimester) of female caucasians. Using a sensitive radioimmunoassay, 17β-oestradiol was measured, and the gingival index system of Loe (1967) was used to assess the gingival condition of each patient. The results showed that 17β-oestradiol could be measured in saliva but that the levels were extremely low and a very sensitive immunoassay was necessary. In the pregnant group, saliva represented 3 per cent of the plasma level. This was not the case in the non-pregnant group, probably because of the constantly changing free: bound plasma ratio. The results are discussed in relation to the fact that oestrogens are known to bind to the oral epithelium [af

  18. A Combined Metabolomic and Proteomic Analysis of Gestational Diabetes Mellitus

    OpenAIRE

    Hajduk, Joanna; Klupczynska, Agnieszka; Dereziński, Paweł; Matysiak, Jan; Kokot, Piotr; Nowak, Dorota; Gajęcka, Marzena; Nowak-Markwitz, Ewa; Kokot, Zenon

    2015-01-01

    The aim of this pilot study was to apply a novel combined metabolomic and proteomic approach in analysis of gestational diabetes mellitus. The investigation was performed with plasma samples derived from pregnant women with diagnosed gestational diabetes mellitus (n = 18) and a matched control group (n = 13). The mass spectrometry-based analyses allowed to determine 42 free amino acids and low molecular-weight peptide profiles. Different expressions of several peptides and altered amino acid ...

  19. Erosion protection conferred by whole human saliva, dialysed saliva, and artificial saliva

    Science.gov (United States)

    Baumann, T.; Kozik, J.; Lussi, A.; Carvalho, T. S.

    2016-10-01

    During dental erosion, tooth minerals are dissolved, leading to a softening of the surface and consequently to irreversible surface loss. Components from human saliva form a pellicle on the tooth surface, providing some protection against erosion. To assess the effect of different components and compositions of saliva on the protective potential of the pellicle against enamel erosion, we prepared four different kinds of saliva: human whole stimulated saliva (HS), artificial saliva containing only ions (AS), human saliva dialysed against artificial saliva, containing salivary proteins and ions (HS/AS), and human saliva dialysed against deionised water, containing only salivary proteins but no ions (HS/DW). Enamel specimens underwent four cycles of immersion in either HS, AS, HS/AS, HS/DW, or a humid chamber (Ctrl), followed by erosion with citric acid. During the cycling process, the surface hardness and the calcium released from the surface of the specimens were measured. The different kinds of saliva provided different levels of protection, HS/DW exhibiting significantly better protection than all the other groups (p < 0.0001). Different components of saliva, therefore, have different effects on the protective properties of the pellicle and the right proportions of these components in saliva are critical for the ability to form a protective pellicle.

  20. Saliva Preservative for Diagnostic Purposes

    Science.gov (United States)

    Pierson, Duane L.; Mehta, Satish K.

    2012-01-01

    Saliva is an important body fluid for diagnostic purposes. Glycoproteins, glucose, steroids, DNA, and other molecules of diagnostic value are found in saliva. It is easier to collect as compared to blood or urine. Unfortunately, saliva also contains large numbers of bacteria that can release enzymes, which can degrade proteins and nucleic acids. These degradative enzymes destroy or reduce saliva s diagnostic value. This innovation describes the formulation of a chemical preservative that prevents microbial growth and inactivates the degradative enzymes. This extends the time that saliva can be stored or transported without losing its diagnostic value. Multiple samples of saliva can be collected if needed without causing discomfort to the subject and it does not require any special facilities to handle after it is collected.

  1. Circadian Metabolomics in Time and Space

    Directory of Open Access Journals (Sweden)

    Kenneth A. Dyar

    2017-07-01

    Full Text Available Circadian rhythms are widely known to govern human health and disease, but specific pathogenic mechanisms linking circadian disruption to metabolic diseases are just beginning to come to light. This is thanks in part to the development and application of various “omics”-based tools in biology and medicine. Current high-throughput technologies allow for the simultaneous monitoring of multiple dynamic cellular events over time, ranging from gene expression to metabolite abundance and sub-cellular localization. These fundamental temporal and spatial perspectives have allowed for a more comprehensive understanding of how various dynamic cellular events and biochemical processes are related in health and disease. With advances in technology, metabolomics has become a more routine “omics” approach for studying metabolism, and “circadian metabolomics” (i.e., studying the 24-h metabolome has recently been undertaken by several groups. To date, circadian metabolomes have been reported for human serum, saliva, breath, and urine, as well as tissues from several species under specific disease or mutagenesis conditions. Importantly, these studies have consistently revealed that 24-h rhythms are prevalent in almost every tissue and metabolic pathway. Furthermore, these circadian rhythms in tissue metabolism are ultimately linked to and directed by internal 24-h biological clocks. In this review, we will attempt to put these data-rich circadian metabolomics experiments into perspective to find out what they can tell us about metabolic health and disease, and what additional biomarker potential they may reveal.

  2. Cortisol in urine and saliva

    DEFF Research Database (Denmark)

    Hurwitz Eller, N; Netterstrøm, B; Hansen, Åse Marie

    2001-01-01

    The objective of the study was to analyse the relations between excretion of cortisol in urine and saliva and the intima media thickness (IMT) of the artery carotis communis.......The objective of the study was to analyse the relations between excretion of cortisol in urine and saliva and the intima media thickness (IMT) of the artery carotis communis....

  3. Informatics for Metabolomics.

    Science.gov (United States)

    Kusonmano, Kanthida; Vongsangnak, Wanwipa; Chumnanpuen, Pramote

    2016-01-01

    Metabolome profiling of biological systems has the powerful ability to provide the biological understanding of their metabolic functional states responding to the environmental factors or other perturbations. Tons of accumulative metabolomics data have thus been established since pre-metabolomics era. This is directly influenced by the high-throughput analytical techniques, especially mass spectrometry (MS)- and nuclear magnetic resonance (NMR)-based techniques. Continuously, the significant numbers of informatics techniques for data processing, statistical analysis, and data mining have been developed. The following tools and databases are advanced for the metabolomics society which provide the useful metabolomics information, e.g., the chemical structures, mass spectrum patterns for peak identification, metabolite profiles, biological functions, dynamic metabolite changes, and biochemical transformations of thousands of small molecules. In this chapter, we aim to introduce overall metabolomics studies from pre- to post-metabolomics era and their impact on society. Directing on post-metabolomics era, we provide a conceptual framework of informatics techniques for metabolomics and show useful examples of techniques, tools, and databases for metabolomics data analysis starting from preprocessing toward functional interpretation. Throughout the framework of informatics techniques for metabolomics provided, it can be further used as a scaffold for translational biomedical research which can thus lead to reveal new metabolite biomarkers, potential metabolic targets, or key metabolic pathways for future disease therapy.

  4. Metabolomics for laboratory diagnostics.

    Science.gov (United States)

    Bujak, Renata; Struck-Lewicka, Wiktoria; Markuszewski, Michał J; Kaliszan, Roman

    2015-09-10

    Metabolomics is an emerging approach in a systems biology field. Due to continuous development in advanced analytical techniques and in bioinformatics, metabolomics has been extensively applied as a novel, holistic diagnostic tool in clinical and biomedical studies. Metabolome's measurement, as a chemical reflection of a current phenotype of a particular biological system, is nowadays frequently implemented to understand pathophysiological processes involved in disease progression as well as to search for new diagnostic or prognostic biomarkers of various organism's disorders. In this review, we discussed the research strategies and analytical platforms commonly applied in the metabolomics studies. The applications of the metabolomics in laboratory diagnostics in the last 5 years were also reviewed according to the type of biological sample used in the metabolome's analysis. We also discussed some limitations and further improvements which should be considered taking in mind potential applications of metabolomic research and practice. Copyright © 2014 Elsevier B.V. All rights reserved.

  5. Metabolomics and Epidemiology Working Group

    Science.gov (United States)

    The Metabolomics and Epidemiology (MetEpi) Working Group promotes metabolomics analyses in population-based studies, as well as advancement in the field of metabolomics for broader biomedical and public health research.

  6. Saliva tannin interactions.

    Science.gov (United States)

    Prinz, J F; Lucas, P W

    2000-11-01

    Many plant foods contain tannins, compounds that bind proteins, such as mammalian enzymes. Although described as tasteless, tannins can be detected orally by their astringency. However, the actual mechanism of oral detection and the effect of tannins on mastication and swallowing have been little investigated. Here, we show from in vitro tests that tannic acid, a common standard in tests used to detect tannins, significantly reduces the lubricating qualities of human saliva both by decreasing its viscosity and increasing friction, both factors lending support to the notion that astringency is a tactile phenomenon. From the literature, it is clear that this effect depends on the presence of salivary proline-rich proteins (PRP). In a mammalian context, ingestion of tannin-rich foods in a species with salivary PRP will be signalled by interference with bolus formation during mastication while the increase in friction may also be detectable and lead to increased tooth wear if the signal is ignored. In a human context, cross-cultural preferences for tannin-rich beverages such as tea, coffee and red wine at the end of meals may be explained by reduction in adhesion of food particles to the oral mucosa allowing their rapid oral clearance.

  7. SALIVA AS A DIAGNOSTIC FLUID

    Directory of Open Access Journals (Sweden)

    Pezelj-Ribarić Sonja

    2015-12-01

    Full Text Available Saliva is a readily available oral fluid with many functions, from digestion, maintenance of oral tissues' integrity, to caries prevention. Changes regarding its secretion may be divided into qualitative and quantitative: both of them are a consequence of certain conditions/diseases (e.g. internal factors or nutrients/drugs ingested (e.g. external factors. During the last 15 years, technological advances gave a significant momentum to utilization of saliva as a diagnostic tool. Analysis of saliva, just like the blood analysis, has two main objectives: to identify the subjects suffering from a certain disorder, and to follow the development and progress of therapy. This paper provides an overview of possibilities for the use of saliva for diagnostic purposes and gives specific examples of some clinical investigations, with the final aim to stimulate the use of this noninvasive means for the health care promotion.

  8. Metabolomic Studies in Drosophila.

    Science.gov (United States)

    Cox, James E; Thummel, Carl S; Tennessen, Jason M

    2017-07-01

    Metabolomic analysis provides a powerful new tool for studies of Drosophila physiology. This approach allows investigators to detect thousands of chemical compounds in a single sample, representing the combined contributions of gene expression, enzyme activity, and environmental context. Metabolomics has been used for a wide range of studies in Drosophila , often providing new insights into gene function and metabolic state that could not be obtained using any other approach. In this review, we survey the uses of metabolomic analysis since its entry into the field. We also cover the major methods used for metabolomic studies in Drosophila and highlight new directions for future research. Copyright © 2017 by the Genetics Society of America.

  9. Metabolomics: A Primer.

    Science.gov (United States)

    Liu, Xiaojing; Locasale, Jason W

    2017-04-01

    Metabolomics generates a profile of small molecules that are derived from cellular metabolism and can directly reflect the outcome of complex networks of biochemical reactions, thus providing insights into multiple aspects of cellular physiology. Technological advances have enabled rapid and increasingly expansive data acquisition with samples as small as single cells; however, substantial challenges in the field remain. In this primer we provide an overview of metabolomics, especially mass spectrometry (MS)-based metabolomics, which uses liquid chromatography (LC) for separation, and discuss its utilities and limitations. We identify and discuss several areas at the frontier of metabolomics. Our goal is to give the reader a sense of what might be accomplished when conducting a metabolomics experiment, now and in the near future. Copyright © 2017 Elsevier Ltd. All rights reserved.

  10. Centrosome isolation and analysis by mass spectrometry-based proteomics

    DEFF Research Database (Denmark)

    Jakobsen, Lis; Schrøder, Jacob Morville; Larsen, Katja M

    2013-01-01

    Centrioles are microtubule-based scaffolds that are essential for the formation of centrosomes, cilia, and flagella with important functions throughout the cell cycle, in physiology and during development. The ability to purify centriole-containing organelles on a large scale, combined with advan...... to isolate centrosomes from human cells and strategies to selectively identify and study the properties of the associated proteins using quantitative mass spectrometry-based proteomics.......Centrioles are microtubule-based scaffolds that are essential for the formation of centrosomes, cilia, and flagella with important functions throughout the cell cycle, in physiology and during development. The ability to purify centriole-containing organelles on a large scale, combined...... with advances in protein identification using mass spectrometry-based proteomics, have revealed multiple centriole-associated proteins that are conserved during evolution in eukaryotes. Despite these advances, the molecular basis for the plethora of processes coordinated by cilia and centrosomes is not fully...

  11. Radiation Metabolomics: Current Status and Future Directions

    Directory of Open Access Journals (Sweden)

    Smrithi eSugumaran Menon

    2016-02-01

    Full Text Available Human exposure to ionizing radiation disrupts normal metabolic processes in cells and organs by inducing complex biological responses that interfere with gene and protein expression. Conventional dosimetry, monitoring of prodromal symptoms and peripheral lymphocyte counts are of limited value as organ and tissue specific biomarkers for personnel exposed to radiation, particularly, weeks or months after exposure. Analysis of metabolites generated in known stress-responsive pathways by molecular profiling helps to predict the physiological status of an individual in response to environmental or genetic perturbations. Thus, a multi-metabolite profile obtained from a high resolution mass spectrometry-based metabolomics platform offers potential for identification of robust biomarkers to predict radiation toxicity of organs and tissues resulting from exposures to therapeutic or non-therapeutic ionizing radiation. Here, we review the status of radiation metabolomics and explore applications as a standalone technology, as well as its integration in systems biology, to facilitate a better understanding of the molecular basis of radiation response. Finally, we draw attention to the identification of specific pathways that can be targeted for the development of therapeutics to alleviate or mitigate harmful effects of radiation exposure.

  12. The functions of human saliva

    DEFF Research Database (Denmark)

    Dawes, C; Pedersen, Anne Marie Lynge; Villa, A

    2015-01-01

    This narrative review of the functions of saliva was conducted in the PubMed, Embase and Web of Science databases. Additional references relevant to the topic were used, as our key words did not generate references which covered all known functions of saliva. These functions include maintaining a...... of oral wounds. Clearly, saliva has many functions which are needed for proper protection and functioning of the human body....... a moist oral mucosa which is less susceptible to abrasion, and removal of micro-organisms, desquamated epithelial cells, leucocytes and food debris by swallowing. The mucins form a slimy coating on all surfaces in the mouth and act as a lubricant during such processes as mastication, formation of a food...

  13. The Human Serum Metabolome

    Science.gov (United States)

    Psychogios, Nikolaos; Hau, David D.; Peng, Jun; Guo, An Chi; Mandal, Rupasri; Bouatra, Souhaila; Sinelnikov, Igor; Krishnamurthy, Ramanarayan; Eisner, Roman; Gautam, Bijaya; Young, Nelson; Xia, Jianguo; Knox, Craig; Dong, Edison; Huang, Paul; Hollander, Zsuzsanna; Pedersen, Theresa L.; Smith, Steven R.; Bamforth, Fiona; Greiner, Russ; McManus, Bruce; Newman, John W.; Goodfriend, Theodore; Wishart, David S.

    2011-01-01

    Continuing improvements in analytical technology along with an increased interest in performing comprehensive, quantitative metabolic profiling, is leading to increased interest pressures within the metabolomics community to develop centralized metabolite reference resources for certain clinically important biofluids, such as cerebrospinal fluid, urine and blood. As part of an ongoing effort to systematically characterize the human metabolome through the Human Metabolome Project, we have undertaken the task of characterizing the human serum metabolome. In doing so, we have combined targeted and non-targeted NMR, GC-MS and LC-MS methods with computer-aided literature mining to identify and quantify a comprehensive, if not absolutely complete, set of metabolites commonly detected and quantified (with today's technology) in the human serum metabolome. Our use of multiple metabolomics platforms and technologies allowed us to substantially enhance the level of metabolome coverage while critically assessing the relative strengths and weaknesses of these platforms or technologies. Tables containing the complete set of 4229 confirmed and highly probable human serum compounds, their concentrations, related literature references and links to their known disease associations are freely available at http://www.serummetabolome.ca. PMID:21359215

  14. Metabolomics in chemical ecology.

    Science.gov (United States)

    Kuhlisch, Constanze; Pohnert, Georg

    2015-07-01

    Chemical ecology elucidates the nature and role of natural products as mediators of organismal interactions. The emerging techniques that can be summarized under the concept of metabolomics provide new opportunities to study such environmentally relevant signaling molecules. Especially comparative tools in metabolomics enable the identification of compounds that are regulated during interaction situations and that might play a role as e.g. pheromones, allelochemicals or in induced and activated defenses. This approach helps overcoming limitations of traditional bioassay-guided structure elucidation approaches. But the power of metabolomics is not limited to the comparison of metabolic profiles of interacting partners. Especially the link to other -omics techniques helps to unravel not only the compounds in question but the entire biosynthetic and genetic re-wiring, required for an ecological response. This review comprehensively highlights successful applications of metabolomics in chemical ecology and discusses existing limitations of these novel techniques. It focuses on recent developments in comparative metabolomics and discusses the use of metabolomics in the systems biology of organismal interactions. It also outlines the potential of large metabolomics initiatives for model organisms in the field of chemical ecology.

  15. The proteome of human saliva

    Science.gov (United States)

    Griffin, Timothy J.

    2013-05-01

    Human saliva holds tremendous potential for transforming disease and health diagnostics given its richness of molecular information and non-invasive collection. Enumerating its molecular constituents is an important first step towards reaching this potential. Among the molecules in saliva, proteins and peptides arguably have the most value: they can directly indicate biochemical functions linked to a health condition/disease state, and they are attractive targets for biomarker assay development. However, cataloging and defining the human salivary proteome is challenging given the dynamic, chemically heterogeneous and complex nature of the system. In addition, the overall human saliva proteome is composed of several "sub-proteomes" which include: intact full length proteins, proteins carrying post-translational modifications (PTMs), low molecular weight peptides, and the metaproteome, derived from protein products from nonhuman organisms (e.g. microbes) present in the oral cavity. Presented here will be a summary of communal efforts to meet the challenge of characterizing the multifaceted saliva proteome, focusing on the use of mass spectrometry as the proteomic technology of choice. Implications of these efforts to characterize the salivary proteome in the context of disease diagnostics will also be discussed.

  16. Antimicrobial defense systems in saliva

    NARCIS (Netherlands)

    van 't Hof, W.; Veerman, E.C.I.; Nieuw Amerongen, A.V.; Ligtenberg, A.J.M.; Ligtenberg, A.J.M.; Veerman, E.C.I.

    2014-01-01

    The oral cavity is one of the most heavily colonized parts of our body. The warm, nutrient-rich and moist environment promotes the growth of a diverse microflora. One of the factors responsible for the ecological equilibrium in the mouth is saliva, which in several ways affects the colonization and

  17. ARSENIC SPECIATION ANALYSIS IN HUMAN SALIVA

    Science.gov (United States)

    Background: Determination of arsenic species in human saliva is potentially useful for biomonitoring of human exposure to arsenic and for studying arsenic metabolism. However, there is no report on the speciation analysis of arsenic in saliva. Methods: Arsenic species in saliva ...

  18. Metabolomic studies in pulmonology

    Directory of Open Access Journals (Sweden)

    R. R. Furina

    2015-01-01

    Full Text Available The review shows the results of metabolomic studies in pulmonology. The key idea of metabolomics is to detect specific biomarkers in a biological sample for the diagnosis of diseases of the bronchi and lung. Main methods for the separation and identification of volatile organic substances as biomarkers (gas chromatography, mass spectrometry, and nuclear magnetic resonance spectrometry used in metabolomics are given. A solid-phase microextraction method used to pre-prepare a sample is also covered. The results of laboratory tests for biomarkers for lung cancer, acute respiratory distress syndrome, chronic obstructive pulmonary disease, cystic fibrosis, chronic infections, and pulmonary tuberculosis are presented. In addition, emphasis is placed on the possibilities of metabolomics used in experimental medicine, including to the study of asthma. The information is of interest to both theorists and practitioners.

  19. The food metabolome

    DEFF Research Database (Denmark)

    Scalbert, Augustin; Brennan, Lorraine; Manach, Claudine

    2014-01-01

    to the diet. By its very nature it represents a considerable and still largely unexploited source of novel dietary biomarkers that could be used to measure dietary exposures with a high level of detail and precision. Most dietary biomarkers currently have been identified on the basis of our knowledge of food......The food metabolome is defined as the part of the human metabolome directly derived from the digestion and biotransformation of foods and their constituents. With >25,000 compounds known in various foods, the food metabolome is extremely complex, with a composition varying widely according...... by the recent identification of novel biomarkers of intakes for fruit, vegetables, beverages, meats, or complex diets. Moreover, examples also show how the scrutiny of the food metabolome can lead to the discovery of bioactive molecules and dietary factors associated with diseases. However, researchers still...

  20. Current metabolomics: technological advances.

    Science.gov (United States)

    Putri, Sastia P; Yamamoto, Shinya; Tsugawa, Hiroshi; Fukusaki, Eiichiro

    2013-07-01

    Metabolomics, the global quantitative assessment of metabolites in a biological system, has played a pivotal role in various fields of science in the post-genomic era. Metabolites are the result of the interaction of the system's genome with its environment and are not merely the end product of gene expression, but also form part of the regulatory system in an integrated manner. Therefore, metabolomics is often considered a powerful tool to provide an instantaneous snapshot of the physiology of a cell. The power of metabolomics lies on the acquisition of analytical data in which metabolites in a cellular system are quantified, and the extraction of the most meaningful elements of the data by using various data analysis tool. In this review, we discuss the latest development of analytical techniques and data analyses methods in metabolomics study. Copyright © 2013 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

  1. Metabolomics er fremtiden

    DEFF Research Database (Denmark)

    Pedersern, Birger

    2010-01-01

    Forskningen i fødevarer har fået et potent redskab i hånden. Metabolomics er vejen frem, mener professor Søren Balling Engelsen fra Københavns Universitet......Forskningen i fødevarer har fået et potent redskab i hånden. Metabolomics er vejen frem, mener professor Søren Balling Engelsen fra Københavns Universitet...

  2. [Advances in mass spectrometry-based approaches for neuropeptide analysis].

    Science.gov (United States)

    Ji, Qianyue; Ma, Min; Peng, Xin; Jia, Chenxi; Ji, Qianyue

    2017-07-25

    Neuropeptides are an important class of endogenous bioactive substances involved in the function of the nervous system, and connect the brain and other neural and peripheral organs. Mass spectrometry-based neuropeptidomics are designed to study neuropeptides in a large-scale manner and obtain important molecular information to further understand the mechanism of nervous system regulation and the pathogenesis of neurological diseases. This review summarizes the basic strategies for the study of neuropeptides using mass spectrometry, including sample preparation and processing, qualitative and quantitative methods, and mass spectrometry imagining.

  3. Quality assurance of metabolomics.

    Science.gov (United States)

    Bouhifd, Mounir; Beger, Richard; Flynn, Thomas; Guo, Lining; Harris, Georgina; Hogberg, Helena; Kaddurah-Daouk, Rima; Kamp, Hennicke; Kleensang, Andre; Maertens, Alexandra; Odwin-DaCosta, Shelly; Pamies, David; Robertson, Donald; Smirnova, Lena; Sun, Jinchun; Zhao, Liang; Hartung, Thomas

    2015-01-01

    Metabolomics promises a holistic phenotypic characterization of biological responses to toxicants. This technology is based on advanced chemical analytical tools with reasonable throughput, including mass-spectroscopy and NMR. Quality assurance, however - from experimental design, sample preparation, metabolite identification, to bioinformatics data-mining - is urgently needed to assure both quality of metabolomics data and reproducibility of biological models. In contrast to microarray-based transcriptomics, where consensus on quality assurance and reporting standards has been fostered over the last two decades, quality assurance of metabolomics is only now emerging. Regulatory use in safety sciences, and even proper scientific use of these technologies, demand quality assurance. In an effort to promote this discussion, an expert workshop discussed the quality assurance needs of metabolomics. The goals for this workshop were 1) to consider the challenges associated with metabolomics as an emerging science, with an emphasis on its application in toxicology and 2) to identify the key issues to be addressed in order to establish and implement quality assurance procedures in metabolomics-based toxicology. Consensus has still to be achieved regarding best practices to make sure sound, useful, and relevant information is derived from these new tools.

  4. SALIVA SEBAGAI UJI SARING OSTEOPOROSIS

    Directory of Open Access Journals (Sweden)

    Niniarty Z. Djamal

    2015-07-01

    Full Text Available Osteoporosis is a metabolic bone disease, and is characterized by low bone mass and microstructure deterioration of the bone, which leads to increased risk of fracture. Biomarker of bone metabolism can be seen as beginning of bone loss and first detection before imbalanced bone turnover comes. Biomarker of bone formation as serum bone alkaline fosfatase, osteocalcin (OC, procollagen type I, and biomarker of bone resorption as urine pyridinoline (Pyd and deoxypyridinoline (Dpd crosslinks, hydroxyprolin. The simultaneous examination of serum OC and urine Pyd or Dpd as a very good screening test for determination of bone imbalanced at the moment of the menopausal or the beginning of the pasca menopausal. Saliva as a potential diagnostic fluid for the assessment of osteoporosis biomarker concentrations. The study found elevated three classic warning signs for osteopororsis os OC, Dpd and 116 in the saliva of sheep without ovaries, which were similar to the levels of signs found in their blood and urine. Expectations, that the test may become available within five years and one day the test may be able to be performed at home like pregnancy test. Osteoporosis biomarker in saliva suggested detected of bone mass density easier. Beside that can be used as a method of early diagnostic and as a monitor therapy that as salinity of the examinations of bone mass on radiology.

  5. Nanoparticle-Assisted Metabolomics

    Directory of Open Access Journals (Sweden)

    Bo Zhang

    2018-03-01

    Full Text Available Understanding and harnessing the interactions between nanoparticles and biological molecules is at the forefront of applications of nanotechnology to modern biology. Metabolomics has emerged as a prominent player in systems biology as a complement to genomics, transcriptomics and proteomics. Its focus is the systematic study of metabolite identities and concentration changes in living systems. Despite significant progress over the recent past, important challenges in metabolomics remain, such as the deconvolution of the spectra of complex mixtures with strong overlaps, the sensitive detection of metabolites at low abundance, unambiguous identification of known metabolites, structure determination of unknown metabolites and standardized sample preparation for quantitative comparisons. Recent research has demonstrated that some of these challenges can be substantially alleviated with the help of nanoscience. Nanoparticles in particular have found applications in various areas of bioanalytical chemistry and metabolomics. Their chemical surface properties and increased surface-to-volume ratio endows them with a broad range of binding affinities to biomacromolecules and metabolites. The specific interactions of nanoparticles with metabolites or biomacromolecules help, for example, simplify metabolomics spectra, improve the ionization efficiency for mass spectrometry or reveal relationships between spectral signals that belong to the same molecule. Lessons learned from nanoparticle-assisted metabolomics may also benefit other emerging areas, such as nanotoxicity and nanopharmaceutics.

  6. Clinical Metabolomics and Glaucoma.

    Science.gov (United States)

    Barbosa-Breda, João; Himmelreich, Uwe; Ghesquière, Bart; Rocha-Sousa, Amândio; Stalmans, Ingeborg

    2018-01-01

    Glaucoma is one of the leading causes of irreversible blindness worldwide. However, there are no biomarkers that accurately help clinicians perform an early diagnosis or detect patients with a high risk of progression. Metabolomics is the study of all metabolites in an organism, and it has the potential to provide a biomarker. This review summarizes the findings of metabolomics in glaucoma patients and explains why this field is promising for new research. We identified published studies that focused on metabolomics and ophthalmology. After providing an overview of metabolomics in ophthalmology, we focused on human glaucoma studies. Five studies have been conducted in glaucoma patients and all compared patients to healthy controls. Using mass spectrometry, significant differences were found in blood plasma in the metabolic pathways that involve palmitoylcarnitine, sphingolipids, vitamin D-related compounds, and steroid precursors. For nuclear magnetic resonance spectroscopy, a high glutamine-glutamate/creatine ratio was found in the vitreous and lateral geniculate body; no differences were detected in the optic radiations, and a lower N-acetylaspartate/choline ratio was observed in the geniculocalcarine and striate areas. Metabolomics can move glaucoma care towards a personalized approach and provide new knowledge concerning the pathophysiology of glaucoma, which can lead to new therapeutic options. © 2017 S. Karger AG, Basel.

  7. A Combined Metabolomic and Proteomic Analysis of Gestational Diabetes Mellitus

    Directory of Open Access Journals (Sweden)

    Joanna Hajduk

    2015-12-01

    Full Text Available The aim of this pilot study was to apply a novel combined metabolomic and proteomic approach in analysis of gestational diabetes mellitus. The investigation was performed with plasma samples derived from pregnant women with diagnosed gestational diabetes mellitus (n = 18 and a matched control group (n = 13. The mass spectrometry-based analyses allowed to determine 42 free amino acids and low molecular-weight peptide profiles. Different expressions of several peptides and altered amino acid profiles were observed in the analyzed groups. The combination of proteomic and metabolomic data allowed obtaining the model with a high discriminatory power, where amino acids ethanolamine, l-citrulline, l-asparagine, and peptide ions with m/z 1488.59; 4111.89 and 2913.15 had the highest contribution to the model. The sensitivity (94.44% and specificity (84.62%, as well as the total group membership classification value (90.32% calculated from the post hoc classification matrix of a joint model were the highest when compared with a single analysis of either amino acid levels or peptide ion intensities. The obtained results indicated a high potential of integration of proteomic and metabolomics analysis regardless the sample size. This promising approach together with clinical evaluation of the subjects can also be used in the study of other diseases.

  8. An integrated strategy for in vivo metabolite profiling using high-resolution mass spectrometry based data processing techniques

    International Nuclear Information System (INIS)

    Guo, Jian; Zhang, Minli; Elmore, Charles S.; Vishwanathan, Karthick

    2013-01-01

    Graphical abstract: -- Highlights: •Profiling the metabolites of model compounds in rats using high resolution mass spectrometry based data processing techniques. •Demonstrating an integrated strategy in vivo metabolite profiling using data mining tools. •Unusual metabolites generated via thiazole-ring opening were characterized based on processed LC–MS.data. -- Abstract: An ongoing challenge of drug metabolite profiling is to detect and identify unknown or low-level metabolites in complex biological matrices. Here we present a generic strategy for metabolite detection using multiple accurate-mass-based data processing tools via the analysis of rat samples of two model drug candidates, AZD6280 and AZ12488024. First, the function of isotopic pattern recognition was proved to be highly effective in the detection of metabolites derived from [ 14 C]-AZD6280 that possesses a distinct isotopic pattern. The metabolites revealed using this approach were in excellent qualitative correlation to those observed in radiochromatograms. Second, the effectiveness of accurate mass based untargeted data mining tools such as background subtraction, mass defect filtering, or a data mining package (MZmine) used for metabolomic analysis in detection of metabolites of [ 14 C]-AZ12488024 in rat urine, feces, bile and plasma samples was examined and a total of 33 metabolites of AZ12488024 were detected. Among them, at least 16 metabolites were only detected by the aid of the data mining packages and not via radiochromatograms. New metabolic pathways such as S-oxidation and thiomethylation reactions occurring on the thiazole ring were proposed based on the processed data. The results of these experiments also demonstrated that accurate mass-based mass defect filtering (MDF) and data mining techniques used in metabolomics are complementary and can be valuable tools for delineating low-level metabolites in complex matrices. Furthermore, the application of distinct multiple data

  9. Investigation of mixed saliva by optoelectronic methods

    Science.gov (United States)

    Savchenko, Ekaterina; Nepomnyashchaya, Elina; Baranov, Maksim; Velichko, Elena; Aksenov, Evgenii; Bogomaz, Tatyana

    2018-04-01

    At present, saliva and its properties are being actively studied. Human saliva is a unique biological material that has potential in clinical practice. A detailed analysis of the characteristics and properties of saliva is relevant for diagnostic purposes. In this paper, the properties and characteristics of saliva are studied using optoelectronic methods: dynamic light scattering, electrophoretic light scattering and optical microscopy. Mixed saliva from a healthy patient and patient with diabetes mellitus type 2 was used as an object of the study. The dynamics of the behavior of a healthy and patient with diabetes mellitus type 2 is visible according to the results obtained. All three methods confirm hypothesis of structural changes in mixed saliva in the disease of diabetes mellitus type 2.

  10. Gut metabolome meets microbiome

    DEFF Research Database (Denmark)

    Lamichhane, Santosh; Sen, Partho; Dickens, Alex M

    2018-01-01

    It is well established that gut microbes and their metabolic products regulate host metabolism. The interactions between the host and its gut microbiota are highly dynamic and complex. In this review we present and discuss the metabolomic strategies to study the gut microbial ecosystem. We...... highlight the metabolic profiling approaches to study faecal samples aimed at deciphering the metabolic product derived from gut microbiota. We also discuss how metabolomics data can be integrated with metagenomics data derived from gut microbiota and how such approaches may lead to better understanding...

  11. White Light Generation in Human Saliva

    Science.gov (United States)

    Santhosh, C.; Dharmadhikari, A. K.; Dharmadhikari, J. A.; Alti, K.; Mathur, D.

    2011-07-01

    Interaction of intense, femto-second pulses of infrared light (800 nm) with water generates white light supercontinuum due to nonlinear optical effects. This supercontinuum was found to be suppressed by the addition of alpha amylase, a major protein in the human saliva. We have studied the suppression of supper continuum by human saliva, collected from healthy subjects with and without smoking habits. Suppression of the blue-sided components was observed significantly in non-smokers saliva than chain smokers.

  12. Saliva as a diagnostic fluid: literature review

    OpenAIRE

    Martí Álamo, Silvia; Mancheño Franch, Aisha; Marzal Gamarra, Cristina

    2012-01-01

    There is a growing interest in diagnosis based on the analysis of saliva. This is a simple, non-invasive method of obtaining oral samples which is safe for both the health worker and the patient, not to mention allowing for simple and cost-efficient storage. The majority of studies use general saliva samples in their entirety, complex fluids containing both local and systemic sources and whose composition corresponds to that of the blood. General saliva contains a considerable ...

  13. Metabolomics and Personalized Medicine.

    Science.gov (United States)

    Koen, Nadia; Du Preez, Ilse; Loots, Du Toit

    2016-01-01

    Current clinical practice strongly relies on the prognosis, diagnosis, and treatment of diseases using methods determined and averaged for the specific diseased cohort/population. Although this approach complies positively with most patients, misdiagnosis, treatment failure, relapse, and adverse drug effects are common occurrences in many individuals, which subsequently hamper the control and eradication of a number of diseases. These incidences can be explained by individual variation in the genome, transcriptome, proteome, and metabolome of a patient. Various "omics" approaches have investigated the influence of these factors on a molecular level, with the intention of developing personalized approaches to disease diagnosis and treatment. Metabolomics, the newest addition to the "omics" domain and the closest to the observed phenotype, reflects changes occurring at all molecular levels, as well as influences resulting from other internal and external factors. By comparing the metabolite profiles of two or more disease phenotypes, metabolomics can be applied to identify biomarkers related to the perturbation being investigated. These biomarkers can, in turn, be used to develop personalized prognostic, diagnostic, and treatment approaches, and can also be applied to the monitoring of disease progression, treatment efficacy, predisposition to drug-related side effects, and potential relapse. In this review, we discuss the contributions that metabolomics has made, and can potentially still make, towards the field of personalized medicine. © 2016 Elsevier Inc. All rights reserved.

  14. Single cell metabolomics

    NARCIS (Netherlands)

    Heinemann, Matthias; Zenobi, Renato

    Recent discoveries suggest that cells of a clonal population often display multiple metabolic phenotypes at the same time. Motivated by the success of mass spectrometry (MS) in the investigation of population-level metabolomics, the analytical community has initiated efforts towards MS-based single

  15. Novel TIA biomarkers identified by mass spectrometry-based proteomics.

    Science.gov (United States)

    George, Paul M; Mlynash, Michael; Adams, Christopher M; Kuo, Calvin J; Albers, Gregory W; Olivot, Jean-Marc

    2015-12-01

    Transient ischemic attacks remain a clinical diagnosis with significant variability between physicians. Finding reliable biomarkers to identify transient ischemic attacks would improve patient care and optimize treatment. Our aim is to identify novel serum TIA biomarkers through the use of mass spectroscopy-based proteomics. Patients with transient neurologic symptoms were prospectively enrolled. Mass spectrometry-based proteomics, an unbiased method to identify candidate proteins, was used to test the serum of the patients for biomarkers of cerebral ischemia. Three candidate proteins were found, and serum concentrations of these proteins were measured by enzyme-linked immunosorbent assay in a second cohort of prospectively enrolled patients. The Student's t-test was used for comparison. The Benjamini-Hochberg false discovery rate controlling procedure for multiple comparison adjustments determined significance for the proteomic screen. Patients with transient ischemic attacks (n = 20), minor strokes (n = 15), and controls (i.e. migraine, seizure, n = 12) were enrolled in the first cohort. Ceruloplasmin, complement component C8 gamma (C8γ), and platelet basic protein were significantly different between the ischemic group (transient ischemic attack and minor stroke) and the controls (P = 0·0001, P = 0·00027, P = 0·00105, respectively). A second cohort of patients with transient ischemic attack (n = 22), minor stroke (n = 20), and controls' (n = 12) serum was enrolled. Platelet basic protein serum concentrations were increased in the ischemic samples compared with control (for transient ischemic attack alone, P = 0·019, for the ischemic group, P = 0·046). Ceruloplasmin trended towards increased concentrations in the ischemic group (P = 0·127); no significant difference in C8γ (P = 0·44) was found. Utilizing mass spectrometry-based proteomics, platelet basic protein has been identified as a candidate serum

  16. Atmospheric vs. anaerobic processing of metabolome samples for the metabolite profiling of a strict anaerobic bacterium, Clostridium acetobutylicum.

    Science.gov (United States)

    Lee, Sang-Hyun; Kim, Sooah; Kwon, Min-A; Jung, Young Hoon; Shin, Yong-An; Kim, Kyoung Heon

    2014-12-01

    Well-established metabolome sample preparation is a prerequisite for reliable metabolomic data. For metabolome sampling of a Gram-positive strict anaerobe, Clostridium acetobutylicum, fast filtration and metabolite extraction with acetonitrile/methanol/water (2:2:1, v/v) at -20°C under anaerobic conditions has been commonly used. This anaerobic metabolite processing method is laborious and time-consuming since it is conducted in an anaerobic chamber. Also, there have not been any systematic method evaluation and development of metabolome sample preparation for strict anaerobes and Gram-positive bacteria. In this study, metabolome sampling and extraction methods were rigorously evaluated and optimized for C. acetobutylicum by using gas chromatography/time-of-flight mass spectrometry-based metabolomics, in which a total of 116 metabolites were identified. When comparing the atmospheric (i.e., in air) and anaerobic (i.e., in an anaerobic chamber) processing of metabolome sample preparation, there was no significant difference in the quality and quantity of the metabolomic data. For metabolite extraction, pure methanol at -20°C was a better solvent than acetonitrile/methanol/water (2:2:1, v/v/v) at -20°C that is frequently used for C. acetobutylicum, and metabolite profiles were significantly different depending on extraction solvents. This is the first evaluation of metabolite sample preparation under aerobic processing conditions for an anaerobe. This method could be applied conveniently, efficiently, and reliably to metabolome analysis for strict anaerobes in air. © 2014 Wiley Periodicals, Inc.

  17. Variability in Mass Spectrometry-based Quantification of Clinically Relevant Drug Transporters and Drug Metabolizing Enzymes

    NARCIS (Netherlands)

    Wegler, C.; Gaugaz, F.Z.; Andersson, T.B.; Wiśniewski, J.R.; Busch, D.; Gröer, C.; Oswald, S.; Norén, A.; Weiss, F.; Hammer, H.S.; Joos, T.O.; Poetz, O.; Achour, B.; Rostami-Hodjegan, A.; Steeg, E. van de; Wortelboer, H.M.; Artursson, P.

    2017-01-01

    Many different methods are used for mass-spectrometry-based protein quantification in pharmacokinetics and systems pharmacology. It has not been established to what extent the results from these various methods are comparable. Here, we compared six different mass spectrometry-based proteomics

  18. Dissecting plasmodesmata molecular composition by mass spectrometry-based proteomics.

    Directory of Open Access Journals (Sweden)

    Emmanuelle Maria Françoise Bayer

    2013-01-01

    Full Text Available In plants, the intercellular communication through the membranous channels called plasmodesmata (PD; singular plasmodesma plays pivotal roles in the orchestration of development, defence responses and viral propagation. PD are dynamic structures embedded in the plant cell wall that are defined by specialised domains of the endoplasmic reticulum and the plasma membrane. PD structure and unique functions are guaranteed by their particular molecular composition. Yet, up to recent years and despite numerous approaches such as mutant screens, immunolocalisation or screening of random cDNAs, only few PD proteins had been conclusively identified and characterised. A clear breakthrough in the search of PD constituents came from mass-spectrometry-based proteomic approaches coupled with subcellular fractionation strategies. Due to their position, firmly anchored in the extracellular matrix, PD are notoriously difficult to isolate for biochemical analysis. Proteomic-based approaches have therefore first relied on the use of cell wall fractions containing embedded PD then on free PD fractions whereby PD membranes were released from the walls by enzymatic degradation. To discriminate between likely contaminants and PD protein candidates, bioinformatics tools have often been used in combination with proteomic approaches. GFP fusion proteins of selected candidates have confirmed the PD association of several protein families. Here we review the accomplishments and limitations of the proteomic based strategies to unravel the functional and structural complexity of PD. We also discuss the role of the identified PD associated proteins.

  19. Dissecting plasmodesmata molecular composition by mass spectrometry-based proteomics.

    Science.gov (United States)

    Salmon, Magali S; Bayer, Emmanuelle M F

    2012-01-01

    In plants, the intercellular communication through the membranous channels called plasmodesmata (PD; singular plasmodesma) plays pivotal roles in the orchestration of development, defence responses, and viral propagation. PD are dynamic structures embedded in the plant cell wall that are defined by specialized domains of the endoplasmic reticulum (ER) and the plasma membrane (PM). PD structure and unique functions are guaranteed by their particular molecular composition. Yet, up to recent years and despite numerous approaches such as mutant screens, immunolocalization, or screening of random cDNAs, only few PD proteins had been conclusively identified and characterized. A clear breakthrough in the search of PD constituents came from mass-spectrometry-based proteomic approaches coupled with subcellular fractionation strategies. Due to their position, firmly anchored in the extracellular matrix, PD are notoriously difficult to isolate for biochemical analysis. Proteomic-based approaches have therefore first relied on the use of cell wall fractions containing embedded PD then on "free" PD fractions whereby PD membranes were released from the walls by enzymatic degradation. To discriminate between likely contaminants and PD protein candidates, bioinformatics tools have often been used in combination with proteomic approaches. GFP fusion proteins of selected candidates have confirmed the PD association of several protein families. Here we review the accomplishments and limitations of the proteomic-based strategies to unravel the functional and structural complexity of PD. We also discuss the role of the identified PD-associated proteins.

  20. Enhancement of Cellulose Degradation by Cattle Saliva

    Science.gov (United States)

    Seki, Yasutaka; Kikuchi, Yukiko; Kimura, Yoshihiro; Yoshimoto, Ryo; Takahashi, Masatoshi; Aburai, Kenichi; Kanai, Yoshihiro; Ruike, Tatsushi; Iwabata, Kazuki; Sugawara, Fumio; Sakai, Hideki; Abe, Masahiko; Sakaguchi, Kengo

    2015-01-01

    Saccharification of cellulose is a promising technique for producing alternative source of energy. However, the efficiency of conversion of cellulose into soluble sugar using any currently available methodology is too low for industrial application. Many additives, such as surfactants, have been shown to enhance the efficiency of cellulose-to-sugar conversion. In this study, we have examined first whether cattle saliva, as an additive, would enhance the cellulase-catalyzed hydrolysis of cellulose, and subsequently elucidated the mechanism by which cattle saliva enhanced this conversion. Although cattle saliva, by itself, did not degrade cellulose, it enhanced the cellulase-catalyzed degradation of cellulose. Thus, the amount of reducing sugar produced increased approximately 2.9-fold by the addition of cattle saliva. We also found that non-enzymatic proteins, which were present in cattle saliva, were responsible for causing the enhancement effect. Third, the mechanism of cattle saliva mediated enhancement of cellulase activity was probably similar to that of the canonical surfactants. Cattle saliva is available in large amounts easily and cheaply, and it can be used without further purification. Thus, cattle saliva could be a promising additive for efficient saccharification of cellulose on an industrial scale. PMID:26402242

  1. A Comprehensive Workflow of Mass Spectrometry-Based Untargeted Metabolomics in Cancer Metabolic Biomarker Discovery Using Human Plasma and Urine

    Directory of Open Access Journals (Sweden)

    Jianwen She

    2013-09-01

    Full Text Available Current available biomarkers lack sensitivity and/or specificity for early detection of cancer. To address this challenge, a robust and complete workflow for metabolic profiling and data mining is described in details. Three independent and complementary analytical techniques for metabolic profiling are applied: hydrophilic interaction liquid chromatography (HILIC–LC, reversed-phase liquid chromatography (RP–LC, and gas chromatography (GC. All three techniques are coupled to a mass spectrometer (MS in the full scan acquisition mode, and both unsupervised and supervised methods are used for data mining. The univariate and multivariate feature selection are used to determine subsets of potentially discriminative predictors. These predictors are further identified by obtaining accurate masses and isotopic ratios using selected ion monitoring (SIM and data-dependent MS/MS and/or accurate mass MSn ion tree scans utilizing high resolution MS. A list combining all of the identified potential biomarkers generated from different platforms and algorithms is used for pathway analysis. Such a workflow combining comprehensive metabolic profiling and advanced data mining techniques may provide a powerful approach for metabolic pathway analysis and biomarker discovery in cancer research. Two case studies with previous published data are adapted and included in the context to elucidate the application of the workflow.

  2. NMR-based milk metabolomics

    DEFF Research Database (Denmark)

    Sundekilde, Ulrik; Larsen, Lotte Bach; Bertram, Hanne Christine S.

    2013-01-01

    and processing capabilities of bovine milk is closely associated to milk composition. Metabolomics is ideal in the study of the low-molecular-weight compounds in milk, and this review focuses on the recent nuclear magnetic resonance (NMR)-based metabolomics trends in milk research, including applications linking...... compounds. Furthermore, metabolomics applications elucidating how the differential regulated genes affects milk composition are also reported. This review will highlight the recent advances in NMR-based metabolomics on milk, as well as give a brief summary of when NMR spectroscopy can be useful for gaining...

  3. Mass Spectrometry Based Lipidomics: An Overview of Technological Platforms

    Science.gov (United States)

    Köfeler, Harald C.; Fauland, Alexander; Rechberger, Gerald N.; Trötzmüller, Martin

    2012-01-01

    One decade after the genomic and the proteomic life science revolution, new ‘omics’ fields are emerging. The metabolome encompasses the entity of small molecules—Most often end products of a catalytic process regulated by genes and proteins—with the lipidome being its fat soluble subdivision. Within recent years, lipids are more and more regarded not only as energy storage compounds but also as interactive players in various cellular regulation cycles and thus attain rising interest in the bio-medical community. The field of lipidomics is, on one hand, fuelled by analytical technology advances, particularly mass spectrometry and chromatography, but on the other hand new biological questions also drive analytical technology developments. Compared to fairly standardized genomic or proteomic high-throughput protocols, the high degree of molecular heterogeneity adds a special analytical challenge to lipidomic analysis. In this review, we will take a closer look at various mass spectrometric platforms for lipidomic analysis. We will focus on the advantages and limitations of various experimental setups like ‘shotgun lipidomics’, liquid chromatography—Mass spectrometry (LC-MS) and matrix assisted laser desorption ionization-time of flight (MALDI-TOF) based approaches. We will also examine available software packages for data analysis, which nowadays is in fact the rate limiting step for most ‘omics’ workflows. PMID:24957366

  4. Mass Spectrometry Based Lipidomics: An Overview of Technological Platforms

    Directory of Open Access Journals (Sweden)

    Harald C. Köfeler

    2012-01-01

    Full Text Available One decade after the genomic and the proteomic life science revolution, new ‘omics’ fields are emerging. The metabolome encompasses the entity of small molecules—Most often end products of a catalytic process regulated by genes and proteins—with the lipidome being its fat soluble subdivision. Within recent years, lipids are more and more regarded not only as energy storage compounds but also as interactive players in various cellular regulation cycles and thus attain rising interest in the bio-medical community. The field of lipidomics is, on one hand, fuelled by analytical technology advances, particularly mass spectrometry and chromatography, but on the other hand new biological questions also drive analytical technology developments. Compared to fairly standardized genomic or proteomic high-throughput protocols, the high degree of molecular heterogeneity adds a special analytical challenge to lipidomic analysis. In this review, we will take a closer look at various mass spectrometric platforms for lipidomic analysis. We will focus on the advantages and limitations of various experimental setups like ‘shotgun lipidomics’, liquid chromatography—Mass spectrometry (LC-MS and matrix assisted laser desorption ionization-time of flight (MALDI-TOF based approaches. We will also examine available software packages for data analysis, which nowadays is in fact the rate limiting step for most ‘omics’ workflows.

  5. Adrenal status assessed by direct radioimmunoassay of cortisol in whole saliva or parotid saliva

    International Nuclear Information System (INIS)

    Walker, R.F.; Riad-Fahmy, D.; Read, G.F.

    1978-01-01

    We describe a direct radioimmunoassay for cortisol in 10-μl volumes of parotid saliva or whole saliva. Binding proteins are absent from these fluids, as demonstrated by the excellent correlation between results for samples assayed directly and by a comparison procedure involving extraction with 1,2-dichloroethane. The direct assay is specific, precise, and had a lower limit of sensitivity of 4 pg per assay tube. Comparison of cortisol concentrations in plasma, parotid saliva, and whole saliva in persons undergoing investigations for assessing adrenal function, including stimulation with cosyntropin (Synachthen) and suppression with dexamethasone, indicated that changes in plasma cortisol concentration were accurately and immediately reflected in saliva from either the parotid-gland or whole saliva. A marked circadian rhythm has also been demonstrated for cortisol in parotid-gland saliva and whole saliva. We had to modify the 1,2-dichloroethane extraction procedure for accurate determination of cortisol in parotid saliva and whole saliva of patients undergoing treatment with metyrapone

  6. The Human Urine Metabolome

    Science.gov (United States)

    Bouatra, Souhaila; Aziat, Farid; Mandal, Rupasri; Guo, An Chi; Wilson, Michael R.; Knox, Craig; Bjorndahl, Trent C.; Krishnamurthy, Ramanarayan; Saleem, Fozia; Liu, Philip; Dame, Zerihun T.; Poelzer, Jenna; Huynh, Jessica; Yallou, Faizath S.; Psychogios, Nick; Dong, Edison; Bogumil, Ralf; Roehring, Cornelia; Wishart, David S.

    2013-01-01

    Urine has long been a “favored” biofluid among metabolomics researchers. It is sterile, easy-to-obtain in large volumes, largely free from interfering proteins or lipids and chemically complex. However, this chemical complexity has also made urine a particularly difficult substrate to fully understand. As a biological waste material, urine typically contains metabolic breakdown products from a wide range of foods, drinks, drugs, environmental contaminants, endogenous waste metabolites and bacterial by-products. Many of these compounds are poorly characterized and poorly understood. In an effort to improve our understanding of this biofluid we have undertaken a comprehensive, quantitative, metabolome-wide characterization of human urine. This involved both computer-aided literature mining and comprehensive, quantitative experimental assessment/validation. The experimental portion employed NMR spectroscopy, gas chromatography mass spectrometry (GC-MS), direct flow injection mass spectrometry (DFI/LC-MS/MS), inductively coupled plasma mass spectrometry (ICP-MS) and high performance liquid chromatography (HPLC) experiments performed on multiple human urine samples. This multi-platform metabolomic analysis allowed us to identify 445 and quantify 378 unique urine metabolites or metabolite species. The different analytical platforms were able to identify (quantify) a total of: 209 (209) by NMR, 179 (85) by GC-MS, 127 (127) by DFI/LC-MS/MS, 40 (40) by ICP-MS and 10 (10) by HPLC. Our use of multiple metabolomics platforms and technologies allowed us to identify several previously unknown urine metabolites and to substantially enhance the level of metabolome coverage. It also allowed us to critically assess the relative strengths and weaknesses of different platforms or technologies. The literature review led to the identification and annotation of another 2206 urinary compounds and was used to help guide the subsequent experimental studies. An online database containing

  7. Livestock metabolomics and the livestock metabolome: A systematic review.

    Science.gov (United States)

    Goldansaz, Seyed Ali; Guo, An Chi; Sajed, Tanvir; Steele, Michael A; Plastow, Graham S; Wishart, David S

    2017-01-01

    Metabolomics uses advanced analytical chemistry techniques to comprehensively measure large numbers of small molecule metabolites in cells, tissues and biofluids. The ability to rapidly detect and quantify hundreds or even thousands of metabolites within a single sample is helping scientists paint a far more complete picture of system-wide metabolism and biology. Metabolomics is also allowing researchers to focus on measuring the end-products of complex, hard-to-decipher genetic, epigenetic and environmental interactions. As a result, metabolomics has become an increasingly popular "omics" approach to assist with the robust phenotypic characterization of humans, crop plants and model organisms. Indeed, metabolomics is now routinely used in biomedical, nutritional and crop research. It is also being increasingly used in livestock research and livestock monitoring. The purpose of this systematic review is to quantitatively and objectively summarize the current status of livestock metabolomics and to identify emerging trends, preferred technologies and important gaps in the field. In conducting this review we also critically assessed the applications of livestock metabolomics in key areas such as animal health assessment, disease diagnosis, bioproduct characterization and biomarker discovery for highly desirable economic traits (i.e., feed efficiency, growth potential and milk production). A secondary goal of this critical review was to compile data on the known composition of the livestock metabolome (for 5 of the most common livestock species namely cattle, sheep, goats, horses and pigs). These data have been made available through an open access, comprehensive livestock metabolome database (LMDB, available at http://www.lmdb.ca). The LMDB should enable livestock researchers and producers to conduct more targeted metabolomic studies and to identify where further metabolome coverage is needed.

  8. Livestock metabolomics and the livestock metabolome: A systematic review

    Science.gov (United States)

    Guo, An Chi; Sajed, Tanvir; Steele, Michael A.; Plastow, Graham S.; Wishart, David S.

    2017-01-01

    Metabolomics uses advanced analytical chemistry techniques to comprehensively measure large numbers of small molecule metabolites in cells, tissues and biofluids. The ability to rapidly detect and quantify hundreds or even thousands of metabolites within a single sample is helping scientists paint a far more complete picture of system-wide metabolism and biology. Metabolomics is also allowing researchers to focus on measuring the end-products of complex, hard-to-decipher genetic, epigenetic and environmental interactions. As a result, metabolomics has become an increasingly popular “omics” approach to assist with the robust phenotypic characterization of humans, crop plants and model organisms. Indeed, metabolomics is now routinely used in biomedical, nutritional and crop research. It is also being increasingly used in livestock research and livestock monitoring. The purpose of this systematic review is to quantitatively and objectively summarize the current status of livestock metabolomics and to identify emerging trends, preferred technologies and important gaps in the field. In conducting this review we also critically assessed the applications of livestock metabolomics in key areas such as animal health assessment, disease diagnosis, bioproduct characterization and biomarker discovery for highly desirable economic traits (i.e., feed efficiency, growth potential and milk production). A secondary goal of this critical review was to compile data on the known composition of the livestock metabolome (for 5 of the most common livestock species namely cattle, sheep, goats, horses and pigs). These data have been made available through an open access, comprehensive livestock metabolome database (LMDB, available at http://www.lmdb.ca). The LMDB should enable livestock researchers and producers to conduct more targeted metabolomic studies and to identify where further metabolome coverage is needed. PMID:28531195

  9. Identification of putative biomarkers for prediabetes by metabolome analysis of rat models of type 2 diabetes

    OpenAIRE

    Yokoi, Norihide; Beppu, Masayuki; Yoshida, Eri; Hoshikawa, Ritsuko; Hidaka, Shihomi; Matsubara, Toshiya; Shinohara, Masami; Irino, Yasuhiro; Hatano, Naoya; Seino, Susumu

    2015-01-01

    Biomarkers for the development of type 2 diabetes (T2D) are useful for prediction and intervention of the disease at earlier stages. In this study, we performed a longitudinal study of changes in metabolites using an animal model of T2D, the spontaneously diabetic Torii (SDT) rat. Fasting plasma samples of SDT and control Sprague-Dawley (SD) rats were collected from 6 to 24 weeks of age, and subjected to gas chromatography–mass spectrometry-based metabolome analysis. Fifty-nine hydrophilic me...

  10. Analysis for drugs in saliva and breath

    Science.gov (United States)

    1981-09-25

    Collection devices for saliva and breath that involved non-invasive techniques for sample collection were evaluated. Having subjects simply spit into a specially prepared glass vial was found to be an efficient, inexpensive and simple way to collect ...

  11. Analysis for drug in saliva and breath

    Science.gov (United States)

    1981-09-25

    Collection devices for saliva and breath that involved non-invasive : techniques for sample collection were evaluated. Having subjects simply : spit into a specially prepared glass vial was found to be an efficient, : inexpensive and simple way to co...

  12. A hybrid approach to protein differential expression in mass spectrometry-based proteomics

    KAUST Repository

    Wang, X.; Anderson, G. A.; Smith, R. D.; Dabney, A. R.

    2012-01-01

    MOTIVATION: Quantitative mass spectrometry-based proteomics involves statistical inference on protein abundance, based on the intensities of each protein's associated spectral peaks. However, typical MS-based proteomics datasets have substantial

  13. System-Level and Granger Network Analysis of Integrated Proteomic and Metabolomic Dynamics Identifies Key Points of Grape Berry Development at the Interface of Primary and Secondary Metabolism

    OpenAIRE

    Wang, Lei; Sun, Xiaoliang; Weiszmann, Jakob; Weckwerth, Wolfram

    2017-01-01

    Grapevine is a fruit crop with worldwide economic importance. The grape berry undergoes complex biochemical changes from fruit set until ripening. This ripening process and production processes define the wine quality. Thus, a thorough understanding of berry ripening is crucial for the prediction of wine quality. For a systemic analysis of grape berry development we applied mass spectrometry based platforms to analyse the metabolome and proteome of Early Campbell at 12 stages covering major d...

  14. Phenotyping of Chronic Obstructive Pulmonary Disease Based on the Integration of Metabolomes and Clinical Characteristics

    Directory of Open Access Journals (Sweden)

    Kalle Kilk

    2018-02-01

    Full Text Available Apart from the refined management-oriented clinical stratification of chronic obstructive pulmonary disease (COPD, the molecular pathologies behind this highly prevalent disease have remained obscure. The aim of this study was the characterization of patients with COPD, based on the metabolomic profiling of peripheral blood and exhaled breath condensate (EBC within the context of defined clinical and demographic variables. Mass-spectrometry-based targeted analysis of serum metabolites (mainly amino acids and lipid species, untargeted profiles of serum and EBC of patients with COPD of different clinical characteristics (n = 25 and control individuals (n = 21 were performed. From the combined clinical/demographic and metabolomics data, associations between clinical/demographic and metabolic parameters were searched and a de novo phenotyping for COPD was attempted. Adjoining the clinical parameters, sphingomyelins were the best to differentiate COPD patients from controls. Unsaturated fatty acid-containing lipids, ornithine metabolism and plasma protein composition-associated signals from the untargeted analysis differentiated the Global Initiative for COPD (GOLD categories. Hierarchical clustering did not reveal a clinical-metabolomic stratification superior to the strata set by the GOLD consensus. We conclude that while metabolomics approaches are good for finding biomarkers and clarifying the mechanism of the disease, there are no distinct co-variate independent clinical-metabolic phenotypes.

  15. Metabolome Profiling of Partial and Fully Reprogrammed Induced Pluripotent Stem Cells.

    Science.gov (United States)

    Park, Soon-Jung; Lee, Sang A; Prasain, Nutan; Bae, Daekyeong; Kang, Hyunsu; Ha, Taewon; Kim, Jong Soo; Hong, Ki-Sung; Mantel, Charlie; Moon, Sung-Hwan; Broxmeyer, Hal E; Lee, Man Ryul

    2017-05-15

    Acquisition of proper metabolomic fate is required to convert somatic cells toward fully reprogrammed pluripotent stem cells. The majority of induced pluripotent stem cells (iPSCs) are partially reprogrammed and have a transcriptome different from that of the pluripotent stem cells. The metabolomic profile and mitochondrial metabolic functions required to achieve full reprogramming of somatic cells to iPSC status have not yet been elucidated. Clarification of the metabolites underlying reprogramming mechanisms should enable further optimization to enhance the efficiency of obtaining fully reprogrammed iPSCs. In this study, we characterized the metabolites of human fully reprogrammed iPSCs, partially reprogrammed iPSCs, and embryonic stem cells (ESCs). Using capillary electrophoresis time-of-flight mass spectrometry-based metabolomics, we found that 89% of analyzed metabolites were similarly expressed in fully reprogrammed iPSCs and human ESCs (hESCs), whereas partially reprogrammed iPSCs shared only 74% similarly expressed metabolites with hESCs. Metabolomic profiling analysis suggested that converting mitochondrial respiration to glycolytic flux is critical for reprogramming of somatic cells into fully reprogrammed iPSCs. This characterization of metabolic reprogramming in iPSCs may enable the development of new reprogramming parameters for enhancing the generation of fully reprogrammed human iPSCs.

  16. Disposable Collection Kit for Rapid and Reliable Collection of Saliva

    OpenAIRE

    Yamaguchi, Masaki; Tezuka, Yuki; Takeda, Kazunori; Shetty, Vivek

    2015-01-01

    Objectives To describe and evaluate disposable saliva collection kit for rapid, reliable, and reproducible collection of saliva samples. Methods The saliva collection kit comprised of a saliva absorbent swab and an extractor unit was used to retrieve whole saliva samples from 10 subjects. The accuracy and precision of the extracted volumes (3, 10, and 30 ?l) were compared to similar volumes drawn from control samples obtained by passive drool. Additionally, the impact of kit collection method...

  17. Metabolomics of Genetically Modified Crops

    Directory of Open Access Journals (Sweden)

    Carolina Simó

    2014-10-01

    Full Text Available Metabolomic-based approaches are increasingly applied to analyse genetically modified organisms (GMOs making it possible to obtain broader and deeper information on the composition of GMOs compared to that obtained from traditional analytical approaches. The combination in metabolomics of advanced analytical methods and bioinformatics tools provides wide chemical compositional data that contributes to corroborate (or not the substantial equivalence and occurrence of unintended changes resulting from genetic transformation. This review provides insight into recent progress in metabolomics studies on transgenic crops focusing mainly in papers published in the last decade.

  18. Metabolomics of Genetically Modified Crops

    Science.gov (United States)

    Simó, Carolina; Ibáñez, Clara; Valdés, Alberto; Cifuentes, Alejandro; García-Cañas, Virginia

    2014-01-01

    Metabolomic-based approaches are increasingly applied to analyse genetically modified organisms (GMOs) making it possible to obtain broader and deeper information on the composition of GMOs compared to that obtained from traditional analytical approaches. The combination in metabolomics of advanced analytical methods and bioinformatics tools provides wide chemical compositional data that contributes to corroborate (or not) the substantial equivalence and occurrence of unintended changes resulting from genetic transformation. This review provides insight into recent progress in metabolomics studies on transgenic crops focusing mainly in papers published in the last decade. PMID:25334064

  19. Best-Matched Internal Standard Normalization in Liquid Chromatography-Mass Spectrometry Metabolomics Applied to Environmental Samples.

    Science.gov (United States)

    Boysen, Angela K; Heal, Katherine R; Carlson, Laura T; Ingalls, Anitra E

    2018-01-16

    The goal of metabolomics is to measure the entire range of small organic molecules in biological samples. In liquid chromatography-mass spectrometry-based metabolomics, formidable analytical challenges remain in removing the nonbiological factors that affect chromatographic peak areas. These factors include sample matrix-induced ion suppression, chromatographic quality, and analytical drift. The combination of these factors is referred to as obscuring variation. Some metabolomics samples can exhibit intense obscuring variation due to matrix-induced ion suppression, rendering large amounts of data unreliable and difficult to interpret. Existing normalization techniques have limited applicability to these sample types. Here we present a data normalization method to minimize the effects of obscuring variation. We normalize peak areas using a batch-specific normalization process, which matches measured metabolites with isotope-labeled internal standards that behave similarly during the analysis. This method, called best-matched internal standard (B-MIS) normalization, can be applied to targeted or untargeted metabolomics data sets and yields relative concentrations. We evaluate and demonstrate the utility of B-MIS normalization using marine environmental samples and laboratory grown cultures of phytoplankton. In untargeted analyses, B-MIS normalization allowed for inclusion of mass features in downstream analyses that would have been considered unreliable without normalization due to obscuring variation. B-MIS normalization for targeted or untargeted metabolomics is freely available at https://github.com/IngallsLabUW/B-MIS-normalization .

  20. An Innovative Approach for The Integration of Proteomics and Metabolomics Data In Severe Septic Shock Patients Stratified for Mortality.

    Science.gov (United States)

    Cambiaghi, Alice; Díaz, Ramón; Martinez, Julia Bauzá; Odena, Antonia; Brunelli, Laura; Caironi, Pietro; Masson, Serge; Baselli, Giuseppe; Ristagno, Giuseppe; Gattinoni, Luciano; de Oliveira, Eliandre; Pastorelli, Roberta; Ferrario, Manuela

    2018-04-27

    In this work, we examined plasma metabolome, proteome and clinical features in patients with severe septic shock enrolled in the multicenter ALBIOS study. The objective was to identify changes in the levels of metabolites involved in septic shock progression and to integrate this information with the variation occurring in proteins and clinical data. Mass spectrometry-based targeted metabolomics and untargeted proteomics allowed us to quantify absolute metabolites concentration and relative proteins abundance. We computed the ratio D7/D1 to take into account their variation from day 1 (D1) to day 7 (D7) after shock diagnosis. Patients were divided into two groups according to 28-day mortality. Three different elastic net logistic regression models were built: one on metabolites only, one on metabolites and proteins and one to integrate metabolomics and proteomics data with clinical parameters. Linear discriminant analysis and Partial least squares Discriminant Analysis were also implemented. All the obtained models correctly classified the observations in the testing set. By looking at the variable importance (VIP) and the selected features, the integration of metabolomics with proteomics data showed the importance of circulating lipids and coagulation cascade in septic shock progression, thus capturing a further layer of biological information complementary to metabolomics information.

  1. Assessment of extracellular dehydration using saliva osmolality.

    Science.gov (United States)

    Ely, Brett R; Cheuvront, Samuel N; Kenefick, Robert W; Spitz, Marissa G; Heavens, Kristen R; Walsh, Neil P; Sawka, Michael N

    2014-01-01

    When substantial solute losses accompany body water an isotonic hypovolemia (extracellular dehydration) results. The potential for using blood or urine to assess extracellular dehydration is generally poor, but saliva is not a simple ultra-filtrate of plasma and the autonomic regulation of salivary gland function suggests the possibility that saliva osmolality (Sosm) may afford detection of extracellular dehydration via the influence of volume-mediated factors. This study aimed to evaluate the assessment of extracellular dehydration using Sosm. In addition, two common saliva collection methods and their effects on Sosm were compared. Blood, urine, and saliva samples were collected in 24 healthy volunteers during paired euhydration and dehydration trials. Furosemide administration and 12 h fluid restriction were used to produce extracellular dehydration. Expectoration and salivette collection methods were compared in a separate group of eight euhydrated volunteers. All comparisons were made using paired t-tests. The diagnostic potential of body fluids was additionally evaluated. Dehydration (3.1 ± 0.5% loss of body mass) decreased PV (-0.49 ± 0.12 L; -15.12 ± 3.94% change), but Sosm changes were marginal ( 0.05). Extracelluar dehydration was not detectable using plasma, urine, or saliva measures. Salivette and expectoration sampling methods produced similar, consistent results for Sosm, suggesting no methodological influence on Sosm.

  2. Metabolomics Workbench (MetWB)

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Metabolomics Program's Data Repository and Coordinating Center (DRCC), housed at the San Diego Supercomputer Center (SDSC), University of California, San Diego,...

  3. NMR-based metabolomics applications

    DEFF Research Database (Denmark)

    Iaccarino, Nunzia

    Metabolomics is the scientific discipline that identifies and quantifies endogenous and exogenous metabolites in different biological samples. Metabolites are crucial components of a biological system and they are highly informative about its functional state, due to their closeness to the organism...... focused on the analysis of various samples covering a wide range of fields, namely, food and nutraceutical sciences, cell metabolomics and medicine using a metabolomics approach. Indeed, the first part of the thesis describes two exploratory studies performed on Algerian extra virgin olive oil and apple...... juice from ancient Danish apple cultivars. Both studies revealed variety-related peculiarities that would have been difficult to detect by means of traditional analysis. The second part of the project includes four metabolomics studies performed on samples of biological origin. In particular, the first...

  4. The biology of plant metabolomics

    NARCIS (Netherlands)

    Hall, R.D.

    2011-01-01

    Following a general introduction, this book includes details of metabolomics of model species including Arabidopsis and tomato. Further chapters provide in-depth coverage of abiotic stress, data integration, systems biology, genetics, genomics, chemometrics and biostatisitcs. Applications of plant

  5. Evaluation of intensity drift correction strategies using MetaboDrift, a normalization tool for multi-batch metabolomics data.

    Science.gov (United States)

    Thonusin, Chanisa; IglayReger, Heidi B; Soni, Tanu; Rothberg, Amy E; Burant, Charles F; Evans, Charles R

    2017-11-10

    In recent years, mass spectrometry-based metabolomics has increasingly been applied to large-scale epidemiological studies of human subjects. However, the successful use of metabolomics in this context is subject to the challenge of detecting biologically significant effects despite substantial intensity drift that often occurs when data are acquired over a long period or in multiple batches. Numerous computational strategies and software tools have been developed to aid in correcting for intensity drift in metabolomics data, but most of these techniques are implemented using command-line driven software and custom scripts which are not accessible to all end users of metabolomics data. Further, it has not yet become routine practice to assess the quantitative accuracy of drift correction against techniques which enable true absolute quantitation such as isotope dilution mass spectrometry. We developed an Excel-based tool, MetaboDrift, to visually evaluate and correct for intensity drift in a multi-batch liquid chromatography - mass spectrometry (LC-MS) metabolomics dataset. The tool enables drift correction based on either quality control (QC) samples analyzed throughout the batches or using QC-sample independent methods. We applied MetaboDrift to an original set of clinical metabolomics data from a mixed-meal tolerance test (MMTT). The performance of the method was evaluated for multiple classes of metabolites by comparison with normalization using isotope-labeled internal standards. QC sample-based intensity drift correction significantly improved correlation with IS-normalized data, and resulted in detection of additional metabolites with significant physiological response to the MMTT. The relative merits of different QC-sample curve fitting strategies are discussed in the context of batch size and drift pattern complexity. Our drift correction tool offers a practical, simplified approach to drift correction and batch combination in large metabolomics studies

  6. Fluoride in dental biofilm and saliva

    DEFF Research Database (Denmark)

    Larsen, Line Staun

    Dette ph.d.-projekt bidrager med ny viden om fordelingen af fluorid i dental biofilm og saliva. For at udforske koncentrationen af fluorid i naturlig (in vivo) biofilmvæske, biofilmsediment og i saliva, blev der udført to meget forskellige kliniske studier. Resultaterne fra tværsnitsstudiet (Studie...... I), hos en stor gruppe mennesker (n=42) der konsulterede en tandklinik for behandling, bekræfter tidligere viden, at der findes en naturlig biologisk variation i fluoridkoncentrationerne i biofilm fra forskellige intra-orale regioner samt mellem biofilmvæske, biofilmsediment og saliva...... fluoridkoncentrationer i underkæbefronten, intermediære koncentrationer i alle tre overkæberegioner og de laveste koncentrationer i underkæbemolarregionerne. Begge studier viser at biofilmsedimentet indeholder størstedelen af fluorid i biofilm. Set i et bredere perspektiv viser fundene at der er et omvendt forhold...

  7. Proteomic Analysis of Saliva in HIV-positive Heroin Addicts Reveals Proteins Correlated with Cognition

    Energy Technology Data Exchange (ETDEWEB)

    Dominy, Stephen; Brown, Joseph N.; Ryder, Mark I.; Gritsenko, Marina A.; Jacobs, Jon M.; Smith, Richard D.

    2014-04-01

    The prevalence of HIV-associated neurocognitive disorders (HAND) remains high despite effective antiretroviral therapies. Multiple etiologies have been proposed over the last few years to account for this phenomenon, including the neurotoxic effects of antiretrovirals and co-morbid substance abuse. However, no underlying molecular mechanism has been identified. Emerging evidence in several fields has linked the gut to brain diseases, but the effect of the gut on the brain during HIV infection has not been explored. Saliva is the most accessible gut biofluid, and is therefore of great scientific interest for diagnostic and prognostic purposes. This study presents a longitudinal, liquid chromatography-mass spectrometry-based quantitative proteomics study investigating saliva samples taken from 8 HIV-positive (HIV+) and 11 -negative (HIV-) heroin addicts. In the HIV+ group, 58 proteins were identified that show significant correlations with cognitive scores and that implicate disruption of protein quality control pathways by HIV. Notably, no proteins from the HIV- heroin addict cohort showed significant correlations with cognitive scores. In addition, the majority of correlated proteins have been shown to be associated with exosomes, allowing us to propose that the salivary glands and/or oral epithelium may modulate brain function during HIV infection through the release of discrete packets of proteins in the form of exosomes.

  8. Autologous saliva transfusion: treatment for HIV?

    Science.gov (United States)

    Arakeri, Gururaj

    2010-05-01

    The HIV-1 pandemic is a complex mix of diverse epidemics within and between countries and regions of the world, and is undoubtedly the defining public-health crisis of our time. Any therapeutic or prophylactic measure which holds promise or provides clues of eliminating or inhibiting the infection is worthy of investigation. As our body's own saliva is suspiciously escaping from the infection and providing clues regarding the resistance/inhibition of HIV; in this paper, a treatment approach is suggested with the rationale of in vitro effective antiviral action of autogenous saliva may also have a better therapeutic potential by its intravenous administration along with dextran.

  9. A device for the collection of submandibular saliva.

    Science.gov (United States)

    Hanning, Sara; Motoi, Lidia; Medlicott, Natalie; Swindells, Stephen

    2012-03-01

    The objective of this study was to describe the construction of a non-invasive device for the collection of submandibular saliva. Preliminary tests were carried out on saliva collected from a single donor in order to determine whether the rheological properties of submandibular saliva collected using the device were comparable to whole saliva collected using the expectoration (or 'spit') method. The device collected a lower quantity of saliva than that collected using the expectoration method. Stimulated saliva collected using the device had a pH close to that of unstimulated saliva because the sealed collection unit in the device minimised contamination. Saliva exhibited shear-thinning behaviour regardless of the method of collection, although that collected using the device was more viscous. The viscoelasticity of saliva collected using the two methods was different, probably as a result of differences in composition. This difference was greater with stimulated saliva. Despite the discrepancies between whole saliva and submandibular saliva, the device provides a non-invasive method for the collection of high-quality saliva over extended periods.

  10. Metabolomic applications in radiation biodosimetry: exploring radiation effects through small molecules.

    Science.gov (United States)

    Pannkuk, Evan L; Fornace, Albert J; Laiakis, Evagelia C

    2017-10-01

    Exposure of the general population to ionizing radiation has increased in the past decades, primarily due to long distance travel and medical procedures. On the other hand, accidental exposures, nuclear accidents, and elevated threats of terrorism with the potential detonation of a radiological dispersal device or improvised nuclear device in a major city, all have led to increased needs for rapid biodosimetry and assessment of exposure to different radiation qualities and scenarios. Metabolomics, the qualitative and quantitative assessment of small molecules in a given biological specimen, has emerged as a promising technology to allow for rapid determination of an individual's exposure level and metabolic phenotype. Advancements in mass spectrometry techniques have led to untargeted (discovery phase, global assessment) and targeted (quantitative phase) methods not only to identify biomarkers of radiation exposure, but also to assess general perturbations of metabolism with potential long-term consequences, such as cancer, cardiovascular, and pulmonary disease. Metabolomics of radiation exposure has provided a highly informative snapshot of metabolic dysregulation. Biomarkers in easily accessible biofluids and biospecimens (urine, blood, saliva, sebum, fecal material) from mouse, rat, and minipig models, to non-human primates and humans have provided the basis for determination of a radiation signature to assess the need for medical intervention. Here we provide a comprehensive description of the current status of radiation metabolomic studies for the purpose of rapid high-throughput radiation biodosimetry in easily accessible biofluids and discuss future directions of radiation metabolomics research.

  11. Metabolomics Society’s International Affiliations

    NARCIS (Netherlands)

    Roessner, U.; Rolin, D.; Rijswijk, van M.E.C.; Hall, R.D.; Hankemeier, T.

    2015-01-01

    In 2012 the Metabolomics Society established a more formal system for national and regional metabolomics initiatives, interest groups, societies and networks to become an International Affiliate of the Society. A number of groups (http://metabolomicssociety.org/international-affilia

  12. Role of metabolomics in TBI research

    Science.gov (United States)

    Wolahan, Stephanie M.; Hirt, Daniel; Braas, Daniel; Glenn, Thomas C.

    2016-01-01

    Synopsis Metabolomics is an important member of the omics community in that it defines which small molecules may be responsible for disease states. This article reviews the essential principles of metabolomics from specimen preparation, chemical analysis, and advanced statistical methods. Metabolomics in TBI has so far been underutilized. Future metabolomics based studies focused on the diagnoses, prognoses, and treatment effects, need to be conducted across all types of TBI. PMID:27637396

  13. ECMDB: The E. coli Metabolome Database

    OpenAIRE

    Guo, An Chi; Jewison, Timothy; Wilson, Michael; Liu, Yifeng; Knox, Craig; Djoumbou, Yannick; Lo, Patrick; Mandal, Rupasri; Krishnamurthy, Ram; Wishart, David S.

    2012-01-01

    The Escherichia coli Metabolome Database (ECMDB, http://www.ecmdb.ca) is a comprehensively annotated metabolomic database containing detailed information about the metabolome of E. coli (K-12). Modelled closely on the Human and Yeast Metabolome Databases, the ECMDB contains >2600 metabolites with links to ?1500 different genes and proteins, including enzymes and transporters. The information in the ECMDB has been collected from dozens of textbooks, journal articles and electronic databases. E...

  14. Is parotid saliva sterile on entry to the oral cavity?

    DEFF Research Database (Denmark)

    Schrøder, Stine A; Bardow, Allan; Eickhardt-Dalbøge, Steffen

    2017-01-01

    CONCLUSION: The present study indicates that parotid saliva is sterile on entry to the oral cavity. OBJECTIVES: The objective was to investigate if parotid saliva is sterile on entry to the oral cavity and, thus, prior to contamination by oral bacteria. METHOD: Forty healthy volunteers were...... included in sterile parotid saliva collection. Parotid saliva was collected using a sterile Lashley cup, placed over the papilla of the Stensen´s duct, as well as sterile tubes and syringes for collection. All collections were followed by collection of a positive control sample where some of the sterile...... obtained parotid saliva had been exposed to the contralateral mucosal membranes. All samples parotid saliva, as well as the positive controls, were cultivated, and 10 randomly selected parotid saliva samples underwent polymerase chain reaction (PCR) analyses. RESULTS: In 33 of 40 parotid saliva samples...

  15. Detection of phencyclidine usage by radioimmunoassay of saliva

    International Nuclear Information System (INIS)

    McCarron, M.M.; Walberg, C.B.; Soares, J.R.; Gross, S.J.; Baselt, R.C.

    1984-01-01

    Paired serum and saliva samples, obtained from 100 emergency department patients suspected of phencyclidine (PCP) intoxication, were analyzed using a specific PCP radioimmunoassay (RIA). Seventy-four of the 100 saliva samples and 75 of the paired serum samples were positive for PCP. The final clinical diagnosis was PCP intoxication in 79 cases. Of these, both serum and saliva tests were positive in 70 cases, only serum was positive in two cases, and both serum and saliva samples were negative in seven cases. The concentration of PCP in the samples did not correlate with the severity of PCP intoxication. In the remaining 21 cases, with no clinical evidence of PCP intoxication, PCP assays were negative in both serum and saliva in 17 cases, three patients had positive saliva and serum tests, and one other patient had a positive PCP saliva assay. Thus, saliva would appear to be as reliable as serum as a specimen for PCP analysis

  16. Mass spectrometry based proteomics profiling as diagnostic tool in oncology: current status and future perspective.

    Science.gov (United States)

    Findeisen, Peter; Neumaier, Michael

    2009-01-01

    Proteomics analysis has been heralded as a novel tool for identifying new and specific biomarkers that may improve diagnosis and monitoring of various disease states. Recent years have brought a number of proteomics profiling technologies. Although proteomics profiling has resulted in the detection of disease-associated differences and modification of proteins, current proteomics technologies display certain limitations that are hampering the introduction of these new technologies into clinical laboratory diagnostics and routine applications. In this review, we summarize current advances in mass spectrometry based biomarker discovery. The promises and challenges of this new technology are discussed with particular emphasis on diagnostic perspectives of mass-spectrometry based proteomics profiling for malignant diseases.

  17. Modulation of host immunity by tick saliva

    Czech Academy of Sciences Publication Activity Database

    Kotál, Jan; Langhansová, H.; Lieskovská, J.; Andersen, J. F.; Francischetti, I.M.B.; Chavakis, T.; Kopecký, J.; Pedra, J. H. F.; Kotsyfakis, Michalis; Chmelař, J.

    2015-01-01

    Roč. 128, OCT 14 2015 (2015), s. 58-68 ISSN 1874-3919 R&D Projects: GA ČR GAP502/12/2409 Institutional support: RVO:60077344 Keywords : Adaptive immunity * Innate immunity * Saliva * Salivary glands * Tick Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.867, year: 2015

  18. Binding of corroded ions to human saliva.

    Science.gov (United States)

    Mueller, H J

    1985-05-01

    Employing equilibrium dialysis, the binding abilities of Cu, Al, Co and Cr ions from corroded Cu-Al and Co-Cr dental casting alloys towards human saliva and two of its gel chromatographic fractions were determined. Results indicate that both Cu and Co bind to human saliva i.e. 0.045 and 0.027 mg/mg protein, respectively. Besides possessing the largest binding ability, Cu also possessed the largest binding capacity. The saturation of Cu binding was not reached up to the limit of 0.35 mg protein/ml employed in the tests, while Co reached full saturation at about 0.2 mg protein/ml. Chromium showed absolutely no binding to human saliva while Al ions did not pass through the dialysis membranes. Compared to the binding with solutions that were synthetically made up to contain added salivary-type proteins, it is shown that the binding to human saliva is about 1 order of magnitude larger, at least for Cu ions.

  19. Metabolomics: the chemistry between ecology and genetics

    NARCIS (Netherlands)

    Macel, M.; Van Dam, N.M.; Keurentjes, J.J.B.

    2010-01-01

    Metabolomics is a fast developing field of comprehensive untargeted chemical analyses. It has many applications and can in principle be used on any organism without prior knowledge of the metabolome or genome. The amount of functional information that is acquired with metabolomics largely depends on

  20. Comparing Properties (Concentration, PH and mutans streptococcus Saliva in Both Status Resting Saliva and Stimulated Saliva in Preschoolers of Kerman city

    Directory of Open Access Journals (Sweden)

    Elham Farokh-Gisour,

    2016-08-01

    Full Text Available This paper aimed to compare the characteristics (concentration, PH and mutans streptococcus saliva in both status resting saliva and stimulated saliva in preschoolers of Kerman city. In this study, 100 children aged 5 years among patients admitted to the pediatric ward of Kerman dental school and dental offices, some experts in Kerman dental school participated. Resting and stimulated saliva (after chewing oral paraffin children collected and in concentrations, PH and the amount of mutans streptococcus was measured. Mc Nemar test to compare the frequency of positive and negative cultures before and after stimulation as well as paired t-test to compare the saliva pH and concentration of not stimulated saliva and stimulated saliva in two modes was used. The significance level was set less than 0.05.The mean resting salivary osmolality of the population: 30.42 ± 87.41 and the average salivary osmolality of the total population were 79.81. Osmolality differences in saliva before and after stimulation with each other was significant (p = 0.009, paired t-test. The mean of resting saliva in the total population PH 0.45 ± 7.78 and the average PH stimulated saliva in the total population was 8.22 and the difference before and after each significant (p = 0.02, paired t-test. In mutans streptococcus in test samples in all 71 patients (71% positive test and 29 patients (29% had a negative test that number of positive cultures are equal before and after stimulation of saliva and thus the difference between the two groups (p> 0.05 was observed. In terms of comparing the properties of resting and stimulated saliva can conclude that salivary stimulated PH was significantly higher than resting saliva. While stimulated saliva osmolality was significantly less than resting saliva and the frequency of positive test mutans streptococcus in saliva before and after stimulation had no significant difference (p> 0.05. This means that test results on samples of mutans

  1. Inorganic component of saliva during fasting and after fast break

    OpenAIRE

    Samad, Rasmidar

    2016-01-01

    Oral health is closely related to salivary components. Saliva consists of water, inorganic and organic materials. Fasting changes one???s meal and drinking time that in turn can affect the environment in oral cavity, including inorganic componenet of saliva. The purpose of this study is to determine the inorganic component of saliva during fasting and after fast break.

  2. An overview of renal metabolomics.

    Science.gov (United States)

    Kalim, Sahir; Rhee, Eugene P

    2017-01-01

    The high-throughput, high-resolution phenotyping enabled by metabolomics has been applied increasingly to a variety of questions in nephrology research. This article provides an overview of current metabolomics methodologies and nomenclature, citing specific considerations in sample preparation, metabolite measurement, and data analysis that investigators should understand when examining the literature or designing a study. Furthermore, we review several notable findings that have emerged in the literature that both highlight some of the limitations of current profiling approaches, as well as outline specific strengths unique to metabolomics. More specifically, we review data on the following: (i) tryptophan metabolites and chronic kidney disease onset, illustrating the interpretation of metabolite data in the context of established biochemical pathways; (ii) trimethylamine-N-oxide and cardiovascular disease in chronic kidney disease, illustrating the integration of exogenous and endogenous inputs to the blood metabolome; and (iii) renal mitochondrial function in diabetic kidney disease and acute kidney injury, illustrating the potential for rapid translation of metabolite data for diagnostic or therapeutic aims. Finally, we review future directions, including the need to better characterize interperson and intraperson variation in the metabolome, pool existing data sets to identify the most robust signals, and capitalize on the discovery potential of emerging nontargeted methods. Copyright © 2016 International Society of Nephrology. Published by Elsevier Inc. All rights reserved.

  3. Applied metabolomics in drug discovery.

    Science.gov (United States)

    Cuperlovic-Culf, M; Culf, A S

    2016-08-01

    The metabolic profile is a direct signature of phenotype and biochemical activity following any perturbation. Metabolites are small molecules present in a biological system including natural products as well as drugs and their metabolism by-products depending on the biological system studied. Metabolomics can provide activity information about possible novel drugs and drug scaffolds, indicate interesting targets for drug development and suggest binding partners of compounds. Furthermore, metabolomics can be used for the discovery of novel natural products and in drug development. Metabolomics can enhance the discovery and testing of new drugs and provide insight into the on- and off-target effects of drugs. This review focuses primarily on the application of metabolomics in the discovery of active drugs from natural products and the analysis of chemical libraries and the computational analysis of metabolic networks. Metabolomics methodology, both experimental and analytical is fast developing. At the same time, databases of compounds are ever growing with the inclusion of more molecular and spectral information. An increasing number of systems are being represented by very detailed metabolic network models. Combining these experimental and computational tools with high throughput drug testing and drug discovery techniques can provide new promising compounds and leads.

  4. A Rough Guide to Metabolite Identification Using High Resolution Liquid Chromatography Mass Spectrometry in Metabolomic Profiling in Metazoans

    Directory of Open Access Journals (Sweden)

    David G Watson

    2013-01-01

    Full Text Available Compound identification in mass spectrometry based metabolomics can be a problem but sometimes the problem seems to be presented in an over complicated way. The current review focuses on metazoans where the range of metabolites is more restricted than for example in plants. The focus is on liquid chromatography with high resolution mass spectrometry where it is proposed that most of the problems in compound identification relate to structural isomers rather than to isobaric compounds. Thus many of the problems faced relate to separation of isomers, which is usually required even if fragmentation is used to support structural identification. Many papers report the use of MS/MS or MS2 as an adjunct to the identification of known metabolites but there a few examples in metabolomics studies of metazoans of complete structure elucidation of novel metabolites or metabolites where no authentic standards are available for comparison.

  5. Food metabolomics: from farm to human.

    Science.gov (United States)

    Kim, Sooah; Kim, Jungyeon; Yun, Eun Ju; Kim, Kyoung Heon

    2016-02-01

    Metabolomics, one of the latest components in the suite of systems biology, has been used to understand the metabolism and physiology of living systems, including microorganisms, plants, animals and humans. Food metabolomics can be defined as the application of metabolomics in food systems, including food resources, food processing and diet for humans. The study of food metabolomics has increased gradually in the recent years, because food systems are directly related to nutrition and human health. This review describes the recent trends and applications of metabolomics to food systems, from farm to human, including food resource production, industrial food processing and food intake by humans. Copyright © 2015 Elsevier Ltd. All rights reserved.

  6. Experimental Chagas disease-induced perturbations of the fecal microbiome and metabolome.

    Science.gov (United States)

    McCall, Laura-Isobel; Tripathi, Anupriya; Vargas, Fernando; Knight, Rob; Dorrestein, Pieter C; Siqueira-Neto, Jair L

    2018-03-01

    Trypanosoma cruzi parasites are the causative agents of Chagas disease. These parasites infect cardiac and gastrointestinal tissues, leading to local inflammation and tissue damage. Digestive Chagas disease is associated with perturbations in food absorption, intestinal traffic and defecation. However, the impact of T. cruzi infection on the gut microbiota and metabolome have yet to be characterized. In this study, we applied mass spectrometry-based metabolomics and 16S rRNA sequencing to profile infection-associated alterations in fecal bacterial composition and fecal metabolome through the acute-stage and into the chronic stage of infection, in a murine model of Chagas disease. We observed joint microbial and chemical perturbations associated with T. cruzi infection. These included alterations in conjugated linoleic acid (CLA) derivatives and in specific members of families Ruminococcaceae and Lachnospiraceae, as well as alterations in secondary bile acids and members of order Clostridiales. These results highlight the importance of multi-'omics' and poly-microbial studies in understanding parasitic diseases in general, and Chagas disease in particular.

  7. Application of Stable Isotope-Assisted Metabolomics for Cell Metabolism Studies

    Science.gov (United States)

    You, Le; Zhang, Baichen; Tang, Yinjie J.

    2014-01-01

    The applications of stable isotopes in metabolomics have facilitated the study of cell metabolisms. Stable isotope-assisted metabolomics requires: (1) properly designed tracer experiments; (2) stringent sampling and quenching protocols to minimize isotopic alternations; (3) efficient metabolite separations; (4) high resolution mass spectrometry to resolve overlapping peaks and background noises; and (5) data analysis methods and databases to decipher isotopic clusters over a broad m/z range (mass-to-charge ratio). This paper overviews mass spectrometry based techniques for precise determination of metabolites and their isotopologues. It also discusses applications of isotopic approaches to track substrate utilization, identify unknown metabolites and their chemical formulas, measure metabolite concentrations, determine putative metabolic pathways, and investigate microbial community populations and their carbon assimilation patterns. In addition, 13C-metabolite fingerprinting and metabolic models can be integrated to quantify carbon fluxes (enzyme reaction rates). The fluxome, in combination with other “omics” analyses, may give systems-level insights into regulatory mechanisms underlying gene functions. More importantly, 13C-tracer experiments significantly improve the potential of low-resolution gas chromatography-mass spectrometry (GC-MS) for broad-scope metabolism studies. We foresee the isotope-assisted metabolomics to be an indispensable tool in industrial biotechnology, environmental microbiology, and medical research. PMID:24957020

  8. MSQuant, an Open Source Platform for Mass Spectrometry-Based Quantitative Proteomics

    DEFF Research Database (Denmark)

    Mortensen, Peter; Gouw, Joost W; Olsen, Jesper V

    2010-01-01

    Mass spectrometry-based proteomics critically depends on algorithms for data interpretation. A current bottleneck in the rapid advance of proteomics technology is the closed nature and slow development cycle of vendor-supplied software solutions. We have created an open source software environment...

  9. Effective representation and storage of mass spectrometry-based proteomic data sets for the scientific community

    DEFF Research Database (Denmark)

    Olsen, Jesper V; Mann, Matthias

    2011-01-01

    Mass spectrometry-based proteomics has emerged as a technology of choice for global analysis of cell signaling networks. However, reporting and sharing of MS data are often haphazard, limiting the usefulness of proteomics to the signaling community. We argue that raw data should always be provided...... mechanisms for community-wide sharing of these data....

  10. Efek Pengunyahan Permen Karet Gula dan Xylitol terhadap Status Saliva

    Directory of Open Access Journals (Sweden)

    Lisna Kurnia Rezky

    2016-11-01

    Full Text Available Latar belakang. Rongga mulut sebagai pintu masuk makanan ke dalam tubuh selalu dibasahi oleh saliva setiap harinya. Saat ini banyak produk permen karet yang beredar di masyarakat yang mengandung gula dan xylitol. Banyak orang yang gemar mengunyah permen karet dengan kurang memperhatikan komposisinya baik yang mengandung gula ataupun xylitol sehingga kurang mengetahui efek masing-masing jenis permen karet tersebut terhadap kesehatan rongga mulut. Tujuan. Penelitian ini bertujuan untuk mengetahui efek pengunyahan permen karet gula dengan permen karet xylitol terhadap status saliva yang terdiri dari volume, pH, dan viskositas saliva. Metode penelitian. Subjek penelitian berjumlah 30 orang dibagi menjadi 3 kelompok masing-masing 10 orang, terdiri dari kelompok mengunyah permen karet gula, xylitol, dan kontrol dengan mengunyah apel. Pengambilan saliva dilakukan pagi hari dan siang hari. Subjek mengunyah 2 butir permen karet dan tidak diperbolehkan untuk makan dan minum 1 jam sebelum mengunyah. Subjek diinstruksikan meludah ke dalam pot saliva selama 10 menit dalam interval setiap 1 menit. Pengukuran volume saliva menggunakan pipet volume, pH saliva dengan menggunakan pH meter, dan viskositas saliva dengan menggunakan viskometer Ostwald hari ke-1 dan ke-4. Analisis data dengan uji statistik Mann-Whitney. Hasil. penelitian menunjukkan adanya peningkatan bermakna volume dan viskositas saliva pada pengunyahan permen karet xylitol dan gula. Derajat keasaman (pH saliva menurun setelah mengunyah permen karet gula sedangkan pada perm en karet xylitol relatif stabil. Disimpulkan bahwa permen karet xylitollebih baik untuk kestabilan status saliva dibandingkan permen karet gula.

  11. Factors That Influence the Extensional Rheological Property of Saliva.

    Directory of Open Access Journals (Sweden)

    Amrita Vijay

    Full Text Available The spinnbarkeit of saliva reflects the ability of saliva to adhere to surfaces within the mouth, thereby serving as a protective role and aiding in lubrication. Therefore, alterations in the extensional rheology of saliva may result in the loss in adhesiveness or the ability to bind onto surfaces. Mucin glycoproteins and their structures are known to be important factors for the extensional rheological properties of saliva. The conformation of mucin depends on factors such as pH and ionic strength. Chewing is one of the main stimuli for salivary secretion but creates significant sheer stress on the salivary film which could influence mouthfeel perceptions. The current study investigates the possible factors which affect the extensional rheological properties of saliva by comparing submandibular/sublingual saliva with different oral stimuli within the same group of subjects. Unstimulated and stimulated saliva (chew, smell and taste salivas were collected primarily from submandibular/sublingual glands. The saliva samples were measured for Spinnbarkeit followed by the measuring mucin, total protein, total calcium and bicarbonate concentrations. The results indicated correlations between rheological properties and mucin/ion concentrations. However, chewing stimulated submandibular/sublingual saliva is shown to have significantly lower Spinnbarkeit, but factors such as mucin, protein and calcium concentrations did not account for this variation. Analysis of the concentration of bicarbonate and pH appears to suggest that it has a prominent effect on extensional rheology of saliva.

  12. Lutzomyia longipalpis saliva or salivary protein LJM19 protects against Leishmania braziliensis and the saliva of its vector, Lutzomyia intermedia.

    Directory of Open Access Journals (Sweden)

    Natalia M Tavares

    Full Text Available BACKGROUND: Leishmania transmission occurs in the presence of insect saliva. Immunity to Phlebotomus papatasi or Lutzomyia longipalpis saliva or salivary components confers protection against an infection by Leishmania in the presence of the homologous saliva. However, immunization with Lutzomyia intermedia saliva did not protect mice against Leishmania braziliensis plus Lu. intermedia saliva. In the present study, we have studied whether the immunization with Lu. longipalpis saliva or a DNA plasmid coding for LJM19 salivary protein would be protective against L. braziliensis infection in the presence of Lu. intermedia saliva, the natural vector for L. braziliensis. METHODOLOGY/PRINCIPAL FINDINGS: Immunization with Lu. longipalpis saliva or with LJM19 DNA plasmid induced a Delayed-Type Hypersensitivity (DTH response against Lu. longipalpis as well as against a Lu. intermedia saliva challenge. Immunized and unimmunized control hamsters were then intradermally infected in the ears with L. braziliensis in the presence of Lu. longipalpis or Lu. intermedia saliva. Animals immunized with Lu. longipalpis saliva exhibited smaller lesion sizes as well as reduced disease burdens both at lesion site and in the draining lymph nodes. These alterations were associated with a significant decrease in the expression levels of IL-10 and TGF-β. Animals immunized with LJM19 DNA plasmid presented similar findings in protection and immune response and additionally increased IFN-γ expression. CONCLUSIONS/SIGNIFICANCE: Immunization with Lu. longipalpis saliva or with a DNA plasmid coding LJM19 salivary protein induced protection in hamsters challenged with L. braziliensis plus Lu. intermedia saliva. These findings point out an important role of immune response against saliva components, suggesting the possibility to develop a vaccine using a single component of Lu. longipalpis saliva to generate protection against different species of Leishmania, even those

  13. Manganese concentration in human saliva using NAA

    Energy Technology Data Exchange (ETDEWEB)

    Lewgoy, Hugo R., E-mail: hugorl@usp.br [Universidade Bandeirante Anhanguera (UNIBAN), Sao Paulo, SP (Brazil); Zamboni, Cibele B.; Medeiros, Ilca M.M.A.; Medeiros, Jose A.G. de [Instituto de Pesquisas Energeticas e Nucleares (IPEN/CNEN-SP), Sao Paulo, SP (Brazil)

    2013-07-01

    In this investigation the Manganese levels in human whole saliva were determined using Neutron Activation Analysis (NAA) technique for the proposition of an indicative interval. The measurements were performed considering gender and lifestyle factors of Brazilian inhabitants (non-smokers, non-drinkers and no history of toxicological exposure). The results emphasize that the indicative interval is statistically different by gender. These data are useful for identifying or preventing some diseases in the Brazilian population. (author)

  14. Candida in saliva of Brazilian hemophilic patients

    OpenAIRE

    Pereira,Claudio Maranhão; Pires,Fábio Ramôa; Corrêa,Maria Elvira Pizzigatti; di Hipólito Júnior,Osvaldo; Almeida,Oslei Paes de

    2004-01-01

    Hemophilia is a common hereditary hemorrhagic disorder, however little is known about the oral microflora of hemophilic patients. The aim of this study was to quantify the Candida and identify its species in non-stimulated saliva of hemophilic patients, and consider its relationship with clinical factors influencing Candida carriage. This study comprised evaluation of 86 hemophilic patients of the Hematology Center/UNICAMP and 43 healthy subjects as controls. All patients were submitted to an...

  15. Manganese concentration in human saliva using NAA

    International Nuclear Information System (INIS)

    Lewgoy, Hugo R.; Zamboni, Cibele B.; Medeiros, Ilca M.M.A.; Medeiros, Jose A.G. de

    2013-01-01

    In this investigation the Manganese levels in human whole saliva were determined using Neutron Activation Analysis (NAA) technique for the proposition of an indicative interval. The measurements were performed considering gender and lifestyle factors of Brazilian inhabitants (non-smokers, non-drinkers and no history of toxicological exposure). The results emphasize that the indicative interval is statistically different by gender. These data are useful for identifying or preventing some diseases in the Brazilian population. (author)

  16. NMR-based metabolomics in human disease diagnosis: Applications, limitations, and recommendations

    KAUST Repository

    Emwas, Abdul-Hamid M.

    2013-04-03

    Metabolomics is a dynamic and emerging research field, similar to proteomics, transcriptomics and genomics in affording global understanding of biological systems. It is particularly useful in functional genomic studies in which metabolism is thought to be perturbed. Metabolomics provides a snapshot of the metabolic dynamics that reflect the response of living systems to both pathophysiological stimuli and/or genetic modification. Because this approach makes possible the examination of interactions between an organism and its diet or environment, it is particularly useful for identifying biomarkers of disease processes that involve the environment. For example, the interaction of a high fat diet with cardiovascular disease can be studied via such a metabolomics approach by modeling the interaction between genes and diet. The high reproducibility of NMR-based techniques gives this method a number of advantages over other analytical techniques in large-scale and long-term metabolomic studies, such as epidemiological studies. This approach has been used to study a wide range of diseases, through the examination of biofluids, including blood plasma/serum, urine, blister fluid, saliva and semen, as well as tissue extracts and intact tissue biopsies. However, complicating the use of NMR spectroscopy in biomarker discovery is the fact that numerous variables can effect metabolic composition including, fasting, stress, drug administration, diet, gender, age, physical activity, life style and the subject\\'s health condition. To minimize the influence of these variations in the datasets, all experimental conditions including sample collection, storage, preparation as well as NMR spectroscopic parameters and data analysis should be optimized carefully and conducted in an identical manner as described by the local standard operating protocol. This review highlights the potential applications of NMR-based metabolomics studies and gives some recommendations to improve sample

  17. Vitamins, metabolomics, and prostate cancer.

    Science.gov (United States)

    Mondul, Alison M; Weinstein, Stephanie J; Albanes, Demetrius

    2017-06-01

    How micronutrients might influence risk of developing adenocarcinoma of the prostate has been the focus of a large body of research (especially regarding vitamins E, A, and D). Metabolomic profiling has the potential to discover molecular species relevant to prostate cancer etiology, early detection, and prevention, and may help elucidate the biologic mechanisms through which vitamins influence prostate cancer risk. Prostate cancer risk data related to vitamins E, A, and D and metabolomic profiling from clinical, cohort, and nested case-control studies, along with randomized controlled trials, are examined and summarized, along with recent metabolomic data of the vitamin phenotypes. Higher vitamin E serologic status is associated with lower prostate cancer risk, and vitamin E genetic variant data support this. By contrast, controlled vitamin E supplementation trials have had mixed results based on differing designs and dosages. Beta-carotene supplementation (in smokers) and higher circulating retinol and 25-hydroxy-vitamin D concentrations appear related to elevated prostate cancer risk. Our prospective metabolomic profiling of fasting serum collected 1-20 years prior to clinical diagnoses found reduced lipid and energy/TCA cycle metabolites, including inositol-1-phosphate, lysolipids, alpha-ketoglutarate, and citrate, significantly associated with lower risk of aggressive disease. Several active leads exist regarding the role of micronutrients and metabolites in prostate cancer carcinogenesis and risk. How vitamins D and A may adversely impact risk, and whether low-dose vitamin E supplementation remains a viable preventive approach, require further study.

  18. The metabolomics standards initiative (MSI)

    NARCIS (Netherlands)

    Fiehn, O.; Robertson, D.; Griffin, J.; Werf, M. van der; Nikolau, B.; Morrison, N.; Sumner, L.W.; Goodacre, R.; Hardy, N.W.; Taylor, C.; Fostel, J.; Kristal, B.; Kaddurah-Daouk, R.; Mendes, P.; Ommen, B. van; Lindon, J.C.; Sansone, S.-A.

    2007-01-01

    In 2005, the Metabolomics Standards Initiative has been formed. An outline and general introduction is provided to inform about the history, structure, working plan and intentions of this initiative. Comments on any of the suggested minimal reporting standards are welcome to be sent to the open

  19. YMDB: the Yeast Metabolome Database

    Science.gov (United States)

    Jewison, Timothy; Knox, Craig; Neveu, Vanessa; Djoumbou, Yannick; Guo, An Chi; Lee, Jacqueline; Liu, Philip; Mandal, Rupasri; Krishnamurthy, Ram; Sinelnikov, Igor; Wilson, Michael; Wishart, David S.

    2012-01-01

    The Yeast Metabolome Database (YMDB, http://www.ymdb.ca) is a richly annotated ‘metabolomic’ database containing detailed information about the metabolome of Saccharomyces cerevisiae. Modeled closely after the Human Metabolome Database, the YMDB contains >2000 metabolites with links to 995 different genes/proteins, including enzymes and transporters. The information in YMDB has been gathered from hundreds of books, journal articles and electronic databases. In addition to its comprehensive literature-derived data, the YMDB also contains an extensive collection of experimental intracellular and extracellular metabolite concentration data compiled from detailed Mass Spectrometry (MS) and Nuclear Magnetic Resonance (NMR) metabolomic analyses performed in our lab. This is further supplemented with thousands of NMR and MS spectra collected on pure, reference yeast metabolites. Each metabolite entry in the YMDB contains an average of 80 separate data fields including comprehensive compound description, names and synonyms, structural information, physico-chemical data, reference NMR and MS spectra, intracellular/extracellular concentrations, growth conditions and substrates, pathway information, enzyme data, gene/protein sequence data, as well as numerous hyperlinks to images, references and other public databases. Extensive searching, relational querying and data browsing tools are also provided that support text, chemical structure, spectral, molecular weight and gene/protein sequence queries. Because of S. cervesiae's importance as a model organism for biologists and as a biofactory for industry, we believe this kind of database could have considerable appeal not only to metabolomics researchers, but also to yeast biologists, systems biologists, the industrial fermentation industry, as well as the beer, wine and spirit industry. PMID:22064855

  20. Enzymatically Modified Starch Ameliorates Postprandial Serum Triglycerides and Lipid Metabolome in Growing Pigs.

    Science.gov (United States)

    Metzler-Zebeli, Barbara U; Eberspächer, Eva; Grüll, Dietmar; Kowalczyk, Lidia; Molnar, Timea; Zebeli, Qendrim

    2015-01-01

    Developing host digestion-resistant starches to promote human health is of great research interest. Chemically modified starches (CMS) are widely used in processed foods and although the modification of the starch molecule allows specific reduction in digestibility, the metabolic effects of CMS have been less well described. This short-term study evaluated the impact of enzymatically modified starch (EMS) on fasting and postprandial profiles of blood glucose, insulin and lipids, and serum metabolome in growing pigs. Eight jugular-vein catheterized pigs (initial body weight, 37.4 kg; 4 months of age) were fed 2 diets containing 72% purified starch (EMS or waxy corn starch (control)) in a cross-over design for 7 days. On day 8, an 8-hour meal tolerance test (MTT) was performed with serial blood samplings. Besides biochemical analysis, serum was analysed for 201 metabolites through targeted mass spectrometry-based metabolomic approaches. Pigs fed the EMS diet showed increased (Pmetabolome profiling identified characteristic changes in glycerophospholipid, lysophospholipids, sphingomyelins and amino acid metabolome profiles with EMS diet compared to control diet. Results showed rapid adaptations of blood metabolites to dietary starch shifts within 7 days. In conclusion, EMS ingestion showed potential to attenuate postprandial raise in serum lipids and suggested constant alteration in the synthesis or breakdown of sphingolipids and phospholipids which might be a health benefit of EMS consumption. Because serum insulin was not lowered, more research is warranted to reveal possible underlying mechanisms behind the observed changes in the profile of serum lipid metabolome in response to EMS consumption.

  1. Metabolomics analysis of metabolic effects of nicotinamide phosphoribosyltransferase (NAMPT inhibition on human cancer cells.

    Directory of Open Access Journals (Sweden)

    Vladimir Tolstikov

    Full Text Available Nicotinamide phosphoribosyltransferase (NAMPT plays an important role in cellular bioenergetics. It is responsible for converting nicotinamide to nicotinamide adenine dinucleotide, an essential molecule in cellular metabolism. NAMPT has been extensively studied over the past decade due to its role as a key regulator of nicotinamide adenine dinucleotide-consuming enzymes. NAMPT is also known as a potential target for therapeutic intervention due to its involvement in disease. In the current study, we used a global mass spectrometry-based metabolomic approach to investigate the effects of FK866, a small molecule inhibitor of NAMPT currently in clinical trials, on metabolic perturbations in human cancer cells. We treated A2780 (ovarian cancer and HCT-116 (colorectal cancer cell lines with FK866 in the presence and absence of nicotinic acid. Significant changes were observed in the amino acids metabolism and the purine and pyrimidine metabolism. We also observed metabolic alterations in glycolysis, the citric acid cycle (TCA, and the pentose phosphate pathway. To expand the range of the detected polar metabolites and improve data confidence, we applied a global metabolomics profiling platform by using both non-targeted and targeted hydrophilic (HILIC-LC-MS and GC-MS analysis. We used Ingenuity Knowledge Base to facilitate the projection of metabolomics data onto metabolic pathways. Several metabolic pathways showed differential responses to FK866 based on several matches to the list of annotated metabolites. This study suggests that global metabolomics can be a useful tool in pharmacological studies of the mechanism of action of drugs at a cellular level.

  2. Advancement of mass spectrometry-based proteomics technologies to explore triple negative breast cancer.

    Science.gov (United States)

    Miah, Sayem; Banks, Charles A S; Adams, Mark K; Florens, Laurence; Lukong, Kiven E; Washburn, Michael P

    2016-12-20

    Understanding the complexity of cancer biology requires extensive information about the cancer proteome over the course of the disease. The recent advances in mass spectrometry-based proteomics technologies have led to the accumulation of an incredible amount of such proteomic information. This information allows us to identify protein signatures or protein biomarkers, which can be used to improve cancer diagnosis, prognosis and treatment. For example, mass spectrometry-based proteomics has been used in breast cancer research for over two decades to elucidate protein function. Breast cancer is a heterogeneous group of diseases with distinct molecular features that are reflected in tumour characteristics and clinical outcomes. Compared with all other subtypes of breast cancer, triple-negative breast cancer is perhaps the most distinct in nature and heterogeneity. In this review, we provide an introductory overview of the application of advanced proteomic technologies to triple-negative breast cancer research.

  3. Longitudinal Study of Hepatitis A Infection by Saliva Sampling: The Kinetics of HAV Markers in Saliva Revealed the Application of Saliva Tests for Hepatitis A Study

    Science.gov (United States)

    Amado Leon, Luciane Almeida; de Almeida, Adilson José; de Paula, Vanessa Salete; Tourinho, Renata Santos; Villela, Daniel Antunes Maciel; Gaspar, Ana Maria Coimbra; Lewis-Ximenez, Lia Laura; Pinto, Marcelo Alves

    2015-01-01

    Despite the increasing numbers of studies investigating hepatitis A diagnostic through saliva, the frequency and the pattern of hepatitis A virus (HAV) markers in this fluid still remains unknown. To address this issue, we carried on a longitudinal study to examine the kinetics of HAV markers in saliva, in comparison with serum samples. The present study followed-up ten patients with acute hepatitis A infection during 180 days post diagnosis (dpd). Total anti-HAV was detected in paired serum and saliva samples until the end of the follow-up, showing a peak titer at 90th. However, total anti-HAV level was higher in serum than in saliva samples. This HAV marker showed a probability of 100% to be detected in both serum and saliva during 180 dpd. The IgM anti-HAV could be detected in saliva up to 150 dpd, showing the highest frequency at 30th, when it was detected in all individuals. During the first month of HAV infection, this acute HAV marker showed a detection probability of 100% in paired samples. The detection of IgM anti-HAV in saliva was not dependent on its level in serum, HAV-RNA detection and/or viral load, since no association was found between IgM anti-HAV positivity in saliva and any of these parameter (p>0.05). Most of the patients (80%) were found to contain HAV-RNA in saliva, mainly at early acute phase (30th day). However, it was possible to demonstrate the HAV RNA presence in paired samples for more than 90 days, even after seroconversion. No significant relationship was observed between salivary HAV-RNA positivity and serum viral load, demonstrating that serum viral load is not predictive of HAV-RNA detection in saliva. Similar viral load was seen in paired samples (on average 104 copies/mL). These data demonstrate that the best diagnostic coverage can be achieved by salivary anti-HAV antibodies and HAV-RNA tests during 30–90 dpd. The long detection and high probability of specific-HAV antibodies positivity in saliva samples make the assessment of

  4. The next wave in metabolome analysis

    DEFF Research Database (Denmark)

    Nielsen, Jens; Oliver, S.

    2005-01-01

    The metabolome of a cell represents the amplification and integration of signals from other functional genomic levels, such as the transcriptome and the proteome. Although this makes metabolomics a useful tool for the high-throughput analysis of phenotypes, the lack of a direct connection...... to the genome makes it difficult to interpret metabolomic data. Nevertheless, functional genomics has produced examples of the use of metabolomics to elucidate the phenotypes of otherwise silent mutations. Despite several successes, we believe that future metabolomic studies must focus on the accurate...... measurement of the concentrations of unambiguously identified metabolites. The research community must develop databases of metabolite concentrations in cells that are grown in several well-defined conditions if metabolomic data are to be integrated meaningfully with data from the other levels of functional...

  5. Saliva: Physiology and Diagnostic Potential in Health and Disease

    Directory of Open Access Journals (Sweden)

    Sebastien J. C. Farnaud

    2010-01-01

    Full Text Available Saliva has been described as the mirror of the body. In a world of soaring healthcare costs and an environment where rapid diagnosis may be critical to a positive patient outcome, saliva is emerging as a viable alternative to blood sampling. In this review, we discuss the composition and various physiological roles of saliva in the oral cavity, including soft tissue protection, antimicrobial activities, and oral tissue repair. We then explore saliva as a diagnostic marker of local oral disease and focus particularly on oral cancers. The cancer theme continues when we focus on systemic disease diagnosis from salivary biomarkers. Communicable disease is the focus of the next section where we review the literature relating to the direct and indirect detection of pathogenic infections from human saliva. Finally, we discuss hormones involved in appetite regulation and whether saliva is a viable alternative to blood in order to monitor hormones that are involved in satiety.

  6. Metabolomics Application in Maternal-Fetal Medicine

    OpenAIRE

    Fanos, Vassilios; Atzori, Luigi; Makarenko, Karina; Melis, Gian Benedetto; Ferrazzi, Enrico

    2013-01-01

    Metabolomics in maternal-fetal medicine is still an “embryonic” science. However, there is already an increasing interest in metabolome of normal and complicated pregnancies, and neonatal outcomes. Tissues used for metabolomics interrogations of pregnant women, fetuses and newborns are amniotic fluid, blood, plasma, cord blood, placenta, urine, and vaginal secretions. All published papers highlight the strong correlation between biomarkers found in these tissues and fetal malformations, prete...

  7. Factors determining the passage of drugs from blood into saliva.

    OpenAIRE

    Stephen, K W; McCrossan, J; Mackenzie, D; Macfarlane, C B; Speirs, C F

    1980-01-01

    1. Following single oral dosing of ampicillin, cephalexin, tetracycline, erythromycin estolate, clindamycin and rifampicin to six normal volunteers, antibacterial activity was measured at 1, 3 and 6 h in serum, gingival fluid and minor gland saliva from all subjects and in parotid and submandiabular saliva from three. 2. pH values of all gingival fluid and saliva specimens were noted. 3. Partition coefficients between n-octanol and water were measured for erythromycin, clindamycin and rifampi...

  8. Microbial Community Profiling of Human Saliva Using Shotgun Metagenomic Sequencing

    OpenAIRE

    Hasan, Nur A.; Young, Brian A.; Minard-Smith, Angela T.; Saeed, Kelly; Li, Huai; Heizer, Esley M.; McMillan, Nancy J.; Isom, Richard; Abdullah, Abdul Shakur; Bornman, Daniel M.; Faith, Seth A.; Choi, Seon Young; Dickens, Michael L.; Cebula, Thomas A.; Colwell, Rita R.

    2014-01-01

    Human saliva is clinically informative of both oral and general health. Since next generation shotgun sequencing (NGS) is now widely used to identify and quantify bacteria, we investigated the bacterial flora of saliva microbiomes of two healthy volunteers and five datasets from the Human Microbiome Project, along with a control dataset containing short NGS reads from bacterial species representative of the bacterial flora of human saliva. GENIUS, a system designed to identify and quantify ba...

  9. Metabolomics in Toxicology and Preclinical Research

    Science.gov (United States)

    Ramirez, Tzutzuy; Daneshian, Mardas; Kamp, Hennicke; Bois, Frederic Y.; Clench, Malcolm R.; Coen, Muireann; Donley, Beth; Fischer, Steven M.; Ekman, Drew R.; Fabian, Eric; Guillou, Claude; Heuer, Joachim; Hogberg, Helena T.; Jungnickel, Harald; Keun, Hector C.; Krennrich, Gerhard; Krupp, Eckart; Luch, Andreas; Noor, Fozia; Peter, Erik; Riefke, Bjoern; Seymour, Mark; Skinner, Nigel; Smirnova, Lena; Verheij, Elwin; Wagner, Silvia; Hartung, Thomas; van Ravenzwaay, Bennard; Leist, Marcel

    2013-01-01

    Summary Metabolomics, the comprehensive analysis of metabolites in a biological system, provides detailed information about the biochemical/physiological status of a biological system, and about the changes caused by chemicals. Metabolomics analysis is used in many fields, ranging from the analysis of the physiological status of genetically modified organisms in safety science to the evaluation of human health conditions. In toxicology, metabolomics is the -omics discipline that is most closely related to classical knowledge of disturbed biochemical pathways. It allows rapid identification of the potential targets of a hazardous compound. It can give information on target organs and often can help to improve our understanding regarding the mode-of-action of a given compound. Such insights aid the discovery of biomarkers that either indicate pathophysiological conditions or help the monitoring of the efficacy of drug therapies. The first toxicological applications of metabolomics were for mechanistic research, but different ways to use the technology in a regulatory context are being explored. Ideally, further progress in that direction will position the metabolomics approach to address the challenges of toxicology of the 21st century. To address these issues, scientists from academia, industry, and regulatory bodies came together in a workshop to discuss the current status of applied metabolomics and its potential in the safety assessment of compounds. We report here on the conclusions of three working groups addressing questions regarding 1) metabolomics for in vitro studies 2) the appropriate use of metabolomics in systems toxicology, and 3) use of metabolomics in a regulatory context. PMID:23665807

  10. Endocrinology Meets Metabolomics: Achievements, Pitfalls, and Challenges.

    Science.gov (United States)

    Tokarz, Janina; Haid, Mark; Cecil, Alexander; Prehn, Cornelia; Artati, Anna; Möller, Gabriele; Adamski, Jerzy

    2017-10-01

    The metabolome, although very dynamic, is sufficiently stable to provide specific quantitative traits related to health and disease. Metabolomics requires balanced use of state-of-the-art study design, chemical analytics, biostatistics, and bioinformatics to deliver meaningful answers to contemporary questions in human disease research. The technology is now frequently employed for biomarker discovery and for elucidating the mechanisms underlying endocrine-related diseases. Metabolomics has also enriched genome-wide association studies (GWAS) in this area by providing functional data. The contributions of rare genetic variants to metabolome variance and to the human phenotype have been underestimated until now. Copyright © 2017 Elsevier Ltd. All rights reserved.

  11. Functional metabolomics reveals novel active products in the DHA metabolome

    Directory of Open Access Journals (Sweden)

    Masakazu eShinohara

    2012-04-01

    Full Text Available Endogenous mechanisms for successful resolution of an acute inflammatory response and the local return to homeostasis are of interest because excessive inflammation underlies many human diseases. In this review, we provide an update and overview of functional metabolomics that identified a new bioactive metabolome of docosahexaenoic acid (DHA. Systematic studies revealed that DHA was converted to DHEA-derived novel bioactive products as well as aspirin-triggered (AT forms of protectins. The new oxygenated DHEA derived products blocked PMN chemotaxis, reduced P-selectin expression and platelet-leukocyte adhesion, and showed organ protection in ischemia/reperfusion injury. These products activated cannabinoid receptor (CB2 receptor and not CB1 receptors. The AT-PD1 reduced neutrophil (PMN recruitment in murine peritonitis. With human cells, AT-PD1 decreased transendothelial PMN migration as well as enhanced efferocytosis of apoptotic human PMN by macrophages. The recent findings reviewed here indicate that DHEA oxidative metabolism and aspirin-triggered conversion of DHA produce potent novel molecules with anti-inflammatory and organ-protective properties, opening the DHA metabolome functional roles.

  12. Statistical analysis of proteomics, metabolomics, and lipidomics data using mass spectrometry

    CERN Document Server

    Mertens, Bart

    2017-01-01

    This book presents an overview of computational and statistical design and analysis of mass spectrometry-based proteomics, metabolomics, and lipidomics data. This contributed volume provides an introduction to the special aspects of statistical design and analysis with mass spectrometry data for the new omic sciences. The text discusses common aspects of design and analysis between and across all (or most) forms of mass spectrometry, while also providing special examples of application with the most common forms of mass spectrometry. Also covered are applications of computational mass spectrometry not only in clinical study but also in the interpretation of omics data in plant biology studies. Omics research fields are expected to revolutionize biomolecular research by the ability to simultaneously profile many compounds within either patient blood, urine, tissue, or other biological samples. Mass spectrometry is one of the key analytical techniques used in these new omic sciences. Liquid chromatography mass ...

  13. Metabolomics window into diabetic complications.

    Science.gov (United States)

    Wu, Tao; Qiao, Shuxuan; Shi, Chenze; Wang, Shuya; Ji, Guang

    2018-03-01

    Diabetes has become a major global health problem. The elucidation of characteristic metabolic alterations during the diabetic progression is critical for better understanding its pathogenesis, and identifying potential biomarkers and drug targets. Metabolomics is a promising tool to reveal the metabolic changes and the underlying mechanism involved in the pathogenesis of diabetic complications. The present review provides an update on the application of metabolomics in diabetic complications, including diabetic coronary artery disease, diabetic nephropathy, diabetic retinopathy and diabetic neuropathy, and this review provides notes on the prevention and prediction of diabetic complications. © 2017 The Authors. Journal of Diabetes Investigation published by Asian Association for the Study of Diabetes (AASD) and John Wiley & Sons Australia, Ltd.

  14. Metabolomics investigation of whey intake

    DEFF Research Database (Denmark)

    Stanstrup, Jan

    syndrome are complex disorders and are not caused by a high-calorie diet and low exercise level alone. The specific nature of the nutrients, independent of their caloric value, also play a role. The question is which. In the quest to answer this question the qualitative intake of protein is of special...... and prevention of the metabolic syndrome related to obesity and diabetes. In this thesis the effects of whey intake on the human metabolome was investigated using a metabolomics approach. We demonstrated that intake of whey causes a decreased rate of gastric emptying compared to other protein sources....... Therefore this thesis will also present and discuss state-of-the-art tools for computer-assisted compound identification, including: annotation of adducts and fragments, determination of the molecular ion, in silico fragmentation, retention time mapping between analytical systems and de novo retention time...

  15. Metabolomics techniques for nanotoxicity investigations.

    Science.gov (United States)

    Lv, Mengying; Huang, Wanqiu; Chen, Zhipeng; Jiang, Hulin; Chen, Jiaqing; Tian, Yuan; Zhang, Zunjian; Xu, Fengguo

    2015-01-01

    Nanomaterials are commonly defined as engineered structures with at least one dimension of 100 nm or less. Investigations of their potential toxicological impact on biological systems and the environment have yet to catch up with the rapid development of nanotechnology and extensive production of nanoparticles. High-throughput methods are necessary to assess the potential toxicity of nanoparticles. The omics techniques are well suited to evaluate toxicity in both in vitro and in vivo systems. Besides genomic, transcriptomic and proteomic profiling, metabolomics holds great promises for globally evaluating and understanding the molecular mechanism of nanoparticle-organism interaction. This manuscript presents a general overview of metabolomics techniques, summarizes its early application in nanotoxicology and finally discusses opportunities and challenges faced in nanotoxicology.

  16. Candida in saliva of Brazilian hemophilic patients.

    Science.gov (United States)

    Pereira, Claudio Maranhão; Pires, Fábio Ramôa; Corrêa, Maria Elvira Pizzigatti; di Hipólito Júnior, Osvaldo; Almeida, Oslei Paes de

    2004-12-01

    Hemophilia is a common hereditary hemorrhagic disorder, however little is known about the oral microflora of hemophilic patients. The aim of this study was to quantify the Candida and identify its species in non-stimulated saliva of hemophilic patients, and consider its relationship with clinical factors influencing Candida carriage. This study comprised evaluation of 86 hemophilic patients of the Hematology Center/UNICAMP and 43 healthy subjects as controls. All patients were submitted to anamnesis, intraoral examination and unstimulated saliva collection. Candida counts and species identification were performed in salivary samples. Candida was present in 64% of the hemophilic patients and in 44% of the healthy controls. C. albicans represented 65% and 68% of the isolated species, in hemophiliacs and control group respectively, and C. tropicalis was the second most common species in both groups. These results indicate that hemophilic patients carry Candida more frequently and in higher counts than healthy controls, independently of oral clinical parameter considered, as viral infections, complete dentures, transfusions of hemoderivatives, and salivary flow.

  17. The pH changes of artificial saliva after interaction with oral of artificial saliva after interaction with oral micropathogen

    Directory of Open Access Journals (Sweden)

    Basri A. Gani

    2012-12-01

    Full Text Available Backgorund: Saliva contains several protein elements, exocrine proteins and antibodies, such as lactoferrin, sIgA, peroxidase, albumin, polypeptides, and oligopeptides that contribute to the defense of oral mucosa and dental pellicle to prevent infection caused by oral micropathogen, such as Candida albicans, Streptococcus mutans and Aggregatibacter actinomycetemcomitans (A. actinomycetemcomitans. Those micropathogens have a role to change salivary pH as an indicator of oral disease activities. Purpose: This study was aimed to analyze the changes of artificial saliva pH after interaction with S. mutans, C. albicans, and A. Actinomycetemcpmitans. Methods: The materials used in this study consist of S. mutans (ATCC 31987, C. albicans (ATCC 10231, A. actinomycetemcomitans (ATTC 702 358, and artificial saliva. To examine the pH changes of artificial saliva, those three microbiotas were cultured and incubated for 24 hours. Results: The results showed that the interactions of S. mutans, C. albicans, and A. actinomycetemcomitans in the artificial saliva can change the salivary on neutral. There were no significant difference with the control treatment salivary pH 4, 5, 6, 8, and 9 (p>0.05. Similarly, there was also no significant difference when those three microorganism interacted each other in the artificial saliva (p<0.05. Conclusion: It can be concluded that the biological activity of S. mutans, C. albicans, and A. actinomycetemcomitans in artificial saliva can change the salivary pH into neutral. It indicates that those microbiotas mutually supported and cooperated in influencing the biological cycle of the oral cavity with salivary pH as an indicator.Latar belakang: Saliva merupakan cairan eksokrin yang mengandung unsur protein dan antibodi seperti sIgA laktoferin peroksidase, albumin, polipeptida dan oligopeptida yang berperan pada pertahanan mukosa rongga mulut dan gigi guna mencegah infeksi oral mikropatogen seperti C. albicans, S. mutans, dan

  18. The future of metabolomics in ELIXIR

    Science.gov (United States)

    van Rijswijk, Merlijn; Beirnaert, Charlie; Caron, Christophe; Cascante, Marta; Dominguez, Victoria; Dunn, Warwick B.; Ebbels, Timothy M. D.; Giacomoni, Franck; Gonzalez-Beltran, Alejandra; Hankemeier, Thomas; Haug, Kenneth; Izquierdo-Garcia, Jose L.; Jimenez, Rafael C.; Jourdan, Fabien; Kale, Namrata; Klapa, Maria I.; Kohlbacher, Oliver; Koort, Kairi; Kultima, Kim; Le Corguillé, Gildas; Moreno, Pablo; Moschonas, Nicholas K.; Neumann, Steffen; O’Donovan, Claire; Reczko, Martin; Rocca-Serra, Philippe; Rosato, Antonio; Salek, Reza M.; Sansone, Susanna-Assunta; Satagopam, Venkata; Schober, Daniel; Shimmo, Ruth; Spicer, Rachel A.; Spjuth, Ola; Thévenot, Etienne A.; Viant, Mark R.; Weber, Ralf J. M.; Willighagen, Egon L.; Zanetti, Gianluigi; Steinbeck, Christoph

    2017-01-01

    Metabolomics, the youngest of the major omics technologies, is supported by an active community of researchers and infrastructure developers across Europe. To coordinate and focus efforts around infrastructure building for metabolomics within Europe, a workshop on the “Future of metabolomics in ELIXIR” was organised at Frankfurt Airport in Germany. This one-day strategic workshop involved representatives of ELIXIR Nodes, members of the PhenoMeNal consortium developing an e-infrastructure that supports workflow-based metabolomics analysis pipelines, and experts from the international metabolomics community. The workshop established metabolite identification as the critical area, where a maximal impact of computational metabolomics and data management on other fields could be achieved. In particular, the existing four ELIXIR Use Cases, where the metabolomics community - both industry and academia - would benefit most, and which could be exhaustively mapped onto the current five ELIXIR Platforms were discussed. This opinion article is a call for support for a new ELIXIR metabolomics Use Case, which aligns with and complements the existing and planned ELIXIR Platforms and Use Cases. PMID:29043062

  19. The future of metabolomics in ELIXIR.

    Science.gov (United States)

    van Rijswijk, Merlijn; Beirnaert, Charlie; Caron, Christophe; Cascante, Marta; Dominguez, Victoria; Dunn, Warwick B; Ebbels, Timothy M D; Giacomoni, Franck; Gonzalez-Beltran, Alejandra; Hankemeier, Thomas; Haug, Kenneth; Izquierdo-Garcia, Jose L; Jimenez, Rafael C; Jourdan, Fabien; Kale, Namrata; Klapa, Maria I; Kohlbacher, Oliver; Koort, Kairi; Kultima, Kim; Le Corguillé, Gildas; Moreno, Pablo; Moschonas, Nicholas K; Neumann, Steffen; O'Donovan, Claire; Reczko, Martin; Rocca-Serra, Philippe; Rosato, Antonio; Salek, Reza M; Sansone, Susanna-Assunta; Satagopam, Venkata; Schober, Daniel; Shimmo, Ruth; Spicer, Rachel A; Spjuth, Ola; Thévenot, Etienne A; Viant, Mark R; Weber, Ralf J M; Willighagen, Egon L; Zanetti, Gianluigi; Steinbeck, Christoph

    2017-01-01

    Metabolomics, the youngest of the major omics technologies, is supported by an active community of researchers and infrastructure developers across Europe. To coordinate and focus efforts around infrastructure building for metabolomics within Europe, a workshop on the "Future of metabolomics in ELIXIR" was organised at Frankfurt Airport in Germany. This one-day strategic workshop involved representatives of ELIXIR Nodes, members of the PhenoMeNal consortium developing an e-infrastructure that supports workflow-based metabolomics analysis pipelines, and experts from the international metabolomics community. The workshop established metabolite identification as the critical area, where a maximal impact of computational metabolomics and data management on other fields could be achieved. In particular, the existing four ELIXIR Use Cases, where the metabolomics community - both industry and academia - would benefit most, and which could be exhaustively mapped onto the current five ELIXIR Platforms were discussed. This opinion article is a call for support for a new ELIXIR metabolomics Use Case, which aligns with and complements the existing and planned ELIXIR Platforms and Use Cases.

  20. Symbiosis of chemometrics and metabolomics: past, present, and future

    NARCIS (Netherlands)

    van der Greef, J.; Smilde, A. K.

    2005-01-01

    Metabolomics is a growing area in the field of systems biology. Metabolomics has already a long history and also the connection of metabolomics with chemometrics goes back some time. This review discusses the symbiosis of metabolomics and chemometrics with emphasis on the medical domain, puts the

  1. The role of electrostatics in saliva-induced emulsion flocculation

    NARCIS (Netherlands)

    Silletti, Erika; Vingerhoeds, Monique H.; Norde, Willem; Van Aken, George A.

    Upon consumption food emulsions undergo different processes, including mixing with saliva. It has been shown that whole saliva induces emulsion flocculation [van Aken, G. A., Vingerhoeds, M. H., & de Hoog, E. H. A. (2005). Colloidal behaviour of food emulsions under oral conditions. In E. Dickinson

  2. Effects of Lactobacillus rhamnosus GG on saliva-derived microcosms

    NARCIS (Netherlands)

    Pham, L.C.; Hoogenkamp, M.A.; Exterkate, R.A.M.; Terefework, Z.; de Soet, J.J.; ten Cate, J.M.; Crielaard, W.; Zaura, E.

    2011-01-01

    Objective The probiotic strain Lactobacillus rhamnosus GG (LGG) is shown to hamper the presence of mutans streptococci in saliva and may have positive effects on oral health. We investigated the effects of LGG on the cariogenic potential and microbial composition of saliva-derived microcosms. Design

  3. Effects of different tastants on parotid saliva flow and composition

    NARCIS (Netherlands)

    Neyraud, E.; Heinzerling, C.I.; Bult, J.H.F.; Mesmin, C.; Dransfield, E.

    2009-01-01

    Saliva from parotid glands plays a role in taste perception. Parotid saliva is also stimulated by tastants. The aim of this work is to investigate the effects of different tastants on the parotid salivary response in six subjects. Five tastants were given in different concentrations in solution and

  4. Metabolomics and bioactive substances in plants

    DEFF Research Database (Denmark)

    Khakimov, Bekzod

    Metabolomic analysis of plants broadens understanding of how plants may benefit humans, animals and the environment, provide sustainable food and energy, and improve current agricultural, pharmacological and medicinal practices in order to bring about healthier and longer life. The quality...... and amount of the extractible biological information is largely determined by data acquisition, data processing and analysis methodologies of the plant metabolomics studies. This PhD study focused mainly on the development and implementation of new metabolomics methodologies for improved data acquisition...... and data processing. The study mainly concerned the three most commonly applied analytical techniques in plant metabolomics, GC-MS, LC-MS and NMR. In addition, advanced chemometrics methods e.g. PARAFAC2 and ASCA have been extensively used for development of complex metabolomics data processing...

  5. A Metabolomic Perspective on Coeliac Disease

    Science.gov (United States)

    Calabrò, Antonio

    2014-01-01

    Metabolomics is an “omic” science that is now emerging with the purpose of elaborating a comprehensive analysis of the metabolome, which is the complete set of metabolites (i.e., small molecules intermediates) in an organism, tissue, cell, or biofluid. In the past decade, metabolomics has already proved to be useful for the characterization of several pathological conditions and offers promises as a clinical tool. A metabolomics investigation of coeliac disease (CD) revealed that a metabolic fingerprint for CD can be defined, which accounts for three different but complementary components: malabsorption, energy metabolism, and alterations in gut microflora and/or intestinal permeability. In this review, we will discuss the major advancements in metabolomics of CD, in particular with respect to the role of gut microbiome and energy metabolism. PMID:24665364

  6. Factors determining the passage of drugs from blood into saliva.

    Science.gov (United States)

    Stephen, K W; McCrossan, J; Mackenzie, D; Macfarlane, C B; Speirs, C F

    1980-01-01

    1. Following single oral dosing of ampicillin, cephalexin, tetracycline, erythromycin estolate, clindamycin and rifampicin to six normal volunteers, antibacterial activity was measured at 1, 3 and 6 h in serum, gingival fluid and minor gland saliva from all subjects and in parotid and submandiabular saliva from three. 2. pH values of all gingival fluid and saliva specimens were noted. 3. Partition coefficients between n-octanol and water were measured for erythromycin, clindamycin and rifampicin. Published data were used for ampicillin, cephalexin and tetracycline. 4. All antibiotics, but particularly rifampicin, were detected in gingival fluid. Only rifampicin and to a lesser degree, clindamycin were present in the other salivary constituents. 5. In studies of secretion of drugs in saliva, both the physico-chemical characteristics of the drugs and the physiological differences between individual salivary components should be considered. 6. Parotid saliva samples are likely to be of greatest value. PMID:7356893

  7. DNA methylation analysis from saliva samples for epidemiological studies.

    Science.gov (United States)

    Nishitani, Shota; Parets, Sasha E; Haas, Brian W; Smith, Alicia K

    2018-06-18

    Saliva is a non-invasive, easily accessible tissue, which is regularly collected in large epidemiological studies to examine genetic questions. Recently, it is becoming more common to use saliva to assess DNA methylation. However, DNA extracted from saliva is a mixture of both bacterial and human DNA derived from epithelial and immune cells in the mouth. Thus, there are unique challenges to using salivary DNA in methylation studies that can influence data quality. This study assesses: (1) quantification of human DNA after extraction; (2) delineation of human and bacterial DNA; (3) bisulfite conversion (BSC); (4) quantification of BSC DNA; (5) PCR amplification of BSC DNA from saliva and; (6) quantitation of DNA methylation with a targeted assay. The framework proposed will allow saliva samples to be more widely used in targeted epigenetic studies.

  8. Application of mass spectrometry-based proteomics for biomarker discovery in neurological disorders

    Directory of Open Access Journals (Sweden)

    Venugopal Abhilash

    2009-01-01

    Full Text Available Mass spectrometry-based quantitative proteomics has emerged as a powerful approach that has the potential to accelerate biomarker discovery, both for diagnostic as well as therapeutic purposes. Proteomics has traditionally been synonymous with 2D gels but is increasingly shifting to the use of gel-free systems and liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS. Quantitative proteomic approaches have already been applied to investigate various neurological disorders, especially in the context of identifying biomarkers from cerebrospinal fluid and serum. This review highlights the scope of different applications of quantitative proteomics in understanding neurological disorders with special emphasis on biomarker discovery.

  9. Recuperación de veillonellas a partir de saliva Recovery of Veillonella from saliva

    Directory of Open Access Journals (Sweden)

    M.I. Gutiérrez De Ferro

    2005-03-01

    Full Text Available Las veillonellas son cocos gram-negativos anaerobios asociados con salud oral. Para su aislamiento, se han reportado diferentes medios de cultivo. Las colonias de Veillonella spp. producen fluorescencia roja visible con luz ultravioleta, que desaparece en contacto con oxígeno. Esta propiedad sería útil para su identificación presuntiva rápida. Los objetivos de este trabajo fueron: 1- comparar el medio selectivo para Veillonella de Rogosa con los medios de cultivo recomendados por diferentes autores para determinar en cual de ellos se obtiene una mejor recuperación de veillonellas a partir de saliva, ya que esta muestra es generalmente utilizada para determinar la presencia y predominio de esta bacteria; 2- detectar la producción de fluorescencia en estos medios de cultivo como método rápido de identificación. Los medios de cultivo estudiados fueron: medio selectivo para Veillonella, agar Schaedler para anaerobios con vitamina K, agar tioglicolato, agar infusión cerebro corazón, agar Brucella, agar tripteína soja y agar Columbia con y sin el agregado de vancomicina y sangre lacada. La muestra ensayada fue un pool de saliva. Se hicieron recuentos de colonias de veillonellas y de microorganismos totales expresados en UFC/ml de saliva. La mayor recuperación de veillonellas en saliva se obtuvo en el medio selectivo para Veillonella con vancomicina y sangre lacada. Sólo se observó producción de fluorescencia en este medio.Veillonella spp. are anaerobic gram-negative cocci associated to oral health. Different types of cultures have been reported for the isolation of these microorganisms. Veillonella spp. colonies produce a red fluorescence, which is made visible through ultraviolet light and disappears in contact with oxygen. This feature would be very useful for rapid presumptive identification. The aims of this study were: 1. to compare the Rogosa selective medium for Veillonella with the cultures recommended by different authors in

  10. The association between saliva control, silent saliva penetration, aspiration, and videofluoroscopic findings in Parkinson's disease patients

    Science.gov (United States)

    Rajaei, Ali; Ashtari, Fereshteh; Azargoon, Seyed Abolfazl; Chitsaz, Ahmad; Nilforoush, Mohammad Hussein; Taheri, Masoud; Sadeghi, Saba

    2015-01-01

    Background: Dysphagia is a common disorder among patients with Parkinson's disease (PD). It occurs in up to 80% of all (PD) patients during the early stages of the disease and up to 95% in the advanced stages; but professionals may not hear from the patients about dysphagia symptoms until these symptoms reach an advanced stage and lead to medical complications. Materials and Methods: Thirty-three PD patients (mean age 66.09 ± 9.4 years; 24 men, nine women) participated in this study at our Neurology Institute, between April 20, 2013, and October 26, 2013. They were asked two questions; one about saliva control and the other about silent saliva penetration and aspiration. Next, they underwent the videofluoroscopic swallowing study (VFSS). Results: The Pearson Correlation coefficient between the Penetration–Aspiration Scale (PAS) scores and question 1 scores was 0.48 (P < 0.05, =0.25), and there was a significant correlation between the PAS scores and question 2 scores, and also question 1 scores + question 2 scores (r = 0.589, P < 0.05, =0 and r = 0589, P < 0.05, =0). Conclusions: This study showed a significant correlation between the questions about saliva control, silent saliva penetration, and aspiration, and laryngeal penetration and aspiration during VFSS. Therefore, by using these two questions, the potential silent laryngeal penetration and aspiration during meals could be detected before it led to aspiration pneumonia. Taking the benefit of these questions, as a part of the swallowing assessment of PD patients, is recommended. PMID:26261810

  11. Raman spectroscopy of saliva as a perspective method for periodontitis diagnostics Raman spectroscopy of saliva

    Science.gov (United States)

    Gonchukov, S.; Sukhinina, A.; Bakhmutov, D.; Minaeva, S.

    2012-01-01

    In view of its potential for biological tissues analyses at a molecular level, Raman spectroscopy in optical range has been the object of biomedical research for the last years. The main aim of this work is the development of Raman spectroscopy for organic content identifying and determination of biomarkers of saliva at a molecular level for periodontitis diagnostics. Four spectral regions were determined: 1155 and 1525 cm-1, 1033 and 1611 cm-1, which can be used as biomarkers of this widespread disease.

  12. MetaDB a Data Processing Workflow in Untargeted MS-Based Metabolomics Experiments.

    Science.gov (United States)

    Franceschi, Pietro; Mylonas, Roman; Shahaf, Nir; Scholz, Matthias; Arapitsas, Panagiotis; Masuero, Domenico; Weingart, Georg; Carlin, Silvia; Vrhovsek, Urska; Mattivi, Fulvio; Wehrens, Ron

    2014-01-01

    Due to their sensitivity and speed, mass-spectrometry based analytical technologies are widely used to in metabolomics to characterize biological phenomena. To address issues like metadata organization, quality assessment, data processing, data storage, and, finally, submission to public repositories, bioinformatic pipelines of a non-interactive nature are often employed, complementing the interactive software used for initial inspection and visualization of the data. These pipelines often are created as open-source software allowing the complete and exhaustive documentation of each step, ensuring the reproducibility of the analysis of extensive and often expensive experiments. In this paper, we will review the major steps which constitute such a data processing pipeline, discussing them in the context of an open-source software for untargeted MS-based metabolomics experiments recently developed at our institute. The software has been developed by integrating our metaMS R package with a user-friendly web-based application written in Grails. MetaMS takes care of data pre-processing and annotation, while the interface deals with the creation of the sample lists, the organization of the data storage, and the generation of survey plots for quality assessment. Experimental and biological metadata are stored in the ISA-Tab format making the proposed pipeline fully integrated with the Metabolights framework.

  13. Specific metabolomics adaptations define a differential regional vulnerability in the adult human cerebral cortex

    Directory of Open Access Journals (Sweden)

    Rosanna Cabré

    2016-12-01

    Full Text Available Brain neurons offer diverse responses to stresses and detrimental factors during development and aging, and as a result of both neurodegenerative and neuropsychiatric disorders. This multiplicity of responses can be ascribed to the great diversity among neuronal populations. Here we have determined the metabolomic profile of three healthy adult human brain regions—entorhinal cortex, hippocampus, and frontal cortex—using mass spectrometry-based technologies. Our results show the existence of a lessened energy demand, mitochondrial stress, and lower one-carbon metabolism (particularly restricted to the methionine cycle specifically in frontal cortex. These findings, along with the better antioxidant capacity and lower mTOR signaling also seen in frontal cortex, suggest that this brain region is especially resistant to stress compared to the entorhinal cortex and hippocampus, which are more vulnerable regions. Globally, our results show the presence of specific metabolomics adaptations in three mature, healthy human brain regions, confirming the existence of cross-regional differences in cell vulnerability in the human cerebral cortex.

  14. Mass Spectrometry-Based Proteomics in Molecular Diagnostics: Discovery of Cancer Biomarkers Using Tissue Culture

    Science.gov (United States)

    Paul, Debasish; Kumar, Avinash; Gajbhiye, Akshada; Santra, Manas K.; Srikanth, Rapole

    2013-01-01

    Accurate diagnosis and proper monitoring of cancer patients remain a key obstacle for successful cancer treatment and prevention. Therein comes the need for biomarker discovery, which is crucial to the current oncological and other clinical practices having the potential to impact the diagnosis and prognosis. In fact, most of the biomarkers have been discovered utilizing the proteomics-based approaches. Although high-throughput mass spectrometry-based proteomic approaches like SILAC, 2D-DIGE, and iTRAQ are filling up the pitfalls of the conventional techniques, still serum proteomics importunately poses hurdle in overcoming a wide range of protein concentrations, and also the availability of patient tissue samples is a limitation for the biomarker discovery. Thus, researchers have looked for alternatives, and profiling of candidate biomarkers through tissue culture of tumor cell lines comes up as a promising option. It is a rich source of tumor cell-derived proteins, thereby, representing a wide array of potential biomarkers. Interestingly, most of the clinical biomarkers in use today (CA 125, CA 15.3, CA 19.9, and PSA) were discovered through tissue culture-based system and tissue extracts. This paper tries to emphasize the tissue culture-based discovery of candidate biomarkers through various mass spectrometry-based proteomic approaches. PMID:23586059

  15. Catch and measure-mass spectrometry-based immunoassays in biomarker research.

    Science.gov (United States)

    Weiß, Frederik; van den Berg, Bart H J; Planatscher, Hannes; Pynn, Christopher J; Joos, Thomas O; Poetz, Oliver

    2014-05-01

    Mass spectrometry-based (MS) methods are effective tools for discovering protein biomarker candidates that can differentiate between physiological and pathophysiological states. Promising candidates are validated in studies comprising large patient cohorts. Here, targeted protein analytics are used to increase sample throughput. Methods involving antibodies, such as sandwich immunoassays or Western blots, are commonly applied at this stage. Highly-specific and sensitive mass spectrometry-based immunoassays that have been established in recent years offer a suitable alternative to sandwich immunoassays for quantifying proteins. Mass Spectrometric ImmunoAssays (MSIA) and Stable Isotope Standards and Capture by Anti-Peptide Antibodies (SISCAPA/iMALDI) are two prominent types of MS-based immunoassays in which the capture is done either at the protein or the peptide level. We present an overview of these emerging types of immunoassays and discuss their suitability for the discovery and validation of protein biomarkers. This article is part of a Special Issue entitled: Biomarkers: A Proteomic Challenge. © 2013.

  16. Mass Spectrometry-Based Proteomics in Molecular Diagnostics: Discovery of Cancer Biomarkers Using Tissue Culture

    Directory of Open Access Journals (Sweden)

    Debasish Paul

    2013-01-01

    Full Text Available Accurate diagnosis and proper monitoring of cancer patients remain a key obstacle for successful cancer treatment and prevention. Therein comes the need for biomarker discovery, which is crucial to the current oncological and other clinical practices having the potential to impact the diagnosis and prognosis. In fact, most of the biomarkers have been discovered utilizing the proteomics-based approaches. Although high-throughput mass spectrometry-based proteomic approaches like SILAC, 2D-DIGE, and iTRAQ are filling up the pitfalls of the conventional techniques, still serum proteomics importunately poses hurdle in overcoming a wide range of protein concentrations, and also the availability of patient tissue samples is a limitation for the biomarker discovery. Thus, researchers have looked for alternatives, and profiling of candidate biomarkers through tissue culture of tumor cell lines comes up as a promising option. It is a rich source of tumor cell-derived proteins, thereby, representing a wide array of potential biomarkers. Interestingly, most of the clinical biomarkers in use today (CA 125, CA 15.3, CA 19.9, and PSA were discovered through tissue culture-based system and tissue extracts. This paper tries to emphasize the tissue culture-based discovery of candidate biomarkers through various mass spectrometry-based proteomic approaches.

  17. Probing Conformational Changes of Human DNA Polymerase λ Using Mass Spectrometry-Based Protein Footprinting

    Science.gov (United States)

    Fowler, Jason D.; Brown, Jessica A.; Kvaratskhelia, Mamuka; Suo, Zucai

    2009-01-01

    SUMMARY Crystallographic studies of the C-terminal, DNA polymerase β-like domain of human DNA polymerase lambda (fPolλ) suggested that the catalytic cycle might not involve a large protein domain rearrangement as observed with several replicative DNA polymerases and DNA polymerase β. To examine solution-phase protein conformation changes in fPolλ, which also contains a breast cancer susceptibility gene 1 C-terminal domain and a Proline-rich domain at its N-terminus, we used a mass spectrometry - based protein footprinting approach. In parallel experiments, surface accessibility maps for Arg residues were compared for the free fPolλ versus the binary complex of enzyme•gapped DNA and the ternary complex of enzyme•gapped DNA•dNTP. These experiments suggested that fPolλ does not undergo major conformational changes during the catalysis in the solution phase. Furthermore, the mass spectrometry-based protein footprinting experiments revealed that active site residue R386 was shielded from the surface only in the presence of both a gapped DNA substrate and an incoming nucleotide dNTP. Site-directed mutagenesis and pre-steady state kinetic studies confirmed the importance of R386 for the enzyme activity, and indicated the key role for its guanidino group in stabilizing the negative charges of an incoming nucleotide and the leaving pyrophosphate product. We suggest that such interactions could be shared by and important for catalytic functions of other DNA polymerases. PMID:19467241

  18. Functional Analysis of Metabolomics Data.

    Science.gov (United States)

    Chagoyen, Mónica; López-Ibáñez, Javier; Pazos, Florencio

    2016-01-01

    Metabolomics aims at characterizing the repertory of small chemical compounds in a biological sample. As it becomes more massive and larger sets of compounds are detected, a functional analysis is required to convert these raw lists of compounds into biological knowledge. The most common way of performing such analysis is "annotation enrichment analysis," also used in transcriptomics and proteomics. This approach extracts the annotations overrepresented in the set of chemical compounds arisen in a given experiment. Here, we describe the protocols for performing such analysis as well as for visualizing a set of compounds in different representations of the metabolic networks, in both cases using free accessible web tools.

  19. Probabilistic Principal Component Analysis for Metabolomic Data.

    LENUS (Irish Health Repository)

    Nyamundanda, Gift

    2010-11-23

    Abstract Background Data from metabolomic studies are typically complex and high-dimensional. Principal component analysis (PCA) is currently the most widely used statistical technique for analyzing metabolomic data. However, PCA is limited by the fact that it is not based on a statistical model. Results Here, probabilistic principal component analysis (PPCA) which addresses some of the limitations of PCA, is reviewed and extended. A novel extension of PPCA, called probabilistic principal component and covariates analysis (PPCCA), is introduced which provides a flexible approach to jointly model metabolomic data and additional covariate information. The use of a mixture of PPCA models for discovering the number of inherent groups in metabolomic data is demonstrated. The jackknife technique is employed to construct confidence intervals for estimated model parameters throughout. The optimal number of principal components is determined through the use of the Bayesian Information Criterion model selection tool, which is modified to address the high dimensionality of the data. Conclusions The methods presented are illustrated through an application to metabolomic data sets. Jointly modeling metabolomic data and covariates was successfully achieved and has the potential to provide deeper insight to the underlying data structure. Examination of confidence intervals for the model parameters, such as loadings, allows for principled and clear interpretation of the underlying data structure. A software package called MetabolAnalyze, freely available through the R statistical software, has been developed to facilitate implementation of the presented methods in the metabolomics field.

  20. Human Saliva Collection Devices for Proteomics: An Update

    Directory of Open Access Journals (Sweden)

    Zohaib Khurshid

    2016-06-01

    Full Text Available There has been a rapid growth in the interest and adaptation of saliva as a diagnostic specimen over the last decade, and in the last few years in particular, there have been major developments involving the application of saliva as a clinically relevant specimen. Saliva provides a “window” into the oral and systemic health of an individual, and like other bodily fluids, saliva can be analyzed and studied to diagnose diseases. With the advent of new, more sensitive technologies to detect smaller concentrations of analytes in saliva relative to blood levels, there have been a number of critical developments in the field that we will describe. In particular, recent advances in standardized saliva collection devices that were not available three to four years ago, have made it easy for safe, simple, and non-invasive collection of samples to be carried out from patients. With the availability of these new technologies, we believe that in the next decade salivary proteomics will make it possible to predict and diagnose oral as well as systemic diseases, cancer, and infectious diseases, among others. The aim of this article is to review recent developments and advances in the area of saliva specimen collection devices and applications that will advance the field of proteomics.

  1. Trace element measurement in Saliva by NAA and PIXE techniques

    Energy Technology Data Exchange (ETDEWEB)

    Hamidian, M.R.; Vahid Golpayegani, M.; Shojai, S. (Shahid Beheshti Medical Science Univ., Shemiran, Tehran (Iran, Islamic Republic of))

    1993-01-01

    The activity of salivary glands and the chemical and physical properties of saliva, especially in some illnesses in which the activity of salivary glands and the chemical and physical properties alter, sometimes have severe effects on sedimentation and tooth decay. Long-standing investigations have shown the relationship between salivary gland activity and saliva composition in dental carries. Many modern techniques have been employed to measure important elements in saliva. The major elements in saliva include sodium, potassium, calcium, magnesium, chlorine, phosphorus, iodine, and fluorine. It should be pointed out that the amount of minerals changes when the diet changes. The major constituent of saliva is water with a density of 1.007 g/cm[sup 3] in which 0.6% is solid, 0.3% organic material and 0.3% inorganic material. In addition to other effects, the acidity (pH) of saliva has a strong effect on tooth sedimentation. Type of work, degree of stress, and mental condition affect salivary gland activity. When the acidity of salivary fluid in the mouth and consequently over the teeth drops, sedimentation increases. In this paper, the results of trace element measurement in saliva are presented.

  2. Microbial community profiling of human saliva using shotgun metagenomic sequencing.

    Directory of Open Access Journals (Sweden)

    Nur A Hasan

    Full Text Available Human saliva is clinically informative of both oral and general health. Since next generation shotgun sequencing (NGS is now widely used to identify and quantify bacteria, we investigated the bacterial flora of saliva microbiomes of two healthy volunteers and five datasets from the Human Microbiome Project, along with a control dataset containing short NGS reads from bacterial species representative of the bacterial flora of human saliva. GENIUS, a system designed to identify and quantify bacterial species using unassembled short NGS reads was used to identify the bacterial species comprising the microbiomes of the saliva samples and datasets. Results, achieved within minutes and at greater than 90% accuracy, showed more than 175 bacterial species comprised the bacterial flora of human saliva, including bacteria known to be commensal human flora but also Haemophilus influenzae, Neisseria meningitidis, Streptococcus pneumoniae, and Gamma proteobacteria. Basic Local Alignment Search Tool (BLASTn analysis in parallel, reported ca. five times more species than those actually comprising the in silico sample. Both GENIUS and BLAST analyses of saliva samples identified major genera comprising the bacterial flora of saliva, but GENIUS provided a more precise description of species composition, identifying to strain in most cases and delivered results at least 10,000 times faster. Therefore, GENIUS offers a facile and accurate system for identification and quantification of bacterial species and/or strains in metagenomic samples.

  3. Towards Improving Point-of-Care Diagnosis of Non-malaria Febrile Illness: A Metabolomics Approach.

    Directory of Open Access Journals (Sweden)

    Saskia Decuypere

    2016-03-01

    Full Text Available Non-malaria febrile illnesses such as bacterial bloodstream infections (BSI are a leading cause of disease and mortality in the tropics. However, there are no reliable, simple diagnostic tests for identifying BSI or other severe non-malaria febrile illnesses. We hypothesized that different infectious agents responsible for severe febrile illness would impact on the host metabolome in different ways, and investigated the potential of plasma metabolites for diagnosis of non-malaria febrile illness.We conducted a comprehensive mass-spectrometry based metabolomics analysis of the plasma of 61 children with severe febrile illness from a malaria-endemic rural African setting. Metabolite features characteristic for non-malaria febrile illness, BSI, severe anemia and poor clinical outcome were identified by receiver operating curve analysis.The plasma metabolome profile of malaria and non-malaria patients revealed fundamental differences in host response, including a differential activation of the hypothalamic-pituitary-adrenal axis. A simple corticosteroid signature was a good classifier of severe malaria and non-malaria febrile patients (AUC 0.82, 95% CI: 0.70-0.93. Patients with BSI were characterized by upregulated plasma bile metabolites; a signature of two bile metabolites was estimated to have a sensitivity of 98.1% (95% CI: 80.2-100 and a specificity of 82.9% (95% CI: 54.7-99.9 to detect BSI in children younger than 5 years. This BSI signature demonstrates that host metabolites can have a superior diagnostic sensitivity compared to pathogen-detecting tests to identify infections characterized by low pathogen load such as BSI.This study demonstrates the potential use of plasma metabolites to identify causality in children with severe febrile illness in malaria-endemic settings.

  4. Disposable collection kit for rapid and reliable collection of saliva.

    Science.gov (United States)

    Yamaguchi, Masaki; Tezuka, Yuki; Takeda, Kazunori; Shetty, Vivek

    2015-01-01

    To describe and evaluate disposable saliva collection kit for rapid, reliable, and reproducible collection of saliva samples. The saliva collection kit comprised of a saliva absorbent swab and an extractor unit was used to retrieve whole saliva samples from 10 subjects. The accuracy and precision of the extracted volumes (3, 10, and 30 μl) were compared to similar volumes drawn from control samples obtained by passive drool. Additionally, the impact of kit collection method on subsequent immunoassay results was verified by assessing salivary cortisol levels in the samples and comparing them to controls. The recovered volumes for the whole saliva samples were 3.85 ± 0.28, 10.79 ± 0.95, and 31.18 ± 1.72 μl, respectively (CV = 8.76%) and 2.91 ± 0.19, 9.75 ± 0.43, and 29.64 ± 0.91 μl, respectively, (CV = 6.36%) for the controls. There was a close correspondence between the salivary cortisol levels from the saliva samples obtained by the collection kit and the controls (R(2)  > 0.96). The disposable saliva collection kit allows accurate and repeatable collection of fixed amounts of whole saliva and does not interfere with subsequent measurements of salivary cortisol. The simple collection process, lack of elaborate specimen recovery steps, and the short turnaround time (<3 min) should render the kit attractive to test subjects and researchers alike. © 2015 Wiley Periodicals, Inc.

  5. Anti-inflammatory and antinociceptive activities of Rhipicephalus microplus saliva

    Directory of Open Access Journals (Sweden)

    D F Buccini

    2018-01-01

    Full Text Available Objective: To evaluate the antinociceptive and anti-inflammatory activities and the toxic effects of Rhipicephalus microplus saliva for elucidating the modulation mechanism between arthropod saliva and host. Methods: For saliva collection, engorged ticks were obtained from a controlled bovine infestation and collected by natural fall. The ticks were fixed and injected pilocarpine 0.2% for induction of salivation. Saliva was collected, lyophilized and stored at - 80 °C. Cytotoxic activity was assessed by the hemolysis method (25, 50, 100, 200 and 300 μ g/mL and MTT cell viability assay (2.5, 5, 10, 20 and 40 μ g/mL for 24, 48 and 72 h. Anti-inflammatory activity was evaluated using the method of neutrophil migration to the peritoneal cavity of mice at doses of 10, 15 and 20 mg/kg; antinociceptive activity was assessed using the acetic acid-induced writhing test, and formalin-induced paw-licking in mice at dose of 15 mg/kg. Results: Saliva did not cause erythrocytes hemolysis at any concentration tested, as well as did not decrease cell viability in the MTT assay. Saliva inhibited neutrophil migration by 87% and 73% at doses of 15 and 20 mg/kg, respectively. In the nociceptive tests, saliva presented analgesic activity of 69.96% in the abdominal writhing test, and of 84.41% in the formalin test. Conclusions: The study proves that Rhipicephalus microplus saliva has significant in vivo anti-inflammatory and antinociceptive activities. The data presented herein support the development of further studies to elucidate the active principles of Rhipicephalus microplus saliva and its mechanism of action and, in future, to develop novel anti-inflammatory and analgesic drugs.

  6. Metabolomics: beyond biomarkers and towards mechanisms

    Science.gov (United States)

    Johnson, Caroline H.; Ivanisevic, Julijana; Siuzdak, Gary

    2017-01-01

    Metabolomics, which is the profiling of metabolites in biofluids, cells and tissues, is routinely applied as a tool for biomarker discovery. Owing to innovative developments in informatics and analytical technologies, and the integration of orthogonal biological approaches, it is now possible to expand metabolomic analyses to understand the systems-level effects of metabolites. Moreover, because of the inherent sensitivity of metabolomics, subtle alterations in biological pathways can be detected to provide insight into the mechanisms that underlie various physiological conditions and aberrant processes, including diseases. PMID:26979502

  7. Metabolomics applied to the pancreatic islet.

    Science.gov (United States)

    Gooding, Jessica R; Jensen, Mette V; Newgard, Christopher B

    2016-01-01

    Metabolomics, the characterization of the set of small molecules in a biological system, is advancing research in multiple areas of islet biology. Measuring a breadth of metabolites simultaneously provides a broad perspective on metabolic changes as the islets respond dynamically to metabolic fuels, hormones, or environmental stressors. As a result, metabolomics has the potential to provide new mechanistic insights into islet physiology and pathophysiology. Here we summarize advances in our understanding of islet physiology and the etiologies of type-1 and type-2 diabetes gained from metabolomics studies. Copyright © 2015 Elsevier Inc. All rights reserved.

  8. Mathematical Modeling Approaches in Plant Metabolomics.

    Science.gov (United States)

    Fürtauer, Lisa; Weiszmann, Jakob; Weckwerth, Wolfram; Nägele, Thomas

    2018-01-01

    The experimental analysis of a plant metabolome typically results in a comprehensive and multidimensional data set. To interpret metabolomics data in the context of biochemical regulation and environmental fluctuation, various approaches of mathematical modeling have been developed and have proven useful. In this chapter, a general introduction to mathematical modeling is presented and discussed in context of plant metabolism. A particular focus is laid on the suitability of mathematical approaches to functionally integrate plant metabolomics data in a metabolic network and combine it with other biochemical or physiological parameters.

  9. Periodontitis diagnostics using resonance Raman spectroscopy on saliva

    Science.gov (United States)

    Gonchukov, S.; Sukhinina, A.; Bakhmutov, D.; Biryukova, T.; Tsvetkov, M.; Bagratashvily, V.

    2013-07-01

    In view of its wealth of molecular information, Raman spectroscopy has been the subject of active biomedical research. The aim of this work is Raman spectroscopy (RS) application for the determination of molecular biomarkers in saliva with the objective of early periodontitis detection. As was shown in our previous study, carotenoids contained in saliva can be molecular fingerprint information for the periodontitis level. It is shown here that the carotenoid RS lines at wavenumbers of 1156 and 1524 cm-1 can be easily detected and serve as reliable biomarkers of periodontitis using resonance Raman spectroscopy of dry saliva.

  10. Saliva in relation to dental erosion before and after radiotherapy

    DEFF Research Database (Denmark)

    Jensdottir, Thorbjorg; von Buchwald, Christian; Nauntofte, Birgitte

    2013-01-01

    Abstract Objective. Low saliva flow and abnormal saliva composition are common conditions after radiotherapy for oral cavity and pharyngeal cancer. Both conditions increase the susceptibility to dental caries and erosion, which may be further accelerated by changes in food preferences. The aim...... of this study was to determine changes in saliva flow and susceptibility to erosive challenges in pharyngeal cancer patients before and after radiotherapy to the head and neck. Materials and methods: The erosive potential of sucking acidic candies with and without calcium was determined in nine patients (50...

  11. Radioimmunological method for determination of cortisol in saliva

    International Nuclear Information System (INIS)

    Maleeva, A.; Mileva, Zh.; Kekhajova, M.

    1989-01-01

    A method was developed for determination of cortisol in saliva after being previously extracted with dichlormethane. Cortisol concentration in saliva of 19 subjects was determined by this method. The saliva cortisol levels were compared with those of blood plasma. No statistically significant difference was found. The method finds acceptance primarily when frequent measurements of cortisol level are neccessary as a screening technique and when strongly abnormally high levels should be differentiated from the normal ones: in this latter case determination of plasma cortisol is mandatory. 5 tabs., 8 refs

  12. Periodontitis diagnostics using resonance Raman spectroscopy on saliva

    International Nuclear Information System (INIS)

    Gonchukov, S; Sukhinina, A; Bakhmutov, D; Biryukova, T; Tsvetkov, M; Bagratashvily, V

    2013-01-01

    In view of its wealth of molecular information, Raman spectroscopy has been the subject of active biomedical research. The aim of this work is Raman spectroscopy (RS) application for the determination of molecular biomarkers in saliva with the objective of early periodontitis detection. As was shown in our previous study, carotenoids contained in saliva can be molecular fingerprint information for the periodontitis level. It is shown here that the carotenoid RS lines at wavenumbers of 1156 and 1524 cm −1 can be easily detected and serve as reliable biomarkers of periodontitis using resonance Raman spectroscopy of dry saliva. (letter)

  13. A Machine Learning Application Based in Random Forest for Integrating Mass Spectrometry-Based Metabolomic Data: A Simple Screening Method for Patients With Zika Virus

    Directory of Open Access Journals (Sweden)

    Carlos Fernando Odir Rodrigues Melo

    2018-04-01

    Full Text Available Recent Zika outbreaks in South America, accompanied by unexpectedly severe clinical complications have brought much interest in fast and reliable screening methods for ZIKV (Zika virus identification. Reverse-transcriptase polymerase chain reaction (RT-PCR is currently the method of choice to detect ZIKV in biological samples. This approach, nonetheless, demands a considerable amount of time and resources such as kits and reagents that, in endemic areas, may result in a substantial financial burden over affected individuals and health services veering away from RT-PCR analysis. This study presents a powerful combination of high-resolution mass spectrometry and a machine-learning prediction model for data analysis to assess the existence of ZIKV infection across a series of patients that bear similar symptomatic conditions, but not necessarily are infected with the disease. By using mass spectrometric data that are inputted with the developed decision-making algorithm, we were able to provide a set of features that work as a “fingerprint” for this specific pathophysiological condition, even after the acute phase of infection. Since both mass spectrometry and machine learning approaches are well-established and have largely utilized tools within their respective fields, this combination of methods emerges as a distinct alternative for clinical applications, providing a diagnostic screening—faster and more accurate—with improved cost-effectiveness when compared to existing technologies.

  14. A Machine Learning Application Based in Random Forest for Integrating Mass Spectrometry-Based Metabolomic Data: A Simple Screening Method for Patients With Zika Virus.

    Science.gov (United States)

    Melo, Carlos Fernando Odir Rodrigues; Navarro, Luiz Claudio; de Oliveira, Diogo Noin; Guerreiro, Tatiane Melina; Lima, Estela de Oliveira; Delafiori, Jeany; Dabaja, Mohamed Ziad; Ribeiro, Marta da Silva; de Menezes, Maico; Rodrigues, Rafael Gustavo Martins; Morishita, Karen Noda; Esteves, Cibele Zanardi; de Amorim, Aline Lopes Lucas; Aoyagui, Caroline Tiemi; Parise, Pierina Lorencini; Milanez, Guilherme Paier; do Nascimento, Gabriela Mansano; Ribas Freitas, André Ricardo; Angerami, Rodrigo; Costa, Fábio Trindade Maranhão; Arns, Clarice Weis; Resende, Mariangela Ribeiro; Amaral, Eliana; Junior, Renato Passini; Ribeiro-do-Valle, Carolina C; Milanez, Helaine; Moretti, Maria Luiza; Proenca-Modena, Jose Luiz; Avila, Sandra; Rocha, Anderson; Catharino, Rodrigo Ramos

    2018-01-01

    Recent Zika outbreaks in South America, accompanied by unexpectedly severe clinical complications have brought much interest in fast and reliable screening methods for ZIKV (Zika virus) identification. Reverse-transcriptase polymerase chain reaction (RT-PCR) is currently the method of choice to detect ZIKV in biological samples. This approach, nonetheless, demands a considerable amount of time and resources such as kits and reagents that, in endemic areas, may result in a substantial financial burden over affected individuals and health services veering away from RT-PCR analysis. This study presents a powerful combination of high-resolution mass spectrometry and a machine-learning prediction model for data analysis to assess the existence of ZIKV infection across a series of patients that bear similar symptomatic conditions, but not necessarily are infected with the disease. By using mass spectrometric data that are inputted with the developed decision-making algorithm, we were able to provide a set of features that work as a "fingerprint" for this specific pathophysiological condition, even after the acute phase of infection. Since both mass spectrometry and machine learning approaches are well-established and have largely utilized tools within their respective fields, this combination of methods emerges as a distinct alternative for clinical applications, providing a diagnostic screening-faster and more accurate-with improved cost-effectiveness when compared to existing technologies.

  15. Protein Biomarkers of Periodontitis in Saliva

    Science.gov (United States)

    Taylor, John J.

    2014-01-01

    Periodontitis is a chronic inflammatory condition of the tissues that surround and support the teeth and is initiated by inappropriate and excessive immune responses to bacteria in subgingival dental plaque leading to loss of the integrity of the periodontium, compromised tooth function, and eventually tooth loss. Periodontitis is an economically important disease as it is time-consuming and expensive to treat. Periodontitis has a worldwide prevalence of 5–15% and the prevalence of severe disease in western populations has increased in recent decades. Furthermore, periodontitis is more common in smokers, in obesity, in people with diabetes, and in heart disease patients although the pathogenic processes underpinning these links are, as yet, poorly understood. Diagnosis and monitoring of periodontitis rely on traditional clinical examinations which are inadequate to predict patient susceptibility, disease activity, and response to treatment. Studies of the immunopathogenesis of periodontitis and analysis of mediators in saliva have allowed the identification of many potentially useful biomarkers. Convenient measurement of these biomarkers using chairside analytical devices could form the basis for diagnostic tests which will aid the clinician and the patient in periodontitis management; this review will summarise this field and will identify the experimental, technical, and clinical issues that remain to be addressed before such tests can be implemented. PMID:24944840

  16. Radioimmunological determination of chloramphenicol in the saliva of lactating cows

    International Nuclear Information System (INIS)

    Dotter, A.; Kroker, R.; Arnold, D.; Somogyi, A.

    1987-01-01

    In an effort to search for noninvasive methods suitable to monitor compliance with the ban of chloramphenicol (CAP) in milkproducing animals, the pharmacokinetic behavior of this drug in bovine saliva was investigated. As revealed by studies using a radioimmunological assay, CAP appears following its intracisternal (i.c.) or subcutaneous (s.c.) administration in the saliva of lactating cows. The level of sensitivity of the method (1.5 ng CAP per g saliva) was reached 14 and 18 days after i.c. and s.c. administration, respectively. At present, the question must remain open as to whether the concentration of CAP in the saliva can serve as a reliable indicator for the enforcement of the highest permissible level set at 1 ng CAP per g of milk by German regulations. (orig.) [de

  17. Saliva-catalyzed hydrolysis of a ketobemidone ester prodrug

    DEFF Research Database (Denmark)

    Hansen, L.B.; Christrup, Lona Louring; Bundgaard, H.

    1992-01-01

    Saliva enzyme-catalysed hydrolysis of ester prodrugs or drugs containing sensitive ester groups may be a limiting factor for the buccal absorption of such compounds. Using the isopropyl carbonate ester of ketobemidone as a model substance of a hydrolysis-sensitive prodrug the esterase activity...... of human saliva has been characterized as a function of various factors. The esterase activity was found to decrease rapidly upon storage of the saliva at 37°C. The activity increased with increasing pH in the range 4.5-7.4 and with increasing salivation flow rate up to a rate of 0.9 ml min. Under resting...... conditions, the flow rate was about 0.2 ml min which implied a greatly decreased esterase activity. The activity was highest after fasting and decreased after intake of a meal. The intraindividual variation in the saliva esterase activity was small whereas a larger interindividual variation was found....

  18. Radioimmunological determination of chloramphenicol in the saliva of lactating cows

    Energy Technology Data Exchange (ETDEWEB)

    Dotter, A.; Kroker, R.; Arnold, D.; Somogyi, A.

    1987-02-01

    In an effort to search for noninvasive methods suitable to monitor compliance with the ban of chloramphenicol (CAP) in milk-producing animals, the pharmacokinetic behavior of this drug in bovine saliva was investigated. As revealed by studies using a radioimmunological assay, CAP appears following its intracisternal (i.c.) or subcutaneous (s.c.) administration in the saliva of lactating cows. The level of sensitivity of the method (1.5 ng CAP per g saliva) was reached 14 and 18 days after i.c. and s.c. administration, respectively. At present, the question must remain open as to whether the concentration of CAP in the saliva can serve as a reliable indicator for the enforcement of the highest permissible level set at 1 ng CAP per g of milk by German regulations.

  19. MULTI-DIMENSIONAL MASS SPECTROMETRY-BASED SHOTGUN LIPIDOMICS AND NOVEL STRATEGIES FOR LIPIDOMIC ANALYSES

    Science.gov (United States)

    Han, Xianlin; Yang, Kui; Gross, Richard W.

    2011-01-01

    Since our last comprehensive review on multi-dimensional mass spectrometry-based shotgun lipidomics (Mass Spectrom. Rev. 24 (2005), 367), many new developments in the field of lipidomics have occurred. These developments include new strategies and refinements for shotgun lipidomic approaches that use direct infusion, including novel fragmentation strategies, identification of multiple new informative dimensions for mass spectrometric interrogation, and the development of new bioinformatic approaches for enhanced identification and quantitation of the individual molecular constituents that comprise each cell’s lipidome. Concurrently, advances in liquid chromatography-based platforms and novel strategies for quantitative matrix-assisted laser desorption/ionization mass spectrometry for lipidomic analyses have been developed. Through the synergistic use of this repertoire of new mass spectrometric approaches, the power and scope of lipidomics has been greatly expanded to accelerate progress toward the comprehensive understanding of the pleiotropic roles of lipids in biological systems. PMID:21755525

  20. Using metabolomics to evaluate food intake

    DEFF Research Database (Denmark)

    Manach, Claudine; Brennan, Lorraine; Dragsted, Lars Ove

    2015-01-01

    Improving dietary assessment is essential for modern nutritional epidemiology. This chapter discusses the potential of metabolomics for the identification of new biomarkers of intake and presents the first candidate biomarkers discovered using this approach. It then describes the challenges...

  1. Metabolomics in Population-Based Research

    Science.gov (United States)

    Metabolomics is the study of small molecules of both endogenous and exogenous origin, such as metabolic substrates and their products, lipids, small peptides, vitamins and other protein cofactors generated by metabolism, which are downstream from genes.

  2. Proteomic and metabolomic approaches to biomarker discovery

    CERN Document Server

    Issaq, Haleem J

    2013-01-01

    Proteomic and Metabolomic Approaches to Biomarker Discovery demonstrates how to leverage biomarkers to improve accuracy and reduce errors in research. Disease biomarker discovery is one of the most vibrant and important areas of research today, as the identification of reliable biomarkers has an enormous impact on disease diagnosis, selection of treatment regimens, and therapeutic monitoring. Various techniques are used in the biomarker discovery process, including techniques used in proteomics, the study of the proteins that make up an organism, and metabolomics, the study of chemical fingerprints created from cellular processes. Proteomic and Metabolomic Approaches to Biomarker Discovery is the only publication that covers techniques from both proteomics and metabolomics and includes all steps involved in biomarker discovery, from study design to study execution.  The book describes methods, and presents a standard operating procedure for sample selection, preparation, and storage, as well as data analysis...

  3. Metabolomics Application in Maternal-Fetal Medicine

    Directory of Open Access Journals (Sweden)

    Vassilios Fanos

    2013-01-01

    Full Text Available Metabolomics in maternal-fetal medicine is still an “embryonic” science. However, there is already an increasing interest in metabolome of normal and complicated pregnancies, and neonatal outcomes. Tissues used for metabolomics interrogations of pregnant women, fetuses and newborns are amniotic fluid, blood, plasma, cord blood, placenta, urine, and vaginal secretions. All published papers highlight the strong correlation between biomarkers found in these tissues and fetal malformations, preterm delivery, premature rupture of membranes, gestational diabetes mellitus, preeclampsia, neonatal asphyxia, and hypoxic-ischemic encephalopathy. The aim of this review is to summarize and comment on original data available in relevant published works in order to emphasize the clinical potential of metabolomics in obstetrics in the immediate future.

  4. Clinical trial participant characteristics and saliva and DNA metrics

    Directory of Open Access Journals (Sweden)

    Richards Julie

    2009-10-01

    Full Text Available Abstract Background Clinical trial and epidemiological studies need high quality biospecimens from a representative sample of participants to investigate genetic influences on treatment response and disease. Obtaining blood biospecimens presents logistical and financial challenges. As a result, saliva biospecimen collection is becoming more frequent because of the ease of collection and lower cost. This article describes an assessment of saliva biospecimen samples collected through the mail, trial participant demographic and behavioral characteristics, and their association with saliva and DNA quantity and quality. Methods Saliva biospecimens were collected using the Oragene® DNA Self-Collection Kits from participants in a National Cancer Institute funded smoking cessation trial. Saliva biospecimens from 565 individuals were visually inspected for clarity prior to and after DNA extraction. DNA samples were then quantified by UV absorbance, PicoGreen®, and qPCR. Genotyping was performed on 11 SNPs using TaqMan® SNP assays and two VNTR assays. Univariate, correlation, and analysis of variance analyses were conducted to observe the relationship between saliva sample and participant characteristics. Results The biospecimen kit return rate was 58.5% among those invited to participate (n = 967 and 47.1% among all possible COMPASS participants (n = 1202. Significant gender differences were observed with males providing larger saliva volume (4.7 vs. 4.5 ml, p = 0.019, samples that were more likely to be judged as cloudy (39.5% vs. 24.9%, p 0.21, P Conclusion Findings from this study show that demographic and behavioral characteristics of smoking cessation trial participants have significant associations with saliva and DNA metrics, but not with the performance of TaqMan® SNP or VNTR genotyping assays. Trial registration COMPASS; registered as NCT00301145 at clinicaltrials.gov.

  5. Pengaruh Berkumur Air Kelapa Muda Terhadap Ph Saliva

    OpenAIRE

    Mokoginta, Zuthra P

    2017-01-01

    PENGARUH BERKUMUR AIR KELAPA MUDA TERHADAP pH SALIVA Zuthra P. Mokoginta1) , Vonny N.S. Wowor1) , Juliatri1) 1)Program Studi Pendidikan Dokter Gigi, Fakultas Kedokteran UNSRAT Manado, 95115 ABSTRACT Saliva is one factor that contributes to the development of caries, particularly in the process of demineralization. The low pH in the oral cavity will facilitate the growth of acidogenic bacteria such as Streptococcus mutans and Lactobacillus which is the main cause microorganisms in th...

  6. Comparison of Plasma, Saliva, and Hair Levetiracetam Concentrations.

    Science.gov (United States)

    Karaś-Ruszczyk, Katarzyna; Kuczyńska, Julita; Sienkiewicz-Jarosz, Halina; Kurkowska-Jastrzębska, Iwona; Bienkowski, Przemyslaw; Restel, Magdalena; Samochowiec, Jerzy; Mierzejewski, Pawel

    2017-06-01

    Previous findings revealed high correlations between serum/plasma and saliva levetiracetam concentrations, indicating saliva as an alternative matrix for monitoring levetiracetam therapy. Levetiracetam concentration in the hair, which could reflect long-term drug exposure and patients' compliance, has not been systematically tested, as yet. The aim of this study was to determine the correlation between plasma, saliva, and hair levetiracetam concentrations in 47 patients with epilepsy. Plasma, saliva, and hair levetiracetam concentrations were measured by liquid chromatography-tandem mass spectrometry with positive ionization. Levetiracetam saliva and plasma concentrations were highly correlated (r = 0.93). Plasma concentrations were not influenced by sex, age, and other concomitant antiepileptic drugs. Levetiracetam hair concentrations correlated with plasma concentrations (r = 0.36) but not daily dose (mg/kg). Drug hair concentrations were not influenced by hair color or treatment (dyed). The results tend to indicate that saliva may be a reliable alternative to plasma for monitoring levetiracetam concentrations. Levetiracetam can also be detected in human hair.

  7. Protein components in saliva and plaque fluid from irradiated primates

    Energy Technology Data Exchange (ETDEWEB)

    Edgar, W.M.; Bowen, W.H.; Cole, M.F. (Caries Prevention and Research Branch, National Caries Program, NIDR, Bethesda, Maryland, USA)

    1982-01-01

    Irradiation of the major salivary glands of monkeys (Macaca mulatta) fed cariogenic diets leads to caries clinically indistinguishable from radiation caries in man. This study compares the organic compostion of individual samples of plaque fluid and saliva from irradiated and control monkeys receiving the same cariogenic diet. Plaque and saliva were collected from fasting, tranquillised animals. Four irradiated animals were sampled repeatedly as were non-irradiated controls. Total protein, albumin, immunoglobulins A, G, and M, and the third component of complement (C'3) were quantitated in plaque fluid and whole saliva. Salivary amylase and peroxidase activities were also determined. Plaque fluid and saliva samples were also subjected to polyacrylamide gel electrophoresis. The total viable anaerobic count and numbers of Streptococcus mutans were determined in samples of plaque. The results suggest that the major effect of irradiation leading to increased numbers of S. mutans and caries susceptibility is in the amount, and not the composition, of the saliva produced by the residual gland tissue. The scanty flow of saliva may reduce the effectiveness of cleansing, buffering and lubrication mechanisms as well as resulting in a marked reduction in the total amount of specific and non-specific immune factors entering the mouth.

  8. Dynamic changes in saliva after acute mental stress

    Science.gov (United States)

    Naumova, Ella A.; Sandulescu, Tudor; Bochnig, Clemens; Khatib, Philipp Al; Lee, Wing-Kee; Zimmer, Stefan; Arnold, Wolfgang H.

    2014-01-01

    Stress-related variations of fluoride concentration in supernatant saliva and salivary sediment, salivary cortisol, total protein and pH after acute mental stress were assessed. The hypothesis was that stress reactions have no influence on these parameters. Thirty-four male students were distributed into two groups: first received the stress exposure followed by the same protocol two weeks later but without stress exposure, second underwent the protocol without stress exposure followed by the stress exposure two weeks later. The stressor was a public speech followed by tooth brushing. Saliva was collected before, immediately after stress induction and immediately, at 10, 30 and 120 min. after tooth brushing. Cortisol concentrations, total protein, intraoral pH, and fluoride content in saliva were measured. The data were analyzed statistically. Salivary sediment was ca 4.33% by weight of whole unstimulated saliva. Fluoride bioavailability was higher in salivary sediment than in supernatant saliva. The weight and fluoride concentration was not altered during 2 hours after stress exposure. After a public speech, the salivary cortisol concentration significantly increased after 20 minutes compared to the baseline. The salivary protein concentration and pH also increased. Public speaking influences protein concentration and salivary pH but does not alter the fluoride concentration of saliva. PMID:24811301

  9. Protein components in saliva and plaque fluid from irradiated primates

    International Nuclear Information System (INIS)

    Edgar, W.M.; Bowen, W.H.; Cole, M.F.

    1982-01-01

    Irradiation of the major salivary glands of monkeys (Macaca mulatta) fed cariogenic diets leads to caries clinically indistinguishable from radiation caries in man. This study compares the organic compostion of individual samples of plaque fluid and saliva from irradiated and control monkeys receiving the same cariogenic diet. Plaque and saliva were collected from fasting, tranquillised animals. Four irradiated animals were sampled repeatedly as were non-irradiated controls. Total protein, albumin, immunoglobulins A, G, and M, and the third component of complement (C'3) were quantitated in plaque fluid and whole saliva. Salivary amylase and peroxidase activities were also determined. Plaque fluid and saliva samples were also subjected to polyacrylamide gel electrophoresis. The total viable anaerobic count and numbers of Streptococcus mutans were determined in samples of plaque. The results suggest that the major effect of irradiation leading to increased numbers of S. mutans and caries susceptibility is in the amount, and not the composition, of the saliva produced by the residual gland tissue. The scanty flow of saliva may reduce the effectiveness of cleansing, buffering and lubrication mechanisms as well as resulting in a marked reduction in the total amount of specific and non-specific immune factors entering the mouth. (author)

  10. Protein components in saliva and plaque fluid from irradiated primates

    Energy Technology Data Exchange (ETDEWEB)

    Edgar, W M; Bowen, W H; Cole, M F [Caries Prevention and Research Branch, National Caries Program, NIDR, Bethesda, Maryland, USA

    1982-01-01

    Irradiation of the major salivary glands of monkeys (Macaca mulatta) fed cariogenic diets leads to caries clinically indistinguishable from radiation caries in man. This study compares the organic compostion of individual samples of plaque fluid and saliva from irradiated and control monkeys receiving the same cariogenic diet. Plaque and saliva were collected from fasting, tranquillised animals. Four irradiated animals were sampled repeatedly as were non-irradiated controls. Total protein, albumin, immunoglobulins A, G, and M, and the third component of complement (C'3) were quantitated in plaque fluid and whole saliva. Salivary amylase and peroxidase activities were also determined. Plaque fluid and saliva samples were also subjected to polyacrylamide gel electrophoresis. The total viable anaerobic count and numbers of Streptococcus mutans were determined in samples of plaque. The results suggest that the major effect of irradiation leading to increased numbers of S. mutans and caries susceptibility is in the amount, and not the composition, of the saliva produced by the residual gland tissue. The scanty flow of saliva may reduce the effectiveness of cleansing, buffering and lubrication mechanisms as well as resulting in a marked reduction in the total amount of specific and non-specific immune factors entering the mouth.

  11. Sample normalization methods in quantitative metabolomics.

    Science.gov (United States)

    Wu, Yiman; Li, Liang

    2016-01-22

    To reveal metabolomic changes caused by a biological event in quantitative metabolomics, it is critical to use an analytical tool that can perform accurate and precise quantification to examine the true concentration differences of individual metabolites found in different samples. A number of steps are involved in metabolomic analysis including pre-analytical work (e.g., sample collection and storage), analytical work (e.g., sample analysis) and data analysis (e.g., feature extraction and quantification). Each one of them can influence the quantitative results significantly and thus should be performed with great care. Among them, the total sample amount or concentration of metabolites can be significantly different from one sample to another. Thus, it is critical to reduce or eliminate the effect of total sample amount variation on quantification of individual metabolites. In this review, we describe the importance of sample normalization in the analytical workflow with a focus on mass spectrometry (MS)-based platforms, discuss a number of methods recently reported in the literature and comment on their applicability in real world metabolomics applications. Sample normalization has been sometimes ignored in metabolomics, partially due to the lack of a convenient means of performing sample normalization. We show that several methods are now available and sample normalization should be performed in quantitative metabolomics where the analyzed samples have significant variations in total sample amounts. Copyright © 2015 Elsevier B.V. All rights reserved.

  12. PLS-based and regularization-based methods for the selection of relevant variables in non-targeted metabolomics data

    Directory of Open Access Journals (Sweden)

    Renata Bujak

    2016-07-01

    Full Text Available Non-targeted metabolomics constitutes a part of systems biology and aims to determine many metabolites in complex biological samples. Datasets obtained in non-targeted metabolomics studies are multivariate and high-dimensional due to the sensitivity of mass spectrometry-based detection methods as well as complexity of biological matrices. Proper selection of variables which contribute into group classification is a crucial step, especially in metabolomics studies which are focused on searching for disease biomarker candidates. In the present study, three different statistical approaches were tested using two metabolomics datasets (RH and PH study. Orthogonal projections to latent structures-discriminant analysis (OPLS-DA without and with multiple testing correction as well as least absolute shrinkage and selection operator (LASSO were tested and compared. For the RH study, OPLS-DA model built without multiple testing correction, selected 46 and 218 variables based on VIP criteria using Pareto and UV scaling, respectively. In the case of the PH study, 217 and 320 variables were selected based on VIP criteria using Pareto and UV scaling, respectively. In the RH study, OPLS-DA model built with multiple testing correction, selected 4 and 19 variables as statistically significant in terms of Pareto and UV scaling, respectively. For PH study, 14 and 18 variables were selected based on VIP criteria in terms of Pareto and UV scaling, respectively. Additionally, the concept and fundaments of the least absolute shrinkage and selection operator (LASSO with bootstrap procedure evaluating reproducibility of results, was demonstrated. In the RH and PH study, the LASSO selected 14 and 4 variables with reproducibility between 99.3% and 100%. However, apart from the popularity of PLS-DA and OPLS-DA methods in metabolomics, it should be highlighted that they do not control type I or type II error, but only arbitrarily establish a cut-off value for PLS-DA loadings

  13. Saliva as a future potential predictor for various periodontal diseases

    Directory of Open Access Journals (Sweden)

    Zahreni Hamzah

    2011-06-01

    Full Text Available Background: There are many diagnostic biomarkers have been found in saliva. Saliva contains a wide variety of proteins, including bacteria and products, enzymes, inflammatory mediators and host response modifiers, products of tissue breakdown. Purpose: The purpose of the study was studied current development of diagnostic biomarkers in saliva that will lead to the development of simple and accurate diagnostic tools for periodental disease. Reviews: Specifically, the salivary biomarkers divided for three aspects of periodontitis i.e. inflammation, collagen degradation and bone turnover, correlated with clinical features of periodontal disease. The diagnostic biomarkers is in saliva, such as enzyme, immunoglobulin, cytokines, bacteria and bacterial products, hormones. For the past two decades, oral health researchers have been developing salivary diagnostic tools to monitor oral diseases. Conclusion: The indicators of acute periodontitis can detect with ß-glucuronidase and AST, IL-1β, and MMP-8, whereas indicators for chronic periodontitis can detect with ALP. The indicators for collagen degradation and bone turnover suggest ICTP, fibronectin fragments, and osteonectin. The indicators of severity of periodontitis especially can be predict by B. forsythus.Latar belakang: Banyak biomarker telah ditemukan dalam saliva. Saliva terdiri dari berbagai protein unik meliputi bakteri dan produk bakteri, enzim, mediator inflamasi dan modifikasi respon host (immunoglobulin, sitokin, produk kerusakan jaringan (telopeptida kolagen, osteokalsin, proteoglikan, fragmen fibronectin. Tujuan: Mengkaji biomarker dalam saliva untuk pengembangan metode diagnostik sederhana dan akurat untuk penyakit periodontal. Tinjauan Pustaka: Secara khusus, biomarker saliva pada periodontitis dibagi dalam tiga aspek yaitu inflamasi, dan degradasi kolagen serta pergantian tulang. Biomarker diagnostik dalam saliva, meliputi enzim, imunoglobulin, sitokin, bakteri dan produk

  14. Metabolomics, Nutrition, and Potential Biomarkers of Food Quality, Intake, and Health Status.

    Science.gov (United States)

    Sébédio, Jean-Louis

    Diet, dietary patterns, and other environmental factors such as exposure to toxins are playing an important role in the prevention/development of many diseases, like obesity, type 2 diabetes, and consequently on the health status of individuals. A major challenge nowadays is to identify novel biomarkers to detect as early as possible metabolic dysfunction and to predict evolution of health status in order to refine nutritional advices to specific population groups. Omics technologies such as genomics, transcriptomics, proteomics, and metabolomics coupled with statistical and bioinformatics tools have already shown great potential in this research field even if so far only few biomarkers have been validated. For the past two decades, important analytical techniques have been developed to detect as many metabolites as possible in human biofluids such as urine, blood, and saliva. In the field of food science and nutrition, many studies have been carried out for food authenticity, quality, and safety, as well as for food processing. Furthermore, metabolomic investigations have been carried out to discover new early biomarkers of metabolic dysfunction and predictive biomarkers of developing pathologies (obesity, metabolic syndrome, type-2 diabetes, etc.). Great emphasis is also placed in the development of methodologies to identify and validate biomarkers of nutrients exposure. © 2017 Elsevier Inc. All rights reserved.

  15. Comprehensive metabolomic profiling and incident cardiovascular disease: a systematic review

    Science.gov (United States)

    Background: Metabolomics is a promising tool of cardiovascular biomarker discovery. We systematically reviewed the literature on comprehensive metabolomic profiling in association with incident cardiovascular disease (CVD). Methods and Results: We searched MEDLINE and EMBASE from inception to Janua...

  16. Plant Metabolomics : the missiong link in functional genomics strategies

    NARCIS (Netherlands)

    Hall, R.D.; Beale, M.; Fiehn, O.; Hardy, N.; Summer, L.; Bino, R.

    2002-01-01

    After the establishment of technologies for high-throughput DNA sequencing (genomics), gene expression analysis (transcriptomics), and protein analysis (proteomics), the remaining functional genomics challenge is that of metabolomics. Metabolomics is the term coined for essentially comprehensive,

  17. New Methodology for Known Metabolite Identification in Metabonomics/Metabolomics: Topological Metabolite Identification Carbon Efficiency (tMICE).

    Science.gov (United States)

    Sanchon-Lopez, Beatriz; Everett, Jeremy R

    2016-09-02

    A new, simple-to-implement and quantitative approach to assessing the confidence in NMR-based identification of known metabolites is introduced. The approach is based on a topological analysis of metabolite identification information available from NMR spectroscopy studies and is a development of the metabolite identification carbon efficiency (MICE) method. New topological metabolite identification indices are introduced, analyzed, and proposed for general use, including topological metabolite identification carbon efficiency (tMICE). Because known metabolite identification is one of the key bottlenecks in either NMR-spectroscopy- or mass spectrometry-based metabonomics/metabolomics studies, and given the fact that there is no current consensus on how to assess metabolite identification confidence, it is hoped that these new approaches and the topological indices will find utility.

  18. Metabolomics

    DEFF Research Database (Denmark)

    Pedersen, Hans

    fusion where data from different platforms can be combined. Complex data are obtained when samples are analysed using NMR, fluorescence and GC-MS. Chemometrics methods which can be used to extract the relevant information from the obtained data are presented. Focus has been on principal component...... based on NMR data with RRV and known risk markers. The sensitivity and specificity values are 0.80 and 0.79, respectively, for a test set validated model. The second case study is based on plasma samples with verified colorectal cancer and three types of control samples analysed by fluorescence...

  19. Comparative evaluation of qigong on various parameters of saliva

    Directory of Open Access Journals (Sweden)

    Bayat Movahed S.

    2007-05-01

    Full Text Available Background and Aim: Qigong is a type of Chinese psychosomatic exercise that integrates meditation, slow physical movements, and breathing. Numerous physical and mental benefits have been classically ascribed to qigong. On the other hand, unstimulated saliva is thought to play an important role in oral immunity, enamel stability and moisturizing the oral mucous membrane. Impaired salivary secretion leads to dental caries, mucosal deterioration and mouth dryness. The aim of the present study was to analyze the effect of a qigong program on various parameters of saliva such as quantity of unstimulated saliva, pH and SIgA. Materials and Methods: Twenty three subjects participated in this clinical trial study. The experimental subjects underwent a qigong training program, conducted by a qualified instructor. The program consisted of half an hour daily practice for 6 months (spring and winter. Saliva was collected in two periods: once during the spring before the experiment commencement and the second, in the following spring. During each period saliva collection was done on tuesday of each week. pH and quantity of salvia measurements were taken simultaneously. SIgA measurements were also taken based on the values obtained in the last phase of the experiment at the end of each spring. The results were analyzed using paired sample T test, one way repeated measure and Bon Ferroni multiple comparison. P<0.05 was the level of significance. Results: Based on our findings, the change in the amount of unstimulated salvia as well as SIgA was statistically significant (P<0.001; however, there was no significant difference in pH values before and after experiment. Conclusion: These findings demonstrate that after 6 months of practicing qigong, significant changes in amount of unstimulated saliva and SIgA occurred in participants. The authors suggest that qigong may be a beneficial adjunctive treatment that enhances amount of unstimulated saliva and SIgA.

  20. Serum Metabolomics Investigation of Humanized Mouse Model of Dengue Virus Infection.

    Science.gov (United States)

    Cui, Liang; Hou, Jue; Fang, Jinling; Lee, Yie Hou; Costa, Vivian Vasconcelos; Wong, Lan Hiong; Chen, Qingfeng; Ooi, Eng Eong; Tannenbaum, Steven R; Chen, Jianzhu; Ong, Choon Nam

    2017-07-15

    Dengue is an acute febrile illness caused by dengue virus (DENV) and a major cause of morbidity and mortality in tropical and subtropical regions of the world. The lack of an appropriate small-animal model of dengue infection has greatly hindered the study of dengue pathogenesis and the development of therapeutics. In this study, we conducted mass spectrometry-based serum metabolic profiling from a model using humanized mice (humice) with DENV serotype 2 infection at 0, 3, 7, 14, and 28 days postinfection (dpi). Forty-eight differential metabolites were identified, including fatty acids, purines and pyrimidines, acylcarnitines, acylglycines, phospholipids, sphingolipids, amino acids and derivatives, free fatty acids, and bile acid. These metabolites showed a reversible-change trend-most were significantly perturbed at 3 or 7 dpi and returned to control levels at 14 or 28 dpi, indicating that the metabolites might serve as prognostic markers of the disease in humice. The major perturbed metabolic pathways included purine and pyrimidine metabolism, fatty acid β-oxidation, phospholipid catabolism, arachidonic acid and linoleic acid metabolism, sphingolipid metabolism, tryptophan metabolism, phenylalanine metabolism, lysine biosynthesis and degradation, and bile acid biosynthesis. Most of these disturbed pathways are similar to our previous metabolomics findings in a longitudinal cohort of adult human dengue patients across different infection stages. Our analyses revealed the commonalities of host responses to DENV infection between humice and humans and suggested that humice could be a useful small-animal model for the study of dengue pathogenesis and the development of dengue therapeutics. IMPORTANCE Dengue virus is the most widespread arbovirus, causing an estimated 390 million dengue infections worldwide every year. There is currently no effective treatment for the disease, and the lack of an appropriate small-animal model of dengue infection has greatly

  1. Hepatitis B virus DNA in saliva from children with chronic hepatitis B infection: implications for saliva as a potential mode of horizontal transmission

    DEFF Research Database (Denmark)

    Heiberg, Ida Louise; Hoegh, Mette; Ladelund, Steen

    2010-01-01

    To explore the mechanism of horizontal transmission of hepatitis B virus (HBV) among children, we investigated the quantitative relationship between HBV in saliva and blood from 46 children with chronic hepatitis B. We found high levels of HBV DNA in saliva of HBeAg (+) children, suggesting saliva...... as a vehicle for horizontal transmission of HBV among children....

  2. HEPATITIS B VIRUS DNA IN SALIVA FROM CHILDREN WITH CHRONIC HEPATITIS B INFECTION IMPLICATIONS FOR SALIVA AS A POTENTIAL MODE OF HORIZONTAL TRANSMISSION

    NARCIS (Netherlands)

    Heiberg, Ida Louise; Hoegh, Mette; Ladelund, Steen; Niesters, Hubert G. M.; Hogh, Birthe

    2010-01-01

    To explore the mechanism of horizontal transmission of hepatitis B virus (HBV) among children, we investigated the quantitative relationship between HBV in saliva and blood from 46 children with chronic hepatitis B. We found high levels of HBV DNA in saliva of HBeAg (+) children, suggesting saliva

  3. Hepatitis B virus DNA in saliva from children with chronic hepatitis B infection: implications for saliva as a potential mode of horizontal transmission

    DEFF Research Database (Denmark)

    Heiberg, Ida Louise; Hoegh, Mette; Ladelund, Steen

    2010-01-01

    To explore the mechanism of horizontal transmission of hepatitis B virus (HBV) among children, we investigated the quantitative relationship between HBV in saliva and blood from 46 children with chronic hepatitis B. We found high levels of HBV DNA in saliva of HBeAg (+) children, suggesting saliva...

  4. A versatile mass spectrometry-based method to both identify kinase client-relationships and characterize signaling network topology

    Science.gov (United States)

    While more than a thousand protein kinases (PK) have been identified in the Arabidopsis thaliana genome, relatively little progress has been made towards identifying their individual client proteins. Herein we describe use of a mass spectrometry-based in vitro phosphorylation strategy, termed Kinase...

  5. Metabolomics data normalization with EigenMS.

    Directory of Open Access Journals (Sweden)

    Yuliya V Karpievitch

    Full Text Available Liquid chromatography mass spectrometry has become one of the analytical platforms of choice for metabolomics studies. However, LC-MS metabolomics data can suffer from the effects of various systematic biases. These include batch effects, day-to-day variations in instrument performance, signal intensity loss due to time-dependent effects of the LC column performance, accumulation of contaminants in the MS ion source and MS sensitivity among others. In this study we aimed to test a singular value decomposition-based method, called EigenMS, for normalization of metabolomics data. We analyzed a clinical human dataset where LC-MS serum metabolomics data and physiological measurements were collected from thirty nine healthy subjects and forty with type 2 diabetes and applied EigenMS to detect and correct for any systematic bias. EigenMS works in several stages. First, EigenMS preserves the treatment group differences in the metabolomics data by estimating treatment effects with an ANOVA model (multiple fixed effects can be estimated. Singular value decomposition of the residuals matrix is then used to determine bias trends in the data. The number of bias trends is then estimated via a permutation test and the effects of the bias trends are eliminated. EigenMS removed bias of unknown complexity from the LC-MS metabolomics data, allowing for increased sensitivity in differential analysis. Moreover, normalized samples better correlated with both other normalized samples and corresponding physiological data, such as blood glucose level, glycated haemoglobin, exercise central augmentation pressure normalized to heart rate of 75, and total cholesterol. We were able to report 2578 discriminatory metabolite peaks in the normalized data (p<0.05 as compared to only 1840 metabolite signals in the raw data. Our results support the use of singular value decomposition-based normalization for metabolomics data.

  6. Saliva transit in patients with gastroesophageal reflux disease.

    Science.gov (United States)

    Cassiani, R A; Mota, G A; Aprile, L R O; Dantas, R O

    2015-10-01

    Saliva is an important factor in the neutralization of the acidity of the refluxed material that comes from the stomach to the esophagus. The impairment of saliva transit from oral cavity to distal esophagus may be one of the causes of esophagitis and symptoms in gastroesophageal reflux disease (GERD). With the scintigraphic method, the transit of 2 mL of artificial saliva was measured in 30 patients with GERD and 26 controls. The patients with GERD had symptoms of heartburn and acid regurgitation, a 24-hour pH monitoring with more than 4.2% of the time with pH below four, 26 with erosive esophagitis, and four with non-erosive reflux disease. Fourteen had mild dysphagia for solid foods. Twenty-one patients had normal esophageal manometry, and nine had ineffective esophageal motility. They were 15 men and 15 women, aged 21-61 years, mean 39 years. The control group had 14 men and 12 women, aged 19-61 years, mean 35 years. The subjects swallowed in the sitting and supine position 2 mL of artificial saliva labeled with 18 MBq of (99m) Technetium phytate. The time of saliva transit was measured from oral cavity to esophageal-gastric transition, from proximal esophagus to esophageal-gastric transition, and the transit through proximal, middle, and distal esophageal body. There was no difference between patients and controls in the time for saliva to go from oral cavity to esophageal-gastric transition, and from proximal esophagus to esophageal-gastric transition, in the sitting and supine positions. In distal esophagus in the sitting position, the saliva transit duration was shorter in patients with GERD (3.0 ± 0.8 seconds) than in controls (7.6 ± 1.7 seconds, P = 0.03). In conclusion, the saliva transit from oral cavity to the esophageal-gastric transition in patients with GERD has the same duration than in controls. Saliva transit through the distal esophageal body is faster in patients with GERD than controls. © 2014 International Society for Diseases of the

  7. State of the Art: Saliva-Hormonanalyse // State of the art: Saliva analysis

    Directory of Open Access Journals (Sweden)

    Obermayer-Pietsch B

    2017-01-01

    Full Text Available Saliva analyses are widely used for hormone measurements, but also for drug and therapy monitoring, periodontal inflammation and human, viral or microbial nucleic acid (DNA detection. In this review, we focus on preanalytics, and measurement techniques. Clinical applications of steroid hormone analyses are presented with regard to practical use. p bKurzfassung: /bSpeichelanalysen können Hormone, aber auch Drogen- und Medikamenten-Monitoring, parodontale Entzündungsparameter und humane, virale oder mikrobielle Nukleinsäuren (DNA umfassen. In dieser Übersichtsarbeit wird auf Präanalytik, Nachweis-Techniken und Beispiele u.a. aus der Steroidanalyse eingegangen, die derzeit am weitesten entwickelt ist und vielerorts bereits Eingang in die medizinische Routine findet.

  8. CHROMOGRANIN A DETECTION IN SALIVA OF TYPE 2 DIABETES PATIENTS

    Directory of Open Access Journals (Sweden)

    Martine Soell

    2010-02-01

    Full Text Available Chromogranin A is present in secretion granules of nerve, endocrine and immune cells and is a precursor of several peptides with antibacterial and antifungal properties at micromolar concentrations.Our aim in this prospective, double blind study, was to determine the expression of chromogranin A and its peptides at protein level in saliva of type 2 diabetic patients and thereby to obtain a new non-invasive diagnostic means for the future.Saliva was taken from 30 type 2 diabetic patients and 30 healthy individuals at the same time interval in the morning without any oral stimuli. Circadianic periodics in protein productions have been avoided. The presence of chromogranin A and its derived peptides was determined in whole saliva, after centrifugation at 40C for 12 min at 14 000 rpm, by SDS-PAGE electrophoresis and Immunoblotting (Western Blot. To ensure same protein concentrations Bradford protein quantification assay has been performed before.For the first time, we have determined an overexpression of chromogranin A in saliva of diabetic patients in 100% of the individuals.Chromogranin A, a circulating biomarker for epithelial tumours, is also overexpressed in saliva of type 2 diabetic patients. To confirm our results, more studies with a large amount of patients is necessary.

  9. Chromogranin A Detection in Saliva of Type 2 Diabetes Patients

    Directory of Open Access Journals (Sweden)

    Martine Soell

    2010-02-01

    Full Text Available Chromogranin A is present in secretion granules of nerve, endocrine and immune cells and is a precursor of several peptides with antibacterial and antifungal properties at micromolar concentrations.Our aim in this prospective, double blind study, was to determine the expression of chromogranin A and its peptides at protein level in saliva of type 2 diabetic patients and thereby to obtain a new non-invasive diagnostic means for the future.Saliva was taken from 30 type 2 diabetic patients and 30 healthy individuals at the same time interval in the morning without any oral stimuli. Circadianic periodics in protein productions have been avoided. The presence of chromogranin A and its derived peptides was determined in whole saliva, after centrifugation at 4°C for 12 min at 14 000 rpm, by SDS-PAGE electrophoresis and Immunoblotting (Western Blot. To ensure same protein concentrations Bradford protein quantification assay has been performed before.For the first time, we have determined an overexpression of chromogranin A in saliva of diabetic patients in 100% of the individuals.Chromogranin A, a circulating biomarker for epithelial tumours, is also overexpressed in saliva of type 2 diabetic patients. To confirm our results, more studies with a large amount of patients is necessary.

  10. Saliva of obese patients – is it different?

    Directory of Open Access Journals (Sweden)

    Katarzyna Choromańska

    2015-01-01

    Full Text Available Obesity is a major public health concern that increases the risk of cardiovascular disease, type 2 diabetes and cancer. The incidence of obesity has increased significantly in recent years, not only in adults, but also in adolescents and children. This is evidenced by rapidly developing bariatric surgery, the most effective method of treating morbid obesity. Obesity is a multifactorial disease, and its pathogenesis is not completely understood. Numerous studies have been performed to clarify pathogenetic mechanisms, based mostly on blood and sometimes urine samples. Saliva is easily accessible and can be obtained non-invasively. Our aim was to review studies performed on saliva obtained from obese subjects in order to answer the title question.Obese people have different composition of salivary bacteria. Changes in the concentration of sialic acid, phosphorus and peroxidase activity as well as a lower flow rate of stimulated whole saliva promote dental caries and periodontal disease. Concentrations of salivary uric acid, endocannabinoids and CRP are increased in obesity and may provide a useful index of cardiometabolic risk. Assessment of fasting salivary ghrelin might facilitate choosing the best type of bariatric surgery for a specific patient. A significant decrease in salivary cortisol in women with morbid obesity also seems interesting.There is sufficient evidence to state that the saliva of obese and lean subjects is different. Saliva as an easily accessible research material seems promising, as shown by the few studies performed so far.

  11. Noninvasive glucose monitoring using saliva nano-biosensor

    Directory of Open Access Journals (Sweden)

    Wenjun Zhang

    2015-06-01

    Full Text Available Millions of people worldwide live with diabetes and several millions die from it each year. A noninvasive, painless method of glucose testing would highly improve compliance and glucose control while reducing complications and overall disease management costs. To provide accurate, low cost, and continuous glucose monitoring, we have developed a unique, disposable saliva nano-biosensor. More than eight clinical trials on real-time noninvasive salivary glucose monitoring were carried out on two healthy individuals (a 2–3 h-period for each trial, including both regular food and standard glucose beverage intake with more than 35 saliva samples obtained. Excellent clinical accuracy was revealed as compared to the UV Spectrophotometer. By measuring subjects’ salivary glucose and blood glucose in parallel, we found the two generated profiles share the same fluctuation trend but the correlation between them is individual dependent. There is a time lag between the peak glucose values from blood and from saliva. However, the correlation between the two glucose values at fasting is constant for each person enabling noninvasive diagnosis of diabetes through saliva instead of blood. Furthermore, a good correlation of glucose levels in saliva and in blood before and 2 h after glucose intake was observed. Glucose monitoring before and 2 h after meals is usually prescribed by doctors for diabetic patients. Thus, this disposable biosensor will be an alternative for real-time salivary glucose tracking at any time.

  12. Systematic Applications of Metabolomics in Metabolic Engineering

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    Robert A. Dromms

    2012-12-01

    Full Text Available The goals of metabolic engineering are well-served by the biological information provided by metabolomics: information on how the cell is currently using its biochemical resources is perhaps one of the best ways to inform strategies to engineer a cell to produce a target compound. Using the analysis of extracellular or intracellular levels of the target compound (or a few closely related molecules to drive metabolic engineering is quite common. However, there is surprisingly little systematic use of metabolomics datasets, which simultaneously measure hundreds of metabolites rather than just a few, for that same purpose. Here, we review the most common systematic approaches to integrating metabolite data with metabolic engineering, with emphasis on existing efforts to use whole-metabolome datasets. We then review some of the most common approaches for computational modeling of cell-wide metabolism, including constraint-based models, and discuss current computational approaches that explicitly use metabolomics data. We conclude with discussion of the broader potential of computational approaches that systematically use metabolomics data to drive metabolic engineering.

  13. Causal Genetic Variation Underlying Metabolome Differences.

    Science.gov (United States)

    Swain-Lenz, Devjanee; Nikolskiy, Igor; Cheng, Jiye; Sudarsanam, Priya; Nayler, Darcy; Staller, Max V; Cohen, Barak A

    2017-08-01

    An ongoing challenge in biology is to predict the phenotypes of individuals from their genotypes. Genetic variants that cause disease often change an individual's total metabolite profile, or metabolome. In light of our extensive knowledge of metabolic pathways, genetic variants that alter the metabolome may help predict novel phenotypes. To link genetic variants to changes in the metabolome, we studied natural variation in the yeast Saccharomyces cerevisiae We used an untargeted mass spectrometry method to identify dozens of metabolite Quantitative Trait Loci (mQTL), genomic regions containing genetic variation that control differences in metabolite levels between individuals. We mapped differences in urea cycle metabolites to genetic variation in specific genes known to regulate amino acid biosynthesis. Our functional assays reveal that genetic variation in two genes, AUA1 and ARG81 , cause the differences in the abundance of several urea cycle metabolites. Based on knowledge of the urea cycle, we predicted and then validated a new phenotype: sensitivity to a particular class of amino acid isomers. Our results are a proof-of-concept that untargeted mass spectrometry can reveal links between natural genetic variants and metabolome diversity. The interpretability of our results demonstrates the promise of using genetic variants underlying natural differences in the metabolome to predict novel phenotypes from genotype. Copyright © 2017 by the Genetics Society of America.

  14. Application of Metabolomics in Thyroid Cancer Research

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    Anna Wojakowska

    2015-01-01

    Full Text Available Thyroid cancer is the most common endocrine malignancy with four major types distinguished on the basis of histopathological features: papillary, follicular, medullary, and anaplastic. Classification of thyroid cancer is the primary step in the assessment of prognosis and selection of the treatment. However, in some cases, cytological and histological patterns are inconclusive; hence, classification based on histopathology could be supported by molecular biomarkers, including markers identified with the use of high-throughput “omics” techniques. Beside genomics, transcriptomics, and proteomics, metabolomic approach emerges as the most downstream attitude reflecting phenotypic changes and alterations in pathophysiological states of biological systems. Metabolomics using mass spectrometry and magnetic resonance spectroscopy techniques allows qualitative and quantitative profiling of small molecules present in biological systems. This approach can be applied to reveal metabolic differences between different types of thyroid cancer and to identify new potential candidates for molecular biomarkers. In this review, we consider current results concerning application of metabolomics in the field of thyroid cancer research. Recent studies show that metabolomics can provide significant information about the discrimination between different types of thyroid lesions. In the near future, one could expect a further progress in thyroid cancer metabolomics leading to development of molecular markers and improvement of the tumor types classification and diagnosis.

  15. NMR and MS Methods for Metabolomics.

    Science.gov (United States)

    Amberg, Alexander; Riefke, Björn; Schlotterbeck, Götz; Ross, Alfred; Senn, Hans; Dieterle, Frank; Keck, Matthias

    2017-01-01

    Metabolomics, also often referred as "metabolic profiling," is the systematic profiling of metabolites in biofluids or tissues of organisms and their temporal changes. In the last decade, metabolomics has become more and more popular in drug development, molecular medicine, and other biotechnology fields, since it profiles directly the phenotype and changes thereof in contrast to other "-omics" technologies. The increasing popularity of metabolomics has been possible only due to the enormous development in the technology and bioinformatics fields. In particular, the analytical technologies supporting metabolomics, i.e., NMR, UPLC-MS, and GC-MS, have evolved into sensitive and highly reproducible platforms allowing the determination of hundreds of metabolites in parallel. This chapter describes the best practices of metabolomics as seen today. All important steps of metabolic profiling in drug development and molecular medicine are described in great detail, starting from sample preparation to determining the measurement details of all analytical platforms, and finally to discussing the corresponding specific steps of data analysis.

  16. YPED: an integrated bioinformatics suite and database for mass spectrometry-based proteomics research.

    Science.gov (United States)

    Colangelo, Christopher M; Shifman, Mark; Cheung, Kei-Hoi; Stone, Kathryn L; Carriero, Nicholas J; Gulcicek, Erol E; Lam, TuKiet T; Wu, Terence; Bjornson, Robert D; Bruce, Can; Nairn, Angus C; Rinehart, Jesse; Miller, Perry L; Williams, Kenneth R

    2015-02-01

    We report a significantly-enhanced bioinformatics suite and database for proteomics research called Yale Protein Expression Database (YPED) that is used by investigators at more than 300 institutions worldwide. YPED meets the data management, archival, and analysis needs of a high-throughput mass spectrometry-based proteomics research ranging from a single laboratory, group of laboratories within and beyond an institution, to the entire proteomics community. The current version is a significant improvement over the first version in that it contains new modules for liquid chromatography-tandem mass spectrometry (LC-MS/MS) database search results, label and label-free quantitative proteomic analysis, and several scoring outputs for phosphopeptide site localization. In addition, we have added both peptide and protein comparative analysis tools to enable pairwise analysis of distinct peptides/proteins in each sample and of overlapping peptides/proteins between all samples in multiple datasets. We have also implemented a targeted proteomics module for automated multiple reaction monitoring (MRM)/selective reaction monitoring (SRM) assay development. We have linked YPED's database search results and both label-based and label-free fold-change analysis to the Skyline Panorama repository for online spectra visualization. In addition, we have built enhanced functionality to curate peptide identifications into an MS/MS peptide spectral library for all of our protein database search identification results. Copyright © 2015 The Authors. Production and hosting by Elsevier Ltd.. All rights reserved.

  17. Biomarkers of systemic lupus erythematosus identified using mass spectrometry-based proteomics: a systematic review.

    Science.gov (United States)

    Nicolaou, Orthodoxia; Kousios, Andreas; Hadjisavvas, Andreas; Lauwerys, Bernard; Sokratous, Kleitos; Kyriacou, Kyriacos

    2017-05-01

    Advances in mass spectrometry technologies have created new opportunities for discovering novel protein biomarkers in systemic lupus erythematosus (SLE). We performed a systematic review of published reports on proteomic biomarkers identified in SLE patients using mass spectrometry-based proteomics and highlight their potential disease association and clinical utility. Two electronic databases, MEDLINE and EMBASE, were systematically searched up to July 2015. The methodological quality of studies included in the review was performed according to Preferred Reporting Items for Systematic Reviews and Meta-analyses guidelines. Twenty-five studies were included in the review, identifying 241 SLE candidate proteomic biomarkers related to various aspects of the disease including disease diagnosis and activity or pinpointing specific organ involvement. Furthermore, 13 of the 25 studies validated their results for a selected number of biomarkers in an independent cohort, resulting in the validation of 28 candidate biomarkers. It is noteworthy that 11 candidate biomarkers were identified in more than one study. A significant number of potential proteomic biomarkers that are related to a number of aspects of SLE have been identified using mass spectrometry proteomic approaches. However, further studies are required to assess the utility of these biomarkers in routine clinical practice. © 2016 The Authors. Journal of Cellular and Molecular Medicine published by John Wiley & Sons Ltd and Foundation for Cellular and Molecular Medicine.

  18. Mass Spectrometry-Based Proteomics for the Analysis of Chromatin Structure and Dynamics

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    Monica Soldi

    2013-03-01

    Full Text Available Chromatin is a highly structured nucleoprotein complex made of histone proteins and DNA that controls nearly all DNA-dependent processes. Chromatin plasticity is regulated by different associated proteins, post-translational modifications on histones (hPTMs and DNA methylation, which act in a concerted manner to enforce a specific “chromatin landscape”, with a regulatory effect on gene expression. Mass Spectrometry (MS has emerged as a powerful analytical strategy to detect histone PTMs, revealing interplays between neighbouring PTMs and enabling screens for their readers in a comprehensive and quantitative fashion. Here we provide an overview of the recent achievements of state-of-the-art mass spectrometry-based proteomics for the detailed qualitative and quantitative characterization of histone post-translational modifications, histone variants, and global interactomes at specific chromatin regions. This synopsis emphasizes how the advances in high resolution MS, from “Bottom Up” to “Top Down” analysis, together with the uptake of quantitative proteomics methods by chromatin biologists, have made MS a well-established method in the epigenetics field, enabling the acquisition of original information, highly complementary to that offered by more conventional, antibody-based, assays.

  19. A mass spectrometry-based assay for improved quantitative measurements of efflux pump inhibition.

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    Adam R Brown

    Full Text Available Bacterial efflux pumps are active transport proteins responsible for resistance to selected biocides and antibiotics. It has been shown that production of efflux pumps is up-regulated in a number of highly pathogenic bacteria, including methicillin resistant Staphylococcus aureus. Thus, the identification of new bacterial efflux pump inhibitors is a topic of great interest. Existing assays to evaluate efflux pump inhibitory activity rely on fluorescence by an efflux pump substrate. When employing these assays to evaluate efflux pump inhibitory activity of plant extracts and some purified compounds, we observed severe optical interference that gave rise to false negative results. To circumvent this problem, a new mass spectrometry-based method was developed for the quantitative measurement of bacterial efflux pump inhibition. The assay was employed to evaluate efflux pump inhibitory activity of a crude extract of the botanical Hydrastis Canadensis, and to compare the efflux pump inhibitory activity of several pure flavonoids. The flavonoid quercetin, which appeared to be completely inactive with a fluorescence-based method, showed an IC50 value of 75 μg/mL with the new method. The other flavonoids evaluated (apigenin, kaempferol, rhamnetin, luteolin, myricetin, were also active, with IC50 values ranging from 19 μg/mL to 75 μg/mL. The assay described herein could be useful in future screening efforts to identify efflux pump inhibitors, particularly in situations where optical interference precludes the application of methods that rely on fluorescence.

  20. A hybrid approach to protein differential expression in mass spectrometry-based proteomics

    KAUST Repository

    Wang, X.

    2012-04-19

    MOTIVATION: Quantitative mass spectrometry-based proteomics involves statistical inference on protein abundance, based on the intensities of each protein\\'s associated spectral peaks. However, typical MS-based proteomics datasets have substantial proportions of missing observations, due at least in part to censoring of low intensities. This complicates intensity-based differential expression analysis. RESULTS: We outline a statistical method for protein differential expression, based on a simple Binomial likelihood. By modeling peak intensities as binary, in terms of \\'presence/absence,\\' we enable the selection of proteins not typically amenable to quantitative analysis; e.g. \\'one-state\\' proteins that are present in one condition but absent in another. In addition, we present an analysis protocol that combines quantitative and presence/absence analysis of a given dataset in a principled way, resulting in a single list of selected proteins with a single-associated false discovery rate. AVAILABILITY: All R code available here: http://www.stat.tamu.edu/~adabney/share/xuan_code.zip.

  1. Leaching of 210Po in human saliva from smokeless tobacco

    International Nuclear Information System (INIS)

    Syed, U.F.; Bari, A.; Husain, L.; Husain, L.

    2009-01-01

    Use of smokeless tobacco (SLT) is associated with cancer of the oral cavity. 210 Po, a known carcinogen present in SLT may leach into the saliva when the snuff is held in the mouth. Alpha emission from leached 210 Po can cause oral tissue damage, especially in the presence of non healing ulcers seen frequently in snuff users' mouth. Leaching of 210 Po from SLT in human saliva was determined for six popular US snuff brands. 210 Po was leached into human saliva for 30 min, separated radiochemically and its activity was determined by α-counting. Approximately 2-10% of 210 Po present in SLT was observed to leach. Annual exposure from leached 210 Po, based on average daily consumption of 15 g of SLT, was calculated to range from 1.1 to 3.8 Bq year -1 . (author)

  2. Sulfites and the wine metabolome.

    Science.gov (United States)

    Roullier-Gall, Chloé; Hemmler, Daniel; Gonsior, Michael; Li, Yan; Nikolantonaki, Maria; Aron, Alissa; Coelho, Christian; Gougeon, Régis D; Schmitt-Kopplin, Philippe

    2017-12-15

    In a context of societal concern about food preservation, the reduction of sulfite input plays a major role in the wine industry. To improve the understanding of the chemistry involved in the SO 2 protection, a series of bottle aged Chardonnay wines made from the same must, but with different concentrations of SO 2 added at pressing were analyzed by ultrahigh resolution mass spectrometry (FT-ICR-MS) and excitation emission matrix fluorescence (EEMF). Metabolic fingerprints from FT-ICR-MS data could discriminate wines according to the added concentration to the must but they also revealed chemistry-related differences according to the type of stopper, providing a wine metabolomics picture of the impact of distinct stopping strategies. Spearman rank correlation was applied to link the statistically modeled EEMF components (parallel factor analysis (PARAFAC)) and the exact mass information from FT-ICR-MS, and thus revealing the extent of sulfur-containing compounds which could show some correlation with fluorescence fingerprints. Copyright © 2017 Elsevier Ltd. All rights reserved.

  3. Isolation and Analytical Characterization of Local Malaysian Leech Saliva

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    Mohamed Alaama

    2011-12-01

    Full Text Available Leech saliva contains biologically active compounds that are mainly proteins and peptides. In this study a modified and smooth extraction method of saliva was used without leeches' scarification. UV and Bradford Assay protein methods showed that the saliva extract contains high concentrations of proteins. RP-HPLC chromatogram revealed that more than 30 different peaks were observed in leech saliva extract. Gel electrophoresis revealed the existence of proteins and peptides with different molecular weights. The gel showed up to 25 different bands. Comparison of gel electrophoresis data with protein database revealed the closeness of four molecular weights to known proteins from Hirudinaria leech family. Other proteins detected by gel electrophoresis may be related to completely new biologically active proteins and peptides in the saliva extract or to a modification (isoforms of the existing ones or finally to a mixture of both.ABSTRAK: Air liur pacat secara biologinya mengandungi sebahagian besar campuran aktif protein dan peptida. Dalam kajian ini, kaedah pengestrakan air liur pacat yang telah diubah suai digunakan tanpa perlu membunuh pacat. Kaedah protein Cerakin UV dan Bradford menunjukkan air liur pacat yang diekstrak mengandungi konsentrasi protein yang tinggi. Kromatogram RP-HPLC memperlihatkan lebih daripada 30 puncak berbeza diperolehi semasa air liur pacat diekstrak. Gel elektroforesis memperlihatkan kewujudan protein dan peptida dengan berat molekul yang berbeza. Gel menunjukkan hingga 25 jalur yang berbeza. Perbandingan data menggunakan gel elektroforesis seiring dengan pangkalan data protein memperlihatkan persamaan empat berat molekul, dengan protein yang yang dikenali daripada keluarga pacat Hirudinaria. Jenis protein lain yang dikesan dengan menggunakan gel elektrofosis mungkin juga berkait secara biologinya dengan protein dan peptida aktif yang baru, dalam ekstrak air liur atau pengubahsuaian (beberapa jenis yang berbeza daripada

  4. Rapid antemortem detection of CWD prions in deer saliva.

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    Davin M Henderson

    Full Text Available Chronic wasting disease (CWD is an efficiently transmitted prion disease of cervids, now identified in 22 United States, 2 Canadian provinces and Korea. One hallmark of CWD is the shedding of infectious prions in saliva, as demonstrated by bioassay in deer. It is also clear that the concentration of prions in saliva, blood, urine and feces is much lower than in the nervous system or lymphoid tissues. Rapid in vitro detection of CWD (and other prions in body fluids and excreta has been problematic due to the sensitivity limits of direct assays (western blotting, ELISA and the presence of inhibitors in these complex biological materials that hamper detection. Here we use real-time quaking induced conversion (RT-QuIC to demonstrate CWD prions in both diluted and prion-enriched saliva samples from asymptomatic and symptomatic white-tailed deer. CWD prions were detected in 14 of 24 (58.3% diluted saliva samples from CWD-exposed white-tailed deer, including 9 of 14 asymptomatic animals (64.2%. In addition, a phosphotungstic acid enrichment enhanced the RT-QuIC assay sensitivity, enabling detection in 19 of 24 (79.1% of the above saliva samples. Bioassay in Tg[CerPrP] mice confirmed the presence of infectious prions in 2 of 2 RT-QuIC-positive saliva samples so examined. The modified RT-QuIC analysis described represents a non-invasive, rapid ante-mortem detection of prions in complex biologic fluids, excreta, or environmental samples as well as a tool for exploring prion trafficking, peripheralization, and dissemination.

  5. Metabolomics: Definitions and Significance in Systems Biology.

    Science.gov (United States)

    Klassen, Aline; Faccio, Andréa Tedesco; Canuto, Gisele André Baptista; da Cruz, Pedro Luis Rocha; Ribeiro, Henrique Caracho; Tavares, Marina Franco Maggi; Sussulini, Alessandra

    2017-01-01

    Nowadays, there is a growing interest in deeply understanding biological mechanisms not only at the molecular level (biological components) but also the effects of an ongoing biological process in the organism as a whole (biological functionality), as established by the concept of systems biology. Within this context, metabolomics is one of the most powerful bioanalytical strategies that allow obtaining a picture of the metabolites of an organism in the course of a biological process, being considered as a phenotyping tool. Briefly, metabolomics approach consists in identifying and determining the set of metabolites (or specific metabolites) in biological samples (tissues, cells, fluids, or organisms) under normal conditions in comparison with altered states promoted by disease, drug treatment, dietary intervention, or environmental modulation. The aim of this chapter is to review the fundamentals and definitions used in the metabolomics field, as well as to emphasize its importance in systems biology and clinical studies.

  6. Microbiome, Metabolome and Inflammatory Bowel Disease

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    Ishfaq Ahmed

    2016-06-01

    Full Text Available Inflammatory Bowel Disease (IBD is a multifactorial disorder that conceptually occurs as a result of altered immune responses to commensal and/or pathogenic gut microbes in individuals most susceptible to the disease. During Crohn’s Disease (CD or Ulcerative Colitis (UC, two components of the human IBD, distinct stages define the disease onset, severity, progression and remission. Epigenetic, environmental (microbiome, metabolome and nutritional factors are important in IBD pathogenesis. While the dysbiotic microbiota has been proposed to play a role in disease pathogenesis, the data on IBD and diet are still less convincing. Nonetheless, studies are ongoing to examine the effect of pre/probiotics and/or FODMAP reduced diets on both the gut microbiome and its metabolome in an effort to define the healthy diet in patients with IBD. Knowledge of a unique metabolomic fingerprint in IBD could be useful for diagnosis, treatment and detection of disease pathogenesis.

  7. Metabolomics to Explore Impact of Dairy Intake

    Directory of Open Access Journals (Sweden)

    Hong Zheng

    2015-06-01

    Full Text Available Dairy products are an important component in the Western diet and represent a valuable source of nutrients for humans. However, a reliable dairy intake assessment in nutrition research is crucial to correctly elucidate the link between dairy intake and human health. Metabolomics is considered a potential tool for assessment of dietary intake instead of traditional methods, such as food frequency questionnaires, food records, and 24-h recalls. Metabolomics has been successfully applied to discriminate between consumption of different dairy products under different experimental conditions. Moreover, potential metabolites related to dairy intake were identified, although these metabolites need to be further validated in other intervention studies before they can be used as valid biomarkers of dairy consumption. Therefore, this review provides an overview of metabolomics for assessment of dairy intake in order to better clarify the role of dairy products in human nutrition and health.

  8. Blood transcriptomics and metabolomics for personalized medicine.

    Science.gov (United States)

    Li, Shuzhao; Todor, Andrei; Luo, Ruiyan

    2016-01-01

    Molecular analysis of blood samples is pivotal to clinical diagnosis and has been intensively investigated since the rise of systems biology. Recent developments have opened new opportunities to utilize transcriptomics and metabolomics for personalized and precision medicine. Efforts from human immunology have infused into this area exquisite characterizations of subpopulations of blood cells. It is now possible to infer from blood transcriptomics, with fine accuracy, the contribution of immune activation and of cell subpopulations. In parallel, high-resolution mass spectrometry has brought revolutionary analytical capability, detecting > 10,000 metabolites, together with environmental exposure, dietary intake, microbial activity, and pharmaceutical drugs. Thus, the re-examination of blood chemicals by metabolomics is in order. Transcriptomics and metabolomics can be integrated to provide a more comprehensive understanding of the human biological states. We will review these new data and methods and discuss how they can contribute to personalized medicine.

  9. Quantification of anti-Leishmania antibodies in saliva of dogs.

    Science.gov (United States)

    Cantos-Barreda, Ana; Escribano, Damián; Bernal, Luis J; Cerón, José J; Martínez-Subiela, Silvia

    2017-08-15

    Detection of serum anti-Leishmania antibodies by quantitative or qualitative techniques has been the most used method to diagnose Canine Leishmaniosis (CanL). Nevertheless, saliva may represent an alternative to blood because it is easy to collect, painless and non-invasive in comparison with serum. In this study, two time-resolved immunofluorometric assays (TR-IFMAs) for quantification of anti-Leishmania IgG2 and IgA antibodies in saliva were developed and validated and their ability to distinguish Leishmania-seronegative from seropositive dogs was evaluated. The analytical study was performed by evaluation of assay precision, sensitivity and accuracy. In addition, serum from 48 dogs (21 Leishmania-seropositive and 27 Leishmania-seronegative) were analyzed by TR-IFMAs. The assays were precise, with an intra- and inter-assay coefficients of variation lower than 11%, and showed high level of accuracy, as determined by linearity under dilution (R 2 =0.99) and recovery tests (>88.60%). Anti-Leishmania IgG2 antibodies in saliva were significantly higher in the seropositive group compared with the seronegative (pLeishmania IgA antibodies between both groups were observed. Furthermore, TR-IFMA for quantification of anti-Leishmania IgG2 antibodies in saliva showed higher differences between seropositive and seronegative dogs than the commercial assay used in serum. In conclusion, TR-IFMAs developed may be used to quantify anti-Leishmania IgG2 and IgA antibodies in canine saliva with an adequate precision, analytical sensitivity and accuracy. Quantification of anti-Leishmania IgG2 antibodies in saliva could be potentially used to evaluate the humoral response in CanL. However, IgA in saliva seemed not to have diagnostic value for this disease. For future studies, it would be desirable to evaluate the ability of the IgG2 assay to detect dogs with subclinical disease or with low antibody titers in serum and also to study the antibodies behaviour in saliva during the

  10. Some Biological Activities of Malaysian Leech Saliva Extract

    OpenAIRE

    Abdualrahman M. Abdualkader; Ahmed Merzouk; Abbas Mohammed Ghawi; and Mohammed Alaama

    2011-01-01

    Leeches were fed on the phagostimulatory solution through parafilm membrane. The satiated leeches were forced to regurgitate the solution by soaking them in an ice-container. The anticoagulant activity was ascertained using thrombin time assay (TT). The result revealed that the saliva concentration which increases TT by 100% (IC100) is 43.205µg/ml plasma. The antimicrobial activity of the saliva was tested against several bacterial spp. (E.coli, P.aeruginosa, B.cereus, Sal.typhi and S...

  11. Linking metabolomics data to underlying metabolic regulation

    Directory of Open Access Journals (Sweden)

    Thomas eNägele

    2014-11-01

    Full Text Available The comprehensive experimental analysis of a metabolic constitution plays a central role in approaches of organismal systems biology.Quantifying the impact of a changing environment on the homeostasis of cellular metabolism has been the focus of numerous studies applying various metabolomics techniques. It has been proven that approaches which integrate different analytical techniques, e.g. LC-MS, GC-MS, CE-MS and H-NMR, can provide a comprehensive picture of a certain metabolic homeostasis. Identification of metabolic compounds and quantification of metabolite levels represent the groundwork for the analysis of regulatory strategies in cellular metabolism. This significantly promotes our current understanding of the molecular organization and regulation of cells, tissues and whole organisms.Nevertheless, it is demanding to elicit the pertinent information which is contained in metabolomics data sets.Based on the central dogma of molecular biology, metabolite levels and their fluctuations are the result of a directed flux of information from gene activation over transcription to translation and posttranslational modification.Hence, metabolomics data represent the summed output of a metabolic system comprising various levels of molecular organization.As a consequence, the inverse assignment of metabolomics data to underlying regulatory processes should yield information which-if deciphered correctly-provides comprehensive insight into a metabolic system.Yet, the deduction of regulatory principles is complex not only due to the high number of metabolic compounds, but also because of a high level of cellular compartmentalization and differentiation.Motivated by the question how metabolomics approaches can provide a representative view on regulatory biochemical processes, this article intends to present and discuss current metabolomics applications, strategies of data analysis and their limitations with respect to the interpretability in context of

  12. Postmortem interval estimation: a novel approach utilizing gas chromatography/mass spectrometry-based biochemical profiling.

    Science.gov (United States)

    Kaszynski, Richard H; Nishiumi, Shin; Azuma, Takeshi; Yoshida, Masaru; Kondo, Takeshi; Takahashi, Motonori; Asano, Migiwa; Ueno, Yasuhiro

    2016-05-01

    While the molecular mechanisms underlying postmortem change have been exhaustively investigated, the establishment of an objective and reliable means for estimating postmortem interval (PMI) remains an elusive feat. In the present study, we exploit low molecular weight metabolites to estimate postmortem interval in mice. After sacrifice, serum and muscle samples were procured from C57BL/6J mice (n = 52) at seven predetermined postmortem intervals (0, 1, 3, 6, 12, 24, and 48 h). After extraction and isolation, low molecular weight metabolites were measured via gas chromatography/mass spectrometry (GC/MS) and examined via semi-quantification studies. Then, PMI prediction models were generated for each of the 175 and 163 metabolites identified in muscle and serum, respectively, using a non-linear least squares curve fitting program. A PMI estimation panel for muscle and serum was then erected which consisted of 17 (9.7%) and 14 (8.5%) of the best PMI biomarkers identified in muscle and serum profiles demonstrating statistically significant correlations between metabolite quantity and PMI. Using a single-blinded assessment, we carried out validation studies on the PMI estimation panels. Mean ± standard deviation for accuracy of muscle and serum PMI prediction panels was -0.27 ± 2.88 and -0.89 ± 2.31 h, respectively. Ultimately, these studies elucidate the utility of metabolomic profiling in PMI estimation and pave the path toward biochemical profiling studies involving human samples.

  13. COordination of Standards in MetabOlomicS (COSMOS): facilitating integrated metabolomics data access

    NARCIS (Netherlands)

    Salek, R.M.; Neumann, S.; Schober, D.; Hummel, J.; Billiau, K.; Kopka, J.; Correa, E.; Reijmers, T.; Rosato, A.; Tenori, L.; Turano, P.; Marin, S.; Deborde, C.; Jacob, D.; Rolin, D.; Dartigues, B.; Conesa, P.; Haug, K.; Rocca-Serra, P.; O’Hagan, S.; Hao, J.; Vliet, M. van; Sysi-Aho, M.; Ludwig, C.; Bouwman, J.; Cascante, M.; Ebbels, T.; Griffin, J.L.; Moing, A.; Nikolski, M.; Oresic, M.; Sansone, S.A.; Viant, M.R.; Goodacre, R.; Günther, U.L.; Hankemeier, T.; Luchinat, C.; Walther, D.; Steinbeck, C.

    2015-01-01

    Metabolomics has become a crucial phenotyping technique in a range of research fields including medicine, the life sciences, biotechnology and the environmental sciences. This necessitates the transfer of experimental information between research groups, as well as potentially to publishers and

  14. Facilitated saliva secretion and reduced oral inflammation by a novel artificial saliva system in the treatment of salivary hypofunction

    Directory of Open Access Journals (Sweden)

    Kang M

    2017-01-01

    Full Text Available Minkyung Kang,1 Hyounggeun Park,1 Joon-Ho Jun,1 Miwon Son,1 Myung Joo Kang2 1Pharmaceutical Product Research Laboratories, Dong-A ST Research Institute, Gyeonggi, 2Division of Pharmaceutical Sciences, College of Pharmacy, Dankook University, Cheonan, Chungnam, Korea Abstract: Saliva substitutes and/or lubricants are commonly employed to lessen dry mouth symptoms by stimulating and/or substituting for the secretion of saliva. In this study, a novel artificial saliva containing inorganic salts, including sodium chloride and potassium chloride, and bactericidal agents, including potassium thiocyanate and lactoperoxidase, was formulated in the form of a solution (DM-sol or gel (DM-gel. Those in vivo therapeutic efficacies were assessed in terms of saliva secretion and anti-inflammatory activity in rats and mice, respectively. Salivary secretion was promoted by mucosal application of DM-formulations in normal rats. In particular, DM-gel resulted in 2.5- and 1.9-fold greater salivary flow rates compared to normal saline and DM-sol, respectively. In an in vivo efficacy evaluation in diabetic mice with salivary hypofunction, repeated application of DM-formulations alleviated histopathological changes in the buccal mucosa in terms of atrophy and thinning of the epithelium, compared to vehicle, after 4 weeks. Moreover, the DM-sol and DM-gel were comparably effective for relieving periodontal gingivitis, reducing infiltration of inflammatory cells, and normalizing the neutrophil level in the gingival gingiva, after 4 weeks. Therefore, the novel artificial saliva is expected to facilitate salivary secretion and restore physiological conditions in the mouth of patients with salivary hypofunction. Keywords: saliva substitute, carbopol gel, hypothiocyanite–hydrogen peroxide mixture, antimicrobial activity, diabetic rats

  15. Cord Blood Metabolome Is Highly Associated with Birth Weight, but Less Predictive for Later Weight Development

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    Christian Hellmuth

    2017-04-01

    Full Text Available Background/Aims: Fetal metabolism may be changed by the exposure to maternal factors, and the route to obesity may already set in utero. Cord blood metabolites might predict growth patterns and later obesity. We aimed to characterize associations of cord blood with birth weight, postnatal weight gain, and BMI in adolescence. Methods: Over 700 cord blood samples were collected from infants participating in the German birth cohort study LISAplus. Glycerophospholipid fatty acids (GPL-FA, polar lipids, non-esterified fatty acids (NEFA, and amino acids were analyzed with a targeted, liquid chromatography-tandem mass spectrometry based metabolomics platform. Cord blood metabolites were related to growth factors by linear regression models adjusted for confounding variables. Results: Cord blood metabolites were highly associated with birth weight. Lysophosphatidylcholines C16:1, C18:1, C20:3, C18:2, C20:4, C14:0, C16:0, C18:3, GPL-FA C20:3n-9, and GPL-FA C22:5n-6 were positively related to birth weight, while higher cord blood concentrations of NEFA C22:6, NEFA C20:5, GPL-FA C18:3n-3, and PCe C38:0 were associated with lower birth weight. Postnatal weight gain and BMI z-scores in adolescents were not significantly associated with cord blood metabolites after adjustment for multiple testing. Conclusion: Potential long-term programming effects of the intrauterine environment and metabolism on later health cannot be predicted with profiling of the cord blood metabolome.

  16. MPLEx: a Robust and Universal Protocol for Single-Sample Integrative Proteomic, Metabolomic, and Lipidomic Analyses

    Energy Technology Data Exchange (ETDEWEB)

    Nakayasu, Ernesto S.; Nicora, Carrie D.; Sims, Amy C.; Burnum-Johnson, Kristin E.; Kim, Young-Mo; Kyle, Jennifer E.; Matzke, Melissa M.; Shukla, Anil K.; Chu, Rosalie K.; Schepmoes, Athena A.; Jacobs, Jon M.; Baric, Ralph S.; Webb-Robertson, Bobbie-Jo; Smith, Richard D.; Metz, Thomas O.; Chia, Nicholas

    2016-05-03

    ABSTRACT

    Integrative multi-omics analyses can empower more effective investigation and complete understanding of complex biological systems. Despite recent advances in a range of omics analyses, multi-omic measurements of the same sample are still challenging and current methods have not been well evaluated in terms of reproducibility and broad applicability. Here we adapted a solvent-based method, widely applied for extracting lipids and metabolites, to add proteomics to mass spectrometry-based multi-omics measurements. Themetabolite,protein, andlipidextraction (MPLEx) protocol proved to be robust and applicable to a diverse set of sample types, including cell cultures, microbial communities, and tissues. To illustrate the utility of this protocol, an integrative multi-omics analysis was performed using a lung epithelial cell line infected with Middle East respiratory syndrome coronavirus, which showed the impact of this virus on the host glycolytic pathway and also suggested a role for lipids during infection. The MPLEx method is a simple, fast, and robust protocol that can be applied for integrative multi-omic measurements from diverse sample types (e.g., environmental,in vitro, and clinical).

    IMPORTANCEIn systems biology studies, the integration of multiple omics measurements (i.e., genomics, transcriptomics, proteomics, metabolomics, and lipidomics) has been shown to provide a more complete and informative view of biological pathways. Thus, the prospect of extracting different types of molecules (e.g., DNAs, RNAs, proteins, and metabolites) and performing multiple omics measurements on single samples is very attractive, but such studies are challenging due to the fact that the extraction conditions differ according to the molecule type. Here, we adapted an organic solvent-based extraction method that demonstrated

  17. Identification of Metabolomic Biomarkers for Endometrial Cancer and Its Recurrence after Surgery in Postmenopausal Women

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    Yannick Audet-Delage

    2018-03-01

    Full Text Available Endometrial cancer (EC is the most frequent gynecological cancer in developed countries. Most EC occurs after menopause and is diagnosed as endometrioid (type I carcinomas, which exhibit a favorable prognosis. In contrast, non-endometrioid (type II carcinomas such as serous tumors have a poor prognosis. Our goal was to identify novel blood-based markers associated with EC subtypes and recurrence after surgery in postmenopausal women. Using mass spectrometry-based untargeted metabolomics, we examined preoperative serum metabolites among control women (n = 18 and those with non-recurrent (NR and recurrent (R cases of type I endometrioid (n = 24 and type II serous (n = 12 carcinomas. R and NR cases were similar with respect to pathological characteristics, body mass index, and age. A total of 1,592 compounds were analyzed including 14 different lipid classes. When we compared EC cases with controls, 137 metabolites were significantly different. A combination of spermine and isovalerate resulted in an age-adjusted area under the receiver-operating characteristic curve (AUCadj of 0.914 (P < 0.001 for EC detection. The combination of 2-oleoylglycerol and TAG42:2-FA12:0 allowed the distinction of R cases from NR cases with an AUCadj of 0.901 (P < 0.001. Type I R cases were also characterized by much lower levels of bile acids and elevated concentrations of phosphorylated fibrinogen cleavage peptide, whereas type II R cases displayed higher levels of ceramides. The findings from our pilot study provide a detailed metabolomics study of EC and identify putative serum biomarkers for defining clinically relevant risk groups.

  18. Specialized Information Processing Deficits and Distinct Metabolomic Profiles Following TM-Domain Disruption of Nrg1.

    Science.gov (United States)

    O'Tuathaigh, Colm M P; Mathur, Naina; O'Callaghan, Matthew J; MacIntyre, Lynsey; Harvey, Richard; Lai, Donna; Waddington, John L; Pickard, Benjamin S; Watson, David G; Moran, Paula M

    2017-09-01

    Although there is considerable genetic and pathologic evidence for an association between neuregulin 1 (NRG1) dysregulation and schizophrenia, the underlying molecular and cellular mechanisms remain unclear. Mutant mice containing disruption of the transmembrane (TM) domain of the NRG1 gene constitute a heuristic model for dysregulation of NRG1-ErbB4 signaling in schizophrenia. The present study focused on hitherto uncharacterized information processing phenotypes in this mutant line. Using a mass spectrometry-based metabolomics approach, we also quantified levels of unique metabolites in brain. Across 2 different sites and protocols, Nrg1 mutants demonstrated deficits in prepulse inhibition, a measure of sensorimotor gating, that is, disrupted in schizophrenia; these deficits were partially reversed by acute treatment with second, but not first-, generation antipsychotic drugs. However, Nrg1 mutants did not show a specific deficit in latent inhibition, a measure of selective attention that is also disrupted in schizophrenia. In contrast, in a "what-where-when" object recognition memory task, Nrg1 mutants displayed sex-specific (males only) disruption of "what-when" performance, indicative of impaired temporal aspects of episodic memory. Differential metabolomic profiling revealed that these behavioral phenotypes were accompanied, most prominently, by alterations in lipid metabolism pathways. This study is the first to associate these novel physiological mechanisms, previously independently identified as being abnormal in schizophrenia, with disruption of NRG1 function. These data suggest novel mechanisms by which compromised neuregulin function from birth might lead to schizophrenia-relevant behavioral changes in adulthood. © The Author 2017. Published by Oxford University Press on behalf of the Maryland Psychiatric Research Center.

  19. Mass Spectrometry-Based Proteomics for Pre-Eclampsia and Preterm Birth

    Science.gov (United States)

    Law, Kai P.; Han, Ting-Li; Tong, Chao; Baker, Philip N.

    2015-01-01

    Pregnancy-related complications such as pre-eclampsia and preterm birth now represent a notable burden of adverse health. Pre-eclampsia is a hypertensive disorder unique to pregnancy. It is an important cause of maternal death worldwide and a leading cause of fetal growth restriction and iatrogenic prematurity. Fifteen million infants are born preterm each year globally, but more than one million of those do not survive their first month of life. Currently there are no predictive tests available for diagnosis of these pregnancy-related complications and the biological mechanisms of the diseases have not been fully elucidated. Mass spectrometry-based proteomics have all the necessary attributes to provide the needed breakthrough in understanding the pathophysiology of complex human diseases thorough the discovery of biomarkers. The mass spectrometry methodologies employed in the studies for pregnancy-related complications are evaluated in this article. Top-down proteomic and peptidomic profiling by laser mass spectrometry, liquid chromatography or capillary electrophoresis coupled to mass spectrometry, and bottom-up quantitative proteomics and targeted proteomics by liquid chromatography mass spectrometry have been applied to elucidate protein biomarkers and biological mechanism of pregnancy-related complications. The proteomes of serum, urine, amniotic fluid, cervical-vaginal fluid, placental tissue, and cytotrophoblastic cells have all been investigated. Numerous biomarkers or biomarker candidates that could distinguish complicated pregnancies from healthy controls have been proposed. Nevertheless, questions as to the clinically utility and the capacity to elucidate the pathogenesis of the pre-eclampsia and preterm birth remain to be answered. PMID:26006232

  20. Mass Spectrometry-Based Proteomics for Pre-Eclampsia and Preterm Birth

    Directory of Open Access Journals (Sweden)

    Kai P. Law

    2015-05-01

    Full Text Available Pregnancy-related complications such as pre-eclampsia and preterm birth now represent a notable burden of adverse health. Pre-eclampsia is a hypertensive disorder unique to pregnancy. It is an important cause of maternal death worldwide and a leading cause of fetal growth restriction and iatrogenic prematurity. Fifteen million infants are born preterm each year globally, but more than one million of those do not survive their first month of life. Currently there are no predictive tests available for diagnosis of these pregnancy-related complications and the biological mechanisms of the diseases have not been fully elucidated. Mass spectrometry-based proteomics have all the necessary attributes to provide the needed breakthrough in understanding the pathophysiology of complex human diseases thorough the discovery of biomarkers. The mass spectrometry methodologies employed in the studies for pregnancy-related complications are evaluated in this article. Top-down proteomic and peptidomic profiling by laser mass spectrometry, liquid chromatography or capillary electrophoresis coupled to mass spectrometry, and bottom-up quantitative proteomics and targeted proteomics by liquid chromatography mass spectrometry have been applied to elucidate protein biomarkers and biological mechanism of pregnancy-related complications. The proteomes of serum, urine, amniotic fluid, cervical-vaginal fluid, placental tissue, and cytotrophoblastic cells have all been investigated. Numerous biomarkers or biomarker candidates that could distinguish complicated pregnancies from healthy controls have been proposed. Nevertheless, questions as to the clinically utility and the capacity to elucidate the pathogenesis of the pre-eclampsia and preterm birth remain to be answered.

  1. Comparative Analysis of two Helicobacter pylori Strains using Genomics and Mass Spectrometry-Based Proteomics

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    Roger Karlsson

    2016-11-01

    Full Text Available Helicobacter pylori, a gastroenteric pathogen believed to have co-evolved with humans over 100,000 years, shows significant genetic variability. This motivates the study of different H. pylori strains and the diseases they cause in order to identify determinants for disease evolution. In this study, we used proteomics tools to compare two H. pylori strains. Nic25_A was isolated in Nicaragua from a patient with intestinal metaplasia, and P12 was isolated in Europe from a patient with duodenal ulcers. Differences in the abundance of surface proteins between the two strains were determined with two mass spectrometry-based methods, label-free quantification (MaxQuant or the use of tandem mass tags (TMT. Each approach used a lipid-based protein immobilization (LPI™ technique to enrich peptides of surface proteins. Using the MaxQuant software, we found 52 proteins that differed significantly in abundance between the two strains (up- or downregulated by a factor of 1.5; with TMT, we found 18 proteins that differed in abundance between the strains. Strain P12 had a higher abundance of proteins encoded by the cag pathogenicity island, while levels of the acid response regulator ArsR and its regulatory targets (KatA, AmiE, and proteins involved in urease production were higher in strain Nic25_A. Our results show that differences in protein abundance between H. pylori strains can be detected with proteomic approaches; this could have important implications for the study of disease progression.

  2. A Mass Spectrometry-Based Predictive Strategy Reveals ADAP1 is Phosphorylated at Tyrosine 364

    Energy Technology Data Exchange (ETDEWEB)

    Littrell, BobbiJo R [National Renewable Energy Laboratory (NREL), Golden, CO (United States)

    2018-04-16

    The goal of this work was to identify phosphorylation sites within the amino acid sequence of human ADAP1. Using traditional mass spectrometry-based techniques we were unable to produce interpretable spectra demonstrating modification by phosphorylation. This prompted us to employ a strategy in which phosphorylated peptides were first predicted using peptide mapping followed by targeted MS/MS acquisition. ADAP1 was immunoprecipitated from extracts of HEK293 cells stably-transfected with ADAP1 cDNA. Immunoprecipitated ADAP1 was digested with proteolytic enzymes and analyzed by LC-MS in MS1 mode by high-resolution quadrupole time-of-flight mass spectrometry (QTOF-MS). Peptide molecular features were extracted using an untargeted data mining algorithm. Extracted peptide neutral masses were matched against the ADAP1 amino acid sequence with phosphorylation included as a predicted modification. Peptides with predicted phosphorylation sites were analyzed by targeted LC-MS2. Acquired MS2 spectra were then analyzed using database search engines to confirm phosphorylation. Spectra of phosphorylated peptides were validated by manual interpretation. Further confirmation was performed by manipulating phospho-peptide abundance using calf intestinal phosphatase (CIP) and the phorbol ester, phorbol 12-myristate 13-acetate (PMA). Of five predicted phosphopeptides, one, comprised of the sequence AVDRPMLPQEYAVEAHFK, was confirmed to be phosphorylated on a Tyrosine at position 364. Pre-treatment of cells with PMA prior to immunoprecipitation increased the ratio of phosphorylated to unphosphorylated peptide as determined by area counts of extracted ion chromatograms (EIC). Addition of CIP to immunoprecipitation reactions eliminated the phosphorylated form. A novel phosphorylation site was identified at Tyrosine 364. Phosphorylation at this site is increased by treatment with PMA. PMA promotes membrane translocation and activation of protein kinase C (PKC), indicating that Tyrosine 364

  3. Comparative analysis of bacterial profiles in unstimulated and stimulated saliva samples

    DEFF Research Database (Denmark)

    Belstrøm, Daniel; Holmstrup, Palle; Jensen, Allan Bardow

    2016-01-01

    BACKGROUND AND OBJECTIVE: The microbial profiles of stimulated saliva samples have been shown to differentiate between patients with periodontitis, patients with dental caries, and orally healthy individuals. Saliva was stimulated to allow for easy and rapid collection; however, microbial...

  4. Improving mass measurement accuracy in mass spectrometry based proteomics by combining open source tools for chromatographic alignment and internal calibration.

    Science.gov (United States)

    Palmblad, Magnus; van der Burgt, Yuri E M; Dalebout, Hans; Derks, Rico J E; Schoenmaker, Bart; Deelder, André M

    2009-05-02

    Accurate mass determination enhances peptide identification in mass spectrometry based proteomics. We here describe the combination of two previously published open source software tools to improve mass measurement accuracy in Fourier transform ion cyclotron resonance mass spectrometry (FTICRMS). The first program, msalign, aligns one MS/MS dataset with one FTICRMS dataset. The second software, recal2, uses peptides identified from the MS/MS data for automated internal calibration of the FTICR spectra, resulting in sub-ppm mass measurement errors.

  5. The use of saliva markers in psychobiology: mechanisms and methods

    NARCIS (Netherlands)

    Bosch, J.A.; Ligtenberg, A.J.M.; Veerman, E.C.I.

    2014-01-01

    In the social sciences, the use of saliva parameters has greatly expanded in recent years from the measurement of steroid hormones, like cortisol, and now includes a wide range of biochemical parameters. These salivary constituents can be broadly classified into two groups: (1) constituents that

  6. Bacterial composition in whole saliva from patients with severe hyposalivation

    DEFF Research Database (Denmark)

    Belstrøm, Daniel; Holmstrup, Palle; Fiehn, Nils-Erik

    2016-01-01

    OBJECTIVE: The purpose of this study was to compare the microbiota of stimulated whole saliva samples from patients with severe hyposalivation to samples from individuals with normal whole saliva flow rates. It was hypothesized that the two groups differ with regard to salivary bacterial profiles...... with severe hyposalivation do not differ from those of individuals with normal salivary secretion, when there are virtually no untreated active caries lesions present in the oral cavity. This article is protected by copyright. All rights reserved.......OBJECTIVE: The purpose of this study was to compare the microbiota of stimulated whole saliva samples from patients with severe hyposalivation to samples from individuals with normal whole saliva flow rates. It was hypothesized that the two groups differ with regard to salivary bacterial profiles....... METHODS: This cross-sectional study included 36 participants (24 females and 12 males, mean age 58.5 years) with severe hyposalivation and 36 gender-, age- and geographically-matched participants with normal salivary secretion from the Danish Health Examination Survey (DANHES). The microbiota...

  7. Fourier Transform Infrared Spectroscopy and Photoacoustic Spectroscopy for Saliva Analysis.

    Science.gov (United States)

    Mikkonen, Jopi J W; Raittila, Jussi; Rieppo, Lassi; Lappalainen, Reijo; Kullaa, Arja M; Myllymaa, Sami

    2016-09-01

    Saliva provides a valuable tool for assessing oral and systemic diseases, but concentrations of salivary components are very small, calling the need for precise analysis methods. In this work, Fourier transform infrared (FT-IR) spectroscopy using transmission and photoacoustic (PA) modes were compared for quantitative analysis of saliva. The performance of these techniques was compared with a calibration series. The linearity of spectrum output was verified by using albumin-thiocyanate (SCN(-)) solution at different SCN(-) concentrations. Saliva samples used as a comparison were obtained from healthy subjects. Saliva droplets of 15 µL were applied on the silicon sample substrate, 6 drops for each specimen, and dried at 37 ℃ overnight. The measurements were carried out using an FT-IR spectrometer in conjunction with an accessory unit for PA measurements. The findings with both transmission and PA modes mirror each other. The major bands presented were 1500-1750 cm(-1) for proteins and 1050-1200 cm(-1) for carbohydrates. In addition, the distinct spectral band at 2050 cm(-1) derives from SCN(-) anions, which is converted by salivary peroxidases to hypothiocyanate (OSCN(-)). The correlation between the spectroscopic data with SCN(-) concentration (r > 0.990 for transmission and r = 0.967 for PA mode) was found to be significant (P < 0.01), thus promising to be utilized in future applications. © The Author(s) 2016.

  8. DETERMINATION OF CHLORHEXIDINE IN SALIVA AND IN AQUEOUS-SOLUTIONS

    NARCIS (Netherlands)

    de Vries, J.; Ruben, J; Arends, J.

    1991-01-01

    A new method is presented for the determination of chlorhexidine in centrifuged saliva and in aqueous solutions by means of fluorescence spectroscopy. The method relies on complex formation between chlorhexidine and eosin. The fluorescence value of the chlorhexidine-eosin system decreases with

  9. Artificial saliva effect on toxic substances release from acrylic resins

    Directory of Open Access Journals (Sweden)

    Kostić Milena

    2015-01-01

    Full Text Available Background/Aim. Acrylic-based resins are intensively used in dentistry practice as restorative or denture-base materials. The purpose of this study was to analyze the surface structure of denture base resins and the amount of released potentially toxic substances (PTS immediately upon polymerization and incubation in different types of artificial saliva. Methods. Storage of acrylic samples in two models of artificial saliva were performed in a water bath at the temperature of 37 ± 1°C. Analysis of the surface structure of samples was carried out using scanning electronic microscopy analysis immediately after polymerization and after the 30-day incubation. The amounts of PTS per day, week and month extracts were measured using high-pressure liquid chromatography. Results. Surface design and amount of PTS in acrylic materials were different and depended on the types and duration of polymerization. The surfaces of tested acrylates became flatter after immersing in solutions of artificial saliva. The degree of acrylic materials release was not dependent on the applied model of artificial saliva. Conclusion. In order to improve biological features of acrylic resin materials, it was recommended that dentures lined with soft or hard coldpolymerized acrylates should be kept at least 1 to 7 days in water before being given to a patient. So, as to reach high degree of biocompatibility preparation of prosthetic restorations from heat-polymerized acrylate was unnecessary. [Projekat Ministarstva nauke Republike Srbije, br. 41017

  10. The exo-metabolome in filamentous fungi

    DEFF Research Database (Denmark)

    Thrane, Ulf; Andersen, Birgitte; Frisvad, Jens Christian

    2007-01-01

    Filamentous fungi are a diverse group of eukaryotic microorganisms that have a significant impact on human life as spoilers of food and feed by degradation and toxin production. They are also most useful as a source of bulk and fine chemicals and pharmaceuticals. This chapter focuses on the exo-metabolome...

  11. Metabolome analysis of Drosophila melanogaster during embryogenesis.

    Science.gov (United States)

    An, Phan Nguyen Thuy; Yamaguchi, Masamitsu; Bamba, Takeshi; Fukusaki, Eiichiro

    2014-01-01

    The Drosophila melanogaster embryo has been widely utilized as a model for genetics and developmental biology due to its small size, short generation time, and large brood size. Information on embryonic metabolism during developmental progression is important for further understanding the mechanisms of Drosophila embryogenesis. Therefore, the aim of this study is to assess the changes in embryos' metabolome that occur at different stages of the Drosophila embryonic development. Time course samples of Drosophila embryos were subjected to GC/MS-based metabolome analysis for profiling of low molecular weight hydrophilic metabolites, including sugars, amino acids, and organic acids. The results showed that the metabolic profiles of Drosophila embryo varied during the course of development and there was a strong correlation between the metabolome and different embryonic stages. Using the metabolome information, we were able to establish a prediction model for developmental stages of embryos starting from their high-resolution quantitative metabolite composition. Among the important metabolites revealed from our model, we suggest that different amino acids appear to play distinct roles in different developmental stages and an appropriate balance in trehalose-glucose ratio is crucial to supply the carbohydrate source for the development of Drosophila embryo.

  12. Metabolomics in the fight against malaria

    Directory of Open Access Journals (Sweden)

    Jorge L Salinas

    2014-08-01

    Full Text Available Metabolomics uses high-resolution mass spectrometry to provide a chemical fingerprint of thousands of metabolites present in cells, tissues or body fluids. Such metabolic phenotyping has been successfully used to study various biologic processes and disease states. High-resolution metabolomics can shed new light on the intricacies of host-parasite interactions in each stage of the Plasmodium life cycle and the downstream ramifications on the host’s metabolism, pathogenesis and disease. Such data can become integrated with other large datasets generated using top-down systems biology approaches and be utilised by computational biologists to develop and enhance models of malaria pathogenesis relevant for identifying new drug targets or intervention strategies. Here, we focus on the promise of metabolomics to complement systems biology approaches in the quest for novel interventions in the fight against malaria. We introduce the Malaria Host-Pathogen Interaction Center (MaHPIC, a new systems biology research coalition. A primary goal of the MaHPIC is to generate systems biology datasets relating to human and non-human primate (NHP malaria parasites and their hosts making these openly available from an online relational database. Metabolomic data from NHP infections and clinical malaria infections from around the world will comprise a unique global resource.

  13. Metabolomics studies in brain tissue: A review.

    Science.gov (United States)

    Gonzalez-Riano, Carolina; Garcia, Antonia; Barbas, Coral

    2016-10-25

    Brain is still an organ with a composition to be discovered but beyond that, mental disorders and especially all diseases that curse with dementia are devastating for the patient, the family and the society. Metabolomics can offer an alternative tool for unveiling new insights in the discovery of new treatments and biomarkers of mental disorders. Until now, most of metabolomic studies have been based on biofluids: serum/plasma or urine, because brain tissue accessibility is limited to animal models or post mortem studies, but even so it is crucial for understanding the pathological processes. Metabolomics studies of brain tissue imply several challenges due to sample extraction, along with brain heterogeneity, sample storage, and sample treatment for a wide coverage of metabolites with a wide range of concentrations of many lipophilic and some polar compounds. In this review, the current analytical practices for target and non-targeted metabolomics are described and discussed with emphasis on critical aspects: sample treatment (quenching, homogenization, filtration, centrifugation and extraction), analytical methods, as well as findings considering the used strategies. Besides that, the altered analytes in the different brain regions have been associated with their corresponding pathways to obtain a global overview of their dysregulation, trying to establish the link between altered biological pathways and pathophysiological conditions. Copyright © 2016 Elsevier B.V. All rights reserved.

  14. Microbial metabolomics in open microscale platforms

    Science.gov (United States)

    Barkal, Layla J.; Theberge, Ashleigh B.; Guo, Chun-Jun; Spraker, Joe; Rappert, Lucas; Berthier, Jean; Brakke, Kenneth A.; Wang, Clay C. C.; Beebe, David J.; Keller, Nancy P.; Berthier, Erwin

    2016-01-01

    The microbial secondary metabolome encompasses great synthetic diversity, empowering microbes to tune their chemical responses to changing microenvironments. Traditional metabolomics methods are ill-equipped to probe a wide variety of environments or environmental dynamics. Here we introduce a class of microscale culture platforms to analyse chemical diversity of fungal and bacterial secondary metabolomes. By leveraging stable biphasic interfaces to integrate microculture with small molecule isolation via liquid–liquid extraction, we enable metabolomics-scale analysis using mass spectrometry. This platform facilitates exploration of culture microenvironments (including rare media typically inaccessible using established methods), unusual organic solvents for metabolite isolation and microbial mutants. Utilizing Aspergillus, a fungal genus known for its rich secondary metabolism, we characterize the effects of culture geometry and growth matrix on secondary metabolism, highlighting the potential use of microscale systems to unlock unknown or cryptic secondary metabolites for natural products discovery. Finally, we demonstrate the potential for this class of microfluidic systems to study interkingdom communication between fungi and bacteria. PMID:26842393

  15. Exploring the analysis of structured metabolomics data

    NARCIS (Netherlands)

    Verouden, M.P.H.; Westerhuis, J.A.; van der Werf, M.J.; Smilde, A.K.

    2009-01-01

    In metabolomics research a large number of metabolites are measured that reflect the cellular state under the experimental conditions studied. In many occasions the experiments are performed according to an experimental design to make sure that sufficient variation is induced in the metabolite

  16. Analysis of metabolomics data from twin families

    NARCIS (Netherlands)

    Draisma, Hermanus Henricus Maria

    2011-01-01

    Metabolomics is the comprehensive analysis of small molecules involved in metabolism, on the basis of samples that have been obtained from organisms in a given physiological state. Data obtained from measurements of trait levels in twin families can be used to elucidate the importance of genetic and

  17. Data-processing strategies for metabolomics studies

    NARCIS (Netherlands)

    Hendriks, M.M.W.B.; Eeuwijk, van F.A.; Jellema, R.H.; Westerhuis, J.A.; Reijmers, T.H.; Hoefsloot, H.C.J.; Smilde, A.K.

    2011-01-01

    Metabolomics studies aim at a better understanding of biochemical processes by studying relations between metabolites and between metabolites and other types of information (e.g., sensory and phenotypic features). The objectives of these studies are diverse, but the types of data generated and the

  18. Protein buffering in model systems and in whole human saliva.

    Directory of Open Access Journals (Sweden)

    Andreas Lamanda

    Full Text Available The aim of this study was to quantify the buffer attributes (value, power, range and optimum of two model systems for whole human resting saliva, the purified proteins from whole human resting saliva and single proteins. Two model systems, the first containing amyloglucosidase and lysozyme, and the second containing amyloglucosidase and alpha-amylase, were shown to provide, in combination with hydrogencarbonate and di-hydrogenphosphate, almost identical buffer attributes as whole human resting saliva. It was further demonstrated that changes in the protein concentration as small as 0.1% may change the buffer value of a buffer solution up to 15 times. Additionally, it was shown that there was a protein concentration change in the same range (0.16% between saliva samples collected at the time periods of 13:00 and others collected at 9:00 am and 17:00. The mode of the protein expression changed between these samples corresponded to the change in basic buffer power and the change of the buffer value at pH 6.7. Finally, SDS Page and Ruthenium II tris (bathophenantroline disulfonate staining unveiled a constant protein expression in all samples except for one 50 kDa protein band. As the change in the expression pattern of that 50 kDa protein band corresponded to the change in basic buffer power and the buffer value at pH 6.7, it was reasonable to conclude that this 50 kDa protein band may contain the protein(s belonging to the protein buffer system of human saliva.

  19. Observations on saliva osmolality during progressive dehydration and partial rehydration.

    Science.gov (United States)

    Taylor, Nigel A S; van den Heuvel, Anne M J; Kerry, Pete; McGhee, Sheena; Peoples, Gregory E; Brown, Marc A; Patterson, Mark J

    2012-09-01

    A need exists to identify dehydrated individuals under stressful settings beyond the laboratory. A predictive index based on changes in saliva osmolality has been proposed, and its efficacy and sensitivity was appraised across mass (water) losses from 1 to 7%. Twelve euhydrated males [serum osmolality: 286.1 mOsm kg(-1) H(2)O (SD 4.3)] completed three exercise- and heat-induced dehydration trials (35.6°C, 56% relative humidity): 7% dehydration (6.15 h), 3% dehydration (with 60% fluid replacement: 2.37 h), repeat 7% dehydration (5.27 h). Expectorated saliva osmolality, measured at baseline and at each 1% mass change, was used to predict instantaneous hydration state relative to mass losses of 3 and 6%. Saliva osmolality increased linearly with dehydration, although its basal osmolality and its rate of change varied among and within subjects across trials. Receiver operating characteristic curves indicated a good predictive power for saliva osmolality when used with two, single-threshold cutoffs to differentiate between hydrated and dehydrated individuals (area under curve: 3% cutoff = 0.868, 6% cutoff = 0.831). However, when analysed using a double-threshold detection technique (3 and 6%), as might be used in a field-based monitor, <50% of the osmolality data could correctly identify individuals who exceeded 3% dehydration. Indeed, within the 3-6% dehydration range, its sensitivity was 64%, while beyond 6% dehydration, this fell to 42%. Therefore, while expectorated saliva osmolality tracked mass losses within individuals, its large intra- and inter-individual variability limited its predictive power and sensitivity, rendering its utility questionable within a universal dehydration monitor.

  20. Effect of endurance training on dental erosion, caries, and saliva.

    Science.gov (United States)

    Frese, C; Frese, F; Kuhlmann, S; Saure, D; Reljic, D; Staehle, H J; Wolff, D

    2015-06-01

    The aim of this investigation was to give insights into the impact of endurance training on oral health, with regard to tooth erosion, caries, and salivary parameters. The study included 35 triathletes and 35 non-exercising controls. The clinical investigation comprised oral examination, assessment of oral status with special regard to caries and erosion, saliva testing during inactivity, and a self-administered questionnaire about eating, drinking, and oral hygiene behavior. In addition, athletes were asked about their training habits and intake of beverages and sports nutrition. For saliva assessment during exercise, a subsample of n = 15 athletes volunteered in an incremental running field test (IRFT). Athletes showed an increased risk for dental erosion (P = 0.001). No differences were observed with regard to caries prevalence and salivary parameters measured during inactivity between athletes and controls. Among athletes, a significant correlation was found between caries prevalence and the cumulative weekly training time (r = 0.347, P = 0.04). In athletes after IRFT and at maximum workload, saliva flow rates decreased (P = 0.001 stimulated; P = 0.01 unstimulated) and saliva pH increased significantly (P = 0.003). Higher risk for dental erosions, exercise-dependent caries risk, and load-dependent changes in saliva parameters point out the need for risk-adapted preventive dental concepts in the field of sports dentistry. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  1. Quantitative metabolomics based on gas chromatography mass spectrometry: Status and perspectives

    NARCIS (Netherlands)

    Koek, M.M.; Jellema, R.H.; Greef, J. van der; Tas, A.C.; Hankemeier, T.

    2011-01-01

    Metabolomics involves the unbiased quantitative and qualitative analysis of the complete set of metabolites present in cells, body fluids and tissues (the metabolome). By analyzing differences between metabolomes using biostatistics (multivariate data analysis; pattern recognition), metabolites

  2. "Polymeromics": Mass spectrometry based strategies in polymer science toward complete sequencing approaches: a review.

    Science.gov (United States)

    Altuntaş, Esra; Schubert, Ulrich S

    2014-01-15

    Mass spectrometry (MS) is the most versatile and comprehensive method in "OMICS" sciences (i.e. in proteomics, genomics, metabolomics and lipidomics). The applications of MS and tandem MS (MS/MS or MS(n)) provide sequence information of the full complement of biological samples in order to understand the importance of the sequences on their precise and specific functions. Nowadays, the control of polymer sequences and their accurate characterization is one of the significant challenges of current polymer science. Therefore, a similar approach can be very beneficial for characterizing and understanding the complex structures of synthetic macromolecules. MS-based strategies allow a relatively precise examination of polymeric structures (e.g. their molar mass distributions, monomer units, side chain substituents, end-group functionalities, and copolymer compositions). Moreover, tandem MS offer accurate structural information from intricate macromolecular structures; however, it produces vast amount of data to interpret. In "OMICS" sciences, the software application to interpret the obtained data has developed satisfyingly (e.g. in proteomics), because it is not possible to handle the amount of data acquired via (tandem) MS studies on the biological samples manually. It can be expected that special software tools will improve the interpretation of (tandem) MS output from the investigations of synthetic polymers as well. Eventually, the MS/MS field will also open up for polymer scientists who are not MS-specialists. In this review, we dissect the overall framework of the MS and MS/MS analysis of synthetic polymers into its key components. We discuss the fundamentals of polymer analyses as well as recent advances in the areas of tandem mass spectrometry, software developments, and the overall future perspectives on the way to polymer sequencing, one of the last Holy Grail in polymer science. Copyright © 2013 Elsevier B.V. All rights reserved.

  3. Characterisation of the metabolome of ocular tissues and post-mortem changes in the rat retina.

    Science.gov (United States)

    Tan, Shi Z; Mullard, Graham; Hollywood, Katherine A; Dunn, Warwick B; Bishop, Paul N

    2016-08-01

    Time-dependent post-mortem biochemical changes have been demonstrated in donor cornea and vitreous, but there have been no published studies to date that objectively measure post-mortem changes in the retinal metabolome over time. The aim of the study was firstly, to investigate post-mortem, time-dependent changes in the rat retinal metabolome and secondly, to compare the metabolite composition of healthy rat ocular tissues. To study post-mortem changes in the rat retinal metabolome, globes were enucleated and stored at 4 °C and sampled at 0, 2, 4, 8, 24 and 48 h post-mortem. To study the metabolite composition of rat ocular tissues, eyes were dissected immediately after culling to isolate the cornea, lens, vitreous and retina, prior to storing at -80 °C. Tissue extracts were subjected to Gas Chromatograph Mass Spectrometry (GC-MS) and Ultra High Performance Liquid Chromatography Mass Spectrometry (UHPLC-MS). Generally, the metabolic composition of the retina was stable for 8 h post-mortem when eyes were stored at 4 °C, but showed increasing changes thereafter. However, some more rapid changes were observed such as increases in TCA cycle metabolites after 2 h post-mortem, whereas some metabolites such as fatty acids only showed decreases in concentration from 24 h. A total of 42 metabolites were identified across the ocular tissues by GC-MS (MSI level 1) and 2782 metabolites were annotated by UHPLC-MS (MSI level 2) according to MSI reporting standards. Many of the metabolites detected were common to all of the tissues but some metabolites showed partitioning between different ocular structures with 655, 297, 93 and 13 metabolites being uniquely detected in the retina, lens, cornea and vitreous respectively. Only a small percentage (1.6%) of metabolites found in the vitreous were only detected in the retina and not other tissues. In conclusion, mass spectrometry-based techniques have been used for the first time to compare the metabolic composition of

  4. Hierarchical cluster analysis of technical replicates to identify interferents in untargeted mass spectrometry metabolomics.

    Science.gov (United States)

    Caesar, Lindsay K; Kvalheim, Olav M; Cech, Nadja B

    2018-08-27

    all data sets. This work highlights the importance of technical replication in mass spectrometry-based studies, and presents a new application of HCA as a tool for evaluating the effectiveness of data filtering prior to statistical analysis. Copyright © 2018 Elsevier B.V. All rights reserved.

  5. Metabolomics of Clostridial Biofuel Production

    Energy Technology Data Exchange (ETDEWEB)

    Rabinowitz, Joshua D [Princeton Univ., NJ (United States); Aristilde, Ludmilla [Cornell Univ., Ithaca, NY (United States); Amador-Noguez, Daniel [Univ. of Wisconsin, Madison, WI (United States)

    2015-09-08

    Members of the genus Clostridium collectively have the ideal set of the metabolic capabilities for fermentative biofuel production: cellulose degradation, hydrogen production, and solvent excretion. No single organism, however, can effectively convert cellulose into biofuels. Here we developed, using metabolomics and isotope tracers, basic science knowledge of Clostridial metabolism of utility for future efforts to engineer such an organism. In glucose fermentation carried out by the biofuel producer Clostridium acetobutylicum, we observed a remarkably ordered series of metabolite concentration changes as the fermentation progressed from acidogenesis to solventogenesis. In general, high-energy compounds decreased while low-energy species increased during solventogenesis. These changes in metabolite concentrations were accompanied by large changes in intracellular metabolic fluxes, with pyruvate directed towards acetyl-CoA and solvents instead of oxaloacetate and amino acids. Thus, the solventogenic transition involves global remodeling of metabolism to redirect resources from biomass production into solvent production. In contrast to C. acetobutylicum, which is an avid fermenter, C. cellulolyticum metabolizes glucose only slowly. We find that glycolytic intermediate concentrations are radically different from fast fermenting organisms. Associated thermodynamic and isotope tracer analysis revealed that the full glycolytic pathway in C. cellulolyticum is reversible. This arises from changes in cofactor utilization for phosphofructokinase and an alternative pathway from phosphoenolpyruvate to pyruvate. The net effect is to increase the high-energy phosphate bond yield of glycolysis by 150% (from 2 to 5) at the expense of lower net flux. Thus, C. cellulolyticum prioritizes glycolytic energy efficiency over speed. Degradation of cellulose results in other sugars in addition to glucose. Simultaneous feeding of stable isotope-labeled glucose and unlabeled pentose sugars

  6. Software Tools and Approaches for Compound Identification of LC-MS/MS Data in Metabolomics

    Directory of Open Access Journals (Sweden)

    Ivana Blaženović

    2018-05-01

    Full Text Available The annotation of small molecules remains a major challenge in untargeted mass spectrometry-based metabolomics. We here critically discuss structured elucidation approaches and software that are designed to help during the annotation of unknown compounds. Only by elucidating unknown metabolites first is it possible to biologically interpret complex systems, to map compounds to pathways and to create reliable predictive metabolic models for translational and clinical research. These strategies include the construction and quality of tandem mass spectral databases such as the coalition of MassBank repositories and investigations of MS/MS matching confidence. We present in silico fragmentation tools such as MS-FINDER, CFM-ID, MetFrag, ChemDistiller and CSI:FingerID that can annotate compounds from existing structure databases and that have been used in the CASMI (critical assessment of small molecule identification contests. Furthermore, the use of retention time models from liquid chromatography and the utility of collision cross-section modelling from ion mobility experiments are covered. Workflows and published examples of successfully annotated unknown compounds are included.

  7. Binary similarity measures for fingerprint analysis of qualitative metabolomic profiles.

    Science.gov (United States)

    Rácz, Anita; Andrić, Filip; Bajusz, Dávid; Héberger, Károly

    2018-01-01

    Contemporary metabolomic fingerprinting is based on multiple spectrometric and chromatographic signals, used either alone or combined with structural and chemical information of metabolic markers at the qualitative and semiquantitative level. However, signal shifting, convolution, and matrix effects may compromise metabolomic patterns. Recent increase in the use of qualitative metabolomic data, described by the presence (1) or absence (0) of particular metabolites, demonstrates great potential in the field of metabolomic profiling and fingerprint analysis. The aim of this study is a comprehensive evaluation of binary similarity measures for the elucidation of patterns among samples of different botanical origin and various metabolomic profiles. Nine qualitative metabolomic data sets covering a wide range of natural products and metabolomic profiles were applied to assess 44 binary similarity measures for the fingerprinting of plant extracts and natural products. The measures were analyzed by the novel sum of ranking differences method (SRD), searching for the most promising candidates. Baroni-Urbani-Buser (BUB) and Hawkins-Dotson (HD) similarity coefficients were selected as the best measures by SRD and analysis of variance (ANOVA), while Dice (Di1), Yule, Russel-Rao, and Consonni-Todeschini 3 ranked the worst. ANOVA revealed that concordantly and intermediately symmetric similarity coefficients are better candidates for metabolomic fingerprinting than the asymmetric and correlation based ones. The fingerprint analysis based on the BUB and HD coefficients and qualitative metabolomic data performed equally well as the quantitative metabolomic profile analysis. Fingerprint analysis based on the qualitative metabolomic profiles and binary similarity measures proved to be a reliable way in finding the same/similar patterns in metabolomic data as that extracted from quantitative data.

  8. Bacterial profiles of saliva in relation to diet, lifestyle factors, and socioeconomic status

    DEFF Research Database (Denmark)

    Belstrøm, Daniel; Holmstrup, Palle; Nielsen, Claus H

    2014-01-01

    BACKGROUND AND OBJECTIVE: The bacterial profile of saliva is composed of bacteria from different oral surfaces. The objective of this study was to determine whether different diet intake, lifestyle, or socioeconomic status is associated with characteristic bacterial saliva profiles. DESIGN: Stimu...... of saliva. CONCLUSIONS: The bacterial profile of saliva seems independent of diet intake, but influenced by smoking and maybe socioeconomic status.......BACKGROUND AND OBJECTIVE: The bacterial profile of saliva is composed of bacteria from different oral surfaces. The objective of this study was to determine whether different diet intake, lifestyle, or socioeconomic status is associated with characteristic bacterial saliva profiles. DESIGN...... presence and levels (mean HOMIM-value) of bacterial probes as endpoints, the influence of diet intake, lifestyle, and socioeconomic status on the bacterial saliva profile was analyzed by Mann-Whitney tests with Benjamini-Hochberg's correction for multiple comparisons and principal component analysis...

  9. The caries environment: saliva, pellicle, diet, and hard tissue ultrastructure.

    Science.gov (United States)

    Hara, Anderson T; Zero, Domenick T

    2010-07-01

    The pathogenicity of the dental biofilm is modified by salivary and dietary factors, as well as by the characteristics of the tooth structure. The composition of the acquired pellicle can modify the mineral homeostasis of the tooth surfaces and the attachment of bacteria for the development of the biofilm. The substitution of sucrose from the diet by other less cariogenic sugars and/or sugar substitutes can contribute to reducing the pathogenicity of the biofilm. Saliva clears, dilutes, neutralizes, and buffers acids produced by the biofilm. In addition, saliva provides the biofilm/tooth structure with Ca(2+) PO(4)(3-) and F(-) ions, which can positively affect the equilibrium between demineralization-remineralization toward the remineralization and modify the susceptibility of the tooth structure to caries progression. Copyright 2010 Elsevier Inc. All rights reserved.

  10. Investigation of saliva of patients with periodontal disease using NAA

    Energy Technology Data Exchange (ETDEWEB)

    Zamboni, C. B.; Metairon, S.; Medeiros, I. M. M. A. [Instituto de Pesquisas Energeticas e Nucleares, IPEN - CNEN/SP Av. Professor Lineu Prestes 2242- 05508-000 Sao Paulo, SP (Brazil); Lewgoy, H. R. [Universidade Anhanguera Bandeirante, UNIBAN R. Maria Candida, 1813, Bloco G / 6o andar - 02071-013 Sao Paulo, SP (Brazil)

    2013-05-06

    In this study the non-stimulated whole saliva of 26 healthy subjects (mean age 33.9 {+-} 11.0 years, range: 26 to 49 years) and 11 patients with periodontal disease (mean age 41.7 {+-} 11.5 years; range 29 to 55 years) was investigated using Neutron Activation Analysis (NAA) technique. The samples were obtained from donors at Sao Paulo city (Brazil). The analyses were performed in the nuclear reactor IEA-R1 (3.5-4.5MW, pool type) at IPEN/CNEN-SP (Brazil). Considerable changes in Ca and S saliva's level were identified in patients with periodontal disease suggesting they can be used as monitors of periodontal diseases.

  11. Biochemical modifications of human whole saliva induced by pregnancy.

    Science.gov (United States)

    Salvolini, E; Di Giorgio, R; Curatola, A; Mazzanti, L; Fratto, G

    1998-06-01

    To assess human unstimulated whole saliva components during pregnancy, to determine the relation, if any, between pregnancy and oral health, particularly total protein concentration, alpha-amylase activity, sialic acid content and calcium and phosphate concentrations were evaluated. Cross-sectional study. Forty-five healthy primigravid women; 15 nonpregnant women acted as controls. 1. A higher total protein content at 10 and 21 weeks of gestation with respect to the controls and to pregnant women at 40 weeks; 2. a higher alpha-amylase activity at 10 and 21 weeks of gestation compared with the controls and to pregnant women at 40 weeks; 3. an increased sialic acid content at 21 and 40 weeks; 4. decreased calcium and phosphorus concentrations at 21 and 40 weeks of gestation. Pregnancy modifies saliva composition. This could play a pivotal role in the incidence of pregnancy-induced dental caries.

  12. The Effect of Canal Contamination with Saliva on Apical Sealing

    Directory of Open Access Journals (Sweden)

    S Sabaghi

    2014-08-01

    Methods: In this laboratory study, 58 human uni-root teeth were cleaned and shaped for obturation with gutta percha and sealer AH26. In the case group, specimens were contaminated with human saliva immediately before obturation, whereas the teeth in the control group were kept dry. All canals were filled by lateral condensation technique. Moreover, the teeth were placed in methylene blue dye for 3 days. Dye penetration was measured using a stereomicrosope. As a matter of fact, the study data were analyzed via utilizing t-test. Results: A significant difference was found between the two groups in regard with the apical leakage(P<0.001. The microleakage mean of dye in the dry group was 3/48mm, whereas it was 6/36mm in the saliva contaminated group. Conclusion: The study findings revealed that complete drying of canal can improve apical sealing.

  13. Aedes aegypti D7 Saliva Protein Inhibits Dengue Virus Infection.

    Directory of Open Access Journals (Sweden)

    Michael J Conway

    2016-09-01

    Full Text Available Aedes aegypti is the primary vector of several medically relevant arboviruses including dengue virus (DENV types 1-4. Ae. aegypti transmits DENV by inoculating virus-infected saliva into host skin during probing and feeding. Ae. aegypti saliva contains over one hundred unique proteins and these proteins have diverse functions, including facilitating blood feeding. Previously, we showed that Ae. aegypti salivary gland extracts (SGEs enhanced dissemination of DENV to draining lymph nodes. In contrast, HPLC-fractionation revealed that some SGE components inhibited infection. Here, we show that D7 proteins are enriched in HPLC fractions that are inhibitory to DENV infection, and that recombinant D7 protein can inhibit DENV infection in vitro and in vivo. Further, binding assays indicate that D7 protein can directly interact with DENV virions and recombinant DENV envelope protein. These data reveal a novel role for D7 proteins, which inhibits arbovirus transmission to vertebrates through a direct interaction with virions.

  14. Investigation of saliva of patients with periodontal disease using NAA

    Science.gov (United States)

    Zamboni, C. B.; Metairon, S.; Medeiros, I. M. M. A.; Lewgoy, H. R.

    2013-05-01

    In this study the non-stimulated whole saliva of 26 healthy subjects (mean age 33.9 ± 11.0 years, range: 26 to 49 years) and 11 patients with periodontal disease (mean age 41.7 ± 11.5 years; range 29 to 55 years) was investigated using Neutron Activation Analysis (NAA) technique. The samples were obtained from donors at São Paulo city (Brazil). The analyses were performed in the nuclear reactor IEA-R1 (3.5-4.5MW, pool type) at IPEN/CNEN-SP (Brazil). Considerable changes in Ca and S saliva's level were identified in patients with periodontal disease suggesting they can be used as monitors of periodontal diseases.

  15. Investigation of saliva of patients with periodontal disease using NAA

    International Nuclear Information System (INIS)

    Zamboni, C. B.; Metairon, S.; Medeiros, I. M. M. A.; Lewgoy, H. R.

    2013-01-01

    In this study the non-stimulated whole saliva of 26 healthy subjects (mean age 33.9 ± 11.0 years, range: 26 to 49 years) and 11 patients with periodontal disease (mean age 41.7 ± 11.5 years; range 29 to 55 years) was investigated using Neutron Activation Analysis (NAA) technique. The samples were obtained from donors at São Paulo city (Brazil). The analyses were performed in the nuclear reactor IEA-R1 (3.5-4.5MW, pool type) at IPEN/CNEN-SP (Brazil). Considerable changes in Ca and S saliva's level were identified in patients with periodontal disease suggesting they can be used as monitors of periodontal diseases.

  16. Amperometric micro pH measurements in oxygenated saliva.

    Science.gov (United States)

    Chaisiwamongkhol, Korbua; Batchelor-McAuley, Christopher; Compton, Richard G

    2017-07-24

    An amperometric micro pH sensor has been developed based on the chemical oxidation of carbon fibre surfaces (diameter of 9 μm and length of ca. 1 mm) to enhance the population of surface quinone groups for the measurement of salivary pH. The pH analysis utilises the electrochemically reversible two-electron, two-proton behaviour of surface quinone groups on the micro-wire electrodes. A Nernstian response is observed across the pH range 2-8 which is the pH range of many biological fluids. We highlight the measurement of pH in small volumes of biological fluids without the need for oxygen removal and specifically the micro pH electrode is examined by measuring the pH of commercial synthetic saliva and authentic human saliva samples. The results correspond well with those obtained by using commercial glass pH electrodes on large volume samples.

  17. Shear bond strength of metallic brackets: influence of saliva contamination

    Directory of Open Access Journals (Sweden)

    Luciana Borges Retamoso

    2009-06-01

    Full Text Available OBJECTIVE: To evaluate the influence of saliva contamination on shear bond strength and the bond failure pattern of 3 adhesive systems (Transbond XT, AdheSE and Xeno III on orthodontic metallic brackets bonded to human enamel. MATERIAL AND METHODS: Seventy-two permanent human molars were cut longitudinally in a mesiodistal direction, producing seventy-two specimens randomly divided into six groups. Each system was tested under 2 different enamel conditions: no contamination and contaminated with saliva. In T, A and X groups, the adhesive systems were applied to the enamel surface in accordance with manufacturer's instructions. In TS, AS and XS groups, saliva was applied to enamel surface followed by adhesive system application. The samples were stored in distilled water at 37ºC for 24 h, and then tested for shear bond strength in a universal testing machine (Emic, DL 2000 running at a crosshead speed of 1 mm/min. After bond failure, the enamel surfaces were observed under an optical microscope at 40x magnification. RESULTS: The control and contaminated groups showed no significant difference in shear bond strength for the same adhesive system. However, shear bond strength of T group (17.03±4.91 was significantly higher than that of AS (8.58±1.73 and XS (10.39±4.06 groups (p<0.05. Regarding the bond failure pattern, TS group had significantly higher scores of no adhesive remaining on the tooth in the bonding area than other groups considering the adhesive remnant index (ARI used to evaluate the amount of adhesive left on the enamel. CONCLUSIONS: Saliva contamination showed little influence on the 24-h shear bond strength of orthodontic brackets.

  18. The effect of saliva on the fate of nanoparticles.

    Science.gov (United States)

    Teubl, Birgit J; Stojkovic, Biljana; Docter, Dominic; Pritz, Elisabeth; Leitinger, Gerd; Poberaj, Igor; Prassl, Ruth; Stauber, Roland H; Fröhlich, Eleonore; Khinast, Johannes G; Roblegg, Eva

    2018-03-01

    The design of nanocarriers for local drug administration to the lining mucosa requires a sound knowledge of how nanoparticles (NPs) interact with saliva. This contact determines whether NPs agglomerate and become immobile due to size- and interaction-filtering effects or adsorb on the cell surface and are internalized by epithelial cells. The aim of this study was to examine the behavior of NPs in saliva considering physicochemical NP properties. The salivary pore-size distribution was determined, and the viscosity of the fluid inside of the pores was studied with optical tweezers. Distinct functionalized NPs (20 and 200 nm) were dispersed in saliva and salivary buffers and characterized, and surface-bound MUC5B and MUC7 were analyzed by 1D electrophoresis and immunoblotting. NP mobility was recorded, and cellular uptake studies were performed with TR146 cells. The mode diameter of the salivary mesh pores is 0.7 μm with a peak width of 1.9 μm, and pores are filled with a low-viscosity fluid. The physicochemical properties of the NPs affected the colloidal stability and mobility: compared with non-functionalized particles, which did not agglomerate and showed a cellular uptake rate of 2.8%, functionalized particles were immobilized, which was correlated with agglomeration and increased binding to mucins. The present study showed that the salivary microstructure facilitates NP adsorption. However, NP size and surface functionalization determine the colloidal stability and cellular interactions. The sound knowledge of NP interactions with saliva enables the improvement of current treatment strategies for inflammatory oral diseases.

  19. A novel one-step Helicobacter pylori saliva antigen test

    Directory of Open Access Journals (Sweden)

    Bi-Ling Yang

    2015-02-01

    Conclusion: The one-step HPS test exhibited a high sensitivity and low specificity compared with the other tests, indicating that it is not sufficiently accurate for use in a clinical setting for diagnosing H. pylori infection. However, the test is simple to use (requiring only a saliva sample, inexpensive, and noninvasive in its application, and thus appealing for use in population-based prevalence surveys of the epidemiology of H. pylori infection.

  20. Candida na saliva de pacientes hemofílicos brasileiros

    OpenAIRE

    Pereira, Claudio Maranhão; Pires, Fábio Ramôa; Corrêa, Maria Elvira Pizzigatti; di Hipólito Júnior, Osvaldo; Almeida, Oslei Paes de

    2004-01-01

    Hemophilia is a common hereditary hemorrhagic disorder, however little is known about the oral microflora of hemophilic patients. The aim of this study was to quantify the Candida and identify its species in non-stimulated saliva of hemophilic patients, and consider its relationship with clinical factors influencing Candida carriage. This study comprised evaluation of 86 hemophilic patients of the Hematology Center/UNICAMP and 43 healthy subjects as controls. All patients were submitted to an...

  1. Recommendations and Standardization of Biomarker Quantification Using NMR-based Metabolomics with Particular Focus on Urinary Analysis

    KAUST Repository

    Emwas, Abdul-Hamid M.

    2016-01-08

    NMR-based metabolomics has shown considerable promise in disease diagnosis and biomarker discovery because it allows one to non-destructively identify and quantify large numbers of novel metabolite biomarkers in both biofluids and tissues. Indeed, precise metabolite quantification is a necessary prerequisite to move any chemical biomarker or biomarker panel from the lab into the clinic. Among the many biofluids (urine, serum, plasma, cerebrospinal fluid and saliva) commonly used for disease diagnosis and prognosis, urine has several advantages. It is abundant, sterile, easily obtained, needs little sample preparation and does not require any invasive medical procedures for collection. Furthermore, urine captures and concentrates many “unwanted” or “undesirable” compounds throughout the body, thereby providing a rich source of potentially useful disease biomarkers. However, the incredible variation in urine chemical concentrations due to effects such as gender, age, diet, life style, health conditions, and physical activity make the analysis of urine and the identification of useful urinary biomarkers by NMR quite challenging. In this review, we discuss a number of the most significant issues regarding NMR-based urinary metabolomics with a specific emphasis on metabolite quantification for disease biomarker applications. We also propose a number of data collection and instrumental recommendations regarding NMR pulse sequences, acceptable acquisition parameter ranges, relaxation effects on quantitation, proper handling of instrumental differences, as well as recommendations regarding sample preparation and biomarker assessment.

  2. Recommendations and Standardization of Biomarker Quantification Using NMR-based Metabolomics with Particular Focus on Urinary Analysis

    KAUST Repository

    Emwas, Abdul-Hamid M.; Roy, Raja; McKay, Ryan T.; Ryan, Danielle; Brennan, Lorraine; Tenori, Leonardo; Luchinat, Claudio; Gao, Xin; Zeri, Ana Carolina; Gowda, G. A. Nagana; Raftery, Daniel; Steinbeck, Christoph; Salek, Reza M; Wishart, David S.

    2016-01-01

    NMR-based metabolomics has shown considerable promise in disease diagnosis and biomarker discovery because it allows one to non-destructively identify and quantify large numbers of novel metabolite biomarkers in both biofluids and tissues. Indeed, precise metabolite quantification is a necessary prerequisite to move any chemical biomarker or biomarker panel from the lab into the clinic. Among the many biofluids (urine, serum, plasma, cerebrospinal fluid and saliva) commonly used for disease diagnosis and prognosis, urine has several advantages. It is abundant, sterile, easily obtained, needs little sample preparation and does not require any invasive medical procedures for collection. Furthermore, urine captures and concentrates many “unwanted” or “undesirable” compounds throughout the body, thereby providing a rich source of potentially useful disease biomarkers. However, the incredible variation in urine chemical concentrations due to effects such as gender, age, diet, life style, health conditions, and physical activity make the analysis of urine and the identification of useful urinary biomarkers by NMR quite challenging. In this review, we discuss a number of the most significant issues regarding NMR-based urinary metabolomics with a specific emphasis on metabolite quantification for disease biomarker applications. We also propose a number of data collection and instrumental recommendations regarding NMR pulse sequences, acceptable acquisition parameter ranges, relaxation effects on quantitation, proper handling of instrumental differences, as well as recommendations regarding sample preparation and biomarker assessment.

  3. Levels of saliva cotinine in electronic cigarette users.

    Science.gov (United States)

    Etter, Jean-François

    2014-05-01

    To assess saliva cotinine levels in experienced users of e-cigarettes ('vapers'). An internet survey in 2011 and 2012, with collection of saliva vials by mail. Participants were 71 users of e-cigarettes enrolled mainly on websites and online forums dedicated to e-cigarettes. Use of e-cigarettes, tobacco and nicotine medications. Collection of saliva by mail and analysis of cotinine by liquid chromatography-mass spectrometry. Most participants (89%) were former smokers, most (92%) were using e-cigarettes daily, had been using e-cigarettes for 12 months on average and puffed a median of 150 times per day on their e-cigarettes [mean = 220 puffs/day, 95% confidence interval (CI) = 169-271]. The median concentration of nicotine in refill liquids was 16 mg/ml (mean = 16.4, 95% CI = 14.5-18.3). In the 62 e-cigarette users who, in the past 5 days, had not used any tobacco or nicotine medications, the median cotinine level was 353 ng/ml (mean = 374, 95% CI = 318-429), the correlation between cotinine and nicotine concentration in e-liquids was r = 0.33 (P = 0.013), and the correlation between cotinine and the number of cigarettes smoked per day before quitting smoking was r = 0.48 (P Addiction.

  4. The Effect of Canal Contamination with Saliva on Apical Sealing

    Directory of Open Access Journals (Sweden)

    S Sabaghi

    2014-08-01

    Full Text Available Introduction: Root canal obturation aims at sealing the root canal system to prevent re-contamination of canal and periapical space. Presence of moisture in canal before obturation may posit a negative effect on the quality of canal sealing. Therefore, this study was conducted to investigate the effect of canal contamination with saliva on apical microleakage. Methods: In this laboratory study, 58 human uni-root teeth were cleaned and shaped for obturation with gutta percha and sealer AH26. In the case group, specimens were contaminated with human saliva immediately before obturation, whereas the teeth in the control group were kept dry. All canals were filled by lateral condensation technique. Moreover, the teeth were placed in methylene blue dye for 3 days. Dye penetration was measured using a stereomicrosope. As a matter of fact, the study data were analyzed via utilizing t-test. Results: A significant difference was found between the two groups in regard with the apical leakage(P<0.001. The microleakage mean of dye in the dry group was 3/48mm, whereas it was 6/36mm in the saliva contaminated group. Conclusion: The study findings revealed that complete drying of canal can improve apical sealing.

  5. Selected antibacterial factors in the saliva of diabetic patients.

    Science.gov (United States)

    Malicka, Barbara; Kaczmarek, Urszula; Skośkiewicz-Malinowska, Katarzyna

    2015-03-01

    Diabetes mellitus leads to many systemic complications, including changes in the morphology, function of the salivary glands, and the composition of saliva. The study comprised a randomly selected 156 adults, of both genders, aged from 21 to 79, out of which patients with diabetes type 1 and 2, and healthy subjects forming two control age- and gender matched to the ill subjects. In unstimulated mixed saliva, total protein, peroxidase, myeloperoxidase and immunoglobulin A were measured as well as salivary flow rate. The periodontal condition was assessed with the use of GI, mSBI and PSR index. The obtained data were analysed with the use of U Mann-Whitney's test, Spearman's rang correlation and Chi-square test at a significant level of p diabetics in comparison to healthy age and gender matched control group had a lower salivary flow rate (p diabetics in comparison to control subjects had a higher level of total protein concentration (p diabetes type 1 and 2 can cause abnormalities in salivary glands function resulting in the diminishing of salivary flow rate and the increase in total protein content. Higher levels of myeloperoxidase and IgA in the saliva can be linked to worse periodontal condition in the diabetic patients. Copyright © 2014. Published by Elsevier Ltd.

  6. Fluorescence spectroscopy for throat cancer detection using human saliva

    Science.gov (United States)

    Kumar, Pavan; Singh, Ashutosh; Zaffar, Mohammad; Pradhan, Asima

    2018-02-01

    Throat precancer detection using fluorescence from human saliva is reported here. It may be noted that accessing the throat for investigation is cumbersome and use of saliva as a diagnostic medium may ease the process. The study has been conducted on three groups of patients: oral squamous cell carcinoma (OSCC), dysplasia, and normal (control). An in-house developed compact set-up has been used for fluorescence measurements. The compact system consist of a 375 nm laser diode, collimating lens, long pass filter, fibers, and cuvette holder. Major and minor bands of flavin adenine dinucleotide (FAD) and porphyrin are observed in the spectra. A receiver operating characteristic (ROC) analysis has been used to evaluate the diagnostic performance. Area under the spectra has been chosen for discrimination among the groups and is able to differentiate OSCC to normal, dysplasia to normal, and OSCC to dysplasia with sensitivities 100% (48/48), 92% (32/35), 77% (37/48), and specificities 96% (50/52), 96% (50/52), 89% (31/35) with the accuracy of 98%, 94% and 82% respectively. Sensitivity and specificity, when differentiating OSCC to normal and dysplasia to normal, are significantly large, which indicates that human saliva may be an excellent diagnostic medium for early detection of throat cancer.

  7. Tongue-mandible coupling movements during saliva swallowing.

    Science.gov (United States)

    Bourdiol, P; Mishellany-Dutour, A; Peyron, M-A; Woda, A

    2014-03-01

    The purpose of this study was to measure the tongue and mandible positions and displacements in relation to the maxilla in the midsagittal plane to characterize the different saliva swallowing patterns by recording their kinematics. A 2D electromagnetic articulograph using four transducer coils, three attached to the upper surface of the tongue midline plus one attached to the chin anterior part allowed continuous evaluation of tongue and chin movements in twelve young adults in good general health. During 170 s sequences recorded at a frequency of 100 Hz, subjects were at rest, silently reading a text they had chosen. The subjects were free to swallow during the sequence. Deglutition of accumulated saliva was analysed after averaging all values obtained during successive 250 ms periods. We identified three elementary swallowing patterns. Mean duration of tongue-mandible movements were 1·51 ± 0·17 s, 1·63 ± 0·14 s and 2·00 ± 0·08 s for the first, second and third patterns respectively. In the light of other studies based on intra-oral pressure recordings, our results help to understand the tongue-mandible coupling behaviours involved in managing an in-mouth saliva bolus during the three elementary swallowing patterns identified. © 2014 John Wiley & Sons Ltd.

  8. Metabolomic analysis of three Mollicute species.

    Directory of Open Access Journals (Sweden)

    Anna A Vanyushkina

    Full Text Available We present a systematic study of three bacterial species that belong to the class Mollicutes, the smallest and simplest bacteria, Spiroplasma melliferum, Mycoplasma gallisepticum, and Acholeplasma laidlawii. To understand the difference in the basic principles of metabolism regulation and adaptation to environmental conditions in the three species, we analyzed the metabolome of these bacteria. Metabolic pathways were reconstructed using the proteogenomic annotation data provided by our lab. The results of metabolome, proteome and genome profiling suggest a fundamental difference in the adaptation of the three closely related Mollicute species to stress conditions. As the transaldolase is not annotated in Mollicutes, we propose variants of the pentose phosphate pathway catalyzed by annotated enzymes for three species. For metabolite detection we employed high performance liquid chromatography coupled with mass spectrometry. We used liquid chromatography method - hydrophilic interaction chromatography with silica column - as it effectively separates highly polar cellular metabolites prior to their detection by mass spectrometer.

  9. Metabolomics for Quality and food security

    International Nuclear Information System (INIS)

    Diretto, Gianfranco

    2015-01-01

    By the term 'Metabolomics' means the discipline which allows you to determine the set of small molecules (metabolites) produced by an organism in a given time. The metabolomic analysis requires complex technological platforms that allow, in the first place, the separation (chromatography liquid or gaseous) of the different molecules and, subsequently, the identification of the same on the basis of characteristic ratio between their mass and charge (m / z). This study arises by estimates that, between climate change planned for the coming decades, there will also be quick increasing the concentration of Co2 in the atmosphere. In this context, it is essential to predict how these changes weather will impact on product quality plant at the base of our diet. [it

  10. Metabolomics Workbench: An international repository for metabolomics data and metadata, metabolite standards, protocols, tutorials and training, and analysis tools.

    Science.gov (United States)

    Sud, Manish; Fahy, Eoin; Cotter, Dawn; Azam, Kenan; Vadivelu, Ilango; Burant, Charles; Edison, Arthur; Fiehn, Oliver; Higashi, Richard; Nair, K Sreekumaran; Sumner, Susan; Subramaniam, Shankar

    2016-01-04

    The Metabolomics Workbench, available at www.metabolomicsworkbench.org, is a public repository for metabolomics metadata and experimental data spanning various species and experimental platforms, metabolite standards, metabolite structures, protocols, tutorials, and training material and other educational resources. It provides a computational platform to integrate, analyze, track, deposit and disseminate large volumes of heterogeneous data from a wide variety of metabolomics studies including mass spectrometry (MS) and nuclear magnetic resonance spectrometry (NMR) data spanning over 20 different species covering all the major taxonomic categories including humans and other mammals, plants, insects, invertebrates and microorganisms. Additionally, a number of protocols are provided for a range of metabolite classes, sample types, and both MS and NMR-based studies, along with a metabolite structure database. The metabolites characterized in the studies available on the Metabolomics Workbench are linked to chemical structures in the metabolite structure database to facilitate comparative analysis across studies. The Metabolomics Workbench, part of the data coordinating effort of the National Institute of Health (NIH) Common Fund's Metabolomics Program, provides data from the Common Fund's Metabolomics Resource Cores, metabolite standards, and analysis tools to the wider metabolomics community and seeks data depositions from metabolomics researchers across the world. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  11. Blood Transcriptomics and Metabolomics for Personalized Medicine

    Science.gov (United States)

    2015-10-31

    involved in rheumatoid arthritis . PLoS Comput Biol 2011;7. [100] Zhu J. Stitching together multiple data dimensions reveals interacting metabolomic...capability, detecting N10,000 metabo- lites, together with environmental exposure, dietary intake, microbial activity, and pharmaceutical drugs. Thus...research to clinical care has constantly seen huge disap- pointments. With the accumulation of detailed, information-rich data, human subjects start to

  12. Data fusion in metabolomic cancer diagnostics

    DEFF Research Database (Denmark)

    Bro, Rasmus; Nielsen, Hans Jørgen; Savorani, Francesco

    2013-01-01

    We have recently shown that fluorescence spectroscopy of plasma samples has promising abilities regarding early detection of colorectal cancer. In the present paper, these results were further developed by combining fluorescence with the biomarkers, CEA and TIMP-1 and traditional metabolomic meas...... measurements in the form of (1)H NMR spectroscopy. The results indicate that using an extensive profile established by combining such measurements together with the biomarkers is better than using single markers....

  13. Metabolomic Analysis in Brain Research: Opportunities & Challenges

    Directory of Open Access Journals (Sweden)

    Catherine G Vasilopoulou

    2016-05-01

    Full Text Available Metabolism being a fundamental part of molecular physiology, elucidating the structure and regulation of metabolic pathways is crucial for obtaining a comprehensive perspective of cellular function and understanding the underlying mechanisms of its dysfunction(s. Therefore, quantifying an accurate metabolic network activity map under various physiological conditions is among the major objectives of systems biology in the context of many biological applications. Especially for CNS, metabolic network activity analysis can substantially enhance our knowledge about the complex structure of the mammalian brain and the mechanisms of neurological disorders, leading to the design of effective therapeutic treatments. Metabolomics has emerged as the high-throughput quantitative analysis of the concentration profile of small molecular weight metabolites, which act as reactants and products in metabolic reactions and as regulatory molecules of proteins participating in many biological processes. Thus, the metabolic profile provides a metabolic activity fingerprint, through the simultaneous analysis of tens to hundreds of molecules of pathophysiological and pharmacological interest. The application of metabolomics is at its standardization phase in general, and the challenges for paving a standardized procedure are even more pronounced in brain studies. In this review, we support the value of metabolomics in brain research. Moreover, we demonstrate the challenges of designing and setting up a reliable brain metabolomic study, which, among other parameters, has to take into consideration the sex differentiation and the complexity of brain physiology manifested in its regional variation. We finally propose ways to overcome these challenges and design a study that produces reproducible and consistent results.

  14. PAMDB: a comprehensive Pseudomonas aeruginosa metabolome database.

    Science.gov (United States)

    Huang, Weiliang; Brewer, Luke K; Jones, Jace W; Nguyen, Angela T; Marcu, Ana; Wishart, David S; Oglesby-Sherrouse, Amanda G; Kane, Maureen A; Wilks, Angela

    2018-01-04

    The Pseudomonas aeruginosaMetabolome Database (PAMDB, http://pseudomonas.umaryland.edu) is a searchable, richly annotated metabolite database specific to P. aeruginosa. P. aeruginosa is a soil organism and significant opportunistic pathogen that adapts to its environment through a versatile energy metabolism network. Furthermore, P. aeruginosa is a model organism for the study of biofilm formation, quorum sensing, and bioremediation processes, each of which are dependent on unique pathways and metabolites. The PAMDB is modelled on the Escherichia coli (ECMDB), yeast (YMDB) and human (HMDB) metabolome databases and contains >4370 metabolites and 938 pathways with links to over 1260 genes and proteins. The database information was compiled from electronic databases, journal articles and mass spectrometry (MS) metabolomic data obtained in our laboratories. For each metabolite entered, we provide detailed compound descriptions, names and synonyms, structural and physiochemical information, nuclear magnetic resonance (NMR) and MS spectra, enzymes and pathway information, as well as gene and protein sequences. The database allows extensive searching via chemical names, structure and molecular weight, together with gene, protein and pathway relationships. The PAMBD and its future iterations will provide a valuable resource to biologists, natural product chemists and clinicians in identifying active compounds, potential biomarkers and clinical diagnostics. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  15. Integration of metabolomics data into metabolic networks.

    Science.gov (United States)

    Töpfer, Nadine; Kleessen, Sabrina; Nikoloski, Zoran

    2015-01-01

    Metabolite levels together with their corresponding metabolic fluxes are integrative outcomes of biochemical transformations and regulatory processes and they can be used to characterize the response of biological systems to genetic and/or environmental changes. However, while changes in transcript or to some extent protein levels can usually be traced back to one or several responsible genes, changes in fluxes and particularly changes in metabolite levels do not follow such rationale and are often the outcome of complex interactions of several components. The increasing quality and coverage of metabolomics technologies have fostered the development of computational approaches for integrating metabolic read-outs with large-scale models to predict the physiological state of a system. Constraint-based approaches, relying on the stoichiometry of the considered reactions, provide a modeling framework amenable to analyses of large-scale systems and to the integration of high-throughput data. Here we review the existing approaches that integrate metabolomics data in variants of constrained-based approaches to refine model reconstructions, to constrain flux predictions in metabolic models, and to relate network structural properties to metabolite levels. Finally, we discuss the challenges and perspectives in the developments of constraint-based modeling approaches driven by metabolomics data.

  16. Kontrasepsi Hormonal Meningkatkan Kadar α-Amylase Saliva

    Directory of Open Access Journals (Sweden)

    Juni Handajani

    2014-06-01

    Full Text Available Salivary α-amylase atau α-amylase saliva (SAA adalah salah satu enzim dalam saliva yang berperan penting pada inisiasi digesti karbohidrat dan fungsi interaksi bakteri. Kontrasepsi hormonal sangat populer di Indonesia untuk mencegah kehamilan. Penelitian ini bertujuan untuk mengetahui kadar SAA wanita pemakai kontrasepsi pil dan suntik. Subjek penelitian sebanyak 30 perempuan usia 20-35 tahun. Prosedur penelitian telah mendapat persetujuan dari Komite Etik Fakultas Kedokteran Universitas Gadjah Mada Yogyakarta. Subjek dibagi menjadi 3 kelompok (pemakai kontrasepsi pil, suntik, dan kontrol, masing-masing 10 perempuan. Kriteria subjek antara lain subjek sehat, tidak menggunakan alat ortodontik, protesa atau mahkota, serta menggunakan kontrasepsi hormonal lebih dari 3 bulan. Sampel saliva dikumpulkan pada sore hari (16.00-18.00 WIB selama 1 menit dengan metode tanpa stimulasi. Kadar tingkat SAA diukur menggunakan ELISA kit (Salimetrics LLC dengan Optical Density (OD pada 405 nm. Data dianalisis menggunakan ANOVA (p<0,05. Hasil penelitian menunjukkan kadar SAA tertinggi pada perempuan pemakai kontrasepsi  pil dan ada perbedaan yang signifikan diantara tiga kelompok. Disimpulkan bahwa kontrasepsi hormonal meningkatkan kadar SAA. Hormonal Contraceptive Increased The Level of Salivary Α-Amylase. Salivary α-amylase (SAA is one of the most important enzymes in saliva. This enzyme was mainly involved in the initiation of the digestion of starch in the oral cavity and has significant bacterial interactive function. Hormonal contraceptives are very popular in Indonesia to avoid pregnancy. This study aimed to evaluate the level of SAA in woman who taking pill and by injection contraceptives. Thirty women were in subjects, 20-35 years old, approval ethical clearance from Ethic Committee Medical Faculty of Gadjah Mada University, Yogyakarta Indonesia. Subjects were divided into three groups (taking pill contraceptive, by injection contraceptive and

  17. [Concentration of calcium ions in the saliva and the value of the pH of the saliva in female and male smokers].

    Science.gov (United States)

    Nakonieczna-Rudnicka, Marta; Bachanek, Teresa; Rogowska, Wanda

    2009-01-01

    Dental decay is a pathological process of extrasomatic origin which leads to demineralization and proteolytic degradation of hard surfaces of a tooth susceptible to this disease. Saliva composition, including calcium ion concentration and its pH value, is of importance in the development of the carious process. Tobacco smoke contains toxic compounds which negatively influence oral health. The aim of the study was evaluation of the selected saliva components: protein concentration, Ca2+ concentration, pH value both in male and female smokers. The investigated group included 65 patients reporting for the treatment to the Department of Conservative Dentistry of Medical University in Lublin. In the investigated group male smokers constituted 15.38%, female smokers--20.00%, male nicotine abstinents 21.54% and female nicotine abstinent 43.08%. The study included both survey examinations of patients and biochemical examinations of the saliva. Mixed, non-stimulated saliva was used as a material for biochemical examinations. Ca2+ concentration and pH of the saliva were assayed with the use of Rapidlab 348 analyzer. Protein in the saliva was assayed with calorimetric method according to Lowry. Saliva was collected from smokers 10-120 minutes after smoking of several cigarettes. It was stated that Ca2+ and protein concentration as well as pH of the saliva were not correlated with sex and cigarette smoking or non-smoking.

  18. INFRARED STUDIES OF HUMAN SALIVA. IDENTIFICATION OF A FACTOR IN HUMAN SALIVA PRODUCING AN INFRARED ABSORBANCE MAXIMUM AT 4.9 MICRONS

    Science.gov (United States)

    An absorption maximum was observed at 4.9 microns in infrared spectra of human parotid saliva. The factor causing this absorbance was found to be a...nitrate, and heat stability. Thiocyanate was then determined in 16 parotid saliva samples by a spectrophotometric method, which involved formation of

  19. Characterization of the Activity and Stability of Amylase from Saliva and Detergent: Laboratory Practicals for Studying the Activity and Stability of Amylase from Saliva and Various Commercial Detergents

    Science.gov (United States)

    Valls, Cristina; Rojas, Cristina; Pujadas, Gerard; Garcia-Vallve, Santi; Mulero, Miquel

    2012-01-01

    This article presents two integrated laboratory exercises intended to show students the role of [alpha]-amylases (AAMYs) in saliva and detergents. These laboratory practicals are based on the determination of the enzymatic activity of amylase from saliva and different detergents using the Phadebas test (quantitative) and the Lugol test…

  20. The association between saliva control, silent saliva penetration, aspiration, and videofluoroscopic findings in Parkinson′s disease patients

    Directory of Open Access Journals (Sweden)

    Ali Rajaei

    2015-01-01

    Full Text Available Background: Dysphagia is a common disorder among patients with Parkinson′s disease (PD. It occurs in up to 80% of all (PD patients during the early stages of the disease and up to 95% in the advanced stages; but professionals may not hear from the patients about dysphagia symptoms until these symptoms reach an advanced stage and lead to medical complications. Materials and Methods: Thirty-three PD patients (mean age 66.09 ± 9.4 years; 24 men, nine women participated in this study at our Neurology Institute, between April 20, 2013, and October 26, 2013. They were asked two questions; one about saliva control and the other about silent saliva penetration and aspiration. Next, they underwent the videofluoroscopic swallowing study (VFSS. Results: The Pearson Correlation coefficient between the Penetration-Aspiration Scale (PAS scores and question 1 scores was 0.48 (P < 0.05, =0.25, and there was a significant correlation between the PAS scores and question 2 scores, and also question 1 scores + question 2 scores (r = 0.589, P < 0.05, =0 and r = 0589, P < 0.05, =0. Conclusions: This study showed a significant correlation between the questions about saliva control, silent saliva penetration, and aspiration, and laryngeal penetration and aspiration during VFSS. Therefore, by using these two questions, the potential silent laryngeal penetration and aspiration during meals could be detected before it led to aspiration pneumonia. Taking the benefit of these questions, as a part of the swallowing assessment of PD patients, is recommended.

  1. A guide through the computational analysis of isotope-labeled mass spectrometry-based quantitative proteomics data: an application study

    Directory of Open Access Journals (Sweden)

    Haußmann Ute

    2011-06-01

    Full Text Available Abstract Background Mass spectrometry-based proteomics has reached a stage where it is possible to comprehensively analyze the whole proteome of a cell in one experiment. Here, the employment of stable isotopes has become a standard technique to yield relative abundance values of proteins. In recent times, more and more experiments are conducted that depict not only a static image of the up- or down-regulated proteins at a distinct time point but instead compare developmental stages of an organism or varying experimental conditions. Results Although the scientific questions behind these experiments are of course manifold, there are, nevertheless, two questions that commonly arise: 1 which proteins are differentially regulated regarding the selected experimental conditions, and 2 are there groups of proteins that show similar abundance ratios, indicating that they have a similar turnover? We give advice on how these two questions can be answered and comprehensively compare a variety of commonly applied computational methods and their outcomes. Conclusions This work provides guidance through the jungle of computational methods to analyze mass spectrometry-based isotope-labeled datasets and recommends an effective and easy-to-use evaluation strategy. We demonstrate our approach with three recently published datasets on Bacillus subtilis 12 and Corynebacterium glutamicum 3. Special focus is placed on the application and validation of cluster analysis methods. All applied methods were implemented within the rich internet application QuPE 4. Results can be found at http://qupe.cebitec.uni-bielefeld.de.

  2. Clinical diagnosis and typing of systemic amyloidosis in subcutaneous fat aspirates by mass spectrometry-based proteomics.

    Science.gov (United States)

    Vrana, Julie A; Theis, Jason D; Dasari, Surendra; Mereuta, Oana M; Dispenzieri, Angela; Zeldenrust, Steven R; Gertz, Morie A; Kurtin, Paul J; Grogg, Karen L; Dogan, Ahmet

    2014-07-01

    Examination of abdominal subcutaneous fat aspirates is a practical, sensitive and specific method for the diagnosis of systemic amyloidosis. Here we describe the development and implementation of a clinical assay using mass spectrometry-based proteomics to type amyloidosis in subcutaneous fat aspirates. First, we validated the assay comparing amyloid-positive (n=43) and -negative (n=26) subcutaneous fat aspirates. The assay classified amyloidosis with 88% sensitivity and 96% specificity. We then implemented the assay as a clinical test, and analyzed 366 amyloid-positive subcutaneous fat aspirates in a 4-year period as part of routine clinical care. The assay had a sensitivity of 90%, and diverse amyloid types, including immunoglobulin light chain (74%), transthyretin (13%), serum amyloid A (%1), gelsolin (1%), and lysozyme (1%), were identified. Using bioinformatics, we identified a universal amyloid proteome signature, which has high sensitivity and specificity for amyloidosis similar to that of Congo red staining. We curated proteome databases which included variant proteins associated with systemic amyloidosis, and identified clonotypic immunoglobulin variable gene usage in immunoglobulin light chain amyloidosis, and the variant peptides in hereditary transthyretin amyloidosis. In conclusion, mass spectrometry-based proteomic analysis of subcutaneous fat aspirates offers a powerful tool for the diagnosis and typing of systemic amyloidosis. The assay reveals the underlying pathogenesis by identifying variable gene usage in immunoglobulin light chains and the variant peptides in hereditary amyloidosis. Copyright© Ferrata Storti Foundation.

  3. A metabolomics study on human dietary intervention with apples

    DEFF Research Database (Denmark)

    Dragsted, L. O.; Kristensen, M.; Ravn-Haren, Gitte

    2009-01-01

    Metabolomics is a promising tool for searching out new biomarkers and the development of hypotheses in nutrition research. This chapter will describe the design of human dietary intervention studies where samples are collected for metabolomics analyses as well as the analytical issues and data...

  4. Plant metabolomics and its potential application for human nutrition

    NARCIS (Netherlands)

    Hall, R.D.; Brouwer, I.D.; Fitzgerald, M.A.

    2008-01-01

    With the growing interest in the use of metabolomic technologies for a wide range of biological targets, food applications related to nutrition and quality are rapidly emerging. Metabolomics offers us the opportunity to gain deeper insights into, and have better control of, the fundamental

  5. Untargeted Metabolomics Strategies—Challenges and Emerging Directions

    Science.gov (United States)

    Schrimpe-Rutledge, Alexandra C.; Codreanu, Simona G.; Sherrod, Stacy D.; McLean, John A.

    2016-12-01

    Metabolites are building blocks of cellular function. These species are involved in enzyme-catalyzed chemical reactions and are essential for cellular function. Upstream biological disruptions result in a series of metabolomic changes and, as such, the metabolome holds a wealth of information that is thought to be most predictive of phenotype. Uncovering this knowledge is a work in progress. The field of metabolomics is still maturing; the community has leveraged proteomics experience when applicable and developed a range of sample preparation and instrument methodology along with myriad data processing and analysis approaches. Research focuses have now shifted toward a fundamental understanding of the biology responsible for metabolomic changes. There are several types of metabolomics experiments including both targeted and untargeted analyses. While untargeted, hypothesis generating workflows exhibit many valuable attributes, challenges inherent to the approach remain. This Critical Insight comments on these challenges, focusing on the identification process of LC-MS-based untargeted metabolomics studies—specifically in mammalian systems. Biological interpretation of metabolomics data hinges on the ability to accurately identify metabolites. The range of confidence associated with identifications that is often overlooked is reviewed, and opportunities for advancing the metabolomics field are described.

  6. Gas chromatography mass spectrometry : key technology in metabolomics

    NARCIS (Netherlands)

    Koek, Maud Marijtje

    2009-01-01

    Metabolomics involves the unbiased quantitative and qualitative analysis of the complete set of metabolites present in cells, body fluids and tissues. Gas chromatography coupled to mass spectrometry (GC-MS) is very suitable for metabolomics analysis, as it combines high separation power with

  7. Metabolomics to study functional consequences in peroxisomal disorders

    NARCIS (Netherlands)

    Herzog, K.

    2017-01-01

    This thesis focusses on metabolomics approaches performed in cultured cells and blood samples from patients with peroxisomal disorders. By applying both targeted and untargeted metabolomics, the aim of these approaches was to study the functional consequences of the primary genetic defects causing

  8. Metabolomics for Undergraduates: Identification and Pathway Assignment of Mitochondrial Metabolites

    Science.gov (United States)

    Marques, Ana Patrícia; Serralheiro, Maria Luisa; Ferreira, António E. N.; Freire, Ana Ponces; Cordeiro, Carlos; Silva, Marta Sousa

    2016-01-01

    Metabolomics is a key discipline in systems biology, together with genomics, transcriptomics, and proteomics. In this omics cascade, the metabolome represents the biochemical products that arise from cellular processes and is often regarded as the final response of a biological system to environmental or genetic changes. The overall screening…

  9. Environmental metabolomics: a SWOT analysis (strengths, weaknesses, opportunities, and threats).

    Science.gov (United States)

    Miller, Marion G

    2007-02-01

    Metabolomic approaches have the potential to make an exceptional contribution to understanding how chemicals and other environmental stressors can affect both human and environmental health. However, the application of metabolomics to environmental exposures, although getting underway, has not yet been extensively explored. This review will use a SWOT analysis model to discuss some of the strengths, weaknesses, opportunities, and threats that are apparent to an investigator venturing into this relatively new field. SWOT has been used extensively in business settings to uncover new outlooks and identify problems that would impede progress. The field of environmental metabolomics provides great opportunities for discovery, and this is recognized by a high level of interest in potential applications. However, understanding the biological consequence of environmental exposures can be confounded by inter- and intra-individual differences. Metabolomic profiles can yield a plethora of data, the interpretation of which is complex and still being evaluated and researched. The development of the field will depend on the availability of technologies for data handling and that permit ready access metabolomic databases. Understanding the relevance of metabolomic endpoints to organism health vs adaptation vs variation is an important step in understanding what constitutes a substantive environmental threat. Metabolomic applications in reproductive research are discussed. Overall, the development of a comprehensive mechanistic-based interpretation of metabolomic changes offers the possibility of providing information that will significantly contribute to the protection of human health and the environment.

  10. Candida in saliva of Brazilian hemophilic patients Candida na saliva de pacientes hemofílicos brasileiros

    Directory of Open Access Journals (Sweden)

    Claudio Maranhão Pereira

    2004-12-01

    Full Text Available Hemophilia is a common hereditary hemorrhagic disorder, however little is known about the oral microflora of hemophilic patients. The aim of this study was to quantify the Candida and identify its species in non-stimulated saliva of hemophilic patients, and consider its relationship with clinical factors influencing Candida carriage. This study comprised evaluation of 86 hemophilic patients of the Hematology Center/UNICAMP and 43 healthy subjects as controls. All patients were submitted to anamnesis, intraoral examination and unstimulated saliva collection. Candida counts and species identification were performed in salivary samples. Candida was present in 64% of the hemophilic patients and in 44% of the healthy controls. C. albicans represented 65% and 68% of the isolated species, in hemophiliacs and control group respectively, and C. tropicalis was the second most common species in both groups. These results indicate that hemophilic patients carry Candida more frequently and in higher counts than healthy controls, independently of oral clinical parameter considered, as viral infections, complete dentures, transfusions of hemoderivatives, and salivary flow.Hemofilia é uma alteração hemorrágica hereditária comum, entretanto pouco se sabe a respeito da microbiota oral destes indivíduos. O objetivo deste estudo foi quantificar a presença de Candida e identificar as suas espécies na saliva de hemofílicos, correlacionando os resultados com fatores clínicos que possam influenciar a presença deste fungo. Foram avaliados 86 hemofílicos do Hemocentro/UNICAMP e 43 indivíduos saudáveis. Todos os pacientes foram submetidos a anamnese, exame clínico intra-oral e coleta de saliva de forma não estimulada. A quantificação e identificação das espécies de Candida foram realizadas nas amostras de saliva. Candida estava presente em 64% dos hemofílicos e em 44% dos indivíduos saudáveis. C. albicans representou 65% e 68% das esp

  11. Tools for the functional interpretation of metabolomic experiments.

    Science.gov (United States)

    Chagoyen, Monica; Pazos, Florencio

    2013-11-01

    The so-called 'omics' approaches used in modern biology aim at massively characterizing the molecular repertories of living systems at different levels. Metabolomics is one of the last additions to the 'omics' family and it deals with the characterization of the set of metabolites in a given biological system. As metabolomic techniques become more massive and allow characterizing larger sets of metabolites, automatic methods for analyzing these sets in order to obtain meaningful biological information are required. Only recently the first tools specifically designed for this task in metabolomics appeared. They are based on approaches previously used in transcriptomics and other 'omics', such as annotation enrichment analysis. These, together with generic tools for metabolic analysis and visualization not specifically designed for metabolomics will for sure be in the toolbox of the researches doing metabolomic experiments in the near future.

  12. Metabolomics in Sepsis and Its Impact on Public Health.

    Science.gov (United States)

    Evangelatos, Nikolaos; Bauer, Pia; Reumann, Matthias; Satyamoorthy, Kapaettu; Lehrach, Hans; Brand, Angela

    2017-01-01

    Sepsis, with its often devastating consequences for patients and their families, remains a major public health concern that poses an increasing financial burden. Early resuscitation together with the elucidation of the biological pathways and pathophysiological mechanisms with the use of "-omics" technologies have started changing the clinical and research landscape in sepsis. Metabolomics (i.e., the study of the metabolome), an "-omics" technology further down in the "-omics" cascade between the genome and the phenome, could be particularly fruitful in sepsis research with the potential to alter the clinical practice. Apart from its benefit for the individual patient, metabolomics has an impact on public health that extends beyond its applications in medicine. In this review, we present recent developments in metabolomics research in sepsis, with a focus on pneumonia, and we discuss the impact of metabolomics on public health, with a focus on free/libre open source software. © 2018 S. Karger AG, Basel.

  13. New tools and resources in metabolomics: 2016-2017.

    Science.gov (United States)

    Misra, Biswapriya B

    2018-04-01

    Rapid advances in mass spectrometry (MS) and nuclear magnetic resonance (NMR)-based platforms for metabolomics have led to an upsurge of data every single year. Newer high-throughput platforms, hyphenated technologies, miniaturization, and tool kits in data acquisition efforts in metabolomics have led to additional challenges in metabolomics data pre-processing, analysis, interpretation, and integration. Thanks to the informatics, statistics, and computational community, new resources continue to develop for metabolomics researchers. The purpose of this review is to provide a summary of the metabolomics tools, software, and databases that were developed or improved during 2016-2017, thus, enabling readers, developers, and researchers access to a succinct but thorough list of resources for further improvisation, implementation, and application in due course of time. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  14. Compliance with minimum information guidelines in public metabolomics repositories.

    Science.gov (United States)

    Spicer, Rachel A; Salek, Reza; Steinbeck, Christoph

    2017-09-26

    The Metabolomics Standards Initiative (MSI) guidelines were first published in 2007. These guidelines provided reporting standards for all stages of metabolomics analysis: experimental design, biological context, chemical analysis and data processing. Since 2012, a series of public metabolomics databases and repositories, which accept the deposition of metabolomic datasets, have arisen. In this study, the compliance of 399 public data sets, from four major metabolomics data repositories, to the biological context MSI reporting standards was evaluated. None of the reporting standards were complied with in every publicly available study, although adherence rates varied greatly, from 0 to 97%. The plant minimum reporting standards were the most complied with and the microbial and in vitro were the least. Our results indicate the need for reassessment and revision of the existing MSI reporting standards.

  15. Rapid Detection of the Varicella Zoster Virus in Saliva

    Science.gov (United States)

    Pierson, Duane L.; Mehta, Satish K.; Cohrs, Randall J.; Gilden, Don H.; Harding, Robert E.

    2011-01-01

    Varicella zoster virus (VZV) causes chicken pox on first exposure (usually in children), and reactivates from latency causing shingles (usually in adults). Shingles can be extremely painful, causing nerve damage, organ damage, and blindness in some cases. The virus can be life-threatening in immune-compromised individuals. The virus is very difficult to culture for diagnosis, requiring a week or longer. This invention is a rapid test for VZV from a saliva sample and can be performed in a doctor s office. The kit is small, compact, and lightweight. Detec tion is sensitive, specific, and noninvasive (no needles); only a saliva sample is required. The test provides results in minutes. The entire test is performed in a closed system, with no exposure to infectious materials. The components are made mostly of inexpensive plastic injection molded parts, many of which can be purchased off the shelf and merely assembled. All biological waste is contained for fast, efficient disposal. This innovation was made possible because of discovery of a NASA scientists flight experiment showing the presence of VZV in saliva during high stress periods and disease. This finding enables clinicians to quickly screen patients for VZV and treat the ones that show positive results with antiviral medicines. This promotes a rapid recovery, easing of pain and symptoms, and reduces chances of complications from zoster. Screening of high-risk patients could be incorporated as part of a regular physical exam. These patients include the elderly, pregnant women, and immune-compromised individuals. In these patients, VZV can be a life-threatening disease. In both high- and low-risk patients, early detection and treatment with antiviral drugs can dramatically decrease or even eliminate the clinical manifestation of disease.

  16. Some Biological Activities of Malaysian Leech Saliva Extract

    Directory of Open Access Journals (Sweden)

    Abdualrahman M. Abdualkader

    2011-12-01

    Full Text Available Normal 0 21 false false false MS X-NONE AR-SA Leeches were fed on the phagostimulatory solution through parafilm membrane. The satiated leeches were forced to regurgitate the solution by soaking them in an ice-container. The anticoagulant activity was ascertained using thrombin time assay (TT. The result revealed that the saliva concentration which increases TT by 100% (IC100 is 43.205µg/ml plasma. The antimicrobial activity of the saliva was tested against several bacterial spp. (E.coli, P.aeruginosa, B.cereus, Sal.typhi and S.aureus  and fungi spp. (C.albicans and C.neoformans. It was found that saliva has an inhibition activity against Sal.typhi (minimal inhibitory concentration MIC 78.253µg/ml, S.aureus (MIC 78.253µg/ml and E.coli (MIC 121.256µg/ml.ABSTRAK: Pacat-pacat diberi makan larutan phagostimulatory menerusi membran parafilem. Pacat-pacat yang kekenyangan itu dipaksa memuntahkan larutan tersebut dengan direndam di dalam bekas berisi ais. Aktiviti antigumpal ditentukan menggunakan cerakin masa trombin (TT. Keputusan menunjukkan kepekatan air liur pacat menyebabkan pertambahan TT sebanyak 100% (IC100 iaitu 43.205µg/ml plasma. Aktiviti antimikrob air liur telah diuji dengan pelbagai jenis bakteria (E.coli, P.aeruginosa, B.cereus, Sal.typhi dan S.aureus dan pelbagai jenis kulat (C.albicans and C.neoformans. Didapati air liur menghasilkan aktiviti perencatan terhadap Sal.typhi (kepekatan perencat minima (Minimal inhibitory concentration - MIC 78.253µg/ml, S.aureus (MIC 78.253µg/ml dan E.coli (MIC 121.256µg/ml.

  17. Effectiveness of transcutaneous electrical nerve stimulation on saliva production in post-radiated oral cancer patients

    OpenAIRE

    Sakshi Ojha; Thimmarasa V Bhovi; Prashant P Jaju; Manas Gupta; Neha Singh; Kriti Shrivastava

    2016-01-01

    Aims and Objectives: To determine the effectiveness of transcutaneous electrical nerve stimulation (TENS) in stimulating salivary flow in post-radiated oral cancer patients, and to compare the salivary flow rate between unstimulated saliva and saliva stimulated with TENS in post-radiated oral cancer patients. Materials and Methods: In 30 patients who underwent radiotherapy for oral cancer, unstimulated saliva was collected every minute for 5 min in a graduated test tube. The TENS unit was act...

  18. Xylitol concentrations in artificial saliva after application of different xylitol dental varnishes

    OpenAIRE

    Pereira,Agnes de Fátima Faustino; Silva,Thiago Cruvinel da; Silva,Thelma Lopes da; Caldana,Magali de Lourdes; Bastos,José Roberto Magalhães; Buzalaf,Marília Afonso Rabelo

    2012-01-01

    Objective: The present study analyzed xylitol concentrations in artificial saliva over time after application of varnishes containing 10% and 20% xylitol. Material and Methods: Fifteen bovine enamel specimens (8x4 mm) were randomly allocated to 3 groups (n=5/group), according to the type of varnish used: 10% xylitol, 20% xylitol and no xylitol (control). After varnish application (4 mg), specimens were immersed in vials containing 500 mu L of artificial saliva. Saliva samples were collected i...

  19. Metronidazole as a radiosensitizer: a preliminary report on estimation in serum and saliva

    International Nuclear Information System (INIS)

    Karim, A.B.M.F.; Faber, D.B.; Haas, R.E.; Hoekstra, F.H.; Njo, K.H.

    1980-01-01

    Some studies indicate the clinical benefit of hypoxic radiosensitizers in patients who are undergoing radiotherapy. Serum level of sensitizers are usualy advised; however they are very demanding on the patient. Saliva level of the sensitizers may be an alternative method. This study correlated serum level of metronidazole to the saliva level in 10 patients who were undergoing radiotherapy with the sensitizer. A change to the saliva level method appears to relieve the patients

  20. Sensing cocaine in saliva with infrared laser spectroscopy

    Science.gov (United States)

    Hans, Kerstin M.-C.; Müller, Matthias; Gianella, Michele; Wägli, Ph.; Sigrist, Markus W.

    2013-02-01

    Increasing numbers of accidents caused by drivers under the influence of drugs, raise drug tests to worldwide interest. We developed a one-step extraction technique for cocaine in saliva and analyzed reference samples with laser spectroscopy employing two different schemes. The first is based on attenuated total reflection (ATR), which is applied to dried samples. The second scheme uses transmission measurements for the analysis of liquid samples. ATR spectroscopy achieved a limit of detection (LOD) of 3μg/ml. The LOD for the transmission approach in liquid samples is cocaine. An improved stabilization of the set-up should lower the limit of detection significantly.

  1. The determination of antipyrine elimination in saliva by liquid chromatography.

    Science.gov (United States)

    Gartzke, J; Jäger, H

    1991-01-01

    A simple, fast and reliable liquid chromatographic method for the determination of antipyrine in saliva is described. The elimination of antipyrine is a good indicator for general evaluation of the liver function for dispositional purposes for example in occupational and environmental medicine. The described LC method was compared with a more extensive photometric procedure. The results obtained from both methods show very good correlation. Only one measurement is necessary to determine the antipyrine clearance. Furthermore the antipyrine dosage can be minimized, because of the sensitivity of the HPLC-method.

  2. [Saliva: more than just a factor in oral health].

    Science.gov (United States)

    van Nieuw Ameronpn, A; Veerman, E C I; Brand, H S; Vissink, A

    2006-05-01

    Several salivary proteins are involved in the antimicrobial defence within the oral cavity, and are able to eliminate or inhibit a great number of microorganisms that enter the body via the oral cavity. Thus changes in the composition of saliva may not only affect people's oral health, but also have consequences for their general health. Based on salivary proteins, antimicrobial peptides have been synthesized. Potentially, these could be used as a new class of antibiotics. The antimicrobial peptides are hardly cytotoxic to human cells and do not evoke any or only very little resistence in microorganisms.

  3. Pengaruh Stimulus Pengunyahan dan Pengecapan Terhadap Kecepatan Aliran dan pH Saliva

    Directory of Open Access Journals (Sweden)

    Hj. Edeh Rolette Haroen

    2015-09-01

    Full Text Available The aim of the research were to describe how salivary flow rate and pH vary with time during use of chewing and gustatory stimulation. Fifty young adult subjects collected unstimulated saliva by spitting method, and then collected stimulated saliva by chewing paraffin wax, and a few drops of citric acid are usually placed on the subject’s tongue. The mean of saliva flow rate that unstimulated: 0.50 cc/minute; stimulated saliva by chewing paraffin wax: 1.57 cc/minute, and drops of citric acid stimulation showed that saliva flow rate: 2.98 cc/minute; and pH saliva that unstimulated 6.39; stimulated saliva by chewing paraffin wax 7.2; and stimulated saliva by citric acid: 7.55. Statistical paired t test showed that t lower than t table. The conclusion of the research showed that there were significant influences in the unstimulated salivary flow rates and pH with stimulated saliva elicited by chewing and gustatory stimulation.

  4. Understanding of xerostomia and strategies for the development of artificial saliva.

    Science.gov (United States)

    Kho, Hong-Seop

    2014-01-01

    Xerostomia is becoming a major issue in dental and medical clinics with an increase of aged population. Medication is the most common etiology of xerostomia, while the most severe xerostomia generally occurs in patients with a history of head and neck radiotherapy. Xerostomic patients usually suffer from diminished quality of life due to various symptoms and complications. Decreased salivary output is a definite objective sign, but oral mucosal wetness is a more reliable factor for the evaluation of xerostomia. At present there are no effective therapeutic methods for the treatment of xerostomia. Sialogogues may have problematic side effects and their therapeutic effects last only brief duration. Artificial saliva typically does not produce satisfactory results in therapeutic efficacy. Therefore, further research and development of better therapeutic modalities are necessary. The basic concept for the development of ideal and functional artificial saliva is the mimicry of natural human saliva. We need proper candidate molecules and antimicrobial supplements to simulate the rheological and biological properties of human saliva. We also need better understanding of the interactions between the ingredients of artificial saliva themselves and between the ingredients and components of human saliva both in solution and on surface phases. In addition, we need accepted measures to evaluate the efficacy of artificial saliva. In conclusion, for the development of ideal artificial saliva, research based on the understanding of pathophysiology of xerostomia and knowledge about rheological and biological functions of human saliva are necessary.

  5. Sample Stability and Protein Composition of Saliva: Implications for Its Use as a Diagnostic Fluid

    Directory of Open Access Journals (Sweden)

    Han Roelofsen

    2008-01-01

    Full Text Available Saliva is an easy accessible plasma ultra-filtrate. Therefore, saliva can be an attractive alternative to blood for measurement of diagnostic protein markers. Our aim was to determine stability and protein composition of saliva. Protein stability at room temperature was examined by incubating fresh whole saliva with and without inhibitors of proteases and bacterial metabolism followed by Surface Enhanced Laser Desorption/Ionization (SELDI analyses. Protein composition was determined by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE fractionation of saliva proteins followed by digestion of excised bands and identification by liquid chromatography tandem mass spectrometry (LC-MS/MS. Results show that rapid protein degradation occurs within 30 minutes after sample collection. Degradation starts already during collection. Protease inhibitors partly prevented degradation while inhibition of bacterial metabolism did not affect degradation. Three stable degradation products of 2937 Da, 3370 Da and 4132 Da were discovered which can be used as markers to monitor sample quality. Saliva proteome analyses revealed 218 proteins of which 84 can also be found in blood plasma. Based on a comparison with seven other proteomics studies on whole saliva we identified 83 new saliva proteins. We conclude that saliva is a promising diagnostic fl uid when precautions are taken towards protein breakdown.

  6. Mass spectrometry-based cDNA profiling as a potential tool for human body fluid identification.

    Science.gov (United States)

    Donfack, Joseph; Wiley, Anissa

    2015-05-01

    Several mRNA markers have been exhaustively evaluated for the identification of human venous blood, saliva, and semen in forensic genetics. As new candidate human body fluid specific markers are discovered, evaluated, and reported in the scientific literature, there is an increasing trend toward determining the ideal markers for cDNA profiling of body fluids of forensic interest. However, it has not been determined which molecular genetics-based technique(s) should be utilized to assess the performance of these markers. In recent years, only a few confirmatory, mRNA/cDNA-based methods have been evaluated for applications in body fluid identification. The most frequently described methods tested to date include quantitative polymerase chain reaction (qPCR) and capillary electrophoresis (CE). However these methods, in particular qPCR, often favor narrow multiplex PCR due to the availability of a limited number of fluorescent dyes/tags. In an attempt to address this technological constraint, this study explored matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) for human body fluid identification via cDNA profiling of venous blood, saliva, and semen. Using cDNA samples at 20pg input phosphoglycerate kinase 1 (PGK1) amounts, body fluid specific markers for the candidate genes were amplified in their corresponding body fluid (i.e., venous blood, saliva, or semen) and absent in the remaining two (100% specificity). The results of this study provide an initial indication that MALDI-TOF MS is a potential fluorescent dye-free alternative method for body fluid identification in forensic casework. However, the inherent issues of low amounts of mRNA, and the damage caused to mRNA by environmental exposures, extraction processes, and storage conditions are important factors that significantly hinder the implementation of cDNA profiling into forensic casework. Published by Elsevier Ireland Ltd.

  7. Identification of altered metabolic pathways in plasma and CSF in mild cognitive impairment and Alzheimer's disease using metabolomics.

    Directory of Open Access Journals (Sweden)

    Eugenia Trushina

    Full Text Available Alzheimer's Disease (AD currently affects more than 5 million Americans, with numbers expected to grow dramatically as the population ages. The pathophysiological changes in AD patients begin decades before the onset of dementia, highlighting the urgent need for the development of early diagnostic methods. Compelling data demonstrate that increased levels of amyloid-beta compromise multiple cellular pathways; thus, the investigation of changes in various cellular networks is essential to advance our understanding of early disease mechanisms and to identify novel therapeutic targets. We applied a liquid chromatography/mass spectrometry-based non-targeted metabolomics approach to determine global metabolic changes in plasma and cerebrospinal fluid (CSF from the same individuals with different AD severity. Metabolic profiling detected a total of significantly altered 342 plasma and 351 CSF metabolites, of which 22% were identified. Based on the changes of >150 metabolites, we found 23 altered canonical pathways in plasma and 20 in CSF in mild cognitive impairment (MCI vs. cognitively normal (CN individuals with a false discovery rate <0.05. The number of affected pathways increased with disease severity in both fluids. Lysine metabolism in plasma and the Krebs cycle in CSF were significantly affected in MCI vs. CN. Cholesterol and sphingolipids transport was altered in both CSF and plasma of AD vs. CN. Other 30 canonical pathways significantly disturbed in MCI and AD patients included energy metabolism, Krebs cycle, mitochondrial function, neurotransmitter and amino acid metabolism, and lipid biosynthesis. Pathways in plasma that discriminated between all groups included polyamine, lysine, tryptophan metabolism, and aminoacyl-tRNA biosynthesis; and in CSF involved cortisone and prostaglandin 2 biosynthesis and metabolism. Our data suggest metabolomics could advance our understanding of the early disease mechanisms shared in progression from CN to

  8. Comparative Analysis of Compatibility Effects on Invigorating Blood Circulation for Cyperi Rhizoma Series of Herb Pairs Using Untargeted Metabolomics

    Directory of Open Access Journals (Sweden)

    Pei Liu

    2017-09-01

    Full Text Available The mutual-assistance compatibility of Cyperi Rhizoma (Xiangfu, XF and Angelicae Sinensis Radix (Danggui, DG, Chuanxiong Rhizoma (Chuanxiong, CX, Paeoniae Radix Alba (Baishao, BS, or Corydalis Rhizoma (Yanhusuo, YH, found in a traditional Chinese medicine (TCM named Xiang-Fu-Si-Wu Decoction (XFSWD, can produce synergistic and promoting blood effects. Nowadays, XFSWD has been proved to be effective in activating blood circulation and dissipating blood stasis. However, the role of the herb pairs synergistic effects in the formula were poorly understood. In order to quantitatively assess the compatibility effects of herb pairs, mass spectrometry-based untargeted metabolomics studies were performed. The plasma and urine metabolic profiles of acute blood stasis rats induced by adrenaline hydrochloride and ice water and administered with Cyperi Rhizoma—Angelicae Sinensis Radix (XD, Cyperi Rhizoma—Chuanxiong Rhizoma (XC, Cyperi Rhizoma—Paeoniae Radix Alba (XB, Cyperi Rhizoma—Corydalis Rhizoma (XY were compared. Relative peak area of identified metabolites was calculated and principal component analysis (PCA score plot from the potential markers was used to visualize the overall differences. Then, the metabolites results were used with biochemistry indicators and genes expression values as parameters to quantitatively evaluate the compatibility effects of XF series of herb pairs by PCA and correlation analysis. The collective results indicated that the four XF herb pairs regulated glycerophospholipid metabolism, steroid hormone biosynthesis and arachidonic acid metabolism pathway. XD was more prominent in regulating the blood stasis during the four XF herb pairs. This study demonstrated that metabolomics was a useful tool to efficacy evaluation and compatibility effects of TCM elucidation.

  9. Comparison between three different saliva substitutes in patients with hyposalivation.

    Science.gov (United States)

    Skrinjar, Ivana; Vucicevic Boras, Vanja; Bakale, Iva; Andabak Rogulj, Ana; Brailo, Vlaho; Vidovic Juras, Danica; Alajbeg, Ivan; Vrdoljak, Danko Velimir

    2015-04-01

    The aim of the present study was to compare the efficiency of oral spray based on thermal spring water (Buccotherm®) versus commercial saliva substitute (Xeros®) and marshmallow root on the quality of life in patients with hyposalivation. A total of 60 patients with unstimulated salivary flow rate marshmallow root. Therapy lasted for 2 weeks; everyday, patients used one of the products four times a day. Quality of life was measured by the Croatian version of Oral Health Impact Profile 14 questionnaire, and visual analog scale was used to determine the intensity of dry mouth before and after therapy. Statistical analysis was performed by Wilcoxon signed-rank test and Kruskal-Wallis test. Standardized effect size was calculated for OHIP following treatment. Buccotherm® has shown the biggest effect on quality of life in patients with hyposalivation. Intensity of dry mouth was lower after the applied therapy whatever substitute patients used. We recommend the use of all three saliva substitutes for decreasing the intensity of dry mouth symptoms as well as improvement in the quality of life. Although all tested agents showed beneficial effect in alleviating hyposalivation symptoms, it seems that Buccotherm® was superior to Xeros® and marshmallow root.

  10. Updates in metabolomics tools and resources: 2014-2015.

    Science.gov (United States)

    Misra, Biswapriya B; van der Hooft, Justin J J

    2016-01-01

    Data processing and interpretation represent the most challenging and time-consuming steps in high-throughput metabolomic experiments, regardless of the analytical platforms (MS or NMR spectroscopy based) used for data acquisition. Improved machinery in metabolomics generates increasingly complex datasets that create the need for more and better processing and analysis software and in silico approaches to understand the resulting data. However, a comprehensive source of information describing the utility of the most recently developed and released metabolomics resources--in the form of tools, software, and databases--is currently lacking. Thus, here we provide an overview of freely-available, and open-source, tools, algorithms, and frameworks to make both upcoming and established metabolomics researchers aware of the recent developments in an attempt to advance and facilitate data processing workflows in their metabolomics research. The major topics include tools and researches for data processing, data annotation, and data visualization in MS and NMR-based metabolomics. Most in this review described tools are dedicated to untargeted metabolomics workflows; however, some more specialist tools are described as well. All tools and resources described including their analytical and computational platform dependencies are summarized in an overview Table. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Challenges of metabolomics in human gut microbiota research.

    Science.gov (United States)

    Smirnov, Kirill S; Maier, Tanja V; Walker, Alesia; Heinzmann, Silke S; Forcisi, Sara; Martinez, Inés; Walter, Jens; Schmitt-Kopplin, Philippe

    2016-08-01

    The review highlights the role of metabolomics in studying human gut microbial metabolism. Microbial communities in our gut exert a multitude of functions with huge impact on human health and disease. Within the meta-omics discipline, gut microbiome is studied by (meta)genomics, (meta)transcriptomics, (meta)proteomics and metabolomics. The goal of metabolomics research applied to fecal samples is to perform their metabolic profiling, to quantify compounds and classes of interest, to characterize small molecules produced by gut microbes. Nuclear magnetic resonance spectroscopy and mass spectrometry are main technologies that are applied in fecal metabolomics. Metabolomics studies have been increasingly used in gut microbiota related research regarding health and disease with main focus on understanding inflammatory bowel diseases. The elucidated metabolites in this field are summarized in this review. We also addressed the main challenges of metabolomics in current and future gut microbiota research. The first challenge reflects the need of adequate analytical tools and pipelines, including sample handling, selection of appropriate equipment, and statistical evaluation to enable meaningful biological interpretation. The second challenge is related to the choice of the right animal model for studies on gut microbiota. We exemplified this using NMR spectroscopy for the investigation of cross-species comparison of fecal metabolite profiles. Finally, we present the problem of variability of human gut microbiota and metabolome that has important consequences on the concepts of personalized nutrition and medicine. Copyright © 2016 Elsevier GmbH. All rights reserved.

  12. Discovery and characterization of antibody variants using mass spectrometry-based comparative analysis for biosimilar candidates of monoclonal antibody drugs.

    Science.gov (United States)

    Li, Wenhua; Yang, Bin; Zhou, Dongmei; Xu, Jun; Ke, Zhi; Suen, Wen-Chen

    2016-07-01

    Liquid chromatography mass spectrometry (LC-MS) is the most commonly used technique for the characterization of antibody variants. MAb-X and mAb-Y are two approved IgG1 subtype monoclonal antibody drugs recombinantly produced in Chinese hamster ovary (CHO) cells. We report here that two unexpected and rare antibody variants have been discovered during cell culture process development of biosimilars for these two approved drugs through intact mass analysis. We then used comprehensive mass spectrometry-based comparative analysis including reduced light, heavy chains, and domain-specific mass as well as peptide mapping analysis to fully characterize the observed antibody variants. The "middle-up" mass comparative analysis demonstrated that the antibody variant from mAb-X biosimilar candidate was caused by mass variation of antibody crystalline fragment (Fc), whereas a different variant with mass variation in antibody antigen-binding fragment (Fab) from mAb-Y biosimilar candidate was identified. Endoproteinase Lys-C digested peptide mapping and tandem mass spectrometry analysis further revealed that a leucine to glutamine change in N-terminal 402 site of heavy chain was responsible for the generation of mAb-X antibody variant. Lys-C and trypsin coupled non-reduced and reduced peptide mapping comparative analysis showed that the formation of the light-heavy interchain trisulfide bond resulted in the mAb-Y antibody variant. These two cases confirmed that mass spectrometry-based comparative analysis plays a critical role for the characterization of monoclonal antibody variants, and biosimilar developers should start with a comprehensive structural assessment and comparative analysis to decrease the risk of the process development for biosimilars. Copyright © 2016 Elsevier B.V. All rights reserved.

  13. Erosive potential of saliva stimulating tablets with and without fluoride in irradiated head and neck cancer patients

    DEFF Research Database (Denmark)

    Lajer, Christel; Buchwald, Christian; Nauntofte, Birgitte

    2009-01-01

    stimulated saliva without fluoride, and with fluoride. Saliva pH was determined without loss of CO(2) and in combination with inorganic measures used to calculate the degree of saturation of hydroxyapatite (HAp) and fluorapatite (FAp). EP was determined directly in all saliva samples by monitored dissolution......BACKGROUND: Patients irradiated in the head and neck region often suffer from severe dry mouth and use acidic saliva stimulating products, which may cause erosion of teeth. PURPOSE: To determine saliva stimulating effects and erosive potential (EP) of acidic saliva stimulating tablets (Xerodent...

  14. INFLUENCE OF SYSTEMIC DISEASES AND REMOVABLE ORTHODONTIC APPLIANCES ON THE QUALITY OF SALIVA IN CHILDHOOD.

    Directory of Open Access Journals (Sweden)

    Maya Rashkova

    2012-03-01

    Full Text Available During the last 10 years numerous investigations using saliva as a diagnostic tool have been carried out. The aim of present study is to evaluate saliva qualities for various general diseases and conditions that influence its qualities. (1 Evaluation of salivary flow and saliva consistency of children. (2 Evaluation of saliva pH and buffer capacity of children. Material and Methods. The investigation was carried out with 126 children (age 6 to 17 selected by their general diseases and conditions influencing the oral risk environment. The children were divided into 4 groups: 30 children with diabetes, 25 children with asthma treated with local corticosteroids, 27 healthy children with orthodontic treatment, 34 children as a control group (healthy children. The saliva of the children was tested with the help of “Saliva Check” of GC company. The instructions of the company producer were followed.Results. Stimulated saliva current is reliably lower for children with asthma treated with local corticosteroids, diabetes and children with orthodontic appliances. Saliva pH is with lower values for children with diabetes and asthma – diseases predisposing to acid oral environment. The decreased saliva buffer capacity for children with diabetes and asthma is an indicator for the difficult regulation of the dynamically changing oral electrolytic balance of those children.Conclusion. The saliva parameters studied can be used as biomarkers of the liquid oral environment with regard to the risks for caries and periodontal diseases in children. General health status influences saliva qualities increasing thus indirectly the caries risk.

  15. Metabolomics, a promising approach to translational research in cardiology

    Directory of Open Access Journals (Sweden)

    Martino Deidda

    2015-12-01

    In this article, we will provide a description of metabolomics in comparison with other, better known “omics” disciplines such as genomics and proteomics. In addition, we will review the current rationale for the implementation of metabolomics in cardiology, its basic methodology and the available data from human studies in this discipline. The topics covered will delineate the importance of being able to use the metabolomic information to understand the mechanisms of diseases from the perspective of systems biology, and as a non-invasive approach to the diagnosis, grading and treatment of cardiovascular diseases.

  16. Introduction to metabolomics and its applications in ophthalmology

    Science.gov (United States)

    Tan, S Z; Begley, P; Mullard, G; Hollywood, K A; Bishop, P N

    2016-01-01

    Metabolomics is the study of endogenous and exogenous metabolites in biological systems, which aims to provide comparative semi-quantitative information about all metabolites in the system. Metabolomics is an emerging and potentially powerful tool in ophthalmology research. It is therefore important for health professionals and researchers involved in the speciality to understand the basic principles of metabolomics experiments. This article provides an overview of the experimental workflow and examples of its use in ophthalmology research from the study of disease metabolism and pathogenesis to identification of biomarkers. PMID:26987591

  17. Targeting of the hydrophobic metabolome by pathogens.

    Science.gov (United States)

    Helms, J Bernd; Kaloyanova, Dora V; Strating, Jeroen R P; van Hellemond, Jaap J; van der Schaar, Hilde M; Tielens, Aloysius G M; van Kuppeveld, Frank J M; Brouwers, Jos F

    2015-05-01

    The hydrophobic molecules of the metabolome - also named the lipidome - constitute a major part of the entire metabolome. Novel technologies show the existence of a staggering number of individual lipid species, the biological functions of which are, with the exception of only a few lipid species, unknown. Much can be learned from pathogens that have evolved to take advantage of the complexity of the lipidome to escape the immune system of the host organism and to allow their survival and replication. Different types of pathogens target different lipids as shown in interaction maps, allowing visualization of differences between different types of pathogens. Bacterial and viral pathogens target predominantly structural and signaling lipids to alter the cellular phenotype of the host cell. Fungal and parasitic pathogens have complex lipidomes themselves and target predominantly the release of polyunsaturated fatty acids from the host cell lipidome, resulting in the generation of eicosanoids by either the host cell or the pathogen. Thus, whereas viruses and bacteria induce predominantly alterations in lipid metabolites at the host cell level, eukaryotic pathogens focus on interference with lipid metabolites affecting systemic inflammatory reactions that are part of the immune system. A better understanding of the interplay between host-pathogen interactions will not only help elucidate the fundamental role of lipid species in cellular physiology, but will also aid in the generation of novel therapeutic drugs. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  18. The Human Blood Metabolome-Transcriptome Interface

    Science.gov (United States)

    Schramm, Katharina; Adamski, Jerzy; Gieger, Christian; Herder, Christian; Carstensen, Maren; Peters, Annette; Rathmann, Wolfgang; Roden, Michael; Strauch, Konstantin; Suhre, Karsten; Kastenmüller, Gabi; Prokisch, Holger; Theis, Fabian J.

    2015-01-01

    Biological systems consist of multiple organizational levels all densely interacting with each other to ensure function and flexibility of the system. Simultaneous analysis of cross-sectional multi-omics data from large population studies is a powerful tool to comprehensively characterize the underlying molecular mechanisms on a physiological scale. In this study, we systematically analyzed the relationship between fasting serum metabolomics and whole blood transcriptomics data from 712 individuals of the German KORA F4 cohort. Correlation-based analysis identified 1,109 significant associations between 522 transcripts and 114 metabolites summarized in an integrated network, the ‘human blood metabolome-transcriptome interface’ (BMTI). Bidirectional causality analysis using Mendelian randomization did not yield any statistically significant causal associations between transcripts and metabolites. A knowledge-based interpretation and integration with a genome-scale human metabolic reconstruction revealed systematic signatures of signaling, transport and metabolic processes, i.e. metabolic reactions mainly belonging to lipid, energy and amino acid metabolism. Moreover, the construction of a network based on functional categories illustrated the cross-talk between the biological layers at a pathway level. Using a transcription factor binding site enrichment analysis, this pathway cross-talk was further confirmed at a regulatory level. Finally, we demonstrated how the constructed networks can be used to gain novel insights into molecular mechanisms associated to intermediate clinical traits. Overall, our results demonstrate the utility of a multi-omics integrative approach to understand the molecular mechanisms underlying both normal physiology and disease. PMID:26086077

  19. The Human Blood Metabolome-Transcriptome Interface.

    Directory of Open Access Journals (Sweden)

    Jörg Bartel

    2015-06-01

    Full Text Available Biological systems consist of multiple organizational levels all densely interacting with each other to ensure function and flexibility of the system. Simultaneous analysis of cross-sectional multi-omics data from large population studies is a powerful tool to comprehensively characterize the underlying molecular mechanisms on a physiological scale. In this study, we systematically analyzed the relationship between fasting serum metabolomics and whole blood transcriptomics data from 712 individuals of the German KORA F4 cohort. Correlation-based analysis identified 1,109 significant associations between 522 transcripts and 114 metabolites summarized in an integrated network, the 'human blood metabolome-transcriptome interface' (BMTI. Bidirectional causality analysis using Mendelian randomization did not yield any statistically significant causal associations between transcripts and metabolites. A knowledge-based interpretation and integration with a genome-scale human metabolic reconstruction revealed systematic signatures of signaling, transport and metabolic processes, i.e. metabolic reactions mainly belonging to lipid, energy and amino acid metabolism. Moreover, the construction of a network based on functional categories illustrated the cross-talk between the biological layers at a pathway level. Using a transcription factor binding site enrichment analysis, this pathway cross-talk was further confirmed at a regulatory level. Finally, we demonstrated how the constructed networks can be used to gain novel insights into molecular mechanisms associated to intermediate clinical traits. Overall, our results demonstrate the utility of a multi-omics integrative approach to understand the molecular mechanisms underlying both normal physiology and disease.

  20. New approaches for metabolomics by mass spectrometry

    Energy Technology Data Exchange (ETDEWEB)

    Vertes, Akos [George Washington Univ., Washington, DC (United States)

    2017-07-10

    Small molecules constitute a large part of the world around us, including fossil and some renewable energy sources. Solar energy harvested by plants and bacteria is converted into energy rich small molecules on a massive scale. Some of the worst contaminants of the environment and compounds of interest for national security also fall in the category of small molecules. The development of large scale metabolomic analysis methods lags behind the state of the art established for genomics and proteomics. This is commonly attributed to the diversity of molecular classes included in a metabolome. Unlike nucleic acids and proteins, metabolites do not have standard building blocks, and, as a result, their molecular properties exhibit a wide spectrum. This impedes the development of dedicated separation and spectroscopic methods. Mass spectrometry (MS) is a strong contender in the quest for a quantitative analytical tool with extensive metabolite coverage. Although various MS-based techniques are emerging for metabolomics, many of these approaches include extensive sample preparation that make large scale studies resource intensive and slow. New ionization methods are redefining the range of analytical problems that can be solved using MS. This project developed new approaches for the direct analysis of small molecules in unprocessed samples, as well as pushed the limits of ultratrace analysis in volume limited complex samples. The projects resulted in techniques that enabled metabolomics investigations with enhanced molecular coverage, as well as the study of cellular response to stimuli on a single cell level. Effectively individual cells became reaction vessels, where we followed the response of a complex biological system to external perturbation. We established two new analytical platforms for the direct study of metabolic changes in cells and tissues following external perturbation. For this purpose we developed a novel technique, laser ablation electrospray

  1. The MetabolomeExpress Project: enabling web-based processing, analysis and transparent dissemination of GC/MS metabolomics datasets

    Directory of Open Access Journals (Sweden)

    Carroll Adam J

    2010-07-01

    Full Text Available Abstract Background Standardization of analytical approaches and reporting methods via community-wide collaboration can work synergistically with web-tool development to result in rapid community-driven expansion of online data repositories suitable for data mining and meta-analysis. In metabolomics, the inter-laboratory reproducibility of gas-chromatography/mass-spectrometry (GC/MS makes it an obvious target for such development. While a number of web-tools offer access to datasets and/or tools for raw data processing and statistical analysis, none of these systems are currently set up to act as a public repository by easily accepting, processing and presenting publicly submitted GC/MS metabolomics datasets for public re-analysis. Description Here, we present MetabolomeExpress, a new File Transfer Protocol (FTP server and web-tool for the online storage, processing, visualisation and statistical re-analysis of publicly submitted GC/MS metabolomics datasets. Users may search a quality-controlled database of metabolite response statistics from publicly submitted datasets by a number of parameters (eg. metabolite, species, organ/biofluid etc.. Users may also perform meta-analysis comparisons of multiple independent experiments or re-analyse public primary datasets via user-friendly tools for t-test, principal components analysis, hierarchical cluster analysis and correlation analysis. They may interact with chromatograms, mass spectra and peak detection results via an integrated raw data viewer. Researchers who register for a free account may upload (via FTP their own data to the server for online processing via a novel raw data processing pipeline. Conclusions MetabolomeExpress https://www.metabolome-express.org provides a new opportunity for the general metabolomics community to transparently present online the raw and processed GC/MS data underlying their metabolomics publications. Transparent sharing of these data will allow researchers to

  2. Continuous analysis of parotid saliva during resting and short-duration simulated chewing

    NARCIS (Netherlands)

    Neyraud, E.; Bult, J.H.F.; Dransfield, E.

    2009-01-01

    Objective: Parotid saliva flow is increased by mastication and its composition is also modified. The aim of this work was to clarify the relationships between flow rate, pH and protein concentration, during resting and short-duration simulated chewing, using continuous and fractional saliva

  3. Total Protein of Whole Saliva as a Biomarker of Anaerobic Threshold

    Science.gov (United States)

    Bortolini, Miguel Junior Sordi; De Agostini, Guilherme Gularte; Reis, Ismair Teodoro; Lamounier, Romeu Paulo Martins Silva; Blumberg, Jeffrey B.; Espindola, Foued Salmen

    2009-01-01

    Saliva provides a convenient and noninvasive matrix for assessing specific physiological parameters, including some biomarkers of exercise. We investigated whether the total protein concentration of whole saliva (TPWS) would reflect the anaerobic threshold during an incremental exercise test. After a warm-up period, 13 nonsmoking men performed a…

  4. Investigating the Hydrolysis of Starch Using "a"-Amylase Contained in Dishwashing Detergent and Human Saliva

    Science.gov (United States)

    Munegumi, Toratane; Inutsuka, Masato; Hayafuji, Yukitaka

    2016-01-01

    Although saliva has commonly been used to teach about digestion by organisms, the phenomenon of digestion is actually caused by enzymes as catalytic substances. This activity explores the hydrolysis of starch by "a"-amylase in cleaning materials as well as a comparison with the similar reaction using human saliva. The fact that the…

  5. Effects of saliva collection using cotton swab on cortisol enzyme immunoassay.

    Science.gov (United States)

    Kozaki, Tomoaki; Hashiguchi, Nobuko; Kaji, Yumi; Yasukouchi, Akira; Tochihara, Yutaka

    2009-12-01

    Cotton swabs are among the most commonly used devices for collecting saliva, but various studies have reported that their use impacts the results of salivary cortisol assays. These studies, however, estimated this impact by comparing the average of the concentration and/or scatter plots. In the present study, we estimated the impact of cotton swabs on the results of salivary cortisol enzyme immunoassay (EIA) by Bland-Altman plot. Eight healthy males (aged 20-23 years) provided four saliva samples on different days to yield a total of 32 samples. Saliva samples were collected directly in plastic tubes using plastic straws and then pipetted onto cotton swabs (cotton saliva collection) and into clear sterile tubes (passive saliva collection). There was a lower correlation between cotton and passive saliva collection. Individually, four subjects showed a negative correlation between passive and cotton saliva collection. A Bland-Altman plot indicated that cotton swabs causes a proportional bias on the EIA assay result. Our findings indicate a considerable effect of using cotton swabs for saliva collection, and subject-specific variability in the impact. A Bland-Altman plot further suggests possible reasons for this effect.

  6. Antialarmin effect of tick saliva during the transmission of Lyme disease

    NARCIS (Netherlands)

    Marchal, Claire; Schramm, Frederic; Kern, Aurélie; Luft, Benjamin J.; Yang, Xiaohua; Schuijt, Tim J.; Hovius, Joppe W.; Jaulhac, Benoît; Boulanger, Nathalie

    2011-01-01

    Tick saliva has potent immunomodulatory properties. In arthropod-borne diseases, this effect is largely used by microorganisms to increase their pathogenicity and to evade host immune responses. We show that in Lyme borreliosis, tick salivary gland extract and a tick saliva protein, Salp15, inhibit

  7. Determination of epirubicin and its metabolite epirubicinol in saliva and plasma by HPLC

    NARCIS (Netherlands)

    Dodde, WIW; Maring, JG; Hendriks, G; Wachters, FM; Groen, HJM; de Vries, EGE; Uges, DRA

    We present a high-performance liquid chromatography (HPLC) method suitable for the analysis of epirubicin and its metabolite epirubicinol in saliva and plasma. Preparation of saliva and plasma samples was performed by extraction of analytes with a chloroform: 2-propanol mixture (6:1, vol/vol) and

  8. Comparative assessment of saliva and plasma for drug bioavailability and bioequivalence studies in humans

    Directory of Open Access Journals (Sweden)

    Nasir M. Idkaidek

    2017-07-01

    Conclusion: Our results suggest that there is a potential in BA/BE studies for saliva to be considered as a surrogate for plasma concentration, which goes along with drug regulations. The use of saliva instead of plasma in such studies makes them non-invasive, easy and with a lower clinical burden.

  9. Preliminary findings on the correlation of saliva pH, buffering ...

    African Journals Online (AJOL)

    The aim of the present comparative study was to compare some salivary characteristics between exclusive waterpipe smokers (EWPS) and non-smokers. 72 males (36 EWPS) were recruited. The volume of stimulated saliva was determined and divided by the duration of saliva collection. The pH was measured directly ...

  10. Effects of isoflurane anesthesia and pilocarpine on rat parotid saliva flow

    DEFF Research Database (Denmark)

    Knudsen, Jacob Dronninglund; Nauntofte, Birgitte; Josipovic, M

    2011-01-01

    rats was 50% slower than that of the sham-irradiated rats. In conclusion, 1.5% isoflurane was found to be a good compromise between proper anesthesia and isoflurane-induced inhibition of saliva secretion. Pilocarpine induces saliva secretion in a dose-dependent matter, with supra-maximal stimulation...

  11. Corticosteroids in plasma and saliva : the influence of oral contraceptive use and pregnancy

    NARCIS (Netherlands)

    Meulenberg, E.P.M.M.

    1995-01-01

    Cortisol in saliva is considered to be derived from the free, unbound fraction in plasma by simple diffusion through the salivary gland. Despite considerable conversion into cortisone in the salivary gland by the enzyme 11β-hydroxysteroid dehydrogenase, levels of cortisol in saliva form a

  12. Can fluconazole concentrations in saliva be used for therapeutic drug monitoring?

    NARCIS (Netherlands)

    Koks, C. H.; Crommentuyn, K. M.; Hoetelmans, R. M.; Mathôt, R. A.; Beijnen, J. H.

    2001-01-01

    The saliva/plasma concentration ratio of fluconazole was investigated in 22 HIV-1-infected individuals with an oropharyngeal Candida infection to determine whether saliva fluconazole concentrations could provide useful information for therapeutic drug monitoring in this population. Steady-state

  13. The effect of saliva composition on texture perception of semi-solids

    NARCIS (Netherlands)

    Engelen, L.; Keybus, P.A.M. van den; Wijk, R.A. de; Veerman, E.C.I.; Amerongen, A.V.N.; Bosman, F.; Prinz, J.F.; Bilt, A. van der

    2007-01-01

    Saliva is expected to be of significance for the perception of food stimuli in the mouth. Mixing the food with saliva, including breakdown and dilution, is considered to be of large importance for semi-solids as these products are masticated without chewing. It is known that there are large

  14. The functions of human saliva : A review sponsored by the World Workshop on Oral Medicine VI

    NARCIS (Netherlands)

    Dawes, C.; Pedersen, A. M. L.; Villa, A.; Ekstrom, J.; Proctor, G. B.; Vissink, A.; Aframian, D.; McGowan, R.; Aliko, A.; Narayana, N.; Sia, Y. W.; Joshi, R. K.; Jensen, S. B.; Kerr, A. R.; Wolff, A.

    This narrative review of the functions of saliva was conducted in the PubMed, Embase and Web of Science databases. Additional references relevant to the topic were used, as our key words did not generate references which covered all known functions of saliva. These functions include maintaining a

  15. Fluoride level in saliva after bonding orthodontic brackets with a fluoride containing adhesive

    NARCIS (Netherlands)

    Ogaard, B; Arends, J; Helseth, H; Dijkman, G; vanderKuijl, M

    The fluoride level in saliva is considered an important parameter in caries prevention. Elevation of the salivary fluoride level by a fluoride-releasing orthodontic bonding adhesive would most likely be beneficial in the prevention of enamel caries. In this study, the fluoride level in saliva was

  16. A novel one-step Helicobacter pylori saliva antigen test.

    Science.gov (United States)

    Yang, Bi-Ling; Yeh, Chun; Kwong, Wei-Gang; Lee, Shou-Dong

    2015-02-01

    A rapid, reliable, and sufficiently accurate test for diagnosing Helicobacter pylori infection is required for screening dyspeptic patients before a referral for endoscopy. The purpose of this article is two-fold: first, to evaluate the accuracy of a one-step H. pylori saliva antigen (HPS) test; and second, to compare noninvasive and invasive H. pylori tests in Taiwanese population. A total of 104 consecutive dyspeptic patients admitted for gastroenterology into the outpatient department underwent a one-step HPS test, rapid urease test, histology, and (13)C-urea breath test (13)C-UBT (proto C-13 urea kit). The accuracy of the HPS test was compared with a gold standard defined by at least two positive H. pylori test results from three H. pylori tests (histology, rapid urease test, and (13)C-UBT). The 104 patients eligible for analysis (mean age: 58 years, range 22-87 years), 21 (20%) were gold standard positive. Among them, the positive of the one-step H. pylori saliva Ag test, rapid urease test, (13)C-UBT, histology were (52; 50%), (17; 16%), (27; 25%) and (22; 21%) respectively. The sensitivity and specificity of the HPS tests, rapid urease test, (13)C-UBTs, and histology were 71.43% and 55.42%, 76.19% and 98.80%, 100% and 92.77%, and 85.71% and 95.18%, respectively, relative to the gold standard. The one-step HPS test exhibited a sensitivity of 71.43%, nearly equivalent to that of the rapid urea test. The one-step HPS test exhibited a high sensitivity and low specificity compared with the other tests, indicating that it is not sufficiently accurate for use in a clinical setting for diagnosing H. pylori infection. However, the test is simple to use (requiring only a saliva sample), inexpensive, and noninvasive in its application, and thus appealing for use in population-based prevalence surveys of the epidemiology of H. pylori infection. Copyright © 2014. Published by Elsevier Taiwan.

  17. Hubungan Body Mass Index dengan Laju Aliran Saliva (Studi pada Mahasiswa Fakultas Kedokteran Gigi Universitas Andalas

    Directory of Open Access Journals (Sweden)

    Fildzah Nurul Fajrin

    2015-12-01

    Relationship between Body Mass Index and Saliva Flow Rate (A Study in Faculty of Dentistry, Andalas University. Saliva flow rate is an affecting factor of caries formation. Adequate saliva flow rate can prevent cariess formation process and progression of periodontal disease and oral infection. Nutritional status is known as an influencing factor of saliva flow rate. The parameter of nutritional status is Body Mass Index (BMI. The purpose of this study is to discover the relation between BMI and saliva flow rate in College Students of the Dentistry Faculty Andalas University. This observational study with cross sectional design was conducted to 24 college students of the Dentistry Faculty Andalas University whose ages were 18-25 years old who complied with inclussion and exclussion criteria. BMI was calculated with BMI formula. The saliva flow rate was determined with Sialometry Method of Navazesh 2008 with ”ml/minute” unit. The univariat data analysis was caried out to describe each variable. Normality test Kolmogorov Smirnoff was done to see the normal distribution (p > 0,05. After the distribution was proven to be normal, corelation and regression test was executed to discover the relation between BMI and saliva flow rate. Based on the correlation test result, BMI of college students of the Dentistry Faculty Andalas University is χχ ± SD = 24,6 ± 6,02 kg/m2 and saliva flow rate is χχ ± SD = 0,29 ± 0,1 ml/minute. The relation between BMI and saliva flow rate expresses medium correlation with negative direction ( r = - 0,451. The result of linear regression shows that Saliva Flow Rate = 0,404 - 0,008*(BMI. The coefficient of regression BMI 0.008 shows that increasing 1 unit of BMI will decrease saliva flow rate 0,008 ml/minute. This study concludes that there is correlation between Body Mass Index and saliva flow rate. Obesity group has the lowest saliva flow rate, while the saliva flow rate does not decrease in underweight group.

  18. The management of xerostomia in patients on haemodialysis: comparison of artificial saliva and chewing gum.

    Science.gov (United States)

    Bots, Casper P; Brand, Henk S; Veerman, Enno C I; Valentijn-Benz, Marianne; Van Amerongen, Barbara M; Nieuw Amerongen, Arie V; Valentijn, Robert M; Vos, Pieter F; Bijlsma, Joost A; Bezemer, Pieter D; ter Wee, Piet M

    2005-04-01

    Many patients on haemodialysis (HD) therapy suffer from a dry mouth and xerostomia. This can be relieved by mechanical and gustatory stimulation or palliative care. The aim of this crossover study was to investigate the effect and preferences of a sugar-free chewing gum (Freedent White) and a xanthan gum-based artificial saliva (Xialine) in the management of xerostomia in chronic HD patients. Sixty-five HD patients participated in a 6-week crossover trial. The artificial saliva was rated significantly lower than the chewing gum for effectiveness, taste and a global assessment. No preference differences were found for gender and age, although older subjects rated the artificial saliva with a higher mark. Thirty-nine subjects (60%) preferred chewing gum, 15% (n=10) preferred the artificial saliva. Therefore, both chewing gum and artificial saliva could play an important role in the palliative care of xerostomia in HD patients.

  19. Whole Saliva has a Dual Role on the Adherence of Candida albicans to Polymethylmetacrylate.

    Science.gov (United States)

    Elguezabal, N; Maza, J L; Dorronsoro, S; Pontón, J

    2008-01-01

    Adhesion of Candida albicans to acrylic of dental prostheses or to salivary macromolecules adsorbed on their surface is believed to be a critical event in the development of denture stomatitis. In previous studies our group has shown that adhesion of C. albicans germ tubes to polystyrene is decreased by saliva whereas C. albicans yeast cells adhesion to the same material is enhanced. The results presented in this study confirm this dual role played by whole saliva, since it decreased the adhesion of germ tubes but increased the adhesion of yeast cells to polymethylmetacrylate (PMMA). These effects mediated by whole saliva do not seem to be related to an inhibition of the germination of C. albicans, since similar levels of filamentation were observed in presence and absence of saliva. These results may give new insights into the conflicting role of saliva in the adhesion of C. albicans to acrylic resins of dental prostheses.

  20. Microbial metabolomics with gas chromatography/mass spectrometry

    NARCIS (Netherlands)

    Koek, M.M.; Muilwijk, B.; Werf, M.J. van der; Hankemeier, T.

    2006-01-01

    An analytical method was set up suitable for the analysis of microbial metabolomes, consisting of an oximation and silylation derivatization reaction and subsequent analysis by gas chromatography coupled to mass spectrometry. Microbial matrixes contain many compounds that potentially interfere with

  1. Impact of Intestinal Microbiota on Intestinal Luminal Metabolome

    Science.gov (United States)

    Matsumoto, Mitsuharu; Kibe, Ryoko; Ooga, Takushi; Aiba, Yuji; Kurihara, Shin; Sawaki, Emiko; Koga, Yasuhiro; Benno, Yoshimi

    2012-01-01

    Low–molecular-weight metabolites produced by intestinal microbiota play a direct role in health and disease. In this study, we analyzed the colonic luminal metabolome using capillary electrophoresis mass spectrometry with time-of-flight (CE-TOFMS) —a novel technique for analyzing and differentially displaying metabolic profiles— in order to clarify the metabolite profiles in the intestinal lumen. CE-TOFMS identified 179 metabolites from the colonic luminal metabolome and 48 metabolites were present in significantly higher concentrations and/or incidence in the germ-free (GF) mice than in the Ex-GF mice (p metabolome and a comprehensive understanding of intestinal luminal metabolome is critical for clarifying host-intestinal bacterial interactions. PMID:22724057

  2. Sparse Mbplsr for Metabolomics Data and Biomarker Discovery

    DEFF Research Database (Denmark)

    Karaman, İbrahim

    2014-01-01

    the link between high throughput metabolomics data generated on different analytical platforms, discover important metabolites deriving from the digestion processes in the gut, and automate metabolic pathway discovery from mass spectrometry. PLS (partial least squares) based chemometric methods were...

  3. A Review of Applications of Metabolomics in Cancer

    Directory of Open Access Journals (Sweden)

    Richard D. Beger

    2013-07-01

    Full Text Available Cancer is a devastating disease that alters the metabolism of a cell and the surrounding milieu. Metabolomics is a growing and powerful technology capable of detecting hundreds to thousands of metabolites in tissues and biofluids. The recent advances in metabolomics technologies have enabled a deeper investigation into the metabolism of cancer and a better understanding of how cancer cells use glycolysis, known as the “Warburg effect,” advantageously to produce the amino acids, nucleotides and lipids necessary for tumor proliferation and vascularization. Currently, metabolomics research is being used to discover diagnostic cancer biomarkers in the clinic, to better understand its complex heterogeneous nature, to discover pathways involved in cancer that could be used for new targets and to monitor metabolic biomarkers during therapeutic intervention. These metabolomics approaches may also provide clues to personalized cancer treatments by providing useful information to the clinician about the cancer patient’s response to medical interventions.

  4. International NMR-based Environmental Metabolomics Intercomparison Exercise

    Science.gov (United States)

    Several fundamental requirements must be met so that NMR-based metabolomics and the related technique of metabonomics can be formally adopted into environmental monitoring and chemical risk assessment. Here we report an intercomparison exercise which has evaluated the effectivene...

  5. Spectral Relative Standard Deviation: A Practical Benchmark in Metabolomics

    Science.gov (United States)

    Metabolomics datasets, by definition, comprise of measurements of large numbers of metabolites. Both technical (analytical) and biological factors will induce variation within these measurements that is not consistent across all metabolites. Consequently, criteria are required to...

  6. NMR-based metabolomic profiling of overweight adolescents

    DEFF Research Database (Denmark)

    Zheng, Hong; Yde, Christian C; Arnberg, Karina

    2014-01-01

    The plasma and urine metabolome of 192 overweight 12-15-year-old adolescents (BMI of 25.4 ± 2.3 kg/m(2)) were examined in order to elucidate gender, pubertal development measured as Tanner stage, physical activity measured as number of steps taken daily, and intra-/interindividual differences...... and the metabolome could be identified. The present study for the first time provides comprehensive information about associations between the metabolome and gender, pubertal development, and physical activity in overweight adolescents, which is an important subject group to approach in the prevention of obesity...... affecting the metabolome detected by proton NMR spectroscopy. Higher urinary excretion of citrate, creatinine, hippurate, and phenylacetylglutamine and higher plasma level of phosphatidylcholine and unsaturated lipid were found for girls compared with boys. The results suggest that gender differences...

  7. Human gut microbes impact host serum metabolome and insulin sensitivity

    DEFF Research Database (Denmark)

    Pedersen, Helle Krogh; Gudmundsdottir, Valborg; Nielsen, Henrik Bjørn

    2016-01-01

    Insulin resistance is a forerunner state of ischaemic cardiovascular disease and type 2 diabetes. Here we show how the human gut microbiome impacts the serum metabolome and associates with insulin resistance in 277 non-diabetic Danish individuals. The serum metabolome of insulin-resistant individ......Insulin resistance is a forerunner state of ischaemic cardiovascular disease and type 2 diabetes. Here we show how the human gut microbiome impacts the serum metabolome and associates with insulin resistance in 277 non-diabetic Danish individuals. The serum metabolome of insulin......-resistant individuals is characterized by increased levels of branched-chain amino acids (BCAAs), which correlate with a gut microbiome that has an enriched biosynthetic potential for BCAAs and is deprived of genes encoding bacterial inward transporters for these amino acids. Prevotella copri and Bacteroides vulgatus...

  8. Metabolomic profiling of Green Frogs exposed to Mixed Pesticides

    Data.gov (United States)

    U.S. Environmental Protection Agency — GC/MS data from the metabolomic profiling of green frog livers after exposure to pesticides and their mixtures. This dataset is associated with the following...

  9. Corrosion of gold alloys and titanium in artificial saliva

    International Nuclear Information System (INIS)

    Brune, D.; Evje, D.

    1982-01-01

    Two types of gold alloys and one type of pure titanium have been submitted to corrosion in artificial saliva for periods of up to about 2 months. The release of copper, gold and silver from the gold alloys as well as titanium from the titanium matrix was measured with nuclear tracer technique. The physical/chemical state of the corrosion products of gold alloys referring to the ionic state or presence in particulate form has been examined retaining the particulate matter on a glass filter. Copper was observed to be mainly present in the ionic state. Considerable amounts of gold were observed to be retained on the glass filter explained by the presence of gold in particulate form or as a compentent of a dispersed collloidal phase. The estimation of the release of titanium was registered by the tracer nuclide 46 Sc assuming particulate matter to be deteriorated from the titanium surface. (author)

  10. Interactions of hydroxyapatite surfaces: conditioning films of human whole saliva.

    Science.gov (United States)

    Cárdenas, Marité; Valle-Delgado, Juan José; Hamit, Jildiz; Rutland, Mark W; Arnebrant, Thomas

    2008-07-15

    Hydroxyapatite is a very interesting material given that it is the main component in tooth enamel and because of its uses in bone implant applications. Therefore, not only the characterization of its surface is of high relevance but also designing reliable methods to study the interfacial properties of films adsorbed onto it. In this paper we apply the colloidal probe atomic force microscopy method to investigate the surface properties of commercially available hydroxyapatite surfaces (both microscopic particles and macroscopic discs) in terms of interfacial and frictional forces. In this way, we find that hydroxyapatite surfaces at physiological relevant conditions are slightly negatively charged. The surfaces were then exposed to human whole saliva, and the surface properties were re-evaluated. A thick film was formed that was very resistant to mechanical stress. The frictional measurements demonstrated that the film was indeed highly lubricating, supporting the argument that this system may prove to be a relevant model for evaluating dental and implant systems.

  11. Cultural, behavioral, social, and psychological perceptions of saliva: relevance to clinical diagnostics.

    Science.gov (United States)

    Nguyen, Sean; Wong, David T

    2006-04-01

    The search for a resource that can be used to detect a broad range of diseases easily and reliably is akin to a search for the diagnostic Holy Grail. Yet, each of us may have inside our mouths, a key to the pathological and disease biomarker library hidden inside our bodies. Saliva--the source of all this information--is the secretory product of glands located in or around the oral cavity. If one could read the stories of diagnostic information present within saliva, then the abundance of information waiting to be found could be comparable to a vast vault of information, such as the Internet. Upon dissection of this data, it would be seen that the source of this information is from saliva's origin as a filtrate of blood, and that the validity of both mediums should be equal. Although one day this may be the view, most people's hold of saliva, current and past cultures, have fared much more diverse meanings to the secretion. Ivan Pavlov's experiments has shown how closely tied salivation is with the thought of food, one of life's primary indulgences. The relationship between salivation and behaviors within our daily lives is undeniable. Yet most people never appreciate the uniqueness of saliva. Throughout the world, saliva carries definite positive and negative connotations, based upon its social, psychological, behavioral, and cultural settings. The thought of saliva may be viewed as grotesque in one population, yet may be the vehicle of blessing in other cultures. Saliva's double nature brings up some interesting cultural, social, behavioral, and psychological points about how saliva is perceived in the world, some of which are subsequently stated in order to present saliva as the spirited fluid it is.

  12. Effects of saliva collection using cotton swabs on melatonin enzyme immunoassay.

    Science.gov (United States)

    Kozaki, Tomoaki; Lee, Soomin; Nishimura, Takayuki; Katsuura, Tetsuo; Yasukouchi, Akira

    2011-01-10

    Although various acceptable and easy-to-use devices have been used for saliva collection, cotton swabs are among the most common ones. Previous studies reported that cotton swabs yield a lower level of melatonin detection. However, this statistical method is not adequate for detecting an agreement between cotton saliva collection and passive saliva collection, and a test for bias is needed. Furthermore, the effects of cotton swabs have not been examined at lower melatonin level, a level at which melatonin is used for assessment of circadian rhythms, namely dim light melatonin onset (DLMO). In the present study, we estimated the effect of cotton swabs on the results of salivary melatonin assay using the Bland-Altman plot at lower level. Nine healthy males were recruited and each provided four saliva samples on a single day to yield a total of 36 samples. Saliva samples were directly collected in plastic tubes using plastic straws, and subsequently pipetted onto cotton swabs (cotton saliva collection) and into clear sterile tubes (passive saliva collection). The melatonin levels were analyzed in duplicate using commercially available ELISA kits. The mean melatonin concentration in cotton saliva collection samples was significantly lower than that in passive saliva collection samples at higher melatonin level (>6 pg/mL). The Bland-Altman plot indicated that cotton swabs causes relative and proportional biases in the assay results. For lower melatonin level (<6 pg/mL), although the BA plots didn't show proportional and relative biases, there was no significant correlation between passive and cotton saliva collection samples. Our findings indicate an interference effect of cotton swabs on the assay result of salivary melatonin at lower melatonin level. Cotton-based collection devices might, thus, not be suitable for assessment of DLMO.

  13. Serum and saliva levels of cathepsin L in patients with acute coronary syndrome.

    Science.gov (United States)

    Mirzaii-Dizgah, Iraj; Riahi, Esmail

    2011-03-01

    Coronary artery disease (CAD) is the major cause of death nearly all over the world, and accurate and rapid diagnosis of CAD is of major medical and economic importance. The aim of this study was to evaluate the serum and saliva levels of cathepsin L in patients with acute coronary syndrome (ACS). In a cross-sectional study, 39 patients with ACS and 28 with controls were recruited to the study, and cathepsin L levels were measured in serum, resting saliva, and stimulated saliva obtained 12 and 24 h after the onset of ACS by ELISA method. Statistical analyses of Fisher's exact test, the Student's t-test or Kruskal-Wallis test were performed. Stimulated saliva cathepsin L levels in patients with ACS 12 hours but not 24 hours after admission showed significant decrease compared with that in control subjects. However, there were no significant differences in serum and unstimulated saliva cathepsin L levels between groups. Serum and saliva levels of cathepsin L remain unchanged in patients with ACS and hence may not be a promising factor in CAD risk assessment. It seems that serum and saliva cathepsin L may not be a good biomarker for CHD. CAD: Coronary artery disease, ACS: Acute coronary syndrome, CHD: Coronary heart disease, EU: Emergency unit, MI: Myocardial infarction. Cathepsin L, Acute coronary syndrome, Resting saliva, Stimulated saliva. How to cite this article: Mirzaii-Dizgah I, Riahi E. Serum and Saliva Levels of Cathepsin L in Patients with Acute Coronary Syndrome. J Contemp Dent Pract 2011;12(2):114-119.

  14. The food metabolome: a window over dietary exposure.

    Science.gov (United States)

    Scalbert, Augustin; Brennan, Lorraine; Manach, Claudine; Andres-Lacueva, Cristina; Dragsted, Lars O; Draper, John; Rappaport, Stephen M; van der Hooft, Justin J J; Wishart, David S

    2014-06-01

    The food metabolome is defined as the part of the human metabolome directly derived from the digestion and biotransformation of foods and their constituents. With >25,000 compounds known in various foods, the food metabolome is extremely complex, with a composition varying widely according to the diet. By its very nature it represents a considerable and still largely unexploited source of novel dietary biomarkers that could be used to measure dietary exposures with a high level of detail and precision. Most dietary biomarkers currently have been identified on the basis of our knowledge of food compositions by using hypothesis-driven approaches. However, the rapid development of metabolomics resulting from the development of highly sensitive modern analytic instruments, the availability of metabolite databases, and progress in (bio)informatics has made agnostic approaches more attractive as shown by the recent identification of novel biomarkers of intakes for fruit, vegetables, beverages, meats, or complex diets. Moreover, examples also show how the scrutiny of the food metabolome can lead to the discovery of bioactive molecules and dietary factors associated with diseases. However, researchers still face hurdles, which slow progress and need to be resolved to bring this emerging field of research to maturity. These limits were discussed during the First International Workshop on the Food Metabolome held in Glasgow. Key recommendations made during the workshop included more coordination of efforts; development of new databases, software tools, and chemical libraries for the food metabolome; and shared repositories of metabolomic data. Once achieved, major progress can be expected toward a better understanding of the complex interactions between diet and human health. © 2014 American Society for Nutrition.

  15. Metabolomic NMR fingerprinting: an exploratory and predictive tool

    OpenAIRE

    Lauri, Ilaria

    2014-01-01

    Metabolomics is the comprehensive assessment of low molecular weight organic metabolites within biological system. The identification and characterization of several chemical species, or metabolic fingerprinting, is an emergent approach in metabolomics field that provides a valuable “snapshot” of metabolic profiles. This approach is finding an increasing number of applications in many areas including cancer research, drug discovery and food science. The combined use of NMR spectroscopy, data ...

  16. Metabolomics approach for discovering disease biomarkers and understanding metabolic pathway

    Directory of Open Access Journals (Sweden)

    Jeeyoun Jung

    2011-12-01

    Full Text Available Metabolomics, the multi-targeted analysis of endogenous metabolites from biological samples, can be efficiently applied to screen disease biomarkers and investigate pathophysiological processes. Metabolites change rapidly in response to physiological perturbations, making them the closest link to disease phenotypes. This study explored the role of metabolomics in gaining mechanistic insight into disease processes and in searching for novel biomarkers of human diseases

  17. Stable isotope-resolved metabolomics and applications for drug development

    Science.gov (United States)

    Fan, Teresa W-M.; Lorkiewicz, Pawel; Sellers, Katherine; Moseley, Hunter N.B.; Higashi, Richard M.; Lane, Andrew N.

    2012-01-01

    Advances in analytical methodologies, principally nuclear magnetic resonance spectroscopy (NMR) and mass spectrometry (MS), during the last decade have made large-scale analysis of the human metabolome a reality. This is leading to the reawakening of the importance of metabolism in human diseases, particularly cancer. The metabolome is the functional readout of the genome, functional genome, and proteome; it is also an integral partner in molecular regulations for homeostasis. The interrogation of the metabolome, or metabolomics, is now being applied to numerous diseases, largely by metabolite profiling for biomarker discovery, but also in pharmacology and therapeutics. Recent advances in stable isotope tracer-based metabolomic approaches enable unambiguous tracking of individual atoms through compartmentalized metabolic networks directly in human subjects, which promises to decipher the complexity of the human metabolome at an unprecedented pace. This knowledge will revolutionize our understanding of complex human diseases, clinical diagnostics, as well as individualized therapeutics and drug response. In this review, we focus on the use of stable isotope tracers with metabolomics technologies for understanding metabolic network dynamics in both model systems and in clinical applications. Atom-resolved isotope tracing via the two major analytical platforms, NMR and MS, has the power to determine novel metabolic reprogramming in diseases, discover new drug targets, and facilitates ADME studies. We also illustrate new metabolic tracer-based imaging technologies, which enable direct visualization of metabolic processes in vivo. We further outline current practices and future requirements for biochemoinformatics development, which is an integral part of translating stable isotope-resolved metabolomics into clinical reality. PMID:22212615

  18. Metabolomics and Metabolic Diseases: Where Do We Stand?

    Science.gov (United States)

    Newgard, Christopher B

    2017-01-10

    Metabolomics, or the comprehensive profiling of small molecule metabolites in cells, tissues, or whole organisms, has undergone a rapid technological evolution in the past two decades. These advances have led to the application of metabolomics to defining predictive biomarkers for incident cardiometabolic diseases and, increasingly, as a blueprint for understanding those diseases' pathophysiologic mechanisms. Progress in this area and challenges for the future are reviewed here. Copyright © 2017 Elsevier Inc. All rights reserved.

  19. Pediatric obesity: could metabolomics be a useful tool?

    OpenAIRE

    Angelica Dessì; Vassilios Fanos

    2013-01-01

    Pediatric obesity represents an important health issue. In recent years applications of metabolomics have led to evaluation of responses to the various nutrients (nutrigenomics), in particular to lipids, in diseases such as obesity and diabetes. The experimental data and the studies in pediatrics  that evaluated the metabolic condition in infant obesity are presented. It is thus to be hoped that future progress in connection with this new technique, together with a metabolomic study of mother...

  20. UHPLC-Q-TOF-MS-based metabolomics approach to compare the saponin compositions of Xueshuantong injection and Xuesaitong injection.

    Science.gov (United States)

    Yao, Changliang; Yang, Wenzhi; Zhang, Jingxian; Qiu, Shi; Chen, Ming; Shi, Xiaojian; Pan, Huiqin; Wu, Wanying; Guo, Dean

    2017-02-01

    Various traditional Chinese medicine preparations developed from Notoginseng total saponins, including Xueshuantong injection and Xuesaitong injection, are extensively used in China to treat cardiocerebrovascular diseases. However, the difference of their saponin compositions remains unknown. An ultra high performance liquid chromatography with quadrupole time-of-flight mass spectrometry based metabolomics approach was developed to probe the saponin discrimination between Xueshuantong and Xuesaitong and the related factors by large sample analysis. A highly efficient chromatographic separation was achieved on an HSS T3 column within 20 min with the holistic metabolites information recorded in the negative MS E mode. A six-step data pretreatment procedure mainly based on Progenesis QI and mass defect filtering was established. Pattern recognition chemometrics was used to discover the potential saponin markers. The saponin composition of Wuzhou Xueshuantong showed distinct discrimination from the other products. Wuzhou Xueshuantong contains more abundant protopanaxatriol-type noto-R 1 , Rg 1 , Re, and protopanaxadiol-type Rb 1 , but less Rd and other low-polarity protopanaxadiol-type ginsenosides. These differences could not directly correlate to the use of different parts of Panax notoginseng, but possibly to the different preparation techniques employed by different manufacturers. These results are beneficial to the establishment of pharmacopoeia standards and the assessment of the efficacy and adverse drug reactions for these homologous products. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. Metabolomics identifies perturbations in amino acid metabolism in the prefrontal cortex of the learned helplessness rat model of depression.

    Science.gov (United States)

    Zhou, Xinyu; Liu, Lanxiang; Zhang, Yuqing; Pu, Juncai; Yang, Lining; Zhou, Chanjuan; Yuan, Shuai; Zhang, Hanping; Xie, Peng

    2017-02-20

    Major depressive disorder is a serious psychiatric condition associated with high rates of suicide and is a leading cause of health burden worldwide. However, the underlying molecular mechanisms of major depression are still essentially unclear. In our study, a non-targeted gas chromatography-mass spectrometry-based metabolomics approach was used to investigate metabolic changes in the prefrontal cortex of the learned helplessness (LH) rat model of depression. Body-weight measurements and behavioral tests including the active escape test, sucrose preference test, forced swimming test, elevated plus-maze and open field test were used to assess changes in the behavioral spectrum after inescapable footshock stress. Rats in the stress group exhibited significant learned helpless and depression-like behaviors, while without any significant change in anxiety-like behaviors. Using multivariate and univariate statistical analysis, a total of 18 differential metabolites were identified after the footshock stress protocol. Ingenuity Pathways Analysis and MetaboAnalyst were applied for predicted pathways and biological functions analysis. "Amino Acid Metabolism, Molecule Transport, Small Molecule Biochemistry" was the most significantly altered network in the LH model. Amino acid metabolism, particularly glutamate metabolism, cysteine and methionine metabolism, arginine and proline metabolism, was significantly perturbed in the prefrontal cortex of LH rats. Copyright © 2016 IBRO. Published by Elsevier Ltd. All rights reserved.

  2. Ultrasound: a subexploited tool for sample preparation in metabolomics.

    Science.gov (United States)

    Luque de Castro, M D; Delgado-Povedano, M M

    2014-01-02

    Metabolomics, one of the most recently emerged "omics", has taken advantage of ultrasound (US) to improve sample preparation (SP) steps. The metabolomics-US assisted SP step binomial has experienced a dissimilar development that has depended on the area (vegetal or animal) and the SP step. Thus, vegetal metabolomics and US assisted leaching has received the greater attention (encompassing subdisciplines such as metallomics, xenometabolomics and, mainly, lipidomics), but also liquid-liquid extraction and (bio)chemical reactions in metabolomics have taken advantage of US energy. Also clinical and animal samples have benefited from US assisted SP in metabolomics studies but in a lesser extension. The main effects of US have been shortening of the time required for the given step, and/or increase of its efficiency or availability for automation; nevertheless, attention paid to potential degradation caused by US has been scant or nil. Achievements and weak points of the metabolomics-US assisted SP step binomial are discussed and possible solutions to the present shortcomings are exposed. Copyright © 2013 Elsevier B.V. All rights reserved.

  3. Quality assurance procedures for mass spectrometry untargeted metabolomics. a review.

    Science.gov (United States)

    Dudzik, Danuta; Barbas-Bernardos, Cecilia; García, Antonia; Barbas, Coral

    2018-01-05

    Untargeted metabolomics, as a global approach, has already proven its great potential and capabilities for the investigation of health and disease, as well as the wide applicability for other research areas. Although great progress has been made on the feasibility of metabolomics experiments, there are still some challenges that should be faced and that includes all sources of fluctuations and bias affecting every step involved in multiplatform untargeted metabolomics studies. The identification and reduction of the main sources of unwanted variation regarding the pre-analytical, analytical and post-analytical phase of metabolomics experiments is essential to ensure high data quality. Nowadays, there is still a lack of information regarding harmonized guidelines for quality assurance as those available for targeted analysis. In this review, sources of variations to be considered and minimized along with methodologies and strategies for monitoring and improvement the quality of the results are discussed. The given information is based on evidences from different groups among our own experiences and recommendations for each stage of the metabolomics workflow. The comprehensive overview with tools presented here might serve other researchers interested in monitoring, controlling and improving the reliability of their findings by implementation of good experimental quality practices in the untargeted metabolomics study. Copyright © 2017 Elsevier B.V. All rights reserved.

  4. SECIMTools: a suite of metabolomics data analysis tools.

    Science.gov (United States)

    Kirpich, Alexander S; Ibarra, Miguel; Moskalenko, Oleksandr; Fear, Justin M; Gerken, Joseph; Mi, Xinlei; Ashrafi, Ali; Morse, Alison M; McIntyre, Lauren M

    2018-04-20

    Metabolomics has the promise to transform the area of personalized medicine with the rapid development of high throughput technology for untargeted analysis of metabolites. Open access, easy to use, analytic tools that are broadly accessible to the biological community need to be developed. While technology used in metabolomics varies, most metabolomics studies have a set of features identified. Galaxy is an open access platform that enables scientists at all levels to interact with big data. Galaxy promotes reproducibility by saving histories and enabling the sharing workflows among scientists. SECIMTools (SouthEast Center for Integrated Metabolomics) is a set of Python applications that are available both as standalone tools and wrapped for use in Galaxy. The suite includes a comprehensive set of quality control metrics (retention time window evaluation and various peak evaluation tools), visualization techniques (hierarchical cluster heatmap, principal component analysis, modular modularity clustering), basic statistical analysis methods (partial least squares - discriminant analysis, analysis of variance, t-test, Kruskal-Wallis non-parametric test), advanced classification methods (random forest, support vector machines), and advanced variable selection tools (least absolute shrinkage and selection operator LASSO and Elastic Net). SECIMTools leverages the Galaxy platform and enables integrated workflows for metabolomics data analysis made from building blocks designed for easy use and interpretability. Standard data formats and a set of utilities allow arbitrary linkages between tools to encourage novel workflow designs. The Galaxy framework enables future data integration for metabolomics studies with other omics data.

  5. Metabolomics through the lens of precision cardiovascular medicine.

    Science.gov (United States)

    Lam, Sin Man; Wang, Yuan; Li, Bowen; Du, Jie; Shui, Guanghou

    2017-03-20

    Metabolomics, which targets at the extensive characterization and quantitation of global metabolites from both endogenous and exogenous sources, has emerged as a novel technological avenue to advance the field of precision medicine principally driven by genomics-oriented approaches. In particular, metabolomics has revealed the cardinal roles that the environment exerts in driving the progression of major diseases threatening public health. Herein, the existent and potential applications of metabolomics in two key areas of precision cardiovascular medicine will be critically discussed: 1) the use of metabolomics in unveiling novel disease biomarkers and pathological pathways; 2) the contribution of metabolomics in cardiovascular drug development. Major issues concerning the statistical handling of big data generated by metabolomics, as well as its interpretation, will be briefly addressed. Finally, the need for integration of various omics branches and adopting a multi-omics approach to precision medicine will be discussed. Copyright © 2017 Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and Genetics Society of China. Published by Elsevier Ltd. All rights reserved.

  6. A comparison of the effects of added saliva, α-amylase and water on texture perception in semisolids

    NARCIS (Netherlands)

    Engelen, L.; Wijk, R.A. de; Prinz, J.F.; Janssen, A.M.; Bilt, A. van der; Weenen, H.; Bosman, F.

    2003-01-01

    The effect of adding saliva or a saliva-related fluid (α-amylase solution and water) to custard prior to ingestion on the sensory ratings of odour, flavour and lip-tooth-, mouth- and after-feel sensations was investigated. Saliva had previously been collected from the subjects and each subject

  7. Oligosaccharide substrate preferences of human extracellular sulfatase Sulf2 using liquid chromatography-mass spectrometry based glycomics approaches.

    Directory of Open Access Journals (Sweden)

    Yu Huang

    Full Text Available Sulfs are extracellular endosulfatases that selectively remove the 6-O-sulfate groups from cell surface heparan sulfate (HS chain. By altering the sulfation at these particular sites, Sulfs function to remodel HS chains. As a result of the remodeling activity, HSulf2 regulates a multitude of cell-signaling events that depend on interactions between proteins and HS. Previous efforts to characterize the substrate specificity of human Sulfs (HSulfs focused on the analysis of HS disaccharides and synthetic repeating units. In this study, we characterized the substrate preferences of human HSulf2 using HS oligosaccharides with various lengths and sulfation degrees from several naturally occurring HS sources by applying liquid chromatography mass spectrometry based glycomics methods. The results showed that HSulf2 preferentially digests highly sulfated HS oligosaccharides with zero acetyl groups and this preference is length dependent. In terms of length of oligosaccharides, HSulf2 digestion induced more sulfation decrease on DP6 (DP: degree of polymerization compared to DP2, DP4 and DP8. In addition, the HSulf2 preferentially digests the oligosaccharide domain located at the non-reducing end (NRE of the HS and heparin chain. In addition, the HSulf2 digestion products were altered only for specific isomers. HSulf2 treated NRE oligosaccharides also showed greater decrease in cell proliferation than those from internal domains of the HS chain. After further chromatographic separation, we identified the three most preferred unsaturated hexasaccharide for HSulf2.

  8. Mass-Spectrometry-Based Proteomics Reveals Organ-Specific Expression Patterns To Be Used as Forensic Evidence.

    Science.gov (United States)

    Dammeier, Sascha; Nahnsen, Sven; Veit, Johannes; Wehner, Frank; Ueffing, Marius; Kohlbacher, Oliver

    2016-01-04

    Standard forensic procedures to examine bullets after an exchange of fire include a mechanical or ballistic reconstruction of the event. While this is routine to identify which projectile hit a subject by DNA analysis of biological material on the surface of the projectile, it is rather difficult to determine which projectile caused the lethal injury--often the crucial point with regard to legal proceedings. With respect to fundamental law it is the duty of the public authority to make every endeavor to solve every homicide case. To improve forensic examinations, we present a forensic proteomic method to investigate biological material from a projectile's surface and determine the tissues traversed by it. To obtain a range of relevant samples, different major bovine organs were penetrated with projectiles experimentally. After tryptic "on-surface" digestion, mass-spectrometry-based proteome analysis, and statistical data analysis, we were able to achieve a cross-validated organ classification accuracy of >99%. Different types of anticipated external variables exhibited no prominent influence on the findings. In addition, shooting experiments were performed to validate the results. Finally, we show that these concepts could be applied to a real case of murder to substantially improve the forensic reconstruction.

  9. Optimization of information content in a mass spectrometry based flow-chemistry system by investigating different ionization approaches.

    Science.gov (United States)

    Martha, Cornelius T; Hoogendoorn, Jan-Carel; Irth, Hubertus; Niessen, Wilfried M A

    2011-05-15

    Current development in catalyst discovery includes combinatorial synthesis methods for the rapid generation of compound libraries combined with high-throughput performance-screening methods to determine the associated activities. Of these novel methodologies, mass spectrometry (MS) based flow chemistry methods are especially attractive due to the ability to combine sensitive detection of the formed reaction product with identification of introduced catalyst complexes. Recently, such a mass spectrometry based continuous-flow reaction detection system was utilized to screen silver-adducted ferrocenyl bidentate catalyst complexes for activity in a multicomponent synthesis of a substituted 2-imidazoline. Here, we determine the merits of different ionization approaches by studying the combination of sensitive detection of product formation in the continuous-flow system with the ability to simultaneous characterize the introduced [ferrocenyl bidentate+Ag](+) catalyst complexes. To this end, we study the ionization characteristics of electrospray ionization (ESI), atmospheric-pressure chemical ionization (APCI), no-discharge APCI, dual ESI/APCI, and dual APCI/no-discharge APCI. Finally, we investigated the application potential of the different ionization approaches by the investigation of ferrocenyl bidentate catalyst complex responses in different solvents. Copyright © 2011 Elsevier B.V. All rights reserved.

  10. Multiplatform Mass Spectrometry-Based Approach Identifies Extracellular Glycolipids of the Yeast Rhodotorula babjevae UCDFST 04-877.

    Science.gov (United States)

    Cajka, Tomas; Garay, Luis A; Sitepu, Irnayuli R; Boundy-Mills, Kyria L; Fiehn, Oliver

    2016-10-28

    A multiplatform mass spectrometry-based approach was used for elucidating extracellular lipids with biosurfactant properties produced by the oleaginous yeast Rhodotorula babjevae UCDFST 04-877. This strain secreted 8.6 ± 0.1 g/L extracellular lipids when grown in a benchtop bioreactor fed with 100 g/L glucose in medium without addition of hydrophobic substrate, such as oleic acid. Untargeted reversed-phase liquid chromatography-quadrupole/time-of-flight mass spectrometry (QTOFMS) detected native glycolipid molecules with masses of 574-716 Da. After hydrolysis into the fatty acid and sugar components and hydrophilic interaction chromatography-QTOFMS analysis, the extracellular lipids were found to consist of hydroxy fatty acids and sugar alcohols. Derivatization and chiral separation gas chromatography-mass spectrometry (GC-MS) identified these components as d-arabitol, d-mannitol, (R)-3-hydroxymyristate, (R)-3-hydroxypalmitate, and (R)-3-hydroxystearate. In order to assemble these substructures back into intact glycolipids that were detected in the initial screen, potential structures were in-silico acetylated to match the observed molar masses and subsequently characterized by matching predicted and observed MS/MS fragmentation using the Mass Frontier software program. Eleven species of acetylated sugar alcohol esters of hydroxy fatty acids were characterized for this yeast strain.

  11. Classification of Tempranillo wines according to geographic origin: Combination of mass spectrometry based electronic nose and chemometrics

    Energy Technology Data Exchange (ETDEWEB)

    Cynkar, Wies, E-mail: wies.cynkar@awri.com.au [Australian Wine Research Institute, PO Box 197, Glen Osmond, SA 5064 (Australia); Dambergs, Robert [Australian Wine Research Institute, Tasmanian Institute of Agricultural Research, University of Tasmania, Private Bag 98, Hobart Tasmania 7001 (Australia); Smith, Paul; Cozzolino, Daniel [Australian Wine Research Institute, PO Box 197, Glen Osmond, SA 5064 (Australia)

    2010-02-15

    Rapid methods employing instruments such as electronic noses (EN) or gas sensors are used in the food and beverage industries to monitor and assess the composition and quality of products. Similar to other food industries, the wine industry has a clear need for simple, rapid and cost effective techniques for objectively evaluating the quality of grapes, wine and spirits. In this study a mass spectrometry based electronic nose (MS-EN) instrument combined with chemometrics was used to predict the geographical origin of Tempranillo wines produced in Australia and Spain. The MS-EN data generated were analyzed using principal components analysis (PCA), partial least squares discriminant analysis (PLS-DA) and stepwise linear discriminant analysis (SLDA) with full cross validation (leave-one-out method). The SLDA classified correctly 86% of the samples while PLS-DA 85% of Tempranillo wines according to their geographical origin. The relative benefits of using MS-EN will provide capability for rapid screening of wines. However, this technique does not provide the identification and quantitative determination of individual compounds responsible for the different aroma notes in the wine.

  12. Classification of Tempranillo wines according to geographic origin: Combination of mass spectrometry based electronic nose and chemometrics

    International Nuclear Information System (INIS)

    Cynkar, Wies; Dambergs, Robert; Smith, Paul; Cozzolino, Daniel

    2010-01-01

    Rapid methods employing instruments such as electronic noses (EN) or gas sensors are used in the food and beverage industries to monitor and assess the composition and quality of products. Similar to other food industries, the wine industry has a clear need for simple, rapid and cost effective techniques for objectively evaluating the quality of grapes, wine and spirits. In this study a mass spectrometry based electronic nose (MS-EN) instrument combined with chemometrics was used to predict the geographical origin of Tempranillo wines produced in Australia and Spain. The MS-EN data generated were analyzed using principal components analysis (PCA), partial least squares discriminant analysis (PLS-DA) and stepwise linear discriminant analysis (SLDA) with full cross validation (leave-one-out method). The SLDA classified correctly 86% of the samples while PLS-DA 85% of Tempranillo wines according to their geographical origin. The relative benefits of using MS-EN will provide capability for rapid screening of wines. However, this technique does not provide the identification and quantitative determination of individual compounds responsible for the different aroma notes in the wine.

  13. Bond strength of self-etch adhesives after saliva contamination at different application steps.

    Science.gov (United States)

    Cobanoglu, N; Unlu, N; Ozer, F F; Blatz, M B

    2013-01-01

    This study evaluated and compared the effect of saliva contamination and possible decontamination methods on bond strengths of two self-etching adhesive systems (Clearfil SE Bond [CSE], Optibond Solo Plus SE [OSE]). Flat occlusal dentin surfaces were created on 180 extracted human molar teeth. The two bonding systems and corresponding composite resins (Clearfil AP-X, Kerr Point 4) were bonded to the dentin under six surface conditions (n=15/group): group 1 (control): primer/bonding/composite; group 2: saliva/drying/primer/bonding/composite; group 3: primer/saliva/rinsing/drying/primer/bonding/composite; group 4: primer/saliva/rinsing/drying/bonding/composite; group 5: primer/bonding (cured)/saliva/rinsing/drying/primer/bonding/composite; group 6: primer/bonding (cured)/saliva/removing contaminated layer with a bur/rinsing/drying/primer/bonding/composite. Shear bond strength was tested after specimens were stored in distilled water at 37°C for 24 hours. One-way analysis of variance and Tukey post hoc tests were used for statistical analyses. For CSE, groups 2, 3, and 4 and for OSE, groups 6, 2, and 4 showed significantly lower bond strengths than the control group (pcontamination occurred after light polymerization of the bonding agent, repeating the bonding procedure recovered the bonding capacity of both self-etch adhesives. However, saliva contamination before or after primer application negatively affected their bond strength.

  14. Bacterial profiles of saliva in relation to diet, lifestyle factors, and socioeconomic status

    Directory of Open Access Journals (Sweden)

    Daniel Belstrøm

    2014-04-01

    Full Text Available Background and objective: The bacterial profile of saliva is composed of bacteria from different oral surfaces. The objective of this study was to determine whether different diet intake, lifestyle, or socioeconomic status is associated with characteristic bacterial saliva profiles. Design: Stimulated saliva samples from 292 participants with low levels of dental caries and periodontitis, enrolled in the Danish Health Examination Survey (DANHES, were analyzed for the presence of approximately 300 bacterial species by means of the Human Oral Microbe Identification Microarray (HOMIM. Using presence and levels (mean HOMIM-value of bacterial probes as endpoints, the influence of diet intake, lifestyle, and socioeconomic status on the bacterial saliva profile was analyzed by Mann–Whitney tests with Benjamini–Hochberg's correction for multiple comparisons and principal component analysis. Results: Targets for 131 different probes were identified in 292 samples, with Streptococcus and Veillonella being the most predominant genera identified. Two bacterial taxa (Streptococcus sobrinus and Eubacterium [11][G-3] brachy were more associated with smokers than non-smokers (adjusted p-value<0.01. Stratification of the group based on extreme ends of the parameters age, gender, alcohol consumption, body mass index (BMI, and diet intake had no statistical influence on the composition of the bacterial profile of saliva. Conversely, differences in socioeconomic status were reflected by the bacterial profiles of saliva. Conclusions: The bacterial profile of saliva seems independent of diet intake, but influenced by smoking and maybe socioeconomic status.

  15. Real-time PCR quantification of six periodontal pathogens in saliva samples from healthy young adults.

    Science.gov (United States)

    Zhou, Xiaodong; Liu, Xiaoli; Li, Jing; Aprecio, Raydolfo M; Zhang, Wu; Li, Yiming

    2015-05-01

    The use of saliva as a diagnostic fluid for the evaluation of periodontal health has gained attention recently. Most published real-time PCR assays focused on quantification of bacteria in subgingival plaque, not in saliva. The aims of this study were to develop a real-time PCR assay for quantification of six periodontal pathogens in saliva and to establish a relationship between the amount of DNA (fg) and colony-forming unit (CFU). TaqMan primers/probe sets were used for the detection of Aggregatibacter actinomycetemcomitans (Aa), Eikenella corrodens (Ec), Fusobacterium nucleatum (Fn), Porphyromonas gingivalis (Pg), Prevotella intermedia (Pi), Tannerella forsythia (Tf), and total bacteria. Six periodontal pathogens and total bacteria in saliva from 24 periodontally healthy individuals were determined. The relationship between the amount of DNA (fg) and CFU was established by measuring the concentrations of extracted bacterial DNA and CFU per milliliter of bacteria on agar plates. Fn, Ec, and Pi were detected in all saliva samples, while 58.5, 45.8, and 33.3% were detected for Tf, Pg, and Aa, respectively. Numbers of Ec and Fn in saliva were highly correlated (R(2) = 0.93, P periodontal pathogens in saliva and estimate the number of live bacteria (CFU). This real-time PCR assay in combination with the relationship between DNA (fg) and CFU has the potential to be an adjunct in evaluation of periodontal health status.

  16. Cigarette smoke-exposed saliva suppresses cellular and humoral immune responses in an animal model

    International Nuclear Information System (INIS)

    Jafarzadeh, A.; Bakhshi, H.; Rezayati, M.T.; Nemati, M.

    2009-01-01

    To evaluate the effects of cigarette smoke (CS)-exposed saliva on cellular and antibody responses in an animal model. The stimulatory and non-stimulatory saliva samples were collected from 10 healthy subjects and were then exposed to CS for 20 or 80 minutes. The CS-exposed saliva samples were administrated intraperitoneally (i.p) to male Balb/c mice. Then the delayed type hypersensitivity (DTH) and antibody responses to sheep red blood cell (SRBC) was assessed. Moreover, the total white blood cells (WBC) counts and the blood lymphocytes counts were determined. The mean of DTH responses of animal groups received 20 minutes or 80 minutes CS-exposed saliva samples was significantly lower than that observed in control group. Moreover, The mean titer of anti-SRBC antibody was significantly lower in animal groups who received 80 minutes CS-exposed stimulatory or non-stimulatory saliva as compared to control group (P<0.04 and P<0.002, respectively). The mean counts of blood lymphocytes in 80 minutes CS exposed-stimulatory saliva group was also significantly lower as compared to control group (P<0.05). These results show that the CS-exposed saliva samples have profound suppressive effects on both cellular and humoral immune response in a mouse animal model (JPMA 59:760; 2009). (author)

  17. Blood Contamination in Saliva: Impact on the Measurement of Salivary Oxidative Stress Markers

    Directory of Open Access Journals (Sweden)

    Natália Kamodyová

    2015-01-01

    Full Text Available Salivary oxidative stress markers represent a promising tool for monitoring of oral diseases. Saliva can often be contaminated by blood, especially in patients with periodontitis. The aim of our study was to examine the impact of blood contamination on the measurement of salivary oxidative stress markers. Saliva samples were collected from 10 healthy volunteers and were artificially contaminated with blood (final concentration 0.001–10%. Next, saliva was collected from 12 gingivitis and 10 control patients before and after dental hygiene treatment. Markers of oxidative stress were measured in all collected saliva samples. Advanced oxidation protein products (AOPP, advanced glycation end products (AGEs, and antioxidant status were changed in 1% blood-contaminated saliva. Salivary AOPP were increased in control and patients after dental treatment (by 45.7% and 34.1%, p<0.01. Salivary AGEs were decreased in patients after microinjury (by 69.3%, p<0.001. Salivary antioxidant status markers were decreased in both control and patients after dental treatment (p<0.05 and p<0.01. One % blood contamination biased concentrations of salivary oxidative stress markers. Saliva samples with 1% blood contamination are visibly discolored and can be excluded from analyses without any specific biochemic detection of blood constituents. Salivary markers of oxidative stress were significantly altered in blood-contaminated saliva in control and patients with gingivitis after dental hygiene treatment.

  18. Saliva oxytocin measures do not reflect peripheral plasma concentrations after intranasal oxytocin administration in men.

    Science.gov (United States)

    Quintana, Daniel S; Westlye, Lars T; Smerud, Knut T; Mahmoud, Ramy A; Andreassen, Ole A; Djupesland, Per G

    2018-05-16

    Oxytocin plays an important role in social behavior. Thus, there has been significant research interest for the role of the oxytocin system in several psychiatric disorders, and the potential of intranasal oxytocin administration to treat social dysfunction. Measurement of oxytocin concentrations in saliva are sometimes used to approximate peripheral levels of oxytocin; however, the validity of this approach is unclear. In this study, saliva and plasma oxytocin was assessed after two doses of Exhalation Delivery System delivered intranasal oxytocin (8 IU and 24 IU), intravenous oxytocin (1 IU) and placebo in a double-dummy, within-subjects design with men. We found that intranasal oxytocin (8 IU and 24 IU) administration increased saliva oxytocin concentrations in comparison to saliva oxytocin concentration levels after intravenous and placebo administration. Additionally, we found that saliva oxytocin concentrations were not significantly associated with plasma oxytocin concentrations after either intranasal or intravenous oxytocin administration. Altogether, we suggest that saliva oxytocin concentrations do not accurately index peripheral oxytocin after intranasal or intravenous oxytocin administration, at least in men. The data indicates that elevated oxytocin saliva levels after nasal delivery primarily reflect exogenous administered oxytocin that is cleared from the nasal cavity to the oropharynx, and is therefore a weak surrogate for peripheral blood measurements. Copyright © 2018 Elsevier Inc. All rights reserved.

  19. Effects of a prolonged standardized diet on normalizing the human metabolome123

    OpenAIRE

    Winnike, Jason H; Busby, Marjorie G; Watkins, Paul B; O'Connell, Thomas M

    2009-01-01

    Background: Although the effects of acute dietary interventions on the human metabolome have been studied, the extent to which the metabolome can be normalized by extended dietary standardization has not yet been examined.

  20. The role of saliva in the process of oxidative stress – review of literature

    Directory of Open Access Journals (Sweden)

    Anna Krysińska

    2016-12-01

    Full Text Available Background: Saliva constitutes a first line of defence against free radical-mediated oxidative stress, since the process of mastication and digestion promotes lipid peroxidation. During gingival inflammation, gingival crevicular fluid flow increases the change of saliva composition with products from the inflammatory response, modulating oxidative damages in the oral cavity. Authors review the current literature concerning the reactive oxygen species, oxidants, pro-oxidants and antioxidants in saliva, and methods for assessing the antioxidant capacity of saliva. Comparison of salivary antioxidant status in male and female subjects reveales a significant gender-related difference in saliva composition. The current data demonstrate a significant enhancement of the salivary antioxidant system in juvenile idiopathic arthritis patients. Also patients with chronic renal failure, diabetes and on hemodialysis show increase oxidative stress burden in both serum and saliva. The finding of reduced oral peroxidase levels in smoking subjects may represent a contributory mechanism for initiation and progression of cigarette smoke-related oral diseases such as oral cancer. The results of recent studies indicate that the total antioxidant capacity of saliva decreased in children with HIV infection. Conclusion: Whole saliva may contain simply measured indicators of oxidative processes. This may provide a tool for the development and monitoring of new treatment strategies. A non-invasive determination of the salivary concentrations of antioxidants such as superoxide dismutase (SOD and uric acid (UR allows the evaluation of the defensive capacity of the oral mucosa. Still, there is a need for standardization of methods for saliva sampling and testing protocol.

  1. Effects of saliva collection using cotton swabs on melatonin enzyme immunoassay

    Directory of Open Access Journals (Sweden)

    Katsuura Tetsuo

    2011-01-01

    Full Text Available Abstract Background Although various acceptable and easy-to-use devices have been used for saliva collection, cotton swabs are among the most common ones. Previous studies reported that cotton swabs yield a lower level of melatonin detection. However, this statistical method is not adequate for detecting an agreement between cotton saliva collection and passive saliva collection, and a test for bias is needed. Furthermore, the effects of cotton swabs have not been examined at lower melatonin level, a level at which melatonin is used for assessment of circadian rhythms, namely dim light melatonin onset (DLMO. In the present study, we estimated the effect of cotton swabs on the results of salivary melatonin assay using the Bland-Altman plot at lower level. Methods Nine healthy males were recruited and each provided four saliva samples on a single day to yield a total of 36 samples. Saliva samples were directly collected in plastic tubes using plastic straws, and subsequently pipetted onto cotton swabs (cotton saliva collection and into clear sterile tubes (passive saliva collection. The melatonin levels were analyzed in duplicate using commercially available ELISA kits. Results The mean melatonin concentration in cotton saliva collection samples was significantly lower than that in passive saliva collection samples at higher melatonin level (>6 pg/mL. The Bland-Altman plot indicated that cotton swabs causes relative and proportional biases in the assay results. For lower melatonin level ( Conclusion Our findings indicate an interference effect of cotton swabs on the assay result of salivary melatonin at lower melatonin level. Cotton-based collection devices might, thus, not be suitable for assessment of DLMO.

  2. Determination of carbamazepine in serum and saliva samples by high performance liquid chromatography with ultraviolet detection

    Directory of Open Access Journals (Sweden)

    Đorđević Snežana

    2009-01-01

    Full Text Available Background/Aim. Carbamazepine is antiepileptic drug widely used for the treatment of epilepsy. Due to low therapeutic index of carbamazepine there is a need for routine measuring its concentrations in biological fluids. The aim of the study was to describe a method for concomitant determination of carbamazepine in the serum and saliva. Methods. Separation of the drug from matrix is achieved by reversedphase chromatography on a C18 column, with a mobile phase of methanol-water-acetic acid (65:34:1 at a flow-rate of 1.0 ml/min. Detection was effected by ultra-violet absorption at 285 nm. The total run time was 5 min. Samples were prepared by alkaline extraction (pH 10 using chlorophorm. Results. Calibration curves were in the range 0.1-5 μg/mL for serum and saliva samples. Mean recoveries of spiked serum and saliva were 97.59 and 92.30%, respectively. Limits of detection (LOD of carbamazepine in serum and saliva were 0.166 and 0.178 μg/mL, respectively. Limits of quantification (LOQ in the serum and saliva were 0.237 and 0.226 μg/mL, respectively. The method precision was carried out with coefficient of variation of 2.10% and 4.03% for the serum and saliva, respectively. The obtained data showed that there was a strong correlation between saliva and serum concentrations (r = 0.9481, p < 0.001. Conclusion. The method described here is rapid, precise, accurate and simple, and can be used for quantitative determination of carbamazepine in human serum and saliva after therapy applying. Saliva samples could be used as an alternative matrix for therapeutic drug monitoring of this antiepileptic drug.

  3. Determination of carbamazepine in serum and saliva samples by high performance liquid chromatography with ultraviolet detection.

    Science.gov (United States)

    Dordević, Snezana; Kilibarda, Vesna; Stojanović, Tomislav

    2009-05-01

    Carbamazepine is antiepileptic drug widely used for the treatment of epilepsy. Due to low therapeutic index of carbamazepine there is a need for routine measuring its concentrations in biological fluids. The aim of the study was to describe a method for concomitant determination of carbamazepine in the serum and saliva. Separation of the drug from matrix is achieved by reversed-phase chromatography on a C18 column, with a mobile phase of methanol-water-acetic acid (65:34:1) at a flow-rate of 1.0 ml/min. Detection was effected by ultra-violet absorption at 285 nm. The total run time was 5 min. Samples were prepared by alkaline extraction (pH 10) using chlorophorm. Calibration curves were in the range 0.1-5 microg/mL for serum and saliva samples. Mean recoveries of spiked serum and saliva were 97.59 and 92.30%, respectively. Limits of detection (LOD) of carbamazepine in serum and saliva were 0.166 and 0.178 microg/mL, respectively. Limits of quantification (LOQ) in the serum and saliva were 0.237 and 0.226 microg/mL, respectively. The method precision was carried out with coefficient of variation of 2.10% and 4.03% for the serum and saliva, respectively. The obtained data showed that there was a strong correlation between saliva and serum concentrations (r = 0.9481, p < 0.001). The method described here is rapid, precise, accurate and simple, and can be used for quantitative determination of carbamazepine in human serum and saliva after therapy applying. Saliva samples could be used as an alternative matrix for therapeutic drug monitoring of this antiepileptic drug.

  4. An interlaboratory comparison between similar methods for determination of melatonin, cortisol and testosterone in saliva

    DEFF Research Database (Denmark)

    Jensen, Marie Aarrebo; Mortier, Leen; Koh, Eitetsu

    2014-01-01

    /L for melatonin, 0.56 and 6.72 nmol/L for cortisol and 11.9 and 73.8 pmol/L for testosterone. This indicates a large interlaboratory variation. The present study emphasizes the importance of external quality control for the analysis of melatonin, cortisol and testosterone in saliva.......An interlaboratory comparison study for melatonin, cortisol and testosterone in saliva in which five laboratories participated is reported in this study. Each laboratory blindly measured eight samples prepared from natural saliva spiked with melatonin, cortisol and testosterone in the range 0...

  5. Trefoil factors in saliva and gingival tissues of patients with chronic periodontitis

    DEFF Research Database (Denmark)

    Chaiyarit, Ponlatham; Chayasadom, Anek; Wara-Aswapati, Nawarat

    2012-01-01

    BACKGROUND: Trefoil factors (TFFs) are secreted molecules that are involved in cytoprotection against tissue damage and the immune response. TFFs have been detected in saliva and oral tissues, but their clinical significance has never been investigated in patients with chronic periodontitis....... The objective of this study is to determine whether TFF expression in saliva and gingival tissues is associated with periodontal pathology. METHODS: Saliva and gingival tissue samples were collected from 25 non-periodontitis individuals and 25 patients with chronic periodontitis (CP). Enzyme...... observed in patients with CP (P = 0.003 and P periodontal pathology and number of Porphyromonas gingivalis...

  6. Meal-induced compositional changes in blood and saliva in persons with bulimia nervosa

    DEFF Research Database (Denmark)

    Dynesen, Anja Weirsøe; Jensen, Allan Bardow; Astrup, Arne

    2008-01-01

    in controls before and after intake of a meal and whether these changes may be reflected in saliva. Design: Twenty women with bulimia nervosa and 20 age- and sex-matched healthy controls participated. After an overnight fast, the subjects ate a standardized carbohydrate-rich breakfast. Whole saliva and blood...... were collected, and visual analogue scales for hunger and satiety were completed once before and continuously for 5 h after the breakfast. Results: A lower pre- and postprandial whole saliva flow rate was found in subjects with bulimia nervosa, which might have been attributable to a concomitant intake...

  7. Assessing genetic polymorphisms using DNA extracted from cells present in saliva samples

    Directory of Open Access Journals (Sweden)

    Nemoda Zsofia

    2011-12-01

    Full Text Available Abstract Background Technical advances following the Human Genome Project revealed that high-quality and -quantity DNA may be obtained from whole saliva samples. However, usability of previously collected samples and the effects of environmental conditions on the samples during collection have not been assessed in detail. In five studies we document the effects of sample volume, handling and storage conditions, type of collection device, and oral sampling location, on quantity, quality, and genetic assessment of DNA extracted from cells present in saliva. Methods Saliva samples were collected from ten adults in each study. Saliva volumes from .10-1.0 ml, different saliva collection devices, sampling locations in the mouth, room temperature storage, and multiple freeze-thaw cycles were tested. One representative single nucleotide polymorphism (SNP in the catechol-0-methyltransferase gene (COMT rs4680 and one representative variable number of tandem repeats (VNTR in the serotonin transporter gene (5-HTTLPR: serotonin transporter linked polymorphic region were selected for genetic analyses. Results The smallest tested whole saliva volume of .10 ml yielded, on average, 1.43 ± .77 μg DNA and gave accurate genotype calls in both genetic analyses. The usage of collection devices reduced the amount of DNA extracted from the saliva filtrates compared to the whole saliva sample, as 54-92% of the DNA was retained on the device. An "adhered cell" extraction enabled recovery of this DNA and provided good quality and quantity DNA. The DNA from both the saliva filtrates and the adhered cell recovery provided accurate genotype calls. The effects of storage at room temperature (up to 5 days, repeated freeze-thaw cycles (up to 6 cycles, and oral sampling location on DNA extraction and on genetic analysis from saliva were negligible. Conclusions Whole saliva samples with volumes of at least .10 ml were sufficient to extract good quality and quantity DNA. Using

  8. Hubungan PH, Hidrasi, Kapasitas Bufer Saliva, Jumlah Streptococcus Mutans dengan Keparahan Karies pada Anak Rampan Karies

    OpenAIRE

    Subekti, Ani; Kristiani, Nany; Rimbyastuti, Hermin

    2013-01-01

    Rampan caries is the habit of bottle feeding at night, sweets preference and often meals sucking. Saliva is one of the factors that may influence the occurrence of caries. Some of the factors that cause caries saliva such as saliva pH, hydration, microorganisms of the oral cavity and salivary buffer capacity.The research objective was to determine the relationship of hydration, pH, buffer capacity salivary and growth Streptoccoccus mutans against caries severity or deft.A sample of 30 kinderg...

  9. Assessment of two complementary liquid chromatography coupled to high resolution mass spectrometry metabolomics strategies for the screening of anabolic steroid treatment in calves

    International Nuclear Information System (INIS)

    Dervilly-Pinel, Gaud; Weigel, Stefan; Lommen, Arjen; Chereau, Sylvain; Rambaud, Lauriane; Essers, Martien; Antignac, Jean-Philippe; Nielen, Michel W.F.; Le Bizec, Bruno

    2011-01-01

    Anabolic steroids are banned in food producing livestock in Europe. Efficient methods based on mass spectrometry detection have been developed to ensure the control of such veterinary drug residues. Nevertheless, the use of 'cocktails' composed of mixtures of low amounts of several substances as well as the synthesis of new compounds of unknown structure prevent efficient prevention. New analytical tools able to detect such abuse are today mandatory. In this context, metabolomics may represent new emerging strategies for investigating the global physiological effects associated to a family of substances and therefore, to suspect the administration of steroids. The purpose of the present study was to set up, assess and compare two complementary mass spectrometry-based metabolomic strategies as new tools to screen for steroid abuse in cattle and demonstrate the feasibility of such approaches. The protocols were developed in two European laboratories in charge of residues analysis in the field of food safety. Apart from sample preparation, the global process was different in both laboratories from LC-HRMS fingerprinting to multivariate data analysis through data processing and involved both LC-Orbitrap-XCMS and UPLC-ToF-MS-MetAlign strategies. The reproducibility of both sample preparation and MS measurements were assessed in order to guarantee that any differences in the acquired fingerprints were not caused by analytical variability but reflect metabolome modifications upon steroids administration. The protocols were then applied to urine samples collected on a large group of animals consisting of 12 control calves and 12 calves administrated with a mixture of 17β-estradiol 3-benzoate and 17β-nandrolone laureate esters according to a protocol reflecting likely illegal practices. The modifications in urine profiles as indicators of steroid administration have been evaluated in this context and proved the suitability of the approach for discriminating anabolic

  10. Assessment of two complementary liquid chromatography coupled to high resolution mass spectrometry metabolomics strategies for the screening of anabolic steroid treatment in calves

    Energy Technology Data Exchange (ETDEWEB)

    Dervilly-Pinel, Gaud, E-mail: laberca@oniris-nantes.fr [ONIRIS, Ecole nationale veterinaire, agroalimentaire et de l' alimentation Nantes-Atlantique, Laboratoire d' Etude des Residus et Contaminants dans les Aliments (LABERCA), Atlanpole - La Chantrerie, BP 40706, Nantes F-44307 (France); Weigel, Stefan; Lommen, Arjen [RIKILT - Institute of Food Safety, Wageningen UR, P.O. Box 230, 6700 AE Wageningen (Netherlands); Chereau, Sylvain; Rambaud, Lauriane [ONIRIS, Ecole nationale veterinaire, agroalimentaire et de l' alimentation Nantes-Atlantique, Laboratoire d' Etude des Residus et Contaminants dans les Aliments (LABERCA), Atlanpole - La Chantrerie, BP 40706, Nantes F-44307 (France); Essers, Martien [RIKILT - Institute of Food Safety, Wageningen UR, P.O. Box 230, 6700 AE Wageningen (Netherlands); Antignac, Jean-Philippe [ONIRIS, Ecole nationale veterinaire, agroalimentaire et de l' alimentation Nantes-Atlantique, Laboratoire d' Etude des Residus et Contaminants dans les Aliments (LABERCA), Atlanpole - La Chantrerie, BP 40706, Nantes F-44307 (France); Nielen, Michel W.F. [RIKILT - Institute of Food Safety, Wageningen UR, P.O. Box 230, 6700 AE Wageningen (Netherlands); Wageningen University, Laboratory of Organic Chemistry, Wageningen (Netherlands); Le Bizec, Bruno [ONIRIS, Ecole nationale veterinaire, agroalimentaire et de l' alimentation Nantes-Atlantique, Laboratoire d' Etude des Residus et Contaminants dans les Aliments (LABERCA), Atlanpole - La Chantrerie, BP 40706, Nantes F-44307 (France)

    2011-08-26

    Anabolic steroids are banned in food producing livestock in Europe. Efficient methods based on mass spectrometry detection have been developed to ensure the control of such veterinary drug residues. Nevertheless, the use of 'cocktails' composed of mixtures of low amounts of several substances as well as the synthesis of new compounds of unknown structure prevent efficient prevention. New analytical tools able to detect such abuse are today mandatory. In this context, metabolomics may represent new emerging strategies for investigating the global physiological effects associated to a family of substances and therefore, to suspect the administration of steroids. The purpose of the present study was to set up, assess and compare two complementary mass spectrometry-based metabolomic strategies as new tools to screen for steroid abuse in cattle and demonstrate the feasibility of such approaches. The protocols were developed in two European laboratories in charge of residues analysis in the field of food safety. Apart from sample preparation, the global process was different in both laboratories from LC-HRMS fingerprinting to multivariate data analysis through data processing and involved both LC-Orbitrap-XCMS and UPLC-ToF-MS-MetAlign strategies. The reproducibility of both sample preparation and MS measurements were assessed in order to guarantee that any differences in the acquired fingerprints were not caused by analytical variability but reflect metabolome modifications upon steroids administration. The protocols were then applied to urine samples collected on a large group of animals consisting of 12 control calves and 12 calves administrated with a mixture of 17{beta}-estradiol 3-benzoate and 17{beta}-nandrolone laureate esters according to a protocol reflecting likely illegal practices. The modifications in urine profiles as indicators of steroid administration have been evaluated in this context and proved the suitability of the approach for

  11. Saliva characteristics, diet and carioreceptivity in dental students.

    Science.gov (United States)

    Chifor, Ioana; Badea, Iulia; Chifor, Radu; Popa, Dan; Staniste, Liviu; Tarmure, Dragos; Avram, Ramona

    2014-01-01

    The use of sugar by dental plaque microorganisms leads to acid formation from the bacteria metabolism, which determines a decrease of pH onto teeth surfaces. The value of the critical pH is 5.2-5.5. We aimed to evaluate the capacity of patients to change their diet towards caries prevention after acknowledging the values of saliva parameters (pH, buffer capacity). A group of 52 subjects were clinically examined according to the International Caries Assessment and Detection System protocol. They were required to complete a diet questionnaire and salivary tests were made for the oral mucosa hydration level, pH, buffer capacity, salivary flow rate at rest and upon stimulation. 4 pre-calibrated 6th year students and 2 dentists performed the tests and the ICDAS examination. One week after the tests, the subjects were asked to complete the diet questionnaire again. The studied group consisted of students aged between 23-26 years, randomly selected among 6(th) year students of the Faculty of Dentistry from Cluj-Napoca. The mean DMF-S index was 18.39. Most of the patients (65%) had a DMF-S index between 9 and 21. Just 2.5% had an index of 3, which was the lowest value recorded. 5% of the patients had a DMFS of 35, which was the maximal value recorded. The distribution of DMF-S was normal. 50% of the patients had no active caries. Even though most subjects (19.23%) had a pH within the normal interval, most of them were at the bottom value of the interval (6.8). Most subjects had a pH of 6.4, which is moderately acid. The mean pH was 6.7, therefore, a moderately acid one. The Pearson correlation coefficient between DMFS and pH was 0.255. A mild negative correlation (-0.275) was found between the cariogenic food and buffer capacity. A week later we noticed a statistically significant decrease of cariogenic foods and drinks in students with acid pH and with low buffer capacity. A regular intake of cakes, bonbons and chocolate was reported by subjects who had a high DMF-S value

  12. Metabolomic markers of fatigue: Association between circulating metabolome and fatigue in women with chronic widespread pain.

    Science.gov (United States)

    Freidin, Maxim B; Wells, Helena R R; Potter, Tilly; Livshits, Gregory; Menni, Cristina; Williams, Frances M K

    2018-02-01

    Fatigue is a sensation of unbearable tiredness that frequently accompanies chronic widespread musculoskeletal pain (CWP) and inflammatory joint disease. Its mechanisms are poorly understood and there is a lack of effective biomarkers for diagnosis and onset prediction. We studied the circulating metabolome in a population sample characterised for CWP to identify biomarkers showing specificity for fatigue. Untargeted metabolomic profiling was conducted on fasting plasma and serum samples of 1106 females with and without CWP from the TwinsUK cohort. Linear mixed-effects models accounting for covariates were used to determine relationships between fatigue and metabolites. Receiver operating curve (ROC)-analysis was used to determine predictive value of metabolites for fatigue. While no association between fatigue and metabolites was identified in twins without CWP (n=711), in participants with CWP (n=395), levels of eicosapentaenoate (EPA) ω-3 fatty acid were significantly reduced in those with fatigue (β=-0.452±0.116; p=1.2×10 -4 ). A significant association between fatigue and two other metabolites also emerged when BMI was excluded from the model: 3-carboxy-4-methyl-5-propyl-2-furanpropanoate (CMPF), and C-glycosyltryptophan (p=1.5×10 -4 and p=3.1×10 -4 , respectively). ROC analysis has identified a combination of 15 circulating metabolites with good predictive potential for fatigue in CWP (AUC=75%; 95% CI 69-80%). The results of this agnostic metabolomics screening show that fatigue is metabolically distinct from CWP, and is associated with a decrease in circulating levels of EPA. Our panel of circulating metabolites provides the starting point for a diagnostic test for fatigue in CWP. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

  13. Parámetros inflamatorios en saliva y sangre en niños y adolescentes sanos Inflammatory parameters in saliva and blood from healthy children and adolescents

    Directory of Open Access Journals (Sweden)

    Ninoska Tahis Viera Sirit

    2011-09-01

    Full Text Available En la actualidad se ha mostrado interés en el empleo de la saliva para ser utilizada como una alternativa de diagnóstico, predicción y progresión de diversas enfermedades con relación a otros fluidos corporales. Los objetivos trazados para la realización de este trabajo fueron: correlacionar las concentraciones en saliva y sangre de IL-1, IL-6, TNF-a, sustancias reactivas al ácido tiobarbitúrico y O2- de niños y adolescentes sistémicamente sanos. Se realizó un estudio de corte transversal en 23 niños y adolescentes sanos, entre 4 y 17 años de edad. Se les realizaron evaluaciones clínicas para determinar las condiciones bucales y estudios inmunológicos con el propósito de identificar los niveles de citosinas, a través del ensayo inmunoenzimático indirecto, el O2- por método citoquímico y las sustancias reactivas al ácido tiobarbitúrico, a través del ensayo colorimétrico. Hubo diferencia significativa entre las muestras de saliva y las de sangre periférica respecto a las citosinas y sustancias reactivas al ácido tiobarbitúrico estudiadas. Los resultados fueron: IL-1 en sangre= 1,646 ± 0,13 pg/mL y de IL-1 en saliva= 552,36 ± 75,7 pg/mL; IL-6 en sangre= 3,506 ± 1,85 pg/mL, e IL-6 en saliva= 26,89 ± 9,97 pg/mL. Al analizar el TNF-a en sangre fue de 12,91 ± 3,05 pg/mL y en saliva= 43,56 ± 6,44 pg/mL, las sustancias reactivas al ácido tiobarbitúrico en sangre= 9,46 ± 3,26 nmol/mL y en saliva= 1,26 ± 0,03 nmol/mL. No se observó correlación estadísticamente significativa entre las muestras de sangre y saliva para los valores de IL-1, IL-6 y sustancias reactivas al ácido tiobarbitúrico. En cuanto al TNF-a se evidenció una correlación significativa, r s= 0,78. No se evidenciaron células positivas para el O2- en las muestras estudiadas. Los resultados del análisis de correlación obtenido entre las muestras salivales y séricas, no aportaron evidencias suficientes para sugerir que la saliva pueda ser utilizada

  14. Corrosion of dental alloys in artificial saliva with Streptococcus mutans.

    Science.gov (United States)

    Lu, Chunhui; Zheng, Yuanli; Zhong, Qun

    2017-01-01

    A comparative study of the corrosion resistance of CoCr and NiCr alloys in artificial saliva (AS) containing tryptic soy broth (Solution 1) and Streptococcus mutans (S. mutans) species (Solution 2) was performed by electrochemical methods, including open circuit potential measurements, impedance spectroscopy, and potentiodynamic polarization. The adherence of S. mutans to the NiCr and CoCr alloy surfaces immersed in Solution 2 for 24 h was verified by scanning electron microscopy, while the results of electrochemical impedance spectroscopy confirmed the importance of biofilm formation for the corrosion process. The R(QR) equivalent circuit was successfully used to fit the data obtained for the AS mixture without S. mutans, while the R(Q(R(QR))) circuit was found to be more suitable for describing the biofilm properties after treatment with the AS containing S. mutans species. In addition, a negative shift of the open circuit potential with immersion time was observed for all samples regardless of the solution type. Both alloys exhibited higher charge transfer resistance after treatment with Solution 2, and lower corrosion current densities were detected for all samples in the presence of S. mutans. The obtained results suggest that the biofilm formation observed after 24 h of exposure to S. mutans bacteria might enhance the corrosion resistance of the studied samples by creating physical barriers that prevented oxygen interactions with the metal surfaces.

  15. Radioimmunoassay for progesterone in human saliva during the menstrual cycle

    Energy Technology Data Exchange (ETDEWEB)

    Luisi, M.; Franchi, F.; Kicovic, P.M.; Silvestri, D.; Cossu, G.; Catarsi, A.L.; Barletta, D.; Gasperi, M. (Pisa Univ. (Italy))

    1981-10-01

    A sensitive, specific and accurate radioimmunoassay of progesterone in human saliva is described, using /sup 3/H. The assay had a sensitivity of 8 pg/tube and blanks were negligible. The intra- and inter-assay coefficients of variation were 5.2 and 9.4%, respectively. The mean recovery from 60 samples was 93.2 +- 6.3%. Results obtained from nine healthy, normally menstruating women showed that salivary progesterone rose from the 4th day before ovulation to a mean peak (+- SD) of 1.14 +- 0.17 ng/ml on the 8th day after ovulation, followed by a gradual decline. Correlation of salivary and simultaneously obtained plasma progesterone levels was good (r = 0.47; P < 0.001), although the maximum percent increase in salivary progesterone was more than 10 times greater than that of plasma progesterone. Salivary progesterone is thought to reflect the unbound fraction of plasma progesterone and this non-invasive technique can be used for serial investigations in which frequent samplings are required.

  16. Disorders of saliva production and taste sensation after oropharyngeal irradiation

    International Nuclear Information System (INIS)

    Herrmann, T.; Adamski, K.; Stefan, M.

    1984-01-01

    Salivary secretion and disorders of taste sensation during and after radiotherapy of the oropharyngeal region were investigated in 20 patients. Salivary glands and tongue were exposed to radiation in different extent. Telecobalt irradiations were given in daily doses of 1.8 - 2.0 Gy, the total dose being 55 - 60 Gy in the salivary glands (1,590 - 1,760 ret). The patients were asked for subjective statements on salivary secretion, taste disorders were measured by semiquantitative gustometry with different dilution ratios for the four basis qualities of taste. 2 weeks after the onset of irradiation (20.0 Gy) a reduction of saliva production appeared without tendency of recovery. A statistically significant increase of the taste threshold appeared for all qualities of taste after 20 - 30 Gy. The criterion 'bitter' was primarily affected. This radiogen disorder, apparently caused on the cellular level of the taste buds, seems to be reversible also for doses of 60 Gy (1,760 ret) while radiogen functional disorders of the salivary glands are irreversible from 45 Gy (1,500 ret). Considering all sensual and organic effects of xerostomy (dental caries, osteoradionecrosis) it is advisable to keep the dose for at least one third of the salivary gland tissue below this critical value. (author)

  17. Mass spectrometry-based metabolic profiling of gemcitabine-sensitive and gemcitabine-resistant pancreatic cancer cells.

    Science.gov (United States)

    Fujimura, Yoshinori; Ikenaga, Naoki; Ohuchida, Kenoki; Setoyama, Daiki; Irie, Miho; Miura, Daisuke; Wariishi, Hiroyuki; Murata, Masaharu; Mizumoto, Kazuhiro; Hashizume, Makoto; Tanaka, Masao

    2014-03-01

    Gemcitabine resistance (GR) is one of the critical issues for therapy for pancreatic cancer, but the mechanism still remains unclear. Our aim was to increase the understanding of GR by metabolic profiling approach. To establish GR cells, 2 human pancreatic cancer cell lines, SUIT-2 and CAPAN-1, were exposed to increasing concentration of gemcitabine. Both parental and chemoresistant cells obtained by this treatment were subjected to metabolic profiling based on liquid chromatography-mass spectrometry. Multivariate statistical analyses, both principal component analysis and orthogonal partial least squares discriminant analysis, distinguished metabolic signature of responsiveness and resistance to gemcitabine in both SUIT-2 and CAPAN-1 cells. Among significantly different (P metabolic pathways such as amino acid, nucleotide, energy, cofactor, and vitamin pathways. Decreases in glutamine and proline levels as well as increases in aspartate, hydroxyproline, creatine, and creatinine levels were observed in chemoresistant cells from both cell lines. These results suggest that metabolic profiling can isolate distinct features of pancreatic cancer in the metabolome of gemcitabine-sensitive and GR cells. These findings may contribute to the biomarker discovery and an enhanced understanding of GR in pancreatic cancer.

  18. Metabolomics of Small Numbers of Cells: Metabolomic Profiling of 100, 1000, and 10000 Human Breast Cancer Cells.

    Science.gov (United States)

    Luo, Xian; Li, Liang

    2017-11-07

    In cellular metabolomics, it is desirable to carry out metabolomic profiling using a small number of cells in order to save time and cost. In some applications (e.g., working with circulating tumor cells in blood), only a limited number of cells are available for analysis. In this report, we describe a method based on high-performance chemical isotope labeling (CIL) nanoflow liquid chromatography mass spectrometry (nanoLC-MS) for high-coverage metabolomic analysis of small numbers of cells (i.e., ≤10000 cells). As an example, 12 C-/ 13 C-dansyl labeling of the metabolites in lysates of 100, 1000, and 10000 MCF-7 breast cancer cells was carried out using a new labeling protocol tailored to handle small amounts of metabolites. Chemical-vapor-assisted ionization in a captivespray interface was optimized for improving metabolite ionization and increasing robustness of nanoLC-MS. Compared to microflow LC-MS, the nanoflow system provided much improved metabolite detectability with a significantly reduced sample amount required for analysis. Experimental duplicate analyses of biological triplicates resulted in the detection of 1620 ± 148, 2091 ± 89 and 2402 ± 80 (n = 6) peak pairs or metabolites in the amine/phenol submetabolome from the 12 C-/ 13 C-dansyl labeled lysates of 100, 1000, and 10000 cells, respectively. About 63-69% of these peak pairs could be either identified using dansyl labeled standard library or mass-matched to chemical structures in human metabolome databases. We envisage the routine applications of this method for high-coverage quantitative cellular metabolomics using a starting material of 10000 cells. Even for analyzing 100 or 1000 cells, although the metabolomic coverage is reduced from the maximal coverage, this method can still detect thousands of metabolites, allowing the analysis of a large fraction of the metabolome and focused analysis of the detectable metabolites.

  19. Saliva and gastrointestinal functions of mastication, taste and textural perception, swallowing and initial digestion

    DEFF Research Database (Denmark)

    Pedersen, Anne Marie Lynge; Sørensen, Christiane E; Proctor, Gordon

    2018-01-01

    pattern. This review paper provides insight into the mechanisms by which saliva acts in relation to taste, mastication, bolus formation, enzymatic digestion, and swallowing. Also the protective functions of saliva including maintenance of dental and mucosal integrity will be discussed as they indirectly......Saliva exerts multiple functions in relation to the initial digestive processes taking place in the upper parts of the gastrointestinal tract. Ingestion of food and beverages, in turn, is a strong stimulus for secretion of saliva with a differential composition depending on the neuronal stimulation...... influence the digestive process. The final part of this paper focuses on the implications of xerostomia and salivary gland dysfunction on gastrointestinal functions. This article is protected by copyright. All rights reserved....

  20. [The physicochemical and microbiological characteristics of saliva during and after pregnancy].

    Science.gov (United States)

    Martínez-Pabón, María C; Martínez Delgado, Cecilia M; López-Palacio, Ana M; Patiño-Gómez, Lina M; Arango-Pérez, Eduin A

    2014-01-01

    Identify the changes in some physiological and microbiological parameters in the saliva from a group of women during and after their pregnancies. Stimulated whole saliva was collected from a cohort of 35 women during their pregnancy and afterwards to determine each sample's physicochemical (secretion rate, pH and buffer capacity) and microbiological characteristics (acidogenic bacteria count). The pH and buffer capacity of saliva during pregnancy were lower than after pregnancy. There were no statistically significant changes regarding S. mutans and Lactobacillus spp. count, but a tendency towards increased values during pregnancy was noted. Changes occurring in the saliva of pregnant women can lead to an increase of risk of suffering disease affecting one's oral health, such as caries, gingivitis and periodontal disease; this could be prevented by appropriate diagnosis and dental follow-up, including education regarding pregnant women's oral health.

  1. Alkaline phosphatase levels in patients with coronary heart disease saliva and its relation with periodontal status

    Science.gov (United States)

    Yunita, Dina Suci; Masulili, Sri Lelyati C.; Tadjoedin, Fatimah M.; Radi, Basuni

    2017-02-01

    Coronary heart disease (CHD) is a disease that causes narrowing of the coronary arteries. Currently, there is a hypothesis regarding periodontal infection that increases risk for heart disease. Alkaline phosphatase (ALP) as a marker of inflammation will increase in atherosclerosis and periodontal disease. The objective of this research is analyzing the relationship between the levels of alkaline phosphatase in saliva with periodontal status in patients with CHD and non CHD. Here, saliva of 104 subjects were taken, each 1 ml, and levels of Alkaline Phosphatase was analyzed using Abbott ci4100 architect. We found that no significant difference of Alkaline Phosphatase levels in saliva between CHD patients and non CHD. Therefore, it can be concluded that Alkaline Phosphatase levels in patients with CHD saliva was higher than non CHD and no association between ALP levels with periodontal status.

  2. Clinical aspects of Candida species carriage in saliva of xerotomic subjects.

    Science.gov (United States)

    Torres, S R; Peixoto, C B; Caldas, D M; Silva, E B; Magalhães, F A C; Uzeda, M; Nucci, M

    2003-10-01

    In order to investigate the clinical factors that might influence the diversity and the degree of Candida species carriage in saliva, we conducted a cross-sectional study with 133 patients with complaints of xerostomia. Anamnesis, oral examination and collection of chewing-stimulated whole saliva were performed. The samples of saliva were kept refrigerated until they were plated onto CHROMagar Candida; cfu were counted and Candida species were identified by standard methods. There was a high prevalence of mixed Candida colonization. No relationship was found between total Candida cfu counts and variables like gender, age, place of origin, underlying diseases, exposure to medications (except antibiotics), daily habits and salivary flow rates. Oral candidiasis, antibiotic exposure and dental prosthesis wearing were associated with relatively high Candida counts in saliva. Low salivary flow rates predisposed to intense colonization by C. albicans and C. parapsilosis.

  3. LC-MS-BASED METABOLOMICS OF XENOBIOTIC-INDUCED TOXICITIES

    Directory of Open Access Journals (Sweden)

    Chi Chen

    2013-01-01

    Full Text Available Xenobiotic exposure, especially high-dose or repeated exposure of xenobiotics, can elicit detrimental effects on biological systems through diverse mechanisms. Changes in metabolic systems, including formation of reactive metabolites and disruption of endogenous metabolism, are not only the common consequences of toxic xenobiotic exposure, but in many cases are the major causes behind development of xenobiotic-induced toxicities (XIT. Therefore, examining the metabolic events associated with XIT generates mechanistic insights into the initiation and progression of XIT, and provides guidance for prevention and treatment. Traditional bioanalytical platforms that target only a few suspected metabolites are capable of validating the expected outcomes of xenobiotic exposure. However, these approaches lack the capacity to define global changes and to identify unexpected events in the metabolic system. Recent developments in high-throughput metabolomics have dramatically expanded the scope and potential of metabolite analysis. Among all analytical techniques adopted for metabolomics, liquid chromatography-mass spectrometry (LC-MS has been most widely used for metabolomic investigations of XIT due to its versatility and sensitivity in metabolite analysis. In this review, technical platform of LC-MS-based metabolomics, including experimental model, sample preparation, instrumentation, and data analysis, are discussed. Applications of LC-MS-based metabolomics in exploratory and hypothesis-driven investigations of XIT are illustrated by case studies of xenobiotic metabolism and endogenous metabolism associated with xenobiotic exposure.

  4. Can NMR solve some significant challenges in metabolomics?

    Science.gov (United States)

    Gowda, G.A. Nagana; Raftery, Daniel

    2015-01-01

    The field of metabolomics continues to witness rapid growth driven by fundamental studies, methods development, and applications in a number of disciplines that include biomedical science, plant and nutrition sciences, drug development, energy and environmental sciences, toxicology, etc. NMR spectroscopy is one of the two most widely used analytical platforms in the metabolomics field, along with mass spectrometry (MS). NMR's excellent reproducibility and quantitative accuracy, its ability to identify structures of unknown metabolites, its capacity to generate metabolite profiles using intact biospecimens with no need for separation, and its capabilities for tracing metabolic pathways using isotope labeled substrates offer unique strengths for metabolomics applications. However, NMR's limited sensitivity and resolution continue to pose a major challenge and have restricted both the number and the quantitative accuracy of metabolites analyzed by NMR. Further, the analysis of highly complex biological samples has increased the demand for new methods with improved detection, better unknown identification, and more accurate quantitation of larger numbers of metabolites. Recent efforts have contributed significant improvements in these areas, and have thereby enhanced the pool of routinely quantifiable metabolites. Additionally, efforts focused on combining NMR and MS promise opportunities to exploit the combined strength of the two analytical platforms for direct comparison of the metabolite data, unknown identification and reliable biomarker discovery that continue to challenge the metabolomics field. This article presents our perspectives on the emerging trends in NMR-based metabolomics and NMR's continuing role in the field with an emphasis on recent and ongoing research from our laboratory. PMID:26476597

  5. [Development of Plant Metabolomics and Medicinal Plant Genomics].

    Science.gov (United States)

    Saito, Kazuki

    2018-01-01

     A variety of chemicals produced by plants, often referred to as 'phytochemicals', have been used as medicines, food, fuels and industrial raw materials. Recent advances in the study of genomics and metabolomics in plant science have accelerated our understanding of the mechanisms, regulation and evolution of the biosynthesis of specialized plant products. We can now address such questions as how the metabolomic diversity of plants is originated at the levels of genome, and how we should apply this knowledge to drug discovery, industry and agriculture. Our research group has focused on metabolomics-based functional genomics over the last 15 years and we have developed a new research area called 'Phytochemical Genomics'. In this review, the development of a research platform for plant metabolomics is discussed first, to provide a better understanding of the chemical diversity of plants. Then, representative applications of metabolomics to functional genomics in a model plant, Arabidopsis thaliana, are described. The extension of integrated multi-omics analyses to non-model specialized plants, e.g., medicinal plants, is presented, including the identification of novel genes, metabolites and networks for the biosynthesis of flavonoids, alkaloids, sulfur-containing metabolites and terpenoids. Further, functional genomics studies on a variety of medicinal plants is presented. I also discuss future trends in pharmacognosy and related sciences.

  6. Can NMR solve some significant challenges in metabolomics?

    Science.gov (United States)

    Nagana Gowda, G. A.; Raftery, Daniel

    2015-11-01

    The field of metabolomics continues to witness rapid growth driven by fundamental studies, methods development, and applications in a number of disciplines that include biomedical science, plant and nutrition sciences, drug development, energy and environmental sciences, toxicology, etc. NMR spectroscopy is one of the two most widely used analytical platforms in the metabolomics field, along with mass spectrometry (MS). NMR's excellent reproducibility and quantitative accuracy, its ability to identify structures of unknown metabolites, its capacity to generate metabolite profiles using intact bio-specimens with no need for separation, and its capabilities for tracing metabolic pathways using isotope labeled substrates offer unique strengths for metabolomics applications. However, NMR's limited sensitivity and resolution continue to pose a major challenge and have restricted both the number and the quantitative accuracy of metabolites analyzed by NMR. Further, the analysis of highly complex biological samples has increased the demand for new methods with improved detection, better unknown identification, and more accurate quantitation of larger numbers of metabolites. Recent efforts have contributed significant improvements in these areas, and have thereby enhanced the pool of routinely quantifiable metabolites. Additionally, efforts focused on combining NMR and MS promise opportunities to exploit the combined strength of the two analytical platforms for direct comparison of the metabolite data, unknown identification and reliable biomarker discovery that continue to challenge the metabolomics field. This article presents our perspectives on the emerging trends in NMR-based metabolomics and NMR's continuing role in the field with an emphasis on recent and ongoing research from our laboratory.

  7. Metabolomics for functional genomics, systems biology, and biotechnology.

    Science.gov (United States)

    Saito, Kazuki; Matsuda, Fumio

    2010-01-01

    Metabolomics now plays a significant role in fundamental plant biology and applied biotechnology. Plants collectively produce a huge array of chemicals, far more than are produced by most other organisms; hence, metabolomics is of great importance in plant biology. Although substantial improvements have been made in the field of metabolomics, the uniform annotation of metabolite signals in databases and informatics through international standardization efforts remains a challenge, as does the development of new fields such as fluxome analysis and single cell analysis. The principle of transcript and metabolite cooccurrence, particularly transcriptome coexpression network analysis, is a powerful tool for decoding the function of genes in Arabidopsis thaliana. This strategy can now be used for the identification of genes involved in specific pathways in crops and medicinal plants. Metabolomics has gained importance in biotechnology applications, as exemplified by quantitative loci analysis, prediction of food quality, and evaluation of genetically modified crops. Systems biology driven by metabolome data will aid in deciphering the secrets of plant cell systems and their application to biotechnology.

  8. Parámetros inflamatorios en saliva y sangre en niños y adolescentes sanos Inflammatory parameters in saliva and blood from healthy children and adolescents

    OpenAIRE

    Ninoska Tahis Viera Sirit; Thais Teresita Morales Rojas; Alejandra Isabel Morón Medina; Rita Mireya Navas Perozo; Adriana Beatriz Pedreañez Santana

    2011-01-01

    En la actualidad se ha mostrado interés en el empleo de la saliva para ser utilizada como una alternativa de diagnóstico, predicción y progresión de diversas enfermedades con relación a otros fluidos corporales. Los objetivos trazados para la realización de este trabajo fueron: correlacionar las concentraciones en saliva y sangre de IL-1, IL-6, TNF-a, sustancias reactivas al ácido tiobarbitúrico y O2- de niños y adolescentes sistémicamente sanos. Se realizó un estudio de corte transversal en ...

  9. Saliva Polymerase-Chain-Reaction Assay for Cytomegalovirus Screening in Newborns

    Science.gov (United States)

    Boppana, Suresh B.; Ross, Shannon A.; Shimamura, Masako; Palmer, April L.; Ahmed, Amina; Michaels, Marian G.; Sánchez, Pablo J.; Bernstein, David I.; Tolan, Robert W.; Novak, Zdenek; Chowdhury, Nazma; Britt, William J.; Fowler, Karen B.

    2011-01-01

    BACKGROUND Congenital cytomegalovirus (CMV) infection is an important cause of hearing loss, and most infants at risk for CMV-associated hearing loss are not identified early in life because of failure to test for the infection. The standard assay for newborn CMV screening is rapid culture performed on saliva specimens obtained at birth, but this assay cannot be automated. Two alternatives — real-time polymerase-chain-reaction (PCR)–based testing of a liquid-saliva or dried-saliva specimen obtained at birth — have been developed. METHODS In our prospective, multicenter screening study of newborns, we compared real-time PCR assays of liquid-saliva and dried-saliva specimens with rapid culture of saliva specimens obtained at birth. RESULTS A total of 177 of 34,989 infants (0.5%; 95% confidence interval [CI], 0.4 to 0.6) were positive for CMV, according to at least one of the three methods. Of 17,662 newborns screened with the use of the liquid-saliva PCR assay, 17,569 were negative for CMV, and the remaining 85 infants (0.5%; 95% CI, 0.4 to 0.6) had positive results on both culture and PCR assay. The sensitivity and specificity of the liquid-saliva PCR assay were 100% (95% CI, 95.8 to 100) and 99.9% (95% CI, 99.9 to 100), respectively, and the positive and negative predictive values were 91.4% (95% CI, 83.8 to 96.2) and 100% (95% CI, 99.9 to 100), respectively. Of 17,327 newborns screened by means of the dried-saliva PCR assay, 74 were positive for CMV, whereas 76 (0.4%; 95% CI, 0.3 to 0.5) were found to be CMV-positive on rapid culture. Sensitivity and specificity of the dried-saliva PCR assay were 97.4% (95% CI, 90.8 to 99.7) and 99.9% (95% CI, 99.9 to 100), respectively. The positive and negative predictive values were 90.2% (95% CI, 81.7 to 95.7) and 99.9% (95% CI, 99.9 to 100), respectively. CONCLUSIONS Real-time PCR assays of both liquid- and dried-saliva specimens showed high sensitivity and specificity for detecting CMV infection and should be

  10. Pengaruh (pH Saliva terhadap Terjadinya Karies Gigi pada Anak Usia Prasekolah

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    Made Ayu Lely

    2017-12-01

    Full Text Available AbstractDental caries is a multifactorial process that occurs through the interaction between teeth and saliva as host, the bacteria in the oral cavity, as well as easily fermented foods. Saliva is one of the factors that have a major influence on the severity of dental caries. The aim of this study was to determine the relationship of salivary pH with dental caries among 564 preschool-age children in DIY Province and Banten Province. The results showed that pH levels of the preschool-age children’saliva are more than 75% basic ranging between 6.8 to 8.0 and the highest levels are in Serang District. Index def-t in Serang District is highest (8.83 and the lowest one is in Yogyakarta City (4.97. The mean number of cavities/ decay more than missing teeth or filling teeth. The study indicates that the acidity of saliva among preschool children in the two provinces is not associated with the occurrence of dental caries.It is more likely due to the habit of drinking sweet milk or eating sticky foods.Key words: thepH of saliva, dental caries,sweet food, sticky foods, preschool childrenageAbstrakKaries gigi merupakan proses multifaktor yang terjadi melalui interaksi antara gigi dan saliva sebagai pejamu, bakteri didalam rongga mulut, serta makanan yang mudah difermentasikan. Saliva merupakan salah satu faktor yang mempunyai pengaruh besar terhadap keparahan karies gigi. Tujuan dari penelitian ini adalah untuk mengetahui pengaruh pH saliva terhadap terjadinya karies gigi pada anak usia prasekolah. Penelitian dilakukan secara potong lintang pada 564 orang anak usia prasekolah di Provinsi Daerah Istimewa Yogyakarta (Provinsi DIY dan Provinsi Banten. Hasil penelitian menunjukkan bahwa derajat keasaman (pH saliva pada anak-anak usia prasekolah lebih dari 75% bersifat basa berkisar antara 6,8-8,0 dan tertinggi di Kabupaten Serang. Indeks def-t tertinggi 8,83 di Kabupaten Serang dan yang terendah 4,97 di Kotamadya Yogyakarta. Rerata jumlah gigi berlubang

  11. Saliva from nymph and adult females of Haemaphysalis longicornis: a proteomic study.

    Science.gov (United States)

    Tirloni, Lucas; Islam, Mohammad Saiful; Kim, Tae Kwon; Diedrich, Jolene K; Yates, John R; Pinto, Antônio F M; Mulenga, Albert; You, Myung-Jo; Da Silva Vaz, Itabajara

    2015-06-24

    Haemaphysalis longicornis is a major vector of Theileria spp., Anaplasma phagocytophilum, Babesia spp. and Coxiella burnetti in East Asian countries. All life stages of ixodid ticks have a destructive pool-feeding style in which they create a pool-feeding site by lacerating host tissue and secreting a variety of biologically active compounds that allows the tick to evade host responses, enabling the uptake of a blood meal. The identification and functional characterization of tick saliva proteins can be useful to elucidate the molecular mechanisms involved in tick development and to conceive new anti-tick control methods. H. longicornis tick saliva was collected from fully engorged nymphs and fully engorged adults induced by dopamine or pilocarpine, respectively. Saliva was digested with trypsin for LC-MS/MS sequencing and peptides were searched against tick and rabbit sequences. A total of 275 proteins were identified, of which 135 were tick and 100 were rabbit proteins. Of the tick proteins, 30 proteins were identified exclusively in fully engorged nymph saliva, 74 in fully engorged adult females, and 31 were detected in both stages. The identified tick proteins include heme/iron metabolism-related proteins, oxidation/detoxification proteins, enzymes, proteinase inhibitors, tick-specific protein families, and cytoskeletal proteins. Proteins involved in signal transduction, transport and metabolism of carbohydrate, energy, nucleotide, amino acids and lipids were also detected. Of the rabbit proteins, 13 were present in nymph saliva, 48 in adult saliva, and 30 were present in both. The host proteins include immunoglobulins, complement system proteins, antimicrobial proteins, serum albumin, peroxiredoxin, serotransferrin, apolipoprotein, hemopexin, proteinase inhibitors, and hemoglobin/red blood cells-related products. This study allows the identification of H. longicornis saliva proteins. In spontaneously detached tick saliva various proteins were identified

  12. 49 CFR 40.263 - What happens when an employee is unable to provide a sufficient amount of saliva for an alcohol...

    Science.gov (United States)

    2010-10-01

    ... sufficient amount of saliva for an alcohol screening test? (a) As the STT, you must take the following steps if an employee is unable to provide sufficient saliva to complete a test on a saliva screening device (e.g., the employee does not provide sufficient saliva to activate the device). (1) You must conduct...

  13. Arsenic speciation in saliva of acute promyelocytic leukemia patients undergoing arsenic trioxide treatment

    OpenAIRE

    Chen, Baowei; Cao, Fenglin; Yuan, Chungang; Lu, Xiufen; Shen, Shengwen; Zhou, Jin; Le, X. Chris

    2013-01-01

    Arsenic trioxide has been successfully used as a therapeutic in the treatment of acute promyelocytic leukemia (APL). Detailed monitoring of the therapeutic arsenic and its metabolites in various accessible specimens of APL patients can contribute to improving treatment efficacy and minimizing arsenic-induced side effects. This article focuses on the determination of arsenic species in saliva samples from APL patients undergoing arsenic treatment. Saliva samples were collected from nine APL pa...

  14. Influence of artificial saliva in biofilm formation of Candida albicans in vitro

    Directory of Open Access Journals (Sweden)

    Michelle Peneluppi Silva

    2012-02-01

    Full Text Available Due to the increase in life expectancy, new treatments have emerged which, although palliative, provide individuals with a better quality of life. Artificial saliva is a solution that contains substances that moisten a dry mouth, thus mimicking the role of saliva in lubricating the oral cavity and controlling the existing normal oral microbiota. This study aimed to assess the influence of commercially available artificial saliva on biofilm formation by Candida albicans. Artificial saliva I consists of carboxymethylcellulose, while artificial saliva II is composed of glucose oxidase, lactoferrin, lysozyme and lactoperoxidase. A control group used sterile distilled water. Microorganisms from the oral cavity were transferred to Sabouraud Dextrose Agar and incubated at 37°C for 24 hours. Colonies of Candida albicans were suspended in a sterile solution of NaCl 0.9%, and standardisation of the suspension to 106 cells/mL was achieved. The acrylic discs, immersed in artificial saliva and sterile distilled water, were placed in a 24-well plate containing 2 mL of Sabouraud Dextrose Broth plus 5% sucrose and 0.1 mL aliquot of the Candida albicans suspension. The plates were incubated at 37°C for 5 days, the discs were washed in 2 mL of 0.9% NaCl and placed into a tube containing 10 mL of 0.9% NaCl. After decimal dilutions, aliquots of 0.1 mL were seeded on Sabouraud Dextrose Agar and incubated at 37°C for 48 hours. Counts were reported as CFU/mL (Log10. A statistically significant reduction of 29.89% (1.45 CFU/mL of Candida albicans was observed in saliva I when compared to saliva II (p = 0.002, considering p≤0.05.

  15. Investigation of Fe and Ca in non-stimulated human saliva using NAA

    Science.gov (United States)

    de Medeiros, J. A. G.; Zamboni, C. B.; Kovacs, L.; Lewgoy, H. R.

    2015-07-01

    In this study we investigated non-stimulated human whole saliva of healthy subjects and patients with periodontal disease using Neutron Activation Analysis technique (NAA). The measurements were performed in the IEA-R1 nuclear reactor at IPEN-CNEN/SP. We found considerable metabolic changes mainly in Fe and Ca concentration in whole saliva of periodontal patients. These data are useful for identifying or preventing this oral disease in the Brazilian population.

  16. Status Antioksidan Total pada Saliva Pasien Periodontitis Kronis di Instalasi Periodonsia FKG USU

    OpenAIRE

    Khairunnisa, Desi

    2016-01-01

    Chronic periodontitis is caused by the immune reaction between bacteria and host. Some forms of examination have been developed to detect the development of periodontitis disease through saliva. Saliva consists of water, protein, electrolytes, gingival sulcus fluids, bacteria, organic molecules, antioxidant components. Antioxidants are released at inflammation sites by PMNs to protect from theReactive Oxygen Species (ROS).ROSsuch as O2 dan H2O2 are released by PMNs during phagocytosis that ca...

  17. Zika virus infection spread through saliva – a truth or myth?

    Directory of Open Access Journals (Sweden)

    Walter Luiz SIQUEIRA

    2016-01-01

    Full Text Available Abstract In this Point-of-view article we highlighted some features related to saliva and virus infection, in special for zika virus. In addition, we pointed out the potential oral problems caused by a microcephaly originated by a zika virus infection. In the end the, we demonstrated the importance of a more comprehensive exploration of saliva and their components as a fluid for diagnostic and therapeutic approaches on oral and systemic diseases.

  18. Shear Bond Strength of Orthodontic Brackets and Disinclusion Buttons: Effect of Water and Saliva Contamination

    OpenAIRE

    Sfondrini, Maria Francesca; Fraticelli, Danilo; Gandini, Paola; Scribante, Andrea

    2013-01-01

    Purpose. The aim of this study was to assess the effect of water and saliva contamination on the shear bond strength and failure site of orthodontic brackets and lingual buttons. Materials and Methods. 120 bovine permanent mandibular incisors were randomly divided into 6 groups of 20 specimens each. Both orthodontic brackets and disinclusion buttons were tested under three different enamel surface conditions: (a) dry, (b) water contamination, and (c) saliva contamination. Brackets and buttons...

  19. Whole Saliva has a Dual Role on the Adherence of Candida albicans to Polymethylmetacrylate

    OpenAIRE

    Elguezabal, N; Maza, J.L.; Dorronsoro, S.; Pont?n, J.

    2008-01-01

    Adhesion of Candida albicans to acrylic of dental prostheses or to salivary macromolecules adsorbed on their surface is believed to be a critical event in the development of denture stomatitis. In previous studies our group has shown that adhesion of C. albicans germ tubes to polystyrene is decreased by saliva whereas C. albicans yeast cells adhesion to the same material is enhanced. The results presented in this study confirm this dual role played by whole saliva, since it decreased the adhe...

  20. Therapeutic drug monitoring of caffeine in preterm infants: Could saliva be an alternative to serum?

    Science.gov (United States)

    Chaabane, Amel; Chioukh, Fatma Z; Chadli, Zohra; Ben Fredj, Nadia; Ben Ameur, Karim; Ben Hmida, Hayet; Boughattas, Naceur A; Monastiri, Kamel; Aouam, Karim

    2017-12-01

    Evaluate whether saliva could be a useful alternative to serum for routine therapeutic drug monitoring of caffeine in preterm infants using the enzyme multiplied immunoassay technique (EMIT) assay. We conducted a prospective study including preterm infants (less than 34 weeks' amenorrhea) admitted to the intensive care and neonatal medicine department. All infants received 5, 10, 15, 20 and 25mg/kg/day of citrate caffeine intravenously from the first to the fifth day of birth, respectively. For each patient, two concomitant blood and saliva samples corresponding to the trough concentrations were collected 24hours after each caffeine dose. The caffeine concentrations were determined using the EMIT ® 2000 caffeine assay. Thirteen preterm infants were included. The saliva and the serum caffeine concentration increased proportionally to the administered dose. Saliva and serum kinetics were comparable and the saliva caffeine concentrations were correlated to the serum ones (r 2 =0.76). Saliva caffeine monitoring by EMIT is a valid, useful and safe alternative to serum in preterm infants. Copyright © 2017 Société française de pharmacologie et de thérapeutique. Published by Elsevier Masson SAS. All rights reserved.

  1. Correlation between factors associated with the removable partial dentures use and Candida spp. in saliva.

    Science.gov (United States)

    Gusmão, João Milton Rocha; Ferreira dos Santos, Silvana Soleo; Neisser, Maximiliano Piero; Jorge, Antônio Olavo Cardoso; Faria, Ms Ivan

    2011-12-01

    To correlate the presence and number of Candida spp. in the saliva of wearers of removable partial dentures retained with precision attachments with the proportion of metal/acrylic resin present in the dentures. Saliva samples from 40 removable partial denture wearers (test) and one paired sample of individuals, non-wearers of any type of removable denture (control) were collected, seeded, and the colony forming units of Candida counted and identified. The metal/acrylic resin proportion of each denture was quantified, using silicone plates pressed over each denture. Candida spp. was found in the saliva of 80% of the individuals in the test group and 65% of the control, with C. albicans being the most prevalent species. The test group presented with the highest number of colony forming units of Candida per ml of saliva, and there was weak correlation between this number and the metal and resin area of the denture (Pearson's coefficient of correlation). Greater prevalence and a higher number of colony forming units of Candida per ml of saliva occurred in removable partial denture wearers (p = 0.04) with a weak positive correlation between the metal and resin area and the number of colony forming units of Candida per ml of saliva. However, this correlation was more significant for the area of resin. © 2010 The Gerodontology Society and John Wiley & Sons A/S.

  2. Electrochemical behavior and pH stability of artificial salivas for corrosion tests.

    Science.gov (United States)

    Queiroz, Gláucia Maria Oliveira de; Silva, Leandro Freitas; Ferreira, José Tarcísio Lima; Gomes, José Antônio da Cunha P; Sathler, Lúcio

    2007-01-01

    It is assumed that the compositions of artificial salivas are similar to that of human saliva. However, the use of solutions with different compositions in in vitro corrosion studies can lead dissimilar electrolytes to exhibit dissimilar corrosivity and electrochemical stability. This study evaluated four artificial salivas as regards pH stability with time, redox potentials and the polarization response of an inert platinum electrode. The tested solutions were: SAGF medium, Mondelli artificial saliva, UFRJ artificial saliva (prepared at the School of Pharmacy, Federal University of Rio de Janeiro, RJ, Brazil) and USP-RP artificial saliva (prepared at the School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, SP, Brazil). It was observed that pH variations were less than 1 unit during a 50-hour test. The SAGF medium, and the UFRJ and USP-RP solutions exhibited more oxidizing characteristics, whereas the Mondelli solution presented reducing properties. Anodic polarization revealed oxidation of the evaluated electrolytes at potentials below +600 mV SCE. It was observed that the UFRJ and USP-RP solutions presented more intense oxidation and reduction processes as compared to the Mondelli and SAGF solutions.

  3. Saliva levels of Abeta1-42 as potential biomarker of Alzheimer's disease: a pilot study

    Directory of Open Access Journals (Sweden)

    Antequera Desiree

    2010-11-01

    Full Text Available Abstract Background Simple, non-invasive tests for early detection of degenerative dementia by use of biomarkers are urgently required. However, up to the present, no validated extracerebral diagnostic markers for the early diagnosis of Alzheimer disease (AD are available. The clinical diagnosis of probable AD is made with around 90% accuracy using modern clinical, neuropsychological and imaging methods. A biochemical marker that would support the clinical diagnosis and distinguish AD from other causes of dementia would therefore be of great value as a screening test. A total of 126 samples were obtained from subjects with AD, and age-sex-matched controls. Additionally, 51 Parkinson's disease (PD patients were used as an example of another neurodegenerative disorder. We analyzed saliva and plasma levels of β amyloid (Aβ using a highly sensitive ELISA kit. Results We found a small but statistically significant increase in saliva Aβ42 levels in mild AD patients. In addition, there were not differences in saliva concentration of Aβ42 between patients with PD and healthy controls. Saliva Aβ40 expression was unchanged within all the studied sample. The association between saliva Aβ42 levels and AD was independent of established risk factors, including age or Apo E, but was dependent on sex and functional capacity. Conclusions We suggest that saliva Aβ42 levels could be considered a potential peripheral marker of AD and help discrimination from other types of neurodegenerative disorders. We propose a new and promising biomarker for early AD.

  4. Morphology and Differentiation of MG63 Osteoblast Cells on Saliva Contaminated Implant Surfaces

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    Neda Shams

    2015-11-01

    Full Text Available Objectives: Osteoblasts are the most important cells in the osseointegration process. Despite years of study on dental Implants, limited studies have discussed the effect of saliva on the adhesion process of osteoblasts to implant surfaces. The aim of this in vitro study was to evaluate the effect of saliva on morphology and differentiation of osteoblasts attached to implant surfaces.Materials and Methods: Twelve Axiom dental implants were divided into two groups. Implants of the case group were placed in containers, containing saliva, for 40 minutes. Then, all the implants were separately stored in a medium containing MG63 human osteoblasts for a week. Cell morphology and differentiation were assessed using a scanning electron microscope and their alkaline phosphatase (ALP activity was determined. The t-test was used to compare the two groups.Results: Scanning electron microscopic observation of osteoblasts revealed round or square cells with fewer and shorter cellular processes in saliva contaminated samples, whereas elongated, fusiform and well-defined cell processes were seen in the control group. ALP level was significantly lower in case compared to control group (P<0.05.Conclusion: Saliva contamination alters osteoblast morphology and differentiation and may subsequently interfere with successful osseointegration. Thus, saliva contamination of bone and implant must be prevented or minimized.

  5. Effectiveness of transcutaneous electrical nerve stimulation on saliva production in post-radiated oral cancer patients

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    Sakshi Ojha

    2016-01-01

    Full Text Available Aims and Objectives: To determine the effectiveness of transcutaneous electrical nerve stimulation (TENS in stimulating salivary flow in post-radiated oral cancer patients, and to compare the salivary flow rate between unstimulated saliva and saliva stimulated with TENS in post-radiated oral cancer patients. Materials and Methods: In 30 patients who underwent radiotherapy for oral cancer, unstimulated saliva was collected every minute for 5 min in a graduated test tube. The TENS unit was activated and stimulated saliva was collected for 5 min in a separate graduated test tube, and the flow rate was compared with the unstimulated salivary flow rate. Results: A statistically significant improvement was seen in saliva production during stimulation (P < 0.001. In addition, statistically significant increase in TENS stimulated saliva was observed in patients aged ≥50 years compared to that in patients aged <50 years (P < 0.05. There was no significant difference in salivary flow rate between the two genders in both stimulated and unstimulated conditions, however, statistically significant increase in salivary flow rate was observed in males under stimulated condition (P < 0.01. Conclusion: TENS was highly effective in stimulating the whole salivary flow rate in post-radiated oral cancer patients. It is an effective supportive treatment modality in xerostomia patients caused by radiotherapy in oral cancer patients.

  6. Effects of isoflurane anesthesia and pilocarpine on rat parotid saliva flow

    DEFF Research Database (Denmark)

    Knudsen, Jacob Dronninglund; Nauntofte, Birgitte; Josipovic, M

    2011-01-01

    The purpose of this study was to investigate the effects of isoflurane on unstimulated and pilocarpine-stimulated parotid saliva secretion. Ten male Sprague-Dawley rats weighing 350-400 g were randomized into two groups, and the saliva flow rate and lag phase were measured at two doses of isoflur......The purpose of this study was to investigate the effects of isoflurane on unstimulated and pilocarpine-stimulated parotid saliva secretion. Ten male Sprague-Dawley rats weighing 350-400 g were randomized into two groups, and the saliva flow rate and lag phase were measured at two doses...... of isoflurane in a crossover study design. Increasing the isoflurane concentration from 1% to 2% was associated with a 19% decrease in saliva secretion rate, and the lag to saliva secretion was increased by 155%. To clarify whether the effect of isoflurane (1.5%) on the parotid flow varied with stimulus...... intensity, we measured the parotid flow induced by seven different doses of pilocarpine on sham-irradiated rats and rats irradiated with single doses of 15 Gy. A maximal pilocarpine response was obtained with 1.5 mg/kg in both irradiated and sham-irradiated rats; however, the parotid flow of the irradiated...

  7. Microbial profile comparisons of saliva, pooled and site-specific subgingival samples in periodontitis patients.

    Directory of Open Access Journals (Sweden)

    Daniel Belstrøm

    Full Text Available The purpose of this study was to compare microbial profiles of saliva, pooled and site-specific subgingival samples in patients with periodontitis. We tested the hypotheses that saliva can be an alternative to pooled subgingival samples, when screening for presence of periopathogens.Site specific subgingival plaque samples (n = 54, pooled subgingival plaque samples (n = 18 and stimulated saliva samples (n = 18 were collected from 18 patients with generalized chronic periodontitis. Subgingival and salivary microbiotas were characterized by means of HOMINGS (Human Oral Microbe Identification using Next Generation Sequencing and microbial community profiles were compared using Spearman rank correlation coefficient.Pronounced intraindividual differences were recorded in site-specific microbial profiles, and site-specific information was in general not reflected by pooled subgingival samples. Presence of Porphyromonas gingivalis, Treponema denticola, Prevotella intermedia, Filifactor alocis, Tannerella forsythia and Parvimona micra in site-specific subgingival samples were detected in saliva with an AUC of 0.79 (sensitivity: 0.61, specificity: 0.94, compared to an AUC of 0.76 (sensitivity: 0.56, specificity: 0.94 in pooled subgingival samples.Site-specific presence of periodontal pathogens was detected with comparable accuracy in stimulated saliva samples and pooled subgingival plaque samples. Consequently, saliva may be a reasonable surrogate for pooled subgingival samples when screening for presence of periopathogens. Future large-scale studies are needed to confirm findings from this study.

  8. Orthodontic treatment effects on inflammatory marker profiles in saliva before and after 2 archwire changes

    Science.gov (United States)

    Yamamoto, Zulham; Jaafar, Ikmal Mohamad; Rohaya, M. A. W.; Abidin, Intan Zarina Zainol; Senafi, Sahidan; Ariffin, Zaidah Zainal; Ariffin, Shahrul Hisham Zainal

    2013-11-01

    Periodontal tissue changes exerted by external forces in orthodontic treatment allow tooth movement. The changes in periodontal tissues i.e. inflammation can be monitored using gingival crevicular fluid (GCF). GCF is a component of saliva. Saliva could be used to monitor periodontal disease progression. The use of saliva to monitor periodontal tissues changes during orthodontic treatment is still unknown. Therefore, we observed the profiles of inflammatory markers namely creatine kinase ('CK), nitric oxide (NO), lactate dehydrogenase (LDH) and aspartate aminotransferase (AST) in saliva of orthodontic patients to evaluate their importance in orthodontic treatment. A total of 21 subjects (13 female and 8 male) participated in this study. Samples were collected from gingival crevicular fluid at three period of archwire changes: baseline (M0), 2 weeks after 0.014" NiTi archwire (M1), and 2 weeks after 0.018" NiTi archwire (M2). All enzyme activities i.e. CK, LDH and AST were measured spectrophotometrically at 340 nm. Griess assay was used to measure nitric oxide level. CK activity, NO level, LDH activity and AST activity in saliva samples did not show significant differences among period of archwire changes. The use of inflammatory marker profiles in saliva may not represent the changes in periodontal tissues during orthodontic treatment.

  9. Tissue Multiplatform-Based Metabolomics/Metabonomics for Enhanced Metabolome Coverage.

    Science.gov (United States)

    Vorkas, Panagiotis A; Abellona U, M R; Li, Jia V

    2018-01-01

    The use of tissue as a matrix to elucidate disease pathology or explore intervention comes with several advantages. It allows investigation of the target alteration directly at the focal location and facilitates the detection of molecules that could become elusive after secretion into biofluids. However, tissue metabolomics/metabonomics comes with challenges not encountered in biofluid analyses. Furthermore, tissue heterogeneity does not allow for tissue aliquoting. Here we describe a multiplatform, multi-method workflow which enables metabolic profiling analysis of tissue samples, while it can deliver enhanced metabolome coverage. After applying a dual consecutive extraction (organic followed by aqueous), tissue extracts are analyzed by reversed-phase (RP-) and hydrophilic interaction liquid chromatography (HILIC-) ultra-performance liquid chromatography coupled to mass spectrometry (UPLC-MS) and nuclear magnetic resonance (NMR) spectroscopy. This pipeline incorporates the required quality control features, enhances versatility, allows provisional aliquoting of tissue extracts for future guided analyses, expands the range of metabolites robustly detected, and supports data integration. It has been successfully employed for the analysis of a wide range of tissue types.

  10. Diurnal effects of anoxia on the metabolome of the seagrass Zostera marina

    DEFF Research Database (Denmark)

    Hasler-Sheetal, Harald; Holmer, Marianne; Weckwerth, Wolfram

    2014-01-01

    Environmental metabolomics has become interesting in marine ecological studies. One example is the revealing of new insights in stress response of Zostera marina. This is essential to understand how, at which level and to what extend aquatic plants adapt, tolerate and react to environmental...... stressors. We exposed Z. marina to water column anoxia and assessed the diurnal metabolomic response by GC-TOF-MS based metabolomics identifying 109 known and 217 unknown metabolites. During day time photosynthetic oxygen production prevents severe effects of anoxia on the metabolome (complete set of small...... the applicability of metabolomics to assess environmental stress responses of Zostera marina....

  11. Metabolomics in plants and humans: applications in the prevention and diagnosis of diseases.

    Science.gov (United States)

    Gomez-Casati, Diego F; Zanor, Maria I; Busi, María V

    2013-01-01

    In the recent years, there has been an increase in the number of metabolomic approaches used, in parallel with proteomic and functional genomic studies. The wide variety of chemical types of metabolites available has also accelerated the use of different techniques in the investigation of the metabolome. At present, metabolomics is applied to investigate several human diseases, to improve their diagnosis and prevention, and to design better therapeutic strategies. In addition, metabolomic studies are also being carried out in areas such as toxicology and pharmacology, crop breeding, and plant biotechnology. In this review, we emphasize the use and application of metabolomics in human diseases and plant research to improve human health.

  12. Deconstructing the pig sex metabolome: Targeted metabolomics in heavy pigs revealed sexual dimorphisms in plasma biomarkers and metabolic pathways.

    Science.gov (United States)

    Bovo, S; Mazzoni, G; Calò, D G; Galimberti, G; Fanelli, F; Mezzullo, M; Schiavo, G; Scotti, E; Manisi, A; Samoré, A B; Bertolini, F; Trevisi, P; Bosi, P; Dall'Olio, S; Pagotto, U; Fontanesi, L

    2015-12-01

    Metabolomics has opened new possibilities to investigate metabolic differences among animals. In this study, we applied a targeted metabolomic approach to deconstruct the pig sex metabolome as defined by castrated males and entire gilts. Plasma from 545 performance-tested Italian Large White pigs (172 castrated males and 373 females) sampled at about 160 kg live weight were analyzed for 186 metabolites using the Biocrates AbsoluteIDQ p180 Kit. After filtering, 132 metabolites (20 AA, 11 biogenic amines, 1 hexose, 13 acylcarnitines, 11 sphingomyelins, 67 phosphatidylcholines, and 9 lysophosphatidylcholines) were retained for further analyses. The multivariate approach of the sparse partial least squares discriminant analysis was applied, together with a specifically designed statistical pipeline, that included a permutation test and a 10 cross-fold validation procedure that produced stability and effect size statistics for each metabolite. Using this approach, we identified 85 biomarkers (with metabolites from all analyzed chemical families) that contributed to the differences between the 2 groups of pigs ( metabolic shift in castrated males toward energy storage and lipid production. Similar general patterns were observed for most sphingomyelins, phosphatidylcholines, and lysophosphatidylcholines. Metabolomic pathway analysis and pathway enrichment identified several differences between the 2 sexes. This metabolomic overview opened new clues on the biochemical mechanisms underlying sexual dimorphism that, on one hand, might explain differences in terms of economic traits between castrated male pigs and entire gilts and, on the other hand, could strengthen the pig as a model to define metabolic mechanisms related to fat deposition.

  13. A Latitudinal Metabolome of the Atlantic Ocean

    Science.gov (United States)

    Johnson, W.; Kido Soule, M. C.; Longnecker, K.; Kujawinski, E. B.

    2016-02-01

    Microbial consortia function via the exchange and transformation of small organic molecules or metabolites. These metabolites make up a pool of rapidly cycling organic matter in the ocean that is challenging to characterize due to its low concentrations. We seek to determine the distribution of these molecules and the factors that shape their abundance and flux. Through measurements of the abundance of a core set of metabolites, including nucleic acids, amino acids, sugars, vitamins, and signaling molecules, we gain a real-time snapshot of microbial activity. We used a targeted metabolomics technique to profile metabolite abundance in particulate and dissolved organic matter extracts collected from a 14,000 km transect running from 38˚S to 55˚N in the Western Atlantic Ocean. This extensive dataset is the first of its kind in the Atlantic Ocean and allows us to explore connections among metabolites as well as latitudinal trends in metabolite abundance. We found changes in the intracellular abundance of certain metabolites between low and high nutrient regions and a wide distribution of certain dissolved vitamins in the surface ocean. These measurements give us baseline data on the distribution of these metabolites and allow us to extend our understanding of microbial community activity in different regions of the ocean.

  14. Genetic basis of metabolome variation in yeast.

    Directory of Open Access Journals (Sweden)

    Jeffrey S Breunig

    2014-03-01

    Full Text Available Metabolism, the conversion of nutrients into usable energy and biochemical building blocks, is an essential feature of all cells. The genetic factors responsible for inter-individual metabolic variability remain poorly understood. To investigate genetic causes of metabolome variation, we measured the concentrations of 74 metabolites across ~ 100 segregants from a Saccharomyces cerevisiae cross by liquid chromatography-tandem mass spectrometry. We found 52 quantitative trait loci for 34 metabolites. These included linkages due to overt changes in metabolic genes, e.g., linking pyrimidine intermediates to the deletion of ura3. They also included linkages not directly related to metabolic enzymes, such as those for five central carbon metabolites to ira2, a Ras/PKA pathway regulator, and for the metabolites, S-adenosyl-methionine and S-adenosyl-homocysteine to slt2, a MAP kinase involved in cell wall integrity. The variant of ira2 that elevates metabolite levels also increases glucose uptake and ethanol secretion. These results highlight specific examples of genetic variability, including in genes without prior known metabolic regulatory function, that impact yeast metabolism.

  15. Mass spectrometry as a quantitative tool in plant metabolomics

    Science.gov (United States)

    Jorge, Tiago F.; Mata, Ana T.

    2016-01-01

    Metabolomics is a research field used to acquire comprehensive information on the composition of a metabolite pool to provide a functional screen of the cellular state. Studies of the plant metabolome include the analysis of a wide range of chemical species with very diverse physico-chemical properties, and therefore powerful analytical tools are required for the separation, characterization and quantification of this vast compound diversity present in plant matrices. In this review, challenges in the use of mass spectrometry (MS) as a quantitative tool in plant metabolomics experiments are discussed, and important criteria for the development and validation of MS-based analytical methods provided. This article is part of the themed issue ‘Quantitative mass spectrometry’. PMID:27644967

  16. Plant Metabolomics: An Indispensable System Biology Tool for Plant Science

    Science.gov (United States)

    Hong, Jun; Yang, Litao; Zhang, Dabing; Shi, Jianxin

    2016-01-01

    As genomes of many plant species have been sequenced, demand for functional genomics has dramatically accelerated the improvement of other omics including metabolomics. Despite a large amount of metabolites still remaining to be identified, metabolomics has contributed significantly not only to the understanding of plant physiology and biology from the view of small chemical molecules that reflect the end point of biological activities, but also in past decades to the attempts to improve plant behavior under both normal and stressed conditions. Hereby, we summarize the current knowledge on the genetic and biochemical mechanisms underlying plant growth, development, and stress responses, focusing further on the contributions of metabolomics to practical applications in crop quality improvement and food safety assessment, as well as plant metabolic engineering. We also highlight the current challenges and future perspectives in this inspiring area, with the aim to stimulate further studies leading to better crop improvement of yield and quality. PMID:27258266

  17. Plant Metabolomics: An Indispensable System Biology Tool for Plant Science

    Directory of Open Access Journals (Sweden)

    Jun Hong

    2016-06-01

    Full Text Available As genomes of many plant species have been sequenced, demand for functional genomics has dramatically accelerated the improvement of other omics including metabolomics. Despite a large amount of metabolites still remaining to be identified, metabolomics has contributed significantly not only to the understanding of plant physiology and biology from the view of small chemical molecules that reflect the end point of biological activities, but also in past decades to the attempts to improve plant behavior under both normal and stressed conditions. Hereby, we summarize the current knowledge on the genetic and biochemical mechanisms underlying plant growth, development, and stress responses, focusing further on the contributions of metabolomics to practical applications in crop quality improvement and food safety assessment, as well as plant metabolic engineering. We also highlight the current challenges and future perspectives in this inspiring area, with the aim to stimulate further studies leading to better crop improvement of yield and quality.

  18. A primer to nutritional metabolomics by NMR spectroscopy and chemometrics

    DEFF Research Database (Denmark)

    Savorani, Francesco; Rasmussen, Morten Arendt; Mikkelsen, Mette Skau

    2013-01-01

    This paper outlines the advantages and disadvantages of using high throughput NMR metabolomics for nutritional studies with emphasis on the workflow and data analytical methods for generation of new knowledge. The paper describes one-by-one the major research activities in the interdisciplinary...... metabolomics platform and highlights the opportunities that NMR spectra can provide in future nutrition studies. Three areas are emphasized: (1) NMR as an unbiased and non-destructive platform for providing an overview of the metabolome under investigation, (2) NMR for providing versatile information and data...... structures for multivariate pattern recognition methods and (3) NMR for providing a unique fingerprint of the lipoprotein status of the subject. For the first time in history, by combining NMR spectroscopy and chemometrics we are able to perform inductive nutritional research as a complement to the deductive...

  19. Metabolomics in epidemiology: from metabolite concentrations to integrative reaction networks.

    Science.gov (United States)

    Fearnley, Liam G; Inouye, Michael

    2016-10-01

    Metabolomics is becoming feasible for population-scale studies of human disease. In this review, we survey epidemiological studies that leverage metabolomics and multi-omics to gain insight into disease mechanisms. We outline key practical, technological and analytical limitations while also highlighting recent successes in integrating these data. The use of multi-omics to infer reaction rates is discussed as a potential future direction for metabolomics research, as a means of identifying biomarkers as well as inferring causality. Furthermore, we highlight established analysis approaches as well as simulation-based methods currently used in single- and multi-cell levels in systems biology. © The Author 2016. Published by Oxford University Press on behalf of the International Epidemiological Association.

  20. The effects of gliadin on urine metabolome in mice

    DEFF Research Database (Denmark)

    Roager, Henrik Munch; Zhang, Li; Frandsen, Henrik Lauritz

    Gliadin, a proline-rich protein of gluten, is thought to modulate the gut microbiota and affect the intestinal permeability and immune system. However, little is known about the long-term effects of gliadin on the host and microbial metabolism. To study this, we compared the urine metabolome of two...... groups of mice, which were on a high fat diet with and without gliadin, respectively, for 23 weeks. Using liquid chromatography mass-spectrometry (MS) followed by multivariate analyses we were able to show a clear separation of the two groups of mice based on their urine metabolome. Discriminating...... in the gliadin mice. Also, Maillard reaction products and β-oxidized tocopherols were observed in higher levels in the urine of gliadin mice, suggesting increased oxidative stress in the gliadin mice. Indisputably, gliadin affected the urine metabolome. However, the mechanisms behind the observed metabolite...